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/public/UKB-b-9050/UKB-b-9050_data.vcf.gz \
--ref-ld-chr ../reference/eur_w_ld_chr/ \
--out /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-9050/ldsc.txt \
--w-ld-chr ../reference/eur_w_ld_chr/ 

Beginning analysis at Thu Oct 17 14:42:10 2019
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-9050/UKB-b-9050_data.vcf.gz ...
Read summary statistics for 3869992 SNPs.
Dropped 693 SNPs with duplicated rs numbers.
Reading reference panel LD Score from ../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 ../reference/eur_w_ld_chr/[1-22] ...
Read regression weight LD Scores for 1290028 SNPs.
After merging with reference panel LD, 927973 SNPs remain.
After merging with regression SNP LD, 927973 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.007 (0.0038)
Lambda GC: 1.0347
Mean Chi^2: 1.032
Intercept: 1.0093 (0.0084)
Ratio: 0.2898 (0.2628)
Analysis finished at Thu Oct 17 14:42:57 2019
Total time elapsed: 47.65s

QC metrics

Metrics

Metrics

{
    "af_correlation": 0.8703,
    "inflation_factor": 1.0475,
    "mean_EFFECT": -3.894e-06,
    "n": "-Inf",
    "n_snps": 9851866,
    "n_clumped_hits": 0,
    "n_p_sig": 0,
    "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": 31457,
    "n_est": "NA",
    "ratio_se_n": "NA",
    "mean_diff": "NaN",
    "ratio_diff": "NaN",
    "sd_y_est1": "NaN",
    "sd_y_est2": "NA",
    "r2_sum1": 0,
    "r2_sum2": 0,
    "r2_sum3": 0,
    "r2_sum4": 0,
    "ldsc_nsnp_merge_refpanel_ld": 927973,
    "ldsc_nsnp_merge_regression_ld": 927973,
    "ldsc_observed_scale_h2_beta": 0.007,
    "ldsc_observed_scale_h2_se": 0.0038,
    "ldsc_intercept_beta": 1.0093,
    "ldsc_intercept_se": 0.0084,
    "ldsc_lambda_gc": 1.0347,
    "ldsc_mean_chisq": 1.032,
    "ldsc_ratio": 0.2906
}

Flags

name value
af_correlation FALSE
inflation_factor FALSE
n TRUE
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 logical.mean logical.count numeric.mean numeric.sd numeric.p0 numeric.p25 numeric.p50 numeric.p75 numeric.p100 numeric.hist
character ID 0 1.0000000 3 58 0 3869302 0 NA NA 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 NA NA
character ALT 0 1.0000000 1 1 0 4 0 NA NA NA NA NA NA NA NA NA NA
logical N 3869992 0.0000000 NA NA NA NA NA NaN : NA NA NA NA NA NA NA NA
numeric CHROM 0 1.0000000 NA NA NA NA NA NA NA 8.661001e+00 5.767860e+00 1.0000000 4.000000e+00 8.000000e+00 1.300000e+01 2.200000e+01 ▇▅▃▂▂
numeric POS 0 1.0000000 NA NA NA NA NA NA NA 7.857900e+07 5.675732e+07 828.0000000 3.162440e+07 6.892439e+07 1.147272e+08 2.492385e+08 ▇▆▅▂▁
numeric EFFECT 0 1.0000000 NA NA NA NA NA NA NA -3.900000e-06 5.796000e-04 -0.0034073 -3.880000e-04 -4.100000e-06 3.818000e-04 3.279300e-03 ▁▁▇▂▁
numeric SE 0 1.0000000 NA NA NA NA NA NA NA 5.665000e-04 7.250000e-05 0.0004717 5.035000e-04 5.429000e-04 6.166000e-04 1.732000e-03 ▇▁▁▁▁
numeric PVAL 0 1.0000000 NA NA NA NA NA NA NA 4.945635e-01 2.897229e-01 0.0000004 2.399999e-01 4.899999e-01 7.499995e-01 1.000000e+00 ▇▇▇▇▇
numeric PVAL_ztest 0 1.0000000 NA NA NA NA NA NA NA 4.945630e-01 2.896956e-01 0.0000004 2.422526e-01 4.918546e-01 7.462063e-01 9.999997e-01 ▇▇▇▇▇
numeric AF 0 1.0000000 NA NA NA NA NA NA NA 3.995808e-01 2.085150e-01 0.1263540 2.176698e-01 3.541105e-01 5.551322e-01 8.736460e-01 ▇▅▃▃▂
numeric AF_reference 31457 0.9918716 NA NA NA NA NA NA NA 3.879432e-01 2.139128e-01 0.0000000 2.120610e-01 3.498400e-01 5.429310e-01 1.000000e+00 ▅▇▅▃▁

