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"gwas_harmonisation_command": "--json /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ukb-d-import/processed/ukb-d-20079_6/ukb-d-20079_6_data.json --ref /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/QC/genomes/b37/human_g1k_v37.fasta; 1.1.1",
"file_date": "2019-11-25T15:14:46.185206",
"bcftools_annotateVersion": "1.9-74-g6af271c+htslib-1.9-64-g226b4a8",
"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-20079_6/ukb-d-20079_6.vcf.gz -O z /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ukb-d-import/processed/ukb-d-20079_6/ukb-d-20079_6_data.vcf.gz; Date=Mon Nov 25 15:51:52 2019",
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"bcftools_viewCommand": "view -h /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/ukb-d-20079_6/ukb-d-20079_6.vcf.gz; Date=Sun May 10 14:58:01 2020"
}
*********************************************************************
* 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-20079_6/ukb-d-20079_6.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-20079_6/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 16:42:14 2019
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ukb-d-import/processed/ukb-d-20079_6/ukb-d-20079_6.vcf.gz ...
Read summary statistics for 13055795 SNPs.
Dropped 11961 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, 1283403 SNPs remain.
After merging with regression SNP LD, 1283403 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.0102 (0.0082)
Lambda GC: 1.0092
Mean Chi^2: 1.0007
Intercept: 0.9904 (0.0061)
Ratio < 0 (usually indicates GC correction).
Analysis finished at Mon Nov 25 16:44:51 2019
Total time elapsed: 2.0m:37.71s
{
"af_correlation": 0.9513,
"inflation_factor": 0.9996,
"mean_EFFECT": 0.0001,
"n": 51427,
"n_snps": 13055795,
"n_clumped_hits": 0,
"n_p_sig": 0,
"n_mono": 0,
"n_ns": 1231570,
"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": 441147,
"n_est": 51640.6139,
"ratio_se_n": 1.0021,
"mean_diff": 0.0001,
"ratio_diff": 39.9836,
"sd_y_est1": 0.3745,
"sd_y_est2": 0.3752,
"r2_sum1": 0,
"r2_sum2": 0,
"r2_sum3": 0,
"r2_sum4": 0,
"ldsc_nsnp_merge_refpanel_ld": 1283403,
"ldsc_nsnp_merge_regression_ld": 1283403,
"ldsc_observed_scale_h2_beta": 0.0102,
"ldsc_observed_scale_h2_se": 0.0082,
"ldsc_intercept_beta": 0.9904,
"ldsc_intercept_se": 0.0061,
"ldsc_lambda_gc": 1.0092,
"ldsc_mean_chisq": 1.0007,
"ldsc_ratio": -13.7143
}
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 | 13044488 | 0 | NA | NA | NA | NA | NA | NA | NA | NA |
character | REF | 0 | 1.0000000 | 1 | 100 | 0 | 55969 | 0 | NA | NA | NA | NA | NA | NA | NA | NA |
character | ALT | 0 | 1.0000000 | 1 | 342 | 0 | 33002 | 0 | NA | NA | NA | NA | NA | NA | NA | NA |
numeric | CHROM | 0 | 1.0000000 | NA | NA | NA | NA | NA | 9.057671e+00 | 6.185618e+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 | 7.898208e+07 | 5.593685e+07 | 3.02000e+02 | 3.284707e+07 | 7.005784e+07 | 1.148244e+08 | 2.492309e+08 | ▇▆▅▂▁ |
numeric | EFFECT | 0 | 1.0000000 | NA | NA | NA | NA | NA | 6.160000e-05 | 1.191280e-02 | -1.32985e-01 | -3.412100e-03 | 5.800000e-06 | 3.414900e-03 | 1.619610e-01 | ▁▁▇▁▁ |
