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/bce245f4-b327-4bf9-a391-1c1ad5b994bb/call-ldsc/inputs/562856189/ieu-b-32.vcf.gz \
--ref-ld-chr /data/ref/eur_w_ld_chr/ \
--out /data/igd/ieu-b-32/ldsc.txt \
--w-ld-chr /data/ref/eur_w_ld_chr/ 

Beginning analysis at Fri Aug 21 01:26:13 2020
Reading summary statistics from /data/cromwell-executions/qc/bce245f4-b327-4bf9-a391-1c1ad5b994bb/call-ldsc/inputs/562856189/ieu-b-32.vcf.gz ...
Read summary statistics for 26949587 SNPs.
Dropped 127468 SNPs with duplicated rs numbers.
Reading reference panel LD Score from /data/ref/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 /data/ref/eur_w_ld_chr/[1-22] ...
Read regression weight LD Scores for 1290028 SNPs.
After merging with reference panel LD, 1220779 SNPs remain.
After merging with regression SNP LD, 1220779 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.1906 (0.0137)
Lambda GC: 1.8848
Mean Chi^2: 3.4194
Intercept: 1.3202 (0.0301)
Ratio: 0.1324 (0.0125)
Analysis finished at Fri Aug 21 01:30:30 2020
Total time elapsed: 4.0m:16.25s

QC metrics

Metrics

Metrics

{
    "af_correlation": 0.9666,
    "inflation_factor": 1.1987,
    "mean_EFFECT": 0.0018,
    "n": 524923,
    "n_snps": 26949819,
    "n_clumped_hits": 510,
    "n_p_sig": 113184,
    "n_mono": 0,
    "n_ns": 0,
    "n_mac": 50336,
    "is_snpid_unique": false,
    "n_miss_EFFECT": 0,
    "n_miss_SE": 0,
    "n_miss_PVAL": 0,
    "n_miss_AF": 0,
    "n_miss_AF_reference": 2124856,
    "n_est": 384644.6843,
    "ratio_se_n": 0.856,
    "mean_diff": -0.0012,
    "ratio_diff": 1.2183,
    "sd_y_est1": 1.3252,
    "sd_y_est2": 1.1344,
    "r2_sum1": 0.0999,
    "r2_sum2": 0.0569,
    "r2_sum3": 0.0777,
    "r2_sum4": 0.1044,
    "ldsc_nsnp_merge_refpanel_ld": 1220779,
    "ldsc_nsnp_merge_regression_ld": 1220779,
    "ldsc_observed_scale_h2_beta": 0.1906,
    "ldsc_observed_scale_h2_se": 0.0137,
    "ldsc_intercept_beta": 1.3202,
    "ldsc_intercept_se": 0.0301,
    "ldsc_lambda_gc": 1.8848,
    "ldsc_mean_chisq": 3.4194,
    "ldsc_ratio": 0.1323
}

Flags

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 TRUE
n_p_sig TRUE
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 numeric.mean numeric.sd numeric.p0 numeric.p25 numeric.p50 numeric.p75 numeric.p100 numeric.hist
character ID 47 0.9999983 3 64 0 26948015 0 NA NA NA NA NA NA NA NA
character REF 0 1.0000000 1 1 0 4 0 NA NA NA NA NA NA NA NA
character ALT 0 1.0000000 1 1 0 4 0 NA NA NA NA NA NA NA NA
numeric CHROM 0 1.0000000 NA NA NA NA NA 8.653471e+00 5.782425e+00 1.000000 4.000000e+00 8.000000e+00 1.300000e+01 2.200000e+01 ▇▅▃▂▂
numeric POS 0 1.0000000 NA NA NA NA NA 7.897982e+07 5.624823e+07 56.000000 3.283209e+07 6.963139e+07 1.148521e+08 2.492398e+08 ▇▆▅▂▁
numeric EFFECT 0 1.0000000 NA NA NA NA NA 1.781400e-03 1.675324e-01 -80.461900 -2.131700e-02 1.260000e-04 2.328100e-02 5.403410e+01 ▁▁▇▁▁
numeric SE 0 1.0000000 NA NA NA NA NA 8.457680e-02 1.445704e-01 0.001355 6.924000e-03 4.678100e-02 1.186890e-01 7.430190e+01 ▇▁▁▁▁
numeric PVAL 0 1.0000000 NA NA NA NA NA 4.683863e-01 2.997242e-01 0.000000 2.008029e-01 4.602386e-01 7.287105e-01 1.000000e+00 ▇▆▆▆▆
numeric PVAL_ztest 0 1.0000000 NA NA NA NA NA 4.683859e-01 2.997253e-01 0.000000 2.008223e-01 4.602271e-01 7.286975e-01 1.000000e+00 ▇▆▆▆▆
numeric AF 0 1.0000000 NA NA NA NA NA 7.884360e-02 1.925990e-01 0.000025 1.660000e-04 7.890000e-04 2.299700e-02 9.999750e-01 ▇▁▁▁▁
numeric AF_reference 2124856 0.9211551 NA NA NA NA NA 8.966190e-02 1.921834e-01 0.000000 1.397800e-03 7.388200e-03 5.291530e-02 1.000000e+00 ▇▁▁▁▁
numeric N 0 1.0000000 NA NA NA NA NA 4.423522e+05 1.259093e+05 396.000000 4.425430e+05 4.668240e+05 5.234940e+05 5.249230e+05 ▁▁▁▂▇

