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/24df39b7-198e-4de5-8d69-245c79488497/call-ldsc/inputs/562856374/ieu-b-91.vcf.gz \
--ref-ld-chr /data/ref/eur_w_ld_chr/ \
--out /data/igd/ieu-b-91/ldsc.txt \
--w-ld-chr /data/ref/eur_w_ld_chr/ 

Beginning analysis at Thu Dec 17 01:51:29 2020
Reading summary statistics from /data/cromwell-executions/qc/24df39b7-198e-4de5-8d69-245c79488497/call-ldsc/inputs/562856374/ieu-b-91.vcf.gz ...
Read summary statistics for 7295809 SNPs.
Dropped 20619 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, 1100559 SNPs remain.
After merging with regression SNP LD, 1100559 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.6777 (0.3421)
Lambda GC: 1.0303
Mean Chi^2: 1.0222
Intercept: 1.0041 (0.0071)
Ratio: 0.1846 (0.3202)
Analysis finished at Thu Dec 17 01:52:56 2020
Total time elapsed: 1.0m:27.71s

QC metrics

Metrics

Metrics

{
    "af_correlation": 0.9554,
    "inflation_factor": 1.0308,
    "mean_EFFECT": 0.0002,
    "n": 1340,
    "n_snps": 7296720,
    "n_clumped_hits": 0,
    "n_p_sig": 0,
    "n_mono": 1,
    "n_ns": 0,
    "n_mac": 5022,
    "is_snpid_unique": false,
    "n_miss_EFFECT": 0,
    "n_miss_SE": 0,
    "n_miss_PVAL": 0,
    "n_miss_AF": 0,
    "n_miss_AF_reference": 63972,
    "n_est": 1307.3576,
    "ratio_se_n": 0.9877,
    "mean_diff": "Inf",
    "ratio_diff": "NaN",
    "sd_y_est1": 2.1491,
    "sd_y_est2": 2.1228,
    "r2_sum1": 0,
    "r2_sum2": 0,
    "r2_sum3": 0,
    "r2_sum4": 0,
    "ldsc_nsnp_merge_refpanel_ld": 1100559,
    "ldsc_nsnp_merge_regression_ld": 1100559,
    "ldsc_observed_scale_h2_beta": 0.6777,
    "ldsc_observed_scale_h2_se": 0.3421,
    "ldsc_intercept_beta": 1.0041,
    "ldsc_intercept_se": 0.0071,
    "ldsc_lambda_gc": 1.0303,
    "ldsc_mean_chisq": 1.0222,
    "ldsc_ratio": 0.1847
}

Flags

name value
af_correlation FALSE
inflation_factor FALSE
n TRUE
is_snpid_non_unique TRUE
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 896 0.9998772 3 58 0 7295741 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 8.648453e+00 5.753610e+00 1.000e+00 4.000000e+00 8.000000e+00 1.300000e+01 2.200000e+01 ▇▅▅▂▂
numeric POS 0 1.0000000 NA NA NA NA NA 7.875161e+07 5.640896e+07 8.280e+02 3.227602e+07 6.931322e+07 1.146215e+08 2.492164e+08 ▇▆▅▂▁
numeric EFFECT 0 1.0000000 NA NA NA NA NA 2.432000e-04 1.982762e-01 -6.908e+00 -8.900000e-02 1.000000e-03 9.000000e-02 6.545000e+00 ▁▁▇▁▁
numeric SE 0 1.0000000 NA NA NA NA NA 1.637053e-01 1.070411e-01 7.500e-02 9.000000e-02 1.200000e-01 1.990000e-01 6.067000e+00 ▇▁▁▁▁
numeric PVAL 0 1.0000000 NA NA NA NA NA 4.958690e-01 2.891551e-01 1.100e-06 2.444251e-01 4.934805e-01 7.462735e-01 1.000000e+00 ▇▇▇▇▇
numeric PVAL_ztest 0 1.0000000 NA NA NA NA NA 4.958887e-01 2.891843e-01 1.200e-06 2.445714e-01 4.934811e-01 7.465193e-01 1.000000e+00 ▇▇▇▇▇
numeric AF 0 1.0000000 NA NA NA NA NA 2.607939e-01 2.573752e-01 0.000e+00 5.100000e-02 1.610000e-01 4.080000e-01 9.990000e-01 ▇▃▂▁▁
numeric AF_reference 63972 0.9912328 NA NA NA NA NA 2.596056e-01 2.523906e-01 0.000e+00 5.491210e-02 1.695290e-01 4.027560e-01 1.000000e+00 ▇▃▂▁▁
numeric N 0 1.0000000 NA NA NA NA NA 1.339970e+03 8.163405e-01 1.244e+03 1.340000e+03 1.340000e+03 1.340000e+03 1.340000e+03 ▁▁▁▁▇

