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-30660_raw/ukb-d-30660_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-30660_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 14:54:41 2019
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ukb-d-import/processed/ukb-d-30660_raw/ukb-d-30660_raw.vcf.gz ...
Read summary statistics for 13584678 SNPs.
Dropped 12709 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, 1283503 SNPs remain.
After merging with regression SNP LD, 1283503 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.2693 (0.2294)
Lambda GC: 1.1383
Mean Chi^2: 4.2374
Intercept: 1.0111 (0.0116)
Ratio: 0.0034 (0.0036)
Analysis finished at Mon Nov 25 14:57:03 2019
Total time elapsed: 2.0m:21.89s

QC metrics

Metrics

Metrics

{
    "af_correlation": 0.9521,
    "inflation_factor": 1.0848,
    "mean_EFFECT": -0,
    "n": 292933,
    "n_snps": 13584678,
    "n_clumped_hits": 55,
    "n_p_sig": 9918,
    "n_mono": 0,
    "n_ns": 1251740,
    "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": 568790,
    "n_est": 294356.1808,
    "ratio_se_n": 1.0024,
    "mean_diff": -4.0996e-06,
    "ratio_diff": 5.7741,
    "sd_y_est1": 0.8347,
    "sd_y_est2": 0.8367,
    "r2_sum1": 0.0229,
    "r2_sum2": 0.0329,
    "r2_sum3": 0.0328,
    "r2_sum4": 0.032,
    "ldsc_nsnp_merge_refpanel_ld": 1283503,
    "ldsc_nsnp_merge_regression_ld": 1283503,
    "ldsc_observed_scale_h2_beta": 0.2693,
    "ldsc_observed_scale_h2_se": 0.2294,
    "ldsc_intercept_beta": 1.0111,
    "ldsc_intercept_se": 0.0116,
    "ldsc_lambda_gc": 1.1383,
    "ldsc_mean_chisq": 4.2374,
    "ldsc_ratio": 0.0034
}

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 0 1.00000 3 94 0 13572633 0 NA NA NA NA NA NA NA NA
character REF 0 1.00000 1 100 0 57083 0 NA NA NA NA NA NA NA NA
character ALT 0 1.00000 1 342 0 33336 0 NA NA NA NA NA NA NA NA
numeric CHROM 0 1.00000 NA NA NA NA NA 9.051176e+00 6.184940e+00 1.00000e+00 4.000000e+00 8.000000e+00 1.300000e+01 2.300000e+01 ▇▅▅▂▂
numeric POS 0 1.00000 NA NA NA NA NA 7.902513e+07 5.591501e+07 3.02000e+02 3.293034e+07 7.013910e+07 1.148583e+08 2.492309e+08 ▇▆▅▂▁
numeric EFFECT 0 1.00000 NA NA NA NA NA -2.460000e-05 1.328370e-02 -3.22950e-01 -3.663000e-03 -5.900000e-05 3.459500e-03 5.490100e-01 ▁▇▁▁▁
numeric SE 0 1.00000 NA NA NA NA NA 9.161900e-03 8.838500e-03 1.76740e-03 2.609400e-03 4.806800e-03 1.316100e-02 4.468300e-02 ▇▂▁▁▁
numeric PVAL 0 1.00000 NA NA NA NA NA 4.857090e-01 2.935178e-01 0.00000e+00 2.284899e-01 4.823597e-01 7.400806e-01 1.000000e+00 ▇▇▇▇▇
numeric PVAL_ztest 0 1.00000 NA NA NA NA NA 4.857085e-01 2.935181e-01 0.00000e+00 2.284883e-01 4.823613e-01 7.400783e-01 9.999998e-01 ▇▇▇▇▇
numeric AF 0 1.00000 NA NA NA NA NA 1.908228e-01 2.544044e-01 1.00000e-03 7.434300e-03 6.005200e-02 2.953500e-01 9.990000e-01 ▇▂▁▁▁
numeric AF_reference 568790 0.95813 NA NA NA NA NA 1.963483e-01 2.471022e-01 0.00000e+00 5.591000e-03 8.426520e-02 3.081070e-01 1.000000e+00 ▇▂▁▁▁
numeric N 0 1.00000 NA NA NA NA NA 2.929330e+05 0.000000e+00 2.92933e+05 2.929330e+05 2.929330e+05 2.929330e+05 2.929330e+05 ▁▁▇▁▁