Head and tail

CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
1 16141 rs529651976 C T 0.193236 0.217307 0.3738746 0.3738792 0.000510 0.0025958 35266
1 49298 rs200943160 T C 0.010168 0.011325 0.3692462 0.3692726 0.823722 0.7821490 35266
1 54353 rs140052487 C A -0.037909 0.101934 0.7099814 0.7099692 0.001815 0.0089856 35266
1 54564 rs558796213 G T 0.165511 0.113086 0.1432950 0.1433073 0.000143 0.0041933 407277
1 54591 rs561234294 A G -0.138950 0.121122 0.2512829 0.2513029 0.001552 0.0035942 35266
1 54712 rs552304420 T C 0.040937 0.044365 0.3561427 0.3561469 0.010376 0.0109824 35266
1 54815 rs568686875 T C 0.113181 0.188218 0.5476423 0.5476207 0.000481 0.0019968 35266
1 55326 rs3107975 T C 0.002358 0.033370 0.9436479 0.9436665 0.019593 0.0459265 35266
1 55351 rs531766459 T A -0.043908 0.059989 0.4642116 0.4642087 0.000503 0.0007987 407277
1 55405 rs372455836 C T 0.056876 0.056491 0.3140118 0.3140236 0.006822 0.0075879 35266
CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
22 51237137 rs534739169 A C -0.032474 0.088379 0.7133062 0.7132907 0.000213 0.0001997 442543
22 51237410 rs530437591 G A -0.065056 0.057675 0.2593098 0.2593302 0.000351 0.0017971 442543
22 51237486 rs149820726 G C -0.093241 0.160163 0.5604811 0.5604568 0.000539 0.0025958 35266
22 51238275 rs202031343 C T 0.148562 0.104104 0.1535501 0.1535644 0.001276 0.0009984 35266
22 51238307 rs577028785 A G 0.039721 0.239333 0.8681661 0.8681842 0.000241 0.0015974 35266
22 51238349 rs546389903 T C 0.169636 0.284785 0.5514219 0.5514001 0.000170 0.0013978 35266
22 51238660 rs569936315 A G -0.165150 0.152007 0.2772573 0.2772741 0.000066 0.0167732 442543
22 51239586 rs535432390 T G -0.011389 0.021291 0.5927151 0.5927046 0.002955 0.0001997 465812
22 51239678 rs573137567 G T 0.084837 0.086710 0.3278657 0.3278769 0.001843 0.0233626 35266
22 51244163 rs199560686 A G -0.028716 0.205313 0.8887469 0.8887671 0.000054 0.0077875 442543

