├── MANIFEST.in ├── results_gold ├── dataset1_nochr1.h2 ├── dataset1_nochr10.h2 ├── dataset1_nochr2.h2 ├── dataset1_nochr3.h2 ├── dataset1_nochr4.h2 ├── dataset1_nochr5.h2 ├── dataset1_nochr6.h2 ├── dataset1_nochr7.h2 ├── dataset1_nochr8.h2 └── dataset1_nochr9.h2 ├── dataset1 ├── dataset1.bed ├── .pversion └── extracts │ ├── chr4_extract.txt │ ├── chr8_extract.txt │ ├── chr6_extract.txt │ ├── chr9_extract.txt │ ├── chr2_extract.txt │ ├── chr5_extract.txt │ ├── chr7_extract.txt │ ├── chr3_extract.txt │ ├── chr1_extract.txt │ └── chr10_extract.txt ├── leapMain.py ├── findRelated.py ├── eigenDecompose.py ├── leap_gwas.py ├── test.py ├── README.md ├── calc_h2.py ├── LICENSE.md ├── leapUtils.py └── probit.py /MANIFEST.in: -------------------------------------------------------------------------------- 1 | recursive-include leap * 2 | -------------------------------------------------------------------------------- /results_gold/dataset1_nochr1.h2: -------------------------------------------------------------------------------- 1 | 0.457940 2 | -------------------------------------------------------------------------------- /results_gold/dataset1_nochr10.h2: -------------------------------------------------------------------------------- 1 | 0.492799 2 | -------------------------------------------------------------------------------- /results_gold/dataset1_nochr2.h2: -------------------------------------------------------------------------------- 1 | 0.465129 2 | -------------------------------------------------------------------------------- /results_gold/dataset1_nochr3.h2: -------------------------------------------------------------------------------- 1 | 0.460831 2 | -------------------------------------------------------------------------------- /results_gold/dataset1_nochr4.h2: -------------------------------------------------------------------------------- 1 | 0.448058 2 | -------------------------------------------------------------------------------- /results_gold/dataset1_nochr5.h2: -------------------------------------------------------------------------------- 1 | 0.433674 2 | -------------------------------------------------------------------------------- /results_gold/dataset1_nochr6.h2: -------------------------------------------------------------------------------- 1 | 0.460130 2 | -------------------------------------------------------------------------------- /results_gold/dataset1_nochr7.h2: -------------------------------------------------------------------------------- 1 | 0.460162 2 | -------------------------------------------------------------------------------- /results_gold/dataset1_nochr8.h2: -------------------------------------------------------------------------------- 1 | 0.482879 2 | -------------------------------------------------------------------------------- /results_gold/dataset1_nochr9.h2: -------------------------------------------------------------------------------- 1 | 0.470872 2 | -------------------------------------------------------------------------------- /dataset1/dataset1.bed: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/omerwe/LEAP/HEAD/dataset1/dataset1.bed -------------------------------------------------------------------------------- /dataset1/.pversion: -------------------------------------------------------------------------------- 1 | Fri Dec 26 2 | HTTP/1.1 3 | 200 4 | OK 5 | Date: 6 | Fri, 7 | 26 8 | Dec 9 | 2014 10 | 09:29:26 11 | GMT 12 | Server: 13 | Apache/2.2.3 14 | (Linux/SUSE) 15 | Last-Modified: 16 | Thu, 17 | 15 18 | May 19 | 2014 20 | 23:16:43 21 | GMT 22 | ETag: 23 | "2604b-d2-4f9787d742cc0" 24 | Accept-Ranges: 25 | bytes 26 | Content-Length: 27 | 210 28 | Connection: 29 | close 30 | Content-Type: 31 | text/plain 32 | X-Pad: 33 | avoid 34 | browser 35 | bug 36 | PLINK-VERSION 37 | 1.07 38 | Old 39 | versions 40 | of 41 | PLINK 42 | (<1.07) 43 | contain 44 | bugs 45 | fixed 46 | in 47 | 1.07. 48 | \n 49 | END-MESSAGE 50 | MESSAGE-ALL 51 | \n 52 | +++ 53 | PLINK 54 | 1.9 55 | is 56 | now 57 | available! 58 | See 59 | above 60 | website 61 | for 62 | details 63 | +++ 64 | \n 65 | END-MESSAGE 66 | FATAL 67 | --none 68 | END 69 | -------------------------------------------------------------------------------- /leapMain.py: -------------------------------------------------------------------------------- 1 | def eigenDecompose(bed, kinshipFile=None, outFile=None, ignore_neig=False): 2 | from . import eigenDecompose 3 | return eigenDecompose.eigenDecompose(bed, kinshipFile, outFile, ignore_neig) 4 | 5 | def findRelated(bed, outFile=None, cutoff=0.05, kinshipFile=None): 6 | from . import findRelated 7 | return findRelated.findRelated(bed, outFile, cutoff, kinshipFile) 8 | 9 | def calcH2(pheno, prev, eigen, keepArr=None, covar=None, numRemovePCs=10, lowtail=False): 10 | from . import calc_h2 11 | return calc_h2.calc_h2(pheno, prev, eigen, keepArr, covar, numRemovePCs, lowtail) 12 | 13 | def probit(bed, pheno, h2, prev, eigen, outFile=None, keepArr=None, covar=None, thresholds=None, nofail=False, 14 | numSkipTopPCs=0, mineig=1e-3, hess=False, recenter=True, maxFixedIters=100, epsilon=1e-3, treatFixedAsRandom=False): 15 | from . import probit 16 | return probit.probit(bed, pheno, h2, prev, eigen, outFile, keepArr, covar, thresholds, nofail, 17 | numSkipTopPCs, mineig, hess, recenter, maxFixedIters, epsilon, treatFixedAsRandom=treatFixedAsRandom) 18 | 19 | def leapGwas(bedSim, bedTest, pheno, h2, outFile=None, eigenFile=None, covar=None): 20 | from . import leap_gwas 21 | return leap_gwas.gwas(bedSim, bedTest, pheno, h2, outFile, eigenFile, covar) 22 | 23 | 24 | 25 | -------------------------------------------------------------------------------- /findRelated.py: -------------------------------------------------------------------------------- 1 | import numpy as np 2 | import argparse 3 | import time 4 | import scipy.linalg.blas as blas 5 | from . import leapUtils 6 | np.set_printoptions(precision=3, linewidth=200) 7 | from . import leapMain 8 | 9 | 10 | def findRelated(bed, outFile, cutoff, kinshipFile=None): 11 | 12 | bed = leapUtils._fixupBed(bed) 13 | 14 | keepArr = leapUtils.findRelated(bed, cutoff, kinshipFile) 15 | if (outFile is not None): 16 | print('Printing output to', outFile) 17 | f = open(outFile, 'w') 18 | for i, (fid,iid) in enumerate(bed.iid): 19 | if (keepArr[i]): f.write(fid + ' ' + iid + ' 0\n') 20 | else: f.write(fid + ' ' + iid + ' 1\n') 21 | f.close() 22 | return keepArr 23 | 24 | if __name__ == '__main__': 25 | 26 | parser = argparse.ArgumentParser() 27 | parser.add_argument('--bfilesim', metavar='bfilesim', default=None, help='Binary plink file') 28 | parser.add_argument('--kinship', metavar='kinsip', default=None, help='A kinship matrix represented in a text file. Note that this matrix must correspond exactly to the phenotypes file, unlike the bfilesim file option.') 29 | parser.add_argument('--extractSim', metavar='extractSim', default=None, help='extractSim file') 30 | parser.add_argument('--cutoff', metavar='cutoff', type=float, default=0.05, help='Relationship cutoff (default 0.05)') 31 | parser.add_argument('--out', metavar='out', default=None, help='output file') 32 | 33 | parser.add_argument('--pheno', metavar='pheno', default=None, help='Phenotypes file (optional), only used for identifying unphenotyped individuals') 34 | parser.add_argument('--missingPhenotype', metavar='missingPhenotype', default='-9', help='identifier for missing values (default: -9)') 35 | args = parser.parse_args() 36 | 37 | if (args.bfilesim is None and args.kinship is None): raise Exception('bfilesim or kinship must be supplied') 38 | if (args.bfilesim is not None and args.kinship is not None): raise Exception('bfilesim and kinship cannot both be supplied') 39 | if (args.out is None): raise Exception('output file name must be supplied') 40 | if (args.bfilesim is not None): bed, _ = leapUtils.loadData(args.bfilesim, args.extractSim, args.pheno, args.missingPhenotype, loadSNPs=True, standardize=True) 41 | else: bed=None 42 | leapMain.findRelated(bed, args.out, args.cutoff, args.kinship) 43 | 44 | -------------------------------------------------------------------------------- /eigenDecompose.py: -------------------------------------------------------------------------------- 1 | import numpy as np 2 | import argparse 3 | import scipy.linalg as la 4 | import time 5 | from . import leapUtils 6 | import scipy.linalg.blas as blas 7 | from . import leapMain 8 | np.set_printoptions(precision=3, linewidth=200) 9 | 10 | def eigenDecompose(bed, kinshipFile=None, outFile=None, ignore_neig=False): 11 | 12 | if (kinshipFile is None): 13 | #Compute kinship matrix 14 | bed = leapUtils._fixupBed(bed) 15 | t0 = time.time() 16 | print('Computing kinship matrix...') 17 | XXT = leapUtils.symmetrize(blas.dsyrk(1.0, bed.val, lower=1)) / bed.val.shape[1] 18 | print('Done in %0.2f'%(time.time()-t0), 'seconds') 19 | else: 20 | XXT = np.loadtxt(kinshipFile) 21 | 22 | #Compute eigendecomposition 23 | S,U = leapUtils.eigenDecompose(XXT, ignore_neig) 24 | if (outFile is not None): np.savez_compressed(outFile, arr_0=U, arr_1=S, XXT=XXT) 25 | eigen = dict([]) 26 | eigen['XXT'] = XXT 27 | eigen['arr_0'] = U 28 | eigen['arr_1'] = S 29 | return eigen 30 | 31 | 32 | 33 | if __name__ == '__main__': 34 | 35 | parser = argparse.ArgumentParser() 36 | parser.add_argument('--bfilesim', metavar='bfilesim', default=None, help='Binary plink file') 37 | parser.add_argument('--kinship', metavar='kinship', default=None, help='A kinship matrix represented in a text file. Note that this matrix must correspond exactly to the phenotypes file, unlike the bfilesim file option.') 38 | parser.add_argument('--extractSim', metavar='extractSim', default=None, help='SNPs subset to use') 39 | parser.add_argument('--out', metavar='out', default=None, help='output file') 40 | parser.add_argument('--pheno', metavar='pheno', default=None, help='Phenotypes file (optional), only used for identifying unphenotyped individuals') 41 | parser.add_argument('--missingPhenotype', metavar='missingPhenotype', default='-9', help='identifier for missing values (default: -9)') 42 | parser.add_argument('--ignore_neig', metavar='ignore_neig', type=int, default=0, help='if set to 1, negative eigenvalues will be set to 0 and consequently ignored.') 43 | args = parser.parse_args() 44 | 45 | if (args.bfilesim is None and args.kinship is None): raise Exception('bfilesim or kinship must be supplied') 46 | if (args.bfilesim is not None and args.kinship is not None): raise Exception('bfilesim and kinship cannot both be supplied') 47 | if (args.out is None): raise Exception('output file name must be supplied') 48 | 49 | #Read input files 50 | if (args.bfilesim is not None): bed, _ = leapUtils.loadData(args.bfilesim, args.extractSim, args.pheno, args.missingPhenotype, loadSNPs=True) 51 | else: bed=None 52 | 53 | leapMain.eigenDecompose(bed, kinshipFile=args.kinship, outFile=args.out, ignore_neig=args.ignore_neig>0) 54 | 55 | -------------------------------------------------------------------------------- /leap_gwas.py: -------------------------------------------------------------------------------- 1 | import numpy as np 2 | import time 3 | import sys 4 | import argparse 5 | from . import leapUtils 6 | from . import leapMain 7 | import fastlmm.association 8 | np.set_printoptions(precision=4, linewidth=200) 9 | 10 | 11 | def gwas(bedSim, bedTest, pheno, h2, outFile, eigenFile, covar): 12 | 13 | bedSim, pheno = leapUtils._fixupBedAndPheno(bedSim, pheno) 14 | bedTest, pheno = leapUtils._fixupBedAndPheno(bedTest, pheno) 15 | 16 | #Run GWAS 17 | logdelta = np.log(1.0/h2 - 1) 18 | G0 = (bedSim if eigenFile is None else None) 19 | print('Performing LEAP GWAS...') 20 | results_df = fastlmm.association.single_snp(bedTest, pheno, G0=G0, covar=covar, output_file_name=outFile, log_delta=logdelta, cache_file=eigenFile) 21 | return results_df 22 | 23 | 24 | if __name__ == '__main__': 25 | 26 | parser = argparse.ArgumentParser() 27 | parser.add_argument('--bfilesim', metavar='bfilesim', default=None, help='Binary plink file') 28 | parser.add_argument('--bfile', metavar='bfile', default=None, help='Binary plink file to test') 29 | parser.add_argument('--pheno', metavar='pheno', default=None, help='Phenotype file in Plink format') 30 | parser.add_argument('--eigen', metavar='eigen', default=None, help='Eigendecompositon file') 31 | parser.add_argument('--h2', metavar='h2', type=float, default=None, help='h2 value') 32 | parser.add_argument('--extractSim', metavar='extractSim', default=None, help='SNPs subset to use') 33 | parser.add_argument('--extract', metavar='extract', default=None, help='SNPs subset to test') 34 | parser.add_argument('--out', metavar='out', default=None, help='output file') 35 | parser.add_argument('--covar', metavar='covar', default=None, help='Covariates file') 36 | parser.add_argument('--missingPhenotype', metavar='missingPhenotype', default='-9', help='identifier for missing values (default: -9)') 37 | args = parser.parse_args() 38 | 39 | if (args.bfile is None): raise Exception('bfile must be supplied') 40 | if (args.bfilesim is None): raise Exception('bfilesim must be supplied') 41 | if (args.pheno is None): raise Exception('phenotype file must be supplied') 42 | if (args.out is None): raise Exception('output file name must be supplied') 43 | if (args.h2 is None): raise Exception('h2 must be supplied') 44 | 45 | #Read bfile and pheno file 46 | bedSim, _ = leapUtils.loadData(args.bfilesim, args.extractSim, args.pheno, args.missingPhenotype, loadSNPs=True) 47 | bedTest, _ = leapUtils.loadData(args.bfile, args.extract, args.pheno, args.missingPhenotype, loadSNPs=True) 48 | 49 | # #Read covariates 50 | # if (args.covar is not None): 51 | # covar = leapUtils.loadCovars(bedSim, args.covar) 52 | # print 'Read', covar.shape[1], 'covariates from file' 53 | # else: covar = None 54 | 55 | leapMain.leapGwas(bedSim, bedTest, args.pheno, args.h2, args.out, eigenFile=args.eigen, covar=args.covar) 56 | 57 | 58 | -------------------------------------------------------------------------------- /test.py: -------------------------------------------------------------------------------- 1 | import unittest 2 | import logging 3 | import os 4 | import sys 5 | import pandas as pd 6 | import numpy as np 7 | import leapUtils 8 | import leapMain 9 | 10 | class TestLeap(unittest.TestCase): 11 | 12 | tempout_dir = "tempout" 13 | gold_dir = "results_gold" 14 | 15 | @classmethod 16 | def setUpClass(self): 17 | from fastlmm.util.util import create_directory_if_necessary 18 | create_directory_if_necessary(self.tempout_dir, isfile=False) 19 | self.pythonpath = os.path.abspath(os.path.join(os.path.dirname(os.path.realpath(__file__)))) 20 | self.bedbase = os.path.join(self.pythonpath, 'dataset1/dataset1') 21 | self.phen_fn = os.path.join(self.pythonpath, 'dataset1/dataset1.phe') 22 | 23 | #Create eigendecompositions 24 | logging.info("Creating eigendecomposition files") 25 | for i in range(1,11): 26 | output_file = os.path.abspath(os.path.join(self.tempout_dir, 'dataset1_nochr{}.npz'.format(i))) 27 | extractSim = 'dataset1/extracts/nochr{0}_extract.txt'.format(i) 28 | bed, _ = leapUtils.loadData(self.bedbase, extractSim, self.phen_fn, loadSNPs=True) 29 | leapMain.eigenDecompose(bed, output_file) 30 | 31 | 32 | #Note: this is commented out, because the .npz files are too large for storage on pypi 33 | # # def test_eigenDecompose(self): 34 | # # logging.info("Leap test_eigenDecompose") 35 | # # for i in xrange(1,11): 36 | # # output_file = os.path.abspath(os.path.join(self.tempout_dir, 'dataset1_nochr{}.npz'.format(i))) 37 | # # ref_file = os.path.abspath(os.path.join(self.gold_dir, 'dataset1_nochr{}.npz'.format(i))) 38 | # # extractSim = 'dataset1/extracts/nochr{0}_extract.txt'.format(i) 39 | # # leapMain.eigenDecompose(self.bedbase, output_file, extractSim=extractSim) 40 | 41 | # # npz1 = np.load(ref_file) 42 | # # npz2 = np.load(output_file) 43 | # # assert np.max(np.abs((npz1['arr_1']-npz2['arr_1']))) < 1e-8, 'Non-matching eigenvalues found' 44 | 45 | # # U1 = npz1['arr_0'] 46 | # # U2 = npz2['arr_0'] 47 | # # U1 *= [(1 if U1[0,i]>0 else -1) for i in xrange(U1.shape[1])] 48 | # # U2 *= [(1 if U2[0,i]>0 else -1) for i in xrange(U2.shape[1])] 49 | # # assert np.max(np.abs((U1-U2))) < 1e-8, 'Non-matching eigenvectors found' 50 | 51 | 52 | def test_findrelated(self): 53 | logging.info("Leap test_findrelated") 54 | ref_file = os.path.abspath(os.path.join(self.gold_dir, 'dataset1.related')) 55 | output_file = os.path.abspath(os.path.join(self.tempout_dir, 'dataset1.related')) 56 | leapMain.findRelated(self.bedbase, output_file) 57 | self.compare_pheno(ref_file, output_file) 58 | 59 | 60 | def test_calch2(self): 61 | logging.info("Leap test_calch2") 62 | related_file = os.path.abspath(os.path.join(self.gold_dir, 'dataset1.related')) 63 | bed, _ = leapUtils.loadData(self.bedbase, None, self.phen_fn, loadSNPs=False) 64 | keepArr = leapUtils.loadRelatedFile(bed, related_file) 65 | 66 | for i in range(1,11): 67 | h2_file = os.path.abspath(os.path.join(self.gold_dir, 'dataset1_nochr{0}.h2'.format(i))) 68 | eigen_file = os.path.abspath(os.path.join(self.tempout_dir, 'dataset1_nochr{}.npz'.format(i))) 69 | eigen = np.load(eigen_file) 70 | extractSim = 'dataset1/extracts/nochr{0}_extract.txt'.format(i) 71 | expected_h2 = np.loadtxt(h2_file, usecols=[0]) 72 | h2 = leapMain.calcH2(self.phen_fn, 0.001, eigen, keepArr=keepArr, h2coeff=1.0) 73 | assert np.abs(h2-expected_h2)<1e-5, 'Incorrect heritability estimated' 74 | 75 | 76 | def test_probit(self): 77 | logging.info("Leap test_probit") 78 | related_file = os.path.abspath(os.path.join(self.gold_dir, 'dataset1.related')) 79 | bed, _ = leapUtils.loadData(self.bedbase, None, self.phen_fn, loadSNPs=False) 80 | keepArr = leapUtils.loadRelatedFile(bed, related_file) 81 | 82 | for i in range(1,11): 83 | h2_file = os.path.abspath(os.path.join(self.gold_dir, 'dataset1_nochr{0}.h2'.format(i))) 84 | h2 = np.loadtxt(h2_file, usecols=[0]) 85 | eigen_file = os.path.abspath(os.path.join(self.tempout_dir, 'dataset1_nochr{}.npz'.format(i))) 86 | eigen = np.load(eigen_file) 87 | ref_file = os.path.abspath(os.path.join(self.gold_dir, 'dataset1_nochr{}.liabs'.format(i))) 88 | extractSim = 'dataset1/extracts/nochr{0}_extract.txt'.format(i) 89 | bed, _ = leapUtils.loadData(self.bedbase, extractSim, self.phen_fn, loadSNPs=True) 90 | output_file = os.path.abspath(os.path.join(self.tempout_dir, 'dataset1_nochr{}'.format(i))) 91 | leapMain.probit(bed, self.phen_fn, h2=h2, prev=0.001, eigen=eigen, outFile=output_file, keepArr=keepArr, hess=False) 92 | self.compare_pheno(ref_file, output_file+'.liabs') 93 | 94 | 95 | def test_gwas(self): 96 | logging.info("Leap test_gwas") 97 | 98 | for i in range(1,11): 99 | h2_file = os.path.abspath(os.path.join(self.gold_dir, 'dataset1_nochr{0}.h2'.format(i))) 100 | h2 = np.loadtxt(h2_file, usecols=[0]) 101 | ref_file = os.path.abspath(os.path.join(self.gold_dir, 'dataset1_nochr{}.gwas.out.txt'.format(i))) 102 | extractSim = 'dataset1/extracts/nochr{0}_extract.txt'.format(i) 103 | extract = 'dataset1/extracts/chr{0}_extract.txt'.format(i) 104 | bedSim, phe = leapUtils.loadData(self.bedbase, extractSim, self.phen_fn, loadSNPs=True) 105 | bedTest, phe = leapUtils.loadData(self.bedbase, extract, self.phen_fn, loadSNPs=True) 106 | 107 | output_file = os.path.abspath(os.path.join(self.tempout_dir, 'dataset1_nochr{}.gwas.out.txt'.format(i))) 108 | liab_file = os.path.abspath(os.path.join(self.gold_dir, 'dataset1_nochr{}.liabs'.format(i))) 109 | eigen_file = os.path.abspath(os.path.join(self.tempout_dir, 'dataset1_nochr{}.npz'.format(i))) 110 | leapMain.leapGwas(bedSim, bedTest, liab_file, h2, output_file, eigenFile=eigen_file) 111 | self.compare_gwas(ref_file, output_file) 112 | 113 | 114 | def compare_pheno(self, file1, file2, delimiter=' ', header=None): 115 | frame1 = pd.read_csv(file1, delimiter=delimiter, header=header) 116 | frame2 = pd.read_csv(file2, delimiter=delimiter, header=header) 117 | frame1.columns = ['fid', 'iid', 'pheno'] 118 | frame2.columns = ['fid', 'iid', 'pheno'] 119 | assert len(frame1) == len(frame2), '# of lines differs from file "{0}"'.format(file2) 120 | for row_i, row1 in frame1.iterrows(): 121 | row2 = frame2[(frame2['fid']==row1['fid']) & (frame2['iid']==row1['iid'])].iloc[0] 122 | for k in list(row1.keys()): 123 | assert row1[k]==row2[k], "different data for individual '{0}' '{1}'".format(row1['fid'], row1['iid']) 124 | 125 | 126 | def compare_gwas(self, file1, file2): 127 | 128 | ref_frame = pd.read_csv(file1, delimiter='\s', header=0, comment=None) 129 | frame = pd.read_csv(file2, delimiter='\s', header=0, comment=None) 130 | assert len(ref_frame) == len(frame), "# of pairs differs from file '{0}'".format(file1) 131 | for _, row in ref_frame.iterrows(): 132 | sid = row['SNP'] 133 | pvalue = (frame[frame['SNP'] == sid].iloc[0])['PValue'] 134 | assert abs(row['PValue'] - pvalue) < 1e-5, "snp {0} differs too much from file '{1}'".format(sid,file1) 135 | 136 | 137 | 138 | 139 | 140 | 141 | 142 | def getTestSuite(): 143 | 144 | suite1 = unittest.TestLoader().loadTestsFromTestCase(TestLeap) 145 | return unittest.TestSuite([suite1]) 146 | 147 | if __name__ == '__main__': 148 | 149 | suites = unittest.TestSuite([getTestSuite()]) 150 | r = unittest.TextTestRunner(failfast=True) 151 | r.run(suites) 152 | 153 | logging.info("done with testing") 154 | -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- 1 | LEAP 2 | ---------------- 3 | 4 | LEAP is a program for liability estimation in ascertained case-control genome-wide association studies, written in the Python language. 5 | LEAP estimates liabilities, that can then be treated as phenotypes in a GWAS context, which can greatly increase power. 6 | LEAP was published in: 7 | [Accurate liability estimation improves power in ascertained case-control studies. Nat Methods 12, 332-4 (2015)](http://www.nature.com/nmeth/journal/v12/n4/full/nmeth.3285.html) 8 | 9 | 10 | ------------------ 11 | Installation 12 | ------------------ 13 | LEAP has the following dependencies: 14 | * Python 3.6 15 | * [Numpy](http://www.numpy.org/) and [Scipy](http://www.scipy.org/) 16 | * [Scikits-learn](http://scikit-learn.org/stable/) 17 | * The Python [FaST-LMM package](https://github.com/fastlmm/FaST-LMM). 18 | 19 | After installind these dependencies, you can install LEAP via: 20 | `git clone https://github.com/omerwe/LEAP` 21 | 22 | To verify that everything is correctly installed, please run the script test.py. It will run a small example analysis and print an error message if any problem is found. 23 | 24 | 25 | ------------------ 26 | Usage instructions 27 | ---------------------- 28 | There are two ways to run LEAP. 29 | The first is via a Python API. A detailed explanation about this option is provided in the [LEAP Ipython notebook](https://nbviewer.jupyter.org/github/omerwe/LEAP/blob/master/Leap_example.ipynb). 30 | 31 | The second option is to run LEAP though a series of Python scripts, as detailed below. This option is more suitable for those not familiar with Python. The script leap_pipeline.sh runs the full LEAP pipeline on a small example dataset, and can be used for reference. 32 | 33 | Generally, LEAP uses the same file formats as [FaST-LMM](https://github.com/fastlmm/FaST-LMM). 34 | Namely, input files are in [binary Plink format](http://zzz.bwh.harvard.edu/plink/binary.shtml). 35 | When there is a contradiction between file formats used by Plink and by FastLMM, LEAP uses the convention adopted by FastLMM. 36 | Explanations about the parameters used by all the scripts can be seen by typing 37 | ``` 38 | python --help 39 | ``` 40 | 41 | The command-line options for LEAP largely follow the options of the [C++ version of 42 | FaST-LMM](http://research.microsoft.com/en-us/projects/fastlmm/). 43 | 44 | 45 | ### The LEAP pipeline 46 | **1) (optional): Find related individuals to be removed:** 47 | ``` 48 | python findRelated.py --bfilesim --out 49 | ``` 50 | This script creates a file marking the individuals that need to be removed to eliminate relatedness. 51 | 52 | **2) Compute an eigendecomposition of the kinship matrix:** 53 | ``` 54 | python eigenDecompose.py --bfilesim --out [--extractSim --pheno ] 55 | ``` 56 | This script computes a kinship matrix and its eigendecomposition, and saves them to speed up subsequent stages. It is recommended to perform a leave-one-chromosome-out (LOCO) analysis by computing a different kinship matrix for each chromosome, each one consisting of all SNPs except those on the selected chromosome. The optional extractSim file is a text file with a list of SNP names (one SNP per line) to facilitate this. The optional phenotype file is only used to exclude individuals with an unknown phenotype. 57 | 58 | **3) Compute heritability using [PCGC regression](http://www.pnas.org/content/111/49/E5272.long):** 59 | ``` 60 | python calc_h2.py --bfilesim --prev --pheno --h2coeff 1.0 [--eigen --extractSim --related --h2coeff ] 61 | ``` 62 | This script outputs the heritability estimate. The optional eigen file is the one created in stage 2. The optional extractSim file is a text file with a list of SNP names (one SNP per line) that will be used for heritability estimation. It is recommended to perform a different heritability and liability estimation for every excluded chromosome, and then testing the SNPs on the excluded chromosome for association with the estimated liabilities. The bfilesim and extractSim parameters must be the same as the ones used in stage 2. The optional relatedness file should be the output of stage 1, and is used to exclude related individuals from the analysis, which improves analysis results. 