Head and tail

CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
1 692794 rs530212009 CA C -0.0017428 0.0038231 0.6484896 0.6484903 0.1104500 0.1894970 292933
1 693731 rs12238997 A G -0.0029490 0.0036098 0.4139596 0.4139611 0.1157000 0.1417730 292933
1 707522 rs371890604 G C -0.0028161 0.0040595 0.4878699 0.4878665 0.0972250 0.1293930 292933
1 717587 rs144155419 G A -0.0026172 0.0096930 0.7871600 0.7871531 0.0156390 0.0045926 292933
1 723329 rs189787166 A T 0.0362710 0.0285300 0.2036100 0.2036118 0.0017372 0.0003994 292933
1 730087 rs148120343 T C -0.0074234 0.0050365 0.1404999 0.1405030 0.0562820 0.0127796 292933
1 731718 rs142557973 T C -0.0023632 0.0034231 0.4899604 0.4899626 0.1216500 0.1543530 292933
1 732032 rs61770163 A C -0.0027271 0.0036536 0.4554105 0.4554171 0.1210200 0.1555510 292933
1 734349 rs141242758 T C -0.0023545 0.0034249 0.4917802 0.4917895 0.1208900 0.1525560 292933
1 740284 rs61770167 C T -0.0051624 0.0156970 0.7422496 0.7422478 0.0057580 0.0023962 292933
CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
23 154923311 rs141127553 C T 0.0062560 0.0039009 0.1087700 0.1087730 0.056065 0.0309934 292933
23 154923374 rs111332691 T A 0.0032609 0.0042785 0.4459704 0.4459647 0.044826 0.0116556 292933
23 154925045 rs509981 C T 0.0037489 0.0020579 0.0684983 0.0684988 0.246390 0.3634440 292933
23 154925895 rs538470 C T 0.0038993 0.0021049 0.0639588 0.0639559 0.242710 0.3634440 292933
23 154927581 rs644138 G A 0.0048141 0.0019359 0.0128911 0.0128916 0.302850 0.4635760 292933
23 154929412 rs557132 C T 0.0036529 0.0020585 0.0759731 0.0759731 0.246250 0.3568210 292933
23 154929637 rs35185538 CT C 0.0050235 0.0021480 0.0193522 0.0193516 0.230380 0.3011920 292933
23 154929952 rs4012982 CAA C 0.0037057 0.0021648 0.0869341 0.0869339 0.240200 0.3165560 292933
23 154930230 rs781880 A G 0.0037449 0.0020581 0.0688256 0.0688213 0.246680 0.3618540 292933
23 154930487 rs781879 T A 0.0033506 0.0070627 0.6352198 0.6352091 0.019578 0.1263580 292933