Head and tail

CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
1 693731 rs12238997 A G 0.029 0.219 0.8945020 0.8946520 0.126 0.141773 1340
1 729679 rs4951859 C G 0.211 0.168 0.2096081 0.2091332 0.784 0.639976 1340
1 731718 rs142557973 T C 0.129 0.197 0.5111096 0.5125821 0.132 0.154353 1340
1 734349 rs141242758 T C 0.127 0.196 0.5175770 0.5170113 0.131 0.152556 1340
1 752566 rs3094315 G A 0.023 0.099 0.8152999 0.8162870 0.783 0.718251 1340
1 752721 rs3131972 A G 0.067 0.095 0.4828998 0.4806465 0.758 0.653355 1340
1 753405 rs3115860 C A 0.091 0.157 0.5635442 0.5621724 0.830 0.751797 1340
1 753541 rs2073813 G A -0.131 0.152 0.3869430 0.3887744 0.181 0.301917 1340
1 754182 rs3131969 A G 0.178 0.148 0.2288959 0.2290914 0.811 0.678514 1340
1 754192 rs3131968 A G 0.178 0.148 0.2282317 0.2290914 0.811 0.678514 1340
CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
22 51218224 rs9616975 C A -0.138 0.254 0.5859843 0.5869184 0.078 0.0619010 1340
22 51218377 rs2519461 G C -0.143 0.250 0.5691831 0.5673220 0.082 0.0826677 1340
22 51219006 rs28729663 G A -0.327 0.185 0.0763185 0.0771332 0.166 0.2052720 1340
22 51219387 rs9616832 T C -0.124 0.253 0.6235051 0.6240500 0.080 0.0654952 1340
22 51219704 rs147475742 G A -0.147 0.376 0.6945300 0.6958287 0.043 0.0473243 1340
22 51221731 rs115055839 T C -0.146 0.257 0.5703507 0.5699716 0.078 0.0625000 1340
22 51222100 rs114553188 G T -0.624 0.317 0.0493878 0.0490158 0.062 0.0880591 1340
22 51223637 rs375798137 G A -0.580 0.319 0.0690844 0.0690363 0.061 0.0788738 1340
22 51229805 rs9616985 T C -0.192 0.259 0.4583666 0.4585038 0.080 0.0730831 1340
22 51237063 rs3896457 T C -0.179 0.160 0.2649525 0.2632468 0.273 0.2050720 1340

