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/dev/ukb-a-import/processed/ukb-a-31/ukb-a-31.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-31/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 02:58:26 2020
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ukb-a-import/processed/ukb-a-31/ukb-a-31.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: 0.1099 (0.0051)
Lambda GC: 1.3689
Mean Chi^2: 1.4225
Intercept: 1.0575 (0.0088)
Ratio: 0.136 (0.0209)
Analysis finished at Sun Feb 16 03:00:12 2020
Total time elapsed: 1.0m:46.53s

QC metrics

Metrics

Metrics

{
    "af_correlation": 0.9533,
    "inflation_factor": 1.2343,
    "mean_EFFECT": -0.0001,
    "n": 172454,
    "n_snps": 10877936,
    "n_clumped_hits": 15,
    "n_p_sig": 536,
    "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": 171829.3801,
    "ratio_se_n": 0.9982,
    "mean_diff": -0.0001,
    "ratio_diff": 15.5863,
    "sd_y_est1": 0.458,
    "sd_y_est2": 0.4572,
    "r2_sum1": 0.0006,
    "r2_sum2": 0.0031,
    "r2_sum3": 0.0031,
    "r2_sum4": 0.0031,
    "ldsc_nsnp_merge_refpanel_ld": 1281483,
    "ldsc_nsnp_merge_regression_ld": 1281483,
    "ldsc_observed_scale_h2_beta": 0.1099,
    "ldsc_observed_scale_h2_se": 0.0051,
    "ldsc_intercept_beta": 1.0575,
    "ldsc_intercept_se": 0.0088,
    "ldsc_lambda_gc": 1.3689,
    "ldsc_mean_chisq": 1.4225,
    "ldsc_ratio": 0.1361
}

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 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 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 ▇▅▃▂▂
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 ▇▆▅▂▁
numeric EFFECT 0 1.0000000 NA NA NA NA NA -8.430000e-05 9.624200e-03 -1.26657e-01 -2.880100e-03 -4.250000e-05 2.768200e-03 1.135870e-01 ▁▁▇▁▁
numeric SE 0 1.0000000 NA NA NA NA NA 6.717600e-03 6.364500e-03 1.53940e-03 1.903300e-03 3.655500e-03 9.767200e-03 3.396810e-02 ▇▂▁▁▁
numeric PVAL 0 1.0000000 NA NA NA NA NA 4.657218e-01 2.980587e-01 0.00000e+00 1.983960e-01 4.536428e-01 7.237374e-01 1.000000e+00 ▇▆▆▆▆
numeric PVAL_ztest 0 1.0000000 NA NA NA NA NA 4.657208e-01 2.980592e-01 0.00000e+00 1.983947e-01 4.536419e-01 7.237363e-01 9.999999e-01 ▇▆▆▆▆
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 ▇▂▁▁▁
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 ▇▂▁▁▁
numeric N 0 1.0000000 NA NA NA NA NA 1.724540e+05 0.000000e+00 1.72454e+05 1.724540e+05 1.724540e+05 1.724540e+05 1.724540e+05 ▁▁▇▁▁

