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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    "FORMAT.5": "<ID=EZ,Number=A,Type=Float,Description=\"Z-score provided if it was used to derive the EFFECT and SE fields\">",
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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/public/UKB-b-13231/UKB-b-13231_data.vcf.gz \
--ref-ld-chr ../reference/eur_w_ld_chr/ \
--out /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-13231/ldsc.txt \
--w-ld-chr ../reference/eur_w_ld_chr/ 

Beginning analysis at Thu Oct 17 14:42:19 2019
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-13231/UKB-b-13231_data.vcf.gz ...
Read summary statistics for 9851816 SNPs.
Dropped 14738 SNPs with duplicated rs numbers.
Reading reference panel LD Score from ../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 ../reference/eur_w_ld_chr/[1-22] ...
Read regression weight LD Scores for 1290028 SNPs.
After merging with reference panel LD, 1289158 SNPs remain.
After merging with regression SNP LD, 1289158 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.0149 (0.0028)
Lambda GC: 1.9328
Mean Chi^2: 1.9548
Intercept: 1.828 (0.0118)
Ratio: 0.8673 (0.0123)
Analysis finished at Thu Oct 17 14:44:06 2019
Total time elapsed: 1.0m:47.8s

QC metrics

Metrics

Metrics

{
    "af_correlation": 0.9497,
    "inflation_factor": 1.92,
    "mean_EFFECT": 0.0001,
    "n": "-Inf",
    "n_snps": 9851866,
    "n_clumped_hits": 118,
    "n_p_sig": 1514,
    "n_mono": 0,
    "n_ns": 0,
    "n_mac": 0,
    "is_snpid_unique": true,
    "n_miss_EFFECT": 0,
    "n_miss_SE": 0,
    "n_miss_PVAL": 0,
    "n_miss_AF": 0,
    "n_miss_AF_reference": 184849,
    "n_est": "NA",
    "ratio_se_n": "NA",
    "mean_diff": "NaN",
    "ratio_diff": "NaN",
    "sd_y_est1": "NaN",
    "sd_y_est2": "NA",
    "r2_sum1": 0,
    "r2_sum2": 0,
    "r2_sum3": 0,
    "r2_sum4": 0,
    "ldsc_nsnp_merge_refpanel_ld": 1289158,
    "ldsc_nsnp_merge_regression_ld": 1289158,
    "ldsc_observed_scale_h2_beta": 0.0149,
    "ldsc_observed_scale_h2_se": 0.0028,
    "ldsc_intercept_beta": 1.828,
    "ldsc_intercept_se": 0.0118,
    "ldsc_lambda_gc": 1.9328,
    "ldsc_mean_chisq": 1.9548,
    "ldsc_ratio": 0.8672
}

Flags

name value
af_correlation FALSE
inflation_factor TRUE
n TRUE
is_snpid_non_unique FALSE
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 TRUE
ldsc_intercept_beta TRUE
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 logical.mean logical.count numeric.mean numeric.sd numeric.p0 numeric.p25 numeric.p50 numeric.p75 numeric.p100 numeric.hist
character ID 0 1.0000000 3 58 0 9837146 0 NA NA NA NA NA NA NA NA NA NA
character REF 0 1.0000000 1 1 0 4 0 NA NA NA NA NA NA NA NA NA NA
character ALT 0 1.0000000 1 1 0 4 0 NA NA NA NA NA NA NA NA NA NA
logical N 9851816 0.0000000 NA NA NA NA NA NaN : NA NA NA NA NA NA NA NA
numeric CHROM 0 1.0000000 NA NA NA NA NA NA NA 8.622842e+00 5.748290e+00 1.0000000 4.000000e+00 8.000000e+00 1.300000e+01 2.200000e+01 ▇▅▃▂▂
numeric POS 0 1.0000000 NA NA NA NA NA NA NA 7.886030e+07 5.628333e+07 828.0000000 3.259055e+07 6.948877e+07 1.145913e+08 2.492385e+08 ▇▆▅▂▁
numeric EFFECT 0 1.0000000 NA NA NA NA NA NA NA 8.740000e-05 1.178980e-02 -0.1651400 -3.531500e-03 4.150000e-05 3.671000e-03 2.027490e-01 ▁▁▇▁▁
numeric SE 0 1.0000000 NA NA NA NA NA NA NA 6.396600e-03 6.115900e-03 0.0017787 2.181000e-03 3.658200e-03 8.442700e-03 9.300850e-02 ▇▁▁▁▁
numeric PVAL 0 1.0000000 NA NA NA NA NA NA NA 3.997855e-01 3.066608e-01 0.0000000 1.100001e-01 3.500000e-01 6.600001e-01 1.000000e+00 ▇▅▃▃▃
numeric PVAL_ztest 0 1.0000000 NA NA NA NA NA NA NA 3.997871e-01 3.066377e-01 0.0000000 1.135463e-01 3.536261e-01 6.602481e-01 9.999997e-01 ▇▅▃▃▃
numeric AF 0 1.0000000 NA NA NA NA NA NA NA 2.035002e-01 2.569114e-01 0.0008060 1.315200e-02 7.784800e-02 3.164100e-01 9.991870e-01 ▇▂▁▁▁
numeric AF_reference 184849 0.9812371 NA NA NA NA NA NA NA 2.068395e-01 2.482930e-01 0.0000000 1.198080e-02 9.984030e-02 3.202880e-01 1.000000e+00 ▇▂▁▁▁

