Summary

Summary {data-width=650}

Manhattan plot

manhattan_plot

manhattan_plot

QQ plot

qq_plot

qq_plot

AF plot

af_plot

af_plot

P-Z plot

pz_plot

pz_plot

beta_std 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 /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ukb-d-import/processed/ukb-d-30770_raw/ukb-d-30770_raw.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-30770_raw/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 14:55:06 2019
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ukb-d-import/processed/ukb-d-30770_raw/ukb-d-30770_raw.vcf.gz ...
Read summary statistics for 13585999 SNPs.
Dropped 12711 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, 1283504 SNPs remain.
After merging with regression SNP LD, 1283504 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.2011 (0.0138)
Lambda GC: 1.7329
Mean Chi^2: 2.6819
Intercept: 1.1792 (0.0194)
Ratio: 0.1066 (0.0115)
Analysis finished at Mon Nov 25 14:57:50 2019
Total time elapsed: 2.0m:44.6s

QC metrics

Metrics

Metrics

{
    "af_correlation": 0.9521,
    "inflation_factor": 1.4445,
    "mean_EFFECT": -0.0002,
    "n": 342439,
    "n_snps": 13585999,
    "n_clumped_hits": 349,
    "n_p_sig": 88864,
    "n_mono": 0,
    "n_ns": 1251784,
    "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": 569172,
    "n_est": 343760.9317,
    "ratio_se_n": 1.0019,
    "mean_diff": 0.0002,
    "ratio_diff": 408.4986,
    "sd_y_est1": 5.4695,
    "sd_y_est2": 5.4801,
    "r2_sum1": 2.8552,
    "r2_sum2": 0.0954,
    "r2_sum3": 0.0951,
    "r2_sum4": 0.0951,
    "ldsc_nsnp_merge_refpanel_ld": 1283504,
    "ldsc_nsnp_merge_regression_ld": 1283504,
    "ldsc_observed_scale_h2_beta": 0.2011,
    "ldsc_observed_scale_h2_se": 0.0138,
    "ldsc_intercept_beta": 1.1792,
    "ldsc_intercept_se": 0.0194,
    "ldsc_lambda_gc": 1.7329,
    "ldsc_mean_chisq": 2.6819,
    "ldsc_ratio": 0.1065
}

Flags

name value
af_correlation FALSE
inflation_factor TRUE
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 TRUE
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 0 1.000000 3 94 0 13573952 0 NA NA NA NA NA NA NA NA
character REF 0 1.000000 1 100 0 57080 0 NA NA NA NA NA NA NA NA
character ALT 0 1.000000 1 342 0 33338 0 NA NA NA NA NA NA NA NA
numeric CHROM 0 1.000000 NA NA NA NA NA 9.051247e+00 6.184981e+00 1.00000e+00 4.000000e+00 8.000000e+00 1.300000e+01 2.300000e+01 ▇▅▅▂▂
numeric POS 0 1.000000 NA NA NA NA NA 7.902573e+07 5.591519e+07 3.02000e+02 3.293103e+07 7.013957e+07 1.148603e+08 2.492309e+08 ▇▆▅▂▁
numeric EFFECT 0 1.000000 NA NA NA NA NA -1.988000e-04 8.295390e-02 -3.14540e+00 -2.631100e-02 -2.589000e-04 2.589000e-02 1.708800e+00 ▁▁▁▇▁
numeric SE 0 1.000000 NA NA NA NA NA 5.553630e-02 5.357070e-02 1.08660e-02 1.581200e-02 2.913800e-02 7.980900e-02 2.706800e-01 ▇▂▁▁▁
numeric PVAL 0 1.000000 NA NA NA NA NA 4.387261e-01 3.060669e-01 0.00000e+00 1.577001e-01 4.175601e-01 7.035906e-01 1.000000e+00 ▇▅▅▅▅
numeric PVAL_ztest 0 1.000000 NA NA NA NA NA 4.387256e-01 3.060671e-01 0.00000e+00 1.576938e-01 4.175573e-01 7.035914e-01 1.000000e+00 ▇▅▅▅▅
numeric AF 0 1.000000 NA NA NA NA NA 1.908096e-01 2.544043e-01 1.00000e-03 7.431300e-03 6.003900e-02 2.953200e-01 9.990000e-01 ▇▂▁▁▁
numeric AF_reference 569172 0.958106 NA NA NA NA NA 1.963391e-01 2.471024e-01 0.00000e+00 5.591000e-03 8.426520e-02 3.081070e-01 1.000000e+00 ▇▂▁▁▁
numeric N 0 1.000000 NA NA NA NA NA 3.424390e+05 0.000000e+00 3.42439e+05 3.424390e+05 3.424390e+05 3.424390e+05 3.424390e+05 ▁▁▇▁▁

