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-24012_irnt/ukb-d-24012_irnt.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-24012_irnt/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 14:50:57 2019
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ukb-d-import/processed/ukb-d-24012_irnt/ukb-d-24012_irnt.vcf.gz ...
Read summary statistics for 13586415 SNPs.
Dropped 12712 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: 0.0024 (0.0013)
Lambda GC: 1.032
Mean Chi^2: 1.0347
Intercept: 1.0179 (0.006)
Ratio: 0.5155 (0.174)
Analysis finished at Mon Nov 25 14:53:00 2019
Total time elapsed: 2.0m:3.2s

QC metrics

Metrics

Metrics

{
    "af_correlation": 0.9521,
    "inflation_factor": 1.0235,
    "mean_EFFECT": 8.1813e-06,
    "n": 356078,
    "n_snps": 13586415,
    "n_clumped_hits": 0,
    "n_p_sig": 0,
    "n_mono": 0,
    "n_ns": 1251792,
    "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": 569244,
    "n_est": 357427.5802,
    "ratio_se_n": 1.0019,
    "mean_diff": -2.8068e-07,
    "ratio_diff": 1.1277,
    "sd_y_est1": 1.002,
    "sd_y_est2": 1.0039,
    "r2_sum1": 0,
    "r2_sum2": 0,
    "r2_sum3": 0,
    "r2_sum4": 0,
    "ldsc_nsnp_merge_refpanel_ld": 1283504,
    "ldsc_nsnp_merge_regression_ld": 1283504,
    "ldsc_observed_scale_h2_beta": 0.0024,
    "ldsc_observed_scale_h2_se": 0.0013,
    "ldsc_intercept_beta": 1.0179,
    "ldsc_intercept_se": 0.006,
    "ldsc_lambda_gc": 1.032,
    "ldsc_mean_chisq": 1.0347,
    "ldsc_ratio": 0.5159
}

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 FALSE
n_p_sig FALSE
miss_EFFECT FALSE
miss_SE FALSE
miss_PVAL FALSE
ldsc_ratio TRUE
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 0 1.000000 3 94 0 13574367 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 33336 0 NA NA NA NA NA NA NA NA
numeric CHROM 0 1.000000 NA NA NA NA NA 9.051311e+00 6.184978e+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 7.902519e+07 5.591495e+07 3.02000e+02 3.293092e+07 7.013876e+07 1.148595e+08 2.492309e+08 ▇▆▅▂▁
numeric EFFECT 0 1.000000 NA NA NA NA NA 8.200000e-06 1.393990e-02 -1.70298e-01 -3.710700e-03 -1.280000e-05 3.706200e-03 1.736440e-01 ▁▁▇▁▁
numeric SE 0 1.000000 NA NA NA NA NA 9.977800e-03 9.624600e-03 1.95250e-03 2.840700e-03 5.234800e-03 1.433920e-02 4.873740e-02 ▇▂▁▁▁
numeric PVAL 0 1.000000 NA NA NA NA NA 4.959996e-01 2.896490e-01 1.00000e-07 2.441057e-01 4.950135e-01 7.467255e-01 1.000000e+00 ▇▇▇▇▇
numeric PVAL_ztest 0 1.000000 NA NA NA NA NA 4.959992e-01 2.896493e-01 1.00000e-07 2.441047e-01 4.950139e-01 7.467251e-01 1.000000e+00 ▇▇▇▇▇
numeric AF 0 1.000000 NA NA NA NA NA 1.908043e-01 2.544029e-01 1.00000e-03 7.429700e-03 6.003110e-02 2.953120e-01 9.990000e-01 ▇▂▁▁▁
numeric AF_reference 569244 0.958102 NA NA NA NA NA 1.963351e-01 2.471015e-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 3.560780e+05 0.000000e+00 3.56078e+05 3.560780e+05 3.560780e+05 3.560780e+05 3.560780e+05 ▁▁▇▁▁

