Interpolating genetic map positions

README.md

Interpolating genetic maps

In order to run this script you would need to run:

python3 interp_genmap.py --snp test.snp --genmap test_chr20_22.txt --morgans True

the module requirements for this are:

• pandas
• numpy
• tqdm
• scipy
• click

For any questions - please submit an issue on this gist.

interp_genmap.py

#!/usr/local/bin/python3

'''
    Perform linear interpolation of a genetic map
'''

import click
import numpy as np
import pandas as pd
from scipy.interpolate import interp1d
from tqdm import tqdm

@click.command()
@click.option('--snp', required=True, help='Eigenstrat SNP file.')
@click.option('--genmap', required=True, help='Genetic map')
@click.option('--extrapolate', default=True, help='Extrapolate the genetic distance outside of the defined map.')
@click.option('--morgans', default=False, help='Convert to morgans (assumes the map is in cM)')
def main(snp, genmap, extrapolate, morgans):
    """Interpolate genetic distances into a SNP dataset."""
    map_interp_dict = {}
    gen_map_df = pd.read_csv(genmap, sep='\s+', header=None, names=['chrom', 'phys_pos', 'gen_pos'])
    for chrom in tqdm(np.unique(gen_map_df.chrom.values)):
        cur_df = gen_map_df[gen_map_df.chrom == chrom]
        if extrapolate:
            map_interp_dict[chrom] = interp1d(cur_df['phys_pos'].values, cur_df['gen_pos'].values, fill_value='extrapolate')
        else:
            map_interp_dict[chrom] = interp1d(cur_df['phys_pos'].values, cur_df['gen_pos'].values, fill_value='NaN')
    with open(snp, 'r') as snpfile:
        for line in snpfile:
            spltln = line.split()
            cur_chrom = int(spltln[1])
            cur_physpos = int(spltln[3])
            # Run the interpolation operation 
            cur_genpos = map_interp_dict[cur_chrom](cur_physpos)
            if morgans:
                cur_genpos = cur_genpos / 100.
            spltln[2] = str(cur_genpos)
            print('\t'.join(spltln))

if __name__ =='__main__':
	main()

