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-30860_irnt/ukb-d-30860_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-30860_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 15:35:55 2019
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ukb-d-import/processed/ukb-d-30860_irnt/ukb-d-30860_irnt.vcf.gz ...
Read summary statistics for 13585297 SNPs.
Dropped 12710 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, 1283502 SNPs remain.
After merging with regression SNP LD, 1283502 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.1374 (0.0085)
Lambda GC: 1.5171
Mean Chi^2: 1.9959
Intercept: 1.1323 (0.0186)
Ratio: 0.1329 (0.0186)
Analysis finished at Mon Nov 25 15:37:58 2019
Total time elapsed: 2.0m:2.87s

QC metrics

Metrics

Metrics

{
    "af_correlation": 0.9521,
    "inflation_factor": 1.325,
    "mean_EFFECT": 0,
    "n": 314921,
    "n_snps": 13585297,
    "n_clumped_hits": 254,
    "n_p_sig": 55321,
    "n_mono": 0,
    "n_ns": 1251738,
    "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": 568980,
    "n_est": 316149.4304,
    "ratio_se_n": 1.0019,
    "mean_diff": -1.36e-06,
    "ratio_diff": 1.0546,
    "sd_y_est1": 1.0002,
    "sd_y_est2": 1.0022,
    "r2_sum1": 0.0619,
    "r2_sum2": 0.0619,
    "r2_sum3": 0.0617,
    "r2_sum4": 0.0609,
    "ldsc_nsnp_merge_refpanel_ld": 1283502,
    "ldsc_nsnp_merge_regression_ld": 1283502,
    "ldsc_observed_scale_h2_beta": 0.1374,
    "ldsc_observed_scale_h2_se": 0.0085,
    "ldsc_intercept_beta": 1.1323,
    "ldsc_intercept_se": 0.0186,
    "ldsc_lambda_gc": 1.5171,
    "ldsc_mean_chisq": 1.9959,
    "ldsc_ratio": 0.1328
}

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 1.000000 3 94 0 13573251 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 33334 0 NA NA NA NA NA NA NA NA
numeric CHROM 0 1.000000 NA NA NA NA NA 9.051281e+00 6.184965e+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 7.902516e+07 5.591503e+07 3.02000e+02 3.293038e+07 7.013894e+07 1.148598e+08 2.492309e+08 ▇▆▅▂▁
numeric EFFECT 0 1.000000 NA NA NA NA NA 3.260000e-05 1.557700e-02 -3.24320e-01 -4.693400e-03 1.190000e-05 4.721800e-03 2.318700e-01 ▁▁▇▂▁
numeric SE 0 1.000000 NA NA NA NA NA 1.058870e-02 1.021380e-02 2.06960e-03 3.015200e-03 5.555600e-03 1.521600e-02 5.156500e-02 ▇▂▁▁▁
numeric PVAL 0 1.000000 NA NA NA NA NA 4.525855e-01 3.028618e-01 0.00000e+00 1.783101e-01 4.375100e-01 7.151102e-01 1.000000e+00 ▇▆▆▅▅
numeric PVAL_ztest 0 1.000000 NA NA NA NA NA 4.525849e-01 3.028621e-01 0.00000e+00 1.783104e-01 4.375119e-01 7.151087e-01 9.999999e-01 ▇▆▆▅▅
numeric AF 0 1.000000 NA NA NA NA NA 1.908201e-01 2.544081e-01 1.00000e-03 7.433700e-03 6.004400e-02 2.953300e-01 9.990000e-01 ▇▂▁▁▁
numeric AF_reference 568980 0.958118 NA NA NA NA NA 1.963466e-01 2.471053e-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 3.149210e+05 0.000000e+00 3.14921e+05 3.149210e+05 3.149210e+05 3.149210e+05 3.149210e+05 ▁▁▇▁▁

