Summary

Summary {data-width=650}

Manhattan plot

manhattan_plot

QQ plot

qq_plot

AF plot

af_plot

P-Z plot

pz_plot

beta_std plot

beta_std_plot

Metadata

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}

LDSC

*********************************************************************
* 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 /data/cromwell-executions/qc/06a85be2-6cb7-43df-bb40-c76e4f908aab/call-ldsc/inputs/-261043419/ieu-b-4968.vcf.gz \
--ref-ld-chr /data/ref/eur_w_ld_chr/ \
--out /data/igd/ieu-b-4968/ldsc.txt \
--w-ld-chr /data/ref/eur_w_ld_chr/ 

Beginning analysis at Fri Mar  4 17:07:46 2022
Reading summary statistics from /data/cromwell-executions/qc/06a85be2-6cb7-43df-bb40-c76e4f908aab/call-ldsc/inputs/-261043419/ieu-b-4968.vcf.gz ...
Read summary statistics for 8282942 SNPs.
Dropped 146609 SNPs with duplicated rs numbers.
Reading reference panel LD Score from /data/ref/eur_w_ld_chr/[1-22] ... (ldscore_fromlist)
Read reference panel LD Scores for 1290028 SNPs.
Removing partitioned LD Scores with zero variance.
Reading regression weight LD Score from /data/ref/eur_w_ld_chr/[1-22] ... (ldscore_fromlist)
Read regression weight LD Scores for 1290028 SNPs.
After merging with reference panel LD, 1172905 SNPs remain.
After merging with regression SNP LD, 1172905 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.0014 (0.0012)
Lambda GC: 1.0146
Mean Chi^2: 1.0097
Intercept: 0.9988 (0.0062)
Ratio < 0 (usually indicates GC correction).
Analysis finished at Fri Mar  4 17:09:21 2022
Total time elapsed: 1.0m:35.17s

QC metrics

Metrics

Metrics

{
    "af_correlation": 0.9295,
    "inflation_factor": 1,
    "mean_EFFECT": -1.2741e-07,
    "n": "-Inf",
    "n_snps": 8283869,
    "n_clumped_hits": 2,
    "n_p_sig": 73,
    "n_mono": 0,
    "n_ns": 1034429,
    "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": 1033343,
    "n_est": "NA",
    "ratio_se_n": "NA",
    "mean_diff": "NaN",
    "ratio_diff": "NaN",
    "sd_y_est1": "NaN",
    "sd_y_est2": "NA",
    "r2_sum1": 0,
    "r2_sum2": 0,
    "r2_sum3": 0,
    "r2_sum4": 0,
    "ldsc_nsnp_merge_refpanel_ld": 1172905,
    "ldsc_nsnp_merge_regression_ld": 1172905,
    "ldsc_observed_scale_h2_beta": 0.0014,
    "ldsc_observed_scale_h2_se": 0.0012,
    "ldsc_intercept_beta": 0.9988,
    "ldsc_intercept_se": 0.0062,
    "ldsc_lambda_gc": 1.0146,
    "ldsc_mean_chisq": 1.0097,
    "ldsc_ratio": -0.1237
}

Flags

name value
af_correlation FALSE
inflation_factor FALSE
n TRUE
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

Definitions

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 SNPs
  • n_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:
    • alleles other than A, C, G or T.
    • P-values < 0 or > 1.
    • negative or infinite standard errors (<= 0 or = Infinity).
    • infinite beta estimates or allele frequencies < 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.
    • \(\widehat{\beta_j^{std}} = \sqrt{\frac{{z}_j^2 / ({z}_j^2 + n -2)}{2 \times {MAF}_j \times (1 - {MAF}_j)}} \times sign({z}_j)\),
    • \({z}_j = \frac{\beta_j}{{se}_j}\),
    • and \(\beta_j\) is the reported effect size.
  • 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.
    • \(\texttt{mean_diff2} = \sum_{j} \frac{\widehat{\beta_j^{std}} - \beta^{\prime}_j}{\texttt{n_snps}}\)
    • \(\beta^{\prime}_j = \frac{\beta_j}{\widehat{\texttt{sd2}}_{y}}\)
  • 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.
    • \(\widehat{\texttt{sd1}}_{y} = \frac{\sqrt{n} \times median({se}_j)}{C}\),
    • \(C = median(\frac{1}{\sqrt{2 \times {MAF}_j \times (1 - {MAF}_j)}})\),
    • and \({se}_j\) is the reported standard error.
  • 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.
    • \(\widehat{\texttt{sd2}}_{y} = median(\widehat{sd_j})\),
    • \(\widehat{sd_j} = \frac{\beta_j}{\widehat{\beta_j^{std}}}\),

