Mercurial > repos > iuc > plink
changeset 8:16d22eee0fe3 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit b63133897598f2881de7bad1f18fcd69d7d7e9df"
| author | iuc |
|---|---|
| date | Thu, 02 Dec 2021 16:20:30 +0000 |
| parents | 66b35562554d |
| children | 272aca44b3dd |
| files | plink.xml test-data/out.assoc.fisher.adjusted test-data/out.assoc.fisher.mperm test-data/out.assoc.logistic.adjusted |
| diffstat | 4 files changed, 181 insertions(+), 178 deletions(-) [+] |
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line diff
--- a/plink.xml Mon Oct 05 16:08:24 2020 +0000 +++ b/plink.xml Thu Dec 02 16:20:30 2021 +0000 @@ -1,7 +1,7 @@ <tool id='plink' name='plink' version='@TOOL_VERSION@+galaxy@VERSION_SUFFIX@'> <macros> <token name='@TOOL_VERSION@'>1.9.b618</token> - <token name='@VERSION_SUFFIX@'>2</token> + <token name='@VERSION_SUFFIX@'>3</token> <xml name='template_sanitizer'> <sanitizer> <valid initial='default'> @@ -38,6 +38,9 @@ </sanitizer> </xml> </macros> + <xrefs> + <xref type="bio.tools">plink</xref> + </xrefs> <requirements> <requirement type='package' version='1.90b6.18'>plink</requirement> </requirements> @@ -354,7 +357,7 @@ $functions.logistic.beta $functions.logistic.intercept #end if - + --lambda $functions.lambda #elif $functions.func == 'ibd': #if $functions.genome.output_genome: --genome @@ -443,11 +446,11 @@ <when value='filtering'> <conditional name='id_list'> <param name='func' type='select' label='ID list functions'> - <option value='none'/> - <option value='keep'/> - <option value='keep-fam'/> - <option value='remove'/> - <option value='remove-fam'/> + <option value='none'>None</option> + <option value='keep'>Keep by sample IDs</option> + <option value='keep-fam'>Keep by family IDs</option> + <option value='remove'>Remove by sample IDs</option> + <option value='remove-fam'>Remove by family IDs</option> </param> <when value='none'/> <when value='keep'> @@ -465,9 +468,9 @@ </conditional> <conditional name='extraction'> <param name='ex_func' type='select' label='ID extraction functions'> - <option value='none'/> - <option value='extract'/> - <option value='exclude'/> + <option value='none'>None</option> + <option value='extract'>Keep by variant IDs</option> + <option value='exclude'>Remove by variant IDs </option> </param> <when value='none'/> <when value='extract'> @@ -568,8 +571,8 @@ </conditional> <conditional name='thinning'> <param name='thinning' type='select' label='Arbitrary thinning'> - <option value='No'/> - <option value='Yes'/> + <option value='No'>No</option> + <option