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/public/UKB-b-13187/UKB-b-13187_data.vcf.gz \
--ref-ld-chr ../reference/eur_w_ld_chr/ \
--out /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-13187/ldsc.txt \
--w-ld-chr ../reference/eur_w_ld_chr/ 

Beginning analysis at Thu Oct 17 14:42:18 2019
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-13187/UKB-b-13187_data.vcf.gz ...
Read summary statistics for 4427667 SNPs.
Dropped 988 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, 1029005 SNPs remain.
After merging with regression SNP LD, 1029005 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.0376 (0.0158)
Lambda GC: 1.0133
Mean Chi^2: 1.0194
Intercept: 0.9942 (0.0077)
Ratio < 0 (usually indicates GC correction).
Analysis finished at Thu Oct 17 14:43:13 2019
Total time elapsed: 55.33s

QC metrics

Metrics

Metrics

{
    "af_correlation": 0.8913,
    "inflation_factor": 1,
    "mean_EFFECT": -3.5483e-06,
    "n": "-Inf",
    "n_snps": 9851866,
    "n_clumped_hits": 0,
    "n_p_sig": 0,
    "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": 36739,
    "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": 1029005,
    "ldsc_nsnp_merge_regression_ld": 1029005,
    "ldsc_observed_scale_h2_beta": 0.0376,
    "ldsc_observed_scale_h2_se": 0.0158,
    "ldsc_intercept_beta": 0.9942,
    "ldsc_intercept_se": 0.0077,
    "ldsc_lambda_gc": 1.0133,
    "ldsc_mean_chisq": 1.0194,
    "ldsc_ratio": -0.299
}

Flags

name value
af_correlation FALSE
inflation_factor FALSE
n TRUE
is_snpid_non_unique FALSE
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 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 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 4426685 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 4427667 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 8.656450e+00 5.765218e+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 7.860191e+07 5.672756e+07 828.0000000 3.173999e+07 6.896227e+07 1.147179e+08 2.492385e+08 ▇▆▅▂▁
numeric EFFECT 0 1.0000000 NA NA NA NA NA NA NA -3.500000e-06 3.218600e-03 -0.0205357 -2.096300e-03 -1.050000e-05 2.100800e-03 1.937460e-02 ▁▁▇▂▁
numeric SE 0 1.0000000 NA NA NA NA NA NA NA 3.142300e-03 5.353000e-04 0.0024848 2.681500e-03 2.960100e-03 3.499800e-03 9.084200e-03 ▇▂▁▁▁
numeric PVAL 0 1.0000000 NA NA NA NA NA NA NA 4.969782e-01 2.894621e-01 0.0000017 2.500000e-01 5.000000e-01 7.499995e-01 1.000000e+00 ▇▇▇▇▇
numeric PVAL_ztest 0 1.0000000 NA NA NA NA NA NA NA 4.969770e-01 2.894386e-01 0.0000017 2.455312e-01 4.960095e-01 7.477275e-01 9.999994e-01 ▇▇▇▇▇
numeric AF 0 1.0000000 NA NA NA NA NA NA NA 3.759750e-01 2.250074e-01 0.0934580 1.807635e-01 3.205610e-01 5.387310e-01 9.065420e-01 ▇▅▃▂▂
numeric AF_reference 36739 0.9917024 NA NA NA NA NA NA NA 3.670632e-01 2.254031e-01 0.0000000 1.811100e-01 3.194890e-01 5.271570e-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 0.0037932 0.0045849 0.4100001 0.4080612 0.623710 0.7821490 NA
1 54676 rs2462492 C T -0.0024262 0.0045630 0.5900000 0.5949202 0.399162 NA NA
1 86028 rs114608975 T C 0.0079992 0.0072203 0.2700001 0.2679133 0.103756 0.0277556 NA
1 91536 rs6702460 G T 0.0045259 0.0044866 0.3100002 0.3130879 0.455304 0.4207270 NA
1 534192 rs6680723 C T -0.0005431 0.0051450 0.9199999 0.9159346 0.240720 NA NA
1 693731 rs12238997 A G -0.0005193 0.0042743 0.9000000 0.9032999 0.118189 0.1417730 NA
1 706368 rs55727773 A G -0.0041858 0.0031742 0.1900002 0.1872719 0.513640 0.2751600 NA
1 722670 rs116030099 T C 0.0053897 0.0052578 0.3100002 0.3053223 0.100278 0.0413339 NA
1 729679 rs4951859 C G -0.0019147 0.0036945 0.5999997 0.6042838 0.840353 0.6399760 NA
1 731718 rs142557973 T C 0.0010426 0.0040619 0.8000000 0.7974251 0.124107 0.1543530 NA
CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
22 51198027 rs34939255 A G -0.0027492 0.0031539 0.3800004 0.3833848 0.257301 0.0984425 NA
22 51208537 rs72619593 G A -0.0034458 0.0042501 0.4199997 0.4175091 0.120551 0.1142170 NA
22 51210289 rs112565862 C T 0.0032989 0.0042883 0.4400003 0.4417261 0.126382 0.1018370 NA
22 51211106 rs9628250 T C -0.0023324 0.0031312 0.4600002 0.4563271 0.274349 0.1671330 NA
22 51211392 rs3888396 T C 0.0024069 0.0042492 0.5700002 0.5710981 0.128916 0.1641370 NA
22 51212875 rs2238837 A C -0.0002376 0.0030083 0.9400001 0.9370404 0.328738 0.3724040 NA
22 51213613 rs34726907 C T 0.0029520 0.0039351 0.4500005 0.4531579 0.128115 0.1727240 NA
22 51216564 rs9616970 T C 0.0028039 0.0039202 0.4700002 0.4744636 0.128577 0.1563500 NA
22 51219006 rs28729663 G A 0.0027256 0.0038337 0.4799997 0.4771042 0.138957 0.2052720 NA
22 51237063 rs3896457 T C -0.0016748 0.0030752 0.5900000 0.5860234 0.295451 0.2050720 NA