bcf preview

1   693731  rs12238997  A   G   .   PASS    AF=0.126    ES:SE:LP:AF:SS:SI:NC:ID 0.029:0.219:0.0484187:0.126:1340:0.324:613:rs12238997
1   729679  rs4951859   C   G   .   PASS    AF=0.784    ES:SE:LP:AF:SS:SI:NC:ID 0.211:0.168:0.678592:0.784:1340:0.361:613:rs4951859
1   731718  rs58276399  T   C   .   PASS    AF=0.132    ES:SE:LP:AF:SS:SI:NC:ID 0.129:0.197:0.291486:0.132:1340:0.378:613:rs58276399
1   734349  rs141242758 T   C   .   PASS    AF=0.131    ES:SE:LP:AF:SS:SI:NC:ID 0.127:0.196:0.286025:0.131:1340:0.379:613:rs141242758
1   752566  rs3094315   G   A   .   PASS    AF=0.783    ES:SE:LP:AF:SS:SI:NC:ID 0.023:0.099:0.0886826:0.783:1340:1:613:rs3094315
1   752721  rs3131972   A   G   .   PASS    AF=0.758    ES:SE:LP:AF:SS:SI:NC:ID 0.067:0.095:0.316143:0.758:1340:1:613:rs3131972
1   753405  rs3115860   C   A   .   PASS    AF=0.83 ES:SE:LP:AF:SS:SI:NC:ID 0.091:0.157:0.249072:0.83:1340:0.473:613:rs3115860
1   753541  rs1388595942    G   A   .   PASS    AF=0.181    ES:SE:LP:AF:SS:SI:NC:ID -0.131:0.152:0.412353:0.181:1340:0.481:613:rs1388595942
1   754182  rs3131969   A   G   .   PASS    AF=0.811    ES:SE:LP:AF:SS:SI:NC:ID 0.178:0.148:0.640362:0.811:1340:0.493:613:rs3131969
1   754192  rs3131968   A   G   .   PASS    AF=0.811    ES:SE:LP:AF:SS:SI:NC:ID 0.178:0.148:0.641624:0.811:1340:0.494:613:rs3131968
1   754334  rs3131967   T   C   .   PASS    AF=0.812    ES:SE:LP:AF:SS:SI:NC:ID 0.177:0.148:0.636628:0.812:1340:0.494:613:rs3131967
1   754503  rs3115859   G   A   .   PASS    AF=0.781    ES:SE:LP:AF:SS:SI:NC:ID 0.164:0.154:0.542175:0.781:1340:0.417:613:rs3115859
1   754964  rs3131966   C   T   .   PASS    AF=0.782    ES:SE:LP:AF:SS:SI:NC:ID 0.165:0.153:0.549857:0.782:1340:0.42:613:rs3131966
1   755775  rs3131965   A   G   .   PASS    AF=0.8  ES:SE:LP:AF:SS:SI:NC:ID 0.087:0.162:0.229791:0.8:1340:0.403:613:rs3131965
1   755890  rs1280367067    A   T   .   PASS    AF=0.828    ES:SE:LP:AF:SS:SI:NC:ID 0.105:0.156:0.302638:0.828:1340:0.48:613:rs1280367067
1   756604  rs3131962   A   G   .   PASS    AF=0.828    ES:SE:LP:AF:SS:SI:NC:ID 0.101:0.155:0.286129:0.828:1340:0.482:613:rs3131962
1   757640  rs3115853   G   A   .   PASS    AF=0.804    ES:SE:LP:AF:SS:SI:NC:ID 0.148:0.141:0.534341:0.804:1340:0.525:613:rs3115853
1   757734  rs1557551770    C   T   .   PASS    AF=0.828    ES:SE:LP:AF:SS:SI:NC:ID 0.1:0.155:0.284266:0.828:1340:0.484:613:rs1557551770
1   757936  rs1360886751    C   A   .   PASS    AF=0.828    ES:SE:LP:AF:SS:SI:NC:ID 0.1:0.155:0.285296:0.828:1340:0.485:613:rs1360886751
1   758144  rs3131956   A   G   .   PASS    AF=0.828    ES:SE:LP:AF:SS:SI:NC:ID 0.1:0.155:0.28489:0.828:1340:0.485:613:rs3131956
1   758626  rs3131954   C   T   .   PASS    AF=0.829    ES:SE:LP:AF:SS:SI:NC:ID 0.106:0.155:0.305089:0.829:1340:0.484:613:rs3131954
1   760912  rs1048488   C   T   .   PASS    AF=0.798    ES:SE:LP:AF:SS:SI:NC:ID 0.092:0.16:0.245664:0.798:1340:0.408:613:rs1048488
1   761147  rs3115850   T   C   .   PASS    AF=0.798    ES:SE:LP:AF:SS:SI:NC:ID 0.092:0.16:0.245412:0.798:1340:0.409:613:rs3115850
1   761732  rs2286139   C   T   .   PASS    AF=0.793    ES:SE:LP:AF:SS:SI:NC:ID 0.157:0.136:0.603858:0.793:1340:0.532:613:rs2286139
1   766007  rs61768174  A   C   .   PASS    AF=0.108    ES:SE:LP:AF:SS:SI:NC:ID 0.025:0.191:0.0471122:0.108:1340:0.458:613:rs61768174
