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-1090/ieu-a-1090.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-1090/ldsc.txt \
--w-ld-chr /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/reference/eur_w_ld_chr/ 

Beginning analysis at Tue Feb  4 17:15:05 2020
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ieu-a-import/processed/ieu-a-1090/ieu-a-1090.vcf.gz ...
Read summary statistics for 7987990 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, 1234266 SNPs remain.
After merging with regression SNP LD, 1234266 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.0279 (0.0035)
Lambda GC: 0.5139
Mean Chi^2: 1.0945
Intercept: 1.0308 (0.0054)
Ratio: 0.3259 (0.0568)
Analysis finished at Tue Feb  4 17:16:25 2020
Total time elapsed: 1.0m:20.03s

QC metrics

Metrics

Metrics

{
    "af_correlation": 0.9375,
    "inflation_factor": 1,
    "mean_EFFECT": 0.0417,
    "n": 117775,
    "n_snps": 7987990,
    "n_clumped_hits": 2,
    "n_p_sig": 2,
    "n_mono": 0,
    "n_ns": 514654,
    "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": 122902,
    "n_est": 156356.4393,
    "ratio_se_n": 1.1522,
    "mean_diff": -0.043,
    "ratio_diff": 9.4697,
    "sd_y_est1": 11.2645,
    "sd_y_est2": 12.979,
    "r2_sum1": 0.13,
    "r2_sum2": 0.001,
    "r2_sum3": 0.0008,
    "r2_sum4": 0.0005,
    "ldsc_nsnp_merge_refpanel_ld": 1234266,
    "ldsc_nsnp_merge_regression_ld": 1234266,
    "ldsc_observed_scale_h2_beta": 0.0279,
    "ldsc_observed_scale_h2_se": 0.0035,
    "ldsc_intercept_beta": 1.0308,
    "ldsc_intercept_se": 0.0054,
    "ldsc_lambda_gc": 0.5139,
    "ldsc_mean_chisq": 1.0945,
    "ldsc_ratio": 0.3259
}

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 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 numeric.mean numeric.sd numeric.p0 numeric.p25 numeric.p50 numeric.p75 numeric.p100 numeric.hist
character ID 0 1.0000000 3 58 0 7987990 0 NA NA NA NA NA NA NA NA
character REF 0 1.0000000 1 51 0 28564 0 NA NA NA NA NA NA NA NA
character ALT 0 1.0000000 1 51 0 15363 0 NA NA NA NA NA NA NA NA
numeric CHROM 0 1.0000000 NA NA NA NA NA 8.625223e+00 5.750020e+00 1.0000 4.000000e+00 8.000000e+00 1.300000e+01 2.200000e+01 ▇▅▃▂▂
numeric POS 0 1.0000000 NA NA NA NA NA 7.891173e+07 5.640257e+07 302.0000 3.238627e+07 6.954088e+07 1.146095e+08 2.492297e+08 ▇▆▅▂▁
numeric EFFECT 0 1.0000000 NA NA NA NA NA 4.167020e-02 6.761367e-01 -10.4833 -5.129330e-02 0.000000e+00 3.045920e-02 8.935900e+00 ▁▁▇▁▁
numeric SE 0 1.0000000 NA NA NA NA NA 3.870307e+00 3.813164e+01 0.0320 3.900000e-02 6.500000e-02 1.700000e-01 7.200000e+02 ▇▁▁▁▁
numeric PVAL 0 1.0000000 NA NA NA NA NA 5.042269e-01 2.919007e-01 0.0000 2.500000e-01 5.000000e-01 7.600007e-01 1.000000e+00 ▇▇▇▇▇
numeric PVAL_ztest 0 1.0000000 NA NA NA NA NA 5.777851e-01 3.566414e-01 0.0000 2.437777e-01 5.797132e-01 1.000000e+00 1.000000e+00 ▅▃▃▃▇
numeric AF 0 1.0000000 NA NA NA NA NA 2.765923e-01 2.636745e-01 0.0050 5.700000e-02 1.800000e-01 4.380000e-01 9.950000e-01 ▇▃▂▂▁
numeric AF_reference 122902 0.9846142 NA NA NA NA NA 2.728606e-01 2.520354e-01 0.0000 6.549520e-02 1.900960e-01 4.253190e-01 1.000000e+00 ▇▃▂▂▁
numeric N 0 1.0000000 NA NA NA NA NA 1.162499e+05 2.412383e+03 83388.0000 1.159790e+05 1.170760e+05 1.175550e+05 1.177750e+05 ▁▁▁▁▇

