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/ieu-a-import/processed/ieu-a-1112/ieu-a-1112.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/ieu-a-import/processed/ieu-a-1112/ldsc.txt \
--w-ld-chr /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/reference/eur_w_ld_chr/ 

Beginning analysis at Wed Feb  5 08:36:09 2020
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ieu-a-import/processed/ieu-a-1112/ieu-a-1112.vcf.gz ...
Read summary statistics for 6288120 SNPs.
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, 760985 SNPs remain.
After merging with regression SNP LD, 760985 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.301 (0.0455)
Lambda GC: 1.0094
Mean Chi^2: 1.0396
Intercept: 0.9452 (0.0078)
Ratio < 0 (usually indicates GC correction).
Analysis finished at Wed Feb  5 08:37:14 2020
Total time elapsed: 1.0m:5.31s

QC metrics

Metrics

Metrics

{
    "af_correlation": 0.9422,
    "inflation_factor": 1.0744,
    "mean_EFFECT": -0.002,
    "n": 14890,
    "n_snps": 6288120,
    "n_clumped_hits": 18,
    "n_p_sig": 13857,
    "n_mono": 0,
    "n_ns": 364426,
    "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": 167149,
    "n_est": 14879.1299,
    "ratio_se_n": 0.9996,
    "mean_diff": 0.0018,
    "ratio_diff": 2.9812,
    "sd_y_est1": 2.6357,
    "sd_y_est2": 2.6347,
    "r2_sum1": 1.1019,
    "r2_sum2": 0.1586,
    "r2_sum3": 0.1587,
    "r2_sum4": 0.1464,
    "ldsc_nsnp_merge_refpanel_ld": 760985,
    "ldsc_nsnp_merge_regression_ld": 760985,
    "ldsc_observed_scale_h2_beta": 0.301,
    "ldsc_observed_scale_h2_se": 0.0455,
    "ldsc_intercept_beta": 0.9452,
    "ldsc_intercept_se": 0.0078,
    "ldsc_lambda_gc": 1.0094,
    "ldsc_mean_chisq": 1.0396,
    "ldsc_ratio": -1.3838
}

Flags

name value
af_correlation FALSE
inflation_factor FALSE
n FALSE
is_snpid_non_unique FALSE
mean_EFFECT_nonfinite FALSE
mean_EFFECT_05 FALSE
mean_EFFECT_01 FALSE
mean_chisq FALSE
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 TRUE
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 47 0 6288120 0 NA NA NA NA NA NA NA NA
character REF 0 1.0000000 1 49 0 18685 0 NA NA NA NA NA NA NA NA
character ALT 0 1.0000000 1 40 0 7851 0 NA NA NA NA NA NA NA NA
numeric CHROM 0 1.0000000 NA NA NA NA NA 8.756854e+00 6.015344e+00 1.00000 4.000000e+00 8.000000e+00 1.300000e+01 2.30000e+01 ▇▅▅▂▂
numeric POS 0 1.0000000 NA NA NA NA NA 7.798949e+07 5.499881e+07 302.00000 3.244481e+07 6.967919e+07 1.128368e+08 2.49205e+08 ▇▆▅▂▁
numeric EFFECT 0 1.0000000 NA NA NA NA NA -1.963700e-03 8.056120e-02 -3.09802 -3.536710e-02 0.000000e+00 3.440140e-02 3.35536e+00 ▁▁▇▁▁
numeric SE 0 1.0000000 NA NA NA NA NA 6.559130e-02 4.348140e-02 0.02300 3.500000e-02 4.700000e-02 8.200000e-02 7.02000e-01 ▇▁▁▁▁
numeric PVAL 0 1.0000000 NA NA NA NA NA 4.877571e-01 2.931908e-01 0.00000 2.310766e-01 4.844802e-01 7.420634e-01 1.00000e+00 ▇▇▇▇▇
numeric PVAL_ztest 0 1.0000000 NA NA NA NA NA 4.977882e-01 2.907681e-01 0.00000 2.461506e-01 4.980163e-01 7.489516e-01 1.00000e+00 ▇▇▇▇▇
numeric AF 0 1.0000000 NA NA NA NA NA 2.540005e-01 2.642542e-01 0.01000 4.000000e-02 1.500000e-01 4.000000e-01 9.90000e-01 ▇▂▂▁▁
numeric AF_reference 167149 0.9734183 NA NA NA NA NA 2.538424e-01 2.513709e-01 0.00000 5.051920e-02 1.633390e-01 3.945690e-01 1.00000e+00 ▇▃▂▁▁
numeric N 0 1.0000000 NA NA NA NA NA 1.489000e+04 0.000000e+00 14890.00000 1.489000e+04 1.489000e+04 1.489000e+04 1.48900e+04 ▁▁▇▁▁