Head and tail

CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
1 49298 rs200943160 T C 0.0026868 0.0032624 0.4100001 0.4101827 0.623702 0.7821490 NA
1 54676 rs2462492 C T -0.0053713 0.0032326 0.0969996 0.0965941 0.400602 NA NA
1 86028 rs114608975 T C 0.0053485 0.0051689 0.2999998 0.3007810 0.103610 0.0277556 NA
1 91536 rs6702460 G T -0.0022914 0.0031821 0.4700002 0.4714784 0.456923 0.4207270 NA
1 234313 rs8179466 C T 0.0045829 0.0062804 0.4700002 0.4655610 0.074515 NA NA
1 534192 rs6680723 C T -0.0029755 0.0036395 0.4100001 0.4136201 0.240764 NA NA
1 546697 rs12025928 A G -0.0110702 0.0045349 0.0150000 0.0146430 0.913422 NA NA
1 693731 rs12238997 A G -0.0004150 0.0030520 0.8900000 0.8918349 0.116204 0.1417730 NA
1 705882 rs72631875 G A 0.0084751 0.0044700 0.0580003 0.0579587 0.067222 0.0315495 NA
1 706368 rs55727773 A G -0.0015348 0.0022595 0.5000000 0.4969857 0.516628 0.2751600 NA
CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
22 51219704 rs147475742 G A -0.0001117 0.0047756 0.9800000 0.9813407 0.041961 0.0473243 NA
22 51219766 rs182321900 C T 0.0089470 0.0231652 0.6999999 0.6993310 0.001814 NA NA
22 51220146 rs868950473 C T 0.0092633 0.0229280 0.6899999 0.6862003 0.001861 NA NA
22 51221190 rs369304721 G A -0.0024438 0.0047740 0.6100002 0.6087256 0.049625 NA NA
22 51221731 rs115055839 T C -0.0009961 0.0035673 0.7800007 0.7800676 0.073196 0.0625000 NA
22 51222100 rs114553188 G T 0.0072735 0.0041976 0.0830004 0.0831409 0.054505 0.0880591 NA
22 51223637 rs375798137 G A 0.0072479 0.0042180 0.0860003 0.0857376 0.054138 0.0788738 NA
22 51229805 rs9616985 T C -0.0009234 0.0035802 0.8000000 0.7964750 0.073027 0.0730831 NA
22 51232488 rs376461333 A G 0.0227110 0.0084276 0.0070000 0.0070426 0.020044 NA NA
22 51237063 rs3896457 T C -0.0023822 0.0021867 0.2800000 0.2759883 0.298393 0.2050720 NA