value='Yes'>Yes</option> </param> <when value='No'/> <when value='Yes'> @@ -620,8 +623,8 @@ </section> <conditional name='hwe'> <param name='hwe' type='select' help='Set Hardy-Weinberg equilibrium tests'> - <option value='No'/> - <option value='Yes'/> + <option value='No'>No</option> + <option value='Yes'>Yes</option> </param> <when value='No'/> <when value='Yes'> @@ -637,8 +640,8 @@ </conditional> <conditional name='sex_founder_filter'> <param name='filter' type='select' label='Filter on sex and/or founders'> - <option value='No'/> - <option value='Yes'/> + <option value='No'>No</option> + <option value='Yes'>Yes</option> </param> <when value='No'/> <when value='Yes'> @@ -663,8 +666,8 @@ <when value='data_manage'> <conditional name='bmerge'> <param name='set' type='select' label='Merge plink tilesets'> - <option value='No'/> - <option value='Yes'/> + <option value='No'>No</option> + <option value='Yes'>Yes</option> </param> <when value='No'/> <when value='Yes'> @@ -805,8 +808,8 @@ <param name='read_genome' label='Reusing an IBS/IBD calculation' format='tabular,tsv' type='data' optional='true'/> <conditional name='cluster'> <param name='cluster' type='select' help='Use IBS values calculated via --genome to perform complete linkage clustering'> - <option value='No'/> - <option value='Yes'/> + <option value='No'>No</option> + <option value='Yes'>Yes</option> </param> <when value='No'/> <when value='Yes'> @@ -817,8 +820,8 @@ </param> <conditional name='mds'> <param name='mds_scaling' type='select' help='Return a Haploview-friendly multidimensional scaling report'> - <option value='No'/> - <option value='Yes'/> + <option value='No'>No</option> + <option value='Yes'>Yes</option> </param> <when value='No'/> <when value='Yes'> @@ -837,7 +840,7 @@ <conditional name='assoc'> <param name='assoc' label='Perform 1df chi-square allelic test' type='select'> <option value=''>No</option> - <option value='Yes'/> + <option value='Yes'>Yes</option> </param> <when value=''/> <when value='Yes'> @@ -865,8 +868,8 @@ </conditional> <conditional name='adjust'> <param name='adjust' label='Report basic multiple testing corrections for the raw p-values' type='select'> - <option value='No'/> - <option value='Yes'/> + <option value='No'>No</option> + <option value='Yes'>Yes</option> </param> <when value='No'/> <when value='Yes'> @@ -921,8 +924,8 @@ </conditional> --> <conditional name='logistic'> <param name='logistic' type='select' label='Perform logistic regression and return report'> - <option value='No'/> - <option value='Yes'/> + <option