Head and tail

CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
1 748332 rs182373484 T C -0.0732505 0.206 0.6966987 0.7221514 0.01 0.0013978 14890
1 761752 rs1057213 C T -0.0227395 0.043 0.5829885 0.5969265 0.86 0.7490020 14890
1 764191 rs7515915 T G 0.0246926 0.042 0.5561834 0.5565866 0.14 0.2220450 14890
1 769138 rs59306077 CAT C 0.0266419 0.042 0.5169172 0.5258649 0.14 0.2332270 14890
1 769223 rs60320384 C G 0.0266419 0.042 0.5158115 0.5258649 0.14 0.1912940 14890
1 771823 rs2977605 T C -0.0237165 0.042 0.5586168 0.5722924 0.86 0.7503990 14890
1 772755 rs2905039 A C -0.0237165 0.042 0.5625576 0.5722924 0.86 0.7551920 14890
1 775181 rs61768182 A G 0.0237165 0.042 0.5599058 0.5722924 0.14 0.2272360 14890
1 776556 rs151160018 C T -0.1034590 0.182 0.5355845 0.5697253 0.01 0.0015974 14890
1 778745 rs1055606 A G 0.0276152 0.042 0.5062721 0.5108564 0.14 0.2106630 14890
CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
23 154653820 rs181977483 A G -0.1980310 0.114 0.0664676 0.0823670 0.02 0.0301987 14890
23 154661750 rs140976899 C G 0.1124350 0.065 0.0763080 0.0836715 0.03 0.0238411 14890
23 154683663 rs5940510 C T 0.0079682 0.032 0.7882682 0.8033567 0.74 0.6278150 14890
23 154741935 rs6642272 A C 0.0639133 0.054 0.2202363 0.2365795 0.76 0.5835760 14890
23 154826774 rs782306 G A 0.0363319 0.028 0.1826712 0.1944359 0.76 0.6384110 14890
23 154866751 rs191379385 C T 0.1016540 0.065 0.1069109 0.1178392 0.03 0.0386755 14890
23 154878253 rs141771419 A G -0.0898407 0.088 0.2866481 0.3072937 0.02 0.0060927 14890
23 154885405 rs563690 G A 0.0372958 0.028 0.1718502 0.1828625 0.76 0.6378810 14890
23 154894936 rs148915445 T C -0.1914460 0.113 0.0727394 0.0902249 0.02 0.0307285 14890
23 154902105 rs696316 G T 0.0372958 0.028 0.1719428 0.1828625 0.76 0.6360260 14890

