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/60848843-4f44-4195-bfbd-a62de3d56877/call-ldsc/inputs/562856379/ieu-b-96.vcf.gz \
--ref-ld-chr /data/ref/eur_w_ld_chr/ \
--out /data/igd/ieu-b-96/ldsc.txt \
--w-ld-chr /data/ref/eur_w_ld_chr/ 

Beginning analysis at Fri Dec 18 01:00:10 2020
Reading summary statistics from /data/cromwell-executions/qc/60848843-4f44-4195-bfbd-a62de3d56877/call-ldsc/inputs/562856379/ieu-b-96.vcf.gz ...
Read summary statistics for 7292591 SNPs.
Dropped 20616 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, 1100532 SNPs remain.
After merging with regression SNP LD, 1100532 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.2834 (0.1185)
Lambda GC: 1.0466
Mean Chi^2: 1.0406
Intercept: 1.018 (0.0066)
Ratio: 0.4443 (0.1633)
Analysis finished at Fri Dec 18 01:01:40 2020
Total time elapsed: 1.0m:30.09s

QC metrics

Metrics

Metrics

{
    "af_correlation": 0.9366,
    "inflation_factor": 1.053,
    "mean_EFFECT": -0.0011,
    "n": 4018,
    "n_snps": 7293502,
    "n_clumped_hits": 1,
    "n_p_sig": 1,
    "n_mono": 2367,
    "n_ns": 0,
    "n_mac": 2042,
    "is_snpid_unique": false,
    "n_miss_EFFECT": 0,
    "n_miss_SE": 0,
    "n_miss_PVAL": 0,
    "n_miss_AF": 0,
    "n_miss_AF_reference": 64186,
    "n_est": 3960.4234,
    "ratio_se_n": 0.9928,
    "mean_diff": "NaN",
    "ratio_diff": "NaN",
    "sd_y_est1": 2.5266,
    "sd_y_est2": 2.5084,
    "r2_sum1": 0.0766,
    "r2_sum2": 0.012,
    "r2_sum3": 0.0122,
    "r2_sum4": 0.0077,
    "ldsc_nsnp_merge_refpanel_ld": 1100532,
    "ldsc_nsnp_merge_regression_ld": 1100532,
    "ldsc_observed_scale_h2_beta": 0.2834,
    "ldsc_observed_scale_h2_se": 0.1185,
    "ldsc_intercept_beta": 1.018,
    "ldsc_intercept_se": 0.0066,
    "ldsc_lambda_gc": 1.0466,
    "ldsc_mean_chisq": 1.0406,
    "ldsc_ratio": 0.4433
}

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 895 0.9998773 3 58 0 7292524 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 8.648513e+00 5.753498e+00 1.000 4.000000e+00 8.000000e+00 1.300000e+01 2.200000e+01 ▇▅▅▂▂
numeric POS 0 1.0000000 NA NA NA NA NA 7.875108e+07 5.640803e+07 828.000 3.227654e+07 6.931337e+07 1.146214e+08 2.492164e+08 ▇▆▅▂▁
numeric EFFECT 0 1.0000000 NA NA NA NA NA -1.066000e-03 4.901448e-01 -6.908 -6.300000e-02 0.000000e+00 6.200000e-02 5.081260e+02 ▇▁▁▁▁
numeric SE 0 1.0000000 NA NA NA NA NA 1.153228e-01 4.875204e-01 0.053 6.200000e-02 8.300000e-02 1.430000e-01 4.133240e+02 ▇▁▁▁▁
numeric PVAL 0 1.0000000 NA NA NA NA NA 4.918702e-01 2.901473e-01 0.000 2.385900e-01 4.888600e-01 7.424992e-01 1.000000e+00 ▇▇▇▇▇
numeric PVAL_ztest 0 1.0000000 NA NA NA NA NA 4.919067e-01 2.901888e-01 0.000 2.385689e-01 4.887441e-01 7.428638e-01 1.000000e+00 ▇▇▇▇▇
numeric AF 0 1.0000000 NA NA NA NA NA 2.603696e-01 2.623966e-01 0.000 4.600000e-02 1.560000e-01 4.100000e-01 1.000000e+00 ▇▂▂▁▁
numeric AF_reference 64186 0.9911996 NA NA NA NA NA 2.596797e-01 2.523702e-01 0.000 5.491210e-02 1.695290e-01 4.027560e-01 1.000000e+00 ▇▃▂▁▁
numeric N 0 1.0000000 NA NA NA NA NA 4.017808e+03 2.980240e+00 3707.000 4.018000e+03 4.018000e+03 4.018000e+03 4.018000e+03 ▁▁▁▁▇