bcf preview

1   49298   rs10399793  T   C   .   PASS    AF=0.623702 ES:SE:LP:AF:ID  0.00268683:0.00326241:0.387216:0.623702:rs10399793
1   54676   rs2462492   C   T   .   PASS    AF=0.400602 ES:SE:LP:AF:ID  -0.00537132:0.00323263:1.01323:0.400602:rs2462492
1   86028   rs114608975 T   C   .   PASS    AF=0.10361  ES:SE:LP:AF:ID  0.00534853:0.00516886:0.522879:0.10361:rs114608975
1   91536   rs6702460   G   T   .   PASS    AF=0.456923 ES:SE:LP:AF:ID  -0.00229136:0.00318211:0.327902:0.456923:rs6702460
1   234313  rs8179466   C   T   .   PASS    AF=0.074515 ES:SE:LP:AF:ID  0.00458293:0.00628039:0.327902:0.074515:rs8179466
1   534192  rs6680723   C   T   .   PASS    AF=0.240764 ES:SE:LP:AF:ID  -0.00297546:0.00363953:0.387216:0.240764:rs6680723
1   546697  rs12025928  A   G   .   PASS    AF=0.913422 ES:SE:LP:AF:ID  -0.0110702:0.00453494:1.82391:0.913422:rs12025928
1   693731  rs12238997  A   G   .   PASS    AF=0.116204 ES:SE:LP:AF:ID  -0.000415018:0.00305199:0.05061:0.116204:rs12238997
1   705882  rs72631875  G   A   .   PASS    AF=0.067222 ES:SE:LP:AF:ID  0.00847511:0.00446997:1.23657:0.067222:rs72631875
1   706368  rs12029736  A   G   .   PASS    AF=0.516628 ES:SE:LP:AF:ID  -0.00153475:0.00225951:0.30103:0.516628:rs12029736
1   714596  rs149887893 T   C   .   PASS    AF=0.032672 ES:SE:LP:AF:ID  0.00333638:0.00572494:0.251812:0.032672:rs149887893
1   715265  rs12184267  C   T   .   PASS    AF=0.036254 ES:SE:LP:AF:ID  0.00291481:0.00519994:0.236572:0.036254:rs12184267
1   715367  rs12184277  A   G   .   PASS    AF=0.036362 ES:SE:LP:AF:ID  0.00336615:0.00518052:0.283997:0.036362:rs12184277
1   717485  rs12184279  C   A   .   PASS    AF=0.036061 ES:SE:LP:AF:ID  0.0036425:0.005218:0.309804:0.036061:rs12184279
1   717587  rs144155419 G   A   .   PASS    AF=0.016265 ES:SE:LP:AF:ID  0.00265876:0.0080317:0.130768:0.016265:rs144155419
1   720381  rs116801199 G   T   .   PASS    AF=0.036591 ES:SE:LP:AF:ID  0.00264852:0.00516049:0.21467:0.036591:rs116801199
1   721290  rs12565286  G   C   .   PASS    AF=0.036681 ES:SE:LP:AF:ID  0.00280447:0.00514295:0.229148:0.036681:rs12565286
1   722670  rs116030099 T   C   .   PASS    AF=0.1013   ES:SE:LP:AF:ID  -0.00277614:0.00372311:0.337242:0.1013:rs116030099
1   723891  rs2977670   G   C   .   PASS    AF=0.959772 ES:SE:LP:AF:ID  -0.00271992:0.00497588:0.236572:0.959772:rs2977670
1   724849  rs12126395  C   A   .   PASS    AF=0.031571 ES:SE:LP:AF:ID  0.00709699:0.00891522:0.366532:0.031571:rs12126395
1   725060  rs865924913 A   T   .   PASS    AF=0.053333 ES:SE:LP:AF:ID  0.00164196:0.0071164:0.0861861:0.053333:rs865924913
1   726794  rs28454925  C   G   .   PASS    AF=0.036208 ES:SE:LP:AF:ID  0.00293289:0.00517606:0.244125:0.036208:rs28454925
1   729632  rs116720794 C   T   .   PASS    AF=0.036516 ES:SE:LP:AF:ID  0.00289891:0.00512911:0.244125:0.036516:rs116720794
1   729679  rs4951859   C   G   .   PASS    AF=0.843997 ES:SE:LP:AF:ID  -0.000425948:0.00264924:0.0604807:0.843997:rs4951859
1   730087  rs148120343 T   C   .   PASS    AF=0.056012 ES:SE:LP:AF:ID  -0.00159386:0.00427575:0.148742:0.056012:rs148120343
