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/f41a3c71-38dd-45f4-a2c7-6ed4b9d7b987/call-ldsc/inputs/-261043422/ieu-b-4965.vcf.gz \
--ref-ld-chr /data/ref/eur_w_ld_chr/ \
--out /data/igd/ieu-b-4965/ldsc.txt \
--w-ld-chr /data/ref/eur_w_ld_chr/ 

Beginning analysis at Mon Mar  7 19:19:17 2022
Reading summary statistics from /data/cromwell-executions/qc/f41a3c71-38dd-45f4-a2c7-6ed4b9d7b987/call-ldsc/inputs/-261043422/ieu-b-4965.vcf.gz ...
Read summary statistics for 11737600 SNPs.
Dropped 197288 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, 1219564 SNPs remain.
After merging with regression SNP LD, 1219564 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.0077 (0.0015)
Lambda GC: 1.0704
Mean Chi^2: 1.0798
Intercept: 1.0233 (0.0068)
Ratio: 0.2917 (0.0846)
Analysis finished at Mon Mar  7 19:21:24 2022
Total time elapsed: 2.0m:6.66s

QC metrics

Metrics

Metrics

{
    "af_correlation": 0.9489,
    "inflation_factor": 1.0475,
    "mean_EFFECT": -5.1633e-06,
    "n": "-Inf",
    "n_snps": 11738639,
    "n_clumped_hits": 9,
    "n_p_sig": 228,
    "n_mono": 0,
    "n_ns": 1267800,
    "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": 1319471,
    "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": 1219564,
    "ldsc_nsnp_merge_regression_ld": 1219564,
    "ldsc_observed_scale_h2_beta": 0.0077,
    "ldsc_observed_scale_h2_se": 0.0015,
    "ldsc_intercept_beta": 1.0233,
    "ldsc_intercept_se": 0.0068,
    "ldsc_lambda_gc": 1.0704,
    "ldsc_mean_chisq": 1.0798,
    "ldsc_ratio": 0.292
}