Head and tail

CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
1 693731 rs12238997 A G -0.0008011 0.0025689 0.7551531 0.7551522 0.1169260 0.1417730 172454
1 717587 rs144155419 G A 0.0034721 0.0069155 0.6156105 0.6156096 0.0143862 0.0045926 172454
1 730087 rs148120343 T C -0.0024094 0.0035760 0.5004688 0.5004679 0.0554733 0.0127796 172454
1 731718 rs142557973 T C -0.0018392 0.0024404 0.4510514 0.4510495 0.1216580 0.1543530 172454
1 734349 rs141242758 T C -0.0017875 0.0024417 0.4641379 0.4641377 0.1215130 0.1525560 172454
1 740284 rs61770167 C T -0.0077871 0.0111369 0.4844188 0.4844175 0.0058556 0.0023962 172454
1 742813 rs112573343 C T -0.0053626 0.0215681 0.8036440 0.8036437 0.0015525 0.1030350 172454
1 753405 rs3115860 C A 0.0029491 0.0023199 0.2036611 0.2036587 0.8706760 0.7517970 172454
1 753541 rs2073813 G A -0.0030904 0.0023259 0.1839628 0.1839616 0.1288330 0.3019170 172454
1 754182 rs3131969 A G 0.0030290 0.0023174 0.1912000 0.1911976 0.8703180 0.6785140 172454
CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
22 51219387 rs9616832 T C 0.0007110 0.0029904 0.8120579 0.8120571 0.0729806 0.0654952 172454
22 51219704 rs147475742 G A 0.0012175 0.0040062 0.7612039 0.7612045 0.0418225 0.0473243 172454
22 51219766 rs182321900 C T 0.0217183 0.0205019 0.2894490 0.2894490 0.0014546 NA 172454
22 51220088 rs566371895 G A 0.0026164 0.0134149 0.8453641 0.8453635 0.0039843 0.0003994 172454
22 51220146 rs868950473 C T 0.0174842 0.0201620 0.3858398 0.3858402 0.0015139 NA 172454
22 51221731 rs115055839 T C 0.0007676 0.0029917 0.7975200 0.7975202 0.0728101 0.0625000 172454
22 51223637 rs375798137 G A -0.0035217 0.0035338 0.3189686 0.3189676 0.0540289 0.0788738 172454
22 51226692 rs150189434 G A 0.0191422 0.0208986 0.3596889 0.3596899 0.0013983 0.0155751 172454
22 51229805 rs9616985 T C 0.0007263 0.0030026 0.8088580 0.8088577 0.0727671 0.0730831 172454
22 51237063 rs3896457 T C 0.0015668 0.0018286 0.3915363 0.3915343 0.2968410 0.2050720 172454