Head and tail

CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
1 692794 rs530212009 CA C 0.0025169 0.0041567 0.5448450 0.5448443 0.1107130 0.1894970 356078
1 693731 rs12238997 A G 0.0032396 0.0039279 0.4095067 0.4095079 0.1158900 0.1417730 356078
1 707522 rs371890604 G C 0.0014562 0.0044154 0.7415527 0.7415532 0.0973637 0.1293930 356078
1 717587 rs144155419 G A 0.0016711 0.0105306 0.8739140 0.8739132 0.0157121 0.0045926 356078
1 723329 rs189787166 A T 0.0431969 0.0309801 0.1632138 0.1632139 0.0017446 0.0003994 356078
1 730087 rs148120343 T C 0.0063642 0.0054709 0.2447192 0.2447188 0.0565129 0.0127796 356078
1 731718 rs142557973 T C 0.0038498 0.0037249 0.3013499 0.3013491 0.1218180 0.1543530 356078
1 732032 rs61770163 A C 0.0032762 0.0039731 0.4096019 0.4096013 0.1212470 0.1555510 356078
1 734349 rs141242758 T C 0.0038505 0.0037268 0.3015178 0.3015179 0.1210470 0.1525560 356078
1 740284 rs61770167 C T -0.0122189 0.0170476 0.4735295 0.4735272 0.0057913 0.0023962 356078
CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
23 154923311 rs141127553 C T -0.0032561 0.0043063 0.4495759 0.4495755 0.0561325 0.0309934 356078
23 154923374 rs111332691 T A -0.0029264 0.0047307 0.5361755 0.5361762 0.0448090 0.0116556 356078
23 154925045 rs509981 C T -0.0003753 0.0022764 0.8690471 0.8690467 0.2456450 0.3634440 356078
23 154925895 rs538470 C T -0.0006993 0.0023286 0.7639431 0.7639426 0.2419560 0.3634440 356078
23 154927581 rs644138 G A -0.0010799 0.0021408 0.6139585 0.6139589 0.3021670 0.4635760 356078
23 154929412 rs557132 C T -0.0004060 0.0022771 0.8584909 0.8584914 0.2454960 0.3568210 356078
23 154929637 rs35185538 CT C 0.0004954 0.0023765 0.8348770 0.8348768 0.2296940 0.3011920 356078
23 154929952 rs4012982 CAA C -0.0006889 0.0023951 0.7736312 0.7736317 0.2394250 0.3165560 356078
23 154930230 rs781880 A G -0.0005066 0.0022767 0.8239110 0.8239109 0.2459020 0.3618540 356078
23 154930487 rs781879 T A 0.0010439 0.0078048 0.8936019 0.8936018 0.0195825 0.1263580 356078