63 | 64 | **4) Estimate liabilities:** 65 | ``` 66 | python probit.py --bfilesim --pheno --prev --out --h2 [--eigen --extractSim --related ] 67 | ``` 68 | This script creates a file called \.liabs, with estimated liabilities for every individual. The estimated liabilities can be used directly for GWAS by using them as a standard phenotype file. The eigen file is the one computed in stage 2, and the h2 parameter should be the heritability estimate from stage 3. The extractSim and relatedness file parameters should be the same as in stage 3. 69 | 70 | **5) Test for Associations:** 71 | ``` 72 | python leap_gwas.py --bfilesim --bfile --pheno --out --h2 [--eigen --extractSim --extract ] 73 | ``` 74 | This script performs GWAS with a prespecified heritability level (as computed in stage 2). The eigen file is the one from stage 2, and the pheno parameter is the liabilities file computed in stage 4. The syntax largely follows that of the [C++ version of FaST-LMM](http://research.microsoft.com/en-us/projects/fastlmm/). 75 | The bfile and bfilesim parameters can both point to the same file. In this case, the extract and extractSim parameters should be used to guarantee that kinship estimation doesn't use SNPs on the excluded chromosome, and that all tested SNPs are on the excluded chromosome. 76 | 77 | 78 | ----------------- 79 | General comments and tips 80 | ------------------------- 81 | **1)** Fixed effects can be included in stages 3-5 by adding the flag --covar. 82 | Please type 83 | ``` 84 | python probit.py --help 85 | ``` 86 | and 87 | ``` 88 | python leap_gwas.py --help 89 | ``` 90 | for instructions. However, we note that under extreme ascertainment, it is recommded to use covariates only in stages 3-4 (see the paper for details). 91 | 92 | **2)** As described in the main text, it is recommended to perform a different liability estimation for every excluded chromosome, and then testing the SNPs on the excluded chromosome for association with the estimated liabilities. The -extractSim flag is useful for this. Please see the example file leap_pipeline.sh for a usage example. 93 | 94 | **3)** A complete end-to-end usage example is provided with the LEAP source files, and can be invoked via the script leap_pipeline.sh. 95 | This example estimates liabilities for a small balanced case-control dataset. 96 | The dataset was simulated with 50% heritability and 0.1% prevalence. It included 500 cases, 500 controls, 499 causal SNPs and 10000 SNPs differentiated with FST=0.01. Causal SNPs are called csnp\. The original liabilities for this file are available in the file dataset1.phe.liab (but this file is not used by LEAP). 97 | 98 | 99 | ----------------- 100 | Contact 101 | --------- 102 | For questions and comments, please create a Github issue. 103 | 104 | 105 | -------------------------------------------------------------------------------- /calc_h2.py: -------------------------------------------------------------------------------- 1 | import numpy as np 2 | import argparse 3 | import scipy.stats as stats 4 | import scipy.linalg.blas as blas 5 | import sklearn.linear_model 6 | import time 7 | import sys 8 | np.set_printoptions(precision=3, linewidth=200) 9 | from . import leapUtils 10 | from . import leapMain 11 | 12 | 13 | def calcLiabThreholds(U, S, keepArr, phe, numRemovePCs, prev, covar): 14 | 15 | #Run logistic regression 16 | if (numRemovePCs > 0): 17 | G = U[:, -numRemovePCs:] * np.sqrt(S[-numRemovePCs:]) 18 | else: 19 | G = np.empty((phe.shape[0], 0)) 20 | if (covar is not None): G = np.concatenate((G, covar), axis=1) 21 | 22 | Logreg = sklearn.linear_model.LogisticRegression(penalty='l2', C=500000, fit_intercept=True) 23 | Logreg.fit(G[keepArr, :], phe[keepArr]) 24 | 25 | #Compute individual thresholds 26 | Pi = Logreg.predict_proba(G)[:,1] 27 | 28 | #Compute thresholds 29 | P = np.sum(phe==1) / float(phe.shape[0]) 30 | K = prev 31 | Ki = K*(1-P) / (P*(1-K)) * Pi / (1 + K*(1-P) / (P*(1-K))*Pi - Pi) 32 | thresholds = stats.norm(0,1).isf(Ki) 33 | thresholds[Ki>=1.] = -999999999 34 | thresholds[Ki<=0.] = 999999999 35 | 36 | return Pi, thresholds 37 | 38 | 39 | def calcH2Continuous_twotails(XXT, phe, keepArr, prev): 40 | 41 | print('computing h2 for a two-tails ascertained study...') 42 | 43 | XXT = XXT[np.ix_(keepArr, keepArr)] 44 | phe = phe[keepArr] 45 | 46 | t1 = stats.norm(0,1).ppf(prev) 47 | t2 = stats.norm(0,1).isf(prev) 48 | phit1 = stats.norm(0,1).pdf(t1) 49 | phit2 = stats.norm(0,1).pdf(t2) 50 | 51 | K1 = prev 52 | K2 = prev 53 | 54 | xCoeff = ((phit2*t2 - phit1*t1 + K1 + K2)**2 * (K1+K2)**2 - (phit2-phit1)**4) / (K1 + K2)**4 55 | intersect = ((phit2-phit1) / (K1+K2))**2 56 | 57 | pheMean = 0 58 | pheVar = 1 59 | 60 | x = xCoeff * XXT 61 | y = np.outer((phe-pheMean)/np.sqrt(pheVar), (phe-pheMean)/np.sqrt(pheVar)) 62 | y -= intersect 63 | 64 | y = y[np.triu_indices(y.shape[0], 1)] 65 | x = x[np.triu_indices(x.shape[0], 1)] 66 | 67 | slope, intercept, rValue, pValue, stdErr = stats.linregress(x,y) 68 | return slope 69 | 70 | 71 | 72 | def calcH2Continuous(XXT, phe, keepArr, prev): 73 | t = stats.norm(0,1).isf(prev) 74 | phit = stats.norm(0,1).pdf(t) 75 | 76 | K1 = 1 - prev 77 | K2 = 1 - K1 78 | P = np.sum(phe0) / float(phe.shape[0]) 104 | 105 | XXT = XXT[np.ix_(keepArr, keepArr)] 106 | phe = phe[keepArr] 107 | 108 | if (thresholds is None): 109 | t = stats.norm(0,1).isf(K) 110 | phit = stats.norm(0,1).pdf(t) 111 | xCoeff = P*(1-P) / (K**2 * (1-K)**2) * phit**2 112 | y = np.outer((phe-P) / np.sqrt(P*(1-P)), (phe-P) / np.sqrt(P*(1-P))) 113 | x = xCoeff * XXT 114 | 115 | else: 116 | probs = probs[keepArr] 117 | thresholds = thresholds[keepArr] 118 | Ki = K*(1-P) / (P*(1-K)) * probs / (1 + K*(1-P) / (P*(1-K))*probs - probs) 119 | phit = stats.norm(0,1).pdf(thresholds) 120 | probsInvOuter = np.outer(probs*(1-probs), probs*(1-probs)) 121 | y = np.outer(phe-probs, phe-probs) / np.sqrt(probsInvOuter) 122 | sumProbs = np.tile(np.column_stack(probs).T, (1,probs.shape[0])) + np.tile(probs, (probs.shape[0], 1)) 123 | Atag0 = np.outer(phit, phit) * (1 - (sumProbs)*(P-K)/(P*(1-K)) + np.outer(probs, probs)*(((P-K)/(P*(1-K)))**2)) / np.sqrt(probsInvOuter) 124 | B0 = np.outer(Ki + (1-Ki)*(K*(1-P))/(P*(1-K)), Ki + (1-Ki)*(K*(1-P))/(P*(1-K))) 125 | x = Atag0 / B0 * XXT 126 | 127 | y = y[np.triu_indices(y.shape[0], 1)] 128 | x = x[np.triu_indices(x.shape[0], 1)] 129 | 130 | slope, intercept, rValue, pValue, stdErr = stats.linregress(x,y) 131 | return slope 132 | 133 | 134 | 135 | def calc_h2(pheno, prev, eigen, keepArr, covar, numRemovePCs, lowtail): 136 | 137 | pheno = leapUtils._fixup_pheno(pheno) 138 | 139 | #Extract phenotype 140 | if isinstance(pheno, dict): phe = pheno['vals'] 141 | else: phe = pheno 142 | if (len(phe.shape)==2): 143 | if (phe.shape[1]==1): phe=phe[:,0] 144 | else: raise Exception('More than one phenotype found') 145 | if (keepArr is None): keepArr = np.ones(phe.shape[0], dtype=np.bool) 146 | 147 | #Compute kinship matrix 148 | XXT = eigen['XXT'] 149 | 150 | #Remove top PCs from kinship matrix 151 | if (numRemovePCs > 0): 152 | if (eigen is None): S,U = leapUtils.eigenDecompose(XXT) 153 | else: S, U = eigen['arr_1'], eigen['arr_0'] 154 | print('Removing the top', numRemovePCs, 'PCs from the kinship matrix') 155 | XXT -= (U[:, -numRemovePCs:]*S[-numRemovePCs:]).dot(U[:, -numRemovePCs:].T) 156 | else: 157 | U, S = None, None 158 | 159 | #Determine if this is a case-control study 160 | pheUnique = np.unique(phe) 161 | if (pheUnique.shape[0] < 2): raise Exception('Less than two different phenotypes observed') 162 | isCaseControl = (pheUnique.shape[0] == 2) 163 | 164 | if isCaseControl: 165 | print('Computing h2 for a binary phenotype') 166 | pheMean = phe.mean() 167 | phe[phe <= pheMean] = 0 168 | phe[phe > pheMean] = 1 169 | if (numRemovePCs > 0 or covar is not None): 170 | probs, thresholds = calcLiabThreholds(U, S, keepArr, phe, numRemovePCs, prev, covar) 171 | h2 = calcH2Binary(XXT, phe, probs, thresholds, keepArr, prev) 172 | else: h2 = calcH2Binary(XXT, phe, None, None, keepArr, prev) 173 | else: 174 | if (covar is not None): raise Exception('Covariates with a continuous phenotype are currently not supported') 175 | print('Computing h2 for a continuous phenotype') 176 | if (not lowtail): h2 = calcH2Continuous(XXT, phe, keepArr, prev) 177 | else: h2 = calcH2Continuous_twotails(XXT, phe, keepArr, prev) 178 | 179 | if (h2 <= 0): raise Exception("Negative heritability found. Exitting...") 180 | if (np.isnan(h2)): raise Exception("Invalid heritability estimate. Please double-check your input for any errors.") 181 | 182 | print('h2: %0.6f'%h2) 183 | return h2 184 | 185 | 186 | if __name__ == '__main__': 187 | 188 | parser = argparse.ArgumentParser() 189 | parser.add_argument('--bfilesim', metavar='bfilesim', default=None, help='Binary plink file') 190 | parser.add_argument('--extractSim', metavar='extractSim', default=None, help='SNPs subset to use') 191 | parser.add_argument('--prev', metavar='prev', type=float, default=None, help='Trait prevalence') 192 | parser.add_argument('--numRemovePCs', metavar='numRemovePCs', type=int, default=10, help='Number of principal components to fit') 193 | parser.add_argument('--pheno', metavar='pheno', default=None, help='Phenotype file in Plink format') 194 | parser.add_argument('--eigen', metavar='eigen', default=None, help='eigen file') 195 | parser.add_argument('--related', metavar='related', default=None, help='relatedness file') 196 | parser.add_argument('--covar', metavar='covar', default=None, help='covariates file') 197 | 198 | parser.add_argument('--lowtail', metavar='lowtail', type=int, default=0, help='Assume that both tails of the liabilities distribution are oversampled (0 or 1 - default 0)') 199 | parser.add_argument('--relCutoff', metavar='relCutoff', type=float, default=0.05, help='relatedness cutoff (set to negative value to override relatedness check)') 200 | parser.add_argument('--missingPhenotype', metavar='missingPhenotype', default='-9', help='identifier for missing values (default: -9)') 201 | args = parser.parse_args() 202 | 203 | 204 | if (args.bfilesim is None): raise Exception('--bfilesim must be supplied') 205 | if (args.prev is None): raise Exception('--prev must be supplied') 206 | if (args.pheno is None): raise Exception('--pheno must be supplied') 207 | 208 | #Read bfilesim and pheno file for heritability computation 209 | bed, phe = leapUtils.loadData(args.bfilesim, args.extractSim, args.pheno, args.missingPhenotype, loadSNPs=(args.eigen is None), standardize=True) 210 | 211 | #Read/create eigendecomposition 212 | if (args.eigen is not None): eigen = np.load(args.eigen) 213 | else: 214 | from . import eigenDecompose 215 | eigen = eigenDecompose.eigenDecompose(bed) 216 | 217 | #Compute relatedness 218 | if (args.relCutoff <= 0): keepArr = np.ones(bed.iid.shape[0], dtype=bool) 219 | else: 220 | if (args.related is None): 221 | bed2 = bed 222 | if (args.extractSim is not None or args.eigen is not None): bed2, _ = leapUtils.loadData(args.bfilesim, None, args.pheno, args.missingPhenotype, loadSNPs=True) 223 | keepArr = leapUtils.findRelated(bed2, args.relCutoff) 224 | else: 225 | keepArr = leapUtils.loadRelatedFile(bed, args.related) 226 | 227 | 228 | #Read covar file 229 | if (args.covar is not None): 230 | covar = leapUtils.loadCovars(bed, args.covar) 231 | covar -= covar.mean() 232 | covar /= covar.std() 233 | print('Read', covar.shape[1], 'covariates from file') 234 | else: 235 | covar = None 236 | 237 | leapMain.calcH2(phe, args.prev, eigen, keepArr, covar, args.numRemovePCs, args.lowtail==1) 238 | 239 | 240 | 241 | 242 | 243 | -------------------------------------------------------------------------------- /LICENSE.md: -------------------------------------------------------------------------------- 1 | 2 | Apache License 3 | Version 2.0, January 2004 4 | http://www.apache.org/licenses/ 5 | 6 | TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION 7 | 8 | 1. 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The text should be enclosed in the appropriate 185 | comment syntax for the file format. We also recommend that a 186 | file or class name and description of purpose be included on the 187 | same "printed page" as the copyright notice for easier 188 | identification within third-party archives. 189 | 190 | Copyright 2014 Omer Weissbrod 191 | 192 | Licensed under the Apache License, Version 2.0 (the "License"); 193 | you may not use this file except in compliance with the License. 194 | You may obtain a copy of the License at 195 | 196 | http://www.apache.org/licenses/LICENSE-2.0 197 | 198 | Unless required by applicable law or agreed to in writing, software 199 | distributed under the License is distributed on an "AS IS" BASIS, 200 | WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. 201 | See the License for the specific language governing permissions and 202 | limitations under the License. 203 | -------------------------------------------------------------------------------- /leapUtils.py: -------------------------------------------------------------------------------- 1 | import numpy as np 2 | from optparse import OptionParser 3 | import scipy.linalg as la 4 | import scipy.stats as stats 5 | import scipy.linalg.blas as blas 6 | import pandas as pd 7 | import csv 8 | import time 9 | import fastlmm.util.VertexCut as vc 10 | from pysnptools.snpreader.bed import Bed 11 | import pysnptools.util as pstutil 12 | import pysnptools.util.pheno as phenoUtils 13 | np.set_printoptions(precision=3, linewidth=200) 14 | 15 | 16 | 17 | def loadData(bfile, extractSim, phenoFile, missingPhenotype='-9', loadSNPs=False, standardize=True): 18 | bed = Bed(bfile, count_A1=True) 19 | 20 | if (extractSim is not None): 21 | f = open(extractSim) 22 | csvReader = csv.reader(f) 23 | extractSnpsSet = set([]) 24 | for l in csvReader: extractSnpsSet.add(l[0]) 25 | f.close() 26 | keepSnpsInds = [i for i in range(bed.sid.shape[0]) if bed.sid[i] in extractSnpsSet] 27 | bed = bed[:, keepSnpsInds] 28 | 29 | phe = None 30 | if (phenoFile is not None): bed, phe = loadPheno(bed, phenoFile, missingPhenotype) 31 | 32 | if (loadSNPs): 33 | bed = bed.read() 34 | if (standardize): bed = bed.standardize() 35 | 36 | return bed, phe 37 | 38 | 39 | def loadPheno(bed, phenoFile, missingPhenotype='-9', keepDict=False): 40 | pheno = phenoUtils.loadOnePhen(phenoFile, missing=missingPhenotype, vectorize=True) 41 | checkIntersection(bed, pheno, 'phenotypes') 42 | bed, pheno = pstutil.intersect_apply([bed, pheno]) 43 | if (not keepDict): pheno = pheno['vals'] 44 | return bed, pheno 45 | 46 | 47 | def checkIntersection(bed, fileDict, fileStr, checkSuperSet=False): 48 | bedSet = set((b[0], b[1]) for b in bed.iid) 49 | fileSet = set((b[0], b[1]) for b in fileDict['iid']) 50 | 51 | if checkSuperSet: 52 | if (not fileSet.issuperset(bedSet)): raise Exception(fileStr + " file does not include all individuals in the bfile") 53 | 54 | intersectSet = bedSet.intersection(fileSet) 55 | if (len(intersectSet) != len (bedSet)): 56 | print(len(intersectSet), 'individuals appear in both the plink file and the', fileStr, 'file') 57 | 58 | 59 | def symmetrize(a): 60 | return a + a.T - np.diag(a.diagonal()) 61 | 62 | 63 | 64 | def loadRelatedFile(bed, relFile): 65 | relatedDict = phenoUtils.loadOnePhen(relFile, vectorize=True) 66 | checkIntersection(bed, relatedDict, 'relatedness', checkSuperSet=True) 67 | _, relatedDict = pstutil.intersect_apply([bed, relatedDict]) 68 | related = relatedDict['vals'] 69 | keepArr = (related < 0.5) 70 | print(np.sum(~keepArr), 'individuals will be removed due to high relatedness') 71 | return keepArr 72 | 73 | 74 | def findRelated(bed, cutoff, kinshipFile=None): 75 | 76 | if (kinshipFile is None): 77 | print('Computing kinship matrix...') 78 | t0 = time.time() 79 | XXT = symmetrize(blas.dsyrk(1.0, bed.val, lower=1) / bed.val.shape[1]) 80 | print('Done in %0.2f'%(time.time()-t0), 'seconds') 81 | else: 82 | XXT = np.loadtxt(kinshipFile) 83 | 84 | #Find related individuals 85 | removeSet = set(np.sort(vc.VertexCut().work(XXT, cutoff))) #These are the indexes of the IIDs to remove 86 | print('Marking', len(removeSet), 'individuals to be removed due to high relatedness') 87 | 88 | #keepArr = np.array([(1 if iid in keepSet else 0) for iid in bed.iid], dtype=bool) 89 | keepArr = np.ones(bed.iid.shape[0], dtype=bool) 90 | for i in removeSet: keepArr[i] = False 91 | return keepArr 92 | 93 | 94 | 95 | def eigenDecompose(XXT, ignore_neig=False): 96 | t0 = time.time() 97 | print('Computing eigendecomposition...') 98 | s,U = la.eigh(XXT) 99 | if (not ignore_neig and (np.min(s) < -1e-4)): raise Exception('Negative eigenvalues found') 100 | s[s<0]=0 101 | ind = np.argsort(s) 102 | ind = ind[s>1e-12] 103 | U = U[:, ind] 104 | s = s[ind] 105 | print('Done in %0.2f'%(time.time()-t0), 'seconds') 106 | return s,U 107 | 108 | 109 | 110 | def loadCovars(bed, covarFile): 111 | covarsDict = phenoUtils.loadPhen(covarFile) 112 | checkIntersection(bed, covarsDict, 'covariates', checkSuperSet=True) 113 | _, covarsDict = pstutil.intersect_apply([bed, covarsDict]) 114 | covar = covarsDict['vals'] 115 | return covar 116 | 117 | def getSNPCovarsMatrix(bed, resfile, pthresh, mindist): 118 | snpNameToNumDict = dict([]) 119 | for i,s in enumerate(bed.sid): snpNameToNumDict[s] = i 120 | 121 | f = open(resfile) 122 | csvReader = csv.reader(f, delimiter="\t") 123 | next(csvReader) 124 | significantSNPs = [] 125 | significantSNPNames = [] 126 | lastPval = 0 127 | featuresPosList = [] 128 | for l in csvReader: 129 | snpName, pVal = l[0], float(l[4]) 130 | if (pVal < lastPval): raise Exception('P-values are not sorted in descending order: ' + str(pVal) + ">" + str(lastPval)) 131 | lastPval = pVal 132 | if (pVal > pthresh): break 133 | if (snpName not in snpNameToNumDict): continue 134 | significantSNPNames.append(snpName) 135 | if (mindist == 0): 136 | significantSNPs.append(snpNameToNumDict[snpName]) 137 | print('Using SNP', snpName, 'with p<%0.2e'%pVal, 'as a fixed effect') 138 | else: 139 | posArr = bed.pos[snpNameToNumDict[snpName]] 140 | chrom, pos = posArr[0], int(posArr[2]) 141 | addSNP = True 142 | for (c,p) in featuresPosList: 143 | if (chrom == c and abs(pos-p) < mindist): 144 | addSNP = False 145 | break 146 | if addSNP: 147 | significantSNPs.append(snpNameToNumDict[snpName]) 148 | featuresPosList.append((chrom, pos)) 149 | print('Using SNP', snpName, '('+str(int(chrom))+':'+str(pos)+') with p<%0.2e'%pVal, 'as a fixed effect') 150 | f.close() 151 | 152 | snpCovarsMat = bed.val[:, significantSNPs] 153 | return snpCovarsMat 154 | 155 | 156 | 157 | def getExcludedChromosome(bfile, chrom): 158 | bed = Bed(bfile, count_A1=True) 159 | indsToKeep = (bed.pos[:,0] != chrom) 160 | bed = bed[:, indsToKeep] 161 | return bed.read().standardize() 162 | 163 | def getChromosome(bfile, chrom): 164 | bed = Bed(bfile, count_A1=True) 165 | indsToKeep = (bed.pos[:,0] == chrom) 166 | bed = bed[:, indsToKeep] 167 | return bed.read().standardize() 168 | 169 | 170 | def _fixupBedAndPheno(bed, pheno, missingPhenotype='-9'): 171 | bed = _fixupBed(bed) 172 | bed, pheno = _fixup_pheno(pheno, bed, missingPhenotype) 173 | return bed, pheno 174 | 175 | def _fixupBed(bed): 176 | if isinstance(bed, str): 177 | return Bed(bed, count_A1=True).read().standardize() 178 | else: return bed 179 | 180 | def _fixup_pheno(pheno, bed=None, missingPhenotype='-9'): 181 | if (isinstance(pheno, str)): 182 | if (bed is not None): 183 | bed, pheno = loadPheno(bed, pheno, missingPhenotype, keepDict=True) 184 | return bed, pheno 185 | else: 186 | phenoDict = phenoUtils.loadOnePhen(pheno, missing=missingPhenotype, vectorize=True) 187 | return phenoDict 188 | else: 189 | if (bed is not None): return bed, pheno 190 | else: return pheno 191 | 192 | def linreg(bed, pheno): 193 | 194 | #Extract snps and phenotype 195 | bed, pheno = _fixupBedAndPheno(bed, pheno) 196 | if isinstance(pheno, dict): phe = pheno['vals'] 197 | else: phe = pheno 198 | if (len(phe.shape)==2): 199 | if (phe.shape[1]==1): phe=phe[:,0] 200 | else: raise Exception('More than one phenotype found') 201 | 202 | #Normalize y. We assume X is already normalized. 203 | y = phe - phe.mean(); y /= y.std() 204 | 205 | #Compute p-values 206 | Xy = bed.val.T.dot(y) / y.shape[0] 207 | Xy[Xy>1.0] = 1.0 208 | Xy[Xy<-1.0] = -1.0 209 | df = y.shape[0]-2 210 | TINY = 1.0e-20 211 | t = Xy * np.sqrt(df / ((1.0-Xy+TINY) * (1.0+Xy+TINY))) 212 | pValT = stats.t.sf(np.abs(t), df)*2 213 | 214 | #Create pandas data frame 215 | items = [ 216 | ('SNP', bed.sid), 217 | ('Chr', bed.pos[:,0]), 218 | ('GenDist', bed.pos[:,1]), 219 | ('ChrPos', bed.pos[:,2]), 220 | ('PValue', pValT), 221 | ] 222 | frame = pd.DataFrame.from_items(items) 223 | frame.sort("PValue", inplace=True) 224 | frame.index = np.arange(len(frame)) 225 | return frame 226 | 227 | def powerPlot(df, causalSNPs, title=''): 228 | import pylab 229 | causalSNPs = set(causalSNPs) 230 | csnpPvals = df[df['SNP'].isin(causalSNPs)]["PValue"] 231 | pvalPoints = np.logspace(-6, -2, num=1000) 232 | power = [np.mean(csnpPvals < p ) for p in list(pvalPoints)] 233 | pylab.plot(-np.log10(pvalPoints), power) 234 | pylab.xlabel("-log10(Significance Threshold)") 235 | pylab.ylabel("Power") 236 | pylab.title(title) 237 | 238 | 239 | def computeCovar(bed, shrinkMethod, fitIndividuals): 240 | eigen = dict([]) 241 | 242 | if (shrinkMethod in ['lw', 'oas', 'l1', 'cv']): 243 | import sklearn.covariance as cov 244 | t0 = time.time() 245 | print('Estimating shrunk covariance using', shrinkMethod, 'estimator...') 246 | 247 | if (shrinkMethod == 'lw'): covEstimator = cov.LedoitWolf(assume_centered=True, block_size = 5*bed.val.shape[0]) 248 | elif (shrinkMethod == 'oas'): covEstimator = cov.OAS(assume_centered=True) 249 | elif (shrinkMethod == 'l1'): covEstimator = cov.GraphLassoCV(assume_centered=True, verbose=True) 250 | elif (shrinkMethod == 'cv'): 251 | shrunkEstimator = cov.ShrunkCovariance(assume_centered=True) 252 | param_grid = {'shrinkage': [0.01, 0.1, 0.3, 0.5, 0.7, 0.9, 0.99]} 253 | covEstimator = sklearn.grid_search.GridSearchCV(shrunkEstimator, param_grid) 254 | else: raise Exception('unknown covariance regularizer') 255 | 256 | covEstimator.fit(bed.val[fitIndividuals, :].T) 257 | if (shrinkMethod == 'l1'): 258 | alpha = covEstimator.alpha_ 259 | print('l1 alpha chosen:', alpha) 260 | covEstimator2 = cov.GraphLasso(alpha=alpha, assume_centered=True, verbose=True) 261 | else: 262 | if (shrinkMethod == 'cv'): shrinkEstimator = clf.best_params_['shrinkage'] 263 | else: shrinkEstimator = covEstimator.shrinkage_ 264 | print('shrinkage estimator:', shrinkEstimator) 265 | covEstimator2 = cov.ShrunkCovariance(shrinkage=shrinkEstimator, assume_centered=True) 266 | covEstimator2.fit(bed.val.T) 267 | XXT = covEstimator2.covariance_ * bed.val.shape[1] 268 | print('Done in %0.2f'%(time.time()-t0), 'seconds') 269 | 270 | else: 271 | print('Computing kinship matrix...') 272 | t0 = time.time() 273 | XXT = symmetrize(blas.dsyrk(1.0, bed.val, lower=1)) 274 | print('Done in %0.2f'%(time.time()-t0), 'seconds') 275 | try: shrinkParam = float(shrinkMethod) 276 | except: shrinkParam = -1 277 | if (shrinkMethod == 'mylw'): 278 | XXT_fit = XXT[np.ix_(fitIndividuals, fitIndividuals)] 279 | sE2R = (np.sum(XXT_fit**2) - np.sum(np.diag(XXT_fit)**2)) / (bed.val.shape[1]**2) 280 | #temp = (bed.val**2).dot((bed.val.T)**2) 281 | temp = symmetrize(blas.dsyrk(1.0, bed.val[fitIndividuals, :]**2, lower=1)) 282 | sER2 = (temp.sum() - np.diag(temp).sum()) / bed.val.shape[1] 283 | shrinkParam = (sER2 - sE2R) / (sE2R * (bed.val.shape[1]-1)) 284 | if (shrinkParam > 0): 285 | print('shrinkage estimator:', 1-shrinkParam) 286 | XXT = (1-shrinkParam)*XXT + bed.val.shape[1]*shrinkParam*np.eye(XXT.shape[0]) 287 | 288 | return XXT 289 | 290 | 291 | 292 | 293 | def standardize(X, method, optionsDict): 294 | fitIndividuals = np.ones(X.shape[0], dtype=np.bool) 295 | if (method == 'frq'): 296 | empMean = X.mean(axis=0) / 2.0 297 | X[:, empMean>0.5] = 2 - X[:, empMean>0.5] 298 | print('regularizng SNPs according to frq file...') 299 | frqFile = (optionsDict['bfilesim']+'.frq' if (optionsDict['frq'] is None) else optionsDict['frq']) 300 | mafs = np.loadtxt(frqFile, usecols=[1,2]).mean(axis=1) 301 | snpsMean = 2*mafs 302 | snpsStd = np.sqrt(2*mafs*(1-mafs)) 303 | elif (method == 'related'): 304 | if (optionsDict['related'] is None): raise Exception('related file not supplied') 305 | print('regularizng SNPs according to non-related individuals...') 