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/7cffe21d-2475-4960-acc5-47787a5d018d/call-ldsc/inputs/562856381/ieu-b-98.vcf.gz \
--ref-ld-chr /data/ref/eur_w_ld_chr/ \
--out /data/igd/ieu-b-98/ldsc.txt \
--w-ld-chr /data/ref/eur_w_ld_chr/ 

Beginning analysis at Fri Dec 18 01:12:45 2020
Reading summary statistics from /data/cromwell-executions/qc/7cffe21d-2475-4960-acc5-47787a5d018d/call-ldsc/inputs/562856381/ieu-b-98.vcf.gz ...
Read summary statistics for 7291205 SNPs.
Dropped 20610 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, 1100537 SNPs remain.
After merging with regression SNP LD, 1100537 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.9954 (0.4005)
Lambda GC: 1.0231
Mean Chi^2: 1.0128
Intercept: 0.9948 (0.0063)
Ratio < 0 (usually indicates GC correction).
Analysis finished at Fri Dec 18 01:14:10 2020
Total time elapsed: 1.0m:24.71s

QC metrics

Metrics

Metrics

{
    "af_correlation": 0.9557,
    "inflation_factor": 1.0221,
    "mean_EFFECT": -0.0124,
    "n": 932,
    "n_snps": 7292112,
    "n_clumped_hits": 0,
    "n_p_sig": 0,
    "n_mono": 1,
    "n_ns": 0,
    "n_mac": 5644,
    "is_snpid_unique": false,
    "n_miss_EFFECT": 0,
    "n_miss_SE": 0,
    "n_miss_PVAL": 0,
    "n_miss_AF": 0,
    "n_miss_AF_reference": 63815,
    "n_est": 911.7967,
    "ratio_se_n": 0.9891,
    "mean_diff": "Inf",
    "ratio_diff": "NaN",
    "sd_y_est1": 2.6138,
    "sd_y_est2": 2.5853,
    "r2_sum1": 0,
    "r2_sum2": 0,
    "r2_sum3": 0,
    "r2_sum4": 0,
    "ldsc_nsnp_merge_refpanel_ld": 1100537,
    "ldsc_nsnp_merge_regression_ld": 1100537,
    "ldsc_observed_scale_h2_beta": 0.9954,
    "ldsc_observed_scale_h2_se": 0.4005,
    "ldsc_intercept_beta": 0.9948,
    "ldsc_intercept_se": 0.0063,
    "ldsc_lambda_gc": 1.0231,
    "ldsc_mean_chisq": 1.0128,
    "ldsc_ratio": -0.4063
}

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 892 0.9998777 3 58 0 7291137 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 8.648362e+00 5.753590e+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 7.875352e+07 5.640878e+07 8.280e+02 3.227585e+07 6.931741e+07 1.146228e+08 2.492164e+08 ▇▆▅▂▁
numeric EFFECT 0 1.0000000 NA NA NA NA NA -1.244940e-02 3.081691e-01 -6.908e+00 -1.310000e-01 -1.000000e-03 1.280000e-01 7.602200e+01 ▇▁▁▁▁
numeric SE 0 1.0000000 NA NA NA NA NA 2.417035e-01 1.751097e-01 1.090e-01 1.310000e-01 1.750000e-01 2.900000e-01 6.898400e+01 ▇▁▁▁▁
numeric PVAL 0 1.0000000 NA NA NA NA NA 4.973739e-01 2.887003e-01 1.300e-06 2.467584e-01 4.952996e-01 7.474928e-01 1.000000e+00 ▇▇▇▇▇
numeric PVAL_ztest 0 1.0000000 NA NA NA NA NA 4.973824e-01 2.887130e-01 1.300e-06 2.467525e-01 4.953539e-01 7.474270e-01 1.000000e+00 ▇▇▇▇▇
numeric AF 0 1.0000000 NA NA NA NA NA 2.608986e-01 2.573206e-01 0.000e+00 5.100000e-02 1.610000e-01 4.080000e-01 9.990000e-01 ▇▃▂▁▁
numeric AF_reference 63815 0.9912488 NA NA NA NA NA 2.597567e-01 2.523850e-01 0.000e+00 5.511180e-02 1.697280e-01 4.029550e-01 1.000000e+00 ▇▃▂▁▁
numeric N 0 1.0000000 NA NA NA NA NA 9.319785e+02 6.023453e-01 8.570e+02 9.320000e+02 9.320000e+02 9.320000e+02 9.320000e+02 ▁▁▁▁▇

