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-489/ukb-a-489.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-489/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 01:55:56 2020
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ukb-a-import/processed/ukb-a-489/ukb-a-489.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: 0.088 (0.0047)
Lambda GC: 1.2376
Mean Chi^2: 1.2976
Intercept: 1.0299 (0.0084)
Ratio: 0.1004 (0.0283)
Analysis finished at Sun Feb 16 01:57:44 2020
Total time elapsed: 1.0m:47.72s

QC metrics

Metrics

Metrics

{
    "af_correlation": 0.9533,
    "inflation_factor": 1.1335,
    "mean_EFFECT": -0,
    "n": 154702,
    "n_snps": 10877936,
    "n_clumped_hits": 43,
    "n_p_sig": 1335,
    "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": 154180.928,
    "ratio_se_n": 0.9983,
    "mean_diff": -0,
    "ratio_diff": 11.6216,
    "sd_y_est1": 0.4748,
    "sd_y_est2": 0.474,
    "r2_sum1": 0.0029,
    "r2_sum2": 0.0129,
    "r2_sum3": 0.0129,
    "r2_sum4": 0.013,
    "ldsc_nsnp_merge_refpanel_ld": 1281483,
    "ldsc_nsnp_merge_regression_ld": 1281483,
    "ldsc_observed_scale_h2_beta": 0.088,
    "ldsc_observed_scale_h2_se": 0.0047,
    "ldsc_intercept_beta": 1.0299,
    "ldsc_intercept_se": 0.0084,
    "ldsc_lambda_gc": 1.2376,
    "ldsc_mean_chisq": 1.2976,
    "ldsc_ratio": 0.1005
}

Flags

name value
af_correlation FALSE
inflation_factor FALSE
n FALSE
is_snpid_non_unique FALSE
mean_EFFECT_nonfinite FALSE
mean_EFFECT_05 FALSE
mean_EFFECT_01 FALSE
mean_chisq FALSE
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 -1.820000e-05 1.024510e-02 -1.25282e-01 -2.946800e-03 3.800000e-06 2.955700e-03 1.195370e-01 <U+2581><U+2581><U+2587><U+2581><U+2581>
numeric SE 0 1.0000000 NA NA NA NA NA 7.354500e-03 6.969100e-03 1.68530e-03 2.083300e-03 4.001300e-03 1.069280e-02 3.991860e-02 <U+2587><U+2582><U+2581><U+2581><U+2581>
numeric PVAL 0 1.0000000 NA NA NA NA NA 4.794596e-01 2.950838e-01 0.00000e+00 2.193618e-01 4.726863e-01 7.352584e-01 1.000000e+00 <U+2587><U+2587><U+2587><U+2586><U+2586>
numeric PVAL_ztest 0 1.0000000 NA NA NA NA NA 4.794585e-01 2.950844e-01 0.00000e+00 2.193605e-01 4.726852e-01 7.352574e-01 1.000000e+00 <U+2587><U+2587><U+2587><U+2586><U+2586>
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 1.547020e+05 0.000000e+00 1.54702e+05 1.547020e+05 1.547020e+05 1.547020e+05 1.547020e+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 0.0006330 0.0028210 0.8224451 0.8224444 0.1169260 0.1417730 154702
1 717587 rs144155419 G A -0.0001009 0.0075729 0.9893720 0.9893721 0.0143862 0.0045926 154702
1 730087 rs148120343 T C -0.0008611 0.0039274 0.8264559 0.8264561 0.0554733 0.0127796 154702
1 731718 rs142557973 T C 0.0000421 0.0026771 0.9874590 0.9874594 0.1216580 0.1543530 154702
1 734349 rs141242758 T C 0.0002480 0.0026787 0.9262340 0.9262341 0.1215130 0.1525560 154702
1 740284 rs61770167 C T -0.0041834 0.0123016 0.7338056 0.7338041 0.0058556 0.0023962 154702
1 742813 rs112573343 C T 0.0411531 0.0228425 0.0716094 0.0716080 0.0015525 0.1030350 154702
1 753405 rs3115860 C A -0.0003347 0.0025439 0.8953351 0.8953351 0.8706760 0.7517970 154702
1 753541 rs2073813 G A -0.0002532 0.0025503 0.9209230 0.9209227 0.1288330 0.3019170 154702
1 754182 rs3131969 A G -0.0000370 0.0025407 0.9883830 0.9883833 0.8703180 0.6785140 154702
CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
22 51219387 rs9616832 T C -0.0018673 0.0032770 0.5688110 0.5688099 0.0729806 0.0654952 154702
22 51219704 rs147475742 G A -0.0024978 0.0043909 0.5694636 0.5694620 0.0418225 0.0473243 154702
22 51219766 rs182321900 C T 0.0079372 0.0222358 0.7211241 0.7211235 0.0014546 NA 154702
22 51220088 rs566371895 G A -0.0118237 0.0146704 0.4202696 0.4202681 0.0039843 0.0003994 154702
22 51220146 rs868950473 C T 0.0134098 0.0219251 0.5407917 0.5407901 0.0015139 NA 154702
22 51221731 rs115055839 T C -0.0016717 0.0032802 0.6103163 0.6103158 0.0728101 0.0625000 154702
22 51223637 rs375798137 G A 0.0004513 0.0038641 0.9070190 0.9070191 0.0540289 0.0788738 154702
22 51226692 rs150189434 G A 0.0098831 0.0229354 0.6665335 0.6665339 0.0013983 0.0155751 154702
22 51229805 rs9616985 T C -0.0016828 0.0032931 0.6093418 0.6093402 0.0727671 0.0730831 154702
22 51237063 rs3896457 T C -0.0018418 0.0019999 0.3570738 0.3570712 0.2968410 0.2050720 154702

