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-30870_raw/ukb-d-30870_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-30870_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 15:26:24 2019
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ukb-d-import/processed/ukb-d-30870_raw/ukb-d-30870_raw.vcf.gz ...
Read summary statistics for 13586006 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: 0.1632 (0.0245)
Lambda GC: 1.5236
Mean Chi^2: 2.304
Intercept: 1.1196 (0.017)
Ratio: 0.0917 (0.013)
Analysis finished at Mon Nov 25 15:28:41 2019
Total time elapsed: 2.0m:17.42s

QC metrics

Metrics

Metrics

{
    "af_correlation": 0.9521,
    "inflation_factor": 1.3329,
    "mean_EFFECT": 0,
    "n": 343992,
    "n_snps": 13586006,
    "n_clumped_hits": 197,
    "n_p_sig": 47169,
    "n_mono": 0,
    "n_ns": 1251783,
    "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": 569174,
    "n_est": 345334.4669,
    "ratio_se_n": 1.0019,
    "mean_diff": 9.1176e-07,
    "ratio_diff": 1.0253,
    "sd_y_est1": 0.9973,
    "sd_y_est2": 0.9993,
    "r2_sum1": 0.0776,
    "r2_sum2": 0.078,
    "r2_sum3": 0.0777,
    "r2_sum4": 0.0771,
    "ldsc_nsnp_merge_refpanel_ld": 1283504,
    "ldsc_nsnp_merge_regression_ld": 1283504,
    "ldsc_observed_scale_h2_beta": 0.1632,
    "ldsc_observed_scale_h2_se": 0.0245,
    "ldsc_intercept_beta": 1.1196,
    "ldsc_intercept_se": 0.017,
    "ldsc_lambda_gc": 1.5236,
    "ldsc_mean_chisq": 2.304,
    "ldsc_ratio": 0.0917
}

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 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 1.0000000 3 94 0 13573959 0 NA NA NA NA NA NA NA NA
character REF 0 1.0000000 1 100 0 57083 0 NA NA NA NA NA NA NA NA
character ALT 0 1.0000000 1 342 0 33337 0 NA NA NA NA NA NA NA NA
numeric CHROM 0 1.0000000 NA NA NA NA NA 9.051253e+00 6.184969e+00 1.00000e+00 4.000000e+00 8.000000e+00 1.300000e+01 2.300000e+01 ▇▅▅▂▂
numeric POS 0 1.0000000 NA NA NA NA NA 7.902586e+07 5.591530e+07 3.02000e+02 3.293100e+07 7.013949e+07 1.148608e+08 2.492309e+08 ▇▆▅▂▁
numeric EFFECT 0 1.0000000 NA NA NA NA NA 3.010000e-05 1.492800e-02 -8.77230e-01 -4.478100e-03 1.800000e-06 4.497600e-03 5.046500e-01 ▁▁▁▇▁
numeric SE 0 1.0000000 NA NA NA NA NA 1.010390e-02 9.746400e-03 1.97690e-03 2.876800e-03 5.301000e-03 1.452000e-02 4.921200e-02 ▇▂▁▁▁
numeric PVAL 0 1.0000000 NA NA NA NA NA 4.520637e-01 3.025041e-01 0.00000e+00 1.776499e-01 4.361602e-01 7.140506e-01 1.000000e+00 ▇▆▆▅▅
numeric PVAL_ztest 0 1.0000000 NA NA NA NA NA 4.520632e-01 3.025043e-01 0.00000e+00 1.776527e-01 4.361579e-01 7.140522e-01 1.000000e+00 ▇▆▆▅▅
numeric AF 0 1.0000000 NA NA NA NA NA 1.908098e-01 2.544046e-01 1.00000e-03 7.431400e-03 6.003900e-02 2.953200e-01 9.990000e-01 ▇▂▁▁▁
numeric AF_reference 569174 0.9581059 NA NA NA NA NA 1.963393e-01 2.471027e-01 0.00000e+00 5.591000e-03 8.426520e-02 3.081070e-01 1.000000e+00 ▇▂▁▁▁
numeric N 0 1.0000000 NA NA NA NA NA 3.439920e+05 0.000000e+00 3.43992e+05 3.439920e+05 3.439920e+05 3.439920e+05 3.439920e+05 ▁▁▇▁▁