bcf preview

1   49298   rs10399793  T   C   .   PASS    AF=0.62371  ES:SE:LP:AF:ID  0.00379316:0.00458493:0.387216:0.62371:rs10399793
1   54676   rs2462492   C   T   .   PASS    AF=0.399162 ES:SE:LP:AF:ID  -0.00242621:0.00456295:0.229148:0.399162:rs2462492
1   86028   rs114608975 T   C   .   PASS    AF=0.103756 ES:SE:LP:AF:ID  0.00799922:0.00722029:0.568636:0.103756:rs114608975
1   91536   rs6702460   G   T   .   PASS    AF=0.455304 ES:SE:LP:AF:ID  0.00452591:0.00448659:0.508638:0.455304:rs6702460
1   534192  rs6680723   C   T   .   PASS    AF=0.24072  ES:SE:LP:AF:ID  -0.000543086:0.005145:0.0362122:0.24072:rs6680723
1   693731  rs12238997  A   G   .   PASS    AF=0.118189 ES:SE:LP:AF:ID  -0.0005193:0.00427429:0.0457575:0.118189:rs12238997
1   706368  rs12029736  A   G   .   PASS    AF=0.51364  ES:SE:LP:AF:ID  -0.00418582:0.00317422:0.721246:0.51364:rs12029736
1   722670  rs116030099 T   C   .   PASS    AF=0.100278 ES:SE:LP:AF:ID  0.00538968:0.00525778:0.508638:0.100278:rs116030099
1   729679  rs4951859   C   G   .   PASS    AF=0.840353 ES:SE:LP:AF:ID  -0.00191468:0.00369451:0.221849:0.840353:rs4951859
1   731718  rs58276399  T   C   .   PASS    AF=0.124107 ES:SE:LP:AF:ID  0.00104262:0.00406193:0.09691:0.124107:rs58276399
1   734349  rs141242758 T   C   .   PASS    AF=0.123373 ES:SE:LP:AF:ID  0.0011431:0.0040636:0.107905:0.123373:rs141242758
1   736289  rs79010578  T   A   .   PASS    AF=0.134053 ES:SE:LP:AF:ID  0.00277184:0.00400789:0.309804:0.134053:rs79010578
1   752566  rs3094315   G   A   .   PASS    AF=0.835828 ES:SE:LP:AF:ID  -0.000524411:0.0035873:0.0555173:0.835828:rs3094315
1   752721  rs3131972   A   G   .   PASS    AF=0.835345 ES:SE:LP:AF:ID  -0.000709393:0.00358091:0.0757207:0.835345:rs3131972
1   753405  rs3115860   C   A   .   PASS    AF=0.866915 ES:SE:LP:AF:ID  0.000139033:0.00383842:0.0132283:0.866915:rs3115860
1   753541  rs2073813   G   A   .   PASS    AF=0.132666 ES:SE:LP:AF:ID  0.000282472:0.00384822:0.0268721:0.132666:rs2073813
1   754182  rs3131969   A   G   .   PASS    AF=0.866153 ES:SE:LP:AF:ID  -0.000241028:0.00382859:0.0222764:0.866153:rs3131969
1   754192  rs3131968   A   G   .   PASS    AF=0.866318 ES:SE:LP:AF:ID  -0.000277675:0.00383067:0.0268721:0.866318:rs3131968
1   754334  rs3131967   T   C   .   PASS    AF=0.86615  ES:SE:LP:AF:ID  -0.000227032:0.00382823:0.0222764:0.86615:rs3131967
1   754503  rs3115859   G   A   .   PASS    AF=0.834923 ES:SE:LP:AF:ID  -0.00107929:0.00357513:0.119186:0.834923:rs3115859
1   754964  rs3131966   C   T   .   PASS    AF=0.835586 ES:SE:LP:AF:ID  -0.00110802:0.00358595:0.119186:0.835586:rs3131966
1   755775  rs3131965   A   G   .   PASS    AF=0.836772 ES:SE:LP:AF:ID  -0.000641812:0.0036325:0.0655015:0.836772:rs3131965
1   755890  rs3115858   A   T   .   PASS    AF=0.866643 ES:SE:LP:AF:ID  -0.000101643:0.00382694:0.00877392:0.866643:rs3115858
1   756604  rs3131962   A   G   .   PASS    AF=0.866271 ES:SE:LP:AF:ID  -2.89931e-05:0.00381769:0.00436481:0.866271:rs3131962
1   757640  rs3115853   G   A   .   PASS    AF=0.864793 ES:SE:LP:AF:ID  0.000209261:0.0038049:0.0177288:0.864793:rs3115853