Head and tail

CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
1 692794 rs530212009 CA C -0.053161 0.023142 0.0216108 0.0216093 0.1105800 0.1894970 342439
1 693731 rs12238997 A G -0.049784 0.021859 0.0227562 0.0227560 0.1158400 0.1417730 342439
1 707522 rs371890604 G C -0.049539 0.024585 0.0439066 0.0439037 0.0972800 0.1293930 342439
1 717587 rs144155419 G A -0.101350 0.058693 0.0841957 0.0842069 0.0156720 0.0045926 342439
1 723329 rs189787166 A T -0.165280 0.172830 0.3389300 0.3389129 0.0017381 0.0003994 342439
1 730087 rs148120343 T C -0.069906 0.030463 0.0217490 0.0217455 0.0564480 0.0127796 342439
1 731718 rs142557973 T C -0.043805 0.020732 0.0346123 0.0346079 0.1217400 0.1543530 342439
1 732032 rs61770163 A C -0.049844 0.022123 0.0242560 0.0242566 0.1211400 0.1555510 342439
1 734349 rs141242758 T C -0.044565 0.020743 0.0316818 0.0316792 0.1209600 0.1525560 342439
1 740284 rs61770167 C T 0.078380 0.095136 0.4100096 0.4100116 0.0057601 0.0023962 342439
CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
23 154923311 rs141127553 C T -0.0539930 0.023948 0.0241630 0.0241589 0.056253 0.0309934 342439
23 154923374 rs111332691 T A -0.0445210 0.026303 0.0905357 0.0905277 0.044881 0.0116556 342439
23 154925045 rs509981 C T 0.0005920 0.012671 0.9627400 0.9627370 0.245620 0.3634440 342439
23 154925895 rs538470 C T 0.0005610 0.012962 0.9654800 0.9654799 0.241940 0.3634440 342439
23 154927581 rs644138 G A -0.0131480 0.011916 0.2698603 0.2698577 0.302260 0.4635760 342439
23 154929412 rs557132 C T 0.0003743 0.012675 0.9764401 0.9764421 0.245480 0.3568210 342439
23 154929637 rs35185538 CT C 0.0123830 0.013228 0.3491797 0.3492112 0.229770 0.3011920 342439
23 154929952 rs4012982 CAA C 0.0008075 0.013330 0.9517001 0.9516962 0.239460 0.3165560 342439
23 154930230 rs781880 A G -0.0004907 0.012673 0.9691201 0.9691161 0.245880 0.3618540 342439
23 154930487 rs781879 T A 0.0621790 0.043420 0.1521399 0.1521335 0.019573 0.1263580 342439