Head and tail

CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
1 692794 rs530212009 CA C -0.0024042 0.0042115 0.5680898 0.5680908 0.1105200 0.1894970 343992
1 693731 rs12238997 A G -0.0016415 0.0039775 0.6798295 0.6798291 0.1158100 0.1417730 343992
1 707522 rs371890604 G C 0.0005364 0.0044741 0.9045700 0.9045685 0.0972480 0.1293930 343992
1 717587 rs144155419 G A -0.0156760 0.0106790 0.1421399 0.1421239 0.0156650 0.0045926 343992
1 723329 rs189787166 A T -0.0260000 0.0314500 0.4083899 0.4084020 0.0017377 0.0003994 343992
1 730087 rs148120343 T C 0.0007841 0.0055435 0.8875199 0.8875156 0.0564240 0.0127796 343992
1 731718 rs142557973 T C -0.0016378 0.0037726 0.6642002 0.6641938 0.1217000 0.1543530 343992
1 732032 rs61770163 A C -0.0003349 0.0040255 0.9337001 0.9336968 0.1211100 0.1555510 343992
1 734349 rs141242758 T C -0.0015071 0.0037747 0.6896901 0.6896990 0.1209200 0.1525560 343992
1 740284 rs61770167 C T -0.0018787 0.0173160 0.9136099 0.9136030 0.0057545 0.0023962 343992
CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
23 154923311 rs141127553 C T -0.0066514 0.0043597 0.1271001 0.1270957 0.056185 0.0309934 343992
23 154923374 rs111332691 T A 0.0050313 0.0047859 0.2931298 0.2931320 0.044864 0.0116556 343992
23 154925045 rs509981 C T -0.0107140 0.0023050 0.0000033 0.0000033 0.245690 0.3634440 343992
23 154925895 rs538470 C T -0.0108960 0.0023578 0.0000038 0.0000038 0.242030 0.3634440 343992
23 154927581 rs644138 G A -0.0112360 0.0021678 0.0000002 0.0000002 0.302260 0.4635760 343992
23 154929412 rs557132 C T -0.0106320 0.0023056 0.0000040 0.0000040 0.245550 0.3568210 343992
23 154929637 rs35185538 CT C -0.0118840 0.0024065 0.0000008 0.0000008 0.229790 0.3011920 343992
23 154929952 rs4012982 CAA C -0.0110650 0.0024248 0.0000050 0.0000050 0.239530 0.3165560 343992
23 154930230 rs781880 A G -0.0107300 0.0023053 0.0000033 0.0000032 0.245950 0.3618540 343992
23 154930487 rs781879 T A -0.0055748 0.0079039 0.4806102 0.4806094 0.019560 0.1263580 343992

