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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    "gwas_harmonisation_command": "--out /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/ukbiobank/vcf_09_19b/bgzip_vcf/data.batch_20084_468.vcf.gz --id UKB-b:15835 --data /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/ukbiobank/raw-output/data.batch_20084_468.txt.gz --cohort_cases 4810 --cohort_controls 60139 --ref /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/ukbiobank/human_g1k_v37.fasta --json /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/ukbiobank/ukb_gwas.json; 1.1.1",
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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-15835/UKB-b-15835_data.vcf.gz \
--ref-ld-chr ../reference/eur_w_ld_chr/ \
--out /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-15835/ldsc.txt \
--w-ld-chr ../reference/eur_w_ld_chr/ 

Beginning analysis at Thu Oct 17 14:44:30 2019
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-15835/UKB-b-15835_data.vcf.gz ...
Read summary statistics for 4843538 SNPs.
Dropped 1278 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, 1093973 SNPs remain.
After merging with regression SNP LD, 1093973 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: -0.0084 (0.0071)
Lambda GC: 1.0058
Mean Chi^2: 0.9999
Intercept: 1.0115 (0.0072)
Ratio: NA (mean chi^2 < 1)
Analysis finished at Thu Oct 17 14:45:26 2019
Total time elapsed: 56.06s

QC metrics

Metrics

Metrics

{
    "af_correlation": 0.9027,
    "inflation_factor": 1,
    "mean_EFFECT": 1.4362e-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": 41029,
    "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": 1093973,
    "ldsc_nsnp_merge_regression_ld": 1093973,
    "ldsc_observed_scale_h2_beta": "NA",
    "ldsc_observed_scale_h2_se": "NA",
    "ldsc_intercept_beta": 1.0115,
    "ldsc_intercept_se": 0.0072,
    "ldsc_lambda_gc": 1.0058,
    "ldsc_mean_chisq": 0.9999,
    "ldsc_ratio": -115
}

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 4842269 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 4843538 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 8.666442e+00 5.767004e+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 7.858381e+07 5.666348e+07 828.0000000 3.185847e+07 6.894733e+07 1.146591e+08 2.492385e+08 ▇▆▅▂▁
numeric EFFECT 0 1.0000000 NA NA NA NA NA NA NA 1.400000e-06 1.886100e-03 -0.0127680 -1.213400e-03 -3.500000e-06 1.209400e-03 1.228090e-02 ▁▁▇▁▁
numeric SE 0 1.0000000 NA NA NA NA NA NA NA 1.843500e-03 3.832000e-04 0.0014033 1.517200e-03 1.708200e-03 2.092100e-03 5.343100e-03 ▇▂▁▁▁
numeric PVAL 0 1.0000000 NA NA NA NA NA NA NA 4.989706e-01 2.885066e-01 0.0000018 2.500000e-01 5.000000e-01 7.499995e-01 1.000000e+00 ▇▇▇▇▇
numeric PVAL_ztest 0 1.0000000 NA NA NA NA NA NA NA 4.989716e-01 2.884815e-01 0.0000018 2.489185e-01 4.980593e-01 7.485946e-01 9.999996e-01 ▇▇▇▇▇
numeric AF 0 1.0000000 NA NA NA NA NA NA NA 3.583976e-01 2.350904e-01 0.0727660 1.555460e-01 2.956160e-01 5.243187e-01 9.272340e-01 ▇▅▃▂▂
numeric AF_reference 41029 0.9915291 NA NA NA NA NA NA NA 3.511562e-01 2.327284e-01 0.0000000 1.591450e-01 2.969250e-01 5.133790e-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 -0.0034067 0.0025862 0.1900002 0.1877490 0.623812 0.7821490 NA
1 54676 rs2462492 C T 0.0010860 0.0025787 0.6700003 0.6736612 0.399144 NA NA
1 86028 rs114608975 T C 0.0058879 0.0041049 0.1499999 0.1514638 0.103536 0.0277556 NA
1 91536 rs6702460 G T 0.0004410 0.0025363 0.8600001 0.8619611 0.455916 0.4207270 NA
1 234313 rs8179466 C T 0.0056212 0.0050159 0.2599998 0.2624309 0.074455 NA NA
1 534192 rs6680723 C T 0.0030127 0.0028887 0.2999998 0.2969925 0.242057 NA NA
1 546697 rs12025928 A G 0.0078427 0.0035843 0.0290001 0.0286636 0.912862 NA NA
1 693731 rs12238997 A G 0.0015250 0.0024087 0.5300002 0.5266631 0.117313 0.1417730 NA
1 706368 rs55727773 A G 0.0002168 0.0017879 0.9000000 0.9034856 0.513304 0.2751600 NA
1 722670 rs116030099 T C -0.0016900 0.0029177 0.5600000 0.5624447 0.102736 0.0413339 NA
CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
22 51202748 rs9616963 A G -0.0007703 0.0028018 0.7800007 0.7833761 0.073992 0.0391374 NA
22 51208537 rs72619593 G A -0.0018102 0.0023815 0.4500005 0.4471817 0.120936 0.1142170 NA
22 51210289 rs112565862 C T 0.0005007 0.0023751 0.8300000 0.8330428 0.129762 0.1018370 NA
22 51211106 rs9628250 T C 0.0006005 0.0017678 0.7300002 0.7340812 0.271468 0.1671330 NA
22 51211392 rs3888396 T C 0.0007504 0.0023539 0.7499995 0.7498759 0.132383 0.1641370 NA
22 51212875 rs2238837 A C 0.0001949 0.0016804 0.9100000 0.9076713 0.331351 0.3724040 NA
22 51213613 rs34726907 C T -0.0010796 0.0022300 0.6300007 0.6282950 0.126422 0.1727240 NA
22 51216564 rs9616970 T C -0.0013455 0.0022213 0.5400003 0.5446880 0.126887 0.1563500 NA
22 51219006 rs28729663 G A -0.0017149 0.0021746 0.4299995 0.4303559 0.136315 0.2052720 NA
22 51237063 rs3896457 T C -0.0005276 0.0017168 0.7600007 0.7586107 0.298393 0.2050720 NA