bcf preview

1   692794  rs530212009 CA  C   .   PASS    AF=0.11058  ES:SE:LP:AF:SS:ID   -0.053161:0.023142:1.66533:0.11058:342439:1_692794_CA_C
1   693731  rs12238997  A   G   .   PASS    AF=0.11584  ES:SE:LP:AF:SS:ID   -0.049784:0.021859:1.6429:0.11584:342439:rs12238997
1   707522  rs371890604 G   C   .   PASS    AF=0.09728  ES:SE:LP:AF:SS:ID   -0.049539:0.024585:1.35747:0.09728:342439:rs371890604
1   717587  rs144155419 G   A   .   PASS    AF=0.015672 ES:SE:LP:AF:SS:ID   -0.10135:0.058693:1.07471:0.015672:342439:rs144155419
1   723329  rs189787166 A   T   .   PASS    AF=0.0017381    ES:SE:LP:AF:SS:ID   -0.16528:0.17283:0.46989:0.0017381:342439:rs189787166
1   730087  rs148120343 T   C   .   PASS    AF=0.056448 ES:SE:LP:AF:SS:ID   -0.069906:0.030463:1.66256:0.056448:342439:rs148120343
1   731718  rs58276399  T   C   .   PASS    AF=0.12174  ES:SE:LP:AF:SS:ID   -0.043805:0.020732:1.46077:0.12174:342439:rs58276399
1   732032  rs61770163  A   C   .   PASS    AF=0.12114  ES:SE:LP:AF:SS:ID   -0.049844:0.022123:1.61518:0.12114:342439:rs61770163
1   734349  rs141242758 T   C   .   PASS    AF=0.12096  ES:SE:LP:AF:SS:ID   -0.044565:0.020743:1.49919:0.12096:342439:rs141242758
1   740284  rs61770167  C   T   .   PASS    AF=0.0057601    ES:SE:LP:AF:SS:ID   0.07838:0.095136:0.387206:0.0057601:342439:rs61770167
1   742813  rs112573343 C   T   .   PASS    AF=0.0018641    ES:SE:LP:AF:SS:ID   0.12741:0.18026:0.319039:0.0018641:342439:rs112573343
1   749963  rs529266287 T   TAA .   PASS    AF=0.86976  ES:SE:LP:AF:SS:ID   0.052075:0.020452:1.96289:0.86976:342439:rs529266287
1   750230  rs190826124 G   C   .   PASS    AF=0.0015221    ES:SE:LP:AF:SS:ID   0.063273:0.18573:0.134689:0.0015221:342439:rs190826124
1   751343  rs28544273  T   A   .   PASS    AF=0.12291  ES:SE:LP:AF:SS:ID   -0.050362:0.020253:1.88954:0.12291:342439:rs28544273
1   751488  rs200141114 G   GA  .   PASS    AF=0.14275  ES:SE:LP:AF:SS:ID   -0.049656:0.020016:1.8824:0.14275:342439:rs200141114
1   751756  rs28527770  T   C   .   PASS    AF=0.12303  ES:SE:LP:AF:SS:ID   -0.050216:0.020225:1.88496:0.12303:342439:rs28527770
1   753405  rs3115860   C   A   .   PASS    AF=0.87092  ES:SE:LP:AF:SS:ID   0.045573:0.019712:1.68238:0.87092:342439:rs3115860
1   753425  rs3131970   T   C   .   PASS    AF=0.87549  ES:SE:LP:AF:SS:ID   0.048556:0.020036:1.81324:0.87549:342439:rs3131970
1   753541  rs2073813   G   A   .   PASS    AF=0.12862  ES:SE:LP:AF:SS:ID   -0.045249:0.01976:1.65704:0.12862:342439:rs2073813
1   754105  rs12184325  C   T   .   PASS    AF=0.036325 ES:SE:LP:AF:SS:ID   -0.04002:0.035879:0.577279:0.036325:342439:rs12184325
1   754182  rs3131969   A   G   .   PASS    AF=0.87051  ES:SE:LP:AF:SS:ID   0.044739:0.019691:1.63669:0.87051:342439:rs3131969
1   754192  rs3131968   A   G   .   PASS    AF=0.87061  ES:SE:LP:AF:SS:ID   0.044755:0.0197:1.63646:0.87061:342439:rs3131968
1   754334  rs3131967   T   C   .   PASS    AF=0.87051  ES:SE:LP:AF:SS:ID   0.045063:0.01969:1.65557:0.87051:342439:rs3131967
1   754433  rs150578204 G   A   .   PASS    AF=0.0050432    ES:SE:LP:AF:SS:ID   0.0041155:0.10108:0.01434:0.0050432:342439:rs150578204
1   754458  rs142682604 G   T   .   PASS    AF=0.0050102    ES:SE:LP:AF:SS:ID   0.003092:0.10135:0.0107015:0.0050102:342439:rs142682604
