Summary

Summary {data-width=650}

Manhattan plot

manhattan_plot

QQ plot

qq_plot

AF plot

af_plot

P-Z plot

pz_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 /data/cromwell-executions/qc/9376eb31-d2ad-4425-a10f-88b1ab82260d/call-ldsc/inputs/562856373/ieu-b-90.vcf.gz \
--ref-ld-chr /data/ref/eur_w_ld_chr/ \
--out /data/igd/ieu-b-90/ldsc.txt \
--w-ld-chr /data/ref/eur_w_ld_chr/ 

Beginning analysis at Thu Dec 17 01:55:36 2020
Reading summary statistics from /data/cromwell-executions/qc/9376eb31-d2ad-4425-a10f-88b1ab82260d/call-ldsc/inputs/562856373/ieu-b-90.vcf.gz ...
Read summary statistics for 7297324 SNPs.
Dropped 20622 SNPs with duplicated rs numbers.
Reading reference panel LD Score from /data/ref/eur_w_ld_chr/[1-22] ... (ldscore_fromlist)
Read reference panel LD Scores for 1290028 SNPs.
Removing partitioned LD Scores with zero variance.
Reading regression weight LD Score from /data/ref/eur_w_ld_chr/[1-22] ... (ldscore_fromlist)
Read regression weight LD Scores for 1290028 SNPs.
After merging with reference panel LD, 1102830 SNPs remain.
After merging with regression SNP LD, 1102830 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.0593 (0.0984)
Lambda GC: 1.0219
Mean Chi^2: 1.0228
Intercept: 1.0173 (0.0059)
Ratio: 0.7596 (0.2613)
Analysis finished at Thu Dec 17 01:57:05 2020
Total time elapsed: 1.0m:29.36s

QC metrics

Metrics

Metrics

{
    "af_correlation": 0.9367,
    "inflation_factor": 1.0239,
    "mean_EFFECT": "Inf",
    "n": 4671,
    "n_snps": 7298218,
    "n_clumped_hits": 0,
    "n_p_sig": 0,
    "n_mono": 4471,
    "n_ns": 2,
    "n_mac": 3938,
    "is_snpid_unique": false,
    "n_miss_EFFECT": 0,
    "n_miss_SE": 0,
    "n_miss_PVAL": 0,
    "n_miss_AF": 0,
    "n_miss_AF_reference": 64416,
    "n_est": 4619.9978,
    "ratio_se_n": 0.9945,
    "mean_diff": "NaN",
    "ratio_diff": "NaN",
    "sd_y_est1": 2.1334,
    "sd_y_est2": 2.1217,
    "r2_sum1": 0,
    "r2_sum2": 0,
    "r2_sum3": 0,
    "r2_sum4": 0,
    "ldsc_nsnp_merge_refpanel_ld": 1102830,
    "ldsc_nsnp_merge_regression_ld": 1102830,
    "ldsc_observed_scale_h2_beta": 0.0593,
    "ldsc_observed_scale_h2_se": 0.0984,
    "ldsc_intercept_beta": 1.0173,
    "ldsc_intercept_se": 0.0059,
    "ldsc_lambda_gc": 1.0219,
    "ldsc_mean_chisq": 1.0228,
    "ldsc_ratio": 0.7588
}

Flags

name value
af_correlation FALSE
inflation_factor FALSE
n TRUE
is_snpid_non_unique TRUE
mean_EFFECT_nonfinite TRUE
mean_EFFECT_05 TRUE
mean_EFFECT_01 TRUE
mean_chisq FALSE
n_p_sig FALSE
miss_EFFECT FALSE
miss_SE FALSE
miss_PVAL FALSE
ldsc_ratio TRUE
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 878 0.9998797 3 58 0 7297257 0 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
character ALT 0 1.0000000 1 1 0 4 0 NA NA NA NA NA NA NA NA
numeric CHROM 0 1.0000000 NA NA NA NA NA 8.648716e+00 5.753598e+00 1.000e+00 4.000000e+00 8.000000e+00 1.300000e+01 22 ▇▅▅▂▂
numeric POS 0 1.0000000 NA NA NA NA NA 7.875129e+07 5.640877e+07 8.280e+02 3.227741e+07 6.931213e+07 1.146217e+08 249216384 ▇▆▅▂▁
numeric EFFECT 0 1.0000000 NA NA NA NA NA Inf Inf -6.908e+00 -4.800000e-02 0.000000e+00 4.900000e-02 Inf ▇▁▁▁▁
numeric SE 0 1.0000000 NA NA NA NA NA 1.178975e-01 7.463653e+01 4.100e-02 4.800000e-02 6.500000e-02 1.120000e-01 201628 ▇▁▁▁▁
numeric PVAL 0 1.0000000 NA NA NA NA NA 4.960696e-01 2.892700e-01 4.000e-07 2.451834e-01 4.949200e-01 7.465570e-01 1 ▇▇▇▇▇
numeric PVAL_ztest 0 1.0000000 NA NA NA NA NA 4.961280e-01 2.893217e-01 0.000e+00 2.454230e-01 4.953539e-01 7.467094e-01 1 ▇▇▇▇▇
numeric AF 0 1.0000000 NA NA NA NA NA 2.602918e-01 2.624152e-01 0.000e+00 4.600000e-02 1.560000e-01 4.100000e-01 1 ▇▂▂▁▁
numeric AF_reference 64416 0.9911737 NA NA NA NA NA 2.596757e-01 2.523726e-01 0.000e+00 5.491210e-02 1.697280e-01 4.029550e-01 1 ▇▃▂▁▁
numeric N 0 1.0000000 NA NA NA NA NA 4.670871e+03 3.181319e+00 4.389e+03 4.671000e+03 4.671000e+03 4.671000e+03 4671 ▁▁▁▁▇