bcf preview

1   748332  rs182373484 T   C   .   PASS    AF=0.01 ES:SE:LP:AF:SS:ID   -0.0732505:0.206:0.156955:0.01:14890:rs182373484
1   761752  rs1057213   C   T   .   PASS    AF=0.86 ES:SE:LP:AF:SS:ID   -0.0227395:0.043:0.23434:0.86:14890:rs1057213
1   764191  rs7515915   T   G   .   PASS    AF=0.14 ES:SE:LP:AF:SS:ID   0.0246926:0.042:0.254782:0.14:14890:rs7515915
1   769138  rs59306077  CAT C   .   PASS    AF=0.14 ES:SE:LP:AF:SS:ID   0.0266419:0.042:0.286579:0.14:14890:rs59306077
1   769223  rs60320384  C   G   .   PASS    AF=0.14 ES:SE:LP:AF:SS:ID   0.0266419:0.042:0.287509:0.14:14890:rs60320384
1   771823  rs2977605   T   C   .   PASS    AF=0.86 ES:SE:LP:AF:SS:ID   -0.0237165:0.042:0.252886:0.86:14890:rs2977605
1   772755  rs2905039   A   C   .   PASS    AF=0.86 ES:SE:LP:AF:SS:ID   -0.0237165:0.042:0.249833:0.86:14890:rs2905039
1   775181  rs61768182  A   G   .   PASS    AF=0.14 ES:SE:LP:AF:SS:ID   0.0237165:0.042:0.251885:0.14:14890:rs61768182
1   776556  rs151160018 C   T   .   PASS    AF=0.01 ES:SE:LP:AF:SS:ID   -0.103459:0.182:0.271172:0.01:14890:rs151160018
1   778745  rs1055606   A   G   .   PASS    AF=0.14 ES:SE:LP:AF:SS:ID   0.0276152:0.042:0.295616:0.14:14890:rs1055606
1   780785  rs2977612   T   A   .   PASS    AF=0.86 ES:SE:LP:AF:SS:ID   -0.0382587:0.049:0.376324:0.86:14890:rs2977612
1   782981  rs6594026   C   T   .   PASS    AF=0.14 ES:SE:LP:AF:SS:ID   0.0353671:0.049:0.332078:0.14:14890:rs6594026
1   783318  rs6686696   A   G   .   PASS    AF=0.14 ES:SE:LP:AF:SS:ID   0.0266419:0.042:0.277918:0.14:14890:rs6686696
1   785050  rs2905062   G   A   .   PASS    AF=0.86 ES:SE:LP:AF:SS:ID   -0.0372958:0.049:0.357233:0.86:14890:rs2905062
1   786995  rs61768202  G   A   .   PASS    AF=0.14 ES:SE:LP:AF:SS:ID   0.0276152:0.042:0.302274:0.14:14890:rs61768202
1   787121  rs12077234  T   A   .   PASS    AF=0.14 ES:SE:LP:AF:SS:ID   0.0421012:0.049:0.418708:0.14:14890:rs12077234
1   787151  rs2519065   G   A   .   PASS    AF=0.14 ES:SE:LP:AF:SS:ID   0.0372958:0.049:0.354208:0.14:14890:rs2519065
1   787606  rs3863622   G   T   .   PASS    AF=0.14 ES:SE:LP:AF:SS:ID   0.0285875:0.042:0.305992:0.14:14890:rs3863622
1   787844  rs2905053   C   T   .   PASS    AF=0.86 ES:SE:LP:AF:SS:ID   -0.0401818:0.049:0.396625:0.86:14890:rs2905053
1   791191  rs111818025 G   A   .   PASS    AF=0.14 ES:SE:LP:AF:SS:ID   -0.0198026:0.085:0.0913778:0.14:14890:rs111818025
1   794332  rs12127425  G   A   .   PASS    AF=0.08 ES:SE:LP:AF:SS:ID   0.0852598:0.064:0.762341:0.08:14890:rs12127425
1   795222  rs12131377  C   G   .   PASS    AF=0.08 ES:SE:LP:AF:SS:ID   0.0760347:0.064:0.650351:0.08:14890:rs12131377
1   796100  rs12132398  C   T   .   PASS    AF=0.08 ES:SE:LP:AF:SS:ID   0.0723207:0.065:0.607311:0.08:14890:rs12132398
1   797281  rs76631953  G   C   .   PASS    AF=0.08 ES:SE:LP:AF:SS:ID   0.07139:0.065:0.59429:0.08:14890:rs76631953
1   797325  rs111739932 T   C   .   PASS    AF=0.08 ES:SE:LP:AF:SS:ID   0.076961:0.064:0.661816:0.08:14890:rs111739932