bcf preview

1   49298   rs10399793  T   C   .   PASS    AF=0.623812 ES:SE:LP:AF:ID  -0.00340673:0.00258621:0.721246:0.623812:rs10399793
1   54676   rs2462492   C   T   .   PASS    AF=0.399144 ES:SE:LP:AF:ID  0.00108596:0.00257869:0.173925:0.399144:rs2462492
1   86028   rs114608975 T   C   .   PASS    AF=0.103536 ES:SE:LP:AF:ID  0.00588793:0.00410486:0.823909:0.103536:rs114608975
1   91536   rs6702460   G   T   .   PASS    AF=0.455916 ES:SE:LP:AF:ID  0.000441011:0.00253632:0.0655015:0.455916:rs6702460
1   234313  rs8179466   C   T   .   PASS    AF=0.074455 ES:SE:LP:AF:ID  0.00562115:0.00501591:0.585027:0.074455:rs8179466
1   534192  rs6680723   C   T   .   PASS    AF=0.242057 ES:SE:LP:AF:ID  0.00301268:0.00288874:0.522879:0.242057:rs6680723
1   546697  rs12025928  A   G   .   PASS    AF=0.912862 ES:SE:LP:AF:ID  0.00784272:0.00358429:1.5376:0.912862:rs12025928
1   693731  rs12238997  A   G   .   PASS    AF=0.117313 ES:SE:LP:AF:ID  0.00152498:0.00240872:0.275724:0.117313:rs12238997
1   706368  rs12029736  A   G   .   PASS    AF=0.513304 ES:SE:LP:AF:ID  0.000216802:0.00178792:0.0457575:0.513304:rs12029736
1   722670  rs116030099 T   C   .   PASS    AF=0.102736 ES:SE:LP:AF:ID  -0.00168995:0.00291766:0.251812:0.102736:rs116030099
1   729679  rs4951859   C   G   .   PASS    AF=0.841441 ES:SE:LP:AF:ID  -0.00231903:0.00208309:0.568636:0.841441:rs4951859
1   731718  rs58276399  T   C   .   PASS    AF=0.123078 ES:SE:LP:AF:ID  0.00161136:0.002288:0.318759:0.123078:rs58276399
1   734349  rs141242758 T   C   .   PASS    AF=0.12233  ES:SE:LP:AF:ID  0.00167664:0.00228874:0.337242:0.12233:rs141242758
1   736289  rs79010578  T   A   .   PASS    AF=0.134139 ES:SE:LP:AF:ID  0.00377704:0.00224677:1.03152:0.134139:rs79010578
1   752566  rs3094315   G   A   .   PASS    AF=0.837029 ES:SE:LP:AF:ID  -0.00273355:0.00201514:0.769551:0.837029:rs3094315
1   752721  rs3131972   A   G   .   PASS    AF=0.836733 ES:SE:LP:AF:ID  -0.00281799:0.00201366:0.79588:0.836733:rs3131972
1   753405  rs3115860   C   A   .   PASS    AF=0.868562 ES:SE:LP:AF:ID  -0.00214371:0.00216378:0.49485:0.868562:rs3115860
1   753541  rs2073813   G   A   .   PASS    AF=0.131004 ES:SE:LP:AF:ID  0.0025522:0.00216934:0.619789:0.131004:rs2073813
1   754182  rs3131969   A   G   .   PASS    AF=0.867976 ES:SE:LP:AF:ID  -0.00227633:0.00216031:0.537602:0.867976:rs3131969
1   754192  rs3131968   A   G   .   PASS    AF=0.86805  ES:SE:LP:AF:ID  -0.00225878:0.00216119:0.522879:0.86805:rs3131968
1   754334  rs3131967   T   C   .   PASS    AF=0.867987 ES:SE:LP:AF:ID  -0.00228604:0.00216025:0.537602:0.867987:rs3131967
1   754503  rs3115859   G   A   .   PASS    AF=0.836159 ES:SE:LP:AF:ID  -0.00293102:0.00200777:0.853872:0.836159:rs3115859
1   754964  rs3131966   C   T   .   PASS    AF=0.836793 ES:SE:LP:AF:ID  -0.00301971:0.00201327:0.886057:0.836793:rs3131966
1   755775  rs3131965   A   G   .   PASS    AF=0.838109 ES:SE:LP:AF:ID  -0.00281772:0.00204161:0.769551:0.838109:rs3131965
1   755890  rs3115858   A   T   .   PASS    AF=0.868228 ES:SE:LP:AF:ID  -0.00212874:0.00215747:0.49485:0.868228:rs3115858