value='No'>No</option> + <option value='Yes'>Yes</option> </param> <when value='No'/> <when value='Yes'> @@ -967,7 +970,7 @@ <conditional name='genome'> <param name='output_genome' type='select' help='Perform and return results of IBS/IBD computation'> <option value=''>No</option> - <option value='Yes'/> + <option value='Yes'>Yes</option> </param> <when value=''/> <when value='Yes'> @@ -1373,4 +1376,4 @@ <citations> <citation type='doi'>10.1186/s13742-015-0047-8</citation> </citations> -</tool> \ No newline at end of file +</tool>
--- a/test-data/out.assoc.fisher.adjusted Mon Oct 05 16:08:24 2020 +0000 +++ b/test-data/out.assoc.fisher.adjusted Thu Dec 02 16:20:30 2021 +0000 @@ -1,51 +1,51 @@ CHR SNP UNADJ GC QQ BONF HOLM SIDAK_SS SIDAK_SD FDR_BH FDR_BY - 1 snp13 1.369 1.369 2 0 0 0.05171 0.05171 0.05883 0 - 1 snp45 1.276 1.276 1.523 0 0 0.02964 0.03136 0.05883 0 - 1 snp22 1.188 1.188 1.301 0 0 0.01545 0.01771 0.05883 0 - 1 snp1 1.019 1.019 1.155 0 0 0.002837 0.003842 0.05883 0 - 1 snp5 0.8623 0.8623 1.046 0 0 0.0002697 0.000487 0.05883 0 - 1 snp15 0.7893 0.7893 0.9586 0 0 6.152e-05 0.0001493 0.05883 0 - 1 snp33 0.7185 0.7185 0.8861 0 0 1.07e-05 3.822e-05 0.05883 0 - 1 snp36 0.717 0.717 0.8239 0 0 1.028e-05 3.822e-05 0.05883 0 - 1 snp21 0.6489 0.6489 0.7696 0 0 1.314e-06 1.004e-05 0.05883 0 - 1 snp18 0.6487 0.6487 0.7212 0 0 1.303e-06 1.004e-05 0.05883 0 - 1 snp23 0.5838 0.5838 0.6778 0 0 1.195e-07 2.452e-06 0.05883 0 - 1 snp12 0.5228 0.5228 0.6383 0 0 7.772e-09 3.935e-07 0.05883 0 - 1 snp41 0.5219 0.5219 0.6021 0 0 7.455e-09 3.935e-07 0.05883 0 - 1 snp17 0.4642 0.4642 0.5686 0 0 3.191e-10 7.563e-08 0.05883 0 - 1 snp2 0.4625 0.4625 0.5376 0 0 2.869e-10 7.563e-08 0.05883 0 - 1 snp35 0.4622 0.4622 0.5086 0 0 2.825e-10 7.563e-08 0.05883 0 - 1 snp28 0.4103 0.4103 0.4815 0 0 8.864e-12 2.336e-08 0.05883 0 - 1 snp38 0.4069 0.4069 0.4559 0 0 6.895e-12 2.336e-08 0.05883 0 - 1 snp43 0.4064 0.4064 0.4318 0 0 6.662e-12 2.336e-08 0.05883 0 - 1 snp8 0.4062 0.4062 0.4089 0 0 6.539e-12 2.336e-08 0.05883 0 - 1 snp9 0.3537 0.3537 0.3872 0 0 8.607e-14 1.038e-08 0.05883 0 - 1 snp19 0.3524 0.3524 0.3665 0 0 7.618e-14 1.038e-08 0.05883 0 - 1 snp44 0.3523 0.3523 0.3468 0 0 7.575e-14 1.038e-08 0.05883 0 - 1 snp31 0.352 0.352 0.3279 0 0 7.348e-14 1.038e-08 0.05883 0 - 1 snp29 0.3018 0.3018 0.3098 0 0 4.339e-16 6.787e-09 0.05883 0 - 1 snp30 0.3011 0.3011 0.2924 0 0 3.857e-16 6.787e-09 0.05883 0 - 1 snp42 0.3011 0.3011 0.2757 0 0 3.857e-16 6.787e-09 0.05883 0 - 1 snp49 0.3011 0.3011 0.2596 0 0 3.857e-16 6.787e-09 0.05883 0 - 1 snp34 0.253 