test.snp

rs6078030 20 0 61098 T C
rs4814683 20 0 61795 T G
rs34147676 20 0 62731 A C
rs6076506 20 0 63231 G T
rs6139074 20 0 63244 C A
rs115017123 20 0 63452 G C
rs75670495 20 0 63733 T C
rs1418258 20 0 63799 T C
rs76004960 20 0 63808 C G
rs116770801 20 0 63967 G A
rs13043000 20 0 65288 T G
rs6053810 20 0 65900 G A
rs147948890 20 0 65951 C T
rs6054257 20 0 66370 G A
rs113878089 20 0 67760 T C
rs60878529 20 0 68264 C T
rs75510087 20 0 68618 A G
rs79067206 20 0 68799 C T
rs6039403 20 0 69094 A G
rs17685809 20 0 69408 T C
rs60263736 20 0 70980 A G
rs6040382 20 0 71079 T C
rs6040395 20 0 71093 A G
rs74812991 20 0 71509 G T
rs11698144 20 0 72719 T C
rs16987437 20 0 72892 A G
rs6135141 20 0 74347 A G
rs187470882 20 0 74545 A T
rs892665 20 0 75254 A C
rs80207627 20 0 75729 G C
rs6111385 20 0 76962 T C
rs76306444 20 0 77707 C T
rs74684343 20 0 78063 T C
rs6045990 20 0 79234 T C
rs6046657 20 0 80071 A G
rs73068355 20 0 80481 C G
rs2196239 20 0 80655 A G
rs150100613 20 0 81666 T C
rs6036079 20 0 82204 C T
rs6036082 20 0 82215 A G
rs141424247 20 0 82223 T C
rs62190471 20 0 82701 C T
rs62190472 20 0 83196 T A
rs7268260 20 0 85116 T C
rs34383360 20 0 87112 A G
rs139816670 20 0 87362 G A
rs1935386 20 0 87416 A C
rs6051504 20 0 88827 A C
rs139544739 20 0 88924 T A
rs1858595 20 0 90008 A C
rs75507632 20 0 90814 C T
rs1077784 20 0 90984 G A
rs2002370 20 0 91088 C T
rs74477741 20 0 91341 T C
rs11698455 20 0 91346 A G
rs6051659 20 0 91508 G A
rs13039134 20 0 92366 G A
rs1418260 20 0 92527 A G
rs140671032 20 0 92865 C T
rs6051804 20 0 92891 G A
rs114727387 20 0 93406 C T
rs6051847 20 0 93440 G A
rs117194009 20 0 93442 A T
rs6051856 20 0 93499 C T
rs112380741 20 0 93718 C T
rs146425143 20 0 93863 A G
rs6051884 20 0 93931 A G
rs6051892 20 0 94091 C T
rs59920385 20 0 94528 G T
rs60976651 20 0 94592 A T
rs75872669 20 0 94760 G A
rs1857092 20 0 94952 T G
rs146467726 20 0 95052 C T
rs6037629 20 0 95093 G T
rs149322979 20 0 96166 T C
rs6052070 20 0 96931 G A
rs6515824 20 0 97122 T C
rs6052094 20 0 97394 G A
rs74402254 20 0 97395 A G
rs75956702 20 0 98008 C T
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rs6107455 20 0 102799 A G
rs76231363 20 0 103351 A C
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rs1954267 20 0 108328 A C
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rs75338579 20 0 121188 A G
rs6053983 20 0 121310 C A
rs75750015 20 0 121823 G A
rs6038402 20 0 121824 T C
rs6038405 20 0 121976 A G
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rs45556640 20 0 123164 T G
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rs6117364 20 0 125538 C G
rs75442118 20 0 126149 C T
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rs74717966 20 0 126224 G A
rs77106211 20 0 126285 C T
rs6133348 20 0 126529 A G
rs6117403 20 0 126600 A C
rs6117404 20 0 126614 C T
rs6117416 20 0 126730 C T
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rs73600341 20 0 126914 T C
rs4815938 20 0 126923 C A
rs6085677 20 0 126930 A T
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rs78468075 20 0 127444 C T
rs753217 20 0 127720 A C
rs75987765 20 0 127887 T C
rs16994392 20 0 127952 T C
rs73071808 20 0 128432 A G
rs80163995 20 0 128708 G A
rs735669 20 0 128713 G C
rs78031171 20 0 128863 C G
rs16994490 20 0 129063 G A