bcf preview

1   692794  rs530212009 CA  C   .   PASS    AF=0.11052  ES:SE:LP:AF:SS:ID   -0.0024042:0.0042115:0.245583:0.11052:343992:1_692794_CA_C
1   693731  rs12238997  A   G   .   PASS    AF=0.11581  ES:SE:LP:AF:SS:ID   -0.0016415:0.0039775:0.1676:0.11581:343992:rs12238997
1   707522  rs371890604 G   C   .   PASS    AF=0.097248 ES:SE:LP:AF:SS:ID   0.00053641:0.0044741:0.0435578:0.097248:343992:rs371890604
1   717587  rs144155419 G   A   .   PASS    AF=0.015665 ES:SE:LP:AF:SS:ID   -0.015676:0.010679:0.847284:0.015665:343992:rs144155419
1   723329  rs189787166 A   T   .   PASS    AF=0.0017377    ES:SE:LP:AF:SS:ID   -0.026:0.03145:0.388925:0.0017377:343992:rs189787166
1   730087  rs148120343 T   C   .   PASS    AF=0.056424 ES:SE:LP:AF:SS:ID   0.00078412:0.0055435:0.0518219:0.056424:343992:rs148120343
1   731718  rs58276399  T   C   .   PASS    AF=0.1217   ES:SE:LP:AF:SS:ID   -0.0016378:0.0037726:0.177701:0.1217:343992:rs58276399
1   732032  rs61770163  A   C   .   PASS    AF=0.12111  ES:SE:LP:AF:SS:ID   -0.0003349:0.0040255:0.0297926:0.12111:343992:rs61770163
1   734349  rs141242758 T   C   .   PASS    AF=0.12092  ES:SE:LP:AF:SS:ID   -0.0015071:0.0037747:0.161346:0.12092:343992:rs141242758
1   740284  rs61770167  C   T   .   PASS    AF=0.0057545    ES:SE:LP:AF:SS:ID   -0.0018787:0.017316:0.0392392:0.0057545:343992:rs61770167
1   742813  rs112573343 C   T   .   PASS    AF=0.0018592    ES:SE:LP:AF:SS:ID   -0.031286:0.032848:0.467398:0.0018592:343992:rs112573343
1   749963  rs529266287 T   TAA .   PASS    AF=0.8698   ES:SE:LP:AF:SS:ID   0.0012021:0.0037214:0.126871:0.8698:343992:rs529266287
1   750230  rs190826124 G   C   .   PASS    AF=0.0015212    ES:SE:LP:AF:SS:ID   -0.0049627:0.033805:0.0538967:0.0015212:343992:rs190826124
1   751343  rs28544273  T   A   .   PASS    AF=0.12288  ES:SE:LP:AF:SS:ID   -0.00089545:0.0036853:0.0925779:0.12288:343992:rs28544273
1   751488  rs200141114 G   GA  .   PASS    AF=0.1427   ES:SE:LP:AF:SS:ID   9.3126e-05:0.0036423:0.00895122:0.1427:343992:rs200141114
1   751756  rs28527770  T   C   .   PASS    AF=0.123    ES:SE:LP:AF:SS:ID   -0.00074446:0.0036801:0.075881:0.123:343992:rs28527770
1   753405  rs3115860   C   A   .   PASS    AF=0.87096  ES:SE:LP:AF:SS:ID   0.0012158:0.0035868:0.133931:0.87096:343992:rs3115860
1   753425  rs3131970   T   C   .   PASS    AF=0.87552  ES:SE:LP:AF:SS:ID   0.00039365:0.0036458:0.0390491:0.87552:343992:rs3131970
1   753541  rs2073813   G   A   .   PASS    AF=0.12857  ES:SE:LP:AF:SS:ID   -0.0011118:0.0035956:0.120812:0.12857:343992:rs2073813
1   754105  rs12184325  C   T   .   PASS    AF=0.036308 ES:SE:LP:AF:SS:ID   -0.0053016:0.0065289:0.380093:0.036308:343992:rs12184325
1   754182  rs3131969   A   G   .   PASS    AF=0.87056  ES:SE:LP:AF:SS:ID   0.0014272:0.0035831:0.160899:0.87056:343992:rs3131969
1   754192  rs3131968   A   G   .   PASS    AF=0.87066  ES:SE:LP:AF:SS:ID   0.0015983:0.0035847:0.183295:0.87066:343992:rs3131968
1   754334  rs3131967   T   C   .   PASS    AF=0.87055  ES:SE:LP:AF:SS:ID   0.0014223:0.0035829:0.160271:0.87055:343992:rs3131967
1   754433  rs150578204 G   A   .   PASS    AF=0.0050469    ES:SE:LP:AF:SS:ID   0.0032281:0.018382:0.0651987:0.0050469:343992:rs150578204
1   754458  rs142682604 G   T   .   PASS    AF=0.0050139    ES:SE:LP:AF:SS:ID   0.0029837:0.018431:0.0597824:0.0050139:343992:rs142682604