Head and tail

CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
1 692794 rs530212009 CA C 0.0009945 0.0044138 0.8217399 0.8217352 0.1105500 0.1894970 314921
1 693731 rs12238997 A G 0.0006121 0.0041696 0.8832999 0.8832988 0.1158600 0.1417730 314921
1 707522 rs371890604 G C 0.0019025 0.0046916 0.6851001 0.6851012 0.0972210 0.1293930 314921
1 717587 rs144155419 G A 0.0146360 0.0111720 0.1901599 0.1901752 0.0157110 0.0045926 314921
1 723329 rs189787166 A T -0.0323010 0.0330210 0.3279797 0.3279775 0.0017318 0.0003994 314921
1 730087 rs148120343 T C 0.0004867 0.0058086 0.9332300 0.9332251 0.0564790 0.0127796 314921
1 731718 rs142557973 T C 0.0013689 0.0039552 0.7292593 0.7292666 0.1217400 0.1543530 314921
1 732032 rs61770163 A C 0.0026749 0.0042209 0.5262596 0.5262587 0.1210900 0.1555510 314921
1 734349 rs141242758 T C 0.0013685 0.0039573 0.7294894 0.7294806 0.1209700 0.1525560 314921
1 740284 rs61770167 C T -0.0102820 0.0181440 0.5709197 0.5709257 0.0057554 0.0023962 314921
CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
23 154923311 rs141127553 C T -0.0006138 0.0045671 0.8930801 0.8930842 0.056102 0.0309934 314921
23 154923374 rs111332691 T A 0.0046447 0.0049975 0.3526801 0.3526794 0.045013 0.0116556 314921
23 154925045 rs509981 C T 0.0021236 0.0024131 0.3788497 0.3788431 0.245720 0.3634440 314921
23 154925895 rs538470 C T 0.0018967 0.0024685 0.4422797 0.4422725 0.242010 0.3634440 314921
23 154927581 rs644138 G A 0.0016831 0.0022696 0.4583498 0.4583392 0.302210 0.4635760 314921
23 154929412 rs557132 C T 0.0019896 0.0024138 0.4097802 0.4097916 0.245570 0.3568210 314921
23 154929637 rs35185538 CT C 0.0002677 0.0025189 0.9153599 0.9153629 0.229950 0.3011920 314921
23 154929952 rs4012982 CAA C 0.0015107 0.0025386 0.5517699 0.5517821 0.239500 0.3165560 314921
23 154930230 rs781880 A G 0.0018173 0.0024135 0.4514805 0.4514662 0.245950 0.3618540 314921
23 154930487 rs781879 T A 0.0086507 0.0082944 0.2969703 0.2969684 0.019469 0.1263580 314921