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 673 0.9999427 3 58 0 11697857 0 NA NA NA NA NA NA NA NA NA NA
character REF 0 1.0000000 1 88 0 17184 0 NA NA NA NA NA NA NA NA NA NA
character ALT 0 1.0000000 1 662 0 70214 0 NA NA NA NA NA NA NA NA NA NA
logical N 11738639 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 8.775733e+00 5.896723e+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 7.865155e+07 5.626903e+07 302.0000000 3.243834e+07 6.916468e+07 1.144115e+08 2.492405e+08 ▇▆▅▂▁
numeric EFFECT 0 1.0000000 NA NA NA NA NA NA NA -5.200000e-06 1.025600e-03 -0.0121854 -3.754000e-04 -3.800000e-06 3.644000e-04 1.490580e-02 ▁▁▇▁▁
numeric SE 0 1.0000000 NA NA NA NA NA NA NA 7.885000e-04 6.391000e-04 0.0002296 3.207000e-04 4.906000e-04 1.057200e-03 7.813500e-03 ▇▁▁▁▁
numeric PVAL 0 1.0000000 NA NA NA NA NA NA NA 4.917787e-01 2.910336e-01 0.0000000 2.399999e-01 4.899999e-01 7.400005e-01 1.000000e+00 ▇▇▇▇▇
numeric PVAL_ztest 0 1.0000000 NA NA NA NA NA NA NA 4.917805e-01 2.910079e-01 0.0000000 2.376360e-01 4.889925e-01 7.437431e-01 1.000000e+00 ▇▇▇▇▇
numeric AF 0 1.0000000 NA NA NA NA NA NA NA 2.691709e-01 3.015666e-01 0.0022100 2.161200e-02 1.308070e-01 4.547400e-01 9.977900e-01 ▇▂▂▁▂
numeric AF_reference 1319471 0.8875959 NA NA NA NA NA NA NA 2.211791e-01 2.524355e-01 0.0000000 1.557510e-02 1.172120e-01 3.520370e-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 -0.0000393 0.0004172 0.9299999 0.9250133 0.601337 NA NA
1 10352 rs1557426776 TA T 0.0006253 0.0004298 0.1499999 0.1456892 0.607073 NA NA
1 11008 rs575272151 C G 0.0002234 0.0007140 0.7499995 0.7543427 0.086202 0.0880591 NA
1 11012 rs544419019 C G 0.0002234 0.0007140 0.7499995 0.7543427 0.086202 0.0880591 NA
1 13110 rs540538026 G A -0.0002769 0.0009493 0.7700005 0.7705462 0.058734 0.0267572 NA
1 13116 rs62635286 T G -0.0002636 0.0005621 0.6400000 0.6390521 0.189405 0.0970447 NA
1 13118 rs200579949 A G -0.0002636 0.0005621 0.6400000 0.6390521 0.189405 0.0970447 NA
1 13273 rs531730856 G C 0.0012218 0.0006587 0.0640000 0.0636288 0.133989 0.0950479 NA
1 14464 rs546169444 A T 0.0003245 0.0005982 0.5900000 0.5875178 0.157073 0.0958466 NA
1 14599 rs531646671 T A -0.0003869 0.0005455 0.4799997 0.4781620 0.191546 0.1475640 NA
CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
23 154901936 rs697727 A G 0.0000882 0.0002670 0.7400005 0.7411494 0.751518 0.643179 NA
23 154901964 rs697726 G A -0.0003363 0.0002819 0.2300001 0.2328416 0.347391 0.117616 NA
23 154902105 rs696316 G T 0.0000832 0.0002670 0.7600007 0.7553055 0.751469 0.636026 NA
23 154902889 rs697725 A T 0.0000745 0.0002669 0.7800007 0.7801665 0.751138 0.584106 NA
23 154903118 rs479770 G A 0.0000915 0.0002670 0.7300002 0.7317538 0.751561 0.643444 NA
23 154903224 rs480725 A T 0.0000915 0.0002670 0.7300002 0.7318678 0.751564 0.643444 NA
23 154903937 rs674707 G A 0.0000917 0.0002670 0.7300002 0.7312046 0.751574 0.643444 NA
23 154909055 rs473529 C G -0.0000482 0.0002515 0.8499999 0.8479165 0.305103 0.463046 NA
23 154918266 rs642043 C T -0.0000199 0.0002523 0.9400001 0.9372241 0.302976 0.478675 NA
23 154927581 rs644138 G A -0.0000214 0.0002523 0.9299999 0.9323849 0.302848 0.463576 NA