Head and tail

CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
1 693731 rs12238997 A G -0.227 0.152 0.1340834 0.1353270 0.118 0.141773 4018
1 729679 rs4951859 C G 0.168 0.135 0.2139661 0.2133360 0.830 0.639976 4018
1 731718 rs142557973 T C -0.184 0.136 0.1769938 0.1760744 0.126 0.154353 4018
1 734349 rs141242758 T C -0.192 0.136 0.1572280 0.1580193 0.125 0.152556 4018
1 752566 rs3094315 G A 0.080 0.077 0.2971002 0.2988229 0.823 0.718251 4016
1 752721 rs3131972 A G 0.073 0.076 0.3437004 0.3367904 0.822 0.653355 4016
1 753405 rs3115860 C A 0.211 0.120 0.0799392 0.0786908 0.859 0.751797 4018
1 753541 rs2073813 G A -0.197 0.120 0.1002164 0.1006591 0.142 0.301917 4018
1 754182 rs3131969 A G 0.202 0.119 0.0883324 0.0896061 0.856 0.678514 4018
1 754192 rs3131968 A G 0.202 0.119 0.0884036 0.0896061 0.856 0.678514 4018
CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
22 51218224 rs9616975 C A 0.127 0.163 0.4371646 0.4358966 0.074 0.0619010 4018
22 51218377 rs2519461 G C 0.125 0.163 0.4436332 0.4431581 0.074 0.0826677 4018
22 51219006 rs28729663 G A 0.033 0.120 0.7807446 0.7833162 0.144 0.2052720 4018
22 51219387 rs9616832 T C 0.131 0.164 0.4256611 0.4244177 0.074 0.0654952 4018
22 51219704 rs147475742 G A 0.255 0.233 0.2731184 0.2737706 0.040 0.0473243 4018
22 51221731 rs115055839 T C 0.129 0.165 0.4315906 0.4343214 0.074 0.0625000 4018
22 51222100 rs114553188 G T 0.081 0.182 0.6587961 0.6562800 0.057 0.0880591 4018
22 51223637 rs375798137 G A 0.081 0.184 0.6600913 0.6597797 0.057 0.0788738 4018
22 51229805 rs9616985 T C 0.130 0.167 0.4359563 0.4363078 0.074 0.0730831 4018
22 51237063 rs3896457 T C 0.044 0.099 0.6572779 0.6567213 0.287 0.2050720 4018