rs148720584 20 0 129503 T C
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rs62190499 20 0 130133 T C
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rs74635036 20 0 130679 G A
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rs1592157 20 0 131657 A G
rs74271532 20 0 132142 A C
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rs13036802 20 0 132775 C T
rs79240204 20 0 132937 T C
rs6054966 20 0 133158 T A
rs2316225 20 0 133433 C A
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rs142919054 20 0 134349 T A
rs7353361 20 0 134400 A G
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rs6055084 20 0 134476 T C
rs6086092 20 0 134539 T A
rs6038867 20 0 134643 C T
rs79048929 20 0 134842 A G
rs1342845 20 0 134844 T C
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rs1342846 20 0 135488 C T
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rs6086162 20 0 136025 T C
rs6086171 20 0 136374 A G
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rs2298109 20 0 138148 T C
rs6077288 20 0 138460 G A
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rs1858592 20 0 138606 G A
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rs6077293 20 0 138620 C A
rs12626088 20 0 139154 G A
rs11087789 20 0 139173 C T
rs6055460 20 0 139362 G A
rs12624951 20 0 139409 A G
rs16995668 20 0 139419 T C
rs12624954 20 0 139456 A G
rs16995685 20 0 139576 A C
rs4142304 20 0 139745 T C
rs4142303 20 0 139841 A T
rs6039029 20 0 140086 A G
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rs6039035 20 0 140280 C T
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rs11087790 20 0 140505 T C
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rs9712517 20 0 141769 C G
rs1594917 20 0 143723 A G
rs1594918 20 0 143754 T C
rs1836440 20 0 143918 C T
rs74672635 20 0 144050 A C
rs6055874 20 0 144382 C T
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rs7264822 20 0 144551 T G
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rs6039198 20 0 144899 T C
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rs75517673 20 0 145965 C A
rs74575908 20 0 145976 A G
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rs73892049 20 0 146291 C T
rs73892050 20 0 146612 G A
rs1865432 20 0 146951 G A
rs6086589 20 0 146995 A T
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rs76166497 20 0 147203 G A
rs75485610 20 0 147273 G A
rs77528617 20 0 147370 G A
rs74481808 20 0 147486 C T
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rs1858597 20 0 147685 C A
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rs1858598 20 0 147915 T C
rs1858599 20 0 147917 C A
rs4816104 20 0 148084 T C
rs60417500 20 0 148301 C T
rs115728963 20 0 148597 T C
rs964794 20 0 148703 A G
rs77778096 20 0 148754 A C
rs76332318 20 0 148801 G T
rs57957087 20 0 149048 G A
rs79028865 20 0 149381 C T
rs6056336 20 0 149407 C G
rs114816383 20 0 149599 A G
rs76734698 20 0 149913 A G
rs6077481 20 0 149975 T C
rs751596 20 0 151330 T C
rs116753505 20 0 151677 T C
rs6056559 20 0 152570 G A
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rs6039451 20 0 152992 C G
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rs6039463 20 0 153393 C A
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rs74181519 20 0 154162 A G
