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_41202_K297.vcf.gz --id UKB-b:18822 --data /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/ukbiobank/raw-output/data.batch_41202_K297.txt.gz --cohort_cases 6247 --cohort_controls 456763 --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-18822/UKB-b-18822_data.vcf.gz \
--ref-ld-chr ../reference/eur_w_ld_chr/ \
--out /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-18822/ldsc.txt \
--w-ld-chr ../reference/eur_w_ld_chr/ 

Beginning analysis at Thu Oct 17 14:40:19 2019
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-18822/UKB-b-18822_data.vcf.gz ...
Read summary statistics for 5254988 SNPs.
Dropped 1687 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, 1146905 SNPs remain.
After merging with regression SNP LD, 1146905 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.0024 (0.001)
Lambda GC: 1.0451
Mean Chi^2: 1.0466
Intercept: 1.023 (0.0071)
Ratio: 0.4934 (0.1522)
Analysis finished at Thu Oct 17 14:41:22 2019
Total time elapsed: 1.0m:3.1s

QC metrics

Metrics

Metrics

{
    "af_correlation": 0.9119,
    "inflation_factor": 1.0475,
    "mean_EFFECT": 3.297e-07,
    "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": 45451,
    "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": 1146905,
    "ldsc_nsnp_merge_regression_ld": 1146905,
    "ldsc_observed_scale_h2_beta": 0.0024,
    "ldsc_observed_scale_h2_se": 0.001,
    "ldsc_intercept_beta": 1.023,
    "ldsc_intercept_se": 0.0071,
    "ldsc_lambda_gc": 1.0451,
    "ldsc_mean_chisq": 1.0466,
    "ldsc_ratio": 0.4936
}

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 5253314 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 5254988 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 8.673036e+00 5.763479e+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 7.852737e+07 5.658624e+07 828.0000000 3.190790e+07 6.891307e+07 1.144813e+08 2.492385e+08 ▇▆▅▂▁
numeric EFFECT 0 1.0000000 NA NA NA NA NA NA NA 3.000000e-07 3.357000e-04 -0.0022993 -2.113000e-04 -8.000000e-07 2.101000e-04 2.522800e-03 ▁▁▇▁▁
numeric SE 0 1.0000000 NA NA NA NA NA NA NA 3.191000e-04 7.960000e-05 0.0002314 2.521000e-04 2.899000e-04 3.686000e-04 1.063000e-03 ▇▂▁▁▁
numeric PVAL 0 1.0000000 NA NA NA NA NA NA NA 4.926634e-01 2.901450e-01 0.0000016 2.399999e-01 4.899999e-01 7.400005e-01 1.000000e+00 ▇▇▇▇▇
numeric PVAL_ztest 0 1.0000000 NA NA NA NA NA NA NA 4.926678e-01 2.901178e-01 0.0000016 2.396512e-01 4.904298e-01 7.433305e-01 9.999998e-01 ▇▇▇▇▇
numeric AF 0 1.0000000 NA NA NA NA NA NA NA 3.410998e-01 2.430127e-01 0.0560270 1.323830e-01 2.713225e-01 5.079290e-01 9.439730e-01 ▇▃▂▂▂
numeric AF_reference 45451 0.9913509 NA NA NA NA NA NA NA 3.353990e-01 2.385666e-01 0.0000000 1.387780e-01 2.749600e-01 4.974040e-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 0.0002945 0.0004258 0.4899999 0.4890883 0.623765 0.7821490 NA
1 54676 rs2462492 C T 0.0001241 0.0004218 0.7700005 0.7686645 0.400401 NA NA
1 86028 rs114608975 T C -0.0001453 0.0006744 0.8300000 0.8294252 0.103556 0.0277556 NA
1 91536 rs6702460 G T 0.0002672 0.0004153 0.5199996 0.5200532 0.456846 0.4207270 NA
1 234313 rs8179466 C T 0.0007292 0.0008190 0.3700002 0.3732779 0.074506 NA NA
1 534192 rs6680723 C T -0.0003784 0.0004744 0.4299995 0.4251241 0.240959 NA NA
1 546697 rs12025928 A G 0.0003220 0.0005919 0.5900000 0.5864048 0.913475 NA NA
1 693731 rs12238997 A G -0.0000639 0.0003976 0.8700001 0.8722645 0.116329 0.1417730 NA
1 705882 rs72631875 G A -0.0008856 0.0005826 0.1299999 0.1285055 0.067288 0.0315495 NA
1 706368 rs55727773 A G -0.0000956 0.0002945 0.7499995 0.7454818 0.515645 0.2751600 NA
CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
22 51213613 rs34726907 C T -0.0002069 0.0003645 0.5700002 0.5703442 0.127814 0.1727240 NA
22 51216564 rs9616970 T C -0.0002408 0.0003630 0.5099998 0.5071413 0.128328 0.1563500 NA
22 51217954 rs9616974 G A 0.0001061 0.0004606 0.8200001 0.8177627 0.073312 0.0621006 NA
22 51218224 rs9616975 C A 0.0001029 0.0004608 0.8200001 0.8233671 0.073333 0.0619010 NA
22 51218377 rs2519461 G C 0.0001229 0.0004602 0.7899998 0.7893815 0.073622 0.0826677 NA
22 51219006 rs28729663 G A -0.0002619 0.0003553 0.4600002 0.4609531 0.137950 0.2052720 NA
22 51219387 rs9616832 T C 0.0001234 0.0004612 0.7899998 0.7889956 0.073744 0.0654952 NA
22 51221731 rs115055839 T C 0.0001033 0.0004615 0.8200001 0.8227896 0.073235 0.0625000 NA
22 51229805 rs9616985 T C 0.0000862 0.0004631 0.8499999 0.8522748 0.073071 0.0730831 NA
22 51237063 rs3896457 T C 0.0004008 0.0002833 0.1600000 0.1570861 0.297974 0.2050720 NA

