Summary

Summary {data-width=650}

Manhattan plot

manhattan_plot

QQ plot

qq_plot

AF plot

af_plot

P-Z plot

pz_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/ukb-a-import/processed/ukb-a-336/ukb-a-336.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/ukb-a-import/processed/ukb-a-336/ldsc.txt \
--w-ld-chr /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/reference/eur_w_ld_chr/ 

Beginning analysis at Sun Feb 16 01:57:10 2020
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ukb-a-import/processed/ukb-a-336/ukb-a-336.vcf.gz ...
Read summary statistics for 10877936 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, 1281483 SNPs remain.
After merging with regression SNP LD, 1281483 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.1605 (0.006)
Lambda GC: 1.7288
Mean Chi^2: 2.1119
Intercept: 1.1199 (0.0127)
Ratio: 0.1079 (0.0114)
Analysis finished at Sun Feb 16 01:58:55 2020
Total time elapsed: 1.0m:44.97s

QC metrics

Metrics

Metrics

{
    "af_correlation": 0.9533,
    "inflation_factor": 1.4211,
    "mean_EFFECT": -0,
    "n": 307638,
    "n_snps": 10877936,
    "n_clumped_hits": 223,
    "n_p_sig": 27039,
    "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": 356865,
    "n_est": 306331.5775,
    "ratio_se_n": 0.9979,
    "mean_diff": -9.4964e-06,
    "ratio_diff": 2.8819,
    "sd_y_est1": 0.7781,
    "sd_y_est2": 0.7765,
    "r2_sum1": 0.0245,
    "r2_sum2": 0.0404,
    "r2_sum3": 0.0406,
    "r2_sum4": 0.0405,
    "ldsc_nsnp_merge_refpanel_ld": 1281483,
    "ldsc_nsnp_merge_regression_ld": 1281483,
    "ldsc_observed_scale_h2_beta": 0.1605,
    "ldsc_observed_scale_h2_se": 0.006,
    "ldsc_intercept_beta": 1.1199,
    "ldsc_intercept_se": 0.0127,
    "ldsc_lambda_gc": 1.7288,
    "ldsc_mean_chisq": 2.1119,
    "ldsc_ratio": 0.1078
}

Flags

name value
af_correlation FALSE
inflation_factor TRUE
n FALSE
is_snpid_non_unique FALSE
mean_EFFECT_nonfinite FALSE
mean_EFFECT_05 FALSE
mean_EFFECT_01 FALSE
mean_chisq TRUE
n_p_sig TRUE
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 10877936 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 8.598638e+00 5.745666e+00 1.00000e+00 4.000000e+00 8.000000e+00 1.300000e+01 2.200000e+01 <U+2587><U+2585><U+2583><U+2582><U+2582>
numeric POS 0 1.0000000 NA NA NA NA NA 7.911383e+07 5.624931e+07 8.28000e+02 3.287294e+07 6.988889e+07 1.148258e+08 2.492251e+08 <U+2587><U+2586><U+2585><U+2582><U+2581>
numeric EFFECT 0 1.0000000 NA NA NA NA NA -4.440000e-05 1.248670e-02 -1.46895e-01 -3.991300e-03 -1.250000e-05 3.956700e-03 1.616010e-01 <U+2581><U+2581><U+2587><U+2581><U+2581>
numeric SE 0 1.0000000 NA NA NA NA NA 8.544400e-03 8.092900e-03 1.96020e-03 2.421000e-03 4.649800e-03 1.242540e-02 4.416650e-02 <U+2587><U+2582><U+2581><U+2581><U+2581>
numeric PVAL 0 1.0000000 NA NA NA NA NA 4.421568e-01 3.041962e-01 0.00000e+00 1.642869e-01 4.213655e-01 7.051979e-01 1.000000e+00 <U+2587><U+2586><U+2585><U+2585><U+2585>
numeric PVAL_ztest 0 1.0000000 NA NA NA NA NA 4.421562e-01 3.041964e-01 0.00000e+00 1.642863e-01 4.213657e-01 7.051981e-01 1.000000e+00 <U+2587><U+2586><U+2585><U+2585><U+2585>
numeric AF 0 1.0000000 NA NA NA NA NA 1.820865e-01 2.503832e-01 1.00090e-03 6.878700e-03 5.191440e-02 2.739880e-01 9.989990e-01 <U+2587><U+2582><U+2581><U+2581><U+2581>
numeric AF_reference 356865 0.9671937 NA NA NA NA NA 1.877709e-01 2.439191e-01 0.00000e+00 5.191700e-03 7.468050e-02 2.873400e-01 1.000000e+00 <U+2587><U+2582><U+2581><U+2581><U+2581>
numeric N 0 1.0000000 NA NA NA NA NA 3.076380e+05 0.000000e+00 3.07638e+05 3.076380e+05 3.076380e+05 3.076380e+05 3.076380e+05 <U+2581><U+2581><U+2587><U+2581><U+2581>