306 | relLines = np.loadtxt(optionsDict['related'], usecols=[2]) 307 | keepArr = (relLines != 1) 308 | print('Excluding', np.sum(~keepArr), 'from the covariance matrix standardization') 309 | snpsMean = X[keepArr, :].mean(axis=0) 310 | snpsStd = X[keepArr, :].std(axis=0) 311 | fitIndividuals = keepArr 312 | elif (method == 'controls'): 313 | phe = optionsDict['pheno'] 314 | pheThreshold = phe.mean() 315 | controls = (phe 0): 78 | thresholdsEM = np.zeros(X.shape[0]) + thresholds 79 | 80 | for i in range(maxFixedIters): 81 | print('Beginning fixed effects iteration', i+1) 82 | t0 = time.time() 83 | prevBeta = beta.copy() 84 | 85 | #Learn fixed effects 86 | thresholdsTemp = thresholdsEM - X[:, numFixedFeatures:].dot(beta[numFixedFeatures:]) 87 | args = (X[:, :numFixedFeatures], cases, controls, thresholdsTemp, 0, normPDF, h2) 88 | 89 | optObj = opt.minimize(funcToSolve, x0=beta[:numFixedFeatures], args=args, jac=True, method=method, hess=hess) 90 | if (not optObj.success): print(optObj.message); #raise Exception('Learning failed with message: ' + optObj.message) 91 | beta[:numFixedFeatures] = optObj.x 92 | 93 | #Learn random effects 94 | thresholdsTemp = thresholdsEM - X[:, :numFixedFeatures].dot(beta[:numFixedFeatures]) 95 | args = (X[:, numFixedFeatures:], cases, controls, thresholdsTemp, invRegParam, normPDF, h2) 96 | optObj = opt.minimize(funcToSolve, x0=beta[numFixedFeatures:], args=args, jac=True, method=method, hess=hess) 97 | if (not optObj.success): print(optObj.message); #raise Exception('Learning failed with message: ' + optObj.message) 98 | beta[numFixedFeatures:] = optObj.x 99 | 100 | diff = np.sqrt(np.mean(beta[:numFixedFeatures]**2 - prevBeta[:numFixedFeatures]**2)) 101 | print('Done in', '%0.2f'%(time.time()-t0), 'seconds') 102 | print('Diff:', '%0.4e'%diff) 103 | if (diff < epsilon): break 104 | return beta 105 | 106 | 107 | 108 | def probit(bed, pheno, h2, prev, eigen, outFile, keepArr, covar, thresholds, nofail, 109 | numSkipTopPCs, mineig, hess, recenter, maxFixedIters, epsilon, treatFixedAsRandom=False): 110 | 111 | bed, pheno = leapUtils._fixupBedAndPheno(bed, pheno) 112 | 113 | #Extract phenotype 114 | if isinstance(pheno, dict): phe = pheno['vals'] 115 | else: phe = pheno 116 | if (len(phe.shape)==2): 117 | if (phe.shape[1]==1): phe=phe[:,0] 118 | else: raise Exception('More than one phenotype found') 119 | if (keepArr is None): keepArr = np.ones(phe.shape[0], dtype=np.bool) 120 | 121 | S = eigen['arr_1'] * bed.sid.shape[0] 122 | U = eigen['arr_0'] 123 | S = np.sqrt(S) 124 | goodS = (S>mineig) 125 | if (numSkipTopPCs > 0): goodS[-numSkipTopPCs:] = False 126 | if (np.sum(~goodS) > 0): print('Removing', np.sum(~goodS), 'PCs with low variance') 127 | G = U[:, goodS]*S[goodS] 128 | 129 | #Set binary vector 130 | pheUnique = np.unique(phe) 131 | if (pheUnique.shape[0] != 2): raise Exception('phenotype file has more than two values') 132 | pheMean = phe.mean() 133 | cases = (phe>pheMean) 134 | phe[~cases] = 0 135 | phe[cases] = 1 136 | 137 | #run probit regression 138 | t = stats.norm(0,1).isf(prev) 139 | if (thresholds is not None): t = thresholds 140 | 141 | #Recenter G to only consider the unrelated individuals 142 | if recenter: G -= np.mean(G[keepArr, :], axis=0) 143 | else: G -= np.mean(G, axis=0) 144 | 145 | numFixedFeatures = 0 146 | if (covar is not None): 147 | covar -= covar.mean() 148 | covar /= covar.std() 149 | covar *= np.mean(np.std(G, axis=0)) 150 | G = np.concatenate((covar, G), axis=1) 151 | if (not treatFixedAsRandom): numFixedFeatures += covar.shape[1] 152 | 153 | #Run Probit regression 154 | probitThresh = (t if thresholds is None else t[keepArr]) 155 | beta = probitRegression(G[keepArr, :], phe[keepArr], probitThresh, bed.sid.shape[0], numFixedFeatures, h2, hess, maxFixedIters, epsilon, nofail) 156 | 157 | #Predict liabilities for all individuals 158 | meanLiab = G.dot(beta) 159 | liab = meanLiab.copy() 160 | indsToFlip = ((liab <= t) & (phe>0.5)) | ((liab > t) & (phe<0.5)) 161 | liab[indsToFlip] = stats.norm(0,1).isf(prev) 162 | 163 | if (outFile is not None): 164 | #save liabilities 165 | f = open(outFile+'.liabs', 'w') 166 | for ind_i,[fid,iid] in enumerate(bed.iid): f.write(' '.join([fid, iid, '%0.3f'%liab[ind_i]]) + '\n') 167 | f.close() 168 | 169 | #save liabilities after regressing out the fixed effects 170 | if (numFixedFeatures > 0): 171 | liab_nofixed = liab - G[:, :numFixedFeatures].dot(beta[:numFixedFeatures]) 172 | f = open(outFile+'.liab_nofixed', 'w') 173 | for ind_i,[fid,iid] in enumerate(bed.iid): f.write(' '.join([fid, iid, '%0.3f'%liab_nofixed[ind_i]]) + '\n') 174 | f.close() 175 | 176 | liab_nofixed2 = meanLiab - G[:, :numFixedFeatures].dot(beta[:numFixedFeatures]) 177 | indsToFlip = ((liab_nofixed2 <= t) & (phe>0.5)) | ((liab_nofixed2 > t) & (phe<0.5)) 178 | liab_nofixed2[indsToFlip] = stats.norm(0,1).isf(prev) 179 | f = open(outFile+'.liab_nofixed2', 'w') 180 | for ind_i,[fid,iid] in enumerate(bed.iid): f.write(' '.join([fid, iid, '%0.3f'%liab_nofixed2[ind_i]]) + '\n') 181 | f.close() 182 | 183 | #Return phenotype struct with liabilities 184 | liabsStruct = { 185 | 'header':[None], 186 | 'vals':liab, 187 | 'iid':bed.iid 188 | } 189 | return liabsStruct 190 | 191 | 192 | 193 | if __name__ == '__main__': 194 | 195 | parser = argparse.ArgumentParser() 196 | parser.add_argument('--bfilesim', metavar='bfilesim', default=None, help='Binary plink file') 197 | parser.add_argument('--pheno', metavar='pheno', default=None, help='Phenotype file in Plink format') 198 | parser.add_argument('--h2', metavar='h2', type=float, default=None, help='Liability heritability') 199 | parser.add_argument('--eigen', metavar='eigen', default=None, help='eigen file') 200 | parser.add_argument('--prev', metavar='prev', type=float, default=None, help='Trait prevalence') 201 | parser.add_argument('--extractSim', metavar='extractSim', default=None, help='SNPs subset to use') 202 | parser.add_argument('--out', metavar='out', default=None, help='output file') 203 | 204 | parser.add_argument('--covar', metavar='covar', default=None, help='covariates file in FastLMM format') 205 | parser.add_argument('--thresholds', metavar='thresholds', default=None, help="liability thresholds file") 206 | parser.add_argument('--nofail', metavar='nofail', type=int, default=0, help="Do not raise exception if Probit fitting failed") 207 | parser.add_argument('--treatFixedAsRandom', metavar='treatFixedAsRandom', type=int, default=0, help="Whether to treat fixed effects as random effects") 208 | 209 | parser.add_argument('--relCutoff', metavar='relCutoff', type=float, default=0.05, help='Relatedness cutoff') 210 | parser.add_argument('--numSkipTopPCs', metavar='numSkipTopPCs', type=int, default=0, help='Number of PCs to skip') 211 | parser.add_argument('--numFixedPCs', metavar='numFixedPCs', type=int, default=0, help='Number of PCs to use as fixed effects') 212 | parser.add_argument('--hess', metavar='hess', type=int, default=1, help='Whether to compute Hessian analytically (1) or not (0)') 213 | parser.add_argument('--bfile', metavar='bfile', default=None, help='Binary plink file with SNPs that can be used as fixed effects') 214 | parser.add_argument('--resfile', metavar='resfile', default=None, help='A linear regression results file in FastLMM format, used to choose SNPs that will be used as fixed effects') 215 | parser.add_argument('--pthresh', metavar='pthresh', type=float, default=5e-8, help='p-value cutoff below which SNPs will be used as fixed effects') 216 | parser.add_argument('--mineig', metavar='mineig', type=float, default=1e-3, help='eigenvectors with singular value below this value will not be used') 217 | parser.add_argument('--extract', metavar='extract', default=None, help='subset of SNPs to be considered as fixed effects') 218 | parser.add_argument('--related', metavar='related', default=None, help='File with info about related individuals to remove') 219 | parser.add_argument('--mindist', metavar='mindist', type=int, default=0, help='Minimum distance between fixed effects SNPs') 220 | parser.add_argument('--recenter', metavar='recenter', type=int, default=1, help='Whether to recenter features matrix so that only individuals participating in the model fitting stage will have zero mean for every feature (1 or 0)') 221 | parser.add_argument('--maxFixedIters', metavar='maxFixedIters', type=int, default=100, help='Max number of iterations for fitting of fixed effects') 222 | parser.add_argument('--epsilon', metavar='epsilon', type=float, default=1e-3, help='Convergence cutoff for fitting of fixed effects') 223 | parser.add_argument('--missingPhenotype', metavar='missingPhenotype', default='-9', help='identifier for missing values (default: -9)') 224 | args = parser.parse_args() 225 | 226 | 227 | if (args.extract is not None and args.bfile is None): raise Exception('--extract cannot be used without --bfile') 228 | if (args.bfile is not None and args.resfile is None): raise Exception('--bfile cannot be used without --resfile') 229 | if (args.bfilesim is None): raise Exception('bfilesim must be supplied') 230 | if (args.pheno is None): raise Exception('phenotype file must be supplied') 231 | if (args.out is None): raise Exception('output file name must be supplied') 232 | if (args.prev is None): raise Exception('prevlence must be supplied') 233 | if (args.h2 is None): raise Exception('heritability must be supplied') 234 | 235 | #Read bfilesim and pheno file for heritability computation 236 | bed, phe = leapUtils.loadData(args.bfilesim, args.extractSim, args.pheno, args.missingPhenotype, loadSNPs=(args.eigen is None), standardize=True) 237 | 238 | #Read/create eigendecomposition 239 | if (args.eigen is not None): eigen = np.load(args.eigen) 240 | else: 241 | from . import eigenDecompose 242 | eigen = eigenDecompose.eigenDecompose(bed) 243 | 244 | #Compute relatedness 245 | if (args.relCutoff <= 0): keepArr = np.ones(bed.iid.shape[0], dtype=bool) 246 | else: 247 | if (args.related is None): 248 | bed2 = bed 249 | if (args.extractSim is not None or args.eigen is not None): bed2, _ = leapUtils.loadData(args.bfilesim, None, args.pheno, args.missingPhenotype, loadSNPs=True) 250 | keepArr = leapUtils.findRelated(bed2, args.relCutoff) 251 | else: 252 | keepArr = leapUtils.loadRelatedFile(bed, args.related) 253 | 254 | 255 | #Add significant SNPs as fixed effects 256 | covar = None 257 | if (args.resfile is not None): 258 | bed_fixed, _ = leapUtils.loadData(args.bfile, args.extract, args.pheno, args.missingPhenotype, loadSNPs=True) 259 | covar = leapUtils.getSNPCovarsMatrix(bed_fixed, args.resfile, args.pthresh, args.mindist) 260 | print('using', covar.shape[1], 'SNPs as covariates') 261 | #Read covar file 262 | if (args.covar is not None): 263 | covarsMat = leapUtils.loadCovars(bed, args.covar) 264 | print('Read', covarsMat.shape[1], 'covariates from file') 265 | if (covar is None): covar = covarsMat 266 | else: covar = np.concatenate((covar, covarsMat), axis=1) 267 | 268 | if (args.thresholds is not None): thresholds = np.loadtxt(args.thresholds, usecols=[0]) 269 | else: thresholds = None 270 | 271 | leapMain.probit(bed, phe, args.h2, args.prev, eigen, args.out, keepArr, covar, thresholds, args.nofail==1, 272 | args.numSkipTopPCs, args.mineig, args.hess==1, args.recenter==1, args.maxFixedIters, args.epsilon, treatFixedAsRandom=args.treatFixedAsRandom>=1) 273 | 274 | -------------------------------------------------------------------------------- /dataset1/extracts/chr4_extract.txt: -------------------------------------------------------------------------------- 1 | csnp1 2 | csnp8 3 | csnp9 4 | csnp11 5 | csnp15 6 | csnp21 7 | csnp24 8 | csnp31 9 | csnp32 10 | csnp47 11 | csnp82 12 | csnp83 13 | csnp94 14 | csnp105 15 | csnp111 16 | csnp114 17 | csnp144 18 | csnp153 19 | csnp160 20 | csnp164 21 | csnp180 22 | csnp184 23 | csnp185 24 | csnp190 25 | csnp203 26 | csnp205 27 | csnp212 28 | csnp217 29 | csnp224 30 | csnp231 31 | csnp233 32 | csnp234 33 | csnp243 34 | csnp253 35 | csnp261 36 | csnp262 37 | csnp263 38 | csnp271 39 | csnp276 40 | csnp285 41 | csnp288 42 | csnp293 43 | csnp308 44 | csnp314 45 | csnp316 46 | csnp324 47 | csnp328 48 | csnp331 49 | csnp340 50 | csnp348 51 | csnp350 52 | csnp358 53 | csnp360 54 | csnp371 55 | csnp375 56 | csnp383 57 | csnp392 58 | csnp396 59 | csnp408 60 | csnp410 61 | csnp418 62 | csnp426 63 | csnp465 64 | csnp472 65 | snp505 66 | snp506 67 | snp530 68 | snp531 69 | snp536 70 | snp541 71 | snp544 72 | snp547 73 | snp548 74 | snp550 75 | snp553 76 | snp556 77 | snp565 78 | snp570 79 | snp575 80 | snp604 81 | snp619 82 | snp630 83 | snp632 84 | snp636 85 | snp638 86 | snp652 87 | snp655 88 | snp662 89 | snp667 90 | snp682 91 | snp704 92 | snp722 93 | snp724 94 | snp728 95 | snp738 96 | snp745 97 | snp767 98 | snp773 99 | snp780 100 | snp781 101 | snp786 102 | snp791 103 | snp793 104 | snp799 105 | snp803 106 | snp813 107 | snp842 108 | snp860 109 | snp865 110 | snp873 111 | snp889 112 | snp893 113 | snp930 114 | snp934 115 | snp949 116 | snp961 117 | snp972 118 | snp978 119 | snp980 120 | snp1011 121 | snp1017 122 | snp1031 123 | snp1040 124 | snp1068 125 | snp1076 126 | snp1090 127 | snp1091 128 | snp1115 129 | snp1124 130 | snp1142 131 | snp1165 132 | snp1168 133 | snp1182 134 | snp1192 135 | snp1220 136 | snp1234 137 | snp1235 138 | snp1239 139 | snp1244 140 | snp1272 141 | snp1286 142 | snp1293 143 | snp1298 144 | snp1303 145 | snp1306 146 | snp1323 147 | snp1335 148 | snp1370 149 | snp1380 150 | snp1386 151 | snp1387 152 | snp1399 153 | snp1411 154 | snp1416 155 | snp1428 156 | snp1438 157 | snp1452 158 | snp1464 159 | snp1466 160 | snp1468 161 | snp1479 162 | snp1502 163 | snp1507 164 | snp1511 165 | snp1549 166 | snp1579 167 | snp1581 168 | snp1592 169 | snp1597 170 | snp1602 171 | snp1608 172 | snp1626 173 | snp1628 174 | snp1636 175 | snp1647 176 | snp1656 177 | snp1660 178 | snp1672 179 | snp1678 180 | snp1687 181 | snp1696 182 | snp1710 183 | snp1714 184 | snp1718 185 | snp1721 186 | snp1723 187 | snp1727 188 | snp1728 189 | snp1738 190 | snp1754 191 | snp1773 192 | snp1774 193 | snp1783 194 | snp1793 195 | snp1806 196 | snp1814 197 | snp1815 198 | snp1837 199 | snp1855 200 | snp1876 201 | snp1881 202 | snp1883 203 | snp1890 204 | snp1891 205 | snp1904 206 | snp1913 207 | snp1915 208 | snp1918 209 | snp1927 210 | snp1935 211 | snp1982 212 | snp1989 213 | snp2017 214 | snp2041 215 | snp2042 216 | snp2043 217 | snp2069 218 | snp2070 219 | snp2081 220 | snp2104 221 | snp2109 222 | snp2115 223 | snp2119 224 | snp2120 225 | snp2122 226 | snp2129 227 | snp2130 228 | snp2137 229 | snp2139 230 | snp2155 231 | snp2166 232 | snp2171 233 | snp2201 234 | snp2218 235 | snp2224 236 | snp2226 237 | snp2229 238 | snp2275 239 | snp2276 240 | snp2284 241 | snp2286 242 | snp2292 243 | snp2293 244 | snp2300 245 | snp2313 246 | snp2318 247 | snp2322 248 | snp2346 249 | snp2361 250 | snp2363 251 | snp2372 252 | snp2373 253 | snp2376 254 | snp2381 255 | snp2382 256 | snp2383 257 | snp2385 258 | snp2386 259 | snp2397 260 | snp2399 261 | snp2416 262 | snp2425 263 | snp2431 264 | snp2432 265 | snp2440 266 | snp2448 267 | snp2449 268 | snp2473 269 | snp2475 270 | snp2476 271 | snp2482 272 | snp2483 273 | snp2492 274 | snp2496 275 | snp2508 276 | snp2522 277 | snp2530 278 | snp2531 279 | snp2534 280 | snp2536 281 | snp2542 282 | snp2549 283 | snp2552 284 | snp2561 285 | snp2565 286 | snp2566 287 | snp2601 288 | snp2605 289 | snp2622 290 | snp2624 291 | snp2625 292 | snp2632 293 | snp2643 294 | snp2660 295 | snp2665 296 | snp2672 297 | snp2675 298 | snp2682 299 | snp2696 300 | snp2719 301 | snp2720 302 | snp2727 303 | snp2734 304 | snp2738 305 | snp2740 306 | snp2742 307 | snp2750 308 | snp2763 309 | snp2791 310 | snp2793 311 | snp2800 312 | snp2818 313 | snp2819 314 | snp2838 315 | snp2852 316 | snp2854 317 | snp2855 318 | snp2860 319 | snp2880 320 | snp2881 321 | snp2893 322 | snp2901 323 | snp2910 324 | snp2925 325 | snp2936 326 | snp2974 327 | snp2980 328 | snp2992 329 | snp2993 330 | snp2996 331 | snp2997 332 | snp2999 333 | snp3022 334 | snp3033 335 | snp3041 336 | snp3043 337 | snp3051 338 | snp3087 339 | snp3097 340 | snp3101 341 | snp3106 342 | snp3128 343 | snp3130 344 | snp3136 345 | snp3151 346 | snp3155 347 | snp3160 348 | snp3164 349 | snp3170 350 | snp3180 351 | snp3181 352 | snp3185 353 | snp3200 354 | snp3222 355 | snp3229 356 | snp3231 357 | snp3244 358 | snp3256 359 | snp3265 360 | snp3267 361 | snp3272 362 | snp3281 363 | snp3286 364 | snp3306 365 | snp3313 366 | snp3317 367 | snp3319 368 | snp3333 369 | snp3334 370 | snp3342 371 | snp3352 372 | snp3354 373 | snp3355 374 | snp3359 375 | snp3361 376 | snp3370 377 | snp3379 378 | snp3392 379 | snp3404 380 | snp3411 381 | snp3425 382 | snp3427 383 | snp3431 384 | snp3446 385 | snp3447 386 | snp3478 387 | snp3479 388 | snp3482 389 | snp3501 390 | snp3503 391 | snp3523 392 | snp3526 393 | snp3530 394 | snp3532 395 | snp3539 396 | snp3550 397 | snp3564 398 | snp3586 399 | snp3588 400 | snp3590 401 | snp3623 402 | snp3627 403 | snp3646 404 | snp3649 405 | snp3657 406 | snp3659 407 | snp3670 408 | snp3676 409 | snp3686 410 | snp3697 411 | snp3713 412 | snp3717 413 | snp3733 414 | snp3737 415 | snp3744 416 | snp3754 417 | snp3755 418 | snp3757 419 | snp3760 420 | snp3776 421 | snp3791 422 | snp3805 423 | snp3827 424 | snp3828 425 | snp3851 426 | snp3854 427 | snp3860 428 | snp3861 429 | snp3873 430 | snp3880 431 | snp3900 432 | snp3901 433 | snp3920 434 | snp3927 435 | snp3932 436 | snp3933 437 | snp3946 438 | snp3951 439 | snp3965 440 | snp3968 441 | snp3981 442 | snp3996 443 | snp4002 444 | snp4005 445 | snp4014 446 | snp4020 447 | snp4023 448 | snp4043 449 | snp4079 450 | snp4083 451 | snp4111 452 | snp4113 453 | snp4119 454 | snp4128 455 | snp4134 456 | snp4145 457 | snp4149 458 | snp4169 459 | snp4172 460 | snp4176 461 | snp4177 462 | snp4186 463 | snp4232 464 | snp4253 465 | snp4260 466 | snp4263 467 | snp4275 468 | snp4279 469 | snp4303 470 | snp4321 471 | snp4325 472 | snp4335 473 | snp4343 474 | snp4363 475 | snp4374 476 | snp4396 477 | snp4401 478 | snp4410 479 | snp4415 480 | snp4426 481 | snp4430 482 | snp4447 483 | snp4454 484 | snp4456 485 | snp4462 486 | snp4483 487 | snp4487 488 | snp4490 489 | snp4491 490 | snp4518 491 | snp4539 492 | snp4558 493 | snp4566 494 | snp4567 495 | snp4568 496 | snp4569 497 | snp4570 498 | snp4590 499 | snp4598 500 | snp4611 501 | snp4623 502 | snp4647 503 | snp4663 504 | snp4681 505 | snp4687 506 | snp4688 507 | snp4694 508 | snp4701 509 | snp4707 510 | snp4717 511 | snp4726 512 | snp4731 513 | snp4744 514 | snp4752 515 | snp4753 516 | snp4776 517 | snp4777 518 | snp4782 519 | snp4784 520 | snp4788 521 | snp4803 522 | snp4838 523 | snp4842 524 | snp4861 525 | snp4866 526 | snp4868 527 | snp4887 528 | snp4902 529 | snp4906 530 | snp4912 531 | snp4919 532 | snp4922 533 | snp4929 534 | snp4954 535 | snp4963 536 | snp4985 537 | snp4990 538 | snp4992 539 | snp4994 540 | snp4996 541 | snp5019 542 | snp5024 543 | snp5025 544 | snp5027 545 | snp5040 546 | snp5044 547 | snp5066 548 | snp5097 549 | snp5107 550 | snp5118 551 | snp5119 552 | snp5120 553 | snp5138 554 | snp5140 555 | snp5150 556 | snp5178 557 | snp5179 558 | snp5183 559 | snp5198 560 | snp5215 561 | snp5217 562 | snp5223 563 | snp5234 564 | snp5241 565 | snp5250 566 | snp5254 567 | snp5276 568 | snp5291 569 | snp5300 570 | snp5302 571 | snp5306 572 | snp5309 573 | snp5312 574 | snp5343 575 | snp5352 576 | snp5359 577 | snp5366 578 | snp5375 579 | snp5381 580 | snp5383 581 | snp5391 582 | snp5399 583 | snp5400 584 | snp5410 585 | snp5425 586 | snp5427 587 | snp5435 588 | snp5446 589 | snp5460 590 | snp5491 591 | snp5499 592 | snp5500 593 | snp5505 594 | snp5510 595 | snp5518 596 | snp5521 597 | snp5533 598 | snp5537 599 | snp5539 600 | snp5541 601 | snp5550 602 | snp5552 603 | snp5554 604 | snp5593 605 | snp5601 606 | snp5606 607 | snp5608 608 | snp5626 609 | snp5627 610 | snp5668 611 | snp5678 612 | snp5684 613 | snp5704 614 | snp5705 615 | snp5731 616 | snp5738 617 | snp5741 618 | snp5746 619 | snp5749 620 | snp5761 621 | snp5762 622 | snp5775 623 | snp5791 624 | snp5796 625 | snp5799 626 | snp5803 627 | snp5811 628 | snp5828 629 | snp5835 630 | snp5840 631 | snp5872 632 | snp5873 633 | snp5876 634 | snp5882 635 | snp5901 636 | snp5921 637 | snp5928 638 | snp5967 639 | snp5979 640 | snp5981 641 | snp5990 642 | snp5994 643 | snp6004 644 | snp6006 645 | snp6038 646 | snp6039 647 | snp6059 648 | snp6071 649 | snp6079 650 | snp6109 651 | snp6112 652 | snp6158 653 | snp6160 654 | snp6171 655 | snp6172 656 | snp6210 657 | snp6218 658 | snp6244 659 | snp6250 660 | snp6252 661 | snp6256 662 | snp6257 663 | snp6278 664 | snp6281 665 | snp6294 666 | snp6300 667 | snp6311 668 | snp6323 669 | snp6336 670 | snp6339 671 | snp6341 672 | snp6365 673 | snp6376 674 | snp6381 675 | snp6395 676 | snp6422 677 | snp6426 678 | snp6427 679 | snp6442 680 | snp6448 681 | snp6459 682 | snp6482 683 | snp6493 684 | snp6499 685 | snp6524 686 | snp6525 687 | snp6529 688 | snp6545 689 | snp6552 690 | snp6553 691 | snp6559 692 | snp6564 693 | snp6566 694 | snp6567 695 | snp6576 696 | snp6584 697 | snp6596 698 | snp6605 699 | snp6610 700 | snp6622 701 | snp6633 702 | snp6642 703 | snp6658 704 | snp6674 705 | snp6675 706 | snp6679 707 | snp6693 708 | snp6697 709 | snp6723 710 | snp6734 711 | snp6749 712 | snp6751 713 | snp6761 714 | snp6762 715 | snp6774 716 | snp6775 717 | snp6783 718 | snp6798 719 | snp6818 720 | snp6824 721 | snp6842 722 | snp6848 723 | snp6855 724 | snp6858 725 | snp6874 726 | snp6894 727 | snp6897 728 | snp6899 729 | snp6921 730 | snp6924 731 | snp6935 732 | snp6950 733 | snp6958 734 | snp6964 735 | snp6975 736 | snp6999 737 | snp7014 738 | snp7017 739 | snp7037 740 | snp7065 741 | snp7069 742 | snp7081 743 | snp7110 744 | snp7144 745 | snp7146 746 | snp7161 747 | snp7193 748 | snp7208 749 | snp7221 750 | snp7229 751 | snp7240 752 | snp7241 753 | snp7242 754 | snp7245 755 | snp7246 756 | snp7251 757 | snp7276 758 | snp7294 759 | snp7309 760 | snp7318 761 | snp7321 762 | snp7339 763 | snp7344 764 | snp7345 765 | snp7397 766 | snp7411 767 | snp7414 768 | snp7429 769 | snp7435 770 | snp7438 771 | snp7445 772 | snp7455 773 | snp7459 774 | snp7460 775 | snp7461 776 | snp7480 777 | snp7490 778 | snp7526 779 | snp7531 780 | snp7534 781 | snp7536 782 | snp7574 783 | snp7596 784 | snp7604 785 | snp7611 786 | snp7613 787 | snp7618 788 | snp7633 789 | snp7639 790 | snp7676 791 | snp7678 792 | snp7684 793 | snp7700 794 | snp7701 795 | snp7715 796 | snp7727 797 | snp7731 798 | snp7748 799 | snp7769 800 | snp7774 801 | snp7785 802 | snp7789 803 | snp7805 804 | snp7818 805 | snp7824 806 | snp7835 807 | snp7854 808 | snp7860 809 | snp7866 810 | snp7868 811 | snp7874 812 | snp7895 813 | snp7898 814 | snp7905 815 | snp7909 816 | snp7922 817 | snp7946 818 | snp7950 819 | snp7968 820 | snp7970 821 | snp7990 822 | snp8004 823 | snp8005 824 | snp8015 825 | snp8022 826 | snp8040 827 | snp8044 828 | snp8053 829 | snp8079 830 | snp8103 831 | snp8106 832 | snp8109 833 | snp8113 834 | snp8139 835 | snp8145 836 | snp8150 837 | snp8160 838 | snp8162 839 | snp8173 840 | snp8177 841 | snp8182 842 | snp8186 843 | snp8194 844 | snp8202 845 | snp8212 846 | snp8217 847 | snp8232 848 | snp8239 849 | snp8245 850 | snp8264 851 | snp8265 852 | snp8269 853 | snp8278 854 | snp8299 855 | snp8324 856 | snp8327 857 | snp8340 858 | snp8354 859 | snp8358 860 | snp8396 861 | snp8406 862 | snp8410 863 | snp8440 864 | snp8472 865 | snp8474 866 | snp8475 867 | snp8514 868 | snp8529 869 | snp8540 870 | snp8552 871 | snp8563 872 | snp8568 873 | snp8588 874 | snp8602 875 | snp8609 876 | snp8614 877 | snp8615 878 | snp8627 879 | snp8633 880 | snp8644 881 | snp8648 882 | snp8675 883 | snp8693 884 | snp8694 885 | snp8698 886 | snp8703 887 | snp8708 888 | snp8711 889 | snp8713 890 | snp8716 891 | snp8723 892 | snp8732 893 | snp8741 894 | snp8748 895 | snp8752 896 | snp8759 897 | snp8763 898 | snp8769 899 | snp8789 900 | snp8795 901 | snp8809 902 | snp8831 903 | snp8837 904 | snp8839 905 | snp8846 906 | snp8857 907 | snp8861 908 | snp8864 909 | snp8875 910 | snp8890 911 | snp8911 912 | snp8913 913 | snp8920 914 | snp8936 915 | snp8937 916 | snp8956 917 | snp8983 918 | snp8988 919 | snp8989 920 | snp9001 921 | snp9003 922 | snp9019 923 | snp9025 924 | snp9037 925 | snp9041 926 | snp9055 927 | snp9056 928 | snp9081 929 | snp9088 930 | snp9101 931 | snp9115 932 | snp9118 933 | snp9122 934 | snp9128 935 | snp9129 936 | snp9140 937 | snp9160 938 | snp9166 939 | snp9184 940 | snp9204 941 | snp9217 942 | snp9222 943 | snp9231 944 | snp9232 945 | snp9241 946 | snp9242 947 | snp9251 948 | snp9253 949 | snp9316 950 | snp9323 951 | snp9331 952 | snp9335 953 | snp9358 954 | snp9360 955 | snp9362 956 | snp9370 957 | snp9372 958 | snp9380 959 | snp9401 960 | snp9428 961 | snp9432 962 | snp9459 963 | snp9461 964 | snp9515 965 | snp9517 966 | snp9539 967 | snp9600 968 | snp9624 969 | snp9630 970 | snp9637 971 | snp9644 972 | snp9655 973 | snp9659 974 | snp9677 975 | snp9680 976 | snp9696 977 | snp9724 978 | snp9758 979 | snp9787 980 | snp9795 981 | snp9798 982 | snp9801 983 | snp9807 984 | snp9822 985 | snp9825 986 | snp9826 987 | snp9840 988 | snp9841 989 | snp9845 990 | snp9846 991 | snp9847 992 | snp9858 993 | snp9875 994 | snp9878 995 | snp9880 996 | snp9883 997 | snp9886 998 | snp9893 999 | snp9896 1000 | snp9922 1001 | snp9926 1002 | snp9961 1003 | snp9977 1004 | snp9996 1005 | snp10022 1006 | snp10024 1007 | snp10079 1008 | snp10092 1009 | snp10100 1010 | snp10117 1011 | snp10121 1012 | snp10124 1013 | snp10135 1014 | snp10155 1015 | snp10163 1016 | snp10165 1017 | snp10172 1018 | snp10173 1019 | snp10232 1020 | snp10236 1021 | snp10246 1022 | snp10257 1023 | snp10263 1024 | snp10265 1025 | snp10266 1026 | snp10272 1027 | snp10278 1028 | snp10279 1029 | snp10284 1030 | snp10296 1031 | snp10311 1032 | snp10321 1033 | snp10340 1034 | snp10341 1035 | snp10345 1036 | snp10349 1037 | snp10354 1038 | snp10358 1039 | snp10366 1040 | snp10369 1041 | snp10385 1042 | snp10401 1043 | snp10412 1044 | snp10431 1045 | snp10435 1046 | snp10436 1047 | snp10449 1048 | snp10455 1049 | snp10484 1050 | snp10489 1051 | snp10492 1052 | dsnp10507 1053 | dsnp10519 1054 | dsnp10521 1055 | dsnp10539 1056 | dsnp10540 1057 | dsnp10558 1058 | dsnp10564 1059 | dsnp10576 1060 | dsnp10597 1061 | -------------------------------------------------------------------------------- /dataset1/extracts/chr8_extract.txt: -------------------------------------------------------------------------------- 1 | csnp6 2 | csnp7 3 | csnp14 4 | csnp29 5 | csnp43 6 | csnp46 7 | csnp61 8 | csnp66 9 | csnp80 10 | csnp102 11 | csnp120 12 | csnp130 13 | csnp145 14 | csnp157 15 | csnp158 16 | csnp168 17 | csnp170 18 | csnp189 19 | csnp219 20 | csnp223 21 | csnp237 22 | csnp258 23 | csnp259 24 | csnp267 25 | csnp270 26 | csnp277 27 | csnp291 28 | csnp306 29 | csnp312 30 | csnp321 31 | csnp327 32 | csnp329 33 | csnp338 34 | csnp342 35 | csnp345 36 | csnp353 37 | csnp368 38 | csnp386 39 | csnp394 40 | csnp409 41 | csnp413 42 | csnp417 43 | csnp427 44 | csnp428 45 | csnp446 46 | csnp449 47 | csnp458 48 | csnp460 49 | csnp468 50 | csnp470 51 | csnp494 52 | snp520 53 | snp522 54 | snp523 55 | snp529 56 | snp538 57 | snp549 58 | snp564 