bcf preview

1   692794  rs530212009 CA  C   .   PASS    AF=0.11055  ES:SE:LP:AF:SS:ID   0.00099449:0.0044138:0.0852656:0.11055:314921:1_692794_CA_C
1   693731  rs12238997  A   G   .   PASS    AF=0.11586  ES:SE:LP:AF:SS:ID   0.00061205:0.0041696:0.0538918:0.11586:314921:rs12238997
1   707522  rs371890604 G   C   .   PASS    AF=0.097221 ES:SE:LP:AF:SS:ID   0.0019025:0.0046916:0.164246:0.097221:314921:rs371890604
1   717587  rs144155419 G   A   .   PASS    AF=0.015711 ES:SE:LP:AF:SS:ID   0.014636:0.011172:0.720881:0.015711:314921:rs144155419
1   723329  rs189787166 A   T   .   PASS    AF=0.0017318    ES:SE:LP:AF:SS:ID   -0.032301:0.033021:0.484153:0.0017318:314921:rs189787166
1   730087  rs148120343 T   C   .   PASS    AF=0.056479 ES:SE:LP:AF:SS:ID   0.00048669:0.0058086:0.0300113:0.056479:314921:rs148120343
1   731718  rs58276399  T   C   .   PASS    AF=0.12174  ES:SE:LP:AF:SS:ID   0.0013689:0.0039552:0.137118:0.12174:314921:rs58276399
1   732032  rs61770163  A   C   .   PASS    AF=0.12109  ES:SE:LP:AF:SS:ID   0.0026749:0.0042209:0.2788:0.12109:314921:rs61770163
1   734349  rs141242758 T   C   .   PASS    AF=0.12097  ES:SE:LP:AF:SS:ID   0.0013685:0.0039573:0.136981:0.12097:314921:rs141242758
1   740284  rs61770167  C   T   .   PASS    AF=0.0057554    ES:SE:LP:AF:SS:ID   -0.010282:0.018144:0.243425:0.0057554:314921:rs61770167
1   742813  rs112573343 C   T   .   PASS    AF=0.0018557    ES:SE:LP:AF:SS:ID   0.013512:0.034447:0.158103:0.0018557:314921:rs112573343
1   749963  rs529266287 T   TAA .   PASS    AF=0.86972  ES:SE:LP:AF:SS:ID   -0.0032569:0.0039012:0.393823:0.86972:314921:rs529266287
1   750230  rs190826124 G   C   .   PASS    AF=0.0015197    ES:SE:LP:AF:SS:ID   -0.066241:0.035449:1.20988:0.0015197:314921:rs190826124
1   751343  rs28544273  T   A   .   PASS    AF=0.12294  ES:SE:LP:AF:SS:ID   0.0010848:0.0038639:0.108513:0.12294:314921:rs28544273
1   751488  rs200141114 G   GA  .   PASS    AF=0.14276  ES:SE:LP:AF:SS:ID   0.000895:0.0038184:0.0890129:0.14276:314921:rs200141114
1   751756  rs28527770  T   C   .   PASS    AF=0.12305  ES:SE:LP:AF:SS:ID   0.0012095:0.0038585:0.122669:0.12305:314921:rs28527770
1   753405  rs3115860   C   A   .   PASS    AF=0.87094  ES:SE:LP:AF:SS:ID   -0.0018862:0.003761:0.210419:0.87094:314921:rs3115860
1   753425  rs3131970   T   C   .   PASS    AF=0.87547  ES:SE:LP:AF:SS:ID   -0.001373:0.0038223:0.143011:0.87547:314921:rs3131970
1   753541  rs2073813   G   A   .   PASS    AF=0.12862  ES:SE:LP:AF:SS:ID   0.0016281:0.00377:0.176624:0.12862:314921:rs2073813
1   754105  rs12184325  C   T   .   PASS    AF=0.036323 ES:SE:LP:AF:SS:ID   -0.0037102:0.0068421:0.230889:0.036323:314921:rs12184325
1   754182  rs3131969   A   G   .   PASS    AF=0.87052  ES:SE:LP:AF:SS:ID   -0.0018219:0.0037569:0.202241:0.87052:314921:rs3131969
1   754192  rs3131968   A   G   .   PASS    AF=0.87063  ES:SE:LP:AF:SS:ID   -0.0016649:0.0037588:0.181893:0.87063:314921:rs3131968
1   754334  rs3131967   T   C   .   PASS    AF=0.87052  ES:SE:LP:AF:SS:ID   -0.0017868:0.0037568:0.197678:0.87052:314921:rs3131967
1   754433  rs150578204 G   A   .   PASS    AF=0.0050401    ES:SE:LP:AF:SS:ID   0.025688:0.01927:0.738713:0.0050401:314921:rs150578204
1   754458  rs142682604 G   T   .   PASS    AF=0.0050067    ES:SE:LP:AF:SS:ID   0.025885:0.019322:0.743884:0.0050067:314921:rs142682604