1   755435  rs184270342 T   G   .   PASS    AF=0.0055455    ES:SE:LP:AF:SS:ID   -0.0079565:0.017885:0.182825:0.0055455:343992:rs184270342
1   755890  rs3115858   A   T   .   PASS    AF=0.87064  ES:SE:LP:AF:SS:ID   0.0010334:0.0035768:0.112017:0.87064:343992:rs3115858
1   756434  rs61768170  G   C   .   PASS    AF=0.12592  ES:SE:LP:AF:SS:ID   -0.00083666:0.0036493:0.0868964:0.12592:343992:rs61768170
1   756604  rs3131962   A   G   .   PASS    AF=0.87021  ES:SE:LP:AF:SS:ID   0.0012598:0.0035683:0.140237:0.87021:343992:rs3131962
1   757640  rs3115853   G   A   .   PASS    AF=0.86949  ES:SE:LP:AF:SS:ID   0.0012551:0.003565:0.139782:0.86949:343992:rs3115853
1   757734  rs4951929   C   T   .   PASS    AF=0.87036  ES:SE:LP:AF:SS:ID   0.0011255:0.0035712:0.123407:0.87036:343992:rs4951929
1   757936  rs4951862   C   A   .   PASS    AF=0.87036  ES:SE:LP:AF:SS:ID   0.0011254:0.0035715:0.123384:0.87036:343992:rs4951862
1   758144  rs3131956   A   G   .   PASS    AF=0.87037  ES:SE:LP:AF:SS:ID   0.0011324:0.0035716:0.124239:0.87037:343992:rs3131956
1   758626  rs3131954   C   T   .   PASS    AF=0.87081  ES:SE:LP:AF:SS:ID   0.0010071:0.0035806:0.10873:0.87081:343992:rs3131954
1   759293  rs10157329  T   A   .   PASS    AF=0.09879  ES:SE:LP:AF:SS:ID   -2.9815e-05:0.0041614:0.0024913:0.09879:343992:rs10157329
1   759600  rs545998451 AGT A   .   PASS    AF=0.0064326    ES:SE:LP:AF:SS:ID   -0.0054655:0.016156:0.133624:0.0064326:343992:1_759600_AGT_A
1   759837  rs3115851   T   A   .   PASS    AF=0.8747   ES:SE:LP:AF:SS:ID   0.00099959:0.0036337:0.1061:0.8747:343992:rs3115851
1   761732  rs2286139   C   T   .   PASS    AF=0.86411  ES:SE:LP:AF:SS:ID   0.0017209:0.0035642:0.201197:0.86411:343992:rs2286139
1   761752  rs1057213   C   T   .   PASS    AF=0.86949  ES:SE:LP:AF:SS:ID   0.0013268:0.0035981:0.147331:0.86949:343992:rs1057213
1   762273  rs3115849   G   A   .   PASS    AF=0.86643  ES:SE:LP:AF:SS:ID   0.001759:0.0035988:0.20412:0.86643:343992:rs3115849
1   762485  rs12095200  C   A   .   PASS    AF=0.098749 ES:SE:LP:AF:SS:ID   -0.0011985:0.0043079:0.107427:0.098749:343992:rs12095200
1   762589  rs3115848   G   C   .   PASS    AF=0.87161  ES:SE:LP:AF:SS:ID   0.0014554:0.0036399:0.161611:0.87161:343992:rs3115848
1   762592  rs3131950   C   G   .   PASS    AF=0.87161  ES:SE:LP:AF:SS:ID   0.001456:0.0036399:0.161686:0.87161:343992:rs3131950
1   762601  rs3131949   T   C   .   PASS    AF=0.87161  ES:SE:LP:AF:SS:ID   0.001484:0.00364:0.165261:0.87161:343992:rs3131949
1   762632  rs3131948   T   A   .   PASS    AF=0.87199  ES:SE:LP:AF:SS:ID   0.001383:0.003642:0.152335:0.87199:343992:rs3131948
1   764191  rs7515915   T   G   .   PASS    AF=0.12551  ES:SE:LP:AF:SS:ID   -0.0008975:0.0036445:0.0939452:0.12551:343992:rs7515915
1   766007  rs61768174  A   C   .   PASS    AF=0.10539  ES:SE:LP:AF:SS:ID   0.0005419:0.0039686:0.0499322:0.10539:343992:rs61768174
1   766105  rs2519015   T   A   .   PASS    AF=0.85546  ES:SE:LP:AF:SS:ID   0.0018529:0.0035627:0.219675:0.85546:343992:rs2519015
1   767393  rs538667473 A   C   .   PASS    AF=0.0016564    ES:SE:LP:AF:SS:ID   -0.025618:0.031529:0.380395:0.0016564:343992:rs538667473
1   768116  rs376645387 A   AGTTTT  .   PASS    AF=0.83825  ES:SE:LP:AF:SS:ID   -0.0027342:0.0035078:0.360802:0.83825:343992:rs376645387