Head and tail

CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
1 49298 rs200943160 T C -0.0002955 0.0008693 0.7300002 0.7338972 0.623755 0.782149 NA
1 54676 rs2462492 C T -0.0005445 0.0008622 0.5300002 0.5276710 0.399226 NA NA
1 91536 rs6702460 G T -0.0013476 0.0008493 0.1100001 0.1125735 0.456028 0.420727 NA
1 534192 rs6680723 C T -0.0002840 0.0009690 0.7700005 0.7694502 0.241037 NA NA
1 706368 rs55727773 A G -0.0002876 0.0006002 0.6300007 0.6318297 0.515025 0.275160 NA
1 729679 rs4951859 C G -0.0004856 0.0007013 0.4899999 0.4886361 0.841466 0.639976 NA
1 736289 rs79010578 T A 0.0007325 0.0007580 0.3300000 0.3338820 0.133330 0.139577 NA
1 752566 rs3094315 G A -0.0003538 0.0006786 0.5999997 0.6020643 0.837165 0.718251 NA
1 752721 rs3131972 A G -0.0003738 0.0006778 0.5800000 0.5812667 0.836738 0.653355 NA
1 753405 rs3115860 C A -0.0004500 0.0007272 0.5400003 0.5360188 0.868304 0.751797 NA
CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
22 51197266 rs61290853 A G 0.0001396 0.0005282 0.7899998 0.7915785 0.386987 0.4229230 NA
22 51198027 rs34939255 A G -0.0007631 0.0005988 0.2000000 0.2025372 0.254430 0.0984425 NA
22 51210289 rs112565862 C T 0.0000020 0.0007980 1.0000000 0.9979969 0.129945 0.1018370 NA
22 51211106 rs9628250 T C -0.0010363 0.0005942 0.0810009 0.0811712 0.271050 0.1671330 NA
22 51211392 rs3888396 T C -0.0000600 0.0007908 0.9400001 0.9394891 0.132649 0.1641370 NA
22 51212875 rs2238837 A C 0.0007624 0.0005640 0.1800002 0.1764756 0.331587 0.3724040 NA
22 51213613 rs34726907 C T 0.0009911 0.0007447 0.1800002 0.1832732 0.127190 0.1727240 NA
22 51216564 rs9616970 T C 0.0009433 0.0007416 0.2000000 0.2033728 0.127722 0.1563500 NA
22 51219006 rs28729663 G A 0.0007578 0.0007253 0.2999998 0.2960877 0.137511 0.2052720 NA
22 51237063 rs3896457 T C 0.0006902 0.0005765 0.2300001 0.2312525 0.298254 0.2050720 NA