bcf preview

1   693731  rs12238997  A   G   .   PASS    AF=0.116926 ES:SE:LP:AF:SS:ID   0.000633043:0.00282102:0.0848931:0.116926:154702:rs12238997
1   717587  rs144155419 G   A   .   PASS    AF=0.0143862    ES:SE:LP:AF:SS:ID   -0.000100874:0.00757286:0.00464038:0.0143862:154702:rs144155419
1   730087  rs148120343 T   C   .   PASS    AF=0.0554733    ES:SE:LP:AF:SS:ID   -0.000861074:0.00392738:0.0827803:0.0554733:154702:rs148120343
1   731718  rs58276399  T   C   .   PASS    AF=0.121658 ES:SE:LP:AF:SS:ID   4.20789e-05:0.00267713:0.00548093:0.121658:154702:rs58276399
1   734349  rs141242758 T   C   .   PASS    AF=0.121513 ES:SE:LP:AF:SS:ID   0.000248001:0.00267866:0.0332793:0.121513:154702:rs141242758
1   740284  rs61770167  C   T   .   PASS    AF=0.00585559   ES:SE:LP:AF:SS:ID   -0.0041834:0.0123016:0.134419:0.00585559:154702:rs61770167
1   742813  rs112573343 C   T   .   PASS    AF=0.0015525    ES:SE:LP:AF:SS:ID   0.0411531:0.0228425:1.14503:0.0015525:154702:rs112573343
1   753405  rs3115860   C   A   .   PASS    AF=0.870676 ES:SE:LP:AF:SS:ID   -0.000334664:0.00254388:0.0480144:0.870676:154702:rs3115860
1   753541  rs2073813   G   A   .   PASS    AF=0.128833 ES:SE:LP:AF:SS:ID   -0.000253171:0.00255029:0.0357767:0.128833:154702:rs2073813
1   754182  rs3131969   A   G   .   PASS    AF=0.870318 ES:SE:LP:AF:SS:ID   -3.69924e-05:0.0025407:0.00507473:0.870318:154702:rs3131969
1   754192  rs3131968   A   G   .   PASS    AF=0.870409 ES:SE:LP:AF:SS:ID   -1.58994e-05:0.00254206:0.00217255:0.870409:154702:rs3131968
1   754334  rs3131967   T   C   .   PASS    AF=0.870037 ES:SE:LP:AF:SS:ID   -3.30205e-05:0.00254065:0.00452715:0.870037:154702:rs3131967
1   754433  rs150578204 G   A   .   PASS    AF=0.00465304   ES:SE:LP:AF:SS:ID   -0.00165436:0.012904:0.04673:0.00465304:154702:rs150578204
1   754458  rs142682604 G   T   .   PASS    AF=0.00464711   ES:SE:LP:AF:SS:ID   -0.00231563:0.0129404:0.0665228:0.00464711:154702:rs142682604
1   755435  rs184270342 T   G   .   PASS    AF=0.00590897   ES:SE:LP:AF:SS:ID   0.0116971:0.0126948:0.447528:0.00590897:154702:rs184270342
1   755890  rs3115858   A   T   .   PASS    AF=0.870329 ES:SE:LP:AF:SS:ID   -0.000434285:0.00253665:0.0634546:0.870329:154702:rs3115858
1   756604  rs3131962   A   G   .   PASS    AF=0.87002  ES:SE:LP:AF:SS:ID   -0.000345155:0.00253062:0.0498728:0.87002:154702:rs3131962
1   757640  rs3115853   G   A   .   PASS    AF=0.869421 ES:SE:LP:AF:SS:ID   0.000106299:0.00252746:0.0148193:0.869421:154702:rs3115853
1   757734  rs4951929   C   T   .   PASS    AF=0.870219 ES:SE:LP:AF:SS:ID   -0.00041052:0.00253265:0.0598647:0.870219:154702:rs4951929
1   757936  rs4951862   C   A   .   PASS    AF=0.870219 ES:SE:LP:AF:SS:ID   -0.000412357:0.00253284:0.0601449:0.870219:154702:rs4951862
1   758144  rs3131956   A   G   .   PASS    AF=0.870222 ES:SE:LP:AF:SS:ID   -0.00041232:0.00253293:0.0601369:0.870222:154702:rs3131956
1   758626  rs3131954   C   T   .   PASS    AF=0.870396 ES:SE:LP:AF:SS:ID   -0.000361126:0.00253953:0.0521151:0.870396:154702:rs3131954
1   761732  rs2286139   C   T   .   PASS    AF=0.867743 ES:SE:LP:AF:SS:ID   -0.00040789:0.00252634:0.0596155:0.867743:154702:rs2286139
1   766007  rs61768174  A   C   .   PASS    AF=0.106958 ES:SE:LP:AF:SS:ID   0.000504028:0.00281712:0.0665107:0.106958:154702:rs61768174
1   768253  rs2977608   A   C   .   PASS    AF=0.763932 ES:SE:LP:AF:SS:ID   -0.00047084:0.00200334:0.0892753:0.763932:154702:rs2977608
1   768448  rs12562034  G   A   .   PASS    AF=0.105257 ES:SE:LP:AF:SS:ID   0.000168225:0.00275727:0.0216597:0.105257:154702:rs12562034
1   768819  rs12562811  C   T   .   PASS    AