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"bcftools_annotateCommand": "annotate -a /mnt/storage/home/gh13047/mr-eve/vcf-reference-datasets/dbsnp/dbsnp.v153.b37.vcf.gz -c ID -o /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ukb-d-import/processed/ukb-d-M13_DORSALGIA/ukb-d-M13_DORSALGIA.vcf.gz -O z /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ukb-d-import/processed/ukb-d-M13_DORSALGIA/ukb-d-M13_DORSALGIA_data.vcf.gz; Date=Mon Nov 25 14:04:28 2019",
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}
*********************************************************************
* LD Score Regression (LDSC)
* Version 1.0.1
* (C) 2014-2019 Brendan Bulik-Sullivan and Hilary Finucane
* Broad Institute of MIT and Harvard / MIT Department of Mathematics
* GNU General Public License v3
*********************************************************************
Call:
./ldsc.py \
--h2 /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ukb-d-import/processed/ukb-d-M13_DORSALGIA/ukb-d-M13_DORSALGIA.vcf.gz \
--ref-ld-chr /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/reference/eur_w_ld_chr/ \
--out /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ukb-d-import/processed/ukb-d-M13_DORSALGIA/ldsc.txt \
--w-ld-chr /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/reference/eur_w_ld_chr/
Beginning analysis at Mon Nov 25 14:52:16 2019
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ukb-d-import/processed/ukb-d-M13_DORSALGIA/ukb-d-M13_DORSALGIA.vcf.gz ...
Read summary statistics for 13041944 SNPs.
Dropped 11939 SNPs with duplicated rs numbers.
Reading reference panel LD Score from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/reference/eur_w_ld_chr/[1-22] ...
Read reference panel LD Scores for 1290028 SNPs.
Removing partitioned LD Scores with zero variance.
Reading regression weight LD Score from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/reference/eur_w_ld_chr/[1-22] ...
Read regression weight LD Scores for 1290028 SNPs.
After merging with reference panel LD, 1283387 SNPs remain.
After merging with regression SNP LD, 1283387 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.0136 (0.0015)
Lambda GC: 1.0872
Mean Chi^2: 1.0975
Intercept: 0.9995 (0.0066)
Ratio < 0 (usually indicates GC correction).
Analysis finished at Mon Nov 25 14:54:17 2019
Total time elapsed: 2.0m:0.74s
{
"af_correlation": 0.9512,
"inflation_factor": 1.0576,
"mean_EFFECT": 1.9339e-06,
"n": 361194,
"n_snps": 13041944,
"n_clumped_hits": 1,
"n_p_sig": 27,
"n_mono": 0,
"n_ns": 1230724,
"n_mac": 0,
"is_snpid_unique": false,
"n_miss_EFFECT": 0,
"n_miss_SE": 0,
"n_miss_PVAL": 0,
"n_miss_AF": 0,
"n_miss_AF_reference": 440053,
"n_est": 362572.891,
"ratio_se_n": 1.0019,
"mean_diff": 9.9034e-06,
"ratio_diff": 15.3778,
"sd_y_est1": 0.1547,
"sd_y_est2": 0.1549,
"r2_sum1": 2.3131e-06,
"r2_sum2": 0.0001,
"r2_sum3": 0.0001,
"r2_sum4": 0.0001,
"ldsc_nsnp_merge_refpanel_ld": 1283387,
"ldsc_nsnp_merge_regression_ld": 1283387,
"ldsc_observed_scale_h2_beta": 0.0136,
"ldsc_observed_scale_h2_se": 0.0015,
"ldsc_intercept_beta": 0.9995,
"ldsc_intercept_se": 0.0066,
"ldsc_lambda_gc": 1.0872,
"ldsc_mean_chisq": 1.0975,
"ldsc_ratio": -0.0051
}
name | value |
---|---|
af_correlation | FALSE |
inflation_factor | FALSE |
n | FALSE |
is_snpid_non_unique | TRUE |
mean_EFFECT_nonfinite | FALSE |
mean_EFFECT_05 | FALSE |
mean_EFFECT_01 | FALSE |
mean_chisq | FALSE |
n_p_sig | FALSE |
miss_EFFECT | FALSE |
miss_SE | FALSE |
miss_PVAL | FALSE |
ldsc_ratio | FALSE |
ldsc_intercept_beta | FALSE |
n_clumped_hits | FALSE |
r2_sum1 | FALSE |
r2_sum2 | FALSE |
r2_sum3 | FALSE |
r2_sum4 | FALSE |
General metrics
af_correlation
: Correlation coefficient between AF
and AF_reference
.inflation_factor
(lambda
): Genomic inflation factor.mean_EFFECT
: Mean of EFFECT
size.n
: Maximum value of reported sample size across all SNPs, \(n\).n_clumped_hits
: Number of clumped hits.n_snps
: Number of SNPsn_p_sig
: Number of SNPs with pvalue below 5e-8
.n_mono
: Number of monomorphic (MAF == 1
or MAF == 0
) SNPs.n_ns
: Number of SNPs with nonsense values:
A, C, G or T
.< 0
or > 1
.<= 0
or = Infinity
).< 0
or > 1
.n_mac
: Number of cases where MAC
(\(2 \times N \times MAF\)) is less than 6
.is_snpid_unique
: true
if the combination of ID
REF
ALT
is unique and therefore no duplication in snpid.n_miss_<*>
: Number of NA
observations for <*>
column.se_n metrics
n_est
: Estimated sample size value, \(\widehat{n}\).ratio_se_n
: \(\texttt{ratio_se_n} = \frac{\sqrt{\widehat{n}}}{\sqrt{n}}\). We expect ratio_se_n
to be 1. When it is not 1, it implies that the trait did not have a variance of 1, the reported sample size is wrong, or that the SNP-level effective sample sizes differ markedly from the reported sample size.mean_diff
: \(\texttt{mean_diff} = \sum_{j} \frac{\widehat{\beta_j^{std}} - \beta_j}{\texttt{n_snps}}\), mean difference between the standardised beta, predicted from P-values, and the observed beta. The difference should be very close to zero if trait has a variance of 1.
ratio_diff
: \(\texttt{ratio_diff} = |\frac{\texttt{mean_diff}}{\texttt{mean_diff2}}|\), absolute ratio between the mean of diff
and the mean of diff2
(expected difference between the standardised beta predicted from P-values, and the standardised beta derived from the observed beta divided by the predicted SD; NOT reported). The ratio should be close to 1. If different from 1, then implies that the betas are not in a standard deviation scale.
sd_y_est1
: The standard deviation for the trait inferred from the reported sample size, median standard errors for the SNP-trait assocations and SNP variances.
sd_y_est2
: The standard deviation for the trait inferred from the reported sample size, Z statistics for the SNP-trait effects (beta/se) and allele frequency.
r2 metrics
Sum of variance explained, calculated from the clumped top hits sample.
r2_sum<*>
: r2
statistics under various assumptions
1
: \(r^2 = \sum_j{\frac{2 \times \beta_j^2 \times {MAF}_j \times (1 - {MAF}_j)}{\texttt{var1}}}\), \(\texttt{var1} = 1\).2
: \(r^2 = \sum_j{\frac{2 \times \beta_j^2 \times {MAF}_j \times (1 - {MAF}_j)}{\texttt{var2}}}\), \(\texttt{var2} = {\widehat{\texttt{sd1}}_{y}}^2\),3
: \(r^2 = \sum_j{\frac{2 \times \beta_j^2 \times {MAF}_j \times (1 - {MAF}_j)}{\texttt{var3}}}\), \(\texttt{var3} = {\widehat{\texttt{sd2}}_{y}}^2\),4
: \(r^2 = \sum_j{\frac{F_j}{F_j + n - 2}}\), \(F = \frac{\beta_j^2}{{se}_j^2}\).LDSC metrics
Metrics from LD regression
ldsc_nsnp_merge_refpanel_ld
: Number of remaining SNPs after merging with reference panel LD.ldsc_nsnp_merge_regression_ld
: Number of remaining SNPs after merging with regression SNP LD.ldsc_observed_scale_h2_{beta,se}
Coefficient value and SE for total observed scale h2.ldsc_intercept_{beta,se}
: Coefficient value and SE for intercept. Intercept is expected to be 1.ldsc_lambda_gc
: Lambda GC statistics.ldsc_mean_chisq
: Mean \(\chi^2\) statistics.ldsc_ratio
: \(\frac{\texttt{ldsc_intercept_beta} - 1}{\texttt{ldsc_mean_chisq} - 1}\), the proportion of the inflation in the mean \(\chi^2\) that the LD Score regression intercepts ascribes to causes other than polygenic heritability. The value of ratio should be close to zero, though in practice values of 0.1-0.2 are not uncommon, probably due to sample/reference LD Score mismatch or model misspecification (e.g., low LD variants have slightly higher \(h^2\) per SNP).Flags
When a metric needs attention, the flag should return TRUE.
af_correlation
: abs(af_correlation)
< 0.7.inflation_factor
: inflation_factor
> 1.2.n
: n
(max reported sample size) < 10000.is_snpid_non_unique
: NOT is_snpid_unique
.mean_EFFECT_nonfinite
: mean(EFFECT)
is NA
, NaN
, or Inf
.mean_EFFECT_05
: abs(mean(EFFECT))
> 0.5.mean_EFFECT_01
: abs(mean(EFFECT))
> 0.1.mean_chisq
: ldsc_mean_chisq
> 1.3 or ldsc_mean_chisq
< 0.7.n_p_sig
: n_p_sig
> 1000.miss_<*>
: n_miss_<*>
/ n_snps
> 0.01.ldsc_ratio
: ldsc_ratio
> 0.5ldsc_intercept_beta
: ldsc_intercept_beta
> 1.5n_clumped_hits
: n_clumped_hits
> 1000r2_sum<*>
: r2_sum<*>
> 0.5Plots
skim_type | skim_variable | n_missing | complete_rate | character.min | character.max | character.empty | character.n_unique | character.whitespace | numeric.mean | numeric.sd | numeric.p0 | numeric.p25 | numeric.p50 | numeric.p75 | numeric.p100 | numeric.hist |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
character | ID | 0 | 1.0000000 | 3 | 94 | 0 | 13030660 | 0 | NA | NA | NA | NA | NA | NA | NA | NA |
character | REF | 0 | 1.0000000 | 1 | 100 | 0 | 55903 | 0 | NA | NA | NA | NA | NA | NA | NA | NA |
character | ALT | 0 | 1.0000000 | 1 | 342 | 0 | 32988 | 0 | NA | NA | NA | NA | NA | NA | NA | NA |
numeric | CHROM | 0 | 1.0000000 | NA | NA | NA | NA | NA | 9.057880e+00 | 6.185700e+00 | 1.00000e+00 | 4.000000e+00 | 8.000000e+00 | 1.300000e+01 | 2.300000e+01 | ▇▅▅▂▂ |
numeric | POS | 0 | 1.0000000 | NA | NA | NA | NA | NA | 7.898181e+07 | 5.593612e+07 | 3.02000e+02 | 3.284806e+07 | 7.006148e+07 | 1.148167e+08 | 2.492309e+08 | ▇▆▅▂▁ |
numeric | EFFECT | 0 | 1.0000000 | NA | NA | NA | NA | NA | 1.900000e-06 | 1.867000e-03 | -2.26580e-02 | -5.563000e-04 | -2.400000e-06 | 5.461000e-04 | 2.595020e-02 | ▁▁▇▁▁ |
numeric | SE | 0 | 1.0000000 | NA | NA | NA | NA | NA | 1.363900e-03 | 1.255600e-03 | 2.99400e-04 | 4.294000e-04 | 7.499000e-04 | 1.936600e-03 | 6.960900e-03 | ▇▂▁▁▁ |
numeric | PVAL | 0 | 1.0000000 | NA | NA | NA | NA | NA | 4.909332e-01 | 2.912981e-01 | 0.00000e+00 | 2.359462e-01 | 4.879069e-01 | 7.432809e-01 | 1.000000e+00 | ▇▇▇▇▇ |
numeric | PVAL_ztest | 0 | 1.0000000 | NA | NA | NA | NA | NA | 4.909328e-01 | 2.912983e-01 | 0.00000e+00 | 2.359450e-01 | 4.879062e-01 | 7.432805e-01 | 9.999998e-01 | ▇▇▇▇▇ |
numeric | AF | 0 | 1.0000000 | NA | NA | NA | NA | NA | 1.983322e-01 | 2.561765e-01 | 1.42060e-03 | 9.507600e-03 | 6.975940e-02 | 3.102640e-01 | 9.985790e-01 | ▇▂▁▁▁ |
numeric | AF_reference | 440053 | 0.9662586 | NA | NA | NA | NA | NA | 2.020998e-01 | 2.483571e-01 | 0.00000e+00 | 6.988800e-03 | 9.225240e-02 | 3.189400e-01 | 1.000000e+00 | ▇▂▁▁▁ |
numeric | N | 0 | 1.0000000 | NA | NA | NA | NA | NA | 3.611940e+05 | 0.000000e+00 | 3.61194e+05 | 3.611940e+05 | 3.611940e+05 | 3.611940e+05 | 3.611940e+05 | ▁▁▇▁▁ |
CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
---|---|---|---|---|---|---|---|---|---|---|---|
1 | 692794 | rs530212009 | CA | C | -0.0002678 | 0.0006376 | 0.6744550 | 0.6744538 | 0.1106400 | 0.1894970 | 361194 |
1 | 693731 | rs12238997 | A | G | -0.0007476 | 0.0006025 | 0.2146560 | 0.2146555 | 0.1158300 | 0.1417730 | 361194 |
1 | 707522 | rs371890604 | G | C | -0.0009354 | 0.0006773 | 0.1672688 | 0.1672677 | 0.0973034 | 0.1293930 | 361194 |
1 | 717587 | rs144155419 | G | A | -0.0006608 | 0.0016162 | 0.6826294 | 0.6826294 | 0.0156880 | 0.0045926 | 361194 |
1 | 723329 | rs189787166 | A | T | 0.0014913 | 0.0047684 | 0.7544753 | 0.7544755 | 0.0017336 | 0.0003994 | 361194 |
1 | 730087 | rs148120343 | T | C | -0.0019480 | 0.0008393 | 0.0202918 | 0.0202908 | 0.0564602 | 0.0127796 | 361194 |
1 | 731718 | rs142557973 | T | C | -0.0006356 | 0.0005714 | 0.2659592 | 0.2659576 | 0.1217380 | 0.1543530 | 361194 |
1 | 732032 | rs61770163 | A | C | -0.0007012 | 0.0006095 | 0.2499413 | 0.2499400 | 0.1211710 | 0.1555510 | 361194 |
1 | 734349 | rs141242758 | T | C | -0.0006769 | 0.0005717 | 0.2364248 | 0.2364238 | 0.1209650 | 0.1525560 | 361194 |
1 | 740284 | rs61770167 | C | T | 0.0011401 | 0.0026155 | 0.6629137 | 0.6629146 | 0.0057851 | 0.0023962 | 361194 |
CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
---|---|---|---|---|---|---|---|---|---|---|---|
23 | 154923311 | rs141127553 | C | T | 0.0011699 | 0.0006601 | 0.0763519 | 0.0763514 | 0.0561667 | 0.0309934 | 361194 |
23 | 154923374 | rs111332691 | T | A | 0.0005844 | 0.0007255 | 0.4204768 | 0.4204763 | 0.0447862 | 0.0116556 | 361194 |
23 | 154925045 | rs509981 | C | T | 0.0003726 | 0.0003491 | 0.2858018 | 0.2858007 | 0.2456060 | 0.3634440 | 361194 |
23 | 154925895 | rs538470 | C | T | 0.0002913 | 0.0003571 | 0.4146513 | 0.4146495 | 0.2419150 | 0.3634440 | 361194 |
23 | 154927581 | rs644138 | G | A | 0.0006186 | 0.0003283 | 0.0594977 | 0.0594974 | 0.3021620 | 0.4635760 | 361194 |
23 | 154929412 | rs557132 | C | T | 0.0003639 | 0.0003492 | 0.2972727 | 0.2972718 | 0.2454590 | 0.3568210 | 361194 |
23 | 154929637 | rs35185538 | CT | C | 0.0006488 | 0.0003644 | 0.0749842 | 0.0749843 | 0.2296970 | 0.3011920 | 361194 |
23 | 154929952 | rs4012982 | CAA | C | 0.0004853 | 0.0003672 | 0.1863198 | 0.1863197 | 0.2394250 | 0.3165560 | 361194 |
23 | 154930230 | rs781880 | A | G | 0.0003770 | 0.0003491 | 0.2802199 | 0.2802187 | 0.2458690 | 0.3618540 | 361194 |
23 | 154930487 | rs781879 | T | A | 0.0008979 | 0.0011976 | 0.4533963 | 0.4533940 | 0.0195623 | 0.1263580 | 361194 |
1 692794 rs530212009 CA C . PASS AF=0.11064 ES:SE:LP:AF:SS:ID -0.000267823:0.000637608:0.171047:0.11064:361194:1_692794_CA_C
1 693731 rs12238997 A G . PASS AF=0.11583 ES:SE:LP:AF:SS:ID -0.000747573:0.000602461:0.668257:0.11583:361194:rs12238997
1 707522 rs371890604 G C . PASS AF=0.0973034 ES:SE:LP:AF:SS:ID -0.000935361:0.000677289:0.776585:0.0973034:361194:rs371890604
1 717587 rs144155419 G A . PASS AF=0.015688 ES:SE:LP:AF:SS:ID -0.000660824:0.00161619:0.165815:0.015688:361194:rs144155419
1 723329 rs189787166 A T . PASS AF=0.00173363 ES:SE:LP:AF:SS:ID 0.00149128:0.00476838:0.122355:0.00173363:361194:rs189787166
1 730087 rs148120343 T C . PASS AF=0.0564602 ES:SE:LP:AF:SS:ID -0.00194796:0.000839303:1.69268:0.0564602:361194:rs148120343
1 731718 rs58276399 T C . PASS AF=0.121738 ES:SE:LP:AF:SS:ID -0.000635609:0.000571375:0.575185:0.121738:361194:rs58276399
1 732032 rs61770163 A C . PASS AF=0.121171 ES:SE:LP:AF:SS:ID -0.000701206:0.000609482:0.602162:0.121171:361194:rs61770163
1 734349 rs141242758 T C . PASS AF=0.120965 ES:SE:LP:AF:SS:ID -0.000676856:0.000571682:0.626307:0.120965:361194:rs141242758
1 740284 rs61770167 C T . PASS AF=0.00578512 ES:SE:LP:AF:SS:ID 0.00114006:0.00261546:0.178543:0.00578512:361194:rs61770167
1 742813 rs112573343 C T . PASS AF=0.00187787 ES:SE:LP:AF:SS:ID -0.00553674:0.00493955:0.581149:0.00187787:361194:rs112573343
1 749963 rs529266287 T TAA . PASS AF=0.869742 ES:SE:LP:AF:SS:ID 0.000441341:0.000563589:0.362936:0.869742:361194:rs529266287
1 750230 rs190826124 G C . PASS AF=0.00153021 ES:SE:LP:AF:SS:ID -0.0062207:0.00510214:0.652169:0.00153021:361194:rs190826124
1 751343 rs28544273 T A . PASS AF=0.122916 ES:SE:LP:AF:SS:ID -0.00049389:0.000558161:0.424538:0.122916:361194:rs28544273
1 751488 rs200141114 G GA . PASS AF=0.142712 ES:SE:LP:AF:SS:ID -0.000141733:0.000551712:0.0984006:0.142712:361194:rs200141114
1 751756 rs28527770 T C . PASS AF=0.123031 ES:SE:LP:AF:SS:ID -0.000492912:0.000557384:0.424214:0.123031:361194:rs28527770
1 753405 rs3115860 C A . PASS AF=0.87089 ES:SE:LP:AF:SS:ID 0.000560465:0.000543152:0.519805:0.87089:361194:rs3115860
1 753425 rs3131970 T C . PASS AF=0.875472 ES:SE:LP:AF:SS:ID 0.000603125:0.000552152:0.561149:0.875472:361194:rs3131970
1 753541 rs2073813 G A . PASS AF=0.128631 ES:SE:LP:AF:SS:ID -0.000503329:0.000544514:0.449407:0.128631:361194:rs2073813
1 754105 rs12184325 C T . PASS AF=0.0363613 ES:SE:LP:AF:SS:ID -0.00148515:0.000987872:0.876998:0.0363613:361194:rs12184325
1 754182 rs3131969 A G . PASS AF=0.870484 ES:SE:LP:AF:SS:ID 0.000572855:0.000542587:0.536006:0.870484:361194:rs3131969
1 754192 rs3131968 A G . PASS AF=0.870589 ES:SE:LP:AF:SS:ID 0.000564755:0.000542835:0.525545:0.870589:361194:rs3131968
1 754334 rs3131967 T C . PASS AF=0.870481 ES:SE:LP:AF:SS:ID 0.000557923:0.000542567:0.517401:0.870481:361194:rs3131967
1 754433 rs150578204 G A . PASS AF=0.00504367 ES:SE:LP:AF:SS:ID 0.00105994:0.00278545:0.152703:0.00504367:361194:rs150578204
1 754458 rs142682604 G T . PASS AF=0.00501064 ES:SE:LP:AF:SS:ID 0.00110797:0.0027929:0.160156:0.00501064:361194:rs142682604
1 755435 rs184270342 T G . PASS AF=0.00558665 ES:SE:LP:AF:SS:ID -0.00348517:0.00269777:0.706854:0.00558665:361194:rs184270342
1 755890 rs3115858 A T . PASS AF=0.870563 ES:SE:LP:AF:SS:ID 0.000511717:0.000541612:0.462483:0.870563:361194:rs3115858
1 756434 rs61768170 G C . PASS AF=0.125985 ES:SE:LP:AF:SS:ID -0.000382347:0.000552643:0.310664:0.125985:361194:rs61768170
1 756604 rs3131962 A G . PASS AF=0.870127 ES:SE:LP:AF:SS:ID 0.00049624:0.000540309:0.445644:0.870127:361194:rs3131962
1 757640 rs3115853 G A . PASS AF=0.869414 ES:SE:LP:AF:SS:ID 0.000501589:0.000539816:0.452479:0.869414:361194:rs3115853
1 757734 rs4951929 C T . PASS AF=0.870281 ES:SE:LP:AF:SS:ID 0.000489183:0.000540774:0.4369:0.870281:361194:rs4951929
1 757936 rs4951862 C A . PASS AF=0.870287 ES:SE:LP:AF:SS:ID 0.000489751:0.000540812:0.43752:0.870287:361194:rs4951862
1 758144 rs3131956 A G . PASS AF=0.870295 ES:SE:LP:AF:SS:ID 0.000488151:0.000540829:0.435642:0.870295:361194:rs3131956
1 758626 rs3131954 C T . PASS AF=0.870739 ES:SE:LP:AF:SS:ID 0.000511623:0.000542206:0.461707:0.870739:361194:rs3131954
1 759293 rs10157329 T A . PASS AF=0.0988442 ES:SE:LP:AF:SS:ID -0.000707963:0.000630076:0.583065:0.0988442:361194:rs10157329
1 759600 rs545998451 AGT A . PASS AF=0.00647588 ES:SE:LP:AF:SS:ID -0.00299794:0.00243717:0.660225:0.00647588:361194:1_759600_AGT_A
1 759837 rs3115851 T A . PASS AF=0.874635 ES:SE:LP:AF:SS:ID 0.00056911:0.000550287:0.521374:0.874635:361194:rs3115851
1 761732 rs2286139 C T . PASS AF=0.864027 ES:SE:LP:AF:SS:ID 0.00062355:0.000539638:0.605746:0.864027:361194:rs2286139
1 761752 rs1057213 C T . PASS AF=0.869425 ES:SE:LP:AF:SS:ID 0.000491295:0.000544877:0.435054:0.869425:361194:rs1057213
1 762273 rs3115849 G A . PASS AF=0.866371 ES:SE:LP:AF:SS:ID 0.000584566:0.000544988:0.547537:0.866371:361194:rs3115849
1 762485 rs12095200 C A . PASS AF=0.0987831 ES:SE:LP:AF:SS:ID -0.000612941:0.000652452:0.45904:0.0987831:361194:rs12095200
1 762589 rs3115848 G C . PASS AF=0.871556 ES:SE:LP:AF:SS:ID 0.000625046:0.000551196:0.590398:0.871556:361194:rs3115848
1 762592 rs3131950 C G . PASS AF=0.871556 ES:SE:LP:AF:SS:ID 0.000625057:0.000551196:0.590413:0.871556:361194:rs3131950
1 762601 rs3131949 T C . PASS AF=0.871555 ES:SE:LP:AF:SS:ID 0.000624353:0.000551207:0.589493:0.871555:361194:rs3131949
1 762632 rs3131948 T A . PASS AF=0.871929 ES:SE:LP:AF:SS:ID 0.000591944:0.000551521:0.547999:0.871929:361194:rs3131948
1 764191 rs7515915 T G . PASS AF=0.125562 ES:SE:LP:AF:SS:ID -0.000469817:0.000551957:0.403769:0.125562:361194:rs7515915
1 766007 rs61768174 A C . PASS AF=0.105428 ES:SE:LP:AF:SS:ID -0.000289661:0.000600881:0.200823:0.105428:361194:rs61768174
1 766105 rs2519015 T A . PASS AF=0.855376 ES:SE:LP:AF:SS:ID 0.000344624:0.000539436:0.28157:0.855376:361194:rs2519015
1 767393 rs538667473 A C . PASS AF=0.00165444 ES:SE:LP:AF:SS:ID 0.00107198:0.00477863:0.084863:0.00165444:361194:rs538667473
1 768116 rs376645387 A AGTTTT . PASS AF=0.838358 ES:SE:LP:AF:SS:ID -7.4219e-06:0.000531442:0.00486651:0.838358:361194:rs376645387