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rs74181520 20 0 154241 A C
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rs6056705 20 0 154837 T C
rs143484317 20 0 154921 C T
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rs114321147 20 0 155621 A G
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rs112184954 20 0 156797 T A
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rs4813900 20 0 157157 T C
rs147615770 20 0 157523 A G
rs6141061 20 0 157746 A C
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rs76689844 20 0.159078 8035567 A T
rs6055500 20 0.159078 8035672 G A
rs78748350 20 0.159078 8035702 C T
rs76984985 20 0.159078 8035812 C T
rs112338742 20 0.159078 8036007 T C
rs12480395 20 0.159078 8036018 T A
rs11906344 20 0.159078 8036240 A G
rs6133533 20 0.159078 8036950 T G
rs1024167 20 0.159078 8037480 A G
rs4315603 20 0.159078 8037545 C G
rs113152509 20 0.159078 8037586 T G
rs3859674 20 0.159078 8037651 G C
rs147592119 20 0.159078 8037975 A G
rs6133534 20 0.159078 8038554 T G
rs12624652 20 0.159078 8038640 A G
rs6133535 20 0.159078 8038649 G A
rs6133536 20 0.159078 8038670 A G
rs6140512 20 0.159078 8038722 G A
rs112514182 20 0.159078 8039235 T C
rs116196448 20 0.159078 8039247 C A
rs79458554 20 0.159078 8039410 T A
rs6133537 20 0.159078 8039501 A T
rs6133539 20 0.159078 8039808 C T
rs6140513 20 0.159078 8039890 G C
rs77109720 20 0.159078 8039918 A G
rs6133540 20 0.159078 8039987 A C
rs6055504 20 0.159078 8040976 A G
rs113131293 20 0.159084 8041377 T C
rs6140514 20 0.159085 8041458 G T
rs145560642 20 0.159088 8041671 C T
rs6140515 20 0.15909 8041815 G A
rs6140517 20 0.159097 8042329 G A
rs6039021 20 0.159098 8042423 T C
rs16994386 20 0.159106 8042960 C T
rs6055505 20 0.159107 8043033 T C
rs6055506 20 0.159109 8043141 A C
rs73087744 20 0.159113 8043429 A T
rs73603830 20 0.159114 8043485 A T
rs6055508 20 0.159118 8043751 A G
rs6039023 20 0.159119 8043837 A G
rs61638775 20 0.159155 8044542 G A
rs6039025 20 0.159176 8044962 T A
rs73087748 20 0.159181 8045056 A G
rs73895507 20 0.15922 8045840 G A
rs6118046 20 0.159222 8045872 T C
rs6140518 20 0.159257 8047718 G T
rs6140519 20 0.15926 8047856 T C
rs6133541 20 0.15928 8048921 A G
rs80131716 20 0.159299 8049903 G A
rs139095251 20 0.159308 8050399 T C
rs6055510 20 0.159313 8050666 T C
rs4816042 20 0.15932 8051032 A G
rs6118048 20 0.159321 8051081 A T
rs4816043 20 0.159326 8051353 G A
rs4816044 20 0.159326 8051376 T A
rs6055512 20 0.159326 8051783 G A
rs6055513 20 0.159326 8052158 G A
rs6133542 20 0.15933 8052280 C T
rs6118049 20 0.159342 8052719 C T
rs66992049 20 0.159353 8053116 C A
rs13037901 20 0.159354 8053134 T C
rs8123568 20 0.159359 8053312 A G
rs8123629 20 0.159362 8053420 A G
rs8117871 20 0.159363 8053455 G A
rs6133543 20 0.159363 8053473 T C
rs6140523 20 0.159365 8053527 C T
rs6133544 20 0.159365 8053551 A G
rs6118050 20 0.159365 8053802 C T
rs6086318 20 0.159365 8053857 T C
rs6077302 20 0.159365 8053884 A G
rs6077303 20 0.159365 8053944 G A
rs2223253 20 0.159366 8054298 T C
rs6140524 20 0.159366 8054552 T C
rs6140525 20 0.159366 8054609 T A
rs6086320 20 0.159366 8055776 A C
rs2056932 20 0.159366 8056181 C T
rs78959517 20 0.159366 8056347 G C
rs74724734 20 0.159366 8056714 A C
rs80124440 20 0.159367 8057669 A G
rs972273 20 0.159367 8058069 C G