Head and tail

CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
1 751343 rs28544273 T A 0.0000000 0.079 0.6700003 1.0000000 0.126 0.242612 116172
1 751488 rs200141114 GA G 0.0000000 0.079 0.5800000 1.0000000 0.855 NA 106771
1 753405 rs3115860 C A 0.0000000 0.077 0.5600000 1.0000000 0.872 0.751797 116400
1 753425 rs3131970 T C 0.0000000 0.077 0.5600000 1.0000000 0.872 0.749002 116393
1 753541 rs2073813 G A 0.0000000 0.077 0.6499995 1.0000000 0.127 0.301917 116600
1 754182 rs3131969 A G -0.0953102 0.077 0.5199996 0.2157922 0.871 0.678514 116877
1 754192 rs3131968 A G -0.0953102 0.077 0.5199996 0.2157922 0.871 0.678514 116874
1 754334 rs3131967 T C 0.0000000 0.077 0.5300002 1.0000000 0.871 0.684305 116851
1 755890 rs3115858 A T -0.0953102 0.077 0.5300002 0.2157922 0.871 0.751398 117061
1 756434 rs61768170 G C 0.0953102 0.078 0.4400003 0.2217357 0.128 0.188498 117071
CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
22 51216051 rs376488897 A G -0.0943107 0.082 0.2700001 0.2500901 0.127 0.1365810 108913
22 51216149 rs373165495 C A -0.0943107 0.082 0.2700001 0.2500901 0.127 0.1361820 108933
22 51216564 rs9616970 T C -0.0943107 0.082 0.2599998 0.2500901 0.127 0.1563500 108828
22 51217954 rs9616974 G A 0.0953102 0.170 0.5400003 0.5750374 0.072 0.0621006 112727
22 51218224 rs9616975 C A 0.0953102 0.170 0.5400003 0.5750374 0.072 0.0619010 112729
22 51218377 rs2519461 G C 0.1823220 0.170 0.4000000 0.2835034 0.073 0.0826677 112664
22 51218615 rs9616976 T A 0.0953102 0.170 0.4199997 0.5750374 0.073 0.0858626 112603
22 51219387 rs9616832 T C 0.0953102 0.170 0.4100001 0.5750374 0.073 0.0654952 112285
22 51220249 rs9616977 A T 0.1823220 0.190 0.3200000 0.3372619 0.072 0.0595048 111867
22 51220319 rs9616978 C G 0.1823220 0.210 0.3100002 0.3852849 0.069 0.0397364 111763