0.253 0.2441 0 0 0 6.732e-09 0.05883 0 - 1 snp37 0.2529 0.2529 0.2291 0 0 0 6.732e-09 0.05883 0 - 1 snp40 0.2528 0.2528 0.2147 0 0 0 6.732e-09 0.05883 0 - 1 snp20 0.2526 0.2526 0.2007 0 0 0 6.732e-09 0.05883 0 - 1 snp48 0.2072 0.2072 0.1871 0 0 0 6.732e-09 0.05814 0 - 1 snp14 0.207 0.207 0.1739 0 0 0 6.732e-09 0.05814 0 - 1 snp0 0.1643 0.1643 0.1612 0 0 0 4.076e-09 0.05814 0 - 1 snp11 0.1642 0.1642 0.1487 0 0 0 4.076e-09 0.05814 0 - 1 snp7 0.1639 0.1639 0.1367 0 0 0 4.076e-09 0.05814 0 - 1 snp26 0.1638 0.1638 0.1249 0 0 0 4.076e-09 0.05814 0 - 1 snp32 0.1235 0.1235 0.1135 0 0 0 4.076e-09 0.05814 0 - 1 snp16 0.1235 0.1235 0.1024 0 0 0 4.076e-09 0.05814 0 - 1 snp25 0.1234 0.1234 0.09151 0 0 0 4.076e-09 0.05814 0 - 1 snp39 0.1233 0.1233 0.08092 0 0 0 4.076e-09 0.05814 0 - 1 snp46 0.1233 0.1233 0.07058 0 0 0 4.076e-09 0.05814 0 - 1 snp47 0.08552 0.08552 0.06048 0 0 0 4.076e-09 0.05814 0 - 1 snp3 0.08512 0.08512 0.05061 0 0 0 4.076e-09 0.05814 0 - 1 snp27 0.08512 0.08512 0.04096 0 0 0 4.076e-09 0.05814 0 - 1 snp4 0.08501 0.08501 0.03152 0 0 0 4.076e-09 0.05814 0 - 1 snp24 0.04939 0.04939 0.02228 0 0 0 4.076e-09 0.03167 0 - 1 snp6 0.0159 0.0159 0.01323 0 0 0 4.076e-09 0.01585 0 - 1 snp10 0.01585 0.01585 0.004365 0 0 0 4.076e-09 0.01585 0 + 1 snp13 1.605 1.605 2 0 0 0.1455 0.1455 0.1672 0 + 1 snp45 1.495 1.495 1.523 0 0 0.09512 0.09865 0.1672 0 + 1 snp22 1.389 1.389 1.301 0 0 0.0577 0.06309 0.1672 0 + 1 snp1 1.187 1.187 1.155 0 0 0.01536 0.01887 0.09243 0 + 1 snp5 1.001 1.001 1.046 0 0 0.00228 0.003475 0.09243 0 + 1 snp15 0.9147 0.9147 0.9586 0 0 0.0006612 0.001266 0.09243 0 + 1 snp33 0.8308 0.8308 0.8861 0 0 0.0001477 0.0003853 0.09243 0 + 1 snp36 0.8291 0.8291 0.8239 0 0 0.0001428 0.0003853 0.09243 0 + 1 snp21 0.7487 0.7487 0.7696 0 0 2.357e-05 0.0001135 0.09243 0 + 1 snp18 0.7485 0.7485 0.7212 0 0 2.34e-05 0.0001135 0.09243 0 + 1 snp23 0.6721 0.6721 0.6778 0 0 2.771e-06 3.032e-05 0.09243 0 + 1 snp12 0.6004 0.6004 0.6383 0 0 2.311e-07 5.548e-06 0.09243 0 + 1 snp41 0.5995 0.5995 0.6021 0 0 2.225e-07 5.548e-06 0.09243 0 + 1 snp17 0.5319 0.5319 0.5686 0 0 1.212e-08 1.116e-06 0.09243 0 + 1 snp2 0.5299 0.5299 0.5376 0 0 1.098e-08 1.116e-06 0.09243 0 + 1 snp35 0.5296 0.5296 0.5086 0 0 1.082e-08 1.116e-06 0.09243 0 + 1 snp28 0.4689 0.4689 0.4815 0 0 4.225e-10 3.233e-07 0.09243 0 + 1 snp38 0.465 0.465 0.4559 0 0 3.334e-10 3.233e-07 0.09243 0 + 1 snp43 0.4644 0.4644 0.4318 0 0 3.228e-10 3.233e-07 0.09243 0 + 1 snp8 0.4641 0.4641 0.4089 0 0 3.171e-10 3.233e-07 0.09243 0 + 1 snp9 0.4031 0.4031 0.3872 0 0 5.202e-12 1.216e-07 