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 > 0.5
  • ldsc_intercept_beta: ldsc_intercept_beta > 1.5
  • n_clumped_hits: n_clumped_hits > 1000
  • r2_sum<*>: r2_sum<*> > 0.5

Plots

  • Manhattan plot
    • Red line: \(-log_{10}^{5 \times 10^{-8}}\)
    • Blue line: \(-log_{10}^{5 \times 10^{-5}}\)
  • QQ plot
  • AF plot
  • P-Z plot
  • beta_std plot: Scatter plot between \(\widehat{\beta_j^{std}}\) and \(\beta_j\)

Diagnostics

Details

Summary stats

skim_type skim_variable n_missing complete_rate character.min character.max character.empty character.n_unique character.whitespace logical.mean logical.count numeric.mean numeric.sd numeric.p0 numeric.p25 numeric.p50 numeric.p75 numeric.p100 numeric.hist
character ID 606 0.9999268 3 58 0 8257441 0 NA NA NA NA NA NA NA NA NA NA
character REF 0 1.0000000 1 88 0 13714 0 NA NA NA NA NA NA NA NA NA NA
character ALT 0 1.0000000 1 662 0 56426 0 NA NA NA NA NA NA NA NA NA NA
logical N 8283869 0.0000000 NA NA NA NA NA NaN : NA NA NA NA NA NA NA NA
numeric CHROM 0 1.0000000 NA NA NA NA NA NA NA 8.860123e+00 5.953355e+00 1.0000000 4.000000e+00 8.000000e+00 1.300000e+01 2.300000e+01 ▇▅▅▂▂
numeric POS 0 1.0000000 NA NA NA NA NA NA NA 7.836656e+07 5.641714e+07 302.0000000 3.195228e+07 6.877570e+07 1.143022e+08 2.492405e+08 ▇▆▅▂▁
numeric EFFECT 0 1.0000000 NA NA NA NA NA NA NA -1.000000e-07 1.419000e-04 -0.0013824 -8.150000e-05 -8.000000e-07 8.030000e-05 1.801600e-03 ▁▂▇▁▁
numeric SE 0 1.0000000 NA NA NA NA NA NA NA 1.317000e-04 5.170000e-05 0.0000693 9.050000e-05 1.107000e-04 1.597000e-04 7.038000e-04 ▇▂▁▁▁
numeric PVAL 0 1.0000000 NA NA NA NA NA NA NA 4.980246e-01 2.893714e-01 0.0000000 2.500000e-01 5.000000e-01 7.499995e-01 1.000000e+00 ▇▇▇▇▇
numeric PVAL_ztest 0 1.0000000 NA NA NA NA NA NA NA 4.980229e-01 2.893446e-01 0.0000000 2.464208e-01 4.969449e-01 7.485545e-01 9.999999e-01 ▇▇▇▇▇
numeric AF 0 1.0000000 NA NA NA NA NA NA NA 3.441455e-01 2.834541e-01 0.0253040 9.333500e-02 2.577890e-01 5.531690e-01 9.746960e-01 ▇▃▂▂▂
numeric AF_reference 1033343 0.8752584 NA NA NA NA NA NA NA 3.009585e-01 2.503216e-01 0.0000000 9.345050e-02 2.278150e-01 4.636580e-01 1.000000e+00 ▇▅▂▂▁