bcf preview

1   692794  rs530212009 CA  C   .   PASS    AF=0.11045  ES:SE:LP:AF:SS:ID   -0.0017428:0.0038231:0.188097:0.11045:292933:1_692794_CA_C
1   693731  rs12238997  A   G   .   PASS    AF=0.1157   ES:SE:LP:AF:SS:ID   -0.002949:0.0036098:0.383042:0.1157:292933:rs12238997
1   707522  rs371890604 G   C   .   PASS    AF=0.097225 ES:SE:LP:AF:SS:ID   -0.0028161:0.0040595:0.311696:0.097225:292933:rs371890604
1   717587  rs144155419 G   A   .   PASS    AF=0.015639 ES:SE:LP:AF:SS:ID   -0.0026172:0.009693:0.103937:0.015639:292933:rs144155419
1   723329  rs189787166 A   T   .   PASS    AF=0.0017372    ES:SE:LP:AF:SS:ID   0.036271:0.02853:0.691201:0.0017372:292933:rs189787166
1   730087  rs148120343 T   C   .   PASS    AF=0.056282 ES:SE:LP:AF:SS:ID   -0.0074234:0.0050365:0.852324:0.056282:292933:rs148120343
1   731718  rs58276399  T   C   .   PASS    AF=0.12165  ES:SE:LP:AF:SS:ID   -0.0023632:0.0034231:0.309839:0.12165:292933:rs58276399
1   732032  rs61770163  A   C   .   PASS    AF=0.12102  ES:SE:LP:AF:SS:ID   -0.0027271:0.0036536:0.341597:0.12102:292933:rs61770163
1   734349  rs141242758 T   C   .   PASS    AF=0.12089  ES:SE:LP:AF:SS:ID   -0.0023545:0.0034249:0.308229:0.12089:292933:rs141242758
1   740284  rs61770167  C   T   .   PASS    AF=0.005758 ES:SE:LP:AF:SS:ID   -0.0051624:0.015697:0.12945:0.005758:292933:rs61770167
1   742813  rs112573343 C   T   .   PASS    AF=0.0018951    ES:SE:LP:AF:SS:ID   -0.016268:0.029471:0.235876:0.0018951:292933:rs112573343
1   749963  rs529266287 T   TAA .   PASS    AF=0.86989  ES:SE:LP:AF:SS:ID   0.0015649:0.0033778:0.191681:0.86989:292933:rs529266287
1   750230  rs190826124 G   C   .   PASS    AF=0.0015135    ES:SE:LP:AF:SS:ID   0.0058263:0.030726:0.0707855:0.0015135:292933:rs190826124
1   751343  rs28544273  T   A   .   PASS    AF=0.1228   ES:SE:LP:AF:SS:ID   -0.0017021:0.0033443:0.214115:0.1228:292933:rs28544273
1   751488  rs200141114 G   GA  .   PASS    AF=0.14259  ES:SE:LP:AF:SS:ID   8.5822e-05:0.0033053:0.00908868:0.14259:292933:rs200141114
1   751756  rs28527770  T   C   .   PASS    AF=0.12291  ES:SE:LP:AF:SS:ID   -0.0016926:0.0033397:0.213043:0.12291:292933:rs28527770
1   753405  rs3115860   C   A   .   PASS    AF=0.87101  ES:SE:LP:AF:SS:ID   0.0022971:0.0032545:0.318487:0.87101:292933:rs3115860
1   753425  rs3131970   T   C   .   PASS    AF=0.87557  ES:SE:LP:AF:SS:ID   0.0015851:0.0033081:0.199393:0.87557:292933:rs3131970
1   753541  rs2073813   G   A   .   PASS    AF=0.1285   ES:SE:LP:AF:SS:ID   -0.0019339:0.0032628:0.256984:0.1285:292933:rs2073813
1   754105  rs12184325  C   T   .   PASS    AF=0.036334 ES:SE:LP:AF:SS:ID   -0.00051195:0.0059221:0.030999:0.036334:292933:rs12184325
1   754182  rs3131969   A   G   .   PASS    AF=0.8706   ES:SE:LP:AF:SS:ID   0.0022366:0.003251:0.308503:0.8706:292933:rs3131969
1   754192  rs3131968   A   G   .   PASS    AF=0.8707   ES:SE:LP:AF:SS:ID   0.0022576:0.0032524:0.311927:0.8707:292933:rs3131968
1   754334  rs3131967   T   C   .   PASS    AF=0.8706   ES:SE:LP:AF:SS:ID   0.0022627:0.0032509:0.31298:0.8706:292933:rs3131967
1   754433  rs150578204 G   A   .   PASS    AF=0.0050477    ES:SE:LP:AF:SS:ID   -0.0084515:0.016673:0.213085:0.0050477:292933:rs150578204
1   754458  rs142682604 G   T   .   PASS    AF=0.005015 ES:SE:LP:AF:SS:ID   -0.008495:0.016718:0.21371:0.005015:292933:rs142682604