bcf preview

1   692794  rs530212009 CA  C   .   PASS    AF=0.110713 ES:SE:LP:AF:SS:ID   0.00251691:0.00415672:0.263727:0.110713:356078:1_692794_CA_C
1   693731  rs12238997  A   G   .   PASS    AF=0.11589  ES:SE:LP:AF:SS:ID   0.00323955:0.00392787:0.387739:0.11589:356078:rs12238997
1   707522  rs371890604 G   C   .   PASS    AF=0.0973637    ES:SE:LP:AF:SS:ID   0.00145617:0.00441535:0.129858:0.0973637:356078:rs371890604
1   717587  rs144155419 G   A   .   PASS    AF=0.0157121    ES:SE:LP:AF:SS:ID   0.0016711:0.0105306:0.0585313:0.0157121:356078:rs144155419
1   723329  rs189787166 A   T   .   PASS    AF=0.00174463   ES:SE:LP:AF:SS:ID   0.0431969:0.0309801:0.787243:0.00174463:356078:rs189787166
1   730087  rs148120343 T   C   .   PASS    AF=0.0565129    ES:SE:LP:AF:SS:ID   0.00636415:0.0054709:0.611332:0.0565129:356078:rs148120343
1   731718  rs58276399  T   C   .   PASS    AF=0.121818 ES:SE:LP:AF:SS:ID   0.00384984:0.00372489:0.520929:0.121818:356078:rs58276399
1   732032  rs61770163  A   C   .   PASS    AF=0.121247 ES:SE:LP:AF:SS:ID   0.0032762:0.0039731:0.387638:0.121247:356078:rs61770163
1   734349  rs141242758 T   C   .   PASS    AF=0.121047 ES:SE:LP:AF:SS:ID   0.00385049:0.00372682:0.520687:0.121047:356078:rs141242758
1   740284  rs61770167  C   T   .   PASS    AF=0.00579128   ES:SE:LP:AF:SS:ID   -0.0122189:0.0170476:0.324653:0.00579128:356078:rs61770167
1   742813  rs112573343 C   T   .   PASS    AF=0.00187621   ES:SE:LP:AF:SS:ID   -0.00921532:0.032228:0.110741:0.00187621:356078:rs112573343
1   749963  rs529266287 T   TAA .   PASS    AF=0.869645 ES:SE:LP:AF:SS:ID   -0.00419705:0.00367394:0.596375:0.869645:356078:rs529266287
1   750230  rs190826124 G   C   .   PASS    AF=0.00154059   ES:SE:LP:AF:SS:ID   -0.0304741:0.0331453:0.446261:0.00154059:356078:rs190826124
1   751343  rs28544273  T   A   .   PASS    AF=0.123008 ES:SE:LP:AF:SS:ID   0.00455894:0.00363846:0.677342:0.123008:356078:rs28544273
1   751488  rs200141114 G   GA  .   PASS    AF=0.142781 ES:SE:LP:AF:SS:ID   0.00636802:0.0035968:1.11549:0.142781:356078:rs200141114
1   751756  rs28527770  T   C   .   PASS    AF=0.123123 ES:SE:LP:AF:SS:ID   0.00461744:0.00363339:0.690821:0.123123:356078:rs28527770
1   753405  rs3115860   C   A   .   PASS    AF=0.870791 ES:SE:LP:AF:SS:ID   -0.00509515:0.00354074:0.823478:0.870791:356078:rs3115860
1   753425  rs3131970   T   C   .   PASS    AF=0.875378 ES:SE:LP:AF:SS:ID   -0.00447205:0.00359935:0.669448:0.875378:356078:rs3131970
1   753541  rs2073813   G   A   .   PASS    AF=0.128727 ES:SE:LP:AF:SS:ID   0.00537278:0.00354968:0.885623:0.128727:356078:rs2073813
1   754105  rs12184325  C   T   .   PASS    AF=0.0363881    ES:SE:LP:AF:SS:ID   0.00694993:0.00644049:0.551999:0.0363881:356078:rs12184325
1   754182  rs3131969   A   G   .   PASS    AF=0.870387 ES:SE:LP:AF:SS:ID   -0.00517236:0.00353716:0.842661:0.870387:356078:rs3131969
1   754192  rs3131968   A   G   .   PASS    AF=0.870493 ES:SE:LP:AF:SS:ID   -0.00508747:0.00353878:0.822351:0.870493:356078:rs3131968
1   754334  rs3131967   T   C   .   PASS    AF=0.870385 ES:SE:LP:AF:SS:ID   -0.00511776:0.00353704:0.829958:0.870385:356078:rs3131967
1   754433  rs150578204 G   A   .   PASS    AF=0.00505302   ES:SE:LP:AF:SS:ID   0.0270008:0.0181465:0.864012:0.00505302:356078:rs150578204
1   754458  rs142682604 G   T   .   PASS    AF=0.00501973   ES:SE:LP:AF:SS:ID   0.0267723:0.0181953:0.850202:0.00501973:356078:rs142682604