0.09243 0 + 1 snp19 0.4016 0.4016 0.3665 0 0 4.628e-12 1.216e-07 0.09243 0 + 1 snp44 0.4015 0.4015 0.3468 0 0 4.604e-12 1.216e-07 0.09243 0 + 1 snp31 0.4011 0.4011 0.3279 0 0 4.473e-12 1.216e-07 0.09243 0 + 1 snp29 0.343 0.343 0.3098 0 0 3.158e-14 6.397e-08 0.09243 0 + 1 snp30 0.3422 0.3422 0.2924 0 0 2.917e-14 6.397e-08 0.09243 0 + 1 snp42 0.3422 0.3422 0.2757 0 0 2.917e-14 6.397e-08 0.09243 0 + 1 snp49 0.3422 0.3422 0.2596 0 0 2.917e-14 6.397e-08 0.09243 0 + 1 snp34 0.2867 0.2867 0.2441 0 0 4.822e-17 4.889e-08 0.09243 0 + 1 snp37 0.2866 0.2866 0.2291 0 0 4.822e-17 4.889e-08 0.09243 0 + 1 snp40 0.2864 0.2864 0.2147 0 0 4.822e-17 4.889e-08 0.09243 0 + 1 snp20 0.2862 0.2862 0.2007 0 0 4.822e-17 4.889e-08 0.09243 0 + 1 snp48 0.234 0.234 0.1871 0 0 0 4.889e-08 0.07281 0 + 1 snp14 0.2338 0.2338 0.1739 0 0 0 4.889e-08 0.07281 0 + 1 snp0 0.185 0.185 0.1612 0 0 0 1.905e-08 0.07281 0 + 1 snp11 0.1848 0.1848 0.1487 0 0 0 1.905e-08 0.07281 0 + 1 snp7 0.1845 0.1845 0.1367 0 0 0 1.905e-08 0.07281 0 + 1 snp26 0.1845 0.1845 0.1249 0 0 0 1.905e-08 0.07281 0 + 1 snp32 0.1386 0.1386 0.1135 0 0 0 1.905e-08 0.07281 0 + 1 snp16 0.1386 0.1386 0.1024 0 0 0 1.905e-08 0.07281 0 + 1 snp25 0.1384 0.1384 0.09151 0 0 0 1.905e-08 0.07281 0 + 1 snp39 0.1384 0.1384 0.08092 0 0 0 1.905e-08 0.07281 0 + 1 snp46 0.1383 0.1383 0.07058 0 0 0 1.905e-08 0.07281 0 + 1 snp47 0.09563 0.09563 0.06048 0 0 0 1.905e-08 0.06819 0 + 1 snp3 0.09519 0.09519 0.05061 0 0 0 1.905e-08 0.06819 0 + 1 snp27 0.09519 0.09519 0.04096 0 0 0 1.905e-08 0.06819 0 + 1 snp4 0.09506 0.09506 0.03152 0 0 0 1.905e-08 0.06819 0 + 1 snp24 0.05503 0.05503 0.02228 0 0 0 1.905e-08 0.03731 0 + 1 snp6 0.01765 0.01765 0.01323 0 0 0 1.905e-08 0.01759 0 + 1 snp10 0.01759 0.01759 0.004365 0 0 0 1.905e-08 0.01759 0
--- a/test-data/out.assoc.fisher.mperm Mon Oct 05 16:08:24 2020 +0000 +++ b/test-data/out.assoc.fisher.mperm Thu Dec 02 16:20:30 2021 +0000 @@ -1,51 +1,51 @@ CHR SNP EMP1 EMP2 - 1 snp0 0.6485 1 - 1 snp1 0.06724 0.9756 - 1 snp2 0.2894 1 - 1 snp3 0.8024 1 - 1 snp4 0.8102 1 - 1 snp5 0.08614 0.9971 + 1 snp0 0.6431 1 + 1 snp1 0.06719 0.9733 + 1 snp2 0.2927 1 + 1 snp3 0.8004 1 + 1 snp4 0.8184 1 + 1 snp5 0.08444 0.9968 1 snp6 0.9608 1 - 1 snp7 0.6315 1 - 1 snp8 0.3596 1 - 1 snp9 0.3878 1 - 1 snp10 0.9566 1 - 1 snp11 0.6523 1 - 1 snp12 0.2271 1 - 1 snp13 0.02575 0.7544 - 1 snp14 0.5918 1 - 1 snp15 0.1154 0.9996 - 1 snp16 0.7294 1 - 1 snp17 0.259 1 - 1 snp18 0.1944 1 - 1 snp19 0.3917 1 - 1 snp20 0.5198 1 - 1 snp21 0.1603 1 - 1 snp22 0.03675 0.8985 - 1 snp23 0.2278 1 - 1 snp24 0.8825 1 - 1 snp25 