bcf preview

1   693731  rs12238997  A   G   .   PASS    AF=0.116926 ES:SE:LP:AF:SS:ID   -0.000801107:0.00256886:0.121965:0.116926:172454:rs12238997
1   717587  rs144155419 G   A   .   PASS    AF=0.0143862    ES:SE:LP:AF:SS:ID   0.00347214:0.00691548:0.210694:0.0143862:172454:rs144155419
1   730087  rs148120343 T   C   .   PASS    AF=0.0554733    ES:SE:LP:AF:SS:ID   -0.00240935:0.00357601:0.300623:0.0554733:172454:rs148120343
1   731718  rs58276399  T   C   .   PASS    AF=0.121658 ES:SE:LP:AF:SS:ID   -0.00183924:0.00244039:0.345774:0.121658:172454:rs58276399
1   734349  rs141242758 T   C   .   PASS    AF=0.121513 ES:SE:LP:AF:SS:ID   -0.00178747:0.00244173:0.333353:0.121513:172454:rs141242758
1   740284  rs61770167  C   T   .   PASS    AF=0.00585559   ES:SE:LP:AF:SS:ID   -0.00778709:0.0111369:0.314779:0.00585559:172454:rs61770167
1   742813  rs112573343 C   T   .   PASS    AF=0.0015525    ES:SE:LP:AF:SS:ID   -0.00536257:0.0215681:0.0949363:0.0015525:172454:rs112573343
1   753405  rs3115860   C   A   .   PASS    AF=0.870676 ES:SE:LP:AF:SS:ID   0.0029491:0.00231994:0.691092:0.870676:172454:rs3115860
1   753541  rs2073813   G   A   .   PASS    AF=0.128833 ES:SE:LP:AF:SS:ID   -0.00309036:0.00232593:0.73527:0.128833:172454:rs2073813
1   754182  rs3131969   A   G   .   PASS    AF=0.870318 ES:SE:LP:AF:SS:ID   0.00302901:0.00231745:0.718512:0.870318:172454:rs3131969
1   754192  rs3131968   A   G   .   PASS    AF=0.870409 ES:SE:LP:AF:SS:ID   0.00304454:0.00231876:0.723118:0.870409:172454:rs3131968
1   754334  rs3131967   T   C   .   PASS    AF=0.870037 ES:SE:LP:AF:SS:ID   0.00301805:0.00231741:0.714891:0.870037:172454:rs3131967
1   754433  rs150578204 G   A   .   PASS    AF=0.00465304   ES:SE:LP:AF:SS:ID   -0.0298522:0.0118341:1.93362:0.00465304:172454:rs150578204
1   754458  rs142682604 G   T   .   PASS    AF=0.00464711   ES:SE:LP:AF:SS:ID   -0.0295784:0.0118717:1.89547:0.00464711:172454:rs142682604
1   755435  rs184270342 T   G   .   PASS    AF=0.00590897   ES:SE:LP:AF:SS:ID   0.0221152:0.0115414:1.25692:0.00590897:172454:rs184270342
1   755890  rs3115858   A   T   .   PASS    AF=0.870329 ES:SE:LP:AF:SS:ID   0.00297151:0.00231344:0.701184:0.870329:172454:rs3115858
1   756604  rs3131962   A   G   .   PASS    AF=0.87002  ES:SE:LP:AF:SS:ID   0.00306896:0.00230761:0.736262:0.87002:172454:rs3131962
1   757640  rs3115853   G   A   .   PASS    AF=0.869421 ES:SE:LP:AF:SS:ID   0.00289239:0.00230568:0.678451:0.869421:172454:rs3115853
1   757734  rs4951929   C   T   .   PASS    AF=0.870219 ES:SE:LP:AF:SS:ID   0.00297484:0.00230964:0.703897:0.870219:172454:rs4951929
1   757936  rs4951862   C   A   .   PASS    AF=0.870219 ES:SE:LP:AF:SS:ID   0.00296584:0.0023098:0.700852:0.870219:172454:rs4951862
1   758144  rs3131956   A   G   .   PASS    AF=0.870222 ES:SE:LP:AF:SS:ID   0.0029866:0.0023099:0.707682:0.870222:172454:rs3131956
1   758626  rs3131954   C   T   .   PASS    AF=0.870396 ES:SE:LP:AF:SS:ID   0.0029478:0.00231605:0.692286:0.870396:172454:rs3131954
1   761732  rs2286139   C   T   .   PASS    AF=0.867743 ES:SE:LP:AF:SS:ID   0.00313851:0.00230426:0.761487:0.867743:172454:rs2286139
1   766007  rs61768174  A   C   .   PASS    AF=0.106958 ES:SE:LP:AF:SS:ID   -0.00212867:0.00256463:0.390902:0.106958:172454:rs61768174
1   768253  rs2977608   A   C   .   PASS    AF=0.763932 ES:SE:LP:AF:SS:ID   0.00167089:0.00182878:0.442619:0.763932:172454:rs2977608