59 | snp569 60 | snp572 61 | snp576 62 | snp582 63 | snp584 64 | snp598 65 | snp599 66 | snp600 67 | snp605 68 | snp611 69 | snp623 70 | snp626 71 | snp651 72 | snp654 73 | snp672 74 | snp675 75 | snp709 76 | snp712 77 | snp730 78 | snp733 79 | snp742 80 | snp756 81 | snp772 82 | snp784 83 | snp785 84 | snp790 85 | snp798 86 | snp812 87 | snp817 88 | snp852 89 | snp864 90 | snp867 91 | snp871 92 | snp890 93 | snp896 94 | snp898 95 | snp912 96 | snp919 97 | snp922 98 | snp927 99 | snp939 100 | snp945 101 | snp948 102 | snp954 103 | snp960 104 | snp962 105 | snp966 106 | snp967 107 | snp988 108 | snp1004 109 | snp1020 110 | snp1024 111 | snp1053 112 | snp1060 113 | snp1083 114 | snp1089 115 | snp1093 116 | snp1112 117 | snp1113 118 | snp1120 119 | snp1131 120 | snp1135 121 | snp1152 122 | snp1170 123 | snp1179 124 | snp1214 125 | snp1222 126 | snp1230 127 | snp1266 128 | snp1326 129 | snp1342 130 | snp1390 131 | snp1395 132 | snp1400 133 | snp1407 134 | snp1419 135 | snp1420 136 | snp1421 137 | snp1429 138 | snp1431 139 | snp1437 140 | snp1451 141 | snp1473 142 | snp1487 143 | snp1489 144 | snp1491 145 | snp1509 146 | snp1510 147 | snp1533 148 | snp1534 149 | snp1544 150 | snp1572 151 | snp1584 152 | snp1589 153 | snp1604 154 | snp1610 155 | snp1621 156 | snp1622 157 | snp1635 158 | snp1641 159 | snp1679 160 | snp1684 161 | snp1692 162 | snp1693 163 | snp1698 164 | snp1719 165 | snp1736 166 | snp1737 167 | snp1741 168 | snp1745 169 | snp1750 170 | snp1751 171 | snp1768 172 | snp1770 173 | snp1784 174 | snp1786 175 | snp1792 176 | snp1803 177 | snp1811 178 | snp1820 179 | snp1831 180 | snp1843 181 | snp1844 182 | snp1895 183 | snp1909 184 | snp1920 185 | snp1931 186 | snp1945 187 | snp1949 188 | snp1959 189 | snp1966 190 | snp1968 191 | snp1972 192 | snp1998 193 | snp2027 194 | snp2029 195 | snp2047 196 | snp2062 197 | snp2063 198 | snp2064 199 | snp2068 200 | snp2076 201 | snp2097 202 | snp2105 203 | snp2111 204 | snp2112 205 | snp2116 206 | snp2135 207 | snp2138 208 | snp2143 209 | snp2145 210 | snp2147 211 | snp2164 212 | snp2165 213 | snp2169 214 | snp2180 215 | snp2204 216 | snp2221 217 | snp2231 218 | snp2239 219 | snp2242 220 | snp2244 221 | snp2246 222 | snp2283 223 | snp2289 224 | snp2299 225 | snp2301 226 | snp2329 227 | snp2330 228 | snp2332 229 | snp2354 230 | snp2357 231 | snp2368 232 | snp2371 233 | snp2375 234 | snp2377 235 | snp2387 236 | snp2392 237 | snp2402 238 | snp2412 239 | snp2437 240 | snp2446 241 | snp2447 242 | snp2450 243 | snp2451 244 | snp2456 245 | snp2478 246 | snp2484 247 | snp2489 248 | snp2498 249 | snp2516 250 | snp2535 251 | snp2537 252 | snp2539 253 | snp2545 254 | snp2558 255 | snp2563 256 | snp2602 257 | snp2607 258 | snp2617 259 | snp2620 260 | snp2630 261 | snp2636 262 | snp2638 263 | snp2641 264 | snp2647 265 | snp2651 266 | snp2658 267 | snp2679 268 | snp2688 269 | snp2690 270 | snp2699 271 | snp2744 272 | snp2749 273 | snp2758 274 | snp2766 275 | snp2769 276 | snp2776 277 | snp2784 278 | snp2787 279 | snp2788 280 | snp2807 281 | snp2820 282 | snp2826 283 | snp2837 284 | snp2857 285 | snp2859 286 | snp2882 287 | snp2891 288 | snp2908 289 | snp2917 290 | snp2921 291 | snp2943 292 | snp2944 293 | snp2945 294 | snp2948 295 | snp2953 296 | snp2956 297 | snp2958 298 | snp2959 299 | snp2963 300 | snp2991 301 | snp3006 302 | snp3019 303 | snp3025 304 | snp3040 305 | snp3059 306 | snp3069 307 | snp3076 308 | snp3077 309 | snp3082 310 | snp3083 311 | snp3084 312 | snp3090 313 | snp3144 314 | snp3146 315 | snp3169 316 | snp3195 317 | snp3207 318 | snp3252 319 | snp3255 320 | snp3297 321 | snp3327 322 | snp3337 323 | snp3338 324 | snp3347 325 | snp3348 326 | snp3366 327 | snp3375 328 | snp3377 329 | snp3390 330 | snp3394 331 | snp3397 332 | snp3401 333 | snp3410 334 | snp3435 335 | snp3437 336 | snp3442 337 | snp3443 338 | snp3468 339 | snp3481 340 | snp3485 341 | snp3487 342 | snp3502 343 | snp3506 344 | snp3515 345 | snp3525 346 | snp3531 347 | snp3535 348 | snp3549 349 | snp3561 350 | snp3563 351 | snp3565 352 | snp3567 353 | snp3575 354 | snp3597 355 | snp3599 356 | snp3605 357 | snp3606 358 | snp3613 359 | snp3616 360 | snp3624 361 | snp3630 362 | snp3651 363 | snp3672 364 | snp3674 365 | snp3688 366 | snp3706 367 | snp3710 368 | snp3711 369 | snp3732 370 | snp3745 371 | snp3749 372 | snp3751 373 | snp3753 374 | snp3763 375 | snp3764 376 | snp3768 377 | snp3794 378 | snp3849 379 | snp3866 380 | snp3867 381 | snp3869 382 | snp3874 383 | snp3875 384 | snp3899 385 | snp3908 386 | snp3913 387 | snp3915 388 | snp3931 389 | snp3942 390 | snp3948 391 | snp3953 392 | snp3982 393 | snp3989 394 | snp3999 395 | snp4022 396 | snp4045 397 | snp4046 398 | snp4047 399 | snp4060 400 | snp4063 401 | snp4081 402 | snp4096 403 | snp4121 404 | snp4124 405 | snp4189 406 | snp4193 407 | snp4214 408 | snp4221 409 | snp4224 410 | snp4227 411 | snp4238 412 | snp4239 413 | snp4246 414 | snp4262 415 | snp4264 416 | snp4286 417 | snp4291 418 | snp4312 419 | snp4313 420 | snp4315 421 | snp4320 422 | snp4332 423 | snp4345 424 | snp4353 425 | snp4388 426 | snp4399 427 | snp4408 428 | snp4417 429 | snp4420 430 | snp4436 431 | snp4464 432 | snp4472 433 | snp4474 434 | snp4475 435 | snp4476 436 | snp4480 437 | snp4493 438 | snp4494 439 | snp4510 440 | snp4519 441 | snp4525 442 | snp4538 443 | snp4560 444 | snp4576 445 | snp4578 446 | snp4585 447 | snp4586 448 | snp4599 449 | snp4609 450 | snp4614 451 | snp4615 452 | snp4626 453 | snp4628 454 | snp4633 455 | snp4650 456 | snp4651 457 | snp4654 458 | snp4664 459 | snp4669 460 | snp4671 461 | snp4672 462 | snp4680 463 | snp4682 464 | snp4704 465 | snp4706 466 | snp4713 467 | snp4729 468 | snp4737 469 | snp4747 470 | snp4772 471 | snp4778 472 | snp4781 473 | snp4786 474 | snp4797 475 | snp4799 476 | snp4816 477 | snp4817 478 | snp4818 479 | snp4823 480 | snp4829 481 | snp4844 482 | snp4867 483 | snp4894 484 | snp4901 485 | snp4905 486 | snp4913 487 | snp4917 488 | snp4925 489 | snp4945 490 | snp4946 491 | snp4967 492 | snp4968 493 | snp4979 494 | snp4988 495 | snp5001 496 | snp5023 497 | snp5036 498 | snp5043 499 | snp5047 500 | snp5058 501 | snp5065 502 | snp5070 503 | snp5071 504 | snp5073 505 | snp5078 506 | snp5092 507 | snp5101 508 | snp5103 509 | snp5124 510 | snp5135 511 | snp5147 512 | snp5156 513 | snp5160 514 | snp5162 515 | snp5163 516 | snp5174 517 | snp5186 518 | snp5192 519 | snp5193 520 | snp5195 521 | snp5197 522 | snp5208 523 | snp5211 524 | snp5228 525 | snp5245 526 | snp5277 527 | snp5285 528 | snp5287 529 | snp5290 530 | snp5304 531 | snp5328 532 | snp5333 533 | snp5358 534 | snp5392 535 | snp5393 536 | snp5416 537 | snp5421 538 | snp5422 539 | snp5431 540 | snp5448 541 | snp5450 542 | snp5473 543 | snp5483 544 | snp5501 545 | snp5503 546 | snp5508 547 | snp5525 548 | snp5527 549 | snp5534 550 | snp5549 551 | snp5565 552 | snp5566 553 | snp5568 554 | snp5579 555 | snp5588 556 | snp5599 557 | snp5604 558 | snp5607 559 | snp5611 560 | snp5612 561 | snp5614 562 | snp5615 563 | snp5617 564 | snp5631 565 | snp5634 566 | snp5651 567 | snp5663 568 | snp5669 569 | snp5676 570 | snp5686 571 | snp5723 572 | snp5737 573 | snp5776 574 | snp5779 575 | snp5792 576 | snp5793 577 | snp5797 578 | snp5813 579 | snp5814 580 | snp5831 581 | snp5846 582 | snp5847 583 | snp5864 584 | snp5874 585 | snp5887 586 | snp5893 587 | snp5909 588 | snp5914 589 | snp5916 590 | snp5924 591 | snp5926 592 | snp5937 593 | snp5962 594 | snp5964 595 | snp5977 596 | snp5996 597 | snp6016 598 | snp6017 599 | snp6054 600 | snp6055 601 | snp6060 602 | snp6066 603 | snp6083 604 | snp6095 605 | snp6097 606 | snp6108 607 | snp6115 608 | snp6124 609 | snp6176 610 | snp6178 611 | snp6182 612 | snp6184 613 | snp6186 614 | snp6212 615 | snp6222 616 | snp6225 617 | snp6226 618 | snp6229 619 | snp6268 620 | snp6283 621 | snp6289 622 | snp6299 623 | snp6309 624 | snp6337 625 | snp6346 626 | snp6355 627 | snp6363 628 | snp6366 629 | snp6369 630 | snp6377 631 | snp6386 632 | snp6406 633 | snp6409 634 | snp6418 635 | snp6431 636 | snp6446 637 | snp6453 638 | snp6477 639 | snp6488 640 | snp6496 641 | snp6504 642 | snp6522 643 | snp6527 644 | snp6533 645 | snp6569 646 | snp6571 647 | snp6583 648 | snp6587 649 | snp6593 650 | snp6595 651 | snp6601 652 | snp6609 653 | snp6611 654 | snp6623 655 | snp6637 656 | snp6639 657 | snp6652 658 | snp6659 659 | snp6661 660 | snp6668 661 | snp6669 662 | snp6673 663 | snp6688 664 | snp6689 665 | snp6695 666 | snp6696 667 | snp6701 668 | snp6704 669 | snp6711 670 | snp6712 671 | snp6718 672 | snp6727 673 | snp6736 674 | snp6738 675 | snp6750 676 | snp6765 677 | snp6768 678 | snp6770 679 | snp6778 680 | snp6788 681 | snp6812 682 | snp6813 683 | snp6829 684 | snp6836 685 | snp6850 686 | snp6861 687 | snp6866 688 | snp6920 689 | snp6928 690 | snp6954 691 | snp6967 692 | snp6972 693 | snp7005 694 | snp7009 695 | snp7025 696 | snp7029 697 | snp7051 698 | snp7053 699 | snp7083 700 | snp7099 701 | snp7100 702 | snp7102 703 | snp7105 704 | snp7126 705 | snp7128 706 | snp7137 707 | snp7145 708 | snp7156 709 | snp7163 710 | snp7174 711 | snp7190 712 | snp7191 713 | snp7199 714 | snp7200 715 | snp7204 716 | snp7211 717 | snp7225 718 | snp7243 719 | snp7249 720 | snp7256 721 | snp7265 722 | snp7274 723 | snp7281 724 | snp7310 725 | snp7317 726 | snp7332 727 | snp7338 728 | snp7350 729 | snp7358 730 | snp7362 731 | snp7366 732 | snp7377 733 | snp7378 734 | snp7382 735 | snp7389 736 | snp7395 737 | snp7398 738 | snp7400 739 | snp7403 740 | snp7404 741 | snp7420 742 | snp7446 743 | snp7472 744 | snp7485 745 | snp7487 746 | snp7493 747 | snp7496 748 | snp7504 749 | snp7511 750 | snp7513 751 | snp7516 752 | snp7520 753 | snp7543 754 | snp7551 755 | snp7557 756 | snp7567 757 | snp7569 758 | snp7593 759 | snp7619 760 | snp7621 761 | snp7643 762 | snp7646 763 | snp7650 764 | snp7663 765 | snp7668 766 | snp7673 767 | snp7699 768 | snp7703 769 | snp7718 770 | snp7720 771 | snp7728 772 | snp7729 773 | snp7737 774 | snp7739 775 | snp7747 776 | snp7752 777 | snp7755 778 | snp7757 779 | snp7776 780 | snp7804 781 | snp7825 782 | snp7826 783 | snp7828 784 | snp7838 785 | snp7845 786 | snp7853 787 | snp7855 788 | snp7856 789 | snp7875 790 | snp7876 791 | snp7892 792 | snp7896 793 | snp7901 794 | snp7902 795 | snp7925 796 | snp7957 797 | snp7977 798 | snp7986 799 | snp8016 800 | snp8033 801 | snp8041 802 | snp8060 803 | snp8073 804 | snp8077 805 | snp8087 806 | snp8088 807 | snp8099 808 | snp8100 809 | snp8112 810 | snp8118 811 | snp8131 812 | snp8134 813 | snp8143 814 | snp8144 815 | snp8154 816 | snp8157 817 | snp8161 818 | snp8178 819 | snp8184 820 | snp8195 821 | snp8229 822 | snp8242 823 | snp8243 824 | snp8259 825 | snp8260 826 | snp8275 827 | snp8286 828 | snp8290 829 | snp8300 830 | snp8303 831 | snp8308 832 | snp8310 833 | snp8313 834 | snp8314 835 | snp8317 836 | snp8357 837 | snp8369 838 | snp8377 839 | snp8378 840 | snp8380 841 | snp8393 842 | snp8414 843 | snp8429 844 | snp8434 845 | snp8445 846 | snp8450 847 | snp8452 848 | snp8478 849 | snp8484 850 | snp8495 851 | snp8499 852 | snp8510 853 | snp8512 854 | snp8515 855 | snp8521 856 | snp8547 857 | snp8551 858 | snp8567 859 | snp8581 860 | snp8586 861 | snp8596 862 | snp8599 863 | snp8601 864 | snp8612 865 | snp8619 866 | snp8624 867 | snp8632 868 | snp8637 869 | snp8650 870 | snp8656 871 | snp8660 872 | snp8679 873 | snp8686 874 | snp8704 875 | snp8738 876 | snp8743 877 | snp8745 878 | snp8747 879 | snp8760 880 | snp8767 881 | snp8778 882 | snp8779 883 | snp8784 884 | snp8787 885 | snp8796 886 | snp8800 887 | snp8801 888 | snp8802 889 | snp8803 890 | snp8806 891 | snp8811 892 | snp8835 893 | snp8851 894 | snp8853 895 | snp8855 896 | snp8874 897 | snp8889 898 | snp8894 899 | snp8905 900 | snp8916 901 | snp8918 902 | snp8925 903 | snp8928 904 | snp8932 905 | snp8935 906 | snp8962 907 | snp8966 908 | snp8970 909 | snp8971 910 | snp8976 911 | snp8981 912 | snp9000 913 | snp9004 914 | snp9014 915 | snp9021 916 | snp9026 917 | snp9040 918 | snp9047 919 | snp9063 920 | snp9071 921 | snp9072 922 | snp9073 923 | snp9085 924 | snp9090 925 | snp9097 926 | snp9102 927 | snp9103 928 | snp9119 929 | snp9124 930 | snp9130 931 | snp9134 932 | snp9145 933 | snp9150 934 | snp9181 935 | snp9197 936 | snp9212 937 | snp9213 938 | snp9216 939 | snp9220 940 | snp9228 941 | snp9247 942 | snp9250 943 | snp9260 944 | snp9276 945 | snp9301 946 | snp9340 947 | snp9344 948 | snp9354 949 | snp9365 950 | snp9381 951 | snp9390 952 | snp9405 953 | snp9411 954 | snp9423 955 | snp9430 956 | snp9453 957 | snp9480 958 | snp9482 959 | snp9490 960 | snp9492 961 | snp9497 962 | snp9500 963 | snp9502 964 | snp9511 965 | snp9520 966 | snp9541 967 | snp9544 968 | snp9553 969 | snp9558 970 | snp9559 971 | snp9565 972 | snp9569 973 | snp9589 974 | snp9601 975 | snp9605 976 | snp9613 977 | snp9618 978 | snp9632 979 | snp9635 980 | snp9642 981 | snp9649 982 | snp9651 983 | snp9666 984 | snp9667 985 | snp9703 986 | snp9720 987 | snp9723 988 | snp9725 989 | snp9726 990 | snp9733 991 | snp9738 992 | snp9742 993 | snp9748 994 | snp9768 995 | snp9776 996 | snp9806 997 | snp9810 998 | snp9815 999 | snp9821 1000 | snp9828 1001 | snp9838 1002 | snp9853 1003 | snp9854 1004 | snp9868 1005 | snp9902 1006 | snp9918 1007 | snp9936 1008 | snp9951 1009 | snp10005 1010 | snp10007 1011 | snp10010 1012 | snp10030 1013 | snp10042 1014 | snp10048 1015 | snp10061 1016 | snp10064 1017 | snp10071 1018 | snp10101 1019 | snp10107 1020 | snp10114 1021 | snp10132 1022 | snp10141 1023 | snp10143 1024 | snp10149 1025 | snp10151 1026 | snp10156 1027 | snp10157 1028 | snp10197 1029 | snp10204 1030 | snp10207 1031 | snp10210 1032 | snp10217 1033 | snp10219 1034 | snp10303 1035 | snp10316 1036 | snp10333 1037 | snp10339 1038 | snp10368 1039 | snp10381 1040 | snp10394 1041 | snp10404 1042 | snp10413 1043 | snp10417 1044 | snp10419 1045 | snp10422 1046 | snp10423 1047 | snp10430 1048 | snp10439 1049 | snp10452 1050 | snp10459 1051 | snp10482 1052 | snp10486 1053 | snp10497 1054 | dsnp10525 1055 | dsnp10572 1056 | dsnp10575 1057 | dsnp10578 1058 | dsnp10592 1059 | dsnp10595 1060 | dsnp10598 1061 | -------------------------------------------------------------------------------- /dataset1/extracts/chr6_extract.txt: -------------------------------------------------------------------------------- 1 | csnp3 2 | csnp38 3 | csnp40 4 | csnp71 5 | csnp74 6 | csnp76 7 | csnp88 8 | csnp116 9 | csnp123 10 | csnp126 11 | csnp127 12 | csnp146 13 | csnp148 14 | csnp156 15 | csnp169 16 | csnp172 17 | csnp183 18 | csnp194 19 | csnp201 20 | csnp202 21 | csnp209 22 | csnp246 23 | csnp279 24 | csnp292 25 | csnp296 26 | csnp303 27 | csnp311 28 | csnp349 29 | csnp354 30 | csnp355 31 | csnp366 32 | csnp367 33 | csnp370 34 | csnp374 35 | csnp384 36 | csnp398 37 | csnp400 38 | csnp438 39 | csnp462 40 | snp501 41 | snp507 42 | snp513 43 | snp514 44 | snp527 45 | snp557 46 | snp583 47 | snp585 48 | snp588 49 | snp607 50 | snp612 51 | snp613 52 | snp615 53 | snp620 54 | snp633 55 | snp668 56 | snp670 57 | snp689 58 | snp694 59 | snp697 60 | snp710 61 | snp737 62 | snp744 63 | snp746 64 | snp770 65 | snp771 66 | snp797 67 | snp805 68 | snp806 69 | snp811 70 | snp820 71 | snp823 72 | snp825 73 | snp841 74 | snp853 75 | snp859 76 | snp866 77 | snp870 78 | snp879 79 | snp886 80 | snp888 81 | snp894 82 | snp895 83 | snp909 84 | snp914 85 | snp925 86 | snp941 87 | snp946 88 | snp953 89 | snp957 90 | snp959 91 | snp970 92 | snp1008 93 | snp1023 94 | snp1027 95 | snp1032 96 | snp1035 97 | snp1044 98 | snp1049 99 | snp1058 100 | snp1069 101 | snp1072 102 | snp1078 103 | snp1081 104 | snp1082 105 | snp1095 106 | snp1105 107 | snp1108 108 | snp1110 109 | snp1117 110 | snp1118 111 | snp1128 112 | snp1129 113 | snp1156 114 | snp1162 115 | snp1163 116 | snp1205 117 | snp1217 118 | snp1218 119 | snp1219 120 | snp1231 121 | snp1240 122 | snp1261 123 | snp1264 124 | snp1284 125 | snp1299 126 | snp1309 127 | snp1322 128 | snp1338 129 | snp1343 130 | snp1345 131 | snp1346 132 | snp1347 133 | snp1350 134 | snp1359 135 | snp1363 136 | snp1368 137 | snp1377 138 | snp1385 139 | snp1388 140 | snp1426 141 | snp1436 142 | snp1455 143 | snp1458 144 | snp1462 145 | snp1467 146 | snp1481 147 | snp1494 148 | snp1505 149 | snp1519 150 | snp1521 151 | snp1524 152 | snp1537 153 | snp1539 154 | snp1547 155 | snp1553 156 | snp1559 157 | snp1562 158 | snp1565 159 | snp1570 160 | snp1571 161 | snp1574 162 | snp1575 163 | snp1601 164 | snp1605 165 | snp1612 166 | snp1619 167 | snp1630 168 | snp1634 169 | snp1655 170 | snp1661 171 | snp1674 172 | snp1677 173 | snp1697 174 | snp1707 175 | snp1708 176 | snp1726 177 | snp1729 178 | snp1740 179 | snp1753 180 | snp1787 181 | snp1798 182 | snp1800 183 | snp1805 184 | snp1807 185 | snp1824 186 | snp1830 187 | snp1845 188 | snp1852 189 | snp1853 190 | snp1860 191 | snp1889 192 | snp1892 193 | snp1923 194 | snp1925 195 | snp1930 196 | snp1934 197 | snp1946 198 | snp1948 199 | snp1952 200 | snp1954 201 | snp1962 202 | snp1974 203 | snp1990 204 | snp2000 205 | snp2031 206 | snp2034 207 | snp2038 208 | snp2059 209 | snp2067 210 | snp2071 211 | snp2077 212 | snp2080 213 | snp2082 214 | snp2085 215 | snp2092 216 | snp2099 217 | snp2101 218 | snp2107 219 | snp2118 220 | snp2148 221 | snp2149 222 | snp2157 223 | snp2159 224 | snp2160 225 | snp2172 226 | snp2185 227 | snp2227 228 | snp2232 229 | snp2294 230 | snp2297 231 | snp2307 232 | snp2308 233 | snp2328 234 | snp2335 235 | snp2337 236 | snp2340 237 | snp2351 238 | snp2369 239 | snp2378 240 | snp2380 241 | snp2401 242 | snp2413 243 | snp2424 244 | snp2433 245 | snp2435 246 | snp2443 247 | snp2464 248 | snp2493 249 | snp2509 250 | snp2510 251 | snp2521 252 | snp2525 253 | snp2550 254 | snp2587 255 | snp2588 256 | snp2609 257 | snp2640 258 | snp2653 259 | snp2663 260 | snp2669 261 | snp2673 262 | snp2681 263 | snp2697 264 | snp2698 265 | snp2735 266 | snp2741 267 | snp2745 268 | snp2751 269 | snp2752 270 | snp2792 271 | snp2798 272 | snp2834 273 | snp2858 274 | snp2861 275 | snp2863 276 | snp2869 277 | snp2870 278 | snp2871 279 | snp2906 280 | snp2914 281 | snp2930 282 | snp2934 283 | snp2937 284 | snp2950 285 | snp2955 286 | snp2970 287 | snp2971 288 | snp3012 289 | snp3018 290 | snp3020 291 | snp3052 292 | snp3075 293 | snp3079 294 | snp3080 295 | snp3088 296 | snp3092 297 | snp3109 298 | snp3121 299 | snp3142 300 | snp3147 301 | snp3150 302 | snp3163 303 | snp3186 304 | snp3190 305 | snp3196 306 | snp3209 307 | snp3216 308 | snp3238 309 | snp3239 310 | snp3249 311 | snp3262 312 | snp3276 313 | snp3278 314 | snp3282 315 | snp3290 316 | snp3301 317 | snp3316 318 | snp3318 319 | snp3320 320 | snp3345 321 | snp3358 322 | snp3380 323 | snp3408 324 | snp3413 325 | snp3419 326 | snp3420 327 | snp3424 328 | snp3426 329 | snp3439 330 | snp3445 331 | snp3454 332 | snp3483 333 | snp3486 334 | snp3490 335 | snp3497 336 | snp3509 337 | snp3522 338 | snp3533 339 | snp3556 340 | snp3557 341 | snp3568 342 | snp3569 343 | snp3580 344 | snp3618 345 | snp3660 346 | snp3665 347 | snp3667 348 | snp3682 349 | snp3687 350 | snp3722 351 | snp3728 352 | snp3740 353 | snp3773 354 | snp3784 355 | snp3785 356 | snp3808 357 | snp3820 358 | snp3822 359 | snp3824 360 | snp3825 361 | snp3834 362 | snp3858 363 | snp3879 364 | snp3884 365 | snp3888 366 | snp3891 367 | snp3904 368 | snp3924 369 | snp3925 370 | snp3926 371 | snp3963 372 | snp3978 373 | snp4009 374 | snp4021 375 | snp4033 376 | snp4036 377 | snp4044 378 | snp4050 379 | snp4069 380 | snp4077 381 | snp4085 382 | snp4088 383 | snp4093 384 | snp4102 385 | snp4112 386 | snp4116 387 | snp4122 388 | snp4123 389 | snp4160 390 | snp4165 391 | snp4168 392 | snp4175 393 | snp4180 394 | snp4188 395 | snp4192 396 | snp4212 397 | snp4213 398 | snp4233 399 | snp4244 400 | snp4255 401 | snp4270 402 | snp4272 403 | snp4281 404 | snp4283 405 | snp4287 406 | snp4293 407 | snp4295 408 | snp4307 409 | snp4319 410 | snp4328 411 | snp4333 412 | snp4344 413 | snp4350 414 | snp4358 415 | snp4370 416 | snp4385 417 | snp4389 418 | snp4392 419 | snp4406 420 | snp4407 421 | snp4418 422 | snp4424 423 | snp4425 424 | snp4437 425 | snp4441 426 | snp4446 427 | snp4448 428 | snp4457 429 | snp4459 430 | snp4486 431 | snp4489 432 | snp4509 433 | snp4544 434 | snp4555 435 | snp4564 436 | snp4580 437 | snp4594 438 | snp4596 439 | snp4601 440 | snp4619 441 | snp4622 442 | snp4625 443 | snp4635 444 | snp4638 445 | snp4641 446 | snp4644 447 | snp4646 448 | snp4649 449 | snp4653 450 | snp4666 451 | snp4689 452 | snp4710 453 | snp4720 454 | snp4727 455 | snp4728 456 | snp4730 457 | snp4735 458 | snp4748 459 | snp4774 460 | snp4808 461 | snp4819 462 | snp4824 463 | snp4832 464 | snp4833 465 | snp4847 466 | snp4873 467 | snp4880 468 | snp4883 469 | snp4888 470 | snp4892 471 | snp4900 472 | snp4920 473 | snp4927 474 | snp4938 475 | snp4941 476 | snp4943 477 | snp4962 478 | snp4969 479 | snp4980 480 | snp4993 481 | snp5000 482 | snp5016 483 | snp5026 484 | snp5033 485 | snp5054 486 | snp5055 487 | snp5061 488 | snp5083 489 | snp5111 490 | snp5112 491 | snp5121 492 | snp5123 493 | snp5125 494 | snp5129 495 | snp5130 496 | snp5133 497 | snp5148 498 | snp5154 499 | snp5168 500 | snp5201 501 | snp5206 502 | snp5224 503 | snp5236 504 | snp5257 505 | snp5258 506 | snp5261 507 | snp5271 508 | snp5279 509 | snp5294 510 | snp5301 511 | snp5311 512 | snp5313 513 | snp5327 514 | snp5336 515 | snp5338 516 | snp5344 517 | snp5347 518 | snp5356 519 | snp5385 520 | snp5398 521 | snp5412 522 | snp5419 523 | snp5432 524 | snp5433 525 | snp5449 526 | snp5461 527 | snp5474 528 | snp5479 529 | snp5481 530 | snp5485 531 | snp5486 532 | snp5487 533 | snp5519 534 | snp5522 535 | snp5544 536 | snp5546 537 | snp5553 538 | snp5570 539 | snp5582 540 | snp5584 541 | snp5589 542 | snp5594 543 | snp5605 544 | snp5636 545 | snp5641 546 | snp5653 547 | snp5656 548 | snp5657 549 | snp5664 550 | snp5672 551 | snp5677 552 | snp5702 553 | snp5706 554 | snp5709 555 | snp5726 556 | snp5742 557 | snp5754 558 | snp5756 559 | snp5757 560 | snp5759 561 | snp5763 562 | snp5782 563 | snp5786 564 | snp5787 565 | snp5788 566 | snp5801 567 | snp5804 568 | snp5805 569 | snp5807 570 | snp5808 571 | snp5820 572 | snp5829 573 | snp5839 574 | snp5848 575 | snp5856 576 | snp5862 577 | snp5863 578 | snp5884 579 | snp5894 580 | snp5908 581 | snp5913 582 | snp5918 583 | snp5923 584 | snp5960 585 | snp5961 586 | snp5978 587 | snp5995 588 | snp6020 589 | snp6028 590 | snp6035 591 | snp6049 592 | snp6061 593 | snp6069 594 | snp6075 595 | snp6086 596 | snp6090 597 | snp6094 598 | snp6117 599 | snp6118 600 | snp6132 601 | snp6150 602 | snp6161 603 | snp6162 604 | snp6175 605 | snp6203 606 | snp6204 607 | snp6207 608 | snp6217 609 | snp6227 610 | snp6230 611 | snp6247 612 | snp6261 613 | snp6264 614 | snp6270 615 | snp6280 616 | snp6307 617 | snp6333 618 | snp6352 619 | snp6359 620 | snp6368 621 | snp6370 622 | snp6371 623 | snp6385 624 | snp6393 625 | snp6396 626 | snp6407 627 | snp6420 628 | snp6424 629 | snp6447 630 | snp6455 631 | snp6461 632 | snp6464 633 | snp6469 634 | snp6472 635 | snp6473 636 | snp6474 637 | snp6481 638 | snp6484 639 | snp6513 640 | snp6520 641 | snp6531 642 | snp6534 643 | snp6535 644 | snp6536 645 | snp6544 646 | snp6548 647 | snp6556 648 | snp6586 649 | snp6588 650 | snp6592 651 | snp6598 652 | snp6600 653 | snp6612 654 | snp6613 655 | snp6619 656 | snp6624 657 | snp6644 658 | snp6649 659 | snp6651 660 | snp6662 661 | snp6681 662 | snp6692 663 | snp6698 664 | snp6709 665 | snp6735 666 | snp6737 667 | snp6744 668 | snp6748 669 | snp6760 670 | snp6767 671 | snp6782 672 | snp6787 673 | snp6794 674 | snp6802 675 | snp6806 676 | snp6807 677 | snp6815 678 | snp6821 679 | snp6831 680 | snp6840 681 | snp6847 682 | snp6875 683 | snp6880 684 | snp6885 685 | snp6888 686 | snp6893 687 | snp6896 688 | snp6903 689 | snp6908 690 | snp6909 691 | snp6913 692 | snp6923 693 | snp6942 694 | snp6955 695 | snp6957 696 | snp6960 697 | snp6968 698 | snp6971 699 | snp6979 700 | snp6987 701 | snp6990 702 | snp7004 703 | snp7007 704 | snp7016 705 | snp7028 706 | snp7030 707 | snp7032 708 | snp7039 709 | snp7046 710 | snp7049 711 | snp7058 712 | snp7066 713 | snp7068 714 | snp7077 715 | snp7089 716 | snp7115 717 | snp7121 718 | snp7124 719 | snp7140 720 | snp7158 721 | snp7159 722 | snp7167 723 | snp7180 724 | snp7183 725 | snp7223 726 | snp7224 727 | snp7253 728 | snp7254 729 | snp7255 730 | snp7260 731 | snp7297 732 | snp7304 733 | snp7312 734 | snp7316 735 | snp7323 736 | snp7327 737 | snp7331 738 | snp7356 739 | snp7368 740 | snp7388 741 | snp7396 742 | snp7451 743 | snp7466 744 | snp7477 745 | snp7488 746 | snp7489 747 | snp7494 748 | snp7506 749 | snp7507 750 | snp7510 751 | snp7533 752 | snp7541 753 | snp7571 754 | snp7577 755 | snp7584 756 | snp7597 757 | snp7609 758 | snp7615 759 | snp7616 760 | snp7622 761 | snp7637 762 | snp7649 763 | snp7651 764 | snp7661 765 | snp7669 766 | snp7741 767 | snp7745 768 | snp7753 769 | snp7763 770 | snp7786 771 | snp7797 772 | snp7801 773 | snp7817 774 | snp7858 775 | snp7863 776 | snp7865 777 | snp7869 778 | snp7877 779 | snp7884 780 | snp7889 781 | snp7906 782 | snp7907 783 | snp7911 784 | snp7921 785 | snp7935 786 | snp7940 787 | snp7954 788 | snp7962 789 | snp7963 790 | snp7964 791 | snp7967 792 | snp7969 793 | snp7976 794 | snp7983 795 | snp7989 796 | snp7993 797 | snp8011 798 | snp8013 799 | snp8017 800 | snp8020 801 | snp8026 802 | snp8027 803 | snp8032 804 | snp8047 805 | snp8048 806 | snp8056 807 | snp8072 808 | snp8078 809 | snp8095 810 | snp8097 811 | snp8105 812 | snp8115 813 | snp8132 814 | snp8136 815 | snp8137 816 | snp8164 817 | snp8170 818 | snp8190 819 | snp8196 820 | snp8199 821 | snp8200 822 | snp8204 823 | snp8205 824 | snp8207 825 | snp8235 826 | snp8237 827 | snp8251 828 | snp8261 829 | snp8276 830 | snp8281 831 | snp8294 832 | snp8304 833 | snp8305 834 | snp8307 835 | snp8316 836 | snp8322 837 | snp8335 838 | snp8337 839 | snp8344 840 | snp8362 841 | snp8365 842 | snp8373 843 | snp8391 844 | snp8394 845 | snp8395 846 | snp8400 847 | snp8405 848 | snp8433 849 | snp8435 850 | snp8441 851 | snp8443 852 | snp8462 853 | snp8480 854 | snp8509 855 | snp8511 856 | snp8530 857 | snp8537 858 | snp8549 859 | snp8550 860 | snp8553 861 | snp8565 862 | snp8573 863 | snp8597 864 | snp8608 865 | snp8617 866 | snp8629 867 | snp8634 868 | snp8666 869 | snp8668 870 | snp8672 871 | snp8676 872 | snp8681 873 | snp8687 874 | snp8692 875 | snp8702 876 | snp8706 877 | snp8722 878 | snp8740 879 | snp8755 880 | snp8756 881 | snp8766 882 | snp8782 883 | snp8786 884 | snp8790 885 | snp8816 886 | snp8829 887 | snp8849 888 | snp8858 889 | snp8921 890 | snp8922 891 | snp8924 892 | snp8926 893 | snp8946 894 | snp8950 895 | snp8954 896 | snp8963 897 | snp8964 898 | snp9008 899 | snp9012 900 | snp9044 901 | snp9046 902 | snp9053 903 | snp9059 904 | snp9080 905 | snp9084 906 | snp9089 907 | snp9105 908 | snp9106 909 | snp9117 910 | snp9123 911 | snp9144 912 | snp9151 913 | snp9152 914 | snp9157 915 | snp9167 916 | snp9178 917 | snp9182 918 | snp9187 919 | snp9188 920 | snp9194 921 | snp9196 922 | snp9198 923 | snp9245 924 | snp9263 925 | snp9280 926 | snp9299 927 | snp9302 928 | snp9309 929 | snp9317 930 | snp9349 931 | snp9353 932 | snp9356 933 | snp9363 934 | snp9368 935 | snp9373 936 | snp9374 937 | snp9384 938 | snp9388 939 | snp9389 940 | snp9399 941 | snp9417 942 | snp9455 943 | snp9470 944 | snp9483 945 | snp9486 946 | snp9495 947 | snp9501 948 | snp9527 949 | snp9531 950 | snp9540 951 | snp9550 952 | snp9564 953 | snp9566 954 | snp9570 955 | snp9580 956 | snp9591 957 | snp9592 958 | snp9598 959 | snp9620 960 | snp9634 961 | snp9657 962 | snp9668 963 | snp9669 964 | snp9684 965 | snp9687 966 | snp9690 967 | snp9712 968 | snp9728 969 | snp9731 970 | snp9734 971 | snp9735 972 | snp9739 973 | snp9745 974 | snp9756 975 | snp9775 976 | snp9779 977 | snp9780 978 | snp9792 979 | snp9796 980 | snp9802 981 | snp9811 982 | snp9832 983 | snp9844 984 | snp9849 985 | snp9877 986 | snp9881 987 | snp9898 988 | snp9908 989 | snp9934 990 | snp9935 991 | snp9939 992 | snp9941 993 | snp9944 994 | snp9945 995 | snp9957 996 | snp9959 997 | snp9960 998 | snp9968 999 | snp9970 1000 | snp9981 1001 | snp9999 1002 | snp10002 1003 | snp10012 1004 | snp10019 1005 | snp10026 1006 | snp10037 1007 | snp10045 1008 | snp10054 1009 | snp10058 1010 | snp10060 1011 | snp10062 1012 | snp10063 1013 | snp10125 1014 | snp10131 1015 | snp10133 1016 | snp10137 1017 | snp10158 1018 | snp10176 1019 | snp10178 1020 | snp10224 1021 | snp10248 1022 | snp10274 1023 | snp10288 1024 | snp10297 1025 | snp10298 1026 | snp10302 1027 | snp10304 1028 | snp10307 1029 | snp10322 1030 | snp10332 1031 | snp10335 1032 | snp10350 1033 | snp10355 1034 | snp10360 1035 | snp10362 1036 | snp10365 1037 | snp10370 1038 | snp10384 1039 | snp10388 1040 | snp10390 1041 | snp10396 1042 | snp10408 1043 | snp10416 1044 | snp10418 1045 | snp10426 1046 | snp10428 1047 | snp10442 1048 | snp10448 1049 | snp10460 1050 | snp10463 1051 | snp10467 1052 | snp10476 1053 | snp10490 1054 | snp10500 1055 | dsnp10501 1056 | dsnp10511 1057 | dsnp10529 1058 | dsnp10544 1059 | dsnp10557 1060 | dsnp10587 1061 | -------------------------------------------------------------------------------- /dataset1/extracts/chr9_extract.txt: -------------------------------------------------------------------------------- 1 | csnp12 2 | csnp13 3 | csnp23 4 | csnp26 5 | csnp45 6 | csnp52 7 | csnp56 8 | csnp60 9 | csnp87 10 | csnp89 11 | csnp91 12 | csnp92 13 | csnp110 14 | csnp122 15 | csnp136 16 | csnp139 17 | csnp161 18 | csnp188 19 | csnp197 20 | csnp214 21 | csnp236 22 | csnp265 23 | csnp290 24 | csnp335 25 | csnp336 26 | csnp347 27 | csnp351 28 | csnp352 29 | csnp372 30 | csnp381 31 | csnp399 32 | csnp414 33 | csnp421 34 | csnp431 35 | csnp474 36 | csnp477 37 | csnp483 38 | csnp484 39 | snp509 40 | snp525 41 | snp533 42 | snp568 43 | snp577 44 | snp578 45 | snp579 46 | snp581 47 | snp590 48 | snp591 49 | snp653 50 | snp660 51 | snp663 52 | snp669 53 | snp676 54 | snp687 55 | snp688 56 | snp707 57 | snp711 58 | snp714 59 | snp721 60 | snp726 61 | snp751 62 | snp761 63 | snp787 64 | snp789 65 | snp794 66 | snp800 67 | snp814 68 | snp821 69 | snp822 70 | snp827 71 | snp830 72 | snp837 73 | snp849 74 | snp851 75 | snp872 76 | snp884 77 | snp885 78 | snp904 79 | snp911 80 | snp918 81 | snp920 82 | snp932 83 | snp937 84 | snp940 85 | snp944 86 | snp952 87 | snp956 88 | snp964 89 | snp975 90 | snp983 91 | snp984 92 | snp993 93 | snp995 94 | snp996 95 | snp1009 96 | snp1018 97 | snp1021 98 | snp1025 99 | snp1026 100 | snp1038 101 | snp1043 102 | snp1057 103 | snp1062 104 | snp1065 105 | snp1075 106 | snp1114 107 | snp1126 108 | snp1130 109 | snp1139 110 | snp1153 111 | snp1188 112 | snp1245 113 | snp1248 114 | snp1251 115 | snp1258 116 | snp1268 117 | snp1270 118 | snp1271 119 | snp1280 120 | snp1281 121 | snp1282 122 | snp1285 123 | snp1292 124 | snp1313 125 | snp1321 126 | snp1344 127 | snp1355 128 | snp1361 129 | snp1367 130 | snp1372 131 | snp1383 132 | snp1404 133 | snp1413 134 | snp1415 135 | snp1430 136 | snp1433 137 | snp1440 138 | snp1444 139 | snp1456 140 | snp1469 141 | snp1474 142 | snp1476 143 | snp1495 144 | snp1503 145 | snp1512 146 | snp1513 147 | snp1529 148 | snp1540 149 | snp1548 150 | snp1554 151 | snp1582 152 | snp1587 153 | snp1594 154 | snp1598 155 | snp1599 156 | snp1606 157 | snp1609 158 | snp1618 159 | snp1623 160 | snp1633 161 | snp1643 162 | snp1658 163 | snp1668 164 | snp1680 165 | snp1689 166 | snp1699 167 | snp1704 168 | snp1705 169 | snp1709 170 | snp1712 171 | snp1747 172 | snp1767 173 | snp1776 174 | snp1785 175 | snp1826 176 | snp1847 177 | snp1859 178 | snp1865 179 | snp1868 180 | snp1893 181 | snp1896 182 | snp1898 183 | snp1903 184 | snp1910 185 | snp1911 186 | snp1933 187 | snp1947 188 | snp1953 189 | snp1977 190 | snp2012 191 | snp2015 192 | snp2026 193 | snp2032 194 | snp2037 195 | snp2048 196 | snp2051 197 | snp2058 198 | snp2089 199 | snp2095 200 | snp2102 201 | snp2117 202 | snp2127 203 | snp2131 204 | snp2192 205 | snp2198 206 | snp2205 207 | snp2222 208 | snp2235 209 | snp2240 210 | snp2265 211 | snp2266 212 | snp2269 213 | snp2271 214 | snp2274 215 | snp2277 216 | snp2317 217 | snp2345 218 | snp2353 219 | snp2393 220 | snp2400 221 | snp2403 222 | snp2411 223 | snp2422 224 | snp2436 225 | snp2486 226 | snp2491 227 | snp2499 228 | snp2500 229 | snp2502 230 | snp2546 231 | snp2548 232 | snp2586 233 | snp2593 234 | snp2594 235 | snp2600 236 | snp2611 237 | snp2623 238 | snp2629 239 | snp2631 240 | snp2655 241 | snp2695 242 | snp2707 243 | snp2709 244 | snp2726 245 | snp2737 246 | snp2739 247 | snp2748 248 | snp2777 249 | snp2797 250 | snp2802 251 | snp2806 252 | snp2815 253 | snp2832 254 | snp2835 255 | snp2840 256 | snp2851 257 | snp2862 258 | snp2867 259 | snp2875 260 | snp2877 261 | snp2878 262 | snp2888 263 | snp2889 264 | snp2890 265 | snp2896 266 | snp2904 267 | snp2905 268 | snp2912 269 | snp2913 270 | snp2928 271 | snp2949 272 | snp2961 273 | snp2984 274 | snp3000 275 | snp3013 276 | snp3017 277 | snp3027 278 | snp3028 279 | snp3031 280 | snp3032 281 | snp3034 282 | snp3036 283 | snp3045 284 | snp3055 285 | snp3056 286 | snp3057 287 | snp3064 288 | snp3074 289 | snp3093 290 | snp3096 291 | snp3115 292 | snp3123 293 | snp3125 294 | snp3126 295 | snp3134 296 | snp3139 297 | snp3159 298 | snp3161 299 | snp3174 300 | snp3179 301 | snp3188 302 | snp3194 303 | snp3197 304 | snp3206 305 | snp3212 306 | snp3214 307 | snp3221 308 | snp3234 309 | snp3235 310 | snp3236 311 | snp3242 312 | snp3243 313 | snp3288 314 | snp3292 315 | snp3312 316 | snp3341 317 | snp3372 318 | snp3373 319 | snp3388 320 | snp3393 321 | snp3398 322 | snp3412 323 | snp3418 324 | snp3423 325 | snp3436 326 | snp3448 327 | snp3458 328 | snp3462 329 | snp3471 330 | snp3480 331 | snp3489 332 | snp3498 333 | snp3504 334 | snp3511 335 | snp3516 336 | snp3517 337 | snp3519 338 | snp3529 339 | snp3538 340 | snp3541 341 | snp3559 342 | snp3570 343 | snp3571 344 | snp3579 345 | snp3589 346 | snp3595 347 | snp3601 348 | snp3607 349 | snp3609 350 | snp3610 351 | snp3614 352 | snp3617 353 | snp3650 354 | snp3680 355 | snp3681 356 | snp3685 357 | snp3691 358 | snp3700 359 | snp3705 360 | snp3715 361 | snp3765 362 | snp3806 363 | snp3814 364 | snp3836 365 | snp3850 366 | snp3855 367 | snp3856 368 | snp3857 369 | snp3859 370 | snp3864 371 | snp3868 372 | snp3882 373 | snp3885 374 | snp3907 375 | snp3910 376 | snp3916 377 | snp3918 378 | snp3930 379 | snp3944 380 | snp3947 381 | snp3950 382 | snp3959 383 | snp3967 384 | snp3974 385 | snp3975 386 | snp3979 387 | snp3984 388 | snp3985 389 | snp3990 390 | snp4000 391 | snp4007 392 | snp4011 393 | snp4015 394 | snp4027 395 | snp4039 396 | snp4051 397 | snp4054 398 | snp4061 399 | snp4094 400 | snp4095 401 | snp4103 402 | snp4108 403 | snp4115 404 | snp4136 405 | snp4144 406 | snp4150 407 | snp4161 408 | snp4162 409 | snp4171 410 | snp4183 411 | snp4216 412 | snp4225 413 | snp4229 414 | snp4234 415 | snp4237 416 | snp4242 417 | snp4247 418 | snp4267 419 | snp4269 420 | snp4296 421 | snp4308 422 | snp4310 423 | snp4311 424 | snp4322 425 | snp4337 426 | snp4341 427 | snp4361 428 | snp4362 429 | snp4379 430 | snp4384 431 | snp4412 432 | snp4435 433 | snp4453 434 | snp4470 435 | snp4473 436 | snp4484 437 | snp4500 438 | snp4501 439 | snp4508 440 | snp4512 441 | snp4514 442 | snp4515 443 | snp4532 444 | snp4533 445 | snp4542 446 | snp4548 447 | snp4562 448 | snp4572 449 | snp4579 450 | snp4581 451 | snp4592 452 | snp4597 453 | snp4606 454 | snp4621 455 | snp4624 456 | snp4648 457 | snp4670 458 | snp4674 459 | snp4678 460 | snp4686 461 | snp4692 462 | snp4696 463 | snp4711 464 | snp4712 465 | snp4721 466 | snp4723 467 | snp4725 468 | snp4742 469 | snp4755 470 | snp4769 471 | snp4770 472 | snp4785 473 | snp4809 474 | snp4837 475 | snp4843 476 | snp4845 477 | snp4856 478 | snp4858 479 | snp4878 480 | snp4897 481 | snp4903 482 | snp4916 483 | snp4928 484 | snp4935 485 | snp4947 486 | snp4957 487 | snp4958 488 | snp4959 489 | snp4971 490 | snp4975 491 | snp4981 492 | snp4986 493 | snp4991 494 | snp5002 495 | snp5007 496 | snp5018 497 | snp5030 498 | snp5048 499 | snp5049 500 | snp5057 501 | snp5064 502 | snp5082 503 | snp5085 504 | snp5087 505 | snp5088 506 | snp5100 507 | snp5114 508 | snp5131 509 | snp5136 510 | snp5151 511 | snp5159 512 | snp5161 513 | snp5165 514 | snp5171 515 | snp5172 516 | snp5180 517 | snp5196 518 | snp5235 519 | snp5237 520 | snp5244 521 | snp5252 522 | snp5255 523 | snp5259 524 | snp5278 525 | snp5286 526 | snp5298 527 | snp5303 528 | snp5315 529 | snp5319 530 | snp5323 531 | snp5331 532 | snp5334 533 | snp5337 534 | snp5341 535 | snp5360 536 | snp5367 537 | snp5368 538 | snp5369 539 | snp5379 540 | snp5380 541 | snp5390 542 | snp5396 543 | snp5409 544 | snp5439 545 | snp5469 546 | snp5498 547 | snp5504 548 | snp5506 549 | snp5513 550 | snp5520 551 | snp5529 552 | snp5530 553 | snp5551 554 | snp5555 555 | snp5563 556 | snp5587 557 | snp5597 558 | snp5598 559 | snp5618 560 | snp5643 561 | snp5644 562 | snp5647 563 | snp5649 564 | snp5652 565 | snp5658 566 | snp5673 567 | snp5682 568 | snp5698 569 | snp5703 570 | snp5712 571 | snp5713 572 | snp5714 573 | snp5719 574 | snp5720 575 | snp5753 576 | snp5758 577 | snp5794 578 | snp5809 579 | snp5827 580 | snp5836 581 | snp5857 582 | snp5903 583 | snp5929 584 | snp5942 585 | snp5945 586 | snp5949 587 | snp5950 588 | snp5973 589 | snp5975 590 | snp5983 591 | snp5989 592 | snp6008 593 | snp6009 594 | snp6014 595 | snp6019 596 | snp6024 597 | snp6026 598 | snp6029 599 | snp6033 600 | snp6036 601 | snp6037 602 | snp6052 603 | snp6073 604 | snp6085 605 | snp6091 606 | snp6093 607 | snp6101 608 | snp6103 609 | snp6104 610 | snp6107 611 | snp6110 612 | snp6111 613 | snp6126 614 | snp6136 615 | snp6137 616 | snp6139 617 | snp6154 618 | snp6164 619 | snp6165 620 | snp6183 621 | snp6192 622 | snp6209 623 | snp6213 624 | snp6224 625 | snp6234 626 | snp6236 627 | snp6238 628 | snp6241 629 | snp6260 630 | snp6275 631 | snp6282 632 | snp6284 633 | snp6288 634 | snp6293 635 | snp6295 636 | snp6298 637 | snp6301 638 | snp6316 639 | snp6340 640 | snp6343 641 | snp6348 642 | snp6350 643 | snp6360 644 | snp6362 645 | snp6372 646 | snp6374 647 | snp6392 648 | snp6416 649 | snp6419 650 | snp6428 651 | snp6436 652 | snp6462 653 | snp6466 654 | snp6470 655 | snp6483 656 | snp6485 657 | snp6489 658 | snp6501 659 | snp6503 660 | snp6526 661 | snp6530 662 | snp6532 663 | snp6538 664 | snp6543 665 | snp6547 666 | snp6550 667 | snp6572 668 | snp6575 669 | snp6589 670 | snp6597 671 | snp6604 672 | snp6617 673 | snp6620 674 | snp6629 675 | snp6641 676 | snp6643 677 | snp6657 678 | snp6678 679 | snp6739 680 | snp6759 681 | snp6771 682 | snp6827 683 | snp6837 684 | snp6839 685 | snp6841 686 | snp6844 687 | snp6879 688 | snp6881 689 | snp6889 690 | snp6898 691 | snp6902 692 | snp6917 693 | snp6930 694 | snp6932 695 | snp6963 696 | snp7018 697 | snp7031 698 | snp7044 699 | snp7050 700 | snp7071 701 | snp7073 702 | snp7080 703 | snp7087 704 | snp7090 705 | snp7093 706 | snp7114 707 | snp7138 708 | snp7143 709 | snp7152 710 | snp7157 711 | snp7162 712 | snp7171 713 | snp7176 714 | snp7179 715 | snp7207 716 | snp7209 717 | snp7239 718 | snp7244 719 | snp7261 720 | snp7266 721 | snp7273 722 | snp7307 723 | snp7313 724 | snp7320 725 | snp7328 726 | snp7343 727 | snp7353 728 | snp7364 729 | snp7376 730 | snp7385 731 | snp7409 732 | snp7412 733 | snp7448 734 | snp7454 735 | snp7463 736 | snp7468 737 | snp7473 738 | snp7514 739 | snp7521 740 | snp7524 741 | snp7528 742 | snp7529 743 | snp7561 744 | snp7570 745 | snp7573 746 | snp7585 747 | snp7586 748 | snp7587 749 | snp7595 750 | snp7598 751 | snp7599 752 | snp7601 753 | snp7606 754 | snp7636 755 | snp7641 756 | snp7671 757 | snp7696 758 | snp7705 759 | snp7712 760 | snp7719 761 | snp7764 762 | snp7779 763 | snp7780 764 | snp7793 765 | snp7807 766 | snp7812 767 | snp7815 768 | snp7840 769 | snp7848 770 | snp7850 771 | snp7870 772 | snp7893 773 | snp7913 774 | snp7914 775 | snp7918 776 | snp7932 777 | snp7941 778 | snp7943 779 | snp7948 780 | snp7975 781 | snp7991 782 | snp7998 783 | snp8002 784 | snp8029 785 | snp8061 786 | snp8068 787 | snp8076 788 | snp8096 789 | snp8110 790 | snp8114 791 | snp8123 792 | snp8124 793 | snp8140 794 | snp8151 795 | snp8155 796 | snp8168 797 | snp8174 798 | snp8176 799 | snp8179 800 | snp8198 801 | snp8215 802 | snp8221 803 | snp8226 804 | snp8228 805 | snp8231 806 | snp8233 807 | snp8256 808 | snp8258 809 | snp8266 810 | snp8272 811 | snp8280 812 | snp8295 813 | snp8298 814 | snp8302 815 | snp8318 816 | snp8320 817 | snp8326 818 | snp8347 819 | snp8353 820 | snp8370 821 | snp8376 822 | snp8382 823 | snp8388 824 | snp8401 825 | snp8404 826 | snp8424 827 | snp8426 828 | snp8455 829 | snp8458 830 | snp8461 831 | snp8471 832 | snp8477 833 | snp8488 834 | snp8491 835 | snp8492 836 | snp8494 837 | snp8500 838 | snp8503 839 | snp8505 840 | snp8525 841 | snp8528 842 | snp8531 843 | snp8538 844 | snp8545 845 | snp8554 846 | snp8574 847 | snp8578 848 | snp8592 849 | snp8598 850 | snp8600 851 | snp8603 852 | snp8604 853 | snp8605 854 | snp8623 855 | snp8645 856 | snp8646 857 | snp8685 858 | snp8699 859 | snp8707 860 | snp8714 861 | snp8718 862 | snp8735 863 | snp8757 864 | snp8761 865 | snp8768 866 | snp8785 867 | snp8792 868 | snp8818 869 | snp8820 870 | snp8821 871 | snp8834 872 | snp8840 873 | snp8841 874 | snp8860 875 | snp8872 876 | snp8878 877 | snp8884 878 | snp8888 879 | snp8892 880 | snp8893 881 | snp8895 882 | snp8915 883 | snp8941 884 | snp8943 885 | snp8969 886 | snp8978 887 | snp8979 888 | snp8980 889 | snp8985 890 | snp9006 891 | snp9034 892 | snp9035 893 | snp9074 894 | snp9075 895 | snp9077 896 | snp9092 897 | snp9104 898 | snp9109 899 | snp9121 900 | snp9126 901 | snp9143 902 | snp9146 903 | snp9148 904 | snp9153 905 | snp9185 906 | snp9186 907 | snp9200 908 | snp9203 909 | snp9205 910 | snp9210 911 | snp9229 912 | snp9237 913 | snp9246 914 | snp9252 915 | snp9255 916 | snp9257 917 | snp9272 918 | snp9287 919 | snp9292 920 | snp9296 921 | snp9303 922 | snp9305 923 | snp9326 924 | snp9333 925 | snp9355 926 | snp9366 927 | snp9376 928 | snp9378 929 | snp9379 930 | snp9386 931 | snp9398 932 | snp9408 933 | snp9419 934 | snp9446 935 | snp9451 936 | snp9466 937 | snp9474 938 | snp9493 939 | snp9494 940 | snp9498 941 | snp9499 942 | snp9507 943 | snp9509 944 | snp9514 945 | snp9523 946 | snp9524 947 | snp9526 948 | snp9528 949 | snp9529 950 | snp9554 951 | snp9560 952 | snp9562 953 | snp9578 954 | snp9579 955 | snp9619 956 | snp9631 957 | snp9638 958 | snp9646 959 | snp9661 960 | snp9676 961 | snp9688 962 | snp9697 963 | snp9708 964 | snp9713 965 | snp9715 966 | snp9718 967 | snp9727 968 | snp9736 969 | snp9744 970 | snp9750 971 | snp9781 972 | snp9783 973 | snp9791 974 | snp9800 975 | snp9816 976 | snp9836 977 | snp9842 978 | snp9855 979 | snp9859 980 | snp9882 981 | snp9914 982 | snp9921 983 | snp9928 984 | snp9940 985 | snp9956 986 | snp9979 987 | snp9986 988 | snp9987 989 | snp9989 990 | snp9998 991 | snp10000 992 | snp10006 993 | snp10016 994 | snp10038 995 | snp10051 996 | snp10067 997 | snp10078 998 | snp10083 999 | snp10094 1000 | snp10097 1001 | snp10108 1002 | snp10111 1003 | snp10112 1004 | snp10134 1005 | snp10142 1006 | snp10177 1007 | snp10185 1008 | snp10194 1009 | snp10198 1010 | snp10199 1011 | snp10200 1012 | snp10212 1013 | snp10214 1014 | snp10220 1015 | snp10223 1016 | snp10229 1017 | snp10238 1018 | snp10270 1019 | snp10273 1020 | snp10289 1021 | snp10290 1022 | snp10292 1023 | snp10301 1024 | snp10305 1025 | snp10308 1026 | snp10323 1027 | snp10328 1028 | snp10330 1029 | snp10338 1030 | snp10357 1031 | snp10375 1032 | snp10386 1033 | snp10391 1034 | snp10409 1035 | snp10411 1036 | snp10414 1037 | snp10421 1038 | snp10438 1039 | snp10441 1040 | snp10474 1041 | snp10479 1042 | snp10495 1043 | snp10496 1044 | dsnp10520 1045 | dsnp10536 1046 | dsnp10546 1047 | dsnp10551 1048 | dsnp10555 1049 | dsnp10556 1050 | dsnp10559 1051 | dsnp10562 1052 | dsnp10565 1053 | dsnp10569 1054 | dsnp10583 1055 | dsnp10584 1056 | dsnp10586 1057 | dsnp10588 1058 | dsnp10599 1059 | dsnp10600 1060 | -------------------------------------------------------------------------------- /dataset1/extracts/chr2_extract.txt: -------------------------------------------------------------------------------- 1 | csnp2 2 | csnp10 3 | csnp16 4 | csnp30 5 | csnp33 6 | csnp34 7 | csnp36 8 | csnp49 9 | csnp50 10 | csnp63 11 | csnp73 12 | csnp75 13 | csnp93 14 | csnp96 15 | csnp118 16 | csnp119 17 | csnp135 18 | csnp137 19 | csnp141 20 | csnp186 21 | csnp193 22 | csnp213 23 | csnp221 24 | csnp248 25 | csnp264 26 | csnp289 27 | csnp313 28 | csnp319 29 | csnp330 30 | csnp339 31 | csnp361 32 | csnp373 33 | csnp376 34 | csnp377 35 | csnp380 36 | csnp390 37 | csnp401 38 | csnp404 39 | csnp433 40 | csnp437 41 | csnp443 42 | csnp444 43 | csnp447 44 | csnp453 45 | csnp475 46 | csnp480 47 | csnp485 48 | csnp488 49 | csnp491 50 | csnp496 51 | csnp497 52 | snp504 53 | snp510 54 | snp516 55 | snp517 56 | snp521 57 | snp534 58 | snp542 59 | snp555 60 | snp560 61 | snp574 62 | snp586 63 | snp594 64 | snp601 65 | snp603 66 | snp625 67 | snp649 68 | snp656 69 | snp664 70 | snp665 71 | snp673 72 | snp679 73 | snp685 74 | snp702 75 | snp706 76 | snp720 77 | snp723 78 | snp752 79 | snp768 80 | snp769 81 | snp796 82 | snp807 83 | snp839 84 | snp844 85 | snp887 86 | snp906 87 | snp908 88 | snp910 89 | snp931 90 | snp938 91 | snp973 92 | snp974 93 | snp989 94 | snp991 95 | snp999 96 | snp1002 97 | snp1007 98 | snp1028 99 | snp1030 100 | snp1039 101 | snp1042 102 | snp1048 103 | snp1050 104 | snp1054 105 | snp1063 106 | snp1079 107 | snp1080 108 | snp1084 109 | snp1087 110 | snp1100 111 | snp1101 112 | snp1103 113 | snp1121 114 | snp1127 115 | snp1140 116 | snp1141 117 | snp1143 118 | snp1149 119 | snp1197 120 | snp1202 121 | snp1233 122 | snp1238 123 | snp1253 124 | snp1257 125 | snp1277 126 | snp1290 127 | snp1305 128 | snp1310 129 | snp1330 130 | snp1331 131 | snp1332 132 | snp1336 133 | snp1341 134 | snp1354 135 | snp1369 136 | snp1371 137 | snp1375 138 | snp1376 139 | snp1394 140 | snp1396 141 | snp1403 142 | snp1409 143 | snp1418 144 | snp1423 145 | snp1477 146 | snp1478 147 | snp1482 148 | snp1490 149 | snp1492 150 | snp1500 151 | snp1501 152 | snp1508 153 | snp1532 154 | snp1545 155 | snp1551 156 | snp1561 157 | snp1563 158 | snp1566 159 | snp1649 160 | snp1652 161 | snp1659 162 | snp1742 163 | snp1744 164 | snp1746 165 | snp1756 166 | snp1758 167 | snp1760 168 | snp1762 169 | snp1764 170 | snp1778 171 | snp1780 172 | snp1790 173 | snp1791 174 | snp1795 175 | snp1801 176 | snp1804 177 | snp1819 178 | snp1825 179 | snp1832 180 | snp1850 181 | snp1858 182 | snp1863 183 | snp1864 184 | snp1866 185 | snp1870 186 | snp1873 187 | snp1877 188 | snp1882 189 | snp1884 190 | snp1921 191 | snp1924 192 | snp1932 193 | snp1940 194 | snp1941 195 | snp1951 196 | snp1969 197 | snp1993 198 | snp2018 199 | snp2028 200 | snp2053 201 | snp2074 202 | snp2075 203 | snp2078 204 | snp2079 205 | snp2084 206 | snp2094 207 | snp2098 208 | snp2108 209 | snp2140 210 | snp2144 211 | snp2153 212 | snp2154 213 | snp2158 214 | snp2161 215 | snp2181 216 | snp2183 217 | snp2189 218 | snp2190 219 | snp2195 220 | snp2206 221 | snp2207 222 | snp2211 223 | snp2215 224 | snp2237 225 | snp2243 226 | snp2245 227 | snp2247 228 | snp2250 229 | snp2251 230 | snp2258 231 | snp2263 232 | snp2290 233 | snp2296 234 | snp2302 235 | snp2305 236 | snp2331 237 | snp2334 238 | snp2352 239 | snp2355 240 | snp2365 241 | snp2379 242 | snp2388 243 | snp2394 244 | snp2398 245 | snp2417 246 | snp2427 247 | snp2457 248 | snp2459 249 | snp2461 250 | snp2467 251 | snp2469 252 | snp2474 253 | snp2479 254 | snp2488 255 | snp2494 256 | snp2495 257 | snp2497 258 | snp2505 259 | snp2507 260 | snp2517 261 | snp2533 262 | snp2551 263 | snp2556 264 | snp2557 265 | snp2564 266 | snp2572 267 | snp2576 268 | snp2578 269 | snp2591 270 | snp2597 271 | snp2604 272 | snp2606 273 | snp2616 274 | snp2635 275 | snp2637 276 | snp2648 277 | snp2664 278 | snp2674 279 | snp2683 280 | snp2684 281 | snp2685 282 | snp2693 283 | snp2705 284 | snp2711 285 | snp2712 286 | snp2718 287 | snp2724 288 | snp2730 289 | snp2731 290 | snp2743 291 | snp2755 292 | snp2757 293 | snp2772 294 | snp2773 295 | snp2774 296 | snp2785 297 | snp2789 298 | snp2790 299 | snp2795 300 | snp2801 301 | snp2804 302 | snp2827 303 | snp2829 304 | snp2841 305 | snp2844 306 | snp2845 307 | snp2846 308 | snp2849 309 | snp2872 310 | snp2886 311 | snp2895 312 | snp2916 313 | snp2923 314 | snp2933 315 | snp2951 316 | snp2960 317 | snp2965 318 | snp2985 319 | snp2988 320 | snp2990 321 | snp3003 322 | snp3014 323 | snp3015 324 | snp3030 325 | snp3039 326 | snp3046 327 | snp3061 328 | snp3081 329 | snp3113 330 | snp3118 331 | snp3122 332 | snp3149 333 | snp3156 334 | snp3191 335 | snp3201 336 | snp3245 337 | snp3253 338 | snp3280 339 | snp3287 340 | snp3291 341 | snp3308 342 | snp3323 343 | snp3340 344 | snp3378 345 | snp3381 346 | snp3387 347 | snp3391 348 | snp3395 349 | snp3403 350 | snp3417 351 | snp3438 352 | snp3466 353 | snp3470 354 | snp3472 355 | snp3476 356 | snp3500 357 | snp3512 358 | snp3542 359 | snp3543 360 | snp3547 361 | snp3548 362 | snp3551 363 | snp3583 364 | snp3585 365 | snp3622 366 | snp3633 367 | snp3634 368 | snp3638 369 | snp3640 370 | snp3647 371 | snp3662 372 | snp3664 373 | snp3692 374 | snp3702 375 | snp3709 376 | snp3716 377 | snp3727 378 | snp3738 379 | snp3750 380 | snp3752 381 | snp3778 382 | snp3812 383 | snp3815 384 | snp3817 385 | snp3831 386 | snp3841 387 | snp3843 388 | snp3883 389 | snp3889 390 | snp3893 391 | snp3902 392 | snp3905 393 | snp3921 394 | snp3943 395 | snp3957 396 | snp3964 397 | snp3972 398 | snp3987 399 | snp4001 400 | snp4028 401 | snp4029 402 | snp4031 403 | snp4040 404 | snp4056 405 | snp4067 406 | snp4070 407 | snp4080 408 | snp4084 409 | snp4090 410 | snp4107 411 | snp4120 412 | snp4126 413 | snp4131 414 | snp4142 415 | snp4178 416 | snp4181 417 | snp4195 418 | snp4198 419 | snp4217 420 | snp4235 421 | snp4240 422 | snp4243 423 | snp4256 424 | snp4265 425 | snp4276 426 | snp4300 427 | snp4301 428 | snp4302 429 | snp4317 430 | snp4330 431 | snp4355 432 | snp4359 433 | snp4360 434 | snp4367 435 | snp4382 436 | snp4386 437 | snp4393 438 | snp4394 439 | snp4395 440 | snp4405 441 | snp4431 442 | snp4439 443 | snp4445 444 | snp4463 445 | snp4468 446 | snp4495 447 | snp4503 448 | snp4504 449 | snp4511 450 | snp4516 451 | snp4528 452 | snp4529 453 | snp4546 454 | snp4552 455 | snp4553 456 | snp4559 457 | snp4563 458 | snp4565 459 | snp4583 460 | snp4584 461 | snp4589 462 | snp4593 463 | snp4600 464 | snp4618 465 | snp4620 466 | snp4636 467 | snp4640 468 | snp4656 469 | snp4657 470 | snp4660 471 | snp4662 472 | snp4667 473 | snp4676 474 | snp4684 475 | snp4703 476 | snp4733 477 | snp4739 478 | snp4743 479 | snp4751 480 | snp4761 481 | snp4763 482 | snp4771 483 | snp4780 484 | snp4789 485 | snp4812 486 | snp4822 487 | snp4828 488 | snp4831 489 | snp4836 490 | snp4848 491 | snp4850 492 | snp4855 493 | snp4875 494 | snp4886 495 | snp4910 496 | snp4924 497 | snp4936 498 | snp4940 499 | snp4965 500 | snp4972 501 | snp4997 502 | snp5004 503 | snp5005 504 | snp5006 505 | snp5009 506 | snp5015 507 | snp5039 508 | snp5046 509 | snp5053 510 | snp5079 511 | snp5093 512 | snp5095 513 | snp5108 514 | snp5110 515 | snp5126 516 | snp5127 517 | snp5132 518 | snp5141 519 | snp5153 520 | snp5173 521 | snp5181 522 | snp5187 523 | snp5188 524 | snp5191 525 | snp5210 526 | snp5218 527 | snp5220 528 | snp5232 529 | snp5239 530 | snp5242 531 | snp5243 532 | snp5260 533 | snp5262 534 | snp5266 535 | snp5272 536 | snp5282 537 | snp5320 538 | snp5326 539 | snp5351 540 | snp5353 541 | snp5355 542 | snp5361 543 | snp5384 544 | snp5394 545 | snp5406 546 | snp5414 