0.7269 1 - 1 snp26 0.6533 1 - 1 snp27 0.8142 1 - 1 snp28 0.3383 1 - 1 snp29 0.4681 1 - 1 snp30 0.458 1 - 1 snp31 0.3922 1 - 1 snp32 0.7283 1 - 1 snp33 0.1654 0.9999 - 1 snp34 0.5148 1 - 1 snp35 0.2918 1 - 1 snp36 0.165 0.9999 - 1 snp37 0.5271 1 - 1 snp38 0.3427 1 - 1 snp39 0.7368 1 - 1 snp40 0.5179 1 - 1 snp41 0.234 1 - 1 snp42 0.4554 1 - 1 snp43 0.3474 1 - 1 snp44 0.4033 1 - 1 snp45 0.02845 0.8325 - 1 snp46 0.7231 1 - 1 snp47 0.7953 1 - 1 snp48 0.5771 1 - 1 snp49 0.4793 1 + 1 snp7 0.6308 1 + 1 snp8 0.3555 1 + 1 snp9 0.3804 1 + 1 snp10 0.9594 1 + 1 snp11 0.6511 1 + 1 snp12 0.2293 1 + 1 snp13 0.02615 0.7451 + 1 snp14 0.5884 1 + 1 snp15 0.1049 0.9996 + 1 snp16 0.729 1 + 1 snp17 0.2644 1 + 1 snp18 0.2046 1 + 1 snp19 0.3887 1 + 1 snp20 0.5381 1 + 1 snp21 0.1646 1 + 1 snp22 0.03845 0.8917 + 1 snp23 0.223 1 + 1 snp24 0.8793 1 + 1 snp25 0.7204 1 + 1 snp26 0.6577 1 + 1 snp27 0.8136 1 + 1 snp28 0.3462 1 + 1 snp29 0.4803 1 + 1 snp30 0.4637 1 + 1 snp31 0.402 1 + 1 snp32 0.7339 1 + 1 snp33 0.1639 0.9999 + 1 snp34 0.5064 1 + 1 snp35 0.2797 1 + 1 snp36 0.1683 0.9999 + 1 snp37 0.5299 1 + 1 snp38 0.3401 1 + 1 snp39 0.7348 1 + 1 snp40 0.5115 1 + 1 snp41 0.2287 1 + 1 snp42 0.4542 1 + 1 snp43 0.3372 1 + 1 snp44 0.3965 1 + 1 snp45 0.029 0.8276 + 1 snp46 0.7211 1 + 1 snp47 0.8059 1 + 1 snp48 0.5881 1 + 1 snp49 0.4842 1
--- a/test-data/out.assoc.logistic.adjusted Mon Oct 05 16:08:24 2020 +0000 +++ b/test-data/out.assoc.logistic.adjusted Thu Dec 02 16:20:30 2021 +0000 @@ -1,51 +1,51 @@ CHR SNP UNADJ GC QQ BONF HOLM SIDAK_SS SIDAK_SD FDR_BH FDR_BY - 1 snp13 1.206 1.206 2 0 0 0.01789 0.01789 0.07645 0 - 1 snp45 1.102 1.102 1.523 0 0 0.00711 0.007727 0.07645 0 - 1 snp17 0.9342 0.9342 1.301 0 0 0.0008958 0.001148 0.07645 0 - 1 snp22 0.8183 0.8183 1.155 0 0 0.0001145 0.0001877 0.07645 0 - 1 snp20 0.8014 0.8014 1.046 0 0 8.017e-05 0.0001595 0.07645 0 - 1 snp44 0.8006 0.8006 0.9586 0 0 7.882e-05 0.0001595 0.07645 0 - 1 snp36 0.7579 0.7579 0.8861 0 0 2.957e-05 9.353e-05 0.07645 0 - 1 snp31 0.6928 0.6928 0.8239 0 0 5.183e-06 2.534e-05 0.07645 0 - 1 snp15 0.6903 0.6903 0.7696 0 0 4.808e-06 2.534e-05 0.07645 0 - 1 snp48 0.6789 0.6789 0.7212 0 0 3.424e-06 2.534e-05 0.07645 0 - 1 snp33 0.6431 0.6431 0.6778 0 0 1.081e-06 1.427e-05 0.07645 0 - 1 snp21 0.603 0.603 0.6383 0 0 2.545e-07 5.98e-06 0.07645 0 - 1 snp12 0.5857 0.5857 0.6021 0 0 1.294e-07 4.766e-06 0.07645 0 - 1 snp1 0.5664 0.5664 0.5686 0 0 5.787e-08 3.548e-06 0.07645 0 - 1 snp38 0.556 0.556 0.5376 0 0 3.669e-08 3.508e-06 0.07645 0 - 1 snp5 0.4872 0.4872 0.5086 0 0 1.204e-09 4.444e-07 0.07645 