bcf preview

1   10177   rs1264289758    AC  A   .   PASS    AF=0.601337 ES:SE:LP:AF:ID  -3.92634e-05:0.00041716:0.0315171:0.601337:rs1264289758
1   10352   rs1557426776    TA  T   .   PASS    AF=0.607073 ES:SE:LP:AF:ID  0.00062528:0.000429767:0.823909:0.607073:rs1557426776
1   11008   rs575272151 C   G   .   PASS    AF=0.086202 ES:SE:LP:AF:ID  0.000223435:0.000714036:0.124939:0.086202:rs575272151
1   11012   rs544419019 C   G   .   PASS    AF=0.086202 ES:SE:LP:AF:ID  0.000223435:0.000714036:0.124939:0.086202:rs544419019
1   13110   rs540538026 G   A   .   PASS    AF=0.058734 ES:SE:LP:AF:ID  -0.000276866:0.000949275:0.113509:0.058734:rs540538026
1   13116   rs62635286  T   G   .   PASS    AF=0.189405 ES:SE:LP:AF:ID  -0.000263642:0.000562107:0.19382:0.189405:rs62635286
1   13118   rs62028691  A   G   .   PASS    AF=0.189405 ES:SE:LP:AF:ID  -0.000263642:0.000562107:0.19382:0.189405:rs62028691
1   13273   rs531730856 G   C   .   PASS    AF=0.133989 ES:SE:LP:AF:ID  0.00122177:0.000658717:1.19382:0.133989:rs531730856
1   14464   rs546169444 A   T   .   PASS    AF=0.157073 ES:SE:LP:AF:ID  0.000324504:0.000598234:0.229148:0.157073:rs546169444
1   14599   rs707680    T   A   .   PASS    AF=0.191546 ES:SE:LP:AF:ID  -0.000386913:0.000545515:0.318759:0.191546:rs707680
1   14604   rs1418508701    A   G   .   PASS    AF=0.191546 ES:SE:LP:AF:ID  -0.000386913:0.000545515:0.318759:0.191546:rs1418508701
1   14930   rs6682385   A   G   .   PASS    AF=0.473969 ES:SE:LP:AF:ID  -0.00029693:0.000423184:0.318759:0.473969:rs6682385
1   14933   rs199856693 G   A   .   PASS    AF=0.045009 ES:SE:LP:AF:ID  -7.40679e-05:0.00104214:0.0268721:0.045009:rs199856693
1   15211   rs3982632   T   G   .   PASS    AF=0.74142  ES:SE:LP:AF:ID  -2.55717e-05:0.000489275:0.0177288:0.74142:rs3982632
1   15820   rs1316988498    G   T   .   PASS    AF=0.275258 ES:SE:LP:AF:ID  0.00055184:0.000501706:0.568636:0.275258:rs1316988498
1   15903   rs557514207 GC  G   .   PASS    AF=0.581116 ES:SE:LP:AF:ID  0.000737527:0.000413764:1.12494:0.581116:rs557514207
1   28590   rs1344649620    T   TTGG    .   PASS    AF=0.956495 ES:SE:LP:AF:ID  -0.000234163:0.00117575:0.0757207:0.956495:rs1344649620
1   30923   rs1165072081    G   T   .   PASS    AF=0.910226 ES:SE:LP:AF:ID  -0.00171374:0.000780713:1.55284:0.910226:rs1165072081
1   47159   rs540662756 T   C   .   PASS    AF=0.062652 ES:SE:LP:AF:ID  -0.000724267:0.000891699:0.376751:0.062652:rs540662756
1   49298   rs10399793  T   C   .   PASS    AF=0.623637 ES:SE:LP:AF:ID  1.28459e-05:0.000496408:0.00877392:0.623637:rs10399793
1   49554   rs539322794 A   G   .   PASS    AF=0.09298  ES:SE:LP:AF:ID  0.000324344:0.000763408:0.173925:0.09298:rs539322794
1   51479   rs116400033 T   A   .   PASS    AF=0.213507 ES:SE:LP:AF:ID  0.00018952:0.000530552:0.142668:0.213507:rs116400033
1   54490   rs141149254 G   A   .   PASS    AF=0.154529 ES:SE:LP:AF:ID  -4.31872e-05:0.000596136:0.0268721:0.154529:rs141149254
1   54676   rs2462492   C   T   .   PASS    AF=0.400412 ES:SE:LP:AF:ID  -0.000143298:0.00049181:0.113509:0.400412:rs2462492
1   54712   rs573184866 TTTTC   T   .   PASS    AF=0.414844 ES:SE:LP:AF:ID  6.37939e-05:0.000388802:0.0604807:0.414844:rs573184866