bcf preview

1   49298   rs10399793  T   C   .   PASS    AF=0.623765 ES:SE:LP:AF:ID  0.000294545:0.000425791:0.309804:0.623765:rs10399793
1   54676   rs2462492   C   T   .   PASS    AF=0.400401 ES:SE:LP:AF:ID  0.000124069:0.000421828:0.113509:0.400401:rs2462492
1   86028   rs114608975 T   C   .   PASS    AF=0.103556 ES:SE:LP:AF:ID  -0.000145295:0.000674414:0.0809219:0.103556:rs114608975
1   91536   rs6702460   G   T   .   PASS    AF=0.456846 ES:SE:LP:AF:ID  0.000267173:0.00041534:0.283997:0.456846:rs6702460
1   234313  rs8179466   C   T   .   PASS    AF=0.074506 ES:SE:LP:AF:ID  0.000729155:0.000818953:0.431798:0.074506:rs8179466
1   534192  rs6680723   C   T   .   PASS    AF=0.240959 ES:SE:LP:AF:ID  -0.000378387:0.000474429:0.366532:0.240959:rs6680723
1   546697  rs12025928  A   G   .   PASS    AF=0.913475 ES:SE:LP:AF:ID  0.000322011:0.000591874:0.229148:0.913475:rs12025928
1   693731  rs12238997  A   G   .   PASS    AF=0.116329 ES:SE:LP:AF:ID  -6.39248e-05:0.000397585:0.0604807:0.116329:rs12238997
1   705882  rs72631875  G   A   .   PASS    AF=0.067288 ES:SE:LP:AF:ID  -0.000885589:0.000582616:0.886057:0.067288:rs72631875
1   706368  rs12029736  A   G   .   PASS    AF=0.515645 ES:SE:LP:AF:ID  -9.56007e-05:0.000294516:0.124939:0.515645:rs12029736
1   722670  rs116030099 T   C   .   PASS    AF=0.1012   ES:SE:LP:AF:ID  0.000151024:0.000485933:0.119186:0.1012:rs116030099
1   729679  rs4951859   C   G   .   PASS    AF=0.843204 ES:SE:LP:AF:ID  -1.17619e-05:0.000344559:0.0132283:0.843204:rs4951859
1   731718  rs58276399  T   C   .   PASS    AF=0.122312 ES:SE:LP:AF:ID  -0.00017243:0.000377149:0.187087:0.122312:rs58276399
1   734349  rs141242758 T   C   .   PASS    AF=0.121554 ES:SE:LP:AF:ID  -0.000148115:0.000377308:0.161151:0.121554:rs141242758
1   736289  rs79010578  T   A   .   PASS    AF=0.132335 ES:SE:LP:AF:ID  0.000356946:0.000371875:0.468521:0.132335:rs79010578
1   752566  rs3094315   G   A   .   PASS    AF=0.838945 ES:SE:LP:AF:ID  4.6073e-05:0.000333682:0.05061:0.838945:rs3094315
1   752721  rs3131972   A   G   .   PASS    AF=0.838573 ES:SE:LP:AF:ID  5.77572e-05:0.000333323:0.0655015:0.838573:rs3131972
1   753405  rs3115860   C   A   .   PASS    AF=0.869776 ES:SE:LP:AF:ID  0.000153251:0.000357668:0.173925:0.869776:rs3115860
1   753541  rs2073813   G   A   .   PASS    AF=0.129876 ES:SE:LP:AF:ID  -0.000219169:0.0003584:0.267606:0.129876:rs2073813
1   754182  rs3131969   A   G   .   PASS    AF=0.869117 ES:SE:LP:AF:ID  0.000164551:0.000356967:0.19382:0.869117:rs3131969
1   754192  rs3131968   A   G   .   PASS    AF=0.869215 ES:SE:LP:AF:ID  0.000154374:0.000357108:0.173925:0.869215:rs3131968
1   754334  rs3131967   T   C   .   PASS    AF=0.869121 ES:SE:LP:AF:ID  0.000153834:0.00035696:0.173925:0.869121:rs3131967
1   754503  rs3115859   G   A   .   PASS    AF=0.838026 ES:SE:LP:AF:ID  6.3077e-05:0.000332398:0.0705811:0.838026:rs3115859
1   754964  rs3131966   C   T   .   PASS    AF=0.838657 ES:SE:LP:AF:ID  7.38061e-05:0.000333332:0.0861861:0.838657:rs3131966
1   755775  rs3131965   A   G   .   PASS    AF=0.83977  ES:SE:LP:AF:ID  7.58523e-05:0.00033784:0.0861861:0.83977:rs3131965