bcf preview

1   693731  rs12238997  A   G   .   PASS    AF=0.118    ES:SE:LP:AF:SS:SI:NC:ID -0.227:0.152:0.872625:0.118:4018:0.324:1090:rs12238997
1   729679  rs4951859   C   G   .   PASS    AF=0.83 ES:SE:LP:AF:SS:SI:NC:ID 0.168:0.135:0.669655:0.83:4018:0.361:1090:rs4951859
1   731718  rs58276399  T   C   .   PASS    AF=0.126    ES:SE:LP:AF:SS:SI:NC:ID -0.184:0.136:0.752042:0.126:4018:0.378:1090:rs58276399
1   734349  rs141242758 T   C   .   PASS    AF=0.125    ES:SE:LP:AF:SS:SI:NC:ID -0.192:0.136:0.80347:0.125:4018:0.379:1090:rs141242758
1   752566  rs3094315   G   A   .   PASS    AF=0.823    ES:SE:LP:AF:SS:SI:NC:ID 0.08:0.077:0.527097:0.823:4016:1:1089:rs3094315
1   752721  rs3131972   A   G   .   PASS    AF=0.822    ES:SE:LP:AF:SS:SI:NC:ID 0.073:0.076:0.46382:0.822:4016:1:1089:rs3131972
1   753405  rs3115860   C   A   .   PASS    AF=0.859    ES:SE:LP:AF:SS:SI:NC:ID 0.211:0.12:1.09724:0.859:4018:0.473:1090:rs3115860
1   753541  rs1388595942    G   A   .   PASS    AF=0.142    ES:SE:LP:AF:SS:SI:NC:ID -0.197:0.12:0.999061:0.142:4018:0.481:1090:rs1388595942
1   754182  rs3131969   A   G   .   PASS    AF=0.856    ES:SE:LP:AF:SS:SI:NC:ID 0.202:0.119:1.05388:0.856:4018:0.493:1090:rs3131969
1   754192  rs3131968   A   G   .   PASS    AF=0.856    ES:SE:LP:AF:SS:SI:NC:ID 0.202:0.119:1.05353:0.856:4018:0.494:1090:rs3131968
1   754334  rs3131967   T   C   .   PASS    AF=0.856    ES:SE:LP:AF:SS:SI:NC:ID 0.202:0.119:1.05271:0.856:4018:0.494:1090:rs3131967
1   754503  rs3115859   G   A   .   PASS    AF=0.824    ES:SE:LP:AF:SS:SI:NC:ID 0.198:0.123:0.972989:0.824:4018:0.417:1090:rs3115859
1   754964  rs3131966   C   T   .   PASS    AF=0.825    ES:SE:LP:AF:SS:SI:NC:ID 0.197:0.122:0.973236:0.825:4018:0.42:1090:rs3131966
1   755775  rs3131965   A   G   .   PASS    AF=0.829    ES:SE:LP:AF:SS:SI:NC:ID 0.2:0.123:0.977414:0.829:4018:0.403:1090:rs3131965
1   755890  rs1280367067    A   T   .   PASS    AF=0.858    ES:SE:LP:AF:SS:SI:NC:ID 0.209:0.119:1.10271:0.858:4018:0.48:1090:rs1280367067
1   756604  rs3131962   A   G   .   PASS    AF=0.858    ES:SE:LP:AF:SS:SI:NC:ID 0.209:0.119:1.10193:0.858:4018:0.482:1090:rs3131962
1   757640  rs3115853   G   A   .   PASS    AF=0.854    ES:SE:LP:AF:SS:SI:NC:ID 0.196:0.117:1.03194:0.854:4018:0.525:1090:rs3115853
1   757734  rs1557551770    C   T   .   PASS    AF=0.858    ES:SE:LP:AF:SS:SI:NC:ID 0.209:0.119:1.10273:0.858:4018:0.484:1090:rs1557551770
1   757936  rs1360886751    C   A   .   PASS    AF=0.858    ES:SE:LP:AF:SS:SI:NC:ID 0.209:0.119:1.10379:0.858:4018:0.485:1090:rs1360886751
1   758144  rs3131956   A   G   .   PASS    AF=0.858    ES:SE:LP:AF:SS:SI:NC:ID 0.209:0.119:1.10281:0.858:4018:0.485:1090:rs3131956
1   758626  rs3131954   C   T   .   PASS    AF=0.859    ES:SE:LP:AF:SS:SI:NC:ID 0.209:0.119:1.10029:0.859:4018:0.484:1090:rs3131954
1   760912  rs1048488   C   T   .   PASS    AF=0.827    ES:SE:LP:AF:SS:SI:NC:ID 0.206:0.122:1.04043:0.827:4018:0.408:1090:rs1048488
1   761147  rs3115850   T   C   .   PASS    AF=0.827    ES:SE:LP:AF:SS:SI:NC:ID 0.211:0.122:1.08054:0.827:4018:0.409:1090:rs3115850
1   761732  rs2286139   C   T   .   PASS    AF=0.847    ES:SE:LP:AF:SS:SI:NC:ID 0.193:0.115:1.03387:0.847:4018:0.532:1090:rs2286139
1   766007  rs61768174  A   C   .   PASS    AF=0.108    ES:SE:LP:AF:SS:SI:NC:ID -0.214:0.129:1.01666:0.108:4018:0.458:1090:rs61768174