Head and tail

CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
1 693731 rs12238997 A G -0.106 0.111 0.3369186 0.3396005 0.126 0.141773 4671
1 729679 rs4951859 C G 0.089 0.101 0.3760651 0.3782160 0.822 0.639976 4671
1 731718 rs142557973 T C -0.097 0.101 0.3398474 0.3368559 0.133 0.154353 4671
1 734349 rs141242758 T C -0.092 0.101 0.3586485 0.3623528 0.132 0.152556 4671
1 752566 rs3094315 G A 0.060 0.059 0.3087003 0.3091776 0.812 0.718251 4671
1 752721 rs3131972 A G 0.058 0.058 0.3246004 0.3173105 0.809 0.653355 4670
1 753405 rs3115860 C A 0.070 0.091 0.4448668 0.4417563 0.854 0.751797 4671
1 753541 rs2073813 G A -0.068 0.090 0.4511085 0.4499157 0.148 0.301917 4671
1 754182 rs3131969 A G 0.065 0.090 0.4703087 0.4701579 0.851 0.678514 4671
1 754192 rs3131968 A G 0.065 0.090 0.4702470 0.4701579 0.851 0.678514 4671
CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
22 51218224 rs9616975 C A -0.091 0.129 0.4815429 0.4805449 0.073 0.0619010 4671
22 51218377 rs2519461 G C -0.100 0.129 0.4395578 0.4382252 0.075 0.0826677 4671
22 51219006 rs28729663 G A 0.011 0.095 0.9091122 0.9078194 0.139 0.2052720 4671
22 51219387 rs9616832 T C -0.093 0.130 0.4756330 0.4743714 0.074 0.0654952 4671
22 51219704 rs147475742 G A -0.109 0.192 0.5687233 0.5702330 0.041 0.0473243 4671
22 51221731 rs115055839 T C -0.090 0.131 0.4940911 0.4920683 0.073 0.0625000 4671
22 51222100 rs114553188 G T 0.031 0.142 0.8272622 0.8271877 0.056 0.0880591 4671
22 51223637 rs375798137 G A 0.031 0.143 0.8319567 0.8283773 0.055 0.0788738 4671
22 51229805 rs9616985 T C -0.086 0.133 0.5197446 0.5178801 0.073 0.0730831 4671
22 51237063 rs3896457 T C 0.036 0.077 0.6363587 0.6401190 0.287 0.2050720 4671

