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-13704/UKB-b-13704_data.vcf.gz \
--ref-ld-chr ../reference/eur_w_ld_chr/ \
--out /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-13704/ldsc.txt \
--w-ld-chr ../reference/eur_w_ld_chr/ 

Beginning analysis at Thu Oct 17 14:42:52 2019
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-13704/UKB-b-13704_data.vcf.gz ...
Read summary statistics for 4459431 SNPs.
Dropped 1007 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, 1034012 SNPs remain.
After merging with regression SNP LD, 1034012 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.006 (0.0012)
Lambda GC: 1.0662
Mean Chi^2: 1.0633
Intercept: 1.0039 (0.0079)
Ratio: 0.0622 (0.1248)
Analysis finished at Thu Oct 17 14:43:46 2019
Total time elapsed: 53.99s

QC metrics

Metrics

Metrics

{
    "af_correlation": 0.8917,
    "inflation_factor": 1.0475,
    "mean_EFFECT": -4.8471e-08,
    "n": "-Inf",
    "n_snps": 9851866,
    "n_clumped_hits": 6,
    "n_p_sig": 379,
    "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": 37061,
    "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": 1034012,
    "ldsc_nsnp_merge_regression_ld": 1034012,
    "ldsc_observed_scale_h2_beta": 0.006,
    "ldsc_observed_scale_h2_se": 0.0012,
    "ldsc_intercept_beta": 1.0039,
    "ldsc_intercept_se": 0.0079,
    "ldsc_lambda_gc": 1.0662,
    "ldsc_mean_chisq": 1.0633,
    "ldsc_ratio": 0.0616
}
 

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 4458430 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 4459431 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 8.656083e+00 5.765309e+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 7.860821e+07 5.673129e+07 828.0000000 3.173377e+07 6.896812e+07 1.147412e+08 2.492385e+08 ▇▆▅▂▁
numeric EFFECT 0 1.0000000 NA NA NA NA NA NA NA 0.000000e+00 2.406000e-04 -0.0025201 -1.569000e-04 -1.000000e-06 1.560000e-04 3.566200e-03 ▁▅▇▁▁
numeric SE 0 1.0000000 NA NA NA NA NA NA NA 2.298000e-04 3.980000e-05 0.0001818 1.955000e-04 2.162000e-04 2.563000e-04 6.650000e-04 ▇▂▁▁▁
numeric PVAL 0 1.0000000 NA NA NA NA NA NA NA 4.902864e-01 2.912490e-01 0.0000000 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 4.902881e-01 2.912235e-01 0.0000000 2.354799e-01 4.864600e-01 7.426005e-01 9.999999e-01 ▇▇▇▇▇
numeric AF 0 1.0000000 NA NA NA NA NA NA NA 3.745821e-01 2.259147e-01 0.0916480 1.787030e-01 3.185020e-01 5.377890e-01 9.083510e-01 ▇▅▃▂▂
numeric AF_reference 37061 0.9916893 NA NA NA NA NA NA NA 3.657341e-01 2.260483e-01 0.0000000 1.791130e-01 3.176920e-01 5.259580e-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 0.0000690 0.0003346 0.8400000 0.8365343 0.623775 0.7821490 NA
1 54676 rs2462492 C T 0.0000224 0.0003314 0.9500000 0.9461080 0.400400 NA NA
1 86028 rs114608975 T C -0.0000374 0.0005299 0.9400001 0.9437188 0.103554 0.0277556 NA
1 91536 rs6702460 G T -0.0001351 0.0003263 0.6800001 0.6789968 0.456851 0.4207270 NA
1 534192 rs6680723 C T 0.0000707 0.0003728 0.8499999 0.8495673 0.240953 NA NA
1 693731 rs12238997 A G 0.0003033 0.0003124 0.3300000 0.3316280 0.116345 0.1417730 NA
1 706368 rs55727773 A G 0.0003863 0.0002314 0.0949992 0.0951020 0.515623 0.2751600 NA
1 722670 rs116030099 T C -0.0007328 0.0003818 0.0549997 0.0549253 0.101232 0.0413339 NA
1 729679 rs4951859 C G -0.0002658 0.0002708 0.3300000 0.3262185 0.843205 0.6399760 NA
1 731718 rs142557973 T C 0.0003792 0.0002964 0.2000000 0.2006719 0.122325 0.1543530 NA
CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
22 51198027 rs34939255 A G -0.0002484 0.0002308 0.2800000 0.2818717 0.254576 0.0984425 NA
22 51208537 rs72619593 G A 0.0005646 0.0003085 0.0669993 0.0672198 0.120740 0.1142170 NA
22 51210289 rs112565862 C T 0.0001048 0.0003073 0.7300002 0.7331356 0.129960 0.1018370 NA
22 51211106 rs9628250 T C -0.0001552 0.0002288 0.5000000 0.4977160 0.271563 0.1671330 NA
22 51211392 rs3888396 T C 0.0000583 0.0003045 0.8499999 0.8481935 0.132634 0.1641370 NA
22 51212875 rs2238837 A C 0.0002219 0.0002174 0.3100002 0.3074705 0.331448 0.3724040 NA
22 51213613 rs34726907 C T 0.0000155 0.0002865 0.9599999 0.9569657 0.127792 0.1727240 NA
22 51216564 rs9616970 T C 0.0000422 0.0002853 0.8800001 0.8823487 0.128308 0.1563500 NA
22 51219006 rs28729663 G A 0.0000588 0.0002792 0.8300000 0.8333100 0.137929 0.2052720 NA
22 51237063 rs3896457 T C 0.0002350 0.0002226 0.2900000 0.2911180 0.297980 0.2050720 NA