1   755435  rs184270342 T   G   .   PASS    AF=0.00558794   ES:SE:LP:AF:SS:ID   0.0118942:0.0175907:0.301953:0.00558794:356078:rs184270342
1   755890  rs3115858   A   T   .   PASS    AF=0.870467 ES:SE:LP:AF:SS:ID   -0.00506144:0.00353075:0.818994:0.870467:356078:rs3115858
1   756434  rs61768170  G   C   .   PASS    AF=0.12608  ES:SE:LP:AF:SS:ID   0.00477518:0.00360261:0.732795:0.12608:356078:rs61768170
1   756604  rs3131962   A   G   .   PASS    AF=0.870031 ES:SE:LP:AF:SS:ID   -0.0049912:0.00352229:0.805555:0.870031:356078:rs3131962
1   757640  rs3115853   G   A   .   PASS    AF=0.869316 ES:SE:LP:AF:SS:ID   -0.00469794:0.00351908:0.740215:0.869316:356078:rs3115853
1   757734  rs4951929   C   T   .   PASS    AF=0.870184 ES:SE:LP:AF:SS:ID   -0.00498786:0.00352527:0.803816:0.870184:356078:rs4951929
1   757936  rs4951862   C   A   .   PASS    AF=0.87019  ES:SE:LP:AF:SS:ID   -0.00499104:0.00352553:0.804466:0.87019:356078:rs4951862
1   758144  rs3131956   A   G   .   PASS    AF=0.870199 ES:SE:LP:AF:SS:ID   -0.00501849:0.00352564:0.810754:0.870199:356078:rs3131956
1   758626  rs3131954   C   T   .   PASS    AF=0.870641 ES:SE:LP:AF:SS:ID   -0.00501265:0.0035346:0.806477:0.870641:356078:rs3131954
1   759293  rs10157329  T   A   .   PASS    AF=0.0988967    ES:SE:LP:AF:SS:ID   0.00394647:0.00410806:0.47273:0.0988967:356078:rs10157329
1   759600  rs545998451 AGT A   .   PASS    AF=0.00647681   ES:SE:LP:AF:SS:ID   -0.00222588:0.0158942:0.051281:0.00647681:356078:1_759600_AGT_A
1   759837  rs3115851   T   A   .   PASS    AF=0.874543 ES:SE:LP:AF:SS:ID   -0.00486489:0.00358732:0.756818:0.874543:356078:rs3115851
1   761732  rs2286139   C   T   .   PASS    AF=0.863929 ES:SE:LP:AF:SS:ID   -0.00506207:0.00351799:0.823397:0.863929:356078:rs2286139
1   761752  rs1057213   C   T   .   PASS    AF=0.869332 ES:SE:LP:AF:SS:ID   -0.00454314:0.003552:0.697052:0.869332:356078:rs1057213
1   762273  rs3115849   G   A   .   PASS    AF=0.866266 ES:SE:LP:AF:SS:ID   -0.0051763:0.0035527:0.838285:0.866266:356078:rs3115849
1   762485  rs12095200  C   A   .   PASS    AF=0.098821 ES:SE:LP:AF:SS:ID   0.00467774:0.00425413:0.566203:0.098821:356078:rs12095200
1   762589  rs3115848   G   C   .   PASS    AF=0.87146  ES:SE:LP:AF:SS:ID   -0.00528423:0.00359321:0.849563:0.87146:356078:rs3115848
1   762592  rs3131950   C   G   .   PASS    AF=0.87146  ES:SE:LP:AF:SS:ID   -0.00528373:0.00359321:0.849446:0.87146:356078:rs3131950
1   762601  rs3131949   T   C   .   PASS    AF=0.871459 ES:SE:LP:AF:SS:ID   -0.00526847:0.00359328:0.845896:0.871459:356078:rs3131949
1   762632  rs3131948   T   A   .   PASS    AF=0.871833 ES:SE:LP:AF:SS:ID   -0.00531871:0.00359532:0.856829:0.871833:356078:rs3131948
1   764191  rs7515915   T   G   .   PASS    AF=0.125656 ES:SE:LP:AF:SS:ID   0.004986:0.00359815:0.780321:0.125656:356078:rs7515915
1   766007  rs61768174  A   C   .   PASS    AF=0.105486 ES:SE:LP:AF:SS:ID   0.00338657:0.00391743:0.411929:0.105486:356078:rs61768174
1   766105  rs2519015   T   A   .   PASS    AF=0.855284 ES:SE:LP:AF:SS:ID   -0.00368098:0.00351685:0.529807:0.855284:356078:rs2519015
1   767393  rs538667473 A   C   .   PASS    AF=0.00166364   ES:SE:LP:AF:SS:ID   0.0398078:0.0310588:0.699076:0.00166364:356078:rs538667473
1   768116  rs376645387 A   AGTTTT  .   PASS    AF=0.838337 ES:SE:LP:AF:SS:ID   -0.0032242:0.00346587:0.453172:0.838337:356078:rs376645387