bcf preview

1   751343  rs28544273  T   A   .   PASS    AF=0.126    ES:SE:LP:AF:SS:ID   0:0.079:0.173925:0.126:116172:rs28544273
1   751488  rs200141114 GA  G   .   PASS    AF=0.855    ES:SE:LP:AF:SS:ID   0:0.079:0.236572:0.855:106771:rs200141114
1   753405  rs3115860   C   A   .   PASS    AF=0.872    ES:SE:LP:AF:SS:ID   0:0.077:0.251812:0.872:116400:rs3115860
1   753425  rs3131970   T   C   .   PASS    AF=0.872    ES:SE:LP:AF:SS:ID   0:0.077:0.251812:0.872:116393:rs3131970
1   753541  rs2073813   G   A   .   PASS    AF=0.127    ES:SE:LP:AF:SS:ID   0:0.077:0.187087:0.127:116600:rs2073813
1   754182  rs3131969   A   G   .   PASS    AF=0.871    ES:SE:LP:AF:SS:ID   -0.0953102:0.077:0.283997:0.871:116877:rs3131969
1   754192  rs3131968   A   G   .   PASS    AF=0.871    ES:SE:LP:AF:SS:ID   -0.0953102:0.077:0.283997:0.871:116874:rs3131968
1   754334  rs3131967   T   C   .   PASS    AF=0.871    ES:SE:LP:AF:SS:ID   0:0.077:0.275724:0.871:116851:rs3131967
1   755890  rs3115858   A   T   .   PASS    AF=0.871    ES:SE:LP:AF:SS:ID   -0.0953102:0.077:0.275724:0.871:117061:rs3115858
1   756434  rs61768170  G   C   .   PASS    AF=0.128    ES:SE:LP:AF:SS:ID   0.0953102:0.078:0.356547:0.128:117071:rs61768170
1   756604  rs3131962   A   G   .   PASS    AF=0.87 ES:SE:LP:AF:SS:ID   -0.0953102:0.076:0.455932:0.87:117775:rs3131962
1   757640  rs3115853   G   A   .   PASS    AF=0.869    ES:SE:LP:AF:SS:ID   -0.0953102:0.076:0.468521:0.869:117363:rs3115853
1   757734  rs4951929   C   T   .   PASS    AF=0.87 ES:SE:LP:AF:SS:ID   -0.0953102:0.076:0.420216:0.87:117627:rs4951929
1   757936  rs4951862   C   A   .   PASS    AF=0.87 ES:SE:LP:AF:SS:ID   -0.0953102:0.076:0.366532:0.87:117629:rs4951862
1   758144  rs3131956   A   G   .   PASS    AF=0.869    ES:SE:LP:AF:SS:ID   -0.0953102:0.076:0.376751:0.869:117007:rs3131956
1   758626  rs3131954   C   T   .   PASS    AF=0.871    ES:SE:LP:AF:SS:ID   0:0.076:0.267606:0.871:117278:rs3131954
1   759293  rs10157329  T   A   .   PASS    AF=0.102    ES:SE:LP:AF:SS:ID   0:0.11:0.0861861:0.102:113169:rs10157329
1   761732  rs2286139   C   T   .   PASS    AF=0.863    ES:SE:LP:AF:SS:ID   -0.0953102:0.075:0.366532:0.863:114476:rs2286139
1   761752  rs1057213   C   T   .   PASS    AF=0.868    ES:SE:LP:AF:SS:ID   -0.0953102:0.077:0.337242:0.868:116246:rs1057213
1   762273  rs3115849   G   A   .   PASS    AF=0.865    ES:SE:LP:AF:SS:ID   -0.0953102:0.076:0.283997:0.865:115084:rs3115849
1   762632  rs3131948   T   A   .   PASS    AF=0.869    ES:SE:LP:AF:SS:ID   0:0.076:0.130768:0.869:115585:rs3131948
1   764191  rs7515915   T   G   .   PASS    AF=0.129    ES:SE:LP:AF:SS:ID   0:0.077:0.259637:0.129:117166:rs7515915
1   766007  rs61768174  A   C   .   PASS    AF=0.099    ES:SE:LP:AF:SS:ID   -0.0100503:0.11:0.0315171:0.099:111851:rs61768174
1   768253  rs2977608   A   C   .   PASS    AF=0.764    ES:SE:LP:AF:SS:ID   -0.0953102:0.046:1.30103:0.764:117268:rs2977608
1   768448  rs12562034  G   A   .   PASS    AF=0.105    ES:SE:LP:AF:SS:ID   0.0953102:0.088:0.267606:0.105:117775:rs12562034