numeric | SE | 0 | 1.0000000 | NA | NA | NA | NA | NA | 8.773100e-03 | 8.085100e-03 | 1.92220e-03 | 2.755600e-03 | 4.819700e-03 | 1.246070e-02 | 4.336630e-02 | ▇▂▁▁▁ |
numeric | PVAL | 0 | 1.0000000 | NA | NA | NA | NA | NA | 5.001533e-01 | 2.884517e-01 | 6.00000e-07 | 2.505601e-01 | 5.000944e-01 | 7.499374e-01 | 1.000000e+00 | ▇▇▇▇▇ |
numeric | PVAL_ztest | 0 | 1.0000000 | NA | NA | NA | NA | NA | 5.001502e-01 | 2.884536e-01 | 6.00000e-07 | 2.505542e-01 | 5.000906e-01 | 7.499357e-01 | 1.000000e+00 | ▇▇▇▇▇ |
numeric | AF | 0 | 1.0000000 | NA | NA | NA | NA | NA | 1.981591e-01 | 2.561495e-01 | 1.41340e-03 | 9.460700e-03 | 6.953970e-02 | 3.098780e-01 | 9.985860e-01 | ▇▂▁▁▁ |
numeric | AF_reference | 441147 | 0.9662106 | NA | NA | NA | NA | NA | 2.019641e-01 | 2.483240e-01 | 0.00000e+00 | 6.988800e-03 | 9.205270e-02 | 3.186900e-01 | 1.000000e+00 | ▇▂▁▁▁ |
numeric | N | 0 | 1.0000000 | NA | NA | NA | NA | NA | 5.142700e+04 | 0.000000e+00 | 5.14270e+04 | 5.142700e+04 | 5.142700e+04 | 5.142700e+04 | 5.142700e+04 | ▁▁▇▁▁ |
CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
---|---|---|---|---|---|---|---|---|---|---|---|
1 | 692794 | rs530212009 | CA | C | -0.0052662 | 0.0040649 | 0.1951390 | 0.1951330 | 0.1121000 | 0.1894970 | 51427 |
1 | 693731 | rs12238997 | A | G | -0.0050217 | 0.0038628 | 0.1935990 | 0.1935932 | 0.1168090 | 0.1417730 | 51427 |
1 | 707522 | rs371890604 | G | C | -0.0051320 | 0.0043324 | 0.2361919 | 0.2361869 | 0.0982930 | 0.1293930 | 51427 |
1 | 717587 | rs144155419 | G | A | -0.0091931 | 0.0104737 | 0.3800949 | 0.3800887 | 0.0154808 | 0.0045926 | 51427 |
1 | 723329 | rs189787166 | A | T | 0.0000017 | 0.0297680 | 0.9999540 | 0.9999536 | 0.0017973 | 0.0003994 | 51427 |
1 | 730087 | rs148120343 | T | C | -0.0035637 | 0.0053794 | 0.5076694 | 0.5076658 | 0.0570822 | 0.0127796 | 51427 |
1 | 731718 | rs142557973 | T | C | -0.0040778 | 0.0036708 | 0.2666257 | 0.2666194 | 0.1225210 | 0.1543530 | 51427 |
1 | 732032 | rs61770163 | A | C | -0.0046025 | 0.0039130 | 0.2395251 | 0.2395198 | 0.1216510 | 0.1555510 | 51427 |
1 | 734349 | rs141242758 | T | C | -0.0037995 | 0.0036728 | 0.3009013 | 0.3008975 | 0.1217650 | 0.1525560 | 51427 |
1 | 740284 | rs61770167 | C | T | 0.0096279 | 0.0160510 | 0.5486242 | 0.5486200 | 0.0062329 | 0.0023962 | 51427 |
CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
---|---|---|---|---|---|---|---|---|---|---|---|
23 | 154923311 | rs141127553 | C | T | 0.0071982 | 0.0043185 | 0.0955564 | 0.0955498 | 0.0542488 | 0.0309934 | 51427 |
23 | 154923374 | rs111332691 | T | A | 0.0039939 | 0.0046781 | 0.3932539 | 0.3932504 | 0.0445389 | 0.0116556 | 51427 |
23 | 154925045 | rs509981 | C | T | -0.0002947 | 0.0022489 | 0.8957411 | 0.8957402 | 0.2434190 | 0.3634440 | 51427 |
23 | 154925895 | rs538470 | C | T | -0.0000940 | 0.0022973 | 0.9673680 | 0.9673684 | 0.2401390 | 0.3634440 | 51427 |
23 | 154927581 | rs644138 | G | A | 0.0014972 | 0.0021154 | 0.4791042 | 0.4790994 | 0.2981050 | 0.4635760 | 51427 |
23 | 154929412 | rs557132 | C | T | -0.0003347 | 0.0022497 | 0.8817419 | 0.8817416 | 0.2432580 | 0.3568210 | 51427 |
23 | 154929637 | rs35185538 | CT | C | 0.0001873 | 0.0023441 | 0.9363120 | 0.9363116 | 0.2278210 | 0.3011920 | 51427 |