1   768253  rs2977608   A   C   .   PASS    AF=0.692    ES:SE:LP:AF:SS:SI:NC:ID 0.032:0.106:0.120762:0.692:1340:0.651:613:rs2977608
1   768448  rs12562034  G   A   .   PASS    AF=0.12 ES:SE:LP:AF:SS:SI:NC:ID 0.124:0.191:0.287901:0.12:1340:0.395:613:rs12562034
1   768819  rs12562811  C   T   .   PASS    AF=0.013    ES:SE:LP:AF:SS:SI:NC:ID 1.358:0.6:1.62754:0.013:1340:0.332:613:rs12562811
1   769223  rs60320384  C   G   .   PASS    AF=0.155    ES:SE:LP:AF:SS:SI:NC:ID -0.015:0.16:0.0332545:0.155:1340:0.491:613:rs60320384
1   770377  rs112563271 A   T   .   PASS    AF=0.013    ES:SE:LP:AF:SS:SI:NC:ID 0.122:0.343:0.141102:0.013:1338:1:611:rs112563271
1   771823  rs2977605   T   C   .   PASS    AF=0.827    ES:SE:LP:AF:SS:SI:NC:ID 0.125:0.15:0.391991:0.827:1340:0.517:613:rs2977605
1   771967  rs59066358  G   A   .   PASS    AF=0.159    ES:SE:LP:AF:SS:SI:NC:ID -0.022:0.157:0.0528577:0.159:1340:0.5:613:rs59066358
1   772755  rs2905039   A   C   .   PASS    AF=0.827    ES:SE:LP:AF:SS:SI:NC:ID 0.114:0.149:0.352592:0.827:1340:0.521:613:rs2905039
1   777122  rs2980319   A   T   .   PASS    AF=0.83 ES:SE:LP:AF:SS:SI:NC:ID 0.083:0.15:0.239614:0.83:1340:0.528:613:rs2980319
1   777232  rs112618790 C   T   .   PASS    AF=0.097    ES:SE:LP:AF:SS:SI:NC:ID -0.014:0.204:0.0251137:0.097:1340:0.426:613:rs112618790
1   778745  rs1055606   A   G   .   PASS    AF=0.155    ES:SE:LP:AF:SS:SI:NC:ID 0.017:0.156:0.0378404:0.155:1340:0.513:613:rs1055606
1   779322  rs4040617   A   G   .   PASS    AF=0.159    ES:SE:LP:AF:SS:SI:NC:ID -0.009:0.154:0.0203873:0.159:1340:0.522:613:rs4040617
1   780785  rs2977612   T   A   .   PASS    AF=0.808    ES:SE:LP:AF:SS:SI:NC:ID 0.138:0.136:0.508584:0.808:1340:0.563:613:rs2977612
1   781845  rs1391043716    A   G   .   PASS    AF=0.101    ES:SE:LP:AF:SS:SI:NC:ID 0.099:0.191:0.218481:0.101:1340:0.485:613:rs1391043716
1   782981  rs6594026   C   T   .   PASS    AF=0.182    ES:SE:LP:AF:SS:SI:NC:ID -0.087:0.14:0.271459:0.182:1340:0.552:613:rs6594026
1   785050  rs2905062   G   A   .   PASS    AF=0.799    ES:SE:LP:AF:SS:SI:NC:ID 0.131:0.13:0.505042:0.799:1340:0.606:613:rs2905062
1   785989  rs2980300   T   C   .   PASS    AF=0.799    ES:SE:LP:AF:SS:SI:NC:ID 0.136:0.129:0.537978:0.799:1340:0.609:613:rs2980300
1   787399  rs2905055   G   T   .   PASS    AF=0.795    ES:SE:LP:AF:SS:SI:NC:ID 0.131:0.131:0.497449:0.795:1340:0.579:613:rs2905055
1   787606  rs3863622   G   T   .   PASS    AF=0.159    ES:SE:LP:AF:SS:SI:NC:ID -0.005:0.15:0.0127557:0.159:1340:0.544:613:rs3863622
1   787685  rs2905054   G   T   .   PASS    AF=0.791    ES:SE:LP:AF:SS:SI:NC:ID 0.142:0.13:0.563796:0.791:1340:0.587:613:rs2905054
1   787844  rs2905053   C   T   .   PASS    AF=0.808    ES:SE:LP:AF:SS:SI:NC:ID 0.116:0.132:0.420297:0.808:1340:0.605:613:rs2905053
1   790465  rs61768207  G   A   .   PASS    AF=0.115    ES:SE:LP:AF:SS:SI:NC:ID 0.032:0.177:0.0671948:0.115:1340:0.522:613:rs61768207
1   791191  rs111818025 G   A   .   PASS    AF=0.158    ES:SE:LP:AF:SS:SI:NC:ID -0.02:0.15:0.048724:0.158:1340:0.549:613:rs111818025
1   791853  rs6684487   G   A   .   PASS    AF=0.098    ES:SE:LP:AF:SS:SI:NC:ID -0.019:0.192:0.0356019:0.098:1340:0.481:613:rs6684487
1   794332  rs12127425  G   A   .   PASS    AF=0.095    ES:SE:LP:AF:SS:SI:NC:ID -0.095:0.184:0.219043:0.095:1340:0.552:613:rs12127425