1   755890  rs3115858   A   T   .   PASS    AF=0.8694   ES:SE:LP:AF:ID  0.000152116:0.000356547:0.173925:0.8694:rs3115858
1   756604  rs3131962   A   G   .   PASS    AF=0.868947 ES:SE:LP:AF:ID  0.000146968:0.00035565:0.167491:0.868947:rs3131962
1   757640  rs3115853   G   A   .   PASS    AF=0.867898 ES:SE:LP:AF:ID  0.000110689:0.000354968:0.119186:0.867898:rs3115853
1   757734  rs4951929   C   T   .   PASS    AF=0.86909  ES:SE:LP:AF:ID  0.00014264:0.000355941:0.161151:0.86909:rs4951929
1   757936  rs4951862   C   A   .   PASS    AF=0.869098 ES:SE:LP:AF:ID  0.000142379:0.000355968:0.161151:0.869098:rs4951862
1   758144  rs3131956   A   G   .   PASS    AF=0.869106 ES:SE:LP:AF:ID  0.000142488:0.000355977:0.161151:0.869106:rs3131956
1   758626  rs3131954   C   T   .   PASS    AF=0.869584 ES:SE:LP:AF:ID  0.000157768:0.000356954:0.180456:0.869584:rs3131954
1   760912  rs1048488   C   T   .   PASS    AF=0.838306 ES:SE:LP:AF:ID  5.927e-05:0.000331768:0.0655015:0.838306:rs1048488
1   761147  rs3115850   T   C   .   PASS    AF=0.838427 ES:SE:LP:AF:ID  6.5853e-05:0.000332002:0.0757207:0.838427:rs3115850
1   761732  rs2286139   C   T   .   PASS    AF=0.862254 ES:SE:LP:AF:ID  0.000128579:0.000354689:0.142668:0.862254:rs2286139
1   763394  rs3115847   G   A   .   PASS    AF=0.706753 ES:SE:LP:AF:ID  0.000362964:0.000345291:0.537602:0.706753:rs3115847
1   766007  rs61768174  A   C   .   PASS    AF=0.105145 ES:SE:LP:AF:ID  5.59024e-05:0.000397769:0.05061:0.105145:rs61768174
1   768253  rs2977608   A   C   .   PASS    AF=0.761297 ES:SE:LP:AF:ID  0.000152323:0.000281818:0.229148:0.761297:rs2977608
1   768448  rs12562034  G   A   .   PASS    AF=0.10649  ES:SE:LP:AF:ID  -0.000144486:0.000388433:0.148742:0.10649:rs12562034
1   769223  rs60320384  C   G   .   PASS    AF=0.129581 ES:SE:LP:AF:ID  -0.000187373:0.000358186:0.221849:0.129581:rs60320384
1   771823  rs2977605   T   C   .   PASS    AF=0.868906 ES:SE:LP:AF:ID  0.000131292:0.000356272:0.148742:0.868906:rs2977605
1   771967  rs59066358  G   A   .   PASS    AF=0.129682 ES:SE:LP:AF:ID  -0.000180766:0.000357955:0.21467:0.129682:rs59066358
1   772755  rs2905039   A   C   .   PASS    AF=0.868916 ES:SE:LP:AF:ID  0.000137346:0.000356279:0.154902:0.868916:rs2905039
1   776546  rs12124819  A   G   .   PASS    AF=0.265385 ES:SE:LP:AF:ID  0.000174522:0.000314801:0.236572:0.265385:rs12124819
1   777122  rs2980319   A   T   .   PASS    AF=0.870039 ES:SE:LP:AF:ID  6.10681e-05:0.000357006:0.0655015:0.870039:rs2980319
1   777232  rs112618790 C   T   .   PASS    AF=0.095141 ES:SE:LP:AF:ID  -0.000213133:0.000413764:0.21467:0.095141:rs112618790
1   778745  rs1055606   A   G   .   PASS    AF=0.12858  ES:SE:LP:AF:ID  -8.75551e-05:0.000358416:0.091515:0.12858:rs1055606
1   779322  rs4040617   A   G   .   PASS    AF=0.128877 ES:SE:LP:AF:ID  -5.98296e-05:0.000357808:0.0604807:0.128877:rs4040617
1   780785  rs2977612   T   A   .   PASS    AF=0.86878  ES:SE:LP:AF:ID  7.49978e-05:0.000356054:0.0809219:0.86878:rs2977612
1   781845  rs61768199  A   G   .   PASS    AF=0.101873 ES:SE:LP:AF:ID  0.000190144:0.000403444:0.19382:0.101873:rs61768199