rs113352364 20 0.159367 8058229 G A
rs6055517 20 0.159367 8058810 C G
rs2327023 20 0.159368 8059865 A T
rs2205778 20 0.159368 8060107 T A
rs73089600 20 0.159369 8061520 T G
rs73091403 20 0.159369 8061521 T C
rs66709406 20 0.159369 8061546 T C
rs61696964 20 0.159369 8061755 G A
rs2223249 20 0.159369 8062057 T A
rs16994407 20 0.159369 8063473 A G
rs12481478 20 0.15937 8064513 G C
rs118172039 20 0.15937 8064554 G A
rs6055520 20 0.15937 8064749 C A
rs34737014 20 0.15937 8065073 C T
rs35082789 20 0.15937 8065079 T A
rs13045064 20 0.15937 8065170 T G
rs79806019 20 0.15937 8065188 C T
rs6039028 20 0.15937 8066213 G A
rs117870680 20 0.15937 8066252 A C
rs79206021 20 0.15937 8066702 C T
rs6086323 20 0.159371 8066888 C T
rs112402384 20 0.159371 8067917 G T
rs6086324 20 0.159371 8068179 A T
rs6118051 20 0.159371 8068274 G A
rs117952492 20 0.159371 8068370 T C
rs6086325 20 0.159371 8069192 A G
rs6108101 20 0.159372 8069396 C T
rs55900834 20 0.159372 8069424 G A
rs74590281 20 0.159372 8069573 C T
rs6108102 20 0.159372 8070078 G T
rs111707660 20 0.159372 8070159 C T
rs55748681 20 0.159372 8070508 C T
rs117481937 20 0.159372 8070892 T C
rs6077304 20 0.159374 8071935 C T
rs6039032 20 0.159374 8072002 A G
rs12329453 20 0.159375 8072005 T C
rs76152256 20 0.159375 8072017 T C
rs142782978 20 0.159375 8072092 A G
rs6108103 20 0.159378 8072489 C T
rs55919500 20 0.159378 8072501 A G
rs2223251 20 0.159382 8072965 G A
rs2038032 20 0.159383 8073136 A G
rs4239774 20 0.159391 8074116 G A
rs73598270 20 0.159392 8074304 G A
rs6055526 20 0.159393 8074417 A G
rs6108104 20 0.159394 8074518 A C
rs6055527 20 0.159395 8074637 G A
rs2205779 20 0.159398 8075023 C T
rs2223252 20 0.159399 8075223 G A
rs2056933 20 0.159408 8075613 A C
rs2056934 20 0.159409 8075713 A G
rs2056935 20 0.159412 8076171 C T
rs6077305 20 0.159417 8076742 C A
rs6055528 20 0.159417 8076795 G A
rs6055529 20 0.159417 8076908 A G
rs6055530 20 0.159417 8076934 C T
rs6055531 20 0.159417 8077056 A G
rs78533593 20 0.159417 8077184 A G
rs12480579 20 0.159417 8077395 G A
rs6140529 20 0.159417 8077523 G A
rs6055532 20 0.159418 8078149 A G
rs58973686 20 0.159419 8078711 T G
rs876880 20 0.159419 8078949 A C
rs876881 20 0.159419 8079019 T C
rs74403391 20 0.15942 8079936 T C
rs2327024 20 0.15942 8080075 T A
rs723458 20 0.159421 8080477 G A
rs79827999 20 0.159421 8080670 G A
rs78332248 20 0.159421 8081137 G A
rs73076227 20 0.159421 8081168 A G
rs73076229 20 0.159422 8081430 A G
rs73076232 20 0.159422 8081611 A C
rs6086329 20 0.159423 8082061 C T
rs6055533 20 0.159423 8082118 T C
rs6086330 20 0.159423 8082272 G T
rs12480533 20 0.159424 8082896 G A
rs6140530 20 0.159424 8082986 A T
rs6086331 20 0.159424 8083296 A G
rs112961871 20 0.159424 8083520 C T
rs6055536 20 0.159425 8083808 C A
rs1079778 20 0.159425 8084107 T A
rs1079779 20 0.159425 8084108 A T
rs6118057 20 0.159425 8084147 A G
rs1079777 20 0.159425 8084404 A G
rs2207316 20 0.159425 8084485 T G
rs2207317 20 0.159425 8084526 A G
rs79564361 20 0.159425 8084609 A G
rs76250331 20 0.159426 8084774 C T
rs80059272 20 0.159426 8084914 C T
rs6039034 20 0.159427 8085071 C T
rs6055541 20 0.159427 8085159 G A
rs6077307 20 0.159428 8085390 A T
rs7265353 20 0.159429 8085660 C G
rs1079909 20 0.159429 8085814 A G
rs6108106 20 0.15943 8086361 A G