1   54716   rs1166278911    C   T   .   PASS    AF=0.417303 ES:SE:LP:AF:ID  0.000737261:0.000448949:1:0.417303:rs1166278911
1   55545   rs28396308  C   T   .   PASS    AF=0.253848 ES:SE:LP:AF:ID  -0.000248018:0.000505054:0.207608:0.253848:rs28396308
1   58814   rs114420996 G   A   .   PASS    AF=0.090046 ES:SE:LP:AF:ID  0.000361032:0.000769029:0.19382:0.090046:rs114420996
1   59040   rs62637815  T   C   .   PASS    AF=0.088883 ES:SE:LP:AF:ID  0.000340258:0.000771941:0.180456:0.088883:rs62637815
1   60351   rs62637817  A   G   .   PASS    AF=0.081036 ES:SE:LP:AF:ID  0.000406998:0.000800772:0.21467:0.081036:rs62637817
1   62777   rs3844233   A   T   .   PASS    AF=0.4385   ES:SE:LP:AF:ID  9.21917e-05:0.000426853:0.0809219:0.4385:rs3844233
1   63268   rs28664618  T   C   .   PASS    AF=0.38209  ES:SE:LP:AF:ID  -0.000243553:0.000458819:0.221849:0.38209:rs28664618
1   63671   rs80011619  G   A   .   PASS    AF=0.158862 ES:SE:LP:AF:ID  0.000337454:0.000584006:0.251812:0.158862:rs80011619
1   63735   rs61158452  C   CCTA    .   PASS    AF=0.683964 ES:SE:LP:AF:ID  -0.000128284:0.000454714:0.107905:0.683964:rs61158452
1   64931   rs62639104  G   A   .   PASS    AF=0.079645 ES:SE:LP:AF:ID  0.000452357:0.000810474:0.236572:0.079645:rs62639104
1   68082   rs367789441 T   C   .   PASS    AF=0.070771 ES:SE:LP:AF:ID  0.000440553:0.00082194:0.229148:0.070771:rs367789441
1   69428   rs140739101 T   G   .   PASS    AF=0.032873 ES:SE:LP:AF:ID  -0.00212506:0.00124536:1.05552:0.032873:rs140739101
1   69761   rs200505207 A   T   .   PASS    AF=0.073917 ES:SE:LP:AF:ID  0.000490461:0.000808462:0.267606:0.073917:rs200505207
1   69897   rs200676709 T   C   .   PASS    AF=0.751183 ES:SE:LP:AF:ID  0.00031219:0.000515128:0.267606:0.751183:rs200676709
1   74790   rs13328700  C   G   .   PASS    AF=0.034027 ES:SE:LP:AF:ID  -0.00121508:0.00118357:0.522879:0.034027:rs13328700
1   74792   rs1335672253    G   A   .   PASS    AF=0.034027 ES:SE:LP:AF:ID  -0.00121508:0.00118357:0.522879:0.034027:rs1335672253
1   76838   rs563953605 T   G   .   PASS    AF=0.077216 ES:SE:LP:AF:ID  0.00051927:0.000825916:0.275724:0.077216:rs563953605
1   76854   rs367666799 A   G   .   PASS    AF=0.077441 ES:SE:LP:AF:ID  -0.000292803:0.000798014:0.148742:0.077441:rs367666799
1   77866   rs563593912 C   T   .   PASS    AF=0.07702  ES:SE:LP:AF:ID  0.000515598:0.000826139:0.275724:0.07702:rs563593912
1   77874   rs62641297  G   A   .   PASS    AF=0.07702  ES:SE:LP:AF:ID  0.000515598:0.000826139:0.275724:0.07702:rs62641297
1   81260   rs571136476 C   T   .   PASS    AF=0.041525 ES:SE:LP:AF:ID  0.000121976:0.00115161:0.0362122:0.041525:rs571136476
1   81587   rs536406113 C   T   .   PASS    AF=0.060962 ES:SE:LP:AF:ID  -0.00014548:0.000875761:0.0604807:0.060962:rs536406113
1   82163   rs139113303 G   A   .   PASS    AF=0.0754   ES:SE:LP:AF:ID  -0.000293267:0.000808096:0.142668:0.0754:rs139113303
1   82609   rs149189449 C   G   .   PASS    AF=0.075427 ES:SE:LP:AF:ID  -0.000303162:0.000807933:0.148742:0.075427:rs149189449
1   83514   rs201754587 C   T   .   PASS    AF=0.352689 ES:SE:LP:AF:ID  -4.12893e-06:0.000462423:0.00436481:0.352689:rs201754587