bcf preview

1   16141   rs529651976 C   T   .   PASS    AF=0.00051  ES:SE:LP:AF:SS:ID   0.193236:0.217307:0.427274:0.00051:35266:rs529651976
1   49298   rs10399793  T   C   .   PASS    AF=0.823722 ES:SE:LP:AF:SS:ID   0.010168:0.011325:0.432684:0.823722:35266:rs10399793
1   54353   rs140052487 C   A   .   PASS    AF=0.001815 ES:SE:LP:AF:SS:ID   -0.037909:0.101934:0.148753:0.001815:35266:rs140052487
1   54564   rs558796213 G   T   .   PASS    AF=0.000143 ES:SE:LP:AF:SS:ID   0.165511:0.113086:0.843769:0.000143:407277:rs558796213
1   54591   rs561234294 A   G   .   PASS    AF=0.001552 ES:SE:LP:AF:SS:ID   -0.13895:0.121122:0.599837:0.001552:35266:rs561234294
1   54712   rs573184866 T   C   .   PASS    AF=0.010376 ES:SE:LP:AF:SS:ID   0.040937:0.044365:0.448376:0.010376:35266:rs573184866
1   54815   rs568686875 T   C   .   PASS    AF=0.000481 ES:SE:LP:AF:SS:ID   0.113181:0.188218:0.261503:0.000481:35266:rs568686875
1   55326   rs3107975   T   C   .   PASS    AF=0.019593 ES:SE:LP:AF:SS:ID   0.002358:0.03337:0.02519:0.019593:35266:rs3107975
1   55351   rs531766459 T   A   .   PASS    AF=0.000503 ES:SE:LP:AF:SS:ID   -0.043908:0.059989:0.333284:0.000503:407277:rs531766459
1   55405   rs372455836 C   T   .   PASS    AF=0.006822 ES:SE:LP:AF:SS:ID   0.056876:0.056491:0.503054:0.006822:35266:rs372455836
1   55416   rs193242050 G   A   .   PASS    AF=9.1e-05  ES:SE:LP:AF:SS:ID   -0.022388:0.167003:0.0489847:9.1e-05:442543:rs193242050
1   55427   rs183189405 T   C   .   PASS    AF=0.002334 ES:SE:LP:AF:SS:ID   -0.064685:0.111397:0.250664:0.002334:35266:rs183189405
1   56586   rs541979596 G   A   .   PASS    AF=0.001466 ES:SE:LP:AF:SS:ID   -0.073516:0.133743:0.234657:0.001466:35266:rs541979596
1   57095   rs553759011 T   C   .   PASS    AF=3.6e-05  ES:SE:LP:AF:SS:ID   0.257077:0.223333:0.602627:3.6e-05:407277:rs553759011
1   57183   rs368339209 A   G   .   PASS    AF=2.8e-05  ES:SE:LP:AF:SS:ID   -0.295778:0.366904:0.376582:2.8e-05:407277:rs368339209
1   61804   rs567421057 G   A   .   PASS    AF=7.4e-05  ES:SE:LP:AF:SS:ID   0.311489:0.163929:1.24088:7.4e-05:407277:rs567421057
1   61993   rs190553843 C   T   .   PASS    AF=9.3e-05  ES:SE:LP:AF:SS:ID   0.226111:0.159972:0.802686:9.3e-05:442543:rs190553843
1   62124   rs528478839 G   A   .   PASS    AF=0.000181 ES:SE:LP:AF:SS:ID   0.768062:0.394577:1.28731:0.000181:35266:rs528478839
1   62157   rs10399597  G   A   .   PASS    AF=0.000138 ES:SE:LP:AF:SS:ID   0.10167:0.097324:0.528459:0.000138:442543:rs10399597
1   62509   rs534313866 T   C   .   PASS    AF=0.000532 ES:SE:LP:AF:SS:ID   0.070227:0.219566:0.125465:0.000532:35266:rs534313866
1   62617   rs543126209 T   G   .   PASS    AF=9e-05    ES:SE:LP:AF:SS:ID   0.01682:0.16617:0.0365186:9e-05:442543:rs543126209
1   64670   rs545257650 A   G   .   PASS    AF=0.000146 ES:SE:LP:AF:SS:ID   0.028092:0.118105:0.0904531:0.000146:442543:rs545257650
1   64908   rs540391097 A   G   .   PASS    AF=0.000639 ES:SE:LP:AF:SS:ID   0.020423:0.053997:0.15164:0.000639:442543:rs540391097
1   65009   rs563233355 G   A   .   PASS    AF=0.000288 ES:SE:LP:AF:SS:ID   0.148768:0.073894:1.35551:0.000288:442543:rs563233355
1   65974   rs531923826 A   G   .   PASS    AF=0.004646 ES:SE:LP:AF:SS:ID   -0.035145:0.069149:0.213748:0.004646:35266:rs531923826
