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-1010/ieu-a-1010.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-1010/ldsc.txt \
--w-ld-chr /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/reference/eur_w_ld_chr/ 

Beginning analysis at Wed Feb  5 09:01:59 2020
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ieu-a-import/processed/ieu-a-1010/ieu-a-1010.vcf.gz ...
Read summary statistics for 7659233 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, 1279622 SNPs remain.
After merging with regression SNP LD, 1279622 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.1291 (0.0062)
Lambda GC: 1.2365
Mean Chi^2: 1.2948
Intercept: 0.9638 (0.0071)
Ratio < 0 (usually indicates GC correction).
Analysis finished at Wed Feb  5 09:03:16 2020
Total time elapsed: 1.0m:16.52s

QC metrics

Metrics

Metrics

{
    "af_correlation": 0.9392,
    "inflation_factor": 1.1903,
    "mean_EFFECT": -0,
    "n": 131695,
    "n_snps": 7659233,
    "n_clumped_hits": 15,
    "n_p_sig": 731,
    "n_mono": 0,
    "n_ns": 0,
    "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": 88513,
    "n_est": 163166.1846,
    "ratio_se_n": 1.1131,
    "mean_diff": -1.1743e-06,
    "ratio_diff": 1.5224,
    "sd_y_est1": 0.8901,
    "sd_y_est2": 0.9908,
    "r2_sum1": 0.0038,
    "r2_sum2": 0.0048,
    "r2_sum3": 0.0039,
    "r2_sum4": 0.004,
    "ldsc_nsnp_merge_refpanel_ld": 1279622,
    "ldsc_nsnp_merge_regression_ld": 1279622,
    "ldsc_observed_scale_h2_beta": 0.1291,
    "ldsc_observed_scale_h2_se": 0.0062,
    "ldsc_intercept_beta": 0.9638,
    "ldsc_intercept_se": 0.0071,
    "ldsc_lambda_gc": 1.2365,
    "ldsc_mean_chisq": 1.2948,
    "ldsc_ratio": -0.1228
}

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 7659233 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 8.647487e+00 5.756361e+00 1.00000e+00 4.000000e+00 8.000000e+00 1.300000e+01 2.300000e+01 ▇▅▅▂▂
numeric POS 0 1.0000000 NA NA NA NA NA 7.892816e+07 5.638935e+07 8.28000e+02 3.256581e+07 6.959205e+07 1.147284e+08 2.492225e+08 ▇▆▅▂▁
numeric EFFECT 0 1.0000000 NA NA NA NA NA -4.340000e-05 9.219000e-03 -1.13000e-01 -4.000000e-03 0.000000e+00 4.000000e-03 1.290000e-01 ▁▁▇▁▁
numeric SE 0 1.0000000 NA NA NA NA NA 7.529400e-03 4.844100e-03 4.00000e-03 4.000000e-03 5.000000e-03 9.000000e-03 4.200000e-02 ▇▁▁▁▁
numeric PVAL 0 1.0000000 NA NA NA NA NA 4.713799e-01 2.972385e-01 0.00000e+00 2.069998e-01 4.618001e-01 7.290998e-01 1.000000e+00 ▇▆▆▆▆
numeric PVAL_ztest 0 1.0000000 NA NA NA NA NA 4.747783e-01 2.999184e-01 0.00000e+00 2.112995e-01 4.532547e-01 7.388827e-01 1.000000e+00 ▇▇▆▆▇
numeric AF 0 1.0000000 NA NA NA NA NA 2.641340e-01 2.602447e-01 1.11900e-02 4.851000e-02 1.642000e-01 4.179000e-01 9.888100e-01 ▇▂▂▁▁
numeric AF_reference 88513 0.9884436 NA NA NA NA NA 2.646849e-01 2.527418e-01 1.99700e-04 5.690890e-02 1.783150e-01 4.135380e-01 1.000000e+00 ▇▃▂▁▁
numeric N 0 1.0000000 NA NA NA NA NA 1.316950e+05 0.000000e+00 1.31695e+05 1.316950e+05 1.316950e+05 1.316950e+05 1.316950e+05 ▁▁▇▁▁