Head and tail

CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
1 10177 rs1264289758 AC A 0.0001419 0.0001259 0.2599998 0.2594920 0.601356 NA NA
1 10352 rs1557426776 TA T -0.0001385 0.0001296 0.2900000 0.2854025 0.606991 NA NA
1 11008 rs575272151 C G 0.0000596 0.0002155 0.7800007 0.7820424 0.086196 0.0880591 NA
1 11012 rs544419019 C G 0.0000596 0.0002155 0.7800007 0.7820424 0.086196 0.0880591 NA
1 13110 rs540538026 G A -0.0001311 0.0002864 0.6499995 0.6471033 0.058736 0.0267572 NA
1 13116 rs62635286 T G 0.0001250 0.0001696 0.4600002 0.4610691 0.189428 0.0970447 NA
1 13118 rs200579949 A G 0.0001250 0.0001696 0.4600002 0.4610691 0.189428 0.0970447 NA
1 13273 rs531730856 G C -0.0000685 0.0001988 0.7300002 0.7304017 0.133929 0.0950479 NA
1 14464 rs546169444 A T 0.0002975 0.0001805 0.0990011 0.0993591 0.157070 0.0958466 NA
1 14599 rs531646671 T A 0.0001813 0.0001646 0.2700001 0.2705048 0.191585 0.1475640 NA
CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
23 154901936 rs697727 A G -2.45e-05 8.06e-05 0.7600007 0.7611177 0.751489 0.643179 NA
23 154901964 rs697726 G A 1.74e-05 8.51e-05 0.8400000 0.8380937 0.347477 0.117616 NA
23 154902105 rs696316 G T -2.43e-05 8.06e-05 0.7600007 0.7626180 0.751442 0.636026 NA
23 154902889 rs697725 A T -2.30e-05 8.06e-05 0.7800007 0.7752291 0.751114 0.584106 NA
23 154903118 rs479770 G A -2.47e-05 8.06e-05 0.7600007 0.7593820 0.751532 0.643444 NA
23 154903224 rs480725 A T -2.47e-05 8.06e-05 0.7600007 0.7592759 0.751535 0.643444 NA
23 154903937 rs674707 G A -2.47e-05 8.06e-05 0.7600007 0.7589290 0.751545 0.643444 NA
23 154909055 rs473529 C G 8.80e-06 7.59e-05 0.9100000 0.9076307 0.305118 0.463046 NA
23 154918266 rs642043 C T 8.70e-06 7.61e-05 0.9100000 0.9088621 0.302982 0.478675 NA
23 154927581 rs644138 G A 7.30e-06 7.62e-05 0.9199999 0.9231424 0.302854 0.463576 NA