rs184717254 20 0.15943 8086379 A G
rs6118058 20 0.159431 8086554 C T
rs116022580 20 0.159431 8086687 T C
rs6118059 20 0.159433 8087217 G A
rs6118060 20 0.159433 8087337 T C
rs76883031 20 0.159433 8087339 T C
rs6055543 20 0.159433 8087342 G T
rs6118061 20 0.159433 8087343 C T
rs6118062 20 0.159434 8087581 C T
rs7264774 20 0.159435 8088334 G A
rs6077310 20 0.159435 8088667 A T
rs6086336 20 0.159435 8088710 T C
rs79285082 20 0.159436 8089171 T C
rs6108107 20 0.159436 8089233 T A
rs73076256 20 0.159436 8089458 C A
rs78830017 20 0.159439 8092494 C T
rs6077316 20 0.159442 8095372 G A
rs6077317 20 0.159442 8095413 A G
rs8114042 20 0.159442 8095416 G C
rs6140538 20 0.159442 8095429 A G
rs6086342 20 0.159443 8096105 A C
rs6055550 20 0.159443 8096130 T C
rs79831805 20 0.159444 8096721 G C
rs6118071 20 0.159444 8096876 G A
rs6086343 20 0.159445 8096952 C T
rs2057146 20 0.159445 8097330 A G
rs6133548 20 0.159446 8097725 C T
rs6055552 20 0.159446 8097884 T G
rs77495146 20 0.159449 8099020 T C
rs6086344 20 0.15945 8099078 C G
rs73076261 20 0.15945 8099106 A T
rs77595936 20 0.15945 8099302 G T
rs6086345 20 0.159451 8099663 C A
rs6055555 20 0.159451 8099774 C G
rs6118073 20 0.159453 8100467 C T
rs73076264 20 0.159454 8100831 A G
rs2179984 20 0.159456 8101337 A G
rs141504108 20 0.159456 8101411 C T
rs57883849 20 0.159457 8101700 A G
rs6055557 20 0.159458 8102034 C A
rs79857902 20 0.159458 8102094 C G
rs6118075 20 0.15946 8102867 G A
rs75032282 20 0.159473 8103027 G T
rs61334244 20 0.159474 8103041 G A
rs6140540 20 0.159498 8103336 A T
rs6140541 20 0.1595 8103360 A C
rs79445176 20 0.159517 8103576 G T
rs12480341 20 0.159519 8103601 A G
rs73076268 20 0.159556 8104065 A G
rs77474761 20 0.159585 8104419 A T
rs6140542 20 0.159617 8104816 T C
rs145952667 20 0.159626 8104930 G A
rs139959418 20 0.159628 8104949 C T
rs6086346 20 0.159648 8105198 A G
rs4816046 20 0.159677 8105561 T C
rs6055558 20 0.15975 8106464 A T
rs6118077 20 0.159761 8106596 C G
rs6039040 20 0.159825 8107397 T C
rs73076272 20 0.159825 8107761 C A
rs77481626 20 0.159825 8108562 C G
rs6118078 20 0.159825 8108714 A C
rs997515 20 0.159825 8108823 G T
rs116955243 20 0.159825 8108896 A G
rs73076273 20 0.159825 8109384 A G
rs61555085 20 0.159825 8110426 G A
rs6039041 20 0.159825 8110530 G A
rs6077319 20 0.159825 8110851 C A
rs932491 20 0.159825 8111284 T C
rs932490 20 0.159825 8111421 T C
rs12481247 20 0.159825 8111723 T C
rs73078237 20 0.159825 8111770 G A
rs79923770 20 0.159825 8111797 G A
rs73078238 20 0.159825 8112290 A G
rs6108110 20 0.159825 8112399 T C
rs6086348 20 0.159825 8112497 T C
rs6086350 20 0.159829 8113405 C T
rs2076695 20 0.159831 8113889 C A
rs2076694 20 0.159831 8113891 C G
rs6140545 20 0.159833 8114261 A T
rs6118083 20 0.159836 8114704 G A
rs79822484 20 0.159838 8115136 T A
rs6140546 20 0.159838 8115237 A G
rs13041373 20 0.159842 8115957 T A
rs4142365 20 0.159844 8116504 A G
rs76555941 20 0.159848 8116513 T C
rs6039042 20 0.159894 8116630 A G
rs73895516 20 0.159939 8116742 A G
rs4813851 20 0.160045 8117011 C A
rs73078246 20 0.160162 8117304 G A
rs16994434 20 0.160249 8117524 G C
rs74946103 20 0.160288 8117622 A G
rs73078247 20 0.160512 8118186 G C
rs57178496 20 0.160578 8118352 G C
rs59885915 20 0.160607 8118426 T C
rs6140549 20 0.160649 8118531 A G