23 | 154929952 | rs4012982 | CAA | C | -0.0000352 | 0.0023670 | 0.9881440 | 0.9881441 | 0.2374290 | 0.3165560 | 51427 |
23 | 154930230 | rs781880 | A | G | -0.0000839 | 0.0022487 | 0.9702519 | 0.9702521 | 0.2438260 | 0.3618540 | 51427 |
23 | 154930487 | rs781879 | T | A | -0.0018318 | 0.0078195 | 0.8147840 | 0.8147834 | 0.0189843 | 0.1263580 | 51427 |
1 692794 rs530212009 CA C . PASS AF=0.1121 ES:SE:LP:AF:SS:ID -0.00526624:0.00406489:0.709656:0.1121:51427:1_692794_CA_C
1 693731 rs12238997 A G . PASS AF=0.116809 ES:SE:LP:AF:SS:ID -0.00502174:0.00386281:0.713097:0.116809:51427:rs12238997
1 707522 rs371890604 G C . PASS AF=0.098293 ES:SE:LP:AF:SS:ID -0.00513205:0.00433241:0.626735:0.098293:51427:rs371890604
1 717587 rs144155419 G A . PASS AF=0.0154808 ES:SE:LP:AF:SS:ID -0.00919311:0.0104737:0.420108:0.0154808:51427:rs144155419
1 723329 rs189787166 A T . PASS AF=0.00179726 ES:SE:LP:AF:SS:ID 1.72978e-06:0.029768:1.9978e-05:0.00179726:51427:rs189787166
1 730087 rs148120343 T C . PASS AF=0.0570822 ES:SE:LP:AF:SS:ID -0.00356374:0.00537942:0.294419:0.0570822:51427:rs148120343
1 731718 rs58276399 T C . PASS AF=0.122521 ES:SE:LP:AF:SS:ID -0.00407779:0.00367077:0.574098:0.122521:51427:rs58276399
1 732032 rs61770163 A C . PASS AF=0.121651 ES:SE:LP:AF:SS:ID -0.00460247:0.00391304:0.620649:0.121651:51427:rs61770163
1 734349 rs141242758 T C . PASS AF=0.121765 ES:SE:LP:AF:SS:ID -0.00379952:0.00367277:0.521576:0.121765:51427:rs141242758
1 740284 rs61770167 C T . PASS AF=0.0062329 ES:SE:LP:AF:SS:ID 0.00962786:0.016051:0.260725:0.0062329:51427:rs61770167
1 742813 rs112573343 C T . PASS AF=0.00176649 ES:SE:LP:AF:SS:ID -0.00395145:0.0333542:0.0430176:0.00176649:51427:rs112573343
1 749963 rs529266287 T TAA . PASS AF=0.868613 ES:SE:LP:AF:SS:ID 0.00308551:0.00361553:0.405124:0.868613:51427:rs529266287
1 750230 rs190826124 G C . PASS AF=0.00158492 ES:SE:LP:AF:SS:ID 0.0178538:0.0324412:0.235014:0.00158492:51427:rs190826124
1 751343 rs28544273 T A . PASS AF=0.123957 ES:SE:LP:AF:SS:ID -0.00364117:0.00358167:0.50956:0.123957:51427:rs28544273
1 751488 rs200141114 G GA . PASS AF=0.143385 ES:SE:LP:AF:SS:ID -0.00346172:0.00355357:0.481504:0.143385:51427:rs200141114
1 751756 rs28527770 T C . PASS AF=0.124126 ES:SE:LP:AF:SS:ID -0.00351385:0.00357573:0.4871:0.124126:51427:rs28527770
1 753405 rs3115860 C A . PASS AF=0.869933 ES:SE:LP:AF:SS:ID 0.00394662:0.00348487:0.589343:0.869933:51427:rs3115860
1 753425 rs3131970 T C . PASS AF=0.874426 ES:SE:LP:AF:SS:ID 0.00417846:0.00354027:0.623606:0.874426:51427:rs3131970
1 753541 rs2073813 G A . PASS AF=0.129659 ES:SE:LP:AF:SS:ID -0.00362709:0.00349347:0.524098:0.129659:51427:rs2073813
1 754105 rs12184325 C T . PASS AF=0.0369164 ES:SE:LP:AF:SS:ID 0.000950993:0.00629226:0.0555825:0.0369164:51427:rs12184325
1 754182 rs3131969 A G . PASS AF=0.869554 ES:SE:LP:AF:SS:ID 0.00401016:0.00348162:0.603095:0.869554:51427:rs3131969
1 754192 rs3131968 A G . PASS AF=0.869648 ES:SE:LP:AF:SS:ID 0.00388587:0.00348343:0.577363:0.869648:51427:rs3131968
1 754334 rs3131967 T C . PASS AF=0.86957 ES:SE:LP:AF:SS:ID 0.00407264:0.00348161:0.615998:0.86957:51427:rs3131967