1   756604  rs3131962   A   G   .   PASS    AF=0.867742 ES:SE:LP:AF:ID  -0.00207295:0.00215175:0.468521:0.867742:rs3131962
1   757640  rs3115853   G   A   .   PASS    AF=0.866644 ES:SE:LP:AF:ID  -0.00208282:0.00214781:0.481486:0.866644:rs3115853
1   757734  rs4951929   C   T   .   PASS    AF=0.867911 ES:SE:LP:AF:ID  -0.00208598:0.00215394:0.481486:0.867911:rs4951929
1   757936  rs4951862   C   A   .   PASS    AF=0.867923 ES:SE:LP:AF:ID  -0.00208901:0.00215409:0.481486:0.867923:rs4951862
1   758144  rs3131956   A   G   .   PASS    AF=0.867932 ES:SE:LP:AF:ID  -0.00209327:0.00215416:0.481486:0.867932:rs3131956
1   758626  rs3131954   C   T   .   PASS    AF=0.868398 ES:SE:LP:AF:ID  -0.00204829:0.00215983:0.468521:0.868398:rs3131954
1   760912  rs1048488   C   T   .   PASS    AF=0.836369 ES:SE:LP:AF:ID  -0.00317196:0.00200276:0.958607:0.836369:rs1048488
1   761147  rs3115850   T   C   .   PASS    AF=0.836495 ES:SE:LP:AF:ID  -0.00307591:0.00200413:0.920819:0.836495:rs3115850
1   761732  rs2286139   C   T   .   PASS    AF=0.860851 ES:SE:LP:AF:ID  -0.00233793:0.00214653:0.552842:0.860851:rs2286139
1   763394  rs3115847   G   A   .   PASS    AF=0.705804 ES:SE:LP:AF:ID  -0.00289929:0.00209464:0.769551:0.705804:rs3115847
1   766007  rs61768174  A   C   .   PASS    AF=0.106094 ES:SE:LP:AF:ID  0.00324431:0.00241028:0.744727:0.106094:rs61768174
1   768253  rs2977608   A   C   .   PASS    AF=0.758252 ES:SE:LP:AF:ID  -0.00156964:0.00169772:0.443698:0.758252:rs2977608
1   768448  rs12562034  G   A   .   PASS    AF=0.108262 ES:SE:LP:AF:ID  0.000202557:0.00233668:0.0315171:0.108262:rs12562034
1   769223  rs60320384  C   G   .   PASS    AF=0.13066  ES:SE:LP:AF:ID  0.00274971:0.00216851:0.69897:0.13066:rs60320384
1   771823  rs2977605   T   C   .   PASS    AF=0.867852 ES:SE:LP:AF:ID  -0.00226226:0.00215667:0.537602:0.867852:rs2977605
1   771967  rs59066358  G   A   .   PASS    AF=0.130756 ES:SE:LP:AF:ID  0.00266058:0.00216706:0.657577:0.130756:rs59066358
1   772755  rs2905039   A   C   .   PASS    AF=0.867878 ES:SE:LP:AF:ID  -0.00225391:0.0021568:0.522879:0.867878:rs2905039
1   776546  rs12124819  A   G   .   PASS    AF=0.263729 ES:SE:LP:AF:ID  -0.00175736:0.00191836:0.443698:0.263729:rs12124819
1   777122  rs2980319   A   T   .   PASS    AF=0.869067 ES:SE:LP:AF:ID  -0.00194458:0.00216247:0.431798:0.869067:rs2980319
1   777232  rs112618790 C   T   .   PASS    AF=0.096639 ES:SE:LP:AF:ID  6.50752e-05:0.00249083:0.00877392:0.096639:rs112618790
1   778745  rs1055606   A   G   .   PASS    AF=0.129594 ES:SE:LP:AF:ID  0.00231268:0.00217072:0.537602:0.129594:rs1055606
1   779322  rs4040617   A   G   .   PASS    AF=0.129863 ES:SE:LP:AF:ID  0.0022445:0.00216702:0.522879:0.129863:rs4040617
1   780785  rs2977612   T   A   .   PASS    AF=0.867843 ES:SE:LP:AF:ID  -0.00203114:0.0021571:0.455932:0.867843:rs2977612
1   781845  rs61768199  A   G   .   PASS    AF=0.102807 ES:SE:LP:AF:ID  0.00390852:0.0024464:0.958607:0.102807:rs61768199
1   782981  rs6594026   C   T   .   PASS    AF=0.130424 ES:SE:LP:AF:ID  0.00236843:0.00216744:0.568636:0.130424:rs6594026