bcf preview

1   10177   rs1264289758    AC  A   .   PASS    AF=0.601356 ES:SE:LP:AF:ID  0.000141947:0.000125885:0.585027:0.601356:rs1264289758
1   10352   rs1557426776    TA  T   .   PASS    AF=0.606991 ES:SE:LP:AF:ID  -0.000138498:0.000129648:0.537602:0.606991:rs1557426776
1   11008   rs575272151 C   G   .   PASS    AF=0.086196 ES:SE:LP:AF:ID  5.96232e-05:0.000215512:0.107905:0.086196:rs575272151
1   11012   rs544419019 C   G   .   PASS    AF=0.086196 ES:SE:LP:AF:ID  5.96232e-05:0.000215512:0.107905:0.086196:rs544419019
1   13110   rs540538026 G   A   .   PASS    AF=0.058736 ES:SE:LP:AF:ID  -0.00013109:0.000286354:0.187087:0.058736:rs540538026
1   13116   rs62635286  T   G   .   PASS    AF=0.189428 ES:SE:LP:AF:ID  0.000124999:0.000169585:0.337242:0.189428:rs62635286
1   13118   rs62028691  A   G   .   PASS    AF=0.189428 ES:SE:LP:AF:ID  0.000124999:0.000169585:0.337242:0.189428:rs62028691
1   13273   rs531730856 G   C   .   PASS    AF=0.133929 ES:SE:LP:AF:ID  -6.85037e-05:0.000198797:0.136677:0.133929:rs531730856
1   14464   rs546169444 A   T   .   PASS    AF=0.15707  ES:SE:LP:AF:ID  0.000297488:0.000180518:1.00436:0.15707:rs546169444
1   14599   rs707680    T   A   .   PASS    AF=0.191585 ES:SE:LP:AF:ID  0.000181342:0.000164572:0.568636:0.191585:rs707680
1   14604   rs1418508701    A   G   .   PASS    AF=0.191585 ES:SE:LP:AF:ID  0.000181342:0.000164572:0.568636:0.191585:rs1418508701
1   14930   rs6682385   A   G   .   PASS    AF=0.474009 ES:SE:LP:AF:ID  6.4187e-05:0.000127665:0.207608:0.474009:rs6682385
1   14933   rs199856693 G   A   .   PASS    AF=0.045012 ES:SE:LP:AF:ID  0.000211193:0.000314366:0.30103:0.045012:rs199856693
1   15211   rs3982632   T   G   .   PASS    AF=0.741432 ES:SE:LP:AF:ID  0.000163829:0.000147644:0.568636:0.741432:rs3982632
1   15820   rs1316988498    G   T   .   PASS    AF=0.275225 ES:SE:LP:AF:ID  0.000110722:0.000151388:0.337242:0.275225:rs1316988498
1   15903   rs557514207 GC  G   .   PASS    AF=0.581024 ES:SE:LP:AF:ID  -5.64609e-06:0.000124833:0.0177288:0.581024:rs557514207
1   28590   rs1344649620    T   TTGG    .   PASS    AF=0.9565   ES:SE:LP:AF:ID  9.54801e-05:0.000354832:0.102373:0.9565:rs1344649620
1   30923   rs1165072081    G   T   .   PASS    AF=0.910285 ES:SE:LP:AF:ID  0.000129643:0.000235701:0.236572:0.910285:rs1165072081
1   47159   rs540662756 T   C   .   PASS    AF=0.062683 ES:SE:LP:AF:ID  0.000574597:0.000268872:1.48149:0.062683:rs540662756
1   49298   rs10399793  T   C   .   PASS    AF=0.623626 ES:SE:LP:AF:ID  -0.000125597:0.000149763:0.39794:0.623626:rs10399793
1   49554   rs539322794 A   G   .   PASS    AF=0.092968 ES:SE:LP:AF:ID  -3.51684e-05:0.00023035:0.0555173:0.092968:rs539322794
1   51479   rs116400033 T   A   .   PASS    AF=0.21349  ES:SE:LP:AF:ID  -4.26085e-05:0.0001601:0.102373:0.21349:rs116400033
1   54490   rs141149254 G   A   .   PASS    AF=0.154533 ES:SE:LP:AF:ID  5.82798e-05:0.000179875:0.124939:0.154533:rs141149254
1   54676   rs2462492   C   T   .   PASS    AF=0.400444 ES:SE:LP:AF:ID  0.000282561:0.000148351:1.24413:0.400444:rs2462492
1   54712   rs573184866 TTTTC   T   .   PASS    AF=0.414825 ES:SE:LP:AF:ID  -0.000120725:0.00011728:0.522879:0.414825:rs573184866