1   755435  rs184270342 T   G   .   PASS    AF=0.005551 ES:SE:LP:AF:SS:ID   -0.20606:0.098226:1.44462:0.005551:342439:rs184270342
1   755890  rs3115858   A   T   .   PASS    AF=0.8706   ES:SE:LP:AF:SS:ID   0.045491:0.019656:1.6851:0.8706:342439:rs3115858
1   756434  rs61768170  G   C   .   PASS    AF=0.12596  ES:SE:LP:AF:SS:ID   -0.051565:0.020055:1.99413:0.12596:342439:rs61768170
1   756604  rs3131962   A   G   .   PASS    AF=0.87016  ES:SE:LP:AF:SS:ID   0.048285:0.019609:1.86003:0.87016:342439:rs3131962
1   757640  rs3115853   G   A   .   PASS    AF=0.86944  ES:SE:LP:AF:SS:ID   0.046266:0.019591:1.73993:0.86944:342439:rs3115853
1   757734  rs4951929   C   T   .   PASS    AF=0.87031  ES:SE:LP:AF:SS:ID   0.047097:0.019626:1.78497:0.87031:342439:rs4951929
1   757936  rs4951862   C   A   .   PASS    AF=0.87032  ES:SE:LP:AF:SS:ID   0.047133:0.019627:1.78696:0.87032:342439:rs4951862
1   758144  rs3131956   A   G   .   PASS    AF=0.87033  ES:SE:LP:AF:SS:ID   0.047088:0.019628:1.78415:0.87033:342439:rs3131956
1   758626  rs3131954   C   T   .   PASS    AF=0.87077  ES:SE:LP:AF:SS:ID   0.045594:0.019677:1.68827:0.87077:342439:rs3131954
1   759293  rs10157329  T   A   .   PASS    AF=0.098815 ES:SE:LP:AF:SS:ID   -0.049512:0.022869:1.51733:0.098815:342439:rs10157329
1   759600  rs545998451 AGT A   .   PASS    AF=0.0064395    ES:SE:LP:AF:SS:ID   -0.19187:0.088757:1.51371:0.0064395:342439:1_759600_AGT_A
1   759837  rs3115851   T   A   .   PASS    AF=0.87466  ES:SE:LP:AF:SS:ID   0.05035:0.019969:1.93215:0.87466:342439:rs3115851
1   761732  rs2286139   C   T   .   PASS    AF=0.86407  ES:SE:LP:AF:SS:ID   0.047683:0.019587:1.82641:0.86407:342439:rs2286139
1   761752  rs1057213   C   T   .   PASS    AF=0.86945  ES:SE:LP:AF:SS:ID   0.046391:0.019774:1.72191:0.86945:342439:rs1057213
1   762273  rs3115849   G   A   .   PASS    AF=0.86639  ES:SE:LP:AF:SS:ID   0.050798:0.019778:1.99068:0.86639:342439:rs3115849
1   762485  rs12095200  C   A   .   PASS    AF=0.098767 ES:SE:LP:AF:SS:ID   -0.04864:0.023676:1.39866:0.098767:342439:rs12095200
1   762589  rs3115848   G   C   .   PASS    AF=0.87158  ES:SE:LP:AF:SS:ID   0.054149:0.020004:2.16796:0.87158:342439:rs3115848
1   762592  rs3131950   C   G   .   PASS    AF=0.87158  ES:SE:LP:AF:SS:ID   0.054148:0.020004:2.16789:0.87158:342439:rs3131950
1   762601  rs3131949   T   C   .   PASS    AF=0.87158  ES:SE:LP:AF:SS:ID   0.054099:0.020005:2.16467:0.87158:342439:rs3131949
1   762632  rs3131948   T   A   .   PASS    AF=0.87195  ES:SE:LP:AF:SS:ID   0.054501:0.020016:2.18902:0.87195:342439:rs3131948
1   764191  rs7515915   T   G   .   PASS    AF=0.12555  ES:SE:LP:AF:SS:ID   -0.051017:0.020029:1.96409:0.12555:342439:rs7515915
1   766007  rs61768174  A   C   .   PASS    AF=0.10543  ES:SE:LP:AF:SS:ID   -0.046011:0.021808:1.45745:0.10543:342439:rs61768174
1   766105  rs2519015   T   A   .   PASS    AF=0.85541  ES:SE:LP:AF:SS:ID   0.047166:0.01958:1.79583:0.85541:342439:rs2519015
1   767393  rs538667473 A   C   .   PASS    AF=0.0016566    ES:SE:LP:AF:SS:ID   -0.14386:0.17327:0.391068:0.0016566:342439:rs538667473
1   768116  rs376645387 A   AGTTTT  .   PASS    AF=0.8382   ES:SE:LP:AF:SS:ID   0.052328:0.019277:2.17789:0.8382:342439:rs376645387