Head and tail

CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
1 693731 rs12238997 A G -0.0073530 0.0032726 0.0246519 0.0246512 0.1169260 0.1417730 307638
1 717587 rs144155419 G A 0.0070179 0.0087859 0.4244241 0.4244233 0.0143862 0.0045926 307638
1 730087 rs148120343 T C -0.0051152 0.0045597 0.2619293 0.2619276 0.0554733 0.0127796 307638
1 731718 rs142557973 T C -0.0068955 0.0031041 0.0263227 0.0263218 0.1216580 0.1543530 307638
1 734349 rs141242758 T C -0.0072219 0.0031059 0.0200595 0.0200589 0.1215130 0.1525560 307638
1 740284 rs61770167 C T -0.0162206 0.0142021 0.2534031 0.2534013 0.0058556 0.0023962 307638
1 742813 rs112573343 C T -0.0287914 0.0263295 0.2741751 0.2741728 0.0015525 0.1030350 307638
1 753405 rs3115860 C A 0.0064681 0.0029508 0.0283831 0.0283821 0.8706760 0.7517970 307638
1 753541 rs2073813 G A -0.0056296 0.0029582 0.0570388 0.0570371 0.1288330 0.3019170 307638
1 754182 rs3131969 A G 0.0061214 0.0029476 0.0378242 0.0378240 0.8703180 0.6785140 307638
CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
22 51219387 rs9616832 T C 0.0014404 0.0038006 0.7046996 0.7046989 0.0729806 0.0654952 307638
22 51219704 rs147475742 G A -0.0018026 0.0050970 0.7235974 0.7235973 0.0418225 0.0473243 307638
22 51219766 rs182321900 C T -0.0539142 0.0260353 0.0383778 0.0383764 0.0014546 NA 307638
22 51220088 rs566371895 G A -0.0321043 0.0171594 0.0613536 0.0613527 0.0039843 0.0003994 307638
22 51220146 rs868950473 C T -0.0507345 0.0256402 0.0478498 0.0478488 0.0015139 NA 307638
22 51221731 rs115055839 T C 0.0011703 0.0038032 0.7583034 0.7583023 0.0728101 0.0625000 307638
22 51223637 rs375798137 G A 0.0079628 0.0044803 0.0755197 0.0755188 0.0540289 0.0788738 307638
22 51226692 rs150189434 G A -0.0458503 0.0266347 0.0851707 0.0851692 0.0013983 0.0155751 307638
22 51229805 rs9616985 T C 0.0008319 0.0038179 0.8275110 0.8275103 0.0727671 0.0730831 307638
22 51237063 rs3896457 T C -0.0014702 0.0023245 0.5270684 0.5270683 0.2968410 0.2050720 307638