1 754433 rs150578204 G A . PASS AF=0.00531261 ES:SE:LP:AF:SS:ID 0.0122305:0.0174501:0.315711:0.00531261:51427:rs150578204
1 754458 rs142682604 G T . PASS AF=0.00527727 ES:SE:LP:AF:SS:ID 0.0119873:0.017496:0.306929:0.00527727:51427:rs142682604
1 755435 rs184270342 T G . PASS AF=0.0057746 ES:SE:LP:AF:SS:ID 0.0257058:0.0170638:0.879568:0.0057746:51427:rs184270342
1 755890 rs3115858 A T . PASS AF=0.869706 ES:SE:LP:AF:SS:ID 0.00381416:0.00347637:0.564517:0.869706:51427:rs3115858
1 756434 rs61768170 G C . PASS AF=0.12702 ES:SE:LP:AF:SS:ID -0.00363932:0.00354552:0.516156:0.12702:51427:rs61768170
1 756604 rs3131962 A G . PASS AF=0.869213 ES:SE:LP:AF:SS:ID 0.00380491:0.00346723:0.564675:0.869213:51427:rs3131962
1 757640 rs3115853 G A . PASS AF=0.868449 ES:SE:LP:AF:SS:ID 0.00374679:0.00346387:0.553772:0.868449:51427:rs3115853
1 757734 rs4951929 C T . PASS AF=0.869419 ES:SE:LP:AF:SS:ID 0.00369457:0.00347105:0.541884:0.869419:51427:rs4951929
1 757936 rs4951862 C A . PASS AF=0.869426 ES:SE:LP:AF:SS:ID 0.00369537:0.00347128:0.541996:0.869426:51427:rs4951862
1 758144 rs3131956 A G . PASS AF=0.869437 ES:SE:LP:AF:SS:ID 0.00368045:0.00347144:0.53902:0.869437:51427:rs3131956
1 758626 rs3131954 C T . PASS AF=0.869848 ES:SE:LP:AF:SS:ID 0.00390589:0.00347954:0.582291:0.869848:51427:rs3131954
1 759293 rs10157329 T A . PASS AF=0.0999077 ES:SE:LP:AF:SS:ID -0.00493616:0.00403507:0.655182:0.0999077:51427:rs10157329
1 759600 rs545998451 AGT A . PASS AF=0.00659027 ES:SE:LP:AF:SS:ID 0.027255:0.0154987:1.10423:0.00659027:51427:1_759600_AGT_A
1 759837 rs3115851 T A . PASS AF=0.87358 ES:SE:LP:AF:SS:ID 0.00419437:0.0035298:0.629428:0.87358:51427:rs3115851
1 761732 rs2286139 C T . PASS AF=0.86295 ES:SE:LP:AF:SS:ID 0.00322544:0.00346294:0.453898:0.86295:51427:rs2286139
1 761752 rs1057213 C T . PASS AF=0.868667 ES:SE:LP:AF:SS:ID 0.00366822:0.0034969:0.531375:0.868667:51427:rs1057213
1 762273 rs3115849 G A . PASS AF=0.8652 ES:SE:LP:AF:SS:ID 0.00370787:0.00349535:0.539422:0.8652:51427:rs3115849
1 762485 rs12095200 C A . PASS AF=0.0992889 ES:SE:LP:AF:SS:ID -0.00583004:0.00419498:0.783552:0.0992889:51427:rs12095200
1 762589 rs3115848 G C . PASS AF=0.870459 ES:SE:LP:AF:SS:ID 0.00394401:0.00353464:0.577566:0.870459:51427:rs3115848
1 762592 rs3131950 C G . PASS AF=0.870459 ES:SE:LP:AF:SS:ID 0.00394409:0.00353464:0.577581:0.870459:51427:rs3131950
1 762601 rs3131949 T C . PASS AF=0.870456 ES:SE:LP:AF:SS:ID 0.00394366:0.00353465:0.577492:0.870456:51427:rs3131949
1 762632 rs3131948 T A . PASS AF=0.870829 ES:SE:LP:AF:SS:ID 0.00397219:0.00353666:0.582726:0.870829:51427:rs3131948
1 764191 rs7515915 T G . PASS AF=0.126636 ES:SE:LP:AF:SS:ID -0.00343777:0.00354062:0.479414:0.126636:51427:rs7515915
1 766007 rs61768174 A C . PASS AF=0.106247 ES:SE:LP:AF:SS:ID -0.00325503:0.0038558:0.399499:0.106247:51427:rs61768174
1 766105 rs2519015 T A . PASS AF=0.854084 ES:SE:LP:AF:SS:ID 0.00214216:0.0034626:0.270717:0.854084:51427:rs2519015
1 767393 rs538667473 A C . PASS AF=0.00168817 ES:SE:LP:AF:SS:ID -0.00869456:0.0300306:0.11228:0.00168817:51427:rs538667473
1 768116 rs376645387 A AGTTTT . PASS AF=0.836377 ES:SE:LP:AF:SS:ID -0.00304822:0.00339104:0.433319:0.836377:51427:rs376645387