1   67179   rs149952626 C   G   .   PASS    AF=0.000128 ES:SE:LP:AF:SS:ID   -0.236124:0.368806:0.2823:0.000128:35266:rs149952626
1   67223   rs78676975  C   T   .   PASS    AF=0.000469 ES:SE:LP:AF:SS:ID   -0.087079:0.262266:0.130839:0.000469:35266:rs78676975
1   67224   rs566526215 G   A   .   PASS    AF=0.000161 ES:SE:LP:AF:SS:ID   -0.019901:0.124739:0.0588753:0.000161:442543:rs566526215
1   67631   rs533896527 G   C   .   PASS    AF=0.000196 ES:SE:LP:AF:SS:ID   -0.120959:0.096635:0.676426:0.000196:442543:rs533896527
1   69594   rs144967600 T   C   .   PASS    AF=0.000759 ES:SE:LP:AF:SS:ID   -0.119808:0.186131:0.28416:0.000759:35266:rs144967600
1   69610   rs376022826 C   T   .   PASS    AF=0.000222 ES:SE:LP:AF:SS:ID   0.312408:0.379227:0.387159:0.000222:35266:rs376022826
1   70317   rs570011908 G   A   .   PASS    AF=0.000636 ES:SE:LP:AF:SS:ID   0.099934:0.208227:0.199764:0.000636:35266:rs570011908
1   72526   rs547237130 A   G   .   PASS    AF=0.038335 ES:SE:LP:AF:SS:ID   -0.00594:0.023372:0.0972407:0.038335:35266:rs547237130
1   73093   rs535508237 G   A   .   PASS    AF=0.003934 ES:SE:LP:AF:SS:ID   0.079574:0.070563:0.585981:0.003934:35266:rs535508237
1   77763   rs557457745 G   A   .   PASS    AF=0.005372 ES:SE:LP:AF:SS:ID   -0.00102:0.062873:0.00566173:0.005372:35266:rs557457745
1   78942   rs372315362 C   G   .   PASS    AF=0.007964 ES:SE:LP:AF:SS:ID   0.019512:0.049537:0.158843:0.007964:35266:rs372315362
1   79033   rs2462495   A   G   .   PASS    AF=0.998705 ES:SE:LP:AF:SS:ID   0.042473:0.047336:0.4323:0.998705:407277:rs2462495
1   79137   rs143777184 A   T   .   PASS    AF=0.001012 ES:SE:LP:AF:SS:ID   -0.001057:0.043297:0.00854797:0.001012:442543:rs143777184
1   79188   rs534350410 G   T   .   PASS    AF=0.001116 ES:SE:LP:AF:SS:ID   -0.130695:0.1496:0.417576:0.001116:35266:rs534350410
1   82957   rs189774606 C   T   .   PASS    AF=0.000456 ES:SE:LP:AF:SS:ID   -0.038191:0.057331:0.296419:0.000456:442543:rs189774606
1   82961   rs537801787 C   T   .   PASS    AF=0.000505 ES:SE:LP:AF:SS:ID   -0.119155:0.21749:0.23373:0.000505:35266:rs537801787
1   82994   rs574556077 A   G   .   PASS    AF=0.000162 ES:SE:LP:AF:SS:ID   0.656357:0.355509:1.18798:0.000162:35266:rs574556077
1   83170   rs562997564 G   T   .   PASS    AF=0.001254 ES:SE:LP:AF:SS:ID   -0.048986:0.139008:0.139931:0.001254:35266:rs562997564
1   83771   rs189906733 T   G   .   PASS    AF=0.000652 ES:SE:LP:AF:SS:ID   -0.035773:0.049778:0.325715:0.000652:442543:rs189906733
1   84139   rs183605470 A   T   .   PASS    AF=0.020783 ES:SE:LP:AF:SS:ID   0.037348:0.031881:0.61729:0.020783:35266:rs183605470
1   84618   rs576633512 C   T   .   PASS    AF=0.000714 ES:SE:LP:AF:SS:ID   0.022133:0.187715:0.0428133:0.000714:35266:rs576633512
1   85622   rs185273034 A   T   .   PASS    AF=0.001251 ES:SE:LP:AF:SS:ID   -0.105834:0.138712:0.351166:0.001251:35266:rs185273034
1   85892   rs147185795 A   G   .   PASS    AF=0.000448 ES:SE:LP:AF:SS:ID   0.021261:0.064969:0.128724:0.000448:442543:rs147185795
1   86028   rs114608975 T   C   .   PASS    AF=0.061277 ES:SE:LP:AF:SS:ID   -0.018873:0.018315:0.518871:0.061277:35266:rs114608975
1   86192   rs548281277 G   A   .   PASS    AF=0.034594 ES:SE:LP:AF:SS:ID   -0.007579:0.024562:0.120527:0.034594:35266:rs548281277