1   757734  rs4951929   C   T   .   PASS    AF=0.866378 ES:SE:LP:AF:ID  -6.48973e-05:0.00382111:0.00436481:0.866378:rs4951929
1   757936  rs4951862   C   A   .   PASS    AF=0.866402 ES:SE:LP:AF:ID  -7.0279e-05:0.00382135:0.00436481:0.866402:rs4951862
1   758144  rs3131956   A   G   .   PASS    AF=0.866407 ES:SE:LP:AF:ID  -7.71088e-05:0.00382144:0.00877392:0.866407:rs3131956
1   758626  rs3131954   C   T   .   PASS    AF=0.86679  ES:SE:LP:AF:ID  -0.000173333:0.00383137:0.0177288:0.86679:rs3131954
1   760912  rs1048488   C   T   .   PASS    AF=0.835422 ES:SE:LP:AF:ID  -0.00100355:0.00357028:0.107905:0.835422:rs1048488
1   761147  rs3115850   T   C   .   PASS    AF=0.835566 ES:SE:LP:AF:ID  -0.00100768:0.0035729:0.107905:0.835566:rs3115850
1   761732  rs2286139   C   T   .   PASS    AF=0.859182 ES:SE:LP:AF:ID  -5.80371e-06:0.00380388:-0:0.859182:rs2286139
1   763394  rs3115847   G   A   .   PASS    AF=0.705081 ES:SE:LP:AF:ID  -0.000715599:0.00370981:0.0705811:0.705081:rs3115847
1   766007  rs61768174  A   C   .   PASS    AF=0.106752 ES:SE:LP:AF:ID  -0.00013963:0.00428521:0.0132283:0.106752:rs61768174
1   768253  rs2977608   A   C   .   PASS    AF=0.756826 ES:SE:LP:AF:ID  0.0003395:0.00302138:0.0409586:0.756826:rs2977608
1   768448  rs12562034  G   A   .   PASS    AF=0.108264 ES:SE:LP:AF:ID  0.000431713:0.00413957:0.0362122:0.108264:rs12562034
1   769223  rs60320384  C   G   .   PASS    AF=0.131879 ES:SE:LP:AF:ID  6.75026e-06:0.00385354:-0:0.131879:rs60320384
1   771823  rs2977605   T   C   .   PASS    AF=0.866392 ES:SE:LP:AF:ID  6.75682e-05:0.00382646:0.00436481:0.866392:rs2977605
1   771967  rs59066358  G   A   .   PASS    AF=0.131995 ES:SE:LP:AF:ID  0.000168183:0.00384995:0.0132283:0.131995:rs59066358
1   772755  rs2905039   A   C   .   PASS    AF=0.866394 ES:SE:LP:AF:ID  7.18401e-05:0.00382633:0.00436481:0.866394:rs2905039
1   776546  rs12124819  A   G   .   PASS    AF=0.264497 ES:SE:LP:AF:ID  -0.000281278:0.00341323:0.0315171:0.264497:rs12124819
1   777122  rs2980319   A   T   .   PASS    AF=0.868007 ES:SE:LP:AF:ID  -0.000941113:0.00383947:0.091515:0.868007:rs2980319
1   777232  rs112618790 C   T   .   PASS    AF=0.096795 ES:SE:LP:AF:ID  0.00279048:0.00441867:0.275724:0.096795:rs112618790
1   778745  rs1055606   A   G   .   PASS    AF=0.130462 ES:SE:LP:AF:ID  0.00121155:0.00385868:0.124939:0.130462:rs1055606
1   779322  rs4040617   A   G   .   PASS    AF=0.130808 ES:SE:LP:AF:ID  0.0010212:0.00385114:0.102373:0.130808:rs4040617
1   780785  rs2977612   T   A   .   PASS    AF=0.866654 ES:SE:LP:AF:ID  -0.000874525:0.00382598:0.0861861:0.866654:rs2977612
1   781845  rs61768199  A   G   .   PASS    AF=0.102937 ES:SE:LP:AF:ID  0.0019894:0.00435374:0.187087:0.102937:rs61768199
1   782981  rs6594026   C   T   .   PASS    AF=0.131418 ES:SE:LP:AF:ID  0.00118542:0.00384825:0.119186:0.131418:rs6594026
1   785050  rs2905062   G   A   .   PASS    AF=0.866227 ES:SE:LP:AF:ID  -0.000462746:0.00382163:0.0457575:0.866227:rs2905062
1   785989  rs2980300   T   C   .   PASS    AF=0.866195 ES:SE:LP:AF:ID  -0.000492972:0.0038248:0.0457575:0.866195:rs2980300