bcf preview

1   693731  rs12238997  A   G   .   PASS    AF=0.116926 ES:SE:LP:AF:SS:ID   -0.00735303:0.00327263:1.60815:0.116926:307638:rs12238997
1   717587  rs144155419 G   A   .   PASS    AF=0.0143862    ES:SE:LP:AF:SS:ID   0.00701792:0.0087859:0.3722:0.0143862:307638:rs144155419
1   730087  rs148120343 T   C   .   PASS    AF=0.0554733    ES:SE:LP:AF:SS:ID   -0.00511524:0.00455966:0.581816:0.0554733:307638:rs148120343
1   731718  rs58276399  T   C   .   PASS    AF=0.121658 ES:SE:LP:AF:SS:ID   -0.00689552:0.00310409:1.57967:0.121658:307638:rs58276399
1   734349  rs141242758 T   C   .   PASS    AF=0.121513 ES:SE:LP:AF:SS:ID   -0.00722193:0.00310588:1.69768:0.121513:307638:rs141242758
1   740284  rs61770167  C   T   .   PASS    AF=0.00585559   ES:SE:LP:AF:SS:ID   -0.0162206:0.0142021:0.596188:0.00585559:307638:rs61770167
1   742813  rs112573343 C   T   .   PASS    AF=0.0015525    ES:SE:LP:AF:SS:ID   -0.0287914:0.0263295:0.561972:0.0015525:307638:rs112573343
1   753405  rs3115860   C   A   .   PASS    AF=0.870676 ES:SE:LP:AF:SS:ID   0.00646809:0.00295082:1.54694:0.870676:307638:rs3115860
1   753541  rs2073813   G   A   .   PASS    AF=0.128833 ES:SE:LP:AF:SS:ID   -0.00562957:0.00295822:1.24383:0.128833:307638:rs2073813
1   754182  rs3131969   A   G   .   PASS    AF=0.870318 ES:SE:LP:AF:SS:ID   0.00612145:0.0029476:1.42223:0.870318:307638:rs3131969
1   754192  rs3131968   A   G   .   PASS    AF=0.870409 ES:SE:LP:AF:SS:ID   0.00618633:0.00294903:1.44457:0.870409:307638:rs3131968
1   754334  rs3131967   T   C   .   PASS    AF=0.870037 ES:SE:LP:AF:SS:ID   0.00619481:0.0029475:1.44881:0.870037:307638:rs3131967
1   754433  rs150578204 G   A   .   PASS    AF=0.00465304   ES:SE:LP:AF:SS:ID   0.00476762:0.0150536:0.124091:0.00465304:307638:rs150578204
1   754458  rs142682604 G   T   .   PASS    AF=0.00464711   ES:SE:LP:AF:SS:ID   0.00456258:0.0150926:0.117806:0.00464711:307638:rs142682604
1   755435  rs184270342 T   G   .   PASS    AF=0.00590897   ES:SE:LP:AF:SS:ID   5.61428e-06:0.014661:0.000132914:0.00590897:307638:rs184270342
1   755890  rs3115858   A   T   .   PASS    AF=0.870329 ES:SE:LP:AF:SS:ID   0.00621327:0.00294245:1.4594:0.870329:307638:rs3115858
1   756604  rs3131962   A   G   .   PASS    AF=0.87002  ES:SE:LP:AF:SS:ID   0.00608443:0.00293534:1.41805:0.87002:307638:rs3131962
1   757640  rs3115853   G   A   .   PASS    AF=0.869421 ES:SE:LP:AF:SS:ID   0.00573117:0.00293245:1.29538:0.869421:307638:rs3115853
1   757734  rs4951929   C   T   .   PASS    AF=0.870219 ES:SE:LP:AF:SS:ID   0.00605168:0.00293782:1.40443:0.870219:307638:rs4951929
1   757936  rs4951862   C   A   .   PASS    AF=0.870219 ES:SE:LP:AF:SS:ID   0.00605154:0.00293803:1.40423:0.870219:307638:rs4951862
1   758144  rs3131956   A   G   .   PASS    AF=0.870222 ES:SE:LP:AF:SS:ID   0.00605755:0.00293813:1.40631:0.870222:307638:rs3131956
1   758626  rs3131954   C   T   .   PASS    AF=0.870396 ES:SE:LP:AF:SS:ID   0.00625274:0.00294566:1.47133:0.870396:307638:rs3131954
1   761732  rs2286139   C   T   .   PASS    AF=0.867743 ES:SE:LP:AF:SS:ID   0.00579386:0.00293159:1.31772:0.867743:307638:rs2286139
1   766007  rs61768174  A   C   .   PASS    AF=0.106958 ES:SE:LP:AF:SS:ID   -0.00939823:0.00326429:2.3992:0.106958:307638:rs61768174
1   768253  rs2977608   A   C   .   PASS    AF=0.763932 ES:SE:LP:AF:SS:ID   0.00420766:0.00232551:1.15244:0.763932:307638:rs2977608