1   755435  rs184270342 T   G   .   PASS    AF=0.0055143    ES:SE:LP:AF:SS:ID   0.028568:0.018796:0.890996:0.0055143:314921:rs184270342
1   755890  rs3115858   A   T   .   PASS    AF=0.87061  ES:SE:LP:AF:SS:ID   -0.0016599:0.0037505:0.181735:0.87061:314921:rs3115858
1   756434  rs61768170  G   C   .   PASS    AF=0.12595  ES:SE:LP:AF:SS:ID   0.0020064:0.0038263:0.221827:0.12595:314921:rs61768170
1   756604  rs3131962   A   G   .   PASS    AF=0.87018  ES:SE:LP:AF:SS:ID   -0.0016641:0.0037416:0.182772:0.87018:314921:rs3131962
1   757640  rs3115853   G   A   .   PASS    AF=0.86946  ES:SE:LP:AF:SS:ID   -0.0015627:0.0037382:0.170105:0.86946:314921:rs3115853
1   757734  rs4951929   C   T   .   PASS    AF=0.87033  ES:SE:LP:AF:SS:ID   -0.0015881:0.0037447:0.17296:0.87033:314921:rs4951929
1   757936  rs4951862   C   A   .   PASS    AF=0.87034  ES:SE:LP:AF:SS:ID   -0.001589:0.003745:0.173051:0.87034:314921:rs4951862
1   758144  rs3131956   A   G   .   PASS    AF=0.87035  ES:SE:LP:AF:SS:ID   -0.0016104:0.0037451:0.17575:0.87035:314921:rs3131956
1   758626  rs3131954   C   T   .   PASS    AF=0.87079  ES:SE:LP:AF:SS:ID   -0.001716:0.0037546:0.18866:0.87079:314921:rs3131954
1   759293  rs10157329  T   A   .   PASS    AF=0.098818 ES:SE:LP:AF:SS:ID   -0.00094256:0.0043636:0.0814559:0.098818:314921:rs10157329
1   759600  rs545998451 AGT A   .   PASS    AF=0.0063971    ES:SE:LP:AF:SS:ID   0.021575:0.016984:0.690391:0.0063971:314921:1_759600_AGT_A
1   759837  rs3115851   T   A   .   PASS    AF=0.87464  ES:SE:LP:AF:SS:ID   -0.0016877:0.0038096:0.181933:0.87464:314921:rs3115851
1   761732  rs2286139   C   T   .   PASS    AF=0.86407  ES:SE:LP:AF:SS:ID   -0.001746:0.0037371:0.193583:0.86407:314921:rs2286139
1   761752  rs1057213   C   T   .   PASS    AF=0.86946  ES:SE:LP:AF:SS:ID   -0.0018555:0.0037726:0.205624:0.86946:314921:rs1057213
1   762273  rs3115849   G   A   .   PASS    AF=0.86641  ES:SE:LP:AF:SS:ID   -0.00095848:0.0037734:0.097187:0.86641:314921:rs3115849
1   762485  rs12095200  C   A   .   PASS    AF=0.098816 ES:SE:LP:AF:SS:ID   0.0019339:0.0045156:0.174931:0.098816:314921:rs12095200
1   762589  rs3115848   G   C   .   PASS    AF=0.87158  ES:SE:LP:AF:SS:ID   -0.0017224:0.0038161:0.185932:0.87158:314921:rs3115848
1   762592  rs3131950   C   G   .   PASS    AF=0.87158  ES:SE:LP:AF:SS:ID   -0.0017221:0.0038161:0.185899:0.87158:314921:rs3131950
1   762601  rs3131949   T   C   .   PASS    AF=0.87158  ES:SE:LP:AF:SS:ID   -0.0017275:0.0038162:0.186566:0.87158:314921:rs3131949
1   762632  rs3131948   T   A   .   PASS    AF=0.87194  ES:SE:LP:AF:SS:ID   -0.0016169:0.0038182:0.17267:0.87194:314921:rs3131948
1   764191  rs7515915   T   G   .   PASS    AF=0.12557  ES:SE:LP:AF:SS:ID   0.0015088:0.003821:0.159304:0.12557:314921:rs7515915
1   766007  rs61768174  A   C   .   PASS    AF=0.10539  ES:SE:LP:AF:SS:ID   -0.0013479:0.0041619:0.127232:0.10539:314921:rs61768174
1   766105  rs2519015   T   A   .   PASS    AF=0.85541  ES:SE:LP:AF:SS:ID   -0.0016947:0.0037354:0.187053:0.85541:314921:rs2519015
1   767393  rs538667473 A   C   .   PASS    AF=0.0016498    ES:SE:LP:AF:SS:ID   -0.028961:0.033112:0.41821:0.0016498:314921:rs538667473
1   768116  rs376645387 A   AGTTTT  .   PASS    AF=0.83825  ES:SE:LP:AF:SS:ID   -0.00032247:0.0036751:0.0314797:0.83825:314921:rs376645387