1   798026  rs4951864   C   T   .   PASS    AF=0.92 ES:SE:LP:AF:SS:ID   -0.0778865:0.064:0.677925:0.92:14890:rs4951864
1   799499  rs147634896 T   C   .   PASS    AF=0.08 ES:SE:LP:AF:SS:ID   0.0741794:0.064:0.63186:0.08:14890:rs147634896
1   801661  rs12132974  C   T   .   PASS    AF=0.08 ES:SE:LP:AF:SS:ID   0.0934903:0.064:0.87534:0.08:14890:rs12132974
1   801680  rs12134490  A   C   .   PASS    AF=0.08 ES:SE:LP:AF:SS:ID   0.0934903:0.064:0.875339:0.08:14890:rs12134490
1   802398  rs111444624 C   T   .   PASS    AF=0.08 ES:SE:LP:AF:SS:ID   0.0778865:0.065:0.667009:0.08:14890:rs111444624
1   802856  rs139867617 C   T   .   PASS    AF=0.08 ES:SE:LP:AF:SS:ID   0.0843411:0.064:0.755688:0.08:14890:rs139867617
1   814870  rs149628520 T   G   .   PASS    AF=0.01 ES:SE:LP:AF:SS:ID   -0.0334348:0.181:0.0742062:0.01:14890:rs149628520
1   832359  rs9697294   C   T   .   PASS    AF=0.02 ES:SE:LP:AF:SS:ID   -0.116894:0.129:0.473484:0.02:14890:rs9697294
1   833223  rs13303211  C   T   .   PASS    AF=0.23 ES:SE:LP:AF:SS:ID   0.0139029:0.04:0.136444:0.23:14890:rs13303211
1   833302  rs28752186  C   T   .   PASS    AF=0.23 ES:SE:LP:AF:SS:ID   0.0109399:0.04:0.109614:0.23:14890:rs28752186
1   833824  rs28484835  T   C   .   PASS    AF=0.23 ES:SE:LP:AF:SS:ID   0.0139029:0.04:0.145004:0.23:14890:rs28484835
1   833927  rs28593608  T   C   .   PASS    AF=0.21 ES:SE:LP:AF:SS:ID   0.0305292:0.042:0.342691:0.21:14890:rs28593608
1   834056  rs28482280  A   C   .   PASS    AF=0.02 ES:SE:LP:AF:SS:ID   -0.131028:0.124:0.579868:0.02:14890:rs28482280
1   834198  rs28385272  T   C   .   PASS    AF=0.21 ES:SE:LP:AF:SS:ID   0.0314987:0.042:0.35907:0.21:14890:rs28385272
1   834263  rs143031236 C   T   .   PASS    AF=0.02 ES:SE:LP:AF:SS:ID   -0.10075:0.13:0.386585:0.02:14890:rs143031236
1   834637  rs34941678  AC  A   .   PASS    AF=0.02 ES:SE:LP:AF:SS:ID   -0.128393:0.124:0.564263:0.02:14890:rs34941678
1   834832  rs4411087   G   C   .   PASS    AF=0.23 ES:SE:LP:AF:SS:ID   0.0129162:0.04:0.134617:0.23:14890:rs4411087
1   834928  rs4422949   A   G   .   PASS    AF=0.21 ES:SE:LP:AF:SS:ID   0.0266419:0.041:0.288483:0.21:14890:rs4422949
1   834956  rs7518581   G   A   .   PASS    AF=0.02 ES:SE:LP:AF:SS:ID   -0.116004:0.125:0.488604:0.02:14890:rs7518581
1   834999  rs28570054  G   A   .   PASS    AF=0.21 ES:SE:LP:AF:SS:ID   0.0266419:0.041:0.285011:0.21:14890:rs28570054
1   836529  rs28731045  C   G   .   PASS    AF=0.21 ES:SE:LP:AF:SS:ID   0.0285875:0.041:0.318259:0.21:14890:rs28731045
1   837553  rs112791300 GGTGT   G   .   PASS    AF=0.02 ES:SE:LP:AF:SS:ID   -0.120446:0.13:0.492798:0.02:14890:rs112791300
1   838329  rs144685080 G   GC  .   PASS    AF=0.21 ES:SE:LP:AF:SS:ID   0.0314987:0.041:0.355331:0.21:14890:rs144685080
1   838387  rs4970384   T   C   .   PASS    AF=0.21 ES:SE:LP:AF:SS:ID   0.0276152:0.041:0.300077:0.21:14890:rs4970384
1   838665  rs28678693  T   C   .   PASS    AF=0.02 ES:SE:LP:AF:SS:ID   -0.107957:0.127:0.436144:0.02:14890:rs28678693