bcf preview

1   49298   rs10399793  T   C   .   PASS    AF=0.623755 ES:SE:LP:AF:ID  -0.000295527:0.000869335:0.136677:0.623755:rs10399793
1   54676   rs2462492   C   T   .   PASS    AF=0.399226 ES:SE:LP:AF:ID  -0.000544533:0.000862196:0.275724:0.399226:rs2462492
1   91536   rs6702460   G   T   .   PASS    AF=0.456028 ES:SE:LP:AF:ID  -0.00134756:0.000849268:0.958607:0.456028:rs6702460
1   534192  rs6680723   C   T   .   PASS    AF=0.241037 ES:SE:LP:AF:ID  -0.000284005:0.000968989:0.113509:0.241037:rs6680723
1   706368  rs12029736  A   G   .   PASS    AF=0.515025 ES:SE:LP:AF:ID  -0.000287604:0.000600234:0.200659:0.515025:rs12029736
1   729679  rs4951859   C   G   .   PASS    AF=0.841466 ES:SE:LP:AF:ID  -0.000485627:0.000701287:0.309804:0.841466:rs4951859
1   736289  rs79010578  T   A   .   PASS    AF=0.13333  ES:SE:LP:AF:ID  0.000732521:0.000758049:0.481486:0.13333:rs79010578
1   752566  rs3094315   G   A   .   PASS    AF=0.837165 ES:SE:LP:AF:ID  -0.000353827:0.000678565:0.221849:0.837165:rs3094315
1   752721  rs3131972   A   G   .   PASS    AF=0.836738 ES:SE:LP:AF:ID  -0.000373834:0.000677806:0.236572:0.836738:rs3131972
1   753405  rs3115860   C   A   .   PASS    AF=0.868304 ES:SE:LP:AF:ID  -0.000450046:0.000727236:0.267606:0.868304:rs3115860
1   753541  rs2073813   G   A   .   PASS    AF=0.131427 ES:SE:LP:AF:ID  0.000482167:0.00072859:0.29243:0.131427:rs2073813
1   754182  rs3131969   A   G   .   PASS    AF=0.867591 ES:SE:LP:AF:ID  -0.000498783:0.000725766:0.309804:0.867591:rs3131969
1   754192  rs3131968   A   G   .   PASS    AF=0.867698 ES:SE:LP:AF:ID  -0.000489134:0.00072609:0.30103:0.867698:rs3131968
1   754334  rs3131967   T   C   .   PASS    AF=0.867589 ES:SE:LP:AF:ID  -0.000501969:0.000725721:0.309804:0.867589:rs3131967
1   754503  rs3115859   G   A   .   PASS    AF=0.836223 ES:SE:LP:AF:ID  -0.000414584:0.000676058:0.267606:0.836223:rs3115859
1   754964  rs3131966   C   T   .   PASS    AF=0.836834 ES:SE:LP:AF:ID  -0.000434391:0.000677871:0.283997:0.836834:rs3131966
1   755775  rs3131965   A   G   .   PASS    AF=0.838125 ES:SE:LP:AF:ID  -0.000350395:0.000687303:0.21467:0.838125:rs3131965
1   755890  rs3115858   A   T   .   PASS    AF=0.867966 ES:SE:LP:AF:ID  -0.000444902:0.000725061:0.267606:0.867966:rs3115858
1   756604  rs3131962   A   G   .   PASS    AF=0.867516 ES:SE:LP:AF:ID  -0.000469175:0.000723245:0.283997:0.867516:rs3131962
1   757640  rs3115853   G   A   .   PASS    AF=0.866267 ES:SE:LP:AF:ID  -0.000536602:0.000721491:0.337242:0.866267:rs3115853
1   757734  rs4951929   C   T   .   PASS    AF=0.867655 ES:SE:LP:AF:ID  -0.000466344:0.0007238:0.283997:0.867655:rs4951929
1   757936  rs4951862   C   A   .   PASS    AF=0.867667 ES:SE:LP:AF:ID  -0.000465666:0.00072386:0.283997:0.867667:rs4951862
1   758144  rs3131956   A   G   .   PASS    AF=0.867675 ES:SE:LP:AF:ID  -0.000467042:0.000723879:0.283997:0.867675:rs3131956
1   758626  rs3131954   C   T   .   PASS    AF=0.868154 ES:SE:LP:AF:ID  -0.000474876:0.000725905:0.29243:0.868154:rs3131954
1   760912  rs1048488   C   T   .   PASS    AF=0.836569 ES:SE:LP:AF:ID  -0.000386408:0.000674795:0.244125:0.836569:rs1048488