Head and tail

CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
1 752566 rs3094315 G A 0.002 0.006 0.7603000 0.7388827 0.8451 0.718251 131695
1 752721 rs3131972 A G 0.001 0.006 0.8867000 0.8676323 0.8414 0.653355 131695
1 752894 rs3131971 T C 0.001 0.007 0.9051001 0.8864030 0.8228 0.753195 131695
1 753474 rs2073814 C G 0.001 0.006 0.8803999 0.8676323 0.8358 0.611422 131695
1 753541 rs2073813 G A -0.003 0.007 0.6639999 0.6682351 0.1213 0.301917 131695
1 754182 rs3131969 A G 0.002 0.007 0.8137000 0.7750970 0.8787 0.678514 131695
1 754192 rs3131968 A G 0.002 0.007 0.7937998 0.7750970 0.8787 0.678514 131695
1 754334 rs3131967 T C 0.002 0.007 0.7770000 0.7750970 0.8638 0.684305 131695
1 754503 rs3115859 G A 0.000 0.006 0.9560000 1.0000000 0.8414 0.663938 131695
1 754964 rs3131966 C T 0.002 0.007 0.7911995 0.7750970 0.8302 0.663339 131695
CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
22 51198027 rs34939255 A G -0.007 0.005 0.1643002 0.1615133 0.23510 0.0984425 131695
22 51198569 rs142671391 G C 0.003 0.011 0.7919997 0.7850629 0.04104 0.1110220 131695
22 51198868 rs185017671 T C 0.006 0.022 0.7929997 0.7850629 0.01119 0.0045926 131695
22 51198998 rs117815989 C A 0.006 0.022 0.7872995 0.7850629 0.01119 0.0045926 131695
22 51199058 rs6010080 T C -0.004 0.010 0.6764006 0.6891565 0.07276 0.0395367 131695
22 51208568 rs148425445 G T 0.006 0.009 0.5570998 0.5049851 0.05410 0.1160140 131695
22 51210289 rs112565862 C T 0.006 0.008 0.4653996 0.4532547 0.15110 0.1018370 131695
22 51211392 rs3888396 T C -0.001 0.007 0.8813001 0.8864030 0.16230 0.1641370 131695
22 51213613 rs34726907 C T 0.002 0.008 0.7657006 0.8025873 0.14740 0.1727240 131695
23 100784211 rs188350543 C A 0.004 0.005 0.3867996 0.4237108 0.72200 0.6498010 131695

bcf preview

1   752566  rs3094315   G   A   .   PASS    AF=0.8451   ES:SE:LP:AF:SS:ID   0.002:0.006:0.119015:0.8451:131695:rs3094315
1   752721  rs3131972   A   G   .   PASS    AF=0.8414   ES:SE:LP:AF:SS:ID   0.001:0.006:0.0522233:0.8414:131695:rs3131972
1   752894  rs3131971   T   C   .   PASS    AF=0.8228   ES:SE:LP:AF:SS:ID   0.001:0.007:0.0433034:0.8228:131695:rs3131971
1   753474  rs2073814   C   G   .   PASS    AF=0.8358   ES:SE:LP:AF:SS:ID   0.001:0.006:0.05532:0.8358:131695:rs2073814
1   753541  rs2073813   G   A   .   PASS    AF=0.1213   ES:SE:LP:AF:SS:ID   -0.003:0.007:0.177832:0.1213:131695:rs2073813
1   754182  rs3131969   A   G   .   PASS    AF=0.8787   ES:SE:LP:AF:SS:ID   0.002:0.007:0.0895357:0.8787:131695:rs3131969
1   754192  rs3131968   A   G   .   PASS    AF=0.8787   ES:SE:LP:AF:SS:ID   0.002:0.007:0.100289:0.8787:131695:rs3131968
1   754334  rs3131967   T   C   .   PASS    AF=0.8638   ES:SE:LP:AF:SS:ID   0.002:0.007:0.109579:0.8638:131695:rs3131967
1   754503  rs3115859   G   A   .   PASS    AF=0.8414   ES:SE:LP:AF:SS:ID   0:0.006:0.0195421:0.8414:131695:rs3115859
1   754964  rs3131966   C   T   .   PASS    AF=0.8302   ES:SE:LP:AF:SS:ID   0.002:0.007:0.101714:0.8302:131695:rs3131966
1   755890  rs3115858   A   T   .   PASS    AF=0.8713   ES:SE:LP:AF:SS:ID   0.001:0.007:0.0778457:0.8713:131695:rs3115858
1   756604  rs3131962   A   G   .   PASS    AF=0.8451   ES:SE:LP:AF:SS:ID   0.003:0.007:0.150765:0.8451:131695:rs3131962
1   757640  rs3115853   G   A   .   PASS    AF=0.8787   ES:SE:LP:AF:SS:ID   0.002:0.007:0.136142:0.8787:131695:rs3115853
1   757734  rs4951929   C   T   .   PASS    AF=0.8787   ES:SE:LP:AF:SS:ID   0.001:0.007:0.0707855:0.8787:131695:rs4951929
1   757936  rs4951862   C   A   .   PASS    AF=0.8769   ES:SE:LP:AF:SS:ID   0.002:0.007:0.129713:0.8769:131695:rs4951862
1   758144  rs3131956   A   G   .   PASS    AF=0.8489   ES:SE:LP:AF:SS:ID   0.003:0.007:0.187287:0.8489:131695:rs3131956
1   758626  rs3131954   C   T   .   PASS    AF=0.8731   ES:SE:LP:AF:SS:ID   0.003:0.007:0.154964:0.8731:131695:rs3131954
1   760912  rs1048488   C   T   .   PASS    AF=0.8172   ES:SE:LP:AF:SS:ID   0.007:0.007:0.470313:0.8172:131695:rs1048488
1   761147  rs3115850   T   C   .   PASS    AF=0.8228   ES:SE:LP:AF:SS:ID   0.006:0.007:0.464326:0.8228:131695:rs3115850
1   761732  rs2286139   C   T   .   PASS    AF=0.8451   ES:SE:LP:AF:SS:ID   0.001:0.007:0.0262719:0.8451:131695:rs2286139
1   761752  rs1057213   C   T   .   PASS    AF=0.8694   ES:SE:LP:AF:SS:ID   0.002:0.007:0.111764:0.8694:131695:rs1057213
1   762273  rs3115849   G   A   .   PASS    AF=0.8507   ES:SE:LP:AF:SS:ID   0.001:0.007:0.0463853:0.8507:131695:rs3115849
1   764191  rs7515915   T   G   .   PASS    AF=0.1213   ES:SE:LP:AF:SS:ID   -0.002:0.007:0.0872998:0.1213:131695:rs7515915
1   766007  rs61768174  A   C   .   PASS    AF=0.1119   ES:SE:LP:AF:SS:ID   0.002:0.008:0.0755656:0.1119:131695:rs61768174
1   768253  rs2977608   A   C   .   PASS    AF=0.7761   ES:SE:LP:AF:SS:ID   0.005:0.006:0.393511:0.7761:131695:rs2977608