1   769138  rs59306077  CAT C   .   PASS    AF=0.129    ES:SE:LP:AF:SS:ID   0.0953102:0.077:0.327902:0.129:117160:rs59306077
1   769223  rs60320384  C   G   .   PASS    AF=0.129    ES:SE:LP:AF:SS:ID   0.0953102:0.077:0.309804:0.129:117431:rs60320384
1   769963  rs7518545   G   A   .   PASS    AF=0.105    ES:SE:LP:AF:SS:ID   0.0953102:0.09:0.283997:0.105:117495:rs7518545
1   770886  rs371458725 G   A   .   PASS    AF=0.104    ES:SE:LP:AF:SS:ID   0:0.09:0.0809219:0.104:116847:rs371458725
1   771823  rs2977605   T   C   .   PASS    AF=0.87 ES:SE:LP:AF:SS:ID   -0.0953102:0.079:0.552842:0.87:117365:rs2977605
1   771967  rs59066358  G   A   .   PASS    AF=0.129    ES:SE:LP:AF:SS:ID   0.0953102:0.079:0.508638:0.129:117362:rs59066358
1   772755  rs2905039   A   C   .   PASS    AF=0.871    ES:SE:LP:AF:SS:ID   -0.0953102:0.079:0.638272:0.871:117340:rs2905039
1   774874  rs28810152  A   C   .   PASS    AF=0.87 ES:SE:LP:AF:SS:ID   -0.0953102:0.08:0.619789:0.87:116628:rs28810152
1   775181  rs61768182  A   G   .   PASS    AF=0.129    ES:SE:LP:AF:SS:ID   0.0953102:0.079:0.60206:0.129:117368:rs61768182
1   775659  rs2905035   A   G   .   PASS    AF=0.87 ES:SE:LP:AF:SS:ID   -0.0953102:0.078:0.537602:0.87:117395:rs2905035
1   777122  rs2980319   A   T   .   PASS    AF=0.871    ES:SE:LP:AF:SS:ID   -0.0953102:0.076:0.49485:0.871:117413:rs2980319
1   777232  rs112618790 C   T   .   PASS    AF=0.096    ES:SE:LP:AF:SS:ID   -0.040822:0.098:0.161151:0.096:114932:rs112618790
1   778745  rs1055606   A   G   .   PASS    AF=0.128    ES:SE:LP:AF:SS:ID   0.0953102:0.077:0.49485:0.128:117516:rs1055606
1   779322  rs4040617   A   G   .   PASS    AF=0.128    ES:SE:LP:AF:SS:ID   0.0953102:0.076:0.522879:0.128:117775:rs4040617
1   780785  rs2977612   T   A   .   PASS    AF=0.87 ES:SE:LP:AF:SS:ID   -0.0953102:0.076:0.522879:0.87:116876:rs2977612
1   781845  rs61768199  A   G   .   PASS    AF=0.095    ES:SE:LP:AF:SS:ID   0.0953102:0.12:0.21467:0.095:111538:rs61768199
1   782981  rs6594026   C   T   .   PASS    AF=0.128    ES:SE:LP:AF:SS:ID   0.0953102:0.078:0.638272:0.128:117064:rs6594026
1   783318  rs6686696   A   G   .   PASS    AF=0.127    ES:SE:LP:AF:SS:ID   0.0953102:0.077:0.468521:0.127:117474:rs6686696
1   785050  rs2905062   G   A   .   PASS    AF=0.87 ES:SE:LP:AF:SS:ID   -0.0953102:0.076:0.431798:0.87:116796:rs2905062
1   785989  rs2980300   T   C   .   PASS    AF=0.87 ES:SE:LP:AF:SS:ID   -0.0953102:0.075:0.39794:0.87:116878:rs2980300
1   786995  rs61768202  G   A   .   PASS    AF=0.127    ES:SE:LP:AF:SS:ID   0.0953102:0.078:0.443698:0.127:117355:rs61768202
1   787399  rs2905055   G   T   .   PASS    AF=0.863    ES:SE:LP:AF:SS:ID   0:0.075:0.124939:0.863:111476:rs2905055
1   787606  rs3863622   G   T   .   PASS    AF=0.127    ES:SE:LP:AF:SS:ID   0:0.078:0.229148:0.127:116131:rs3863622
1   787685  rs2905054   G   T   .   PASS    AF=0.868    ES:SE:LP:AF:SS:ID   0:0.076:0.207608:0.868:114248:rs2905054
1   787844  rs2905053   C   T   .   PASS    AF=0.87 ES:SE:LP:AF:SS:ID   0:0.076:0.113509:0.87:115094:rs2905053