0 - 1 snp3 0.481 0.481 0.4815 0 0 8.504e-10 4.444e-07 0.07645 0 - 1 snp8 0.4704 0.4704 0.4559 0 0 4.595e-10 4.444e-07 0.07645 0 - 1 snp32 0.4704 0.4704 0.4318 0 0 4.595e-10 4.444e-07 0.07645 0 - 1 snp18 0.4704 0.4704 0.4089 0 0 4.595e-10 4.444e-07 0.07645 0 - 1 snp40 0.3898 0.3898 0.3872 0 0 1.868e-12 6.575e-08 0.07645 0 - 1 snp2 0.384 0.384 0.3665 0 0 1.173e-12 6.575e-08 0.07645 0 - 1 snp4 0.3765 0.3765 0.3468 0 0 6.289e-13 6.575e-08 0.07645 0 - 1 snp35 0.3083 0.3083 0.3279 0 0 8.679e-16 5.034e-09 0.07645 0 - 1 snp26 0.3015 0.3015 0.3098 0 0 3.857e-16 5.034e-09 0.07645 0 - 1 snp42 0.3015 0.3015 0.2924 0 0 3.857e-16 5.034e-09 0.07645 0 - 1 snp43 0.2988 0.2988 0.2757 0 0 2.893e-16 5.034e-09 0.07645 0 - 1 snp0 0.2988 0.2988 0.2596 0 0 2.893e-16 5.034e-09 0.07645 0 - 1 snp14 0.2953 0.2953 0.2441 0 0 1.929e-16 5.034e-09 0.07645 0 - 1 snp28 0.2888 0.2888 0.2291 0 0 9.643e-17 5.034e-09 0.07645 0 - 1 snp39 0.2841 0.2841 0.2147 0 0 4.822e-17 5.034e-09 0.07645 0 - 1 snp6 0.23 0.23 0.2007 0 0 0 5.034e-09 0.06545 0 - 1 snp46 0.2257 0.2257 0.1871 0 0 0 5.034e-09 0.06545 0 - 1 snp25 0.2219 0.2219 0.1739 0 0 0 5.034e-09 0.06545 0 - 1 snp37 0.2203 0.2203 0.1612 0 0 0 5.034e-09 0.06545 0 - 1 snp41 0.1538 0.1538 0.1487 0 0 0 5.034e-09 0.04969 0 - 1 snp34 0.1503 0.1503 0.1367 0 0 0 5.034e-09 0.04969 0 - 1 snp19 0.1501 0.1501 0.1249 0 0 0 5.034e-09 0.04969 0 - 1 snp27 0.1497 0.1497 0.1135 0 0 0 5.034e-09 0.04969 0 - 1 snp30 0.1466 0.1466 0.1024 0 0 0 5.034e-09 0.04969 0 - 1 snp10 0.08608 0.08608 0.09151 0 0 0 5.034e-09 0.03893 0 - 1 snp24 0.08365 0.08365 0.08092 0 0 0 5.034e-09 0.03893 0 - 1 snp23 0.08136 0.08136 0.07058 0 0 0 5.034e-09 0.03893 0 - 1 snp16 0.07918 0.07918 0.06048 0 0 0 5.034e-09 0.03893 0 - 1 snp49 0.07711 0.07711 0.05061 0 0 0 5.034e-09 0.03893 0 - 1 snp29 0.07514 0.07514 0.04096 0 0 0 5.034e-09 0.03893 0 - 1 snp47 0.0308 0.0308 0.03152 0 0 0 5.034e-09 0.02352 0 - 1 snp7 0.02483 0.02483 0.02228 0 0 0 5.034e-09 0.02352 0 - 1 snp9 0.02352 0.02352 0.01323 0 0 0 5.034e-09 0.02352 0 - 1 snp11 0.02352 0.02352 0.004365 0 0 0 5.034e-09 0.02352 0 + 1 snp13 1.352 1.352 2 0 0 0.04718 0.04718 0.1215 0 + 1 snp45 1.233 1.233 1.523 0 0 0.02192 0.02332 0.1215 0 + 1 snp17 1.043 1.043 1.301 0 0 0.003779 0.004573 0.1215 0 + 1 snp22 0.9115 0.9115 1.155 0 0 0.0006276 0.0009296 0.1215 0 + 1 snp20 0.8924 0.8924 1.046 0 0 0.000458 0.0007929 0.1215 0 + 1 snp44 0.8915 0.8915 0.9586 0 0 0.0004512 0.0007929 0.1215 0 + 1 snp36 0.8432 0.8432 0.8861 0 0 0.0001884 0.0004772 0.1215 0 + 1 snp31 0.7697 0.7697 0.8239 0 0 3.917e-05 0.0001443 0.1215 