bcf preview

1   49298   rs10399793  T   C   .   PASS    AF=0.623775 ES:SE:LP:AF:ID  6.90371e-05:0.000334598:0.0757207:0.623775:rs10399793
1   54676   rs2462492   C   T   .   PASS    AF=0.4004   ES:SE:LP:AF:ID  2.24037e-05:0.00033144:0.0222764:0.4004:rs2462492
1   86028   rs114608975 T   C   .   PASS    AF=0.103554 ES:SE:LP:AF:ID  -3.74126e-05:0.000529949:0.0268721:0.103554:rs114608975
1   91536   rs6702460   G   T   .   PASS    AF=0.456851 ES:SE:LP:AF:ID  -0.000135053:0.000326347:0.167491:0.456851:rs6702460
1   534192  rs6680723   C   T   .   PASS    AF=0.240953 ES:SE:LP:AF:ID  7.07122e-05:0.000372816:0.0705811:0.240953:rs6680723
1   693731  rs12238997  A   G   .   PASS    AF=0.116345 ES:SE:LP:AF:ID  0.000303303:0.000312413:0.481486:0.116345:rs12238997
1   706368  rs12029736  A   G   .   PASS    AF=0.515623 ES:SE:LP:AF:ID  0.000386288:0.000231438:1.02228:0.515623:rs12029736
1   722670  rs116030099 T   C   .   PASS    AF=0.101232 ES:SE:LP:AF:ID  -0.00073281:0.000381778:1.25964:0.101232:rs116030099
1   729679  rs4951859   C   G   .   PASS    AF=0.843205 ES:SE:LP:AF:ID  -0.000265828:0.000270767:0.481486:0.843205:rs4951859
1   731718  rs58276399  T   C   .   PASS    AF=0.122325 ES:SE:LP:AF:ID  0.000379234:0.00029636:0.69897:0.122325:rs58276399
1   734349  rs141242758 T   C   .   PASS    AF=0.121569 ES:SE:LP:AF:ID  0.00038957:0.000296483:0.721246:0.121569:rs141242758
1   736289  rs79010578  T   A   .   PASS    AF=0.132336 ES:SE:LP:AF:ID  0.000283449:0.00029223:0.481486:0.132336:rs79010578
1   752566  rs3094315   G   A   .   PASS    AF=0.83894  ES:SE:LP:AF:ID  -0.000249659:0.000262219:0.468521:0.83894:rs3094315
1   752721  rs3131972   A   G   .   PASS    AF=0.838567 ES:SE:LP:AF:ID  -0.000234732:0.000261935:0.431798:0.838567:rs3131972
1   753405  rs3115860   C   A   .   PASS    AF=0.869759 ES:SE:LP:AF:ID  -0.000338164:0.000281063:0.638272:0.869759:rs3115860
1   753541  rs2073813   G   A   .   PASS    AF=0.129892 ES:SE:LP:AF:ID  0.000305777:0.000281636:0.552842:0.129892:rs2073813
1   754182  rs3131969   A   G   .   PASS    AF=0.869101 ES:SE:LP:AF:ID  -0.000299469:0.000280512:0.537602:0.869101:rs3131969
1   754192  rs3131968   A   G   .   PASS    AF=0.869199 ES:SE:LP:AF:ID  -0.000297434:0.000280624:0.537602:0.869199:rs3131968
1   754334  rs3131967   T   C   .   PASS    AF=0.869104 ES:SE:LP:AF:ID  -0.000299685:0.000280507:0.537602:0.869104:rs3131967
1   754503  rs3115859   G   A   .   PASS    AF=0.83802  ES:SE:LP:AF:ID  -0.000215522:0.000261209:0.387216:0.83802:rs3115859
1   754964  rs3131966   C   T   .   PASS    AF=0.83865  ES:SE:LP:AF:ID  -0.000218771:0.000261943:0.39794:0.83865:rs3131966
1   755775  rs3131965   A   G   .   PASS    AF=0.839764 ES:SE:LP:AF:ID  -0.000217382:0.000265484:0.387216:0.839764:rs3131965
1   755890  rs3115858   A   T   .   PASS    AF=0.869384 ES:SE:LP:AF:ID  -0.000325253:0.000280183:0.60206:0.869384:rs3115858
1   756604  rs3131962   A   G   .   PASS    AF=0.868931 ES:SE:LP:AF:ID  -0.000317494:0.000279478:0.585027:0.868931:rs3131962
1   757640  rs3115853   G   A   .   PASS    AF=0.867883 ES:SE:LP:AF:ID  -0.000311395:0.000278941:0.585027:0.867883:rs3115853