1   768448  rs12562034  G   A   .   PASS    AF=0.08769  ES:SE:LP:AF:SS:ID   -0.003:0.008:0.141703:0.08769:131695:rs12562034
1   769223  rs60320384  C   G   .   PASS    AF=0.1175   ES:SE:LP:AF:SS:ID   0:0.007:0.0171411:0.1175:131695:rs60320384
1   769963  rs7518545   G   A   .   PASS    AF=0.08582  ES:SE:LP:AF:SS:ID   -0.003:0.008:0.158954:0.08582:131695:rs7518545
1   771823  rs2977605   T   C   .   PASS    AF=0.875    ES:SE:LP:AF:SS:ID   0.001:0.007:0.0484197:0.875:131695:rs2977605
1   771967  rs59066358  G   A   .   PASS    AF=0.1213   ES:SE:LP:AF:SS:ID   -0.001:0.007:0.0433514:0.1213:131695:rs59066358
1   772755  rs2905039   A   C   .   PASS    AF=0.8769   ES:SE:LP:AF:SS:ID   -0.001:0.006:0.0312836:0.8769:131695:rs2905039
1   775181  rs61768182  A   G   .   PASS    AF=0.1213   ES:SE:LP:AF:SS:ID   0.001:0.007:0.07053:0.1213:131695:rs61768182
1   777122  rs2980319   A   T   .   PASS    AF=0.8806   ES:SE:LP:AF:SS:ID   -0.001:0.006:0.0808696:0.8806:131695:rs2980319
1   778745  rs1055606   A   G   .   PASS    AF=0.1175   ES:SE:LP:AF:SS:ID   0.001:0.007:0.0702746:0.1175:131695:rs1055606
1   779322  rs4040617   A   G   .   PASS    AF=0.1175   ES:SE:LP:AF:SS:ID   0.001:0.007:0.0636371:0.1175:131695:rs4040617
1   780785  rs2977612   T   A   .   PASS    AF=0.8787   ES:SE:LP:AF:SS:ID   -0.002:0.006:0.0926962:0.8787:131695:rs2977612
1   781845  rs61768199  A   G   .   PASS    AF=0.09328  ES:SE:LP:AF:SS:ID   0.002:0.007:0.129947:0.09328:131695:rs61768199
1   782981  rs6594026   C   T   .   PASS    AF=0.1325   ES:SE:LP:AF:SS:ID   0.001:0.007:0.0764451:0.1325:131695:rs6594026
1   783318  rs6686696   A   G   .   PASS    AF=0.1101   ES:SE:LP:AF:SS:ID   0.001:0.007:0.0785216:0.1101:131695:rs6686696
1   785050  rs2905062   G   A   .   PASS    AF=0.8806   ES:SE:LP:AF:SS:ID   0:0.006:0.0150229:0.8806:131695:rs2905062
1   785989  rs2980300   T   C   .   PASS    AF=0.8675   ES:SE:LP:AF:SS:ID   0:0.007:0.0189973:0.8675:131695:rs2980300
1   786995  rs61768202  G   A   .   PASS    AF=0.1194   ES:SE:LP:AF:SS:ID   0.002:0.007:0.124071:0.1194:131695:rs61768202
1   787399  rs2905055   G   T   .   PASS    AF=0.8563   ES:SE:LP:AF:SS:ID   -0.001:0.007:0.0548762:0.8563:131695:rs2905055
1   787606  rs3863622   G   T   .   PASS    AF=0.1194   ES:SE:LP:AF:SS:ID   0:0.006:0.00607904:0.1194:131695:rs3863622
1   787685  rs2905054   G   T   .   PASS    AF=0.8582   ES:SE:LP:AF:SS:ID   0:0.007:0.0112627:0.8582:131695:rs2905054
1   787844  rs2905053   C   T   .   PASS    AF=0.8806   ES:SE:LP:AF:SS:ID   0.001:0.006:0.0754106:0.8806:131695:rs2905053
1   790465  rs61768207  G   A   .   PASS    AF=0.08769  ES:SE:LP:AF:SS:ID   0:0.008:0.00326948:0.08769:131695:rs61768207
1   791191  rs111818025 G   A   .   PASS    AF=0.1157   ES:SE:LP:AF:SS:ID   -0.001:0.007:0.044649:0.1157:131695:rs111818025
1   791853  rs6684487   G   A   .   PASS    AF=0.0653   ES:SE:LP:AF:SS:ID   -0.004:0.009:0.201142:0.0653:131695:rs6684487
1   796375  rs12083781  T   C   .   PASS    AF=0.1063   ES:SE:LP:AF:SS:ID   0.007:0.007:0.498804:0.1063:131695:rs12083781