Head and tail

CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
1 693731 rs12238997 A G 0.456 0.305 0.1340331 0.1348931 0.126 0.141773 932
1 729679 rs4951859 C G 0.048 0.240 0.8433520 0.8414806 0.784 0.639976 932
1 731718 rs142557973 T C 0.457 0.277 0.0994031 0.0989799 0.132 0.154353 932
1 734349 rs141242758 T C 0.456 0.277 0.1000341 0.0997207 0.131 0.152556 932
1 752566 rs3094315 G A -0.051 0.143 0.7218999 0.7213588 0.783 0.718251 932
1 752721 rs3131972 A G -0.043 0.136 0.7520003 0.7518686 0.758 0.653355 932
1 753405 rs3115860 C A -0.138 0.223 0.5359756 0.5360257 0.830 0.751797 932
1 753541 rs2073813 G A 0.066 0.218 0.7639871 0.7620786 0.181 0.301917 932
1 754182 rs3131969 A G -0.020 0.211 0.9244250 0.9244842 0.811 0.678514 932
1 754192 rs3131968 A G -0.020 0.211 0.9252257 0.9244842 0.811 0.678514 932
CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
22 51218224 rs9616975 C A -0.311 0.373 0.4049925 0.4044049 0.078 0.0619010 932
22 51218377 rs2519461 G C -0.330 0.368 0.3704026 0.3698581 0.082 0.0826677 932
22 51219006 rs28729663 G A -0.417 0.277 0.1318979 0.1322174 0.166 0.2052720 932
22 51219387 rs9616832 T C -0.362 0.374 0.3320175 0.3330871 0.080 0.0654952 932
22 51219704 rs147475742 G A -0.167 0.542 0.7572704 0.7579925 0.043 0.0473243 932
22 51221731 rs115055839 T C -0.322 0.379 0.3946499 0.3955452 0.078 0.0625000 932
22 51222100 rs114553188 G T -0.722 0.481 0.1340106 0.1333453 0.062 0.0880591 932
22 51223637 rs375798137 G A -0.724 0.487 0.1368113 0.1371065 0.061 0.0788738 932
22 51229805 rs9616985 T C -0.364 0.382 0.3411261 0.3406511 0.080 0.0730831 932
22 51237063 rs3896457 T C -0.313 0.240 0.1915349 0.1921768 0.273 0.2050720 932