1   54716   rs1166278911    C   T   .   PASS    AF=0.417245 ES:SE:LP:AF:ID  0.000186178:0.00013545:0.769551:0.417245:rs1166278911
1   55545   rs28396308  C   T   .   PASS    AF=0.253891 ES:SE:LP:AF:ID  0.000310841:0.000152363:1.38722:0.253891:rs28396308
1   58814   rs114420996 G   A   .   PASS    AF=0.09004  ES:SE:LP:AF:ID  0.000156485:0.000232038:0.30103:0.09004:rs114420996
1   59040   rs62637815  T   C   .   PASS    AF=0.088875 ES:SE:LP:AF:ID  0.00010264:0.000232923:0.180456:0.088875:rs62637815
1   60351   rs62637817  A   G   .   PASS    AF=0.081025 ES:SE:LP:AF:ID  7.78096e-05:0.000241617:0.124939:0.081025:rs62637817
1   62777   rs3844233   A   T   .   PASS    AF=0.43851  ES:SE:LP:AF:ID  0.00022935:0.000128774:1.12494:0.43851:rs3844233
1   63268   rs28664618  T   C   .   PASS    AF=0.382141 ES:SE:LP:AF:ID  0.000317681:0.000138419:1.65758:0.382141:rs28664618
1   63671   rs80011619  G   A   .   PASS    AF=0.15887  ES:SE:LP:AF:ID  0.000489885:0.000176196:2.26761:0.15887:rs80011619
1   63735   rs61158452  C   CCTA    .   PASS    AF=0.68399  ES:SE:LP:AF:ID  0.000169568:0.000137198:0.657577:0.68399:rs61158452
1   64931   rs62639104  G   A   .   PASS    AF=0.079632 ES:SE:LP:AF:ID  4.65778e-05:0.000244548:0.0705811:0.079632:rs62639104
1   68082   rs367789441 T   C   .   PASS    AF=0.070748 ES:SE:LP:AF:ID  -0.000327705:0.000248046:0.721246:0.070748:rs367789441
1   69428   rs140739101 T   G   .   PASS    AF=0.032901 ES:SE:LP:AF:ID  0.000107099:0.000375367:0.107905:0.032901:rs140739101
1   69761   rs200505207 A   T   .   PASS    AF=0.073897 ES:SE:LP:AF:ID  -0.000167097:0.000243967:0.309804:0.073897:rs200505207
1   69897   rs200676709 T   C   .   PASS    AF=0.751155 ES:SE:LP:AF:ID  3.35455e-06:0.000155395:0.00877392:0.751155:rs200676709
1   74790   rs13328700  C   G   .   PASS    AF=0.034042 ES:SE:LP:AF:ID  -0.000212262:0.000356993:0.259637:0.034042:rs13328700
1   74792   rs1335672253    G   A   .   PASS    AF=0.034042 ES:SE:LP:AF:ID  -0.000212262:0.000356993:0.259637:0.034042:rs1335672253
1   76838   rs563953605 T   G   .   PASS    AF=0.077202 ES:SE:LP:AF:ID  4.21854e-05:0.000249207:0.0604807:0.077202:rs563953605
1   76854   rs367666799 A   G   .   PASS    AF=0.077461 ES:SE:LP:AF:ID  0.000403231:0.000240663:1.02687:0.077461:rs367666799
1   77866   rs563593912 C   T   .   PASS    AF=0.077006 ES:SE:LP:AF:ID  4.44618e-05:0.000249273:0.0655015:0.077006:rs563593912
1   77874   rs62641297  G   A   .   PASS    AF=0.077006 ES:SE:LP:AF:ID  4.44618e-05:0.000249273:0.0655015:0.077006:rs62641297
1   81260   rs571136476 C   T   .   PASS    AF=0.041521 ES:SE:LP:AF:ID  -0.000146887:0.000347482:0.173925:0.041521:rs571136476
1   81587   rs536406113 C   T   .   PASS    AF=0.060958 ES:SE:LP:AF:ID  -0.000287314:0.00026426:0.552842:0.060958:rs536406113
1   82163   rs139113303 G   A   .   PASS    AF=0.075421 ES:SE:LP:AF:ID  0.000431188:0.000243699:1.11351:0.075421:rs139113303
1   82609   rs149189449 C   G   .   PASS    AF=0.075448 ES:SE:LP:AF:ID  0.000429255:0.000243649:1.10791:0.075448:rs149189449
1   83514   rs201754587 C   T   .   PASS    AF=0.352679 ES:SE:LP:AF:ID  -0.000109099:0.00013952:0.366532:0.352679:rs201754587