1   761147  rs3115850   T   C   .   PASS    AF=0.836695 ES:SE:LP:AF:ID  -0.000392723:0.00067528:0.251812:0.836695:rs3115850
1   761732  rs2286139   C   T   .   PASS    AF=0.860527 ES:SE:LP:AF:ID  -0.000475271:0.000720992:0.29243:0.860527:rs2286139
1   763394  rs3115847   G   A   .   PASS    AF=0.705447 ES:SE:LP:AF:ID  -0.000642445:0.000703907:0.443698:0.705447:rs3115847
1   768253  rs2977608   A   C   .   PASS    AF=0.759101 ES:SE:LP:AF:ID  -0.00013118:0.000572666:0.0861861:0.759101:rs2977608
1   769223  rs60320384  C   G   .   PASS    AF=0.130972 ES:SE:LP:AF:ID  0.000503872:0.000728394:0.309804:0.130972:rs60320384
1   771823  rs2977605   T   C   .   PASS    AF=0.867541 ES:SE:LP:AF:ID  -0.000463609:0.000724677:0.283997:0.867541:rs2977605
1   771967  rs59066358  G   A   .   PASS    AF=0.131045 ES:SE:LP:AF:ID  0.000469807:0.000727991:0.283997:0.131045:rs59066358
1   772755  rs2905039   A   C   .   PASS    AF=0.867564 ES:SE:LP:AF:ID  -0.000468693:0.000724728:0.283997:0.867564:rs2905039
1   776546  rs12124819  A   G   .   PASS    AF=0.264636 ES:SE:LP:AF:ID  -1.18155e-06:0.000643951:-0:0.264636:rs12124819
1   777122  rs2980319   A   T   .   PASS    AF=0.86872  ES:SE:LP:AF:ID  -0.000385369:0.000726481:0.221849:0.86872:rs2980319
1   778745  rs1055606   A   G   .   PASS    AF=0.12994  ES:SE:LP:AF:ID  0.000401429:0.000729075:0.236572:0.12994:rs1055606
1   779322  rs4040617   A   G   .   PASS    AF=0.130247 ES:SE:LP:AF:ID  0.000363886:0.000727796:0.207608:0.130247:rs4040617
1   780785  rs2977612   T   A   .   PASS    AF=0.86741  ES:SE:LP:AF:ID  -0.000484722:0.000724569:0.30103:0.86741:rs2977612
1   782981  rs6594026   C   T   .   PASS    AF=0.130893 ES:SE:LP:AF:ID  0.000510352:0.000727789:0.318759:0.130893:rs6594026
1   785050  rs2905062   G   A   .   PASS    AF=0.867042 ES:SE:LP:AF:ID  -0.000522153:0.000724155:0.327902:0.867042:rs2905062
1   785989  rs2980300   T   C   .   PASS    AF=0.866961 ES:SE:LP:AF:ID  -0.000516769:0.000724576:0.318759:0.866961:rs2980300
1   787399  rs2905055   G   T   .   PASS    AF=0.859238 ES:SE:LP:AF:ID  -0.000520938:0.000724153:0.327902:0.859238:rs2905055
1   787606  rs3863622   G   T   .   PASS    AF=0.129806 ES:SE:LP:AF:ID  0.000458519:0.000731759:0.275724:0.129806:rs3863622
1   787685  rs2905054   G   T   .   PASS    AF=0.859929 ES:SE:LP:AF:ID  -0.000503867:0.000724683:0.309804:0.859929:rs2905054
1   787844  rs2905053   C   T   .   PASS    AF=0.867709 ES:SE:LP:AF:ID  -0.000513675:0.000727154:0.318759:0.867709:rs2905053
1   791191  rs111818025 G   A   .   PASS    AF=0.129192 ES:SE:LP:AF:ID  0.000465767:0.000736646:0.275724:0.129192:rs111818025
1   795988  rs59380221  C   T   .   PASS    AF=0.144258 ES:SE:LP:AF:ID  0.00122996:0.000752321:1:0.144258:rs59380221
1   798400  rs10900604  A   G   .   PASS    AF=0.208111 ES:SE:LP:AF:ID  -0.000149162:0.000612025:0.091515:0.208111:rs10900604
1   798959  rs11240777  G   A   .   PASS    AF=0.207957 ES:SE:LP:AF:ID  -0.000142437:0.000612266:0.0861861:0.207957:rs11240777
1   808631  rs11240779  G   A   .   PASS    AF=0.770574 ES:SE:LP:AF:ID  -0.000274562:0.000582239:0.19382:0.770574:rs11240779