bcf preview

1   693731  rs12238997  A   G   .   PASS    AF=0.126    ES:SE:LP:AF:SS:SI:NC:ID -0.106:0.111:0.472475:0.126:4671:0.324:2342:rs12238997
1   729679  rs4951859   C   G   .   PASS    AF=0.822    ES:SE:LP:AF:SS:SI:NC:ID 0.089:0.101:0.424737:0.822:4671:0.361:2342:rs4951859
1   731718  rs58276399  T   C   .   PASS    AF=0.133    ES:SE:LP:AF:SS:SI:NC:ID -0.097:0.101:0.468716:0.133:4671:0.378:2342:rs58276399
1   734349  rs141242758 T   C   .   PASS    AF=0.132    ES:SE:LP:AF:SS:SI:NC:ID -0.092:0.101:0.445331:0.132:4671:0.379:2342:rs141242758
1   752566  rs3094315   G   A   .   PASS    AF=0.812    ES:SE:LP:AF:SS:SI:NC:ID 0.06:0.059:0.510463:0.812:4671:1:2342:rs3094315
1   752721  rs3131972   A   G   .   PASS    AF=0.809    ES:SE:LP:AF:SS:SI:NC:ID 0.058:0.058:0.488651:0.809:4670:1:2342:rs3131972
1   753405  rs3115860   C   A   .   PASS    AF=0.854    ES:SE:LP:AF:SS:SI:NC:ID 0.07:0.091:0.35177:0.854:4671:0.473:2342:rs3115860
1   753541  rs1388595942    G   A   .   PASS    AF=0.148    ES:SE:LP:AF:SS:SI:NC:ID -0.068:0.09:0.345719:0.148:4671:0.481:2342:rs1388595942
1   754182  rs3131969   A   G   .   PASS    AF=0.851    ES:SE:LP:AF:SS:SI:NC:ID 0.065:0.09:0.327617:0.851:4671:0.493:2342:rs3131969
1   754192  rs3131968   A   G   .   PASS    AF=0.851    ES:SE:LP:AF:SS:SI:NC:ID 0.065:0.09:0.327674:0.851:4671:0.494:2342:rs3131968
1   754334  rs3131967   T   C   .   PASS    AF=0.851    ES:SE:LP:AF:SS:SI:NC:ID 0.065:0.09:0.325082:0.851:4671:0.494:2342:rs3131967
1   754503  rs3115859   G   A   .   PASS    AF=0.817    ES:SE:LP:AF:SS:SI:NC:ID 0.065:0.092:0.316803:0.817:4671:0.417:2342:rs3115859
1   754964  rs3131966   C   T   .   PASS    AF=0.818    ES:SE:LP:AF:SS:SI:NC:ID 0.066:0.092:0.320284:0.818:4671:0.42:2342:rs3131966
1   755775  rs3131965   A   G   .   PASS    AF=0.822    ES:SE:LP:AF:SS:SI:NC:ID 0.07:0.093:0.350496:0.822:4671:0.403:2342:rs3131965
1   755890  rs1280367067    A   T   .   PASS    AF=0.853    ES:SE:LP:AF:SS:SI:NC:ID 0.071:0.09:0.370308:0.853:4671:0.48:2342:rs1280367067
1   756604  rs3131962   A   G   .   PASS    AF=0.853    ES:SE:LP:AF:SS:SI:NC:ID 0.073:0.09:0.38014:0.853:4671:0.482:2342:rs3131962
1   757640  rs3115853   G   A   .   PASS    AF=0.848    ES:SE:LP:AF:SS:SI:NC:ID 0.064:0.088:0.331598:0.848:4671:0.525:2342:rs3115853
1   757734  rs1557551770    C   T   .   PASS    AF=0.853    ES:SE:LP:AF:SS:SI:NC:ID 0.072:0.09:0.380306:0.853:4671:0.484:2342:rs1557551770
1   757936  rs1360886751    C   A   .   PASS    AF=0.853    ES:SE:LP:AF:SS:SI:NC:ID 0.072:0.09:0.379758:0.853:4671:0.485:2342:rs1360886751
1   758144  rs3131956   A   G   .   PASS    AF=0.853    ES:SE:LP:AF:SS:SI:NC:ID 0.073:0.09:0.38123:0.853:4671:0.485:2342:rs3131956
1   758626  rs3131954   C   T   .   PASS    AF=0.854    ES:SE:LP:AF:SS:SI:NC:ID 0.071:0.09:0.37159:0.854:4671:0.484:2342:rs3131954
1   760912  rs1048488   C   T   .   PASS    AF=0.821    ES:SE:LP:AF:SS:SI:NC:ID 0.066:0.092:0.327308:0.821:4671:0.408:2342:rs1048488
1   761147  rs3115850   T   C   .   PASS    AF=0.821    ES:SE:LP:AF:SS:SI:NC:ID 0.067:0.092:0.32832:0.821:4671:0.409:2342:rs3115850
1   761732  rs2286139   C   T   .   PASS    AF=0.843    ES:SE:LP:AF:SS:SI:NC:ID 0.056:0.087:0.288427:0.843:4671:0.532:2342:rs2286139
1   766007  rs61768174  A   C   .   PASS    AF=0.11 ES:SE:LP:AF:SS:SI:NC:ID -0.041:0.097:0.172791:0.11:4671:0.458:2342:rs61768174