1   768448  rs12562034  G   A   .   PASS    AF=0.105257 ES:SE:LP:AF:SS:ID   -0.000859218:0.00321031:0.102937:0.105257:307638:rs12562034
1   768819  rs12562811  C   T   .   PASS    AF=0.00692766   ES:SE:LP:AF:SS:ID   0.00822112:0.0119286:0.309182:0.00692766:307638:rs12562811
1   769223  rs60320384  C   G   .   PASS    AF=0.128651 ES:SE:LP:AF:SS:ID   -0.00566234:0.00295381:1.25772:0.128651:307638:rs60320384
1   769224  rs141644775 G   A   .   PASS    AF=0.00143239   ES:SE:LP:AF:SS:ID   -0.0554736:0.0277178:1.34339:0.00143239:307638:rs141644775
1   770181  rs146076599 A   G   .   PASS    AF=0.00907328   ES:SE:LP:AF:SS:ID   0.0108187:0.0112949:0.470898:0.00907328:307638:rs146076599
1   770377  rs112563271 A   T   .   PASS    AF=0.00692321   ES:SE:LP:AF:SS:ID   0.00938481:0.0119797:0.363115:0.00692321:307638:rs112563271
1   771823  rs2977605   T   C   .   PASS    AF=0.869934 ES:SE:LP:AF:SS:ID   0.00620434:0.00294074:1.45746:0.869934:307638:rs2977605
1   771967  rs59066358  G   A   .   PASS    AF=0.128709 ES:SE:LP:AF:SS:ID   -0.00549566:0.00295257:1.20273:0.128709:307638:rs59066358
1   772755  rs2905039   A   C   .   PASS    AF=0.870112 ES:SE:LP:AF:SS:ID   0.00616895:0.00294089:1.44446:0.870112:307638:rs2905039
1   774736  rs28830877  A   C   .   PASS    AF=0.998797 ES:SE:LP:AF:SS:ID   0.0702737:0.03029:1.69165:0.998797:307638:rs28830877
1   776556  rs151160018 C   T   .   PASS    AF=0.00851871   ES:SE:LP:AF:SS:ID   -0.00269704:0.0110337:0.0931841:0.00851871:307638:rs151160018
1   777122  rs2980319   A   T   .   PASS    AF=0.871122 ES:SE:LP:AF:SS:ID   0.00644368:0.00294578:1.54194:0.871122:307638:rs2980319
1   777232  rs112618790 C   T   .   PASS    AF=0.0961319    ES:SE:LP:AF:SS:ID   -0.000953466:0.00339984:0.108386:0.0961319:307638:rs112618790
1   778745  rs1055606   A   G   .   PASS    AF=0.127871 ES:SE:LP:AF:SS:ID   -0.00568499:0.0029554:1.26435:0.127871:307638:rs1055606
1   779322  rs4040617   A   G   .   PASS    AF=0.127984 ES:SE:LP:AF:SS:ID   -0.0056975:0.00295139:1.27122:0.127984:307638:rs4040617
1   780785  rs2977612   T   A   .   PASS    AF=0.870455 ES:SE:LP:AF:SS:ID   0.0060842:0.00294103:1.41373:0.870455:307638:rs2977612
1   781367  rs149821290 A   C   .   PASS    AF=0.00989772   ES:SE:LP:AF:SS:ID   0.00936105:0.0104745:0.430061:0.00989772:307638:rs149821290
1   781845  rs61768199  A   G   .   PASS    AF=0.1044   ES:SE:LP:AF:SS:ID   -0.00991453:0.00330728:2.56548:0.1044:307638:rs61768199
1   782721  rs185280546 G   A   .   PASS    AF=0.0143713    ES:SE:LP:AF:SS:ID   0.0266894:0.00895108:2.5426:0.0143713:307638:rs185280546
1   782981  rs6594026   C   T   .   PASS    AF=0.128338 ES:SE:LP:AF:SS:ID   -0.00548498:0.00295317:1.19882:0.128338:307638:rs6594026
1   783193  rs145767270 G   C   .   PASS    AF=0.0143639    ES:SE:LP:AF:SS:ID   0.0272231:0.00899074:2.60858:0.0143639:307638:rs145767270
1   783194  rs138555831 G   T   .   PASS    AF=0.0143713    ES:SE:LP:AF:SS:ID   0.0270652:0.00898963:2.58393:0.0143713:307638:rs138555831
1   783711  rs184266993 G   A   .   PASS    AF=0.00541372   ES:SE:LP:AF:SS:ID   0.0194866:0.014323:0.760273:0.00541372:307638:rs184266993
1   785050  rs2905062   G   A   .   PASS    AF=0.87014  ES:SE:LP:AF:SS:ID   0.00595667:0.00294138:1.368:0.87014:307638:rs2905062
1   785989  rs2980300   T   C   .   PASS    AF=0.87009  ES:SE:LP:AF:SS:ID   0.00604618:0.00294325:1.39846:0.87009:307638:rs2980300