1   768448  rs12562034  G   A   .   PASS    AF=0.105257 ES:SE:LP:AF:SS:ID   0.000384652:0.00252022:0.0561628:0.105257:172454:rs12562034
1   768819  rs12562811  C   T   .   PASS    AF=0.00692766   ES:SE:LP:AF:SS:ID   -0.00308399:0.009455:0.128257:0.00692766:172454:rs12562811
1   769223  rs60320384  C   G   .   PASS    AF=0.128651 ES:SE:LP:AF:SS:ID   -0.00298038:0.00232273:0.700177:0.128651:172454:rs60320384
1   769224  rs141644775 G   A   .   PASS    AF=0.00143239   ES:SE:LP:AF:SS:ID   -0.0178942:0.0216965:0.387731:0.00143239:172454:rs141644775
1   770181  rs146076599 A   G   .   PASS    AF=0.00907328   ES:SE:LP:AF:SS:ID   0.00210453:0.0089009:0.0898608:0.00907328:172454:rs146076599
1   770377  rs112563271 A   T   .   PASS    AF=0.00692321   ES:SE:LP:AF:SS:ID   -0.00372235:0.00950063:0.157886:0.00692321:172454:rs112563271
1   771823  rs2977605   T   C   .   PASS    AF=0.869934 ES:SE:LP:AF:SS:ID   0.00279167:0.00231205:0.643473:0.869934:172454:rs2977605
1   771967  rs59066358  G   A   .   PASS    AF=0.128709 ES:SE:LP:AF:SS:ID   -0.00288532:0.00232136:0.669805:0.128709:172454:rs59066358
1   772755  rs2905039   A   C   .   PASS    AF=0.870112 ES:SE:LP:AF:SS:ID   0.00281587:0.0023122:0.651131:0.870112:172454:rs2905039
1   774736  rs28830877  A   C   .   PASS    AF=0.998797 ES:SE:LP:AF:SS:ID   0.000342927:0.0245743:0.00486256:0.998797:172454:rs28830877
1   776556  rs151160018 C   T   .   PASS    AF=0.00851871   ES:SE:LP:AF:SS:ID   0.00215061:0.00866634:0.0947369:0.00851871:172454:rs151160018
1   777122  rs2980319   A   T   .   PASS    AF=0.871122 ES:SE:LP:AF:SS:ID   0.00287667:0.00231627:0.669057:0.871122:172454:rs2980319
1   777232  rs112618790 C   T   .   PASS    AF=0.0961319    ES:SE:LP:AF:SS:ID   0.000281426:0.00266851:0.0381003:0.0961319:172454:rs112618790
1   778745  rs1055606   A   G   .   PASS    AF=0.127871 ES:SE:LP:AF:SS:ID   -0.00280465:0.00232405:0.642994:0.127871:172454:rs1055606
1   779322  rs4040617   A   G   .   PASS    AF=0.127984 ES:SE:LP:AF:SS:ID   -0.00263146:0.00232114:0.590194:0.127984:172454:rs4040617
1   780785  rs2977612   T   A   .   PASS    AF=0.870455 ES:SE:LP:AF:SS:ID   0.00292479:0.00231216:0.686369:0.870455:172454:rs2977612
1   781367  rs149821290 A   C   .   PASS    AF=0.00989772   ES:SE:LP:AF:SS:ID   -0.00490044:0.00814859:0.261549:0.00989772:172454:rs149821290
1   781845  rs61768199  A   G   .   PASS    AF=0.1044   ES:SE:LP:AF:SS:ID   -0.00254257:0.002597:0.484709:0.1044:172454:rs61768199
1   782721  rs185280546 G   A   .   PASS    AF=0.0143713    ES:SE:LP:AF:SS:ID   0.00669994:0.0070654:0.464717:0.0143713:172454:rs185280546
1   782981  rs6594026   C   T   .   PASS    AF=0.128338 ES:SE:LP:AF:SS:ID   -0.00279703:0.0023216:0.641515:0.128338:172454:rs6594026
1   783193  rs145767270 G   C   .   PASS    AF=0.0143639    ES:SE:LP:AF:SS:ID   0.00756502:0.00710188:0.54245:0.0143639:172454:rs145767270
1   783194  rs138555831 G   T   .   PASS    AF=0.0143713    ES:SE:LP:AF:SS:ID   0.00748816:0.00710124:0.53512:0.0143713:172454:rs138555831
1   783711  rs184266993 G   A   .   PASS    AF=0.00541372   ES:SE:LP:AF:SS:ID   -0.00192734:0.0112786:0.063328:0.00541372:172454:rs184266993
1   785050  rs2905062   G   A   .   PASS    AF=0.87014  ES:SE:LP:AF:SS:ID   0.00282649:0.00231245:0.654432:0.87014:172454:rs2905062
1   785989  rs2980300   T   C   .   PASS    AF=0.87009  ES:SE:LP:AF:SS:ID   0.00282598:0.00231404:0.653647:0.87009:172454:rs2980300