1   768253  rs2977608   A   C   .   PASS    AF=0.731    ES:SE:LP:AF:SS:SI:NC:ID 0.083:0.061:0.766151:0.731:4671:0.651:2342:rs2977608
1   768448  rs12562034  G   A   .   PASS    AF=0.119    ES:SE:LP:AF:SS:SI:NC:ID -0.151:0.102:0.854005:0.119:4671:0.395:2342:rs12562034
1   768819  rs12562811  C   T   .   PASS    AF=0.012    ES:SE:LP:AF:SS:SI:NC:ID -0.338:0.349:0.478375:0.012:4671:0.332:2342:rs12562811
1   769223  rs60320384  C   G   .   PASS    AF=0.144    ES:SE:LP:AF:SS:SI:NC:ID -0.067:0.088:0.354972:0.144:4671:0.491:2342:rs60320384
1   770377  rs112563271 A   T   .   PASS    AF=0.013    ES:SE:LP:AF:SS:SI:NC:ID -0.574:0.244:1.72723:0.013:4669:1:2341:rs112563271
1   771823  rs2977605   T   C   .   PASS    AF=0.854    ES:SE:LP:AF:SS:SI:NC:ID 0.067:0.087:0.357905:0.854:4671:0.517:2342:rs2977605
1   771967  rs59066358  G   A   .   PASS    AF=0.145    ES:SE:LP:AF:SS:SI:NC:ID -0.066:0.087:0.347931:0.145:4671:0.5:2342:rs59066358
1   772755  rs2905039   A   C   .   PASS    AF=0.854    ES:SE:LP:AF:SS:SI:NC:ID 0.067:0.086:0.357371:0.854:4671:0.521:2342:rs2905039
1   777122  rs2980319   A   T   .   PASS    AF=0.855    ES:SE:LP:AF:SS:SI:NC:ID 0.076:0.086:0.424196:0.855:4671:0.528:2342:rs2980319
1   777232  rs112618790 C   T   .   PASS    AF=0.102    ES:SE:LP:AF:SS:SI:NC:ID -0.144:0.106:0.758958:0.102:4671:0.426:2342:rs112618790
1   778745  rs1055606   A   G   .   PASS    AF=0.143    ES:SE:LP:AF:SS:SI:NC:ID -0.076:0.086:0.422305:0.143:4671:0.513:2342:rs1055606
1   779322  rs4040617   A   G   .   PASS    AF=0.144    ES:SE:LP:AF:SS:SI:NC:ID -0.078:0.086:0.442108:0.144:4671:0.522:2342:rs4040617
1   780785  rs2977612   T   A   .   PASS    AF=0.851    ES:SE:LP:AF:SS:SI:NC:ID 0.073:0.084:0.413098:0.851:4671:0.563:2342:rs2977612
1   781845  rs1391043716    A   G   .   PASS    AF=0.106    ES:SE:LP:AF:SS:SI:NC:ID -0.052:0.095:0.232009:0.106:4671:0.485:2342:rs1391043716
1   782981  rs6594026   C   T   .   PASS    AF=0.147    ES:SE:LP:AF:SS:SI:NC:ID -0.073:0.084:0.408633:0.147:4671:0.552:2342:rs6594026
1   785050  rs2905062   G   A   .   PASS    AF=0.85 ES:SE:LP:AF:SS:SI:NC:ID 0.066:0.083:0.369982:0.85:4671:0.606:2342:rs2905062
1   785989  rs2980300   T   C   .   PASS    AF=0.85 ES:SE:LP:AF:SS:SI:NC:ID 0.065:0.082:0.368849:0.85:4671:0.609:2342:rs2980300
1   787399  rs2905055   G   T   .   PASS    AF=0.844    ES:SE:LP:AF:SS:SI:NC:ID 0.057:0.083:0.310285:0.844:4671:0.579:2342:rs2905055
1   787606  rs3863622   G   T   .   PASS    AF=0.144    ES:SE:LP:AF:SS:SI:NC:ID -0.075:0.084:0.429042:0.144:4671:0.544:2342:rs3863622
1   787685  rs2905054   G   T   .   PASS    AF=0.843    ES:SE:LP:AF:SS:SI:NC:ID 0.057:0.083:0.313764:0.843:4671:0.587:2342:rs2905054
1   787844  rs2905053   C   T   .   PASS    AF=0.851    ES:SE:LP:AF:SS:SI:NC:ID 0.063:0.082:0.349695:0.851:4671:0.605:2342:rs2905053
1   790465  rs61768207  G   A   .   PASS    AF=0.104    ES:SE:LP:AF:SS:SI:NC:ID -0.03:0.095:0.123416:0.104:4671:0.522:2342:rs61768207
1   791191  rs111818025 G   A   .   PASS    AF=0.143    ES:SE:LP:AF:SS:SI:NC:ID -0.078:0.084:0.457821:0.143:4671:0.549:2342:rs111818025
1   791853  rs6684487   G   A   .   PASS    AF=0.102    ES:SE:LP:AF:SS:SI:NC:ID -0.129:0.101:0.701766:0.102:4671:0.481:2342:rs6684487
1   794332  rs12127425  G   A   .   PASS    AF=0.089    ES:SE:LP:AF:SS:SI:NC:ID -0.122:0.101:0.648764:0.089:4671:0.552:2342:rs12127425