1   731718  rs58276399  T   C   .   PASS    AF=0.122133 ES:SE:LP:AF:ID  -0.00016987:0.00289578:0.0222764:0.122133:rs58276399
1   732989  rs369030935 C   T   .   PASS    AF=0.025893 ES:SE:LP:AF:ID  -0.006156:0.00709055:0.408935:0.025893:rs369030935
1   734349  rs141242758 T   C   .   PASS    AF=0.121366 ES:SE:LP:AF:ID  -8.20877e-05:0.00289715:0.00877392:0.121366:rs141242758
1   736289  rs79010578  T   A   .   PASS    AF=0.132073 ES:SE:LP:AF:ID  0.00076553:0.00285488:0.102373:0.132073:rs79010578
1   736689  rs181876450 T   C   .   PASS    AF=0.011083 ES:SE:LP:AF:ID  0.0127437:0.0103957:0.657577:0.011083:rs181876450
1   740284  rs61770167  C   T   .   PASS    AF=0.005751 ES:SE:LP:AF:ID  -0.00366305:0.0133201:0.107905:0.005751:rs61770167
1   742813  rs112573343 C   T   .   PASS    AF=0.002083 ES:SE:LP:AF:ID  0.00978479:0.0236583:0.167491:0.002083:rs112573343
1   746189  rs139221807 A   G   .   PASS    AF=0.000945 ES:SE:LP:AF:ID  -0.0468612:0.0390513:0.638272:0.000945:rs139221807
1   752478  rs146277091 G   A   .   PASS    AF=0.036432 ES:SE:LP:AF:ID  0.00284705:0.00507795:0.236572:0.036432:rs146277091
1   752566  rs3094315   G   A   .   PASS    AF=0.83964  ES:SE:LP:AF:ID  0.000501583:0.00256534:0.0757207:0.83964:rs3094315
1   752721  rs3131972   A   G   .   PASS    AF=0.839335 ES:SE:LP:AF:ID  0.000730726:0.00256319:0.107905:0.839335:rs3131972
1   753405  rs3115860   C   A   .   PASS    AF=0.870164 ES:SE:LP:AF:ID  0.00156659:0.00274896:0.244125:0.870164:rs3115860
1   753541  rs2073813   G   A   .   PASS    AF=0.129449 ES:SE:LP:AF:ID  -0.00202048:0.00275493:0.337242:0.129449:rs2073813
1   754063  rs12184312  G   T   .   PASS    AF=0.036956 ES:SE:LP:AF:ID  0.00321539:0.00499051:0.283997:0.036956:rs12184312
1   754105  rs12184325  C   T   .   PASS    AF=0.037199 ES:SE:LP:AF:ID  0.00288884:0.00495887:0.251812:0.037199:rs12184325
1   754182  rs3131969   A   G   .   PASS    AF=0.869587 ES:SE:LP:AF:ID  0.00188181:0.00274436:0.309804:0.869587:rs3131969
1   754192  rs3131968   A   G   .   PASS    AF=0.869684 ES:SE:LP:AF:ID  0.00192818:0.00274544:0.318759:0.869684:rs3131968
1   754211  rs12184313  G   A   .   PASS    AF=0.037157 ES:SE:LP:AF:ID  0.00331327:0.00498042:0.29243:0.037157:rs12184313
1   754334  rs3131967   T   C   .   PASS    AF=0.869589 ES:SE:LP:AF:ID  0.00185074:0.0027443:0.30103:0.869589:rs3131967
1   754433  rs150578204 G   A   .   PASS    AF=0.00511  ES:SE:LP:AF:ID  -0.015564:0.0140565:0.568636:0.00511:rs150578204
1   754458  rs142682604 G   T   .   PASS    AF=0.005076 ES:SE:LP:AF:ID  -0.0154209:0.0140935:0.568636:0.005076:rs142682604
1   754503  rs3115859   G   A   .   PASS    AF=0.838785 ES:SE:LP:AF:ID  0.000573113:0.00255593:0.0861861:0.838785:rs3115859
1   754629  rs10454459  A   G   .   PASS    AF=0.037167 ES:SE:LP:AF:ID  0.00345543:0.00498755:0.309804:0.037167:rs10454459
1   754964  rs3131966   C   T   .   PASS    AF=0.83941  ES:SE:LP:AF:ID  0.000686934:0.00256308:0.102373:0.83941:rs3131966
1   755240  rs181660517 T   G   .   PASS    AF=0.013852 ES:SE:LP:AF:ID  0.0068974:0.00889866:0.356547:0.013852:rs181660517