bcf preview

1   693731  rs12238997  A   G   .   PASS    AF=0.126    ES:SE:LP:AF:SS:SI:NC:ID 0.456:0.305:0.872788:0.126:932:0.324:205:rs12238997
1   729679  rs4951859   C   G   .   PASS    AF=0.784    ES:SE:LP:AF:SS:SI:NC:ID 0.048:0.24:0.0739911:0.784:932:0.361:205:rs4951859
1   731718  rs58276399  T   C   .   PASS    AF=0.132    ES:SE:LP:AF:SS:SI:NC:ID 0.457:0.277:1.0026:0.132:932:0.378:205:rs58276399
1   734349  rs141242758 T   C   .   PASS    AF=0.131    ES:SE:LP:AF:SS:SI:NC:ID 0.456:0.277:0.999852:0.131:932:0.379:205:rs141242758
1   752566  rs3094315   G   A   .   PASS    AF=0.783    ES:SE:LP:AF:SS:SI:NC:ID -0.051:0.143:0.141523:0.783:932:1:205:rs3094315
1   752721  rs3131972   A   G   .   PASS    AF=0.758    ES:SE:LP:AF:SS:SI:NC:ID -0.043:0.136:0.123782:0.758:932:1:205:rs3131972
1   753405  rs3115860   C   A   .   PASS    AF=0.83 ES:SE:LP:AF:SS:SI:NC:ID -0.138:0.223:0.270855:0.83:932:0.473:205:rs3115860
1   753541  rs1388595942    G   A   .   PASS    AF=0.181    ES:SE:LP:AF:SS:SI:NC:ID 0.066:0.218:0.116914:0.181:932:0.481:205:rs1388595942
1   754182  rs3131969   A   G   .   PASS    AF=0.811    ES:SE:LP:AF:SS:SI:NC:ID -0.02:0.211:0.0341283:0.811:932:0.493:205:rs3131969
1   754192  rs3131968   A   G   .   PASS    AF=0.811    ES:SE:LP:AF:SS:SI:NC:ID -0.02:0.211:0.0337523:0.811:932:0.494:205:rs3131968
1   754334  rs3131967   T   C   .   PASS    AF=0.812    ES:SE:LP:AF:SS:SI:NC:ID -0.023:0.211:0.0396962:0.812:932:0.494:205:rs3131967
1   754503  rs3115859   G   A   .   PASS    AF=0.781    ES:SE:LP:AF:SS:SI:NC:ID -0.052:0.219:0.0906051:0.781:932:0.417:205:rs3115859
1   754964  rs3131966   C   T   .   PASS    AF=0.782    ES:SE:LP:AF:SS:SI:NC:ID -0.05:0.219:0.0874744:0.782:932:0.42:205:rs3131966
1   755775  rs3131965   A   G   .   PASS    AF=0.8  ES:SE:LP:AF:SS:SI:NC:ID -0.177:0.229:0.355545:0.8:932:0.403:205:rs3131965
1   755890  rs1280367067    A   T   .   PASS    AF=0.828    ES:SE:LP:AF:SS:SI:NC:ID -0.124:0.221:0.24097:0.828:932:0.48:205:rs1280367067
1   756604  rs3131962   A   G   .   PASS    AF=0.828    ES:SE:LP:AF:SS:SI:NC:ID -0.13:0.22:0.255447:0.828:932:0.482:205:rs3131962
1   757640  rs3115853   G   A   .   PASS    AF=0.804    ES:SE:LP:AF:SS:SI:NC:ID -0.048:0.201:0.091135:0.804:932:0.525:205:rs3115853
1   757734  rs1557551770    C   T   .   PASS    AF=0.828    ES:SE:LP:AF:SS:SI:NC:ID -0.13:0.219:0.257391:0.828:932:0.484:205:rs1557551770
1   757936  rs1360886751    C   A   .   PASS    AF=0.828    ES:SE:LP:AF:SS:SI:NC:ID -0.129:0.219:0.255487:0.828:932:0.485:205:rs1360886751
1   758144  rs3131956   A   G   .   PASS    AF=0.828    ES:SE:LP:AF:SS:SI:NC:ID -0.129:0.219:0.255534:0.828:932:0.485:205:rs3131956
1   758626  rs3131954   C   T   .   PASS    AF=0.829    ES:SE:LP:AF:SS:SI:NC:ID -0.119:0.22:0.228821:0.829:932:0.484:205:rs3131954
1   760912  rs1048488   C   T   .   PASS    AF=0.798    ES:SE:LP:AF:SS:SI:NC:ID -0.146:0.227:0.284872:0.798:932:0.408:205:rs1048488
1   761147  rs3115850   T   C   .   PASS    AF=0.798    ES:SE:LP:AF:SS:SI:NC:ID -0.147:0.227:0.286614:0.798:932:0.409:205:rs3115850
1   761732  rs2286139   C   T   .   PASS    AF=0.793    ES:SE:LP:AF:SS:SI:NC:ID -0.01:0.196:0.0189939:0.793:932:0.532:205:rs2286139
1   766007  rs61768174  A   C   .   PASS    AF=0.108    ES:SE:LP:AF:SS:SI:NC:ID 0.316:0.268:0.624772:0.108:932:0.458:205:rs61768174