547 | snp5417 548 | snp5423 549 | snp5443 550 | snp5445 551 | snp5452 552 | snp5476 553 | snp5490 554 | snp5493 555 | snp5497 556 | snp5514 557 | snp5543 558 | snp5569 559 | snp5572 560 | snp5575 561 | snp5578 562 | snp5586 563 | snp5610 564 | snp5635 565 | snp5655 566 | snp5660 567 | snp5671 568 | snp5699 569 | snp5745 570 | snp5755 571 | snp5770 572 | snp5772 573 | snp5777 574 | snp5778 575 | snp5798 576 | snp5812 577 | snp5821 578 | snp5832 579 | snp5834 580 | snp5842 581 | snp5843 582 | snp5854 583 | snp5858 584 | snp5860 585 | snp5878 586 | snp5879 587 | snp5902 588 | snp5912 589 | snp5917 590 | snp5920 591 | snp5925 592 | snp5934 593 | snp5935 594 | snp5936 595 | snp5952 596 | snp5956 597 | snp5958 598 | snp5987 599 | snp5992 600 | snp5998 601 | snp6000 602 | snp6007 603 | snp6018 604 | snp6053 605 | snp6078 606 | snp6082 607 | snp6087 608 | snp6100 609 | snp6120 610 | snp6128 611 | snp6135 612 | snp6144 613 | snp6155 614 | snp6166 615 | snp6169 616 | snp6170 617 | snp6181 618 | snp6189 619 | snp6199 620 | snp6206 621 | snp6211 622 | snp6221 623 | snp6228 624 | snp6245 625 | snp6251 626 | snp6255 627 | snp6266 628 | snp6326 629 | snp6367 630 | snp6373 631 | snp6402 632 | snp6421 633 | snp6434 634 | snp6439 635 | snp6443 636 | snp6478 637 | snp6486 638 | snp6507 639 | snp6508 640 | snp6511 641 | snp6514 642 | snp6516 643 | snp6517 644 | snp6523 645 | snp6549 646 | snp6577 647 | snp6580 648 | snp6591 649 | snp6603 650 | snp6607 651 | snp6625 652 | snp6627 653 | snp6635 654 | snp6648 655 | snp6656 656 | snp6667 657 | snp6706 658 | snp6715 659 | snp6719 660 | snp6725 661 | snp6728 662 | snp6758 663 | snp6777 664 | snp6790 665 | snp6795 666 | snp6803 667 | snp6804 668 | snp6805 669 | snp6823 670 | snp6838 671 | snp6849 672 | snp6856 673 | snp6884 674 | snp6891 675 | snp6906 676 | snp6912 677 | snp6929 678 | snp6938 679 | snp6944 680 | snp6953 681 | snp6974 682 | snp6976 683 | snp6977 684 | snp6980 685 | snp6985 686 | snp6993 687 | snp6995 688 | snp6996 689 | snp7021 690 | snp7035 691 | snp7038 692 | snp7041 693 | snp7067 694 | snp7076 695 | snp7079 696 | snp7082 697 | snp7094 698 | snp7096 699 | snp7117 700 | snp7120 701 | snp7127 702 | snp7131 703 | snp7135 704 | snp7139 705 | snp7160 706 | snp7166 707 | snp7177 708 | snp7181 709 | snp7182 710 | snp7188 711 | snp7194 712 | snp7197 713 | snp7219 714 | snp7232 715 | snp7237 716 | snp7258 717 | snp7282 718 | snp7286 719 | snp7288 720 | snp7293 721 | snp7298 722 | snp7299 723 | snp7302 724 | snp7329 725 | snp7337 726 | snp7342 727 | snp7348 728 | snp7354 729 | snp7361 730 | snp7365 731 | snp7371 732 | snp7379 733 | snp7383 734 | snp7386 735 | snp7401 736 | snp7405 737 | snp7422 738 | snp7423 739 | snp7425 740 | snp7470 741 | snp7474 742 | snp7479 743 | snp7483 744 | snp7484 745 | snp7499 746 | snp7508 747 | snp7519 748 | snp7523 749 | snp7532 750 | snp7538 751 | snp7546 752 | snp7548 753 | snp7558 754 | snp7560 755 | snp7575 756 | snp7580 757 | snp7594 758 | snp7608 759 | snp7614 760 | snp7624 761 | snp7632 762 | snp7655 763 | snp7656 764 | snp7667 765 | snp7683 766 | snp7706 767 | snp7709 768 | snp7713 769 | snp7714 770 | snp7724 771 | snp7730 772 | snp7733 773 | snp7742 774 | snp7756 775 | snp7768 776 | snp7777 777 | snp7781 778 | snp7783 779 | snp7788 780 | snp7811 781 | snp7822 782 | snp7827 783 | snp7837 784 | snp7851 785 | snp7871 786 | snp7881 787 | snp7887 788 | snp7900 789 | snp7912 790 | snp7938 791 | snp7953 792 | snp7960 793 | snp7961 794 | snp7965 795 | snp7973 796 | snp7981 797 | snp7982 798 | snp7985 799 | snp7996 800 | snp8008 801 | snp8025 802 | snp8028 803 | snp8037 804 | snp8045 805 | snp8050 806 | snp8057 807 | snp8059 808 | snp8066 809 | snp8085 810 | snp8098 811 | snp8121 812 | snp8122 813 | snp8128 814 | snp8130 815 | snp8135 816 | snp8147 817 | snp8185 818 | snp8188 819 | snp8191 820 | snp8197 821 | snp8206 822 | snp8209 823 | snp8211 824 | snp8220 825 | snp8263 826 | snp8277 827 | snp8283 828 | snp8289 829 | snp8291 830 | snp8293 831 | snp8301 832 | snp8339 833 | snp8341 834 | snp8355 835 | snp8364 836 | snp8367 837 | snp8368 838 | snp8374 839 | snp8387 840 | snp8423 841 | snp8436 842 | snp8448 843 | snp8464 844 | snp8467 845 | snp8469 846 | snp8470 847 | snp8479 848 | snp8485 849 | snp8522 850 | snp8524 851 | snp8526 852 | snp8546 853 | snp8580 854 | snp8620 855 | snp8621 856 | snp8625 857 | snp8630 858 | snp8635 859 | snp8636 860 | snp8659 861 | snp8662 862 | snp8673 863 | snp8678 864 | snp8683 865 | snp8684 866 | snp8700 867 | snp8727 868 | snp8739 869 | snp8744 870 | snp8770 871 | snp8771 872 | snp8773 873 | snp8774 874 | snp8777 875 | snp8793 876 | snp8812 877 | snp8813 878 | snp8824 879 | snp8838 880 | snp8848 881 | snp8850 882 | snp8871 883 | snp8877 884 | snp8897 885 | snp8910 886 | snp8947 887 | snp8949 888 | snp8961 889 | snp8982 890 | snp9009 891 | snp9015 892 | snp9032 893 | snp9033 894 | snp9042 895 | snp9043 896 | snp9054 897 | snp9064 898 | snp9087 899 | snp9095 900 | snp9112 901 | snp9116 902 | snp9120 903 | snp9155 904 | snp9156 905 | snp9158 906 | snp9168 907 | snp9176 908 | snp9177 909 | snp9189 910 | snp9207 911 | snp9223 912 | snp9239 913 | snp9243 914 | snp9256 915 | snp9258 916 | snp9261 917 | snp9268 918 | snp9284 919 | snp9288 920 | snp9297 921 | snp9304 922 | snp9310 923 | snp9312 924 | snp9322 925 | snp9343 926 | snp9348 927 | snp9375 928 | snp9382 929 | snp9394 930 | snp9413 931 | snp9433 932 | snp9437 933 | snp9467 934 | snp9472 935 | snp9485 936 | snp9487 937 | snp9506 938 | snp9508 939 | snp9533 940 | snp9537 941 | snp9547 942 | snp9561 943 | snp9571 944 | snp9572 945 | snp9576 946 | snp9584 947 | snp9595 948 | snp9604 949 | snp9606 950 | snp9611 951 | snp9626 952 | snp9639 953 | snp9641 954 | snp9650 955 | snp9662 956 | snp9673 957 | snp9681 958 | snp9682 959 | snp9692 960 | snp9693 961 | snp9699 962 | snp9702 963 | snp9706 964 | snp9714 965 | snp9719 966 | snp9729 967 | snp9747 968 | snp9749 969 | snp9755 970 | snp9757 971 | snp9767 972 | snp9778 973 | snp9786 974 | snp9799 975 | snp9803 976 | snp9813 977 | snp9823 978 | snp9829 979 | snp9830 980 | snp9843 981 | snp9851 982 | snp9857 983 | snp9861 984 | snp9862 985 | snp9863 986 | snp9864 987 | snp9871 988 | snp9897 989 | snp9904 990 | snp9907 991 | snp9913 992 | snp9924 993 | snp9927 994 | snp9929 995 | snp9937 996 | snp9955 997 | snp9972 998 | snp9973 999 | snp9980 1000 | snp9985 1001 | snp9992 1002 | snp9995 1003 | snp10003 1004 | snp10028 1005 | snp10033 1006 | snp10052 1007 | snp10066 1008 | snp10072 1009 | snp10081 1010 | snp10087 1011 | snp10091 1012 | snp10115 1013 | snp10139 1014 | snp10145 1015 | snp10159 1016 | snp10191 1017 | snp10205 1018 | snp10209 1019 | snp10226 1020 | snp10231 1021 | snp10245 1022 | snp10247 1023 | snp10250 1024 | snp10264 1025 | snp10281 1026 | snp10283 1027 | snp10295 1028 | snp10313 1029 | snp10319 1030 | snp10334 1031 | snp10336 1032 | snp10347 1033 | snp10353 1034 | snp10359 1035 | snp10376 1036 | snp10379 1037 | snp10387 1038 | snp10402 1039 | snp10403 1040 | snp10407 1041 | snp10429 1042 | snp10443 1043 | snp10444 1044 | snp10450 1045 | snp10453 1046 | snp10465 1047 | snp10470 1048 | snp10473 1049 | dsnp10509 1050 | dsnp10516 1051 | dsnp10528 1052 | dsnp10535 1053 | dsnp10537 1054 | dsnp10541 1055 | dsnp10543 1056 | dsnp10548 1057 | dsnp10560 1058 | dsnp10561 1059 | dsnp10573 1060 | dsnp10591 1061 | -------------------------------------------------------------------------------- /dataset1/extracts/chr5_extract.txt: -------------------------------------------------------------------------------- 1 | csnp5 2 | csnp20 3 | csnp25 4 | csnp41 5 | csnp64 6 | csnp68 7 | csnp69 8 | csnp70 9 | csnp72 10 | csnp79 11 | csnp84 12 | csnp86 13 | csnp101 14 | csnp125 15 | csnp131 16 | csnp132 17 | csnp133 18 | csnp147 19 | csnp149 20 | csnp165 21 | csnp177 22 | csnp200 23 | csnp215 24 | csnp220 25 | csnp227 26 | csnp232 27 | csnp238 28 | csnp242 29 | csnp250 30 | csnp251 31 | csnp272 32 | csnp273 33 | csnp278 34 | csnp294 35 | csnp298 36 | csnp299 37 | csnp302 38 | csnp326 39 | csnp337 40 | csnp359 41 | csnp369 42 | csnp378 43 | csnp402 44 | csnp403 45 | csnp406 46 | csnp416 47 | csnp419 48 | csnp425 49 | csnp434 50 | csnp450 51 | csnp455 52 | csnp457 53 | csnp479 54 | csnp490 55 | csnp495 56 | snp503 57 | snp524 58 | snp552 59 | snp573 60 | snp589 61 | snp596 62 | snp610 63 | snp618 64 | snp628 65 | snp648 66 | snp650 67 | snp671 68 | snp690 69 | snp700 70 | snp703 71 | snp716 72 | snp725 73 | snp734 74 | snp741 75 | snp755 76 | snp760 77 | snp774 78 | snp788 79 | snp808 80 | snp815 81 | snp818 82 | snp819 83 | snp831 84 | snp832 85 | snp834 86 | snp850 87 | snp855 88 | snp861 89 | snp880 90 | snp901 91 | snp916 92 | snp933 93 | snp936 94 | snp947 95 | snp950 96 | snp951 97 | snp965 98 | snp968 99 | snp985 100 | snp987 101 | snp992 102 | snp997 103 | snp1000 104 | snp1003 105 | snp1006 106 | snp1014 107 | snp1015 108 | snp1034 109 | snp1059 110 | snp1061 111 | snp1064 112 | snp1067 113 | snp1074 114 | snp1123 115 | snp1132 116 | snp1133 117 | snp1145 118 | snp1171 119 | snp1181 120 | snp1186 121 | snp1196 122 | snp1200 123 | snp1207 124 | snp1223 125 | snp1228 126 | snp1252 127 | snp1254 128 | snp1255 129 | snp1259 130 | snp1263 131 | snp1275 132 | snp1276 133 | snp1287 134 | snp1295 135 | snp1302 136 | snp1304 137 | snp1315 138 | snp1328 139 | snp1329 140 | snp1352 141 | snp1365 142 | snp1378 143 | snp1382 144 | snp1384 145 | snp1397 146 | snp1406 147 | snp1414 148 | snp1417 149 | snp1422 150 | snp1439 151 | snp1442 152 | snp1446 153 | snp1460 154 | snp1463 155 | snp1472 156 | snp1475 157 | snp1485 158 | snp1486 159 | snp1493 160 | snp1499 161 | snp1517 162 | snp1546 163 | snp1556 164 | snp1557 165 | snp1573 166 | snp1577 167 | snp1580 168 | snp1586 169 | snp1595 170 | snp1617 171 | snp1642 172 | snp1653 173 | snp1654 174 | snp1664 175 | snp1671 176 | snp1675 177 | snp1688 178 | snp1703 179 | snp1711 180 | snp1713 181 | snp1752 182 | snp1757 183 | snp1766 184 | snp1769 185 | snp1779 186 | snp1781 187 | snp1782 188 | snp1810 189 | snp1813 190 | snp1821 191 | snp1833 192 | snp1834 193 | snp1836 194 | snp1867 195 | snp1888 196 | snp1944 197 | snp1950 198 | snp1967 199 | snp1980 200 | snp1981 201 | snp1995 202 | snp1999 203 | snp2001 204 | snp2002 205 | snp2004 206 | snp2011 207 | snp2016 208 | snp2023 209 | snp2024 210 | snp2030 211 | snp2033 212 | snp2040 213 | snp2050 214 | snp2061 215 | snp2066 216 | snp2088 217 | snp2106 218 | snp2114 219 | snp2124 220 | snp2136 221 | snp2141 222 | snp2146 223 | snp2156 224 | snp2163 225 | snp2170 226 | snp2177 227 | snp2191 228 | snp2199 229 | snp2208 230 | snp2209 231 | snp2233 232 | snp2234 233 | snp2236 234 | snp2249 235 | snp2252 236 | snp2255 237 | snp2256 238 | snp2278 239 | snp2298 240 | snp2316 241 | snp2324 242 | snp2350 243 | snp2356 244 | snp2360 245 | snp2390 246 | snp2396 247 | snp2404 248 | snp2409 249 | snp2414 250 | snp2418 251 | snp2426 252 | snp2428 253 | snp2434 254 | snp2439 255 | snp2454 256 | snp2455 257 | snp2466 258 | snp2480 259 | snp2487 260 | snp2512 261 | snp2514 262 | snp2518 263 | snp2528 264 | snp2562 265 | snp2577 266 | snp2584 267 | snp2596 268 | snp2612 269 | snp2614 270 | snp2649 271 | snp2666 272 | snp2668 273 | snp2670 274 | snp2677 275 | snp2686 276 | snp2713 277 | snp2714 278 | snp2716 279 | snp2736 280 | snp2754 281 | snp2760 282 | snp2767 283 | snp2768 284 | snp2778 285 | snp2781 286 | snp2812 287 | snp2813 288 | snp2825 289 | snp2836 290 | snp2865 291 | snp2894 292 | snp2902 293 | snp2903 294 | snp2915 295 | snp2919 296 | snp2922 297 | snp2926 298 | snp2931 299 | snp2942 300 | snp2964 301 | snp2973 302 | snp2979 303 | snp2998 304 | snp3026 305 | snp3029 306 | snp3047 307 | snp3054 308 | snp3062 309 | snp3085 310 | snp3095 311 | snp3098 312 | snp3102 313 | snp3104 314 | snp3108 315 | snp3120 316 | snp3131 317 | snp3137 318 | snp3138 319 | snp3158 320 | snp3166 321 | snp3176 322 | snp3178 323 | snp3182 324 | snp3208 325 | snp3211 326 | snp3223 327 | snp3225 328 | snp3230 329 | snp3248 330 | snp3258 331 | snp3263 332 | snp3264 333 | snp3268 334 | snp3283 335 | snp3285 336 | snp3289 337 | snp3293 338 | snp3299 339 | snp3307 340 | snp3309 341 | snp3310 342 | snp3314 343 | snp3322 344 | snp3349 345 | snp3353 346 | snp3356 347 | snp3357 348 | snp3365 349 | snp3371 350 | snp3384 351 | snp3416 352 | snp3449 353 | snp3455 354 | snp3456 355 | snp3457 356 | snp3461 357 | snp3496 358 | snp3510 359 | snp3521 360 | snp3536 361 | snp3552 362 | snp3558 363 | snp3560 364 | snp3578 365 | snp3582 366 | snp3584 367 | snp3598 368 | snp3604 369 | snp3608 370 | snp3612 371 | snp3615 372 | snp3639 373 | snp3643 374 | snp3653 375 | snp3655 376 | snp3684 377 | snp3693 378 | snp3694 379 | snp3698 380 | snp3718 381 | snp3720 382 | snp3741 383 | snp3761 384 | snp3762 385 | snp3767 386 | snp3779 387 | snp3786 388 | snp3787 389 | snp3789 390 | snp3793 391 | snp3801 392 | snp3803 393 | snp3835 394 | snp3852 395 | snp3862 396 | snp3881 397 | snp3894 398 | snp3897 399 | snp3923 400 | snp3935 401 | snp3939 402 | snp3941 403 | snp3952 404 | snp3956 405 | snp3958 406 | snp3961 407 | snp3966 408 | snp3969 409 | snp3970 410 | snp3980 411 | snp3997 412 | snp4034 413 | snp4041 414 | snp4049 415 | snp4058 416 | snp4065 417 | snp4066 418 | snp4071 419 | snp4072 420 | snp4073 421 | snp4098 422 | snp4099 423 | snp4100 424 | snp4101 425 | snp4106 426 | snp4110 427 | snp4114 428 | snp4133 429 | snp4143 430 | snp4148 431 | snp4170 432 | snp4184 433 | snp4209 434 | snp4215 435 | snp4219 436 | snp4230 437 | snp4249 438 | snp4250 439 | snp4259 440 | snp4268 441 | snp4289 442 | snp4290 443 | snp4314 444 | snp4316 445 | snp4318 446 | snp4334 447 | snp4346 448 | snp4347 449 | snp4349 450 | snp4378 451 | snp4381 452 | snp4391 453 | snp4397 454 | snp4402 455 | snp4423 456 | snp4438 457 | snp4444 458 | snp4452 459 | snp4460 460 | snp4467 461 | snp4469 462 | snp4471 463 | snp4502 464 | snp4513 465 | snp4520 466 | snp4541 467 | snp4549 468 | snp4554 469 | snp4557 470 | snp4571 471 | snp4577 472 | snp4602 473 | snp4607 474 | snp4610 475 | snp4612 476 | snp4630 477 | snp4668 478 | snp4683 479 | snp4685 480 | snp4700 481 | snp4702 482 | snp4732 483 | snp4756 484 | snp4783 485 | snp4800 486 | snp4804 487 | snp4827 488 | snp4853 489 | snp4854 490 | snp4859 491 | snp4933 492 | snp4934 493 | snp4944 494 | snp4950 495 | snp4961 496 | snp4964 497 | snp4966 498 | snp4970 499 | snp4989 500 | snp5020 501 | snp5021 502 | snp5028 503 | snp5032 504 | snp5041 505 | snp5059 506 | snp5060 507 | snp5072 508 | snp5076 509 | snp5084 510 | snp5094 511 | snp5096 512 | snp5102 513 | snp5116 514 | snp5117 515 | snp5134 516 | snp5149 517 | snp5158 518 | snp5170 519 | snp5176 520 | snp5205 521 | snp5207 522 | snp5230 523 | snp5247 524 | snp5248 525 | snp5265 526 | snp5269 527 | snp5273 528 | snp5280 529 | snp5289 530 | snp5293 531 | snp5310 532 | snp5332 533 | snp5339 534 | snp5354 535 | snp5365 536 | snp5370 537 | snp5386 538 | snp5389 539 | snp5430 540 | snp5437 541 | snp5440 542 | snp5457 543 | snp5471 544 | snp5475 545 | snp5478 546 | snp5484 547 | snp5492 548 | snp5512 549 | snp5540 550 | snp5545 551 | snp5557 552 | snp5577 553 | snp5581 554 | snp5585 555 | snp5591 556 | snp5595 557 | snp5613 558 | snp5619 559 | snp5620 560 | snp5623 561 | snp5632 562 | snp5637 563 | snp5640 564 | snp5645 565 | snp5659 566 | snp5661 567 | snp5679 568 | snp5683 569 | snp5691 570 | snp5697 571 | snp5715 572 | snp5727 573 | snp5735 574 | snp5739 575 | snp5743 576 | snp5748 577 | snp5750 578 | snp5765 579 | snp5767 580 | snp5773 581 | snp5774 582 | snp5800 583 | snp5802 584 | snp5817 585 | snp5819 586 | snp5824 587 | snp5833 588 | snp5838 589 | snp5841 590 | snp5859 591 | snp5866 592 | snp5868 593 | snp5869 594 | snp5881 595 | snp5898 596 | snp5910 597 | snp5930 598 | snp5940 599 | snp5946 600 | snp5951 601 | snp5957 602 | snp5966 603 | snp5971 604 | snp5993 605 | snp5997 606 | snp6005 607 | snp6012 608 | snp6041 609 | snp6043 610 | snp6047 611 | snp6051 612 | snp6056 613 | snp6070 614 | snp6072 615 | snp6081 616 | snp6099 617 | snp6114 618 | snp6121 619 | snp6130 620 | snp6131 621 | snp6138 622 | snp6141 623 | snp6142 624 | snp6146 625 | snp6147 626 | snp6151 627 | snp6177 628 | snp6191 629 | snp6197 630 | snp6253 631 | snp6258 632 | snp6272 633 | snp6274 634 | snp6277 635 | snp6286 636 | snp6287 637 | snp6290 638 | snp6297 639 | snp6306 640 | snp6317 641 | snp6331 642 | snp6332 643 | snp6347 644 | snp6349 645 | snp6358 646 | snp6375 647 | snp6383 648 | snp6389 649 | snp6413 650 | snp6432 651 | snp6437 652 | snp6438 653 | snp6440 654 | snp6445 655 | snp6463 656 | snp6468 657 | snp6471 658 | snp6476 659 | snp6502 660 | snp6512 661 | snp6539 662 | snp6555 663 | snp6562 664 | snp6568 665 | snp6578 666 | snp6594 667 | snp6614 668 | snp6616 669 | snp6618 670 | snp6628 671 | snp6636 672 | snp6680 673 | snp6683 674 | snp6685 675 | snp6687 676 | snp6700 677 | snp6703 678 | snp6708 679 | snp6724 680 | snp6726 681 | snp6729 682 | snp6730 683 | snp6733 684 | snp6743 685 | snp6745 686 | snp6746 687 | snp6755 688 | snp6756 689 | snp6764 690 | snp6799 691 | snp6809 692 | snp6816 693 | snp6819 694 | snp6822 695 | snp6830 696 | snp6832 697 | snp6843 698 | snp6864 699 | snp6867 700 | snp6868 701 | snp6914 702 | snp6915 703 | snp6919 704 | snp6927 705 | snp6937 706 | snp6943 707 | snp6947 708 | snp6962 709 | snp6978 710 | snp6981 711 | snp6983 712 | snp6986 713 | snp7001 714 | snp7003 715 | snp7019 716 | snp7023 717 | snp7034 718 | snp7043 719 | snp7052 720 | snp7060 721 | snp7072 722 | snp7084 723 | snp7098 724 | snp7116 725 | snp7129 726 | snp7175 727 | snp7184 728 | snp7192 729 | snp7196 730 | snp7198 731 | snp7203 732 | snp7228 733 | snp7233 734 | snp7252 735 | snp7269 736 | snp7271 737 | snp7284 738 | snp7295 739 | snp7296 740 | snp7303 741 | snp7326 742 | snp7330 743 | snp7347 744 | snp7359 745 | snp7360 746 | snp7369 747 | snp7375 748 | snp7380 749 | snp7390 750 | snp7394 751 | snp7406 752 | snp7416 753 | snp7417 754 | snp7441 755 | snp7443 756 | snp7449 757 | snp7456 758 | snp7465 759 | snp7475 760 | snp7482 761 | snp7486 762 | snp7491 763 | snp7495 764 | snp7500 765 | snp7518 766 | snp7530 767 | snp7555 768 | snp7564 769 | snp7568 770 | snp7576 771 | snp7579 772 | snp7582 773 | snp7589 774 | snp7591 775 | snp7610 776 | snp7617 777 | snp7620 778 | snp7631 779 | snp7635 780 | snp7648 781 | snp7662 782 | snp7666 783 | snp7672 784 | snp7675 785 | snp7677 786 | snp7681 787 | snp7686 788 | snp7691 789 | snp7698 790 | snp7704 791 | snp7711 792 | snp7732 793 | snp7746 794 | snp7754 795 | snp7762 796 | snp7775 797 | snp7784 798 | snp7787 799 | snp7803 800 | snp7819 801 | snp7820 802 | snp7831 803 | snp7846 804 | snp7847 805 | snp7859 806 | snp7878 807 | snp7886 808 | snp7888 809 | snp7908 810 | snp7923 811 | snp7926 812 | snp7928 813 | snp7929 814 | snp7933 815 | snp7937 816 | snp7944 817 | snp7949 818 | snp7952 819 | snp7972 820 | snp7987 821 | snp7988 822 | snp8010 823 | snp8012 824 | snp8035 825 | snp8049 826 | snp8051 827 | snp8052 828 | snp8062 829 | snp8067 830 | snp8070 831 | snp8080 832 | snp8082 833 | snp8084 834 | snp8086 835 | snp8090 836 | snp8111 837 | snp8125 838 | snp8126 839 | snp8127 840 | snp8129 841 | snp8189 842 | snp8214 843 | snp8224 844 | snp8248 845 | snp8253 846 | snp8267 847 | snp8287 848 | snp8315 849 | snp8319 850 | snp8333 851 | snp8338 852 | snp8343 853 | snp8366 854 | snp8372 855 | snp8375 856 | snp8381 857 | snp8402 858 | snp8409 859 | snp8432 860 | snp8437 861 | snp8449 862 | snp8451 863 | snp8456 864 | snp8459 865 | snp8482 866 | snp8493 867 | snp8498 868 | snp8508 869 | snp8513 870 | snp8533 871 | snp8548 872 | snp8560 873 | snp8591 874 | snp8593 875 | snp8613 876 | snp8618 877 | snp8631 878 | snp8638 879 | snp8640 880 | snp8641 881 | snp8642 882 | snp8643 883 | snp8649 884 | snp8657 885 | snp8664 886 | snp8665 887 | snp8709 888 | snp8725 889 | snp8729 890 | snp8731 891 | snp8733 892 | snp8749 893 | snp8754 894 | snp8758 895 | snp8780 896 | snp8781 897 | snp8797 898 | snp8815 899 | snp8817 900 | snp8822 901 | snp8843 902 | snp8856 903 | snp8859 904 | snp8865 905 | snp8873 906 | snp8885 907 | snp8891 908 | snp8914 909 | snp8919 910 | snp8933 911 | snp8952 912 | snp8955 913 | snp8974 914 | snp8986 915 | snp8999 916 | snp9002 917 | snp9007 918 | snp9011 919 | snp9024 920 | snp9038 921 | snp9039 922 | snp9052 923 | snp9057 924 | snp9078 925 | snp9093 926 | snp9098 927 | snp9108 928 | snp9125 929 | snp9135 930 | snp9136 931 | snp9161 932 | snp9170 933 | snp9179 934 | snp9199 935 | snp9211 936 | snp9215 937 | snp9225 938 | snp9230 939 | snp9234 940 | snp9235 941 | snp9248 942 | snp9249 943 | snp9262 944 | snp9269 945 | snp9270 946 | snp9275 947 | snp9283 948 | snp9308 949 | snp9311 950 | snp9328 951 | snp9332 952 | snp9347 953 | snp9351 954 | snp9367 955 | snp9385 956 | snp9409 957 | snp9420 958 | snp9436 959 | snp9440 960 | snp9442 961 | snp9443 962 | snp9465 963 | snp9468 964 | snp9471 965 | snp9481 966 | snp9530 967 | snp9542 968 | snp9574 969 | snp9582 970 | snp9602 971 | snp9627 972 | snp9653 973 | snp9656 974 | snp9665 975 | snp9670 976 | snp9689 977 | snp9694 978 | snp9704 979 | snp9717 980 | snp9785 981 | snp9809 982 | snp9817 983 | snp9818 984 | snp9827 985 | snp9834 986 | snp9839 987 | snp9865 988 | snp9869 989 | snp9873 990 | snp9876 991 | snp9885 992 | snp9888 993 | snp9891 994 | snp9906 995 | snp9915 996 | snp9938 997 | snp9962 998 | snp9964 999 | snp9965 1000 | snp9967 1001 | snp9982 1002 | snp9984 1003 | snp10031 1004 | snp10036 1005 | snp10044 1006 | snp10047 1007 | snp10068 1008 | snp10085 1009 | snp10090 1010 | snp10096 1011 | snp10104 1012 | snp10110 1013 | snp10130 1014 | snp10152 1015 | snp10154 1016 | snp10174 1017 | snp10180 1018 | snp10182 1019 | snp10183 1020 | snp10184 1021 | snp10196 1022 | snp10201 1023 | snp10218 1024 | snp10234 1025 | snp10240 1026 | snp10253 1027 | snp10261 1028 | snp10277 1029 | snp10286 1030 | snp10294 1031 | snp10309 1032 | snp10318 1033 | snp10326 1034 | snp10344 1035 | snp10363 1036 | snp10364 1037 | snp10392 1038 | snp10397 1039 | snp10400 1040 | snp10410 1041 | snp10437 1042 | snp10447 1043 | snp10462 1044 | snp10466 1045 | snp10468 1046 | snp10471 1047 | snp10485 1048 | snp10494 1049 | dsnp10505 1050 | dsnp10512 1051 | dsnp10515 1052 | dsnp10530 1053 | dsnp10553 1054 | dsnp10567 1055 | dsnp10568 1056 | dsnp10579 1057 | dsnp10581 1058 | dsnp10582 1059 | dsnp10590 1060 | dsnp10594 1061 | -------------------------------------------------------------------------------- /dataset1/extracts/chr7_extract.txt: -------------------------------------------------------------------------------- 1 | csnp17 2 | csnp22 3 | csnp27 4 | csnp39 5 | csnp54 6 | csnp58 7 | csnp62 8 | csnp65 9 | csnp67 10 | csnp81 11 | csnp98 12 | csnp108 13 | csnp113 14 | csnp115 15 | csnp117 16 | csnp151 17 | csnp154 18 | csnp167 19 | csnp181 20 | csnp187 21 | csnp206 22 | csnp235 23 | csnp240 24 | csnp244 25 | csnp254 26 | csnp256 27 | csnp266 28 | csnp268 29 | csnp280 30 | csnp281 31 | csnp307 32 | csnp309 33 | csnp343 34 | csnp365 35 | csnp379 36 | csnp385 37 | csnp388 38 | csnp395 39 | csnp411 40 | csnp429 41 | csnp439 42 | csnp442 43 | csnp445 44 | csnp451 45 | csnp452 46 | csnp454 47 | csnp464 48 | csnp469 49 | csnp471 50 | csnp481 51 | csnp492 52 | csnp498 53 | csnp499 54 | snp502 55 | snp508 56 | snp535 57 | snp543 58 | snp546 59 | snp558 60 | snp566 61 | snp592 62 | snp609 63 | snp621 64 | snp624 65 | snp634 66 | snp642 67 | snp646 68 | snp658 69 | snp659 70 | snp681 71 | snp692 72 | snp695 73 | snp713 74 | snp715 75 | snp718 76 | snp731 77 | snp739 78 | snp749 79 | snp753 80 | snp762 81 | snp765 82 | snp783 83 | snp801 84 | snp802 85 | snp829 86 | snp833 87 | snp840 88 | snp848 89 | snp854 90 | snp856 91 | snp863 92 | snp902 93 | snp913 94 | snp915 95 | snp923 96 | snp924 97 | snp955 98 | snp963 99 | snp969 100 | snp979 101 | snp990 102 | snp1010 103 | snp1013 104 | snp1019 105 | snp1041 106 | snp1070 107 | snp1077 108 | snp1099 109 | snp1102 110 | snp1104 111 | snp1138 112 | snp1154 113 | snp1180 114 | snp1183 115 | snp1187 116 | snp1194 117 | snp1198 118 | snp1199 119 | snp1203 120 | snp1208 121 | snp1212 122 | snp1215 123 | snp1226 124 | snp1229 125 | snp1241 126 | snp1242 127 | snp1246 128 | snp1265 129 | snp1278 130 | snp1289 131 | snp1318 132 | snp1340 133 | snp1348 134 | snp1349 135 | snp1356 136 | snp1373 137 | snp1374 138 | snp1381 139 | snp1389 140 | snp1391 141 | snp1393 142 | snp1410 143 | snp1412 144 | snp1435 145 | snp1480 146 | snp1483 147 | snp1488 148 | snp1496 149 | snp1498 150 | snp1506 151 | snp1522 152 | snp1523 153 | snp1527 154 | snp1528 155 | snp1531 156 | snp1536 157 | snp1543 158 | snp1550 159 | snp1552 160 | snp1588 161 | snp1591 162 | snp1593 163 | snp1596 164 | snp1611 165 | snp1616 166 | snp1620 167 | snp1624 168 | snp1627 169 | snp1631 170 | snp1632 171 | snp1667 172 | snp1700 173 | snp1706 174 | snp1715 175 | snp1716 176 | snp1720 177 | snp1731 178 | snp1733 179 | snp1743 180 | snp1748 181 | snp1763 182 | snp1771 183 | snp1788 184 | snp1828 185 | snp1838 186 | snp1839 187 | snp1840 188 | snp1846 189 | snp1857 190 | snp1869 191 | snp1886 192 | snp1899 193 | snp1902 194 | snp1938 195 | snp1955 196 | snp1958 197 | snp1964 198 | snp1970 199 | snp1975 200 | snp1984 201 | snp1992 202 | snp2020 203 | snp2025 204 | snp2044 205 | snp2052 206 | snp2055 207 | snp2073 208 | snp2090 209 | snp2103 210 | snp2110 211 | snp2113 212 | snp2121 213 | snp2128 214 | snp2167 215 | snp2168 216 | snp2173 217 | snp2178 218 | snp2196 219 | snp2217 220 | snp2225 221 | snp2254 222 | snp2285 223 | snp2291 224 | snp2295 225 | snp2303 226 | snp2306 227 | snp2309 228 | snp2311 229 | snp2321 230 | snp2338 231 | snp2342 232 | snp2344 233 | snp2349 234 | snp2359 235 | snp2364 236 | snp2419 237 | snp2421 238 | snp2442 239 | snp2452 240 | snp2463 241 | snp2465 242 | snp2490 243 | snp2501 244 | snp2504 245 | snp2506 246 | snp2529 247 | snp2538 248 | snp2540 249 | snp2543 250 | snp2559 