1   755435  rs184270342 T   G   .   PASS    AF=0.00555  ES:SE:LP:AF:SS:ID   -0.02885:0.016213:1.12394:0.00555:292933:rs184270342
1   755890  rs3115858   A   T   .   PASS    AF=0.87069  ES:SE:LP:AF:SS:ID   0.0024305:0.0032453:0.34304:0.87069:292933:rs3115858
1   756434  rs61768170  G   C   .   PASS    AF=0.12584  ES:SE:LP:AF:SS:ID   -0.0022573:0.0033114:0.304991:0.12584:292933:rs61768170
1   756604  rs3131962   A   G   .   PASS    AF=0.87025  ES:SE:LP:AF:SS:ID   0.0023867:0.0032374:0.336327:0.87025:292933:rs3131962
1   757640  rs3115853   G   A   .   PASS    AF=0.86953  ES:SE:LP:AF:SS:ID   0.0022613:0.0032341:0.314778:0.86953:292933:rs3115853
1   757734  rs4951929   C   T   .   PASS    AF=0.8704   ES:SE:LP:AF:SS:ID   0.0022783:0.0032401:0.31698:0.8704:292933:rs4951929
1   757936  rs4951862   C   A   .   PASS    AF=0.87041  ES:SE:LP:AF:SS:ID   0.002281:0.0032404:0.317422:0.87041:292933:rs4951862
1   758144  rs3131956   A   G   .   PASS    AF=0.87042  ES:SE:LP:AF:SS:ID   0.0022616:0.0032405:0.314061:0.87042:292933:rs3131956
1   758626  rs3131954   C   T   .   PASS    AF=0.87086  ES:SE:LP:AF:SS:ID   0.0023104:0.0032488:0.321491:0.87086:292933:rs3131954
1   759293  rs10157329  T   A   .   PASS    AF=0.098733 ES:SE:LP:AF:SS:ID   -0.0026319:0.0037764:0.313498:0.098733:292933:rs10157329
1   759600  rs545998451 AGT A   .   PASS    AF=0.0064218    ES:SE:LP:AF:SS:ID   -0.023349:0.014664:0.953388:0.0064218:292933:1_759600_AGT_A
1   759837  rs3115851   T   A   .   PASS    AF=0.87475  ES:SE:LP:AF:SS:ID   0.0020677:0.0032972:0.275241:0.87475:292933:rs3115851
1   761732  rs2286139   C   T   .   PASS    AF=0.8641   ES:SE:LP:AF:SS:ID   0.0017525:0.003233:0.230785:0.8641:292933:rs2286139
1   761752  rs1057213   C   T   .   PASS    AF=0.86954  ES:SE:LP:AF:SS:ID   0.0020644:0.0032643:0.278107:0.86954:292933:rs1057213
1   762273  rs3115849   G   A   .   PASS    AF=0.86648  ES:SE:LP:AF:SS:ID   0.00295:0.0032651:0.436199:0.86648:292933:rs3115849
1   762485  rs12095200  C   A   .   PASS    AF=0.098727 ES:SE:LP:AF:SS:ID   -0.0020741:0.003908:0.225045:0.098727:292933:rs12095200
1   762589  rs3115848   G   C   .   PASS    AF=0.87166  ES:SE:LP:AF:SS:ID   0.0024755:0.0033029:0.343365:0.87166:292933:rs3115848
1   762592  rs3131950   C   G   .   PASS    AF=0.87166  ES:SE:LP:AF:SS:ID   0.0024757:0.0033029:0.343384:0.87166:292933:rs3131950
1   762601  rs3131949   T   C   .   PASS    AF=0.87166  ES:SE:LP:AF:SS:ID   0.0024553:0.003303:0.339827:0.87166:292933:rs3131949
1   762632  rs3131948   T   A   .   PASS    AF=0.87203  ES:SE:LP:AF:SS:ID   0.0025164:0.0033048:0.350266:0.87203:292933:rs3131948
1   764191  rs7515915   T   G   .   PASS    AF=0.12545  ES:SE:LP:AF:SS:ID   -0.0021095:0.0033072:0.281034:0.12545:292933:rs7515915
1   766007  rs61768174  A   C   .   PASS    AF=0.10536  ES:SE:LP:AF:SS:ID   -0.002369:0.0036015:0.291851:0.10536:292933:rs61768174
1   766105  rs2519015   T   A   .   PASS    AF=0.85543  ES:SE:LP:AF:SS:ID   0.0037393:0.0032316:0.606881:0.85543:292933:rs2519015
1   767393  rs538667473 A   C   .   PASS    AF=0.0016586    ES:SE:LP:AF:SS:ID   0.033093:0.028577:0.607567:0.0016586:292933:rs538667473
1   768116  rs376645387 A   AGTTTT  .   PASS    AF=0.83831  ES:SE:LP:AF:SS:ID   -0.00038888:0.0031819:0.0444421:0.83831:292933:rs376645387