1   768253  rs2977608   A   C   .   PASS    AF=0.692    ES:SE:LP:AF:SS:SI:NC:ID -0.124:0.152:0.381261:0.692:932:0.651:205:rs2977608
1   768448  rs12562034  G   A   .   PASS    AF=0.12 ES:SE:LP:AF:SS:SI:NC:ID 0.296:0.283:0.530774:0.12:932:0.395:205:rs12562034
1   768819  rs12562811  C   T   .   PASS    AF=0.013    ES:SE:LP:AF:SS:SI:NC:ID 2.417:0.771:2.76216:0.013:932:0.332:205:rs12562811
1   769223  rs60320384  C   G   .   PASS    AF=0.155    ES:SE:LP:AF:SS:SI:NC:ID 0.251:0.227:0.570301:0.155:932:0.491:205:rs60320384
1   770377  rs112563271 A   T   .   PASS    AF=0.013    ES:SE:LP:AF:SS:SI:NC:ID 0.015:0.525:0.00988323:0.013:932:1:205:rs112563271
1   771823  rs2977605   T   C   .   PASS    AF=0.827    ES:SE:LP:AF:SS:SI:NC:ID -0.088:0.214:0.16747:0.827:932:0.517:205:rs2977605
1   771967  rs59066358  G   A   .   PASS    AF=0.159    ES:SE:LP:AF:SS:SI:NC:ID 0.204:0.223:0.441768:0.159:932:0.5:205:rs59066358
1   772755  rs2905039   A   C   .   PASS    AF=0.827    ES:SE:LP:AF:SS:SI:NC:ID -0.095:0.213:0.184956:0.827:932:0.521:205:rs2905039
1   777122  rs2980319   A   T   .   PASS    AF=0.83 ES:SE:LP:AF:SS:SI:NC:ID -0.139:0.213:0.290914:0.83:932:0.528:205:rs2980319
1   777232  rs112618790 C   T   .   PASS    AF=0.097    ES:SE:LP:AF:SS:SI:NC:ID 0.044:0.309:0.0518417:0.097:932:0.426:205:rs112618790
1   778745  rs1055606   A   G   .   PASS    AF=0.155    ES:SE:LP:AF:SS:SI:NC:ID 0.262:0.222:0.622823:0.155:932:0.513:205:rs1055606
1   779322  rs4040617   A   G   .   PASS    AF=0.159    ES:SE:LP:AF:SS:SI:NC:ID 0.216:0.218:0.491595:0.159:932:0.522:205:rs4040617
1   780785  rs2977612   T   A   .   PASS    AF=0.808    ES:SE:LP:AF:SS:SI:NC:ID -0.021:0.196:0.038672:0.808:932:0.563:205:rs2977612
1   781845  rs1391043716    A   G   .   PASS    AF=0.101    ES:SE:LP:AF:SS:SI:NC:ID 0.407:0.266:0.897008:0.101:932:0.485:205:rs1391043716
1   782981  rs6594026   C   T   .   PASS    AF=0.182    ES:SE:LP:AF:SS:SI:NC:ID 0.081:0.202:0.16156:0.182:932:0.552:205:rs6594026
1   785050  rs2905062   G   A   .   PASS    AF=0.799    ES:SE:LP:AF:SS:SI:NC:ID -0.031:0.186:0.0634213:0.799:932:0.606:205:rs2905062
1   785989  rs2980300   T   C   .   PASS    AF=0.799    ES:SE:LP:AF:SS:SI:NC:ID -0.025:0.186:0.0498463:0.799:932:0.609:205:rs2980300
1   787399  rs2905055   G   T   .   PASS    AF=0.795    ES:SE:LP:AF:SS:SI:NC:ID -0.023:0.189:0.0439867:0.795:932:0.579:205:rs2905055
1   787606  rs3863622   G   T   .   PASS    AF=0.159    ES:SE:LP:AF:SS:SI:NC:ID 0.215:0.214:0.503643:0.159:932:0.544:205:rs3863622
1   787685  rs2905054   G   T   .   PASS    AF=0.791    ES:SE:LP:AF:SS:SI:NC:ID -0.017:0.187:0.0336929:0.791:932:0.587:205:rs2905054
1   787844  rs2905053   C   T   .   PASS    AF=0.808    ES:SE:LP:AF:SS:SI:NC:ID -0.066:0.19:0.137296:0.808:932:0.605:205:rs2905053
1   790465  rs61768207  G   A   .   PASS    AF=0.115    ES:SE:LP:AF:SS:SI:NC:ID 0.457:0.243:1.22279:0.115:932:0.522:205:rs61768207
1   791191  rs111818025 G   A   .   PASS    AF=0.158    ES:SE:LP:AF:SS:SI:NC:ID 0.173:0.214:0.378286:0.158:932:0.549:205:rs111818025
1   791853  rs6684487   G   A   .   PASS    AF=0.098    ES:SE:LP:AF:SS:SI:NC:ID 0.021:0.29:0.0258555:0.098:932:0.481:205:rs6684487
1   794332  rs12127425  G   A   .   PASS    AF=0.095    ES:SE:LP:AF:SS:SI:NC:ID -0.029:0.277:0.0390105:0.095:932:0.552:205:rs12127425