251 | snp2560 252 | snp2570 253 | snp2574 254 | snp2575 255 | snp2583 256 | snp2590 257 | snp2595 258 | snp2603 259 | snp2613 260 | snp2615 261 | snp2626 262 | snp2628 263 | snp2662 264 | snp2671 265 | snp2676 266 | snp2687 267 | snp2694 268 | snp2700 269 | snp2703 270 | snp2728 271 | snp2729 272 | snp2732 273 | snp2759 274 | snp2765 275 | snp2796 276 | snp2803 277 | snp2810 278 | snp2811 279 | snp2830 280 | snp2831 281 | snp2833 282 | snp2847 283 | snp2853 284 | snp2866 285 | snp2868 286 | snp2876 287 | snp2884 288 | snp2887 289 | snp2892 290 | snp2897 291 | snp2898 292 | snp2909 293 | snp2927 294 | snp2929 295 | snp2940 296 | snp2941 297 | snp2946 298 | snp2947 299 | snp2952 300 | snp2966 301 | snp2976 302 | snp2977 303 | snp2983 304 | snp2995 305 | snp3004 306 | snp3009 307 | snp3024 308 | snp3035 309 | snp3042 310 | snp3049 311 | snp3050 312 | snp3053 313 | snp3058 314 | snp3070 315 | snp3073 316 | snp3078 317 | snp3100 318 | snp3107 319 | snp3116 320 | snp3117 321 | snp3153 322 | snp3165 323 | snp3184 324 | snp3192 325 | snp3199 326 | snp3204 327 | snp3205 328 | snp3210 329 | snp3237 330 | snp3247 331 | snp3251 332 | snp3260 333 | snp3274 334 | snp3279 335 | snp3295 336 | snp3302 337 | snp3305 338 | snp3326 339 | snp3328 340 | snp3330 341 | snp3331 342 | snp3343 343 | snp3351 344 | snp3360 345 | snp3362 346 | snp3369 347 | snp3400 348 | snp3415 349 | snp3421 350 | snp3422 351 | snp3430 352 | snp3432 353 | snp3433 354 | snp3451 355 | snp3452 356 | snp3463 357 | snp3491 358 | snp3495 359 | snp3513 360 | snp3518 361 | snp3524 362 | snp3527 363 | snp3528 364 | snp3540 365 | snp3545 366 | snp3572 367 | snp3573 368 | snp3602 369 | snp3625 370 | snp3661 371 | snp3669 372 | snp3671 373 | snp3673 374 | snp3675 375 | snp3695 376 | snp3707 377 | snp3719 378 | snp3721 379 | snp3735 380 | snp3736 381 | snp3746 382 | snp3759 383 | snp3771 384 | snp3777 385 | snp3780 386 | snp3797 387 | snp3800 388 | snp3810 389 | snp3816 390 | snp3823 391 | snp3830 392 | snp3842 393 | snp3886 394 | snp3895 395 | snp3898 396 | snp3909 397 | snp3914 398 | snp3917 399 | snp3929 400 | snp3938 401 | snp3949 402 | snp3954 403 | snp3955 404 | snp3962 405 | snp3986 406 | snp3991 407 | snp4006 408 | snp4012 409 | snp4013 410 | snp4016 411 | snp4018 412 | snp4024 413 | snp4048 414 | snp4052 415 | snp4053 416 | snp4091 417 | snp4105 418 | snp4129 419 | snp4130 420 | snp4135 421 | snp4139 422 | snp4146 423 | snp4158 424 | snp4164 425 | snp4167 426 | snp4185 427 | snp4206 428 | snp4218 429 | snp4248 430 | snp4257 431 | snp4282 432 | snp4297 433 | snp4305 434 | snp4323 435 | snp4336 436 | snp4339 437 | snp4364 438 | snp4369 439 | snp4373 440 | snp4376 441 | snp4387 442 | snp4403 443 | snp4404 444 | snp4411 445 | snp4451 446 | snp4455 447 | snp4466 448 | snp4481 449 | snp4482 450 | snp4505 451 | snp4523 452 | snp4524 453 | snp4531 454 | snp4536 455 | snp4537 456 | snp4550 457 | snp4573 458 | snp4582 459 | snp4605 460 | snp4617 461 | snp4637 462 | snp4643 463 | snp4652 464 | snp4658 465 | snp4661 466 | snp4677 467 | snp4691 468 | snp4695 469 | snp4697 470 | snp4698 471 | snp4709 472 | snp4736 473 | snp4749 474 | snp4759 475 | snp4764 476 | snp4766 477 | snp4775 478 | snp4790 479 | snp4791 480 | snp4793 481 | snp4794 482 | snp4796 483 | snp4798 484 | snp4821 485 | snp4834 486 | snp4835 487 | snp4839 488 | snp4841 489 | snp4857 490 | snp4862 491 | snp4864 492 | snp4871 493 | snp4874 494 | snp4877 495 | snp4879 496 | snp4911 497 | snp4918 498 | snp4921 499 | snp4926 500 | snp4931 501 | snp4937 502 | snp4973 503 | snp4974 504 | snp4977 505 | snp4998 506 | snp5014 507 | snp5022 508 | snp5035 509 | snp5038 510 | snp5081 511 | snp5109 512 | snp5143 513 | snp5144 514 | snp5146 515 | snp5169 516 | snp5175 517 | snp5194 518 | snp5199 519 | snp5212 520 | snp5216 521 | snp5219 522 | snp5221 523 | snp5231 524 | snp5238 525 | snp5240 526 | snp5251 527 | snp5270 528 | snp5275 529 | snp5288 530 | snp5295 531 | snp5305 532 | snp5307 533 | snp5316 534 | snp5324 535 | snp5325 536 | snp5329 537 | snp5330 538 | snp5349 539 | snp5364 540 | snp5402 541 | snp5403 542 | snp5420 543 | snp5447 544 | snp5455 545 | snp5458 546 | snp5468 547 | snp5470 548 | snp5472 549 | snp5477 550 | snp5494 551 | snp5517 552 | snp5532 553 | snp5556 554 | snp5559 555 | snp5562 556 | snp5571 557 | snp5576 558 | snp5600 559 | snp5616 560 | snp5629 561 | snp5639 562 | snp5650 563 | snp5654 564 | snp5665 565 | snp5667 566 | snp5675 567 | snp5681 568 | snp5689 569 | snp5692 570 | snp5694 571 | snp5695 572 | snp5710 573 | snp5733 574 | snp5744 575 | snp5760 576 | snp5789 577 | snp5790 578 | snp5795 579 | snp5810 580 | snp5816 581 | snp5818 582 | snp5830 583 | snp5861 584 | snp5865 585 | snp5870 586 | snp5871 587 | snp5875 588 | snp5877 589 | snp5880 590 | snp5885 591 | snp5895 592 | snp5904 593 | snp5905 594 | snp5906 595 | snp5907 596 | snp5911 597 | snp5932 598 | snp5933 599 | snp5941 600 | snp5965 601 | snp5968 602 | snp5970 603 | snp5976 604 | snp5991 605 | snp5999 606 | snp6002 607 | snp6011 608 | snp6023 609 | snp6045 610 | snp6048 611 | snp6057 612 | snp6063 613 | snp6089 614 | snp6098 615 | snp6102 616 | snp6116 617 | snp6129 618 | snp6133 619 | snp6134 620 | snp6143 621 | snp6152 622 | snp6156 623 | snp6163 624 | snp6173 625 | snp6190 626 | snp6196 627 | snp6201 628 | snp6208 629 | snp6219 630 | snp6240 631 | snp6259 632 | snp6263 633 | snp6267 634 | snp6269 635 | snp6271 636 | snp6285 637 | snp6308 638 | snp6321 639 | snp6325 640 | snp6345 641 | snp6382 642 | snp6390 643 | snp6397 644 | snp6398 645 | snp6400 646 | snp6401 647 | snp6405 648 | snp6423 649 | snp6429 650 | snp6451 651 | snp6456 652 | snp6465 653 | snp6479 654 | snp6487 655 | snp6491 656 | snp6510 657 | snp6519 658 | snp6521 659 | snp6537 660 | snp6540 661 | snp6541 662 | snp6551 663 | snp6558 664 | snp6565 665 | snp6570 666 | snp6602 667 | snp6606 668 | snp6621 669 | snp6630 670 | snp6645 671 | snp6691 672 | snp6702 673 | snp6707 674 | snp6716 675 | snp6720 676 | snp6740 677 | snp6753 678 | snp6772 679 | snp6776 680 | snp6785 681 | snp6792 682 | snp6800 683 | snp6801 684 | snp6817 685 | snp6825 686 | snp6828 687 | snp6845 688 | snp6852 689 | snp6860 690 | snp6876 691 | snp6887 692 | snp6895 693 | snp6910 694 | snp6926 695 | snp6936 696 | snp6941 697 | snp6965 698 | snp6973 699 | snp6984 700 | snp6989 701 | snp6991 702 | snp7000 703 | snp7006 704 | snp7015 705 | snp7024 706 | snp7026 707 | snp7027 708 | snp7033 709 | snp7059 710 | snp7097 711 | snp7104 712 | snp7111 713 | snp7112 714 | snp7122 715 | snp7123 716 | snp7132 717 | snp7150 718 | snp7151 719 | snp7172 720 | snp7178 721 | snp7189 722 | snp7202 723 | snp7216 724 | snp7234 725 | snp7262 726 | snp7263 727 | snp7292 728 | snp7300 729 | snp7301 730 | snp7305 731 | snp7306 732 | snp7314 733 | snp7324 734 | snp7341 735 | snp7363 736 | snp7367 737 | snp7370 738 | snp7444 739 | snp7452 740 | snp7453 741 | snp7458 742 | snp7462 743 | snp7467 744 | snp7469 745 | snp7471 746 | snp7492 747 | snp7497 748 | snp7501 749 | snp7502 750 | snp7535 751 | snp7539 752 | snp7544 753 | snp7565 754 | snp7572 755 | snp7581 756 | snp7583 757 | snp7588 758 | snp7600 759 | snp7623 760 | snp7629 761 | snp7630 762 | snp7647 763 | snp7653 764 | snp7670 765 | snp7674 766 | snp7679 767 | snp7680 768 | snp7688 769 | snp7710 770 | snp7723 771 | snp7734 772 | snp7738 773 | snp7758 774 | snp7765 775 | snp7766 776 | snp7778 777 | snp7790 778 | snp7791 779 | snp7794 780 | snp7798 781 | snp7808 782 | snp7810 783 | snp7813 784 | snp7814 785 | snp7821 786 | snp7830 787 | snp7841 788 | snp7852 789 | snp7857 790 | snp7864 791 | snp7879 792 | snp7897 793 | snp7904 794 | snp7910 795 | snp7919 796 | snp7924 797 | snp7927 798 | snp7936 799 | snp7956 800 | snp7966 801 | snp7980 802 | snp7995 803 | snp8006 804 | snp8007 805 | snp8009 806 | snp8018 807 | snp8021 808 | snp8024 809 | snp8030 810 | snp8038 811 | snp8055 812 | snp8074 813 | snp8091 814 | snp8094 815 | snp8102 816 | snp8119 817 | snp8138 818 | snp8148 819 | snp8156 820 | snp8163 821 | snp8167 822 | snp8169 823 | snp8175 824 | snp8181 825 | snp8183 826 | snp8201 827 | snp8208 828 | snp8210 829 | snp8216 830 | snp8244 831 | snp8249 832 | snp8255 833 | snp8323 834 | snp8345 835 | snp8361 836 | snp8363 837 | snp8383 838 | snp8389 839 | snp8413 840 | snp8417 841 | snp8421 842 | snp8422 843 | snp8425 844 | snp8454 845 | snp8457 846 | snp8460 847 | snp8487 848 | snp8490 849 | snp8506 850 | snp8507 851 | snp8518 852 | snp8519 853 | snp8527 854 | snp8532 855 | snp8536 856 | snp8557 857 | snp8558 858 | snp8572 859 | snp8589 860 | snp8610 861 | snp8616 862 | snp8622 863 | snp8653 864 | snp8658 865 | snp8663 866 | snp8680 867 | snp8682 868 | snp8715 869 | snp8765 870 | snp8776 871 | snp8791 872 | snp8805 873 | snp8832 874 | snp8862 875 | snp8879 876 | snp8882 877 | snp8883 878 | snp8896 879 | snp8899 880 | snp8900 881 | snp8906 882 | snp8907 883 | snp8927 884 | snp8929 885 | snp8931 886 | snp8934 887 | snp8938 888 | snp8939 889 | snp8940 890 | snp8945 891 | snp8959 892 | snp8960 893 | snp8967 894 | snp8968 895 | snp8972 896 | snp8973 897 | snp8975 898 | snp8991 899 | snp8994 900 | snp8996 901 | snp8998 902 | snp9010 903 | snp9017 904 | snp9030 905 | snp9058 906 | snp9079 907 | snp9082 908 | snp9091 909 | snp9096 910 | snp9099 911 | snp9111 912 | snp9137 913 | snp9139 914 | snp9141 915 | snp9142 916 | snp9149 917 | snp9163 918 | snp9165 919 | snp9171 920 | snp9174 921 | snp9175 922 | snp9180 923 | snp9183 924 | snp9193 925 | snp9202 926 | snp9219 927 | snp9224 928 | snp9244 929 | snp9318 930 | snp9329 931 | snp9336 932 | snp9339 933 | snp9357 934 | snp9369 935 | snp9371 936 | snp9395 937 | snp9400 938 | snp9403 939 | snp9406 940 | snp9412 941 | snp9421 942 | snp9438 943 | snp9448 944 | snp9450 945 | snp9454 946 | snp9464 947 | snp9475 948 | snp9478 949 | snp9479 950 | snp9484 951 | snp9491 952 | snp9504 953 | snp9510 954 | snp9516 955 | snp9535 956 | snp9543 957 | snp9556 958 | snp9563 959 | snp9573 960 | snp9583 961 | snp9587 962 | snp9594 963 | snp9597 964 | snp9603 965 | snp9622 966 | snp9633 967 | snp9645 968 | snp9658 969 | snp9660 970 | snp9664 971 | snp9672 972 | snp9700 973 | snp9705 974 | snp9709 975 | snp9711 976 | snp9722 977 | snp9740 978 | snp9752 979 | snp9753 980 | snp9808 981 | snp9820 982 | snp9848 983 | snp9850 984 | snp9852 985 | snp9884 986 | snp9889 987 | snp9919 988 | snp9925 989 | snp9930 990 | snp9932 991 | snp9946 992 | snp9947 993 | snp9963 994 | snp9971 995 | snp9974 996 | snp9975 997 | snp9983 998 | snp9988 999 | snp9993 1000 | snp10008 1001 | snp10013 1002 | snp10018 1003 | snp10027 1004 | snp10029 1005 | snp10032 1006 | snp10034 1007 | snp10039 1008 | snp10043 1009 | snp10055 1010 | snp10057 1011 | snp10070 1012 | snp10093 1013 | snp10095 1014 | snp10106 1015 | snp10109 1016 | snp10116 1017 | snp10119 1018 | snp10138 1019 | snp10146 1020 | snp10170 1021 | snp10171 1022 | snp10203 1023 | snp10213 1024 | snp10215 1025 | snp10221 1026 | snp10222 1027 | snp10243 1028 | snp10258 1029 | snp10260 1030 | snp10275 1031 | snp10276 1032 | snp10285 1033 | snp10293 1034 | snp10306 1035 | snp10314 1036 | snp10317 1037 | snp10327 1038 | snp10329 1039 | snp10348 1040 | snp10361 1041 | snp10371 1042 | snp10398 1043 | snp10415 1044 | snp10427 1045 | snp10433 1046 | snp10440 1047 | snp10451 1048 | snp10454 1049 | snp10456 1050 | snp10488 1051 | snp10491 1052 | dsnp10506 1053 | dsnp10513 1054 | dsnp10523 1055 | dsnp10531 1056 | dsnp10534 1057 | dsnp10545 1058 | dsnp10563 1059 | dsnp10574 1060 | dsnp10585 1061 | -------------------------------------------------------------------------------- /dataset1/extracts/chr3_extract.txt: -------------------------------------------------------------------------------- 1 | csnp48 2 | csnp53 3 | csnp57 4 | csnp77 5 | csnp100 6 | csnp104 7 | csnp106 8 | csnp121 9 | csnp124 10 | csnp140 11 | csnp174 12 | csnp175 13 | csnp176 14 | csnp182 15 | csnp191 16 | csnp192 17 | csnp210 18 | csnp216 19 | csnp218 20 | csnp226 21 | csnp228 22 | csnp229 23 | csnp230 24 | csnp241 25 | csnp247 26 | csnp255 27 | csnp260 28 | csnp275 29 | csnp284 30 | csnp286 31 | csnp305 32 | csnp317 33 | csnp318 34 | csnp323 35 | csnp333 36 | csnp341 37 | csnp362 38 | csnp363 39 | csnp387 40 | csnp389 41 | csnp397 42 | csnp435 43 | csnp436 44 | csnp448 45 | csnp456 46 | csnp461 47 | csnp463 48 | csnp473 49 | csnp486 50 | csnp487 51 | csnp489 52 | snp519 53 | snp532 54 | snp539 55 | snp540 56 | snp554 57 | snp559 58 | snp561 59 | snp567 60 | snp587 61 | snp602 62 | snp627 63 | snp629 64 | snp641 65 | snp647 66 | snp657 67 | snp666 68 | snp677 69 | snp684 70 | snp686 71 | snp693 72 | snp699 73 | snp701 74 | snp705 75 | snp717 76 | snp732 77 | snp740 78 | snp743 79 | snp764 80 | snp816 81 | snp828 82 | snp845 83 | snp846 84 | snp847 85 | snp857 86 | snp862 87 | snp874 88 | snp883 89 | snp905 90 | snp928 91 | snp935 92 | snp976 93 | snp981 94 | snp986 95 | snp1016 96 | snp1037 97 | snp1073 98 | snp1107 99 | snp1111 100 | snp1125 101 | snp1146 102 | snp1148 103 | snp1150 104 | snp1158 105 | snp1160 106 | snp1166 107 | snp1167 108 | snp1174 109 | snp1176 110 | snp1178 111 | snp1193 112 | snp1195 113 | snp1204 114 | snp1209 115 | snp1210 116 | snp1211 117 | snp1216 118 | snp1221 119 | snp1224 120 | snp1236 121 | snp1249 122 | snp1262 123 | snp1267 124 | snp1291 125 | snp1297 126 | snp1301 127 | snp1308 128 | snp1311 129 | snp1316 130 | snp1320 131 | snp1334 132 | snp1337 133 | snp1360 134 | snp1362 135 | snp1366 136 | snp1402 137 | snp1405 138 | snp1408 139 | snp1432 140 | snp1443 141 | snp1450 142 | snp1461 143 | snp1465 144 | snp1515 145 | snp1530 146 | snp1541 147 | snp1558 148 | snp1560 149 | snp1564 150 | snp1567 151 | snp1583 152 | snp1585 153 | snp1614 154 | snp1637 155 | snp1639 156 | snp1648 157 | snp1650 158 | snp1666 159 | snp1685 160 | snp1691 161 | snp1695 162 | snp1725 163 | snp1759 164 | snp1775 165 | snp1802 166 | snp1808 167 | snp1809 168 | snp1817 169 | snp1822 170 | snp1823 171 | snp1827 172 | snp1829 173 | snp1842 174 | snp1849 175 | snp1875 176 | snp1885 177 | snp1887 178 | snp1900 179 | snp1905 180 | snp1914 181 | snp1917 182 | snp1919 183 | snp1922 184 | snp1926 185 | snp1928 186 | snp1957 187 | snp1973 188 | snp1976 189 | snp1979 190 | snp1986 191 | snp1996 192 | snp2006 193 | snp2019 194 | snp2035 195 | snp2054 196 | snp2057 197 | snp2065 198 | snp2083 199 | snp2096 200 | snp2100 201 | snp2123 202 | snp2126 203 | snp2132 204 | snp2134 205 | snp2150 206 | snp2152 207 | snp2162 208 | snp2174 209 | snp2179 210 | snp2182 211 | snp2184 212 | snp2200 213 | snp2213 214 | snp2216 215 | snp2219 216 | snp2223 217 | snp2228 218 | snp2238 219 | snp2253 220 | snp2257 221 | snp2260 222 | snp2261 223 | snp2262 224 | snp2267 225 | snp2273 226 | snp2279 227 | snp2281 228 | snp2282 229 | snp2304 230 | snp2310 231 | snp2312 232 | snp2314 233 | snp2315 234 | snp2319 235 | snp2325 236 | snp2326 237 | snp2336 238 | snp2348 239 | snp2366 240 | snp2395 241 | snp2406 242 | snp2408 243 | snp2410 244 | snp2420 245 | snp2430 246 | snp2438 247 | snp2444 248 | snp2445 249 | snp2453 250 | snp2468 251 | snp2503 252 | snp2513 253 | snp2515 254 | snp2519 255 | snp2541 256 | snp2547 257 | snp2555 258 | snp2567 259 | snp2571 260 | snp2580 261 | snp2589 262 | snp2608 263 | snp2618 264 | snp2634 265 | snp2642 266 | snp2646 267 | snp2650 268 | snp2656 269 | snp2661 270 | snp2678 271 | snp2680 272 | snp2691 273 | snp2701 274 | snp2706 275 | snp2717 276 | snp2725 277 | snp2733 278 | snp2761 279 | snp2762 280 | snp2764 281 | snp2771 282 | snp2780 283 | snp2783 284 | snp2786 285 | snp2799 286 | snp2805 287 | snp2816 288 | snp2817 289 | snp2821 290 | snp2824 291 | snp2839 292 | snp2842 293 | snp2850 294 | snp2873 295 | snp2911 296 | snp2954 297 | snp2968 298 | snp2972 299 | snp2982 300 | snp2986 301 | snp2987 302 | snp3010 303 | snp3060 304 | snp3063 305 | snp3071 306 | snp3072 307 | snp3091 308 | snp3099 309 | snp3103 310 | snp3105 311 | snp3119 312 | snp3132 313 | snp3140 314 | snp3154 315 | snp3162 316 | snp3167 317 | snp3172 318 | snp3173 319 | snp3183 320 | snp3202 321 | snp3217 322 | snp3218 323 | snp3219 324 | snp3220 325 | snp3228 326 | snp3246 327 | snp3254 328 | snp3257 329 | snp3261 330 | snp3269 331 | snp3294 332 | snp3296 333 | snp3304 334 | snp3315 335 | snp3324 336 | snp3325 337 | snp3367 338 | snp3374 339 | snp3376 340 | snp3386 341 | snp3405 342 | snp3407 343 | snp3409 344 | snp3440 345 | snp3441 346 | snp3444 347 | snp3453 348 | snp3465 349 | snp3473 350 | snp3488 351 | snp3499 352 | snp3505 353 | snp3520 354 | snp3553 355 | snp3577 356 | snp3587 357 | snp3591 358 | snp3592 359 | snp3594 360 | snp3600 361 | snp3611 362 | snp3637 363 | snp3648 364 | snp3654 365 | snp3658 366 | snp3663 367 | snp3666 368 | snp3678 369 | snp3690 370 | snp3703 371 | snp3708 372 | snp3712 373 | snp3714 374 | snp3726 375 | snp3729 376 | snp3730 377 | snp3734 378 | snp3739 379 | snp3743 380 | snp3770 381 | snp3772 382 | snp3790 383 | snp3795 384 | snp3798 385 | snp3804 386 | snp3809 387 | snp3819 388 | snp3821 389 | snp3832 390 | snp3840 391 | snp3846 392 | snp3847 393 | snp3863 394 | snp3872 395 | snp3876 396 | snp3878 397 | snp3887 398 | snp3896 399 | snp3906 400 | snp3912 401 | snp3934 402 | snp3936 403 | snp3937 404 | snp3971 405 | snp3973 406 | snp3983 407 | snp3988 408 | snp3994 409 | snp3998 410 | snp4008 411 | snp4010 412 | snp4019 413 | snp4035 414 | snp4037 415 | snp4038 416 | snp4042 417 | snp4086 418 | snp4087 419 | snp4109 420 | snp4117 421 | snp4141 422 | snp4147 423 | snp4152 424 | snp4155 425 | snp4163 426 | snp4166 427 | snp4174 428 | snp4182 429 | snp4191 430 | snp4194 431 | snp4196 432 | snp4197 433 | snp4223 434 | snp4231 435 | snp4251 436 | snp4254 437 | snp4271 438 | snp4278 439 | snp4280 440 | snp4288 441 | snp4292 442 | snp4304 443 | snp4331 444 | snp4340 445 | snp4348 446 | snp4351 447 | snp4352 448 | snp4356 449 | snp4357 450 | snp4365 451 | snp4368 452 | snp4371 453 | snp4377 454 | snp4380 455 | snp4398 456 | snp4416 457 | snp4429 458 | snp4433 459 | snp4434 460 | snp4450 461 | snp4458 462 | snp4465 463 | snp4477 464 | snp4478 465 | snp4497 466 | snp4498 467 | snp4499 468 | snp4506 469 | snp4517 470 | snp4522 471 | snp4545 472 | snp4556 473 | snp4561 474 | snp4574 475 | snp4591 476 | snp4595 477 | snp4603 478 | snp4608 479 | snp4613 480 | snp4673 481 | snp4690 482 | snp4699 483 | snp4714 484 | snp4715 485 | snp4716 486 | snp4722 487 | snp4767 488 | snp4779 489 | snp4787 490 | snp4805 491 | snp4810 492 | snp4811 493 | snp4814 494 | snp4815 495 | snp4820 496 | snp4825 497 | snp4846 498 | snp4849 499 | snp4863 500 | snp4872 501 | snp4881 502 | snp4882 503 | snp4891 504 | snp4893 505 | snp4896 506 | snp4904 507 | snp4907 508 | snp4908 509 | snp4915 510 | snp4923 511 | snp4932 512 | snp4951 513 | snp4956 514 | snp4976 515 | snp4999 516 | snp5010 517 | snp5017 518 | snp5034 519 | snp5042 520 | snp5045 521 | snp5050 522 | snp5051 523 | snp5056 524 | snp5067 525 | snp5069 526 | snp5075 527 | snp5090 528 | snp5122 529 | snp5128 530 | snp5139 531 | snp5152 532 | snp5164 533 | snp5185 534 | snp5189 535 | snp5190 536 | snp5200 537 | snp5202 538 | snp5203 539 | snp5204 540 | snp5209 541 | snp5214 542 | snp5246 543 | snp5253 544 | snp5267 545 | snp5284 546 | snp5308 547 | snp5314 548 | snp5335 549 | snp5346 550 | snp5348 551 | snp5350 552 | snp5371 553 | snp5378 554 | snp5388 555 | snp5405 556 | snp5413 557 | snp5418 558 | snp5436 559 | snp5453 560 | snp5459 561 | snp5463 562 | snp5465 563 | snp5466 564 | snp5480 565 | snp5482 566 | snp5495 567 | snp5507 568 | snp5523 569 | snp5524 570 | snp5528 571 | snp5535 572 | snp5538 573 | snp5558 574 | snp5560 575 | snp5561 576 | snp5583 577 | snp5590 578 | snp5621 579 | snp5624 580 | snp5625 581 | snp5633 582 | snp5642 583 | snp5666 584 | snp5670 585 | snp5674 586 | snp5685 587 | snp5688 588 | snp5693 589 | snp5696 590 | snp5701 591 | snp5716 592 | snp5721 593 | snp5732 594 | snp5734 595 | snp5764 596 | snp5783 597 | snp5815 598 | snp5823 599 | snp5849 600 | snp5853 601 | snp5915 602 | snp5931 603 | snp5939 604 | snp5943 605 | snp5954 606 | snp5959 607 | snp5969 608 | snp5972 609 | snp5974 610 | snp5980 611 | snp5984 612 | snp5988 613 | snp6003 614 | snp6021 615 | snp6025 616 | snp6027 617 | snp6040 618 | snp6042 619 | snp6046 620 | snp6064 621 | snp6067 622 | snp6092 623 | snp6113 624 | snp6119 625 | snp6123 626 | snp6153 627 | snp6159 628 | snp6167 629 | snp6174 630 | snp6187 631 | snp6188 632 | snp6194 633 | snp6195 634 | snp6202 635 | snp6214 636 | snp6215 637 | snp6216 638 | snp6223 639 | snp6233 640 | snp6237 641 | snp6248 642 | snp6249 643 | snp6276 644 | snp6279 645 | snp6304 646 | snp6310 647 | snp6313 648 | snp6318 649 | snp6319 650 | snp6322 651 | snp6335 652 | snp6351 653 | snp6379 654 | snp6384 655 | snp6387 656 | snp6391 657 | snp6408 658 | snp6414 659 | snp6430 660 | snp6435 661 | snp6449 662 | snp6452 663 | snp6457 664 | snp6458 665 | snp6492 666 | snp6506 667 | snp6515 668 | snp6518 669 | snp6554 670 | snp6557 671 | snp6581 672 | snp6582 673 | snp6615 674 | snp6631 675 | snp6632 676 | snp6638 677 | snp6650 678 | snp6655 679 | snp6677 680 | snp6686 681 | snp6699 682 | snp6710 683 | snp6713 684 | snp6741 685 | snp6747 686 | snp6752 687 | snp6763 688 | snp6779 689 | snp6780 690 | snp6793 691 | snp6826 692 | snp6853 693 | snp6859 694 | snp6863 695 | snp6873 696 | snp6877 697 | snp6890 698 | snp6939 699 | snp6948 700 | snp6951 701 | snp6956 702 | snp6961 703 | snp6966 704 | snp6998 705 | snp7002 706 | snp7012 707 | snp7013 708 | snp7020 709 | snp7022 710 | snp7040 711 | snp7042 712 | snp7047 713 | snp7054 714 | snp7057 715 | snp7078 716 | snp7092 717 | snp7107 718 | snp7113 719 | snp7119 720 | snp7133 721 | snp7136 722 | snp7142 723 | snp7147 724 | snp7153 725 | snp7206 726 | snp7214 727 | snp7217 728 | snp7220 729 | snp7231 730 | snp7235 731 | snp7247 732 | snp7250 733 | snp7257 734 | snp7259 735 | snp7264 736 | snp7267 737 | snp7272 738 | snp7277 739 | snp7279 740 | snp7280 741 | snp7315 742 | snp7325 743 | snp7335 744 | snp7336 745 | snp7346 746 | snp7352 747 | snp7357 748 | snp7373 749 | snp7387 750 | snp7391 751 | snp7393 752 | snp7408 753 | snp7410 754 | snp7419 755 | snp7427 756 | snp7428 757 | snp7430 758 | snp7436 759 | snp7437 760 | snp7439 761 | snp7498 762 | snp7509 763 | snp7517 764 | snp7522 765 | snp7525 766 | snp7540 767 | snp7542 768 | snp7547 769 | snp7549 770 | snp7550 771 | snp7553 772 | snp7562 773 | snp7592 774 | snp7626 775 | snp7640 776 | snp7657 777 | snp7658 778 | snp7689 779 | snp7690 780 | snp7695 781 | snp7707 782 | snp7708 783 | snp7722 784 | snp7726 785 | snp7736 786 | snp7740 787 | snp7743 788 | snp7744 789 | snp7750 790 | snp7760 791 | snp7770 792 | snp7782 793 | snp7795 794 | snp7796 795 | snp7829 796 | snp7833 797 | snp7839 798 | snp7844 799 | snp7861 800 | snp7873 801 | snp7882 802 | snp7883 803 | snp7885 804 | snp7890 805 | snp7891 806 | snp7899 807 | snp7920 808 | snp7930 809 | snp7939 810 | snp7945 811 | snp7947 812 | snp7951 813 | snp7984 814 | snp8019 815 | snp8036 816 | snp8039 817 | snp8054 818 | snp8081 819 | snp8092 820 | snp8107 821 | snp8108 822 | snp8120 823 | snp8158 824 | snp8165 825 | snp8166 826 | snp8213 827 | snp8219 828 | snp8225 829 | snp8227 830 | snp8234 831 | snp8238 832 | snp8247 833 | snp8268 834 | snp8279 835 | snp8285 836 | snp8292 837 | snp8297 838 | snp8321 839 | snp8328 840 | snp8331 841 | snp8342 842 | snp8348 843 | snp8351 844 | snp8379 845 | snp8390 846 | snp8408 847 | snp8415 848 | snp8447 849 | snp8463 850 | snp8468 851 | snp8489 852 | snp8497 853 | snp8501 854 | snp8517 855 | snp8539 856 | snp8541 857 | snp8542 858 | snp8570 859 | snp8575 860 | snp8584 861 | snp8626 862 | snp8647 863 | snp8654 864 | snp8655 865 | snp8667 866 | snp8669 867 | snp8688 868 | snp8695 869 | snp8712 870 | snp8717 871 | snp8721 872 | snp8726 873 | snp8728 874 | snp8730 875 | snp8736 876 | snp8737 877 | snp8751 878 | snp8794 879 | snp8804 880 | snp8807 881 | snp8814 882 | snp8823 883 | snp8833 884 | snp8842 885 | snp8847 886 | snp8870 887 | snp8876 888 | snp8881 889 | snp8886 890 | snp8887 891 | snp8898 892 | snp8901 893 | snp8902 894 | snp8903 895 | snp8904 896 | snp8908 897 | snp8930 898 | snp8948 899 | snp8977 900 | snp8984 901 | snp9005 902 | snp9020 903 | snp9028 904 | snp9049 905 | snp9060 906 | snp9065 907 | snp9070 908 | snp9076 909 | snp9083 910 | snp9094 911 | snp9107 912 | snp9113 913 | snp9114 914 | snp9131 915 | snp9133 916 | snp9138 917 | snp9147 918 | snp9154 919 | snp9162 920 | snp9169 921 | snp9173 922 | snp9190 923 | snp9191 924 | snp9201 925 | snp9209 926 | snp9218 927 | snp9233 928 | snp9240 929 | snp9254 930 | snp9266 931 | snp9271 932 | snp9277 933 | snp9285 934 | snp9289 935 | snp9291 936 | snp9295 937 | snp9300 938 | snp9314 939 | snp9321 940 | snp9324 941 | snp9327 942 | snp9330 943 | snp9338 944 | snp9346 945 | snp9359 946 | snp9361 947 | snp9391 948 | snp9393 949 | snp9404 950 | snp9407 951 | snp9414 952 | snp9415 953 | snp9418 954 | snp9434 955 | snp9445 956 | snp9447 957 | snp9452 958 | snp9458 959 | snp9460 960 | snp9462 961 | snp9476 962 | snp9503 963 | snp9512 964 | snp9519 965 | snp9532 966 | snp9534 967 | snp9538 968 | snp9567 969 | snp9568 970 | snp9581 971 | snp9593 972 | snp9599 973 | snp9608 974 | snp9610 975 | snp9621 976 | snp9625 977 | snp9628 978 | snp9654 979 | snp9663 980 | snp9671 981 | snp9675 982 | snp9678 983 | snp9679 984 | snp9683 985 | snp9686 986 | snp9691 987 | snp9716 988 | snp9762 989 | snp9763 990 | snp9766 991 | snp9771 992 | snp9777 993 | snp9790 994 | snp9793 995 | snp9794 996 | snp9831 997 | snp9872 998 | snp9879 999 | snp9890 1000 | snp9895 1001 | snp9899 1002 | snp9901 1003 | snp9912 1004 | snp9952 1005 | snp9958 1006 | snp9966 1007 | snp9978 1008 | snp9990 1009 | snp9991 1010 | snp9997 1011 | snp10009 1012 | snp10011 1013 | snp10020 1014 | snp10046 1015 | snp10050 1016 | snp10059 1017 | snp10073 1018 | snp10082 1019 | snp10084 1020 | snp10105 1021 | snp10113 1022 | snp10136 1023 | snp10153 1024 | snp10162 1025 | snp10167 1026 | snp10168 1027 | snp10188 1028 | snp10193 1029 | snp10195 1030 | snp10206 1031 | snp10208 1032 | snp10211 1033 | snp10227 1034 | snp10230 1035 | snp10237 1036 | snp10242 1037 | snp10251 1038 | snp10271 1039 | snp10291 1040 | snp10310 1041 | snp10312 1042 | snp10342 1043 | snp10343 1044 | snp10351 1045 | snp10352 1046 | snp10432 1047 | snp10446 1048 | snp10461 1049 | snp10475 1050 | snp10477 1051 | snp10493 1052 | dsnp10503 1053 | dsnp10526 1054 | dsnp10527 1055 | dsnp10547 1056 | dsnp10552 1057 | dsnp10554 1058 | dsnp10570 1059 | dsnp10571 1060 | dsnp10577 1061 | -------------------------------------------------------------------------------- /dataset1/extracts/chr1_extract.txt: -------------------------------------------------------------------------------- 1 | csnp18 2 | csnp35 3 | csnp59 4 | csnp78 5 | csnp85 6 | csnp97 7 | csnp103 8 | csnp109 9 | csnp112 10 | csnp129 11 | csnp134 12 | csnp142 13 | csnp150 14 | csnp162 15 | csnp163 16 | csnp166 17 | csnp173 18 | csnp178 19 | csnp199 20 | csnp204 21 | csnp207 22 | csnp211 23 | csnp239 24 | csnp249 25 | csnp252 26 | csnp257 27 | csnp269 28 | csnp282 29 | csnp283 30 | csnp295 31 | csnp300 32 | csnp310 33 | csnp334 34 | csnp344 35 | csnp356 36 | csnp364 37 | csnp412 38 | csnp415 39 | csnp420 40 | csnp422 41 | csnp423 42 | csnp424 43 | csnp432 44 | csnp441 45 | csnp459 46 | csnp478 47 | csnp482 48 | csnp493 49 | snp515 50 | snp526 51 | snp537 52 | snp545 53 | snp562 54 | snp563 55 | snp593 56 | snp606 57 | snp608 58 | snp614 59 | snp617 60 | snp637 61 | snp640 62 | snp644 63 | snp645 64 | snp678 65 | snp680 66 | snp708 67 | snp729 68 | snp747 69 | snp748 70 | snp750 71 | snp757 72 | snp758 73 | snp759 74 | snp766 75 | snp776 76 | snp777 77 | snp795 78 | snp809 79 | snp810 80 | snp824 81 | snp835 82 | snp838 83 | snp858 84 | snp868 85 | snp875 86 | snp881 87 | snp899 88 | snp903 89 | snp907 90 | snp917 91 | snp921 92 | snp926 93 | snp929 94 | snp942 95 | snp958 96 | snp971 97 | snp977 98 | snp982 99 | snp994 100 | snp998 101 | snp1005 102 | snp1012 103 | snp1029 104 | snp1033 105 | snp1045 106 | snp1046 107 | snp1055 108 | snp1085 109 | snp1092 110 | snp1094 111 | snp1096 112 | snp1097 113 | snp1109 114 | snp1116 115 | snp1122 116 | snp1137 117 | snp1144 118 | snp1155 119 | snp1159 120 | snp1161 121 | snp1164 122 | snp1169 123 | snp1173 124 | snp1175 125 | snp1177 126 | snp1184 127 | snp1189 128 | snp1190 129 | snp1201 130 | snp1213 131 | snp1250 132 | snp1260 133 | snp1273 134 | snp1274 135 | snp1279 136 | snp1296 137 | snp1312 138 | snp1314 139 | snp1324 140 | snp1325 141 | snp1327 142 | snp1358 143 | snp1364 144 | snp1392 145 | snp1424 146 | snp1425 147 | snp1427 148 | snp1441 149 | snp1447 150 | snp1454 151 | snp1459 152 | snp1471 153 | snp1484 154 | snp1504 155 | snp1514 156 | snp1535 157 | snp1568 158 | snp1578 159 | snp1600 160 | snp1603 161 | snp1629 162 | snp1640 163 | snp1645 164 | snp1657 165 | snp1662 166 | snp1665 167 | snp1670 168 | snp1673 169 | snp1676 170 | snp1683 171 | snp1694 172 | snp1701 173 | snp1702 174 | snp1717 175 | snp1722 176 | snp1730 177 | snp1772 178 | snp1777 179 | snp1789 180 | snp1794 181 | snp1797 182 | snp1812 183 | snp1816 184 | snp1835 185 | snp1841 186 | snp1848 187 | snp1851 188 | snp1854 189 | snp1856 190 | snp1871 191 | snp1872 192 | snp1874 193 | snp1878 194 | snp1880 195 | snp1901 196 | snp1906 197 | snp1908 198 | snp1916 199 | snp1929 200 | snp1937 201 | snp1939 202 | snp1961 203 | snp1965 204 | snp1987 205 | snp1988 206 | snp1991 207 | snp1997 208 | snp2003 209 | snp2007 210 | snp2009 211 | snp2013 212 | snp2014 213 | snp2036 214 | snp2060 215 | snp2072 216 | snp2087 217 | snp2091 218 | snp2093 219 | snp2142 220 | snp2151 221 | snp2175 222 | snp2188 223 | snp2214 224 | snp2241 225 | snp2264 226 | snp2272 227 | snp2287 228 | snp2323 229 | snp2327 230 | snp2339 231 | snp2343 232 | snp2347 233 | snp2358 234 | snp2362 235 | snp2367 236 | snp2370 237 | snp2384 238 | snp2405 239 | snp2407 240 | snp2415 241 | snp2429 242 | snp2441 243 | snp2462 244 | snp2470 245 | snp2471 246 | snp2477 247 | snp2485 248 | snp2520 249 | snp2524 250 | snp2526 251 | snp2527 252 | snp2532 253 | snp2544 254 | snp2554 255 | snp2573 256 | snp2581 257 | snp2582 258 | snp2585 259 | snp2598 260 | snp2599 261 | snp2627 262 | snp2644 263 | snp2652 264 | snp2657 265 | snp2659 266 | snp2667 267 | snp2692 268 | snp2702 269 | snp2704 270 | snp2708 271 | snp2710 272 | snp2721 273 | snp2722 274 | snp2746 275 | snp2747 276 | snp2753 277 | snp2770 278 | snp2779 279 | snp2808 280 | snp2814 281 | snp2843 282 | snp2848 283 | snp2864 284 | snp2883 285 | snp2899 286 | snp2900 287 | snp2918 288 | snp2924 289 | snp2957 290 | snp2969 291 | snp2975 292 | snp2981 293 | snp2994 294 | snp3001 295 | snp3005 296 | snp3007 297 | snp3008 298 | snp3011 299 | snp3037 300 | snp3038 301 | snp3086 302 | snp3089 303 | snp3094 304 | snp3110 305 | snp3124 306 | snp3133 307 | snp3141 308 | snp3143 309 | snp3148 310 | snp3157 311 | snp3175 312 | snp3177 313 | snp3187 314 | snp3189 315 | snp3198 316 | snp3215 317 | snp3226 318 | snp3233 319 | snp3240 320 | snp3259 321 | snp3266 322 | snp3300 323 | snp3303 324 | snp3311 325 | snp3321 326 | snp3332 327 | snp3335 328 | snp3346 329 | snp3350 330 | snp3363 331 | snp3382 332 | snp3389 333 | snp3399 334 | snp3402 335 | snp3428 336 | snp3434 337 | snp3459 338 | snp3464 339 | snp3469 340 | snp3474 341 | snp3484 342 | snp3492 343 | snp3534 344 | snp3554 345 | snp3555 346 | snp3566 347 | snp3576 348 | snp3596 349 | snp3603 350 | snp3621 351 | snp3629 352 | snp3635 353 | snp3636 354 | snp3641 355 | snp3644 356 | snp3645 357 | snp3668 358 | snp3699 359 | snp3723 360 | snp3725 361 | snp3742 362 | snp3747 363 | snp3748 364 | snp3769 365 | snp3774 366 | snp3775 367 | snp3781 368 | snp3782 369 | snp3792 370 | snp3796 371 | snp3799 372 | snp3813 373 | snp3818 374 | snp3826 375 | snp3837 376 | snp3838 377 | snp3839 378 | snp3844 379 | snp3848 380 | snp3853 381 | snp3871 382 | snp3877 383 | snp3890 384 | snp3903 385 | snp3911 386 | snp3922 387 | snp3945 388 | snp3976 389 | snp3977 390 | snp3993 391 | snp3995 392 | snp4003 393 | snp4004 394 | snp4017 395 | snp4025 396 | snp4057 397 | snp4059 398 | snp4062 399 | snp4064 400 | snp4074 401 | snp4076 402 | snp4092 403 | snp4097 404 | snp4125 405 | snp4127 406 | snp4138 407 | snp4151 408 | snp4153 409 | snp4154 410 | snp4157 411 | snp4159 412 | snp4190 413 | snp4199 414 | snp4204 415 | snp4205 416 | snp4207 417 | snp4208 418 | snp4211 419 | snp4241 420 | snp4245 421 | snp4252 422 | snp4258 423 | snp4261 424 | snp4266 425 | snp4274 426 | snp4284 427 | snp4285 428 | snp4298 429 | snp4306 430 | snp4324 431 | snp4326 432 | snp4327 433 | snp4354 434 | snp4383 435 | snp4390 436 | snp4400 437 | snp4421 438 | snp4422 439 | snp4427 440 | snp4442 441 | snp4443 442 | snp4449 443 | snp4461 444 | snp4488 445 | snp4507 446 | snp4521 447 | snp4526 448 | snp4527 449 | snp4534 450 | snp4535 451 | snp4543 452 | snp4547 453 | snp4551 454 | snp4604 455 | snp4616 456 | snp4627 457 | snp4631 458 | snp4642 459 | snp4645 460 | snp4665 461 | snp4679 462 | snp4693 463 | snp4708 464 | snp4724 465 | snp4734 466 | snp4738 467 | snp4741 468 | snp4746 469 | snp4758 470 | snp4760 471 | snp4765 472 | snp4792 473 | snp4795 474 | snp4806 475 | snp4807 476 | snp4826 477 | snp4840 478 | snp4852 479 | snp4860 480 | snp4865 481 | snp4870 482 | snp4885 483 | snp4890 484 | snp4898 485 | snp4899 486 | snp4930 487 | snp4942 488 | snp4949 489 | snp4952 490 | snp4953 491 | snp4978 492 | snp4982 493 | snp4983 494 | snp5003 495 | snp5008 496 | snp5011 497 | snp5012 498 | snp5013 499 | snp5031 500 | snp5037 501 | snp5074 502 | snp5077 503 | snp5080 504 | snp5086 505 | snp5091 506 | snp5098 507 | snp5106 508 | snp5142 509 | snp5157 510 | snp5166 511 | snp5184 512 | snp5213 513 | snp5225 514 | snp5227 515 | snp5233 516 | snp5249 517 | snp5268 518 | snp5274 519 | snp5281 520 | snp5283 521 | snp5296 522 | snp5299 523 | snp5362 524 | snp5363 525 | snp5374 526 | snp5382 527 | snp5397 528 | snp5408 529 | snp5411 530 | snp5424 531 | snp5426 532 | snp5428 533 | snp5434 534 | snp5438 535 | snp5441 536 | snp5442 537 | snp5451 538 | snp5456 539 | snp5464 540 | snp5467 541 | snp5488 542 | snp5489 543 | snp5516 544 | snp5526 545 | snp5531 546 | snp5536 547 | snp5542 548 | snp5547 549 | snp5574 550 | snp5592 551 | snp5596 552 | snp5609 553 | snp5622 554 | snp5648 555 | snp5662 556 | snp5680 557 | snp5687 558 | snp5690 559 | snp5717 560 | snp5722 561 | snp5724 562 | snp5725 563 | snp5728 564 | snp5730 565 | snp5740 566 | snp5751 567 | snp5771 568 | snp5781 569 | snp5784 570 | snp5785 571 | snp5822 572 | snp5837 573 | snp5886 574 | snp5888 575 | snp5890 576 | snp5891 577 | snp5892 578 | snp5896 579 | snp5899 580 | snp5919 581 | snp5922 582 | snp5927 583 | snp5944 584 | snp5948 585 | snp5953 586 | snp5985 587 | snp6010 588 | snp6013 589 | snp6031 590 | snp6032 591 | snp6034 592 | snp6044 593 | snp6062 594 | snp6065 595 | snp6068 596 | snp6077 597 | snp6080 598 | snp6084 599 | snp6088 600 | snp6122 601 | snp6125 602 | snp6145 603 | snp6149 604 | snp6157 605 | snp6168 606 | snp6180 607 | snp6185 608 | snp6198 609 | snp6200 610 | snp6205 611 | snp6220 612 | snp6235 613 | snp6239 614 | snp6242 615 | snp6262 616 | snp6291 617 | snp6305 618 | snp6314 619 | snp6327 620 | snp6329 621 | snp6334 622 | snp6338 623 | snp6344 624 | snp6353 625 | snp6354 626 | snp6356 627 | snp6357 628 | snp6378 629 | snp6388 630 | snp6404 631 | snp6411 632 | snp6412 633 | snp6415 634 | snp6425 635 | snp6441 636 | snp6450 637 | snp6467 638 | snp6475 639 | snp6480 640 | snp6497 641 | snp6498 642 | snp6500 643 | snp6505 644 | snp6542 645 | snp6561 646 | snp6573 647 | snp6608 648 | snp6626 649 | snp6634 650 | snp6640 651 | snp6646 652 | snp6653 653 | snp6660 654 | snp6663 655 | snp6664 656 | snp6682 657 | snp6684 658 | snp6714 659 | snp6717 660 | snp6721 661 | snp6722 662 | snp6731 663 | snp6754 664 | snp6766 665 | snp6769 666 | snp6773 667 | snp6786 668 | snp6789 669 | snp6791 670 | snp6811 671 | snp6814 672 | snp6820 673 | snp6833 674 | snp6835 675 | snp6854 676 | snp6862 677 | snp6869 678 | snp6872 679 | snp6878 680 | snp6882 681 | snp6883 682 | snp6886 683 | snp6901 684 | snp6907 685 | snp6911 686 | snp6916 687 | snp6925 688 | snp6940 689 | snp6945 690 | snp6949 691 | snp6952 692 | snp6969 693 | snp7010 694 | snp7011 695 | snp7036 696 | snp7045 697 | snp7048 698 | snp7056 699 | snp7061 700 | snp7074 701 | snp7085 702 | snp7088 703 | snp7091 704 | snp7108 705 | snp7134 706 | snp7141 707 | snp7149 708 | snp7154 709 | snp7155 710 | snp7164 711 | snp7173 712 | snp7185 713 | snp7186 714 | snp7187 715 | snp7201 716 | snp7205 717 | snp7210 718 | snp7226 719 | snp7283 720 | snp7287 721 | snp7291 722 | snp7308 723 | snp7311 724 | snp7319 725 | snp7333 726 | snp7340 727 | snp7349 728 | snp7351 729 | snp7384 730 | snp7399 731 | snp7402 732 | snp7415 733 | snp7418 734 | snp7421 735 | snp7431 736 | snp7433 737 | snp7434 738 | snp7442 739 | snp7447 740 | snp7450 741 | snp7478 742 | snp7512 743 | snp7515 744 | snp7537 745 | snp7552 746 | snp7554 747 | snp7556 748 | snp7563 749 | snp7578 750 | snp7590 751 | snp7625 752 | snp7627 753 | snp7628 754 | snp7638 755 | snp7642 756 | snp7644 757 | snp7652 758 | snp7654 759 | snp7660 760 | snp7664 761 | snp7665 762 | snp7682 763 | snp7685 764 | snp7692 765 | snp7697 766 | snp7702 767 | snp7716 768 | snp7717 769 | snp7735 770 | snp7749 771 | snp7759 772 | snp7772 773 | snp7792 774 | snp7799 775 | snp7800 776 | snp7802 777 | snp7809 778 | snp7816 779 | snp7842 780 | snp7843 781 | snp7862 782 | snp7867 783 | snp7872 784 | snp7915 785 | snp7916 786 | snp7917 787 | snp7934 788 | snp7955 789 | snp7958 790 | snp7959 791 | snp7971 792 | snp7978 793 | snp7979 794 | snp8001 795 | snp8034 796 | snp8042 797 | snp8064 798 | snp8065 799 | snp8083 800 | snp8089 801 | snp8101 802 | snp8104 803 | snp8141 804 | snp8142 805 | snp8146 806 | snp8152 807 | snp8153 808 | snp8159 809 | snp8193 810 | snp8218 811 | snp8223 812 | snp8240 813 | snp8246 814 | snp8250 815 | snp8252 816 | snp8254 817 | snp8262 818 | snp8271 819 | snp8282 820 | snp8284 821 | snp8288 822 | snp8312 823 | snp8329 824 | snp8330 825 | snp8334 826 | snp8346 827 | snp8352 828 | snp8356 829 | snp8359 830 | snp8371 831 | snp8392 832 | snp8403 833 | snp8407 834 | snp8411 835 | snp8412 836 | snp8418 837 | snp8420 838 | snp8444 839 | snp8453 840 | snp8476 841 | snp8481 842 | snp8483 843 | snp8486 844 | snp8502 845 | snp8504 846 | snp8516 847 | snp8520 848 | snp8523 849 | snp8534 850 | snp8543 851 | snp8555 852 | snp8559 853 | snp8562 854 | snp8564 855 | snp8569 856 | snp8582 857 | snp8583 858 | snp8587 859 | snp8590 860 | snp8594 861 | snp8595 862 | snp8606 863 | snp8607 864 | snp8628 865 | snp8639 866 | snp8651 867 | snp8661 868 | snp8670 869 | snp8689 870 | snp8690 871 | snp8691 872 | snp8696 873 | snp8701 874 | snp8705 875 | snp8710 876 | snp8720 877 | snp8742 878 | snp8746 879 | snp8764 880 | snp8772 881 | snp8775 882 | snp8783 883 | snp8799 884 | snp8826 885 | snp8836 886 | snp8844 887 | snp8845 888 | snp8852 889 | snp8866 890 | snp8867 891 | snp8869 892 | snp8912 893 | snp8917 894 | snp8944 895 | snp8958 896 | snp8965 897 | snp8987 898 | snp8993 899 | snp8995 900 | snp9031 901 | snp9048 902 | snp9050 903 | snp9061 904 | snp9062 905 | snp9066 906 | snp9067 907 | snp9068 908 | snp9069 909 | snp9100 910 | snp9110 911 | snp9127 912 | snp9172 913 | snp9195 914 | snp9206 915 | snp9214 916 | snp9221 917 | snp9227 918 | snp9236 919 | snp9238 920 | snp9264 921 | snp9267 922 | snp9278 923 | snp9279 924 | snp9281 925 | snp9290 926 | snp9298 927 | snp9306 928 | snp9315 929 | snp9319 930 | snp9325 931 | snp9342 932 | snp9364 933 | snp9377 934 | snp9387 935 | snp9397 936 | snp9402 937 | snp9410 938 | snp9422 939 | snp9425 940 | snp9427 941 | snp9429 942 | snp9444 943 | snp9473 944 | snp9489 945 | snp9521 946 | snp9522 947 | snp9525 948 | snp9545 949 | snp9552 950 | snp9555 951 | snp9557 952 | snp9577 953 | snp9585 954 | snp9586 955 | snp9588 956 | snp9590 957 | snp9596 958 | snp9609 959 | snp9617 960 | snp9623 961 | snp9629 962 | snp9636 963 | snp9640 964 | snp9647 965 | snp9648 966 | snp9652 967 | snp9685 968 | snp9721 969 | snp9730 970 | snp9737 971 | snp9741 972 | snp9764 973 | snp9765 974 | snp9769 975 | snp9770 976 | snp9782 977 | snp9784 978 | snp9788 979 | snp9804 980 | snp9812 981 | snp9824 982 | snp9833 983 | snp9837 984 | snp9856 985 | snp9860 986 | snp9867 987 | snp9874 988 | snp9910 989 | snp9920 990 | snp9949 991 | snp9953 992 | snp9969 993 | snp9976 994 | snp9994 995 | snp10001 996 | snp10004 997 | snp10040 998 | snp10049 999 | snp10053 1000 | snp10065 1001 | snp10076 1002 | snp10080 1003 | snp10088 1004 | snp10102 1005 | snp10103 1006 | snp10120 1007 | snp10128 1008 | snp10140 1009 | snp10144 1010 | snp10147 1011 | snp10160 1012 | snp10166 1013 | snp10175 1014 | snp10179 1015 | snp10186 1016 | snp10202 1017 | snp10225 1018 | snp10233 1019 | snp10235 1020 | snp10241 1021 | snp10249 1022 | snp10252 1023 | snp10255 1024 | snp10256 1025 | snp10259 1026 | snp10267 1027 | snp10268 1028 | snp10287 1029 | snp10315 1030 | snp10320 1031 | snp10324 1032 | snp10325 1033 | snp10331 1034 | snp10373 1035 | snp10374 1036 | snp10377 1037 | snp10378 1038 | snp10393 1039 | snp10395 1040 | snp10405 1041 | snp10406 1042 | snp10420 1043 | snp10434 1044 | snp10472 1045 | snp10478 1046 | snp10487 1047 | snp10498 1048 | snp10499 1049 | dsnp10510 1050 | dsnp10517 1051 | dsnp10524 1052 | dsnp10532 1053 | dsnp10533 1054 | dsnp10538 1055 | dsnp10542 1056 | dsnp10549 1057 | dsnp10550 1058 | dsnp10566 1059 | dsnp10580 1060 | dsnp10596 1061 | -------------------------------------------------------------------------------- /dataset1/extracts/chr10_extract.txt: -------------------------------------------------------------------------------- 1 | csnp4 2 | csnp19 3 | csnp28 4 | csnp37 5 | csnp42 6 | csnp44 7 | csnp51 8 | csnp55 9 | csnp90 10 | csnp95 11 | csnp99 12 | csnp107 13 | csnp128 14 | csnp138 15 | csnp143 16 | csnp152 17 | csnp155 18 | csnp159 19 | csnp171 20 | csnp179 21 | csnp195 22 | csnp196 23 | csnp198 24 | csnp208 25 | csnp222 26 | csnp225 27 | csnp245 28 | csnp274 29 | csnp287 30 | csnp297 31 | csnp301 32 | csnp304 33 | csnp315 34 | csnp320 35 | csnp322 36 | csnp325 37 | csnp332 38 | csnp346 39 | csnp357 40 | csnp382 41 | csnp391 42 | csnp393 43 | csnp405 44 | csnp407 45 | csnp430 46 | csnp440 47 | csnp466 48 | csnp467 49 | csnp476 50 | snp511 51 | snp512 52 | snp518 53 | snp528 54 | snp551 55 | snp571 56 | snp580 57 | snp595 58 | snp597 59 | snp616 60 | snp622 61 | snp631 62 | snp635 63 | snp639 64 | snp643 65 | snp661 66 | snp674 67 | snp683 68 | snp691 69 | snp696 70 | snp698 71 | snp719 72 | snp727 73 | snp735 74 | snp736 75 | snp754 76 | snp763 77 | snp775 78 | snp778 79 | snp779 80 | snp782 81 | snp792 82 | snp804 83 | snp826 84 | snp836 85 | snp843 86 | snp869 87 | snp876 88 | snp877 89 | snp878 90 | snp882 91 | snp891 92 | snp892 93 | snp897 94 | snp900 95 | snp943 96 | snp1001 97 | snp1022 98 | snp1036 99 | snp1047 100 | snp1051 101 | snp1052 102 | snp1056 103 | snp1066 104 | snp1071 105 | snp1086 106 | snp1088 107 | snp1098 108 | snp1106 109 | snp1119 110 | snp1134 111 | snp1136 112 | snp1147 113 | snp1151 114 | snp1157 115 | snp1172 116 | snp1185 117 | snp1191 118 | snp1206 119 | snp1225 120 | snp1227 121 | snp1232 122 | snp1237 123 | snp1243 124 | snp1247 125 | snp1256 126 | snp1269 127 | snp1283 128 | snp1288 129 | snp1294 130 | snp1300 131 | snp1307 132 | snp1317 133 | snp1319 134 | snp1333 135 | snp1339 136 | snp1351 137 | snp1353 138 | snp1357 139 | snp1379 140 | snp1398 141 | snp1401 142 | snp1434 143 | snp1445 144 | snp1448 145 | snp1449 146 | snp1453 147 | snp1457 148 | snp1470 149 | snp1497 150 | snp1516 151 | snp1518 152 | snp1520 153 | snp1525 154 | snp1526 155 | snp1538 156 | snp1542 157 | snp1555 158 | snp1569 159 | snp1576 160 | snp1590 161 | snp1607 162 | snp1613 163 | snp1615 164 | snp1625 165 | snp1638 166 | snp1644 167 | snp1646 168 | snp1651 169 | snp1663 170 | snp1669 171 | snp1681 172 | snp1682 173 | snp1686 174 | snp1690 175 | snp1724 176 | snp1732 177 | snp1734 178 | snp1735 179 | snp1739 180 | snp1749 181 | snp1755 182 | snp1761 183 | snp1765 184 | snp1796 185 | snp1799 186 | snp1818 187 | snp1861 188 | snp1862 189 | snp1879 190 | snp1894 191 | snp1897 192 | snp1907 193 | snp1912 194 | snp1936 195 | snp1942 196 | snp1943 197 | snp1956 198 | snp1960 199 | snp1963 200 | snp1971 201 | snp1978 202 | snp1983 203 | snp1985 204 | snp1994 205 | snp2005 206 | snp2008 207 | snp2010 208 | snp2021 209 | snp2022 210 | snp2039 211 | snp2045 212 | snp2046 213 | snp2049 214 | snp2056 215 | snp2086 216 | snp2125 217 | snp2133 218 | snp2176 219 | snp2186 220 | snp2187 221 | snp2193 222 | snp2194 223 | snp2197 224 | snp2202 225 | snp2203 226 | snp2210 227 | snp2212 228 | snp2220 229 | snp2230 230 | snp2248 231 | snp2259 232 | snp2268 233 | snp2270 234 | snp2280 235 | snp2288 236 | snp2320 237 | snp2333 238 | snp2341 239 | snp2374 240 | snp2389 241 | snp2391 242 | snp2423 243 | snp2458 244 | snp2460 245 | snp2472 246 | snp2481 247 | snp2511 248 | snp2523 249 | snp2553 250 | snp2568 251 | snp2569 252 | snp2579 253 | snp2592 254 | snp2610 255 | snp2619 256 | snp2621 257 | snp2633 258 | snp2639 259 | snp2645 260 | snp2654 261 | snp2689 262 | snp2715 263 | snp2723 264 | snp2756 265 | snp2775 266 | snp2782 267 | snp2794 268 | snp2809 269 | snp2822 270 | snp2823 271 | snp2828 272 | snp2856 273 | snp2874 274 | snp2879 275 | snp2885 276 | snp2907 277 | snp2920 278 | snp2932 279 | snp2935 280 | snp2938 281 | snp2939 282 | snp2962 283 | snp2967 284 | snp2978 285 | snp2989 286 | snp3002 287 | snp3016 288 | snp3021 289 | snp3023 290 | snp3044 291 | snp3048 292 | snp3065 293 | snp3066 294 | snp3067 295 | snp3068 296 | snp3111 297 | snp3112 298 | snp3114 299 | snp3127 300 | snp3129 301 | snp3135 302 | snp3145 303 | snp3152 304 | snp3168 305 | snp3171 306 | snp3193 307 | snp3203 308 | snp3213 309 | snp3224 310 | snp3227 311 | snp3232 312 | snp3241 313 | snp3250 314 | snp3270 315 | snp3271 316 | snp3273 317 | snp3275 318 | snp3277 319 | snp3284 320 | snp3298 321 | snp3329 322 | snp3336 323 | snp3339 324 | snp3344 325 | snp3364 326 | snp3368 327 | snp3383 328 | snp3385 329 | snp3396 330 | snp3406 331 | snp3414 332 | snp3429 333 | snp3450 334 | snp3460 335 | snp3467 336 | snp3475 337 | snp3477 338 | snp3493 339 | snp3494 340 | snp3507 341 | snp3508 342 | snp3514 343 | snp3537 344 | snp3544 345 | snp3546 346 | snp3562 347 | snp3574 348 | snp3581 349 | snp3593 350 | snp3619 351 | snp3620 352 | snp3626 353 | snp3628 354 | snp3631 355 | snp3632 356 | snp3642 357 | snp3652 358 | snp3656 359 | snp3677 360 | snp3679 361 | snp3683 362 | snp3689 363 | snp3696 364 | snp3701 365 | snp3704 366 | snp3724 367 | snp3731 368 | snp3756 369 | snp3758 370 | snp3766 371 | snp3783 372 | snp3788 373 | snp3802 374 | snp3807 375 | snp3811 376 | snp3829 377 | snp3833 378 | snp3845 379 | snp3865 380 | snp3870 381 | snp3892 382 | snp3919 383 | snp3928 384 | snp3940 385 | snp3960 386 | snp3992 387 | snp4026 388 | snp4030 389 | snp4032 390 | snp4055 391 | snp4068 392 | snp4075 393 | snp4078 394 | snp4082 395 | snp4089 396 | snp4104 397 | snp4118 398 | snp4132 399 | snp4137 400 | snp4140 401 | snp4156 402 | snp4173 403 | snp4179 404 | snp4187 405 | snp4200 406 | snp4201 407 | snp4202 408 | snp4203 409 | snp4210 410 | snp4220 411 | snp4222 412 | snp4226 413 | snp4228 414 | snp4236 415 | snp4273 416 | snp4277 417 | snp4294 418 | snp4299 419 | snp4309 420 | snp4329 421 | snp4338 422 | snp4342 423 | snp4366 424 | snp4372 425 | snp4375 426 | snp4409 427 | snp4413 428 | snp4414 429 | snp4419 430 | snp4428 431 | snp4432 432 | snp4440 433 | snp4479 434 | snp4485 435 | snp4492 436 | snp4496 437 | snp4530 438 | snp4540 439 | snp4575 440 | snp4587 441 | snp4588 442 | snp4629 443 | snp4632 444 | snp4634 445 | snp4639 446 | snp4655 447 | snp4659 448 | snp4675 449 | snp4705 450 | snp4718 451 | 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snp5429 523 | snp5444 524 | snp5454 525 | snp5462 526 | snp5496 527 | snp5502 528 | snp5509 529 | snp5511 530 | snp5515 531 | snp5548 532 | snp5564 533 | snp5567 534 | snp5573 535 | snp5580 536 | snp5602 537 | snp5603 538 | snp5628 539 | snp5630 540 | snp5638 541 | snp5646 542 | snp5700 543 | snp5707 544 | snp5708 545 | snp5711 546 | snp5718 547 | snp5729 548 | snp5736 549 | snp5747 550 | snp5752 551 | snp5766 552 | snp5768 553 | snp5769 554 | snp5780 555 | snp5806 556 | snp5825 557 | snp5826 558 | snp5844 559 | snp5845 560 | snp5850 561 | snp5851 562 | snp5852 563 | snp5855 564 | snp5867 565 | snp5883 566 | snp5889 567 | snp5897 568 | snp5900 569 | snp5938 570 | snp5947 571 | snp5955 572 | snp5963 573 | snp5982 574 | snp5986 575 | snp6001 576 | snp6015 577 | snp6022 578 | snp6030 579 | snp6050 580 | snp6058 581 | snp6074 582 | snp6076 583 | snp6096 584 | snp6105 585 | snp6106 586 | snp6127 587 | snp6140 588 | snp6148 589 | snp6179 590 | snp6193 591 | snp6231 592 | snp6232 593 | 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snp8992 878 | snp8997 879 | snp9013 880 | snp9016 881 | snp9018 882 | snp9022 883 | snp9023 884 | snp9027 885 | snp9029 886 | snp9036 887 | snp9045 888 | snp9051 889 | snp9086 890 | snp9132 891 | snp9159 892 | snp9164 893 | snp9192 894 | snp9208 895 | snp9226 896 | snp9259 897 | snp9265 898 | snp9273 899 | snp9274 900 | snp9282 901 | snp9286 902 | snp9293 903 | snp9294 904 | snp9307 905 | snp9313 906 | snp9320 907 | snp9334 908 | snp9337 909 | snp9341 910 | snp9345 911 | snp9350 912 | snp9352 913 | snp9383 914 | snp9392 915 | snp9396 916 | snp9416 917 | snp9424 918 | snp9426 919 | snp9431 920 | snp9435 921 | snp9439 922 | snp9441 923 | snp9449 924 | snp9456 925 | snp9457 926 | snp9463 927 | snp9469 928 | snp9477 929 | snp9488 930 | snp9496 931 | snp9505 932 | snp9513 933 | snp9518 934 | snp9536 935 | snp9546 936 | snp9548 937 | snp9549 938 | snp9551 939 | snp9575 940 | snp9607 941 | snp9612 942 | snp9614 943 | snp9615 944 | snp9616 945 | snp9643 946 | snp9674 947 | snp9695 948 | snp9698 949 | snp9701 950 | snp9707 951 | snp9710 952 | snp9732 953 | snp9743 954 | snp9746 955 | snp9751 956 | snp9754 957 | snp9759 958 | snp9760 959 | snp9761 960 | snp9772 961 | snp9773 962 | snp9774 963 | snp9789 964 | snp9797 965 | snp9805 966 | snp9814 967 | snp9819 968 | snp9835 969 | snp9866 970 | snp9870 971 | snp9887 972 | snp9892 973 | snp9894 974 | snp9900 975 | snp9903 976 | snp9905 977 | snp9909 978 | snp9911 979 | snp9916 980 | snp9917 981 | snp9923 982 | snp9931 983 | snp9933 984 | snp9942 985 | snp9943 986 | snp9948 987 | snp9950 988 | snp9954 989 | snp10014 990 | snp10015 991 | snp10017 992 | snp10021 993 | snp10023 994 | snp10025 995 | snp10035 996 | snp10041 997 | snp10056 998 | snp10069 999 | snp10074 1000 | snp10075 1001 | snp10077 1002 | snp10086 1003 | snp10089 1004 | snp10098 1005 | snp10099 1006 | snp10118 1007 | snp10122 1008 | snp10123 1009 | snp10126 1010 | snp10127 1011 | snp10129 1012 | snp10148 1013 | snp10150 1014 | snp10161 1015 | snp10164 1016 | snp10169 1017 | snp10181 1018 | snp10187 1019 | snp10189 1020 | snp10190 1021 | snp10192 1022 | snp10216 1023 | snp10228 1024 | snp10239 1025 | snp10244 1026 | snp10254 1027 | snp10262 1028 | snp10269 1029 | snp10280 1030 | snp10282 1031 | snp10299 1032 | snp10300 1033 | snp10337 1034 | snp10346 1035 | snp10356 1036 | snp10367 1037 | snp10372 1038 | snp10380 1039 | snp10382 1040 | snp10383 1041 | snp10389 1042 | snp10399 1043 | snp10424 1044 | snp10425 1045 | snp10445 1046 | snp10457 1047 | snp10458 1048 | snp10464 1049 | snp10469 1050 | snp10480 1051 | snp10481 1052 | snp10483 1053 | dsnp10502 1054 | dsnp10504 1055 | dsnp10508 1056 | dsnp10514 1057 | dsnp10518 1058 | dsnp10522 1059 | dsnp10589 1060 | dsnp10593 1061 | --------------------------------------------------------------------------------