rs6055562 20 0.160694 8118643 T C
rs79984192 20 0.16077 8118834 C T
rs16994436 20 0.161055 8119554 T C
rs6039043 20 0.161452 8120553 A T
rs114272445 20 0.161515 8120712 G A
rs1543402 20 0.161562 8120829 G A
rs8114499 20 0.161668 8121097 C T
rs6055563 20 0.161668 8121252 C T
rs6055564 20 0.161668 8121431 C A
rs113126330 20 0.161668 8121467 T C
rs61318841 20 0.161668 8121514 T C
rs143437876 20 0.161668 8121517 A C
rs11908576 20 0.161668 8121605 C A
rs6039044 20 0.161668 8121783 G A
rs13043158 20 0.161668 8121792 C G
rs6039045 20 0.161668 8122062 A G
rs6039046 20 0.161668 8122107 T C
rs6055565 20 0.161668 8122138 C T
rs6039047 20 0.161668 8122162 A C
rs56030692 20 0.161668 8122382 G A
rs73078264 20 0.161668 8122512 G A
rs6039048 20 0.161668 8122525 T C
rs13039823 20 0.161668 8122562 G C
rs6118085 20 0.161668 8123022 G A
rs11907413 20 0.161668 8123057 A G
rs6118086 20 0.161668 8123300 G A
rs60630287 20 0.161668 8123485 A G
rs62198527 20 0.161668 8123737 C T
rs13041008 20 0.161668 8123994 C T
rs6055567 20 0.161668 8124013 C T
rs61159990 20 0.161668 8124164 C T
rs6039049 20 0.161668 8124354 A G
rs8124468 20 0.161668 8124473 A G
rs73078275 20 0.161668 8124588 T A
rs74798078 20 0.161668 8124682 T G
rs4816047 20 0.161668 8125220 T C
rs375871933 20 0.161668 8125223 T G
rs6055568 20 0.161668 8125283 G T
rs8113925 20 0.161668 8125395 G C
rs148024246 20 0.161668 8126338 A G
rs12481262 20 0.161668 8126920 C T
rs75587476 20 0.161668 8127412 C T
rs58635000 20 0.161668 8127449 G A
rs58912867 20 0.161668 8127756 G A
rs56842126 20 0.161668 8127877 T G
rs73078290 20 0.161668 8127991 T G
rs11697830 20 0.161668 8128055 A G
rs2327025 20 0.161668 8128119 T C
rs73605826 20 0.161668 8128163 A G
rs926817 20 0.161668 8128442 A G
rs6055570 20 0.161668 8129324 A C
rs73078300 20 0.161668 8129425 G A
rs8121126 20 0.161668 8129491 A C
rs60650470 20 0.161668 8129914 T C
rs6039051 20 0.161668 8130137 T C
rs73605839 20 0.161668 8130429 G A
rs16994453 20 0.161668 8130943 T C
rs10485719 20 0.161668 8131904 T C
rs544595755 20 0.161668 8132338 A T
rs564617975 20 0.161668 8132339 A C
rs116927882 20 0.161668 8132441 T C
rs57577145 20 0.161668 8132729 A G
rs118012387 20 0.161668 8132979 G A
rs117916143 20 0.161668 8133033 T C
rs62198529 20 0.161668 8133109 T G
rs6055578 20 0.161668 8134628 C T
rs2876122 20 0.161668 8135557 A G
rs76840544 20 0.161668 8136594 G C
rs62198530 20 0.161668 8136686 G A
rs73080209 20 0.161668 8136915 G A
rs79519513 20 0.161668 8137090 G A
rs112341098 20 0.161668 8137939 C T
rs1033398 20 0.161668 8138483 G A
rs1033399 20 0.161668 8138685 A T
rs73080211 20 0.161668 8139186 C A
rs112046158 20 0.161668 8139216 T A
rs6055581 20 0.161668 8139692 A C
rs6055582 20 0.161668 8139753 C T
rs6039059 20 0.161668 8139776 G A
rs113490910 20 0.161668 8140124 T C
rs113396971 20 0.161668 8140158 T G
rs6039060 20 0.161668 8140301 A G
rs2327027 20 0.161668 8140769 A C
rs2327028 20 0.161668 8140925 C T
rs6055584 20 0.161668 8141137 A G
rs73080221 20 0.161668 8141393 C T
rs16994471 20 0.161668 8141433 T G
rs73080222 20 0.161668 8141687 C G
rs62198534 20 0.161668 8141925 G A
rs6055585 20 0.161668 8141956 G A
rs56326021 20 0.161668 8142327 T C
rs58601699 20 0.161668 8143413 A G
rs73080226 20 0.161668 8144117 C G
rs2235212 20 0.161668 8144135 A G