1   757734  rs4951929   C   T   .   PASS    AF=0.869075 ES:SE:LP:AF:ID  -0.000327277:0.000279707:0.619789:0.869075:rs4951929
1   757936  rs4951862   C   A   .   PASS    AF=0.869083 ES:SE:LP:AF:ID  -0.000326867:0.000279728:0.619789:0.869083:rs4951862
1   758144  rs3131956   A   G   .   PASS    AF=0.869091 ES:SE:LP:AF:ID  -0.000326048:0.000279735:0.619789:0.869091:rs3131956
1   758626  rs3131954   C   T   .   PASS    AF=0.869568 ES:SE:LP:AF:ID  -0.000326474:0.000280503:0.619789:0.869568:rs3131954
1   760912  rs1048488   C   T   .   PASS    AF=0.838301 ES:SE:LP:AF:ID  -0.000235676:0.000260714:0.431798:0.838301:rs1048488
1   761147  rs3115850   T   C   .   PASS    AF=0.838422 ES:SE:LP:AF:ID  -0.000239669:0.000260898:0.443698:0.838422:rs3115850
1   761732  rs2286139   C   T   .   PASS    AF=0.862245 ES:SE:LP:AF:ID  -0.000306923:0.00027873:0.568636:0.862245:rs2286139
1   763394  rs3115847   G   A   .   PASS    AF=0.706732 ES:SE:LP:AF:ID  -9.81767e-05:0.000271334:0.142668:0.706732:rs3115847
1   766007  rs61768174  A   C   .   PASS    AF=0.105154 ES:SE:LP:AF:ID  0.000376682:0.000312577:0.638272:0.105154:rs61768174
1   768253  rs2977608   A   C   .   PASS    AF=0.761315 ES:SE:LP:AF:ID  0.00015134:0.000221473:0.309804:0.761315:rs2977608
1   768448  rs12562034  G   A   .   PASS    AF=0.106459 ES:SE:LP:AF:ID  -0.000740259:0.000305282:1.82391:0.106459:rs12562034
1   769223  rs60320384  C   G   .   PASS    AF=0.129596 ES:SE:LP:AF:ID  0.000369938:0.000281467:0.721246:0.129596:rs60320384
1   771823  rs2977605   T   C   .   PASS    AF=0.868891 ES:SE:LP:AF:ID  -0.000378059:0.000279966:0.744727:0.868891:rs2977605
1   771967  rs59066358  G   A   .   PASS    AF=0.129697 ES:SE:LP:AF:ID  0.000360041:0.000281286:0.69897:0.129697:rs59066358
1   772755  rs2905039   A   C   .   PASS    AF=0.868901 ES:SE:LP:AF:ID  -0.000388631:0.000279971:0.769551:0.868901:rs2905039
1   776546  rs12124819  A   G   .   PASS    AF=0.265394 ES:SE:LP:AF:ID  -1.02403e-05:0.000247362:0.0132283:0.265394:rs12124819
1   777122  rs2980319   A   T   .   PASS    AF=0.870021 ES:SE:LP:AF:ID  -0.000372138:0.000280541:0.744727:0.870021:rs2980319
1   777232  rs112618790 C   T   .   PASS    AF=0.095119 ES:SE:LP:AF:ID  -0.000775069:0.000325181:1.76955:0.095119:rs112618790
1   778745  rs1055606   A   G   .   PASS    AF=0.128598 ES:SE:LP:AF:ID  0.000376372:0.000281648:0.744727:0.128598:rs1055606
1   779322  rs4040617   A   G   .   PASS    AF=0.128894 ES:SE:LP:AF:ID  0.000375377:0.00028117:0.744727:0.128894:rs4040617
1   780785  rs2977612   T   A   .   PASS    AF=0.868766 ES:SE:LP:AF:ID  -0.000353894:0.000279799:0.677781:0.868766:rs2977612
1   781845  rs61768199  A   G   .   PASS    AF=0.101887 ES:SE:LP:AF:ID  0.000366199:0.000317029:0.60206:0.101887:rs61768199
1   782981  rs6594026   C   T   .   PASS    AF=0.129533 ES:SE:LP:AF:ID  0.000343065:0.000281085:0.657577:0.129533:rs6594026
1   785050  rs2905062   G   A   .   PASS    AF=0.868519 ES:SE:LP:AF:ID  -0.00036598:0.000279733:0.721246:0.868519:rs2905062
1   785989  rs2980300   T   C   .   PASS    AF=0.86846  ES:SE:LP:AF:ID  -0.000362406:0.000279908:0.69897:0.86846:rs2980300