1   768253  rs2977608   A   C   .   PASS    AF=0.744    ES:SE:LP:AF:SS:SI:NC:ID 0.11:0.079:0.786106:0.744:4018:0.651:1090:rs2977608
1   768448  rs12562034  G   A   .   PASS    AF=0.11 ES:SE:LP:AF:SS:SI:NC:ID -0.03:0.135:0.0837286:0.11:4018:0.395:1090:rs12562034
1   768819  rs12562811  C   T   .   PASS    AF=0.011    ES:SE:LP:AF:SS:SI:NC:ID -0.428:0.515:0.390706:0.011:4018:0.332:1090:rs12562811
1   769223  rs60320384  C   G   .   PASS    AF=0.138    ES:SE:LP:AF:SS:SI:NC:ID -0.214:0.117:1.17562:0.138:4018:0.491:1090:rs60320384
1   770377  rs112563271 A   T   .   PASS    AF=0.013    ES:SE:LP:AF:SS:SI:NC:ID -0.211:0.277:0.349887:0.013:4014:1:1089:rs112563271
1   771823  rs2977605   T   C   .   PASS    AF=0.859    ES:SE:LP:AF:SS:SI:NC:ID 0.209:0.115:1.16403:0.859:4018:0.517:1090:rs2977605
1   771967  rs59066358  G   A   .   PASS    AF=0.139    ES:SE:LP:AF:SS:SI:NC:ID -0.208:0.116:1.1435:0.139:4018:0.5:1090:rs59066358
1   772755  rs2905039   A   C   .   PASS    AF=0.859    ES:SE:LP:AF:SS:SI:NC:ID 0.212:0.114:1.19229:0.859:4018:0.521:1090:rs2905039
1   777122  rs2980319   A   T   .   PASS    AF=0.861    ES:SE:LP:AF:SS:SI:NC:ID 0.202:0.115:1.11104:0.861:4018:0.528:1090:rs2980319
1   777232  rs112618790 C   T   .   PASS    AF=0.093    ES:SE:LP:AF:SS:SI:NC:ID -0.068:0.14:0.203793:0.093:4018:0.426:1090:rs112618790
1   778745  rs1055606   A   G   .   PASS    AF=0.136    ES:SE:LP:AF:SS:SI:NC:ID -0.197:0.115:1.06107:0.136:4018:0.513:1090:rs1055606
1   779322  rs4040617   A   G   .   PASS    AF=0.137    ES:SE:LP:AF:SS:SI:NC:ID -0.196:0.115:1.05761:0.137:4018:0.522:1090:rs4040617
1   780785  rs2977612   T   A   .   PASS    AF=0.857    ES:SE:LP:AF:SS:SI:NC:ID 0.191:0.111:1.06533:0.857:4018:0.563:1090:rs2977612
1   781845  rs1391043716    A   G   .   PASS    AF=0.103    ES:SE:LP:AF:SS:SI:NC:ID -0.184:0.128:0.829521:0.103:4018:0.485:1090:rs1391043716
1   782981  rs6594026   C   T   .   PASS    AF=0.14 ES:SE:LP:AF:SS:SI:NC:ID -0.185:0.112:1.01278:0.14:4018:0.552:1090:rs6594026
1   785050  rs2905062   G   A   .   PASS    AF=0.856    ES:SE:LP:AF:SS:SI:NC:ID 0.186:0.109:1.04774:0.856:4018:0.606:1090:rs2905062
1   785989  rs2980300   T   C   .   PASS    AF=0.856    ES:SE:LP:AF:SS:SI:NC:ID 0.185:0.109:1.04736:0.856:4018:0.609:1090:rs2980300
1   787399  rs2905055   G   T   .   PASS    AF=0.849    ES:SE:LP:AF:SS:SI:NC:ID 0.184:0.11:1.02557:0.849:4018:0.579:1090:rs2905055
1   787606  rs3863622   G   T   .   PASS    AF=0.136    ES:SE:LP:AF:SS:SI:NC:ID -0.192:0.112:1.06066:0.136:4018:0.544:1090:rs3863622
1   787685  rs2905054   G   T   .   PASS    AF=0.848    ES:SE:LP:AF:SS:SI:NC:ID 0.178:0.109:0.984576:0.848:4018:0.587:1090:rs2905054
1   787844  rs2905053   C   T   .   PASS    AF=0.858    ES:SE:LP:AF:SS:SI:NC:ID 0.184:0.109:1.03777:0.858:4018:0.605:1090:rs2905053
1   790465  rs61768207  G   A   .   PASS    AF=0.102    ES:SE:LP:AF:SS:SI:NC:ID -0.177:0.127:0.785601:0.102:4018:0.522:1090:rs61768207
1   791191  rs111818025 G   A   .   PASS    AF=0.135    ES:SE:LP:AF:SS:SI:NC:ID -0.189:0.112:1.04261:0.135:4018:0.549:1090:rs111818025
1   791853  rs6684487   G   A   .   PASS    AF=0.094    ES:SE:LP:AF:SS:SI:NC:ID -0.05:0.133:0.152274:0.094:4018:0.481:1090:rs6684487
1   794332  rs12127425  G   A   .   PASS    AF=0.08 ES:SE:LP:AF:SS:SI:NC:ID -0.052:0.133:0.159713:0.08:4018:0.552:1090:rs12127425