0 + 1 snp15 0.7668 0.7668 0.7696 0 0 3.658e-05 0.0001443 0.1215 0 + 1 snp48 0.754 0.754 0.7212 0 0 2.686e-05 0.0001443 0.1215 0 + 1 snp33 0.7136 0.7136 0.6778 0 0 9.36e-06 8.028e-05 0.1215 0 + 1 snp21 0.6684 0.6684 0.6383 0 0 2.469e-06 3.519e-05 0.1215 0 + 1 snp12 0.649 0.649 0.6021 0 0 1.319e-06 2.783e-05 0.1215 0 + 1 snp1 0.6273 0.6273 0.5686 0 0 6.239e-07 2.062e-05 0.1215 0 + 1 snp38 0.6155 0.6155 0.5376 0 0 4.079e-07 1.987e-05 0.1215 0 + 1 snp5 0.5383 0.5383 0.5086 0 0 1.641e-08 2.766e-06 0.1215 0 + 1 snp3 0.5314 0.5314 0.4815 0 0 1.181e-08 2.766e-06 0.1215 0 + 1 snp8 0.5194 0.5194 0.4559 0 0 6.587e-09 2.766e-06 0.1215 0 + 1 snp32 0.5194 0.5194 0.4318 0 0 6.587e-09 2.766e-06 0.1215 0 + 1 snp18 0.5194 0.5194 0.4089 0 0 6.587e-09 2.766e-06 0.1215 0 + 1 snp40 0.4294 0.4294 0.3872 0 0 3.412e-11 3.758e-07 0.1039 0 + 1 snp2 0.4229 0.4229 0.3665 0 0 2.18e-11 3.758e-07 0.1039 0 + 1 snp4 0.4144 0.4144 0.3468 0 0 1.196e-11 3.758e-07 0.1039 0 + 1 snp35 0.3384 0.3384 0.3279 0 0 2.035e-14 2.753e-08 0.1039 0 + 1 snp26 0.3309 0.3309 0.3098 0 0 9.595e-15 2.753e-08 0.1039 0 + 1 snp42 0.3309 0.3309 0.2924 0 0 9.595e-15 2.753e-08 0.1039 0 + 1 snp43 0.3279 0.3279 0.2757 0 0 7.088e-15 2.753e-08 0.1039 0 + 1 snp0 0.3279 0.3279 0.2596 0 0 7.088e-15 2.753e-08 0.1039 0 + 1 snp14 0.324 0.324 0.2441 0 0 4.725e-15 2.753e-08 0.1039 0 + 1 snp28 0.3169 0.3169 0.2291 0 0 2.218e-15 2.753e-08 0.1039 0 + 1 snp39 0.3115 0.3115 0.2147 0 0 1.254e-15 2.753e-08 0.1039 0 + 1 snp6 0.2516 0.2516 0.2007 0 0 0 2.753e-08 0.08605 0 + 1 snp46 0.2469 0.2469 0.1871 0 0 0 2.753e-08 0.08605 0 + 1 snp25 0.2427 0.2427 0.1739 0 0 0 2.753e-08 0.08605 0 + 1 snp37 0.241 0.241 0.1612 0 0 0 2.753e-08 0.08605 0 + 1 snp41 0.1675 0.1675 0.1487 0 0 0 1.646e-08 0.06276 0 + 1 snp34 0.1638 0.1638 0.1367 0 0 0 1.646e-08 0.06276 0 + 1 snp19 0.1635 0.1635 0.1249 0 0 0 1.646e-08 0.06276 0 + 1 snp27 0.1631 0.1631 0.1135 0 0 0 1.646e-08 0.06276 0 + 1 snp30 0.1597 0.1597 0.1024 0 0 0 1.646e-08 0.06276 0 + 1 snp10 0.09339 0.09339 0.09151 0 0 0 1.646e-08 0.04525 0 + 1 snp24 0.09075 0.09075 0.08092 0 0 0 1.646e-08 0.04525 0 + 1 snp23 0.08824 0.08824 0.07058 0 0 0 1.646e-08 0.04525 0 + 1 snp16 0.08587 0.08587 0.06048 0 0 0 1.646e-08 0.04525 0 + 1 snp49 0.08361 0.08361 0.05061 0 0 0 1.646e-08 0.04525 0 + 1 snp29 0.08146 0.08146 0.04096 0 0 0 1.646e-08 0.04525 0 + 1 snp47 0.03328 0.03328 0.03152 0 0 0 1.646e-08 0.0254 0 + 1 snp7 0.02681 0.02681 0.02228 0 0 0 1.646e-08 0.0254 0 + 1 snp9 0.0254 0.0254 0.01323 0 0 0 1.646e-08 0.0254 0 + 1 snp11 0.0254 0.0254 0.004365 0 0 0 1.646e-08 0.0254 0