rs978266 20 0.161668 8144640 G A
rs10485720 20 0.161668 8144719 C T
rs73080228 20 0.161668 8145149 A G
rs10485721 20 0.161668 8145333 C A
rs73895537 20 0.161668 8145954 G C
rs2423344 20 0.161668 8146642 T C
rs73080231 20 0.161668 8147503 C T
rs73895538 20 0.161668 8147562 G A
rs73895540 20 0.161668 8147870 C T
rs6039061 20 0.161668 8147916 A C
rs12480091 20 0.161668 8148267 G A
rs7266525 20 0.161668 8148902 C T
rs7273266 20 0.161668 8149100 C G
rs1033400 20 0.161668 8149910 A C
rs112624673 20 0.161668 8150078 T A
rs6055590 20 0.161668 8150408 T G
rs4816048 20 0.161668 8150561 C G
rs728213 20 0.161668 8151262 G A
rs2327029 20 0.161668 8151882 C T
rs79944692 20 0.161668 8152040 T C
rs62198558 20 0.161668 8152623 T C
rs117734470 20 0.161668 8152869 C T
rs57133754 20 0.161668 8153141 A G
rs62198559 20 0.161668 8153262 C T
rs62199960 20 0.161668 8153403 T C
rs7271063 20 0.161668 8153919 A G
rs143638856 20 0.161668 8155551 G T
rs59903441 20 0.161668 8156391 C T
rs73080247 20 0.161668 8157097 A G
rs6133550 20 0.161668 8157516 C G
rs371364829 20 0.161668 8157933 A G
rs75673843 20 0.161668 8157934 T G
rs73080249 20 0.161668 8157965 G A
rs57433233 20 0.161668 8158076 T C
rs57183087 20 0.161668 8158078 G T
rs6055593 20 0.161668 8158417 A G
rs6055594 20 0.161668 8158503 A G
rs140097773 20 0.161668 8158558 T G
rs62199963 20 0.161668 8158622 G A
rs111735053 20 0.161668 8158763 A G
rs12480467 20 0.161668 8158910 A G
rs112512551 20 0.161668 8158931 A G
rs6055595 20 0.161668 8159217 C T
rs7268951 20 0.161668 8159313 T C
rs6055596 20 0.161668 8159395 A G
rs6055597 20 0.161668 8159405 T C
rs6055598 20 0.161668 8159412 T C
rs2423345 20 0.161668 8159486 G A
rs4407321 20 0.161668 8159859 A G
rs57440128 20 0.161668 8159913 T C
rs6055600 20 0.161668 8160061 T A
rs56993795 20 0.161668 8160190 G A
rs114118490 20 0.161668 8160216 G A
rs77267831 20 0.161668 8160268 C G
rs148821488 20 0.161668 8160756 T C
rs62199965 20 0.161668 8160757 A G
rs6039071 20 0.161668 8160875 C T
rs6055601 20 0.161668 8161126 A G
rs75237125 20 0.161668 8161328 C A
rs78050101 20 0.161668 8162178 T C
rs11906886 20 0.161668 8162235 A C
rs6055603 20 0.161668 8162278 G A
rs6055604 20 0.161668 8162311 A G
rs61180353 20 0.161668 8162359 T C
rs993482 20 0.161668 8162491 C T
rs55635300 20 0.161668 8162522 T C
rs73080268 20 0.161668 8162984 A G
rs6055605 20 0.161668 8163069 G C
rs62199966 20 0.161668 8163282 T C
rs112208537 20 0.161668 8163283 T G
rs148759848 20 0.161668 8163382 A C
rs8117801 20 0.161668 8163454 C T
rs8116488 20 0.161668 8163466 G A
rs11907373 20 0.161668 8163658 A G
rs6055606 20 0.161668 8163877 T C
rs6055607 20 0.161668 8163994 G A
rs6055608 20 0.161668 8164043 T C
rs6039074 20 0.161668 8164067 C T
rs6039075 20 0.161668 8164425 A T
rs6055609 20 0.161668 8164509 G A
rs6055610 20 0.161668 8164553 C T
rs7267305 20 0.161668 8164581 C T
rs6055611 20 0.161668 8165398 T C
rs6039076 20 0.161668 8165732 T C
rs142775398 20 0.161668 8165743 T C
rs6039077 20 0.161668 8165794 A G
rs2423350 20 0.161668 8165964 A G
rs56328920 20 0.161668 8166071 A G
rs6039078 20 0.161668 8166098 G A
rs73080277 20 0.161668 8166411 A G
rs6039079 20 0.161668 8166493 G A
rs78665898 20 0.161668 8166501 A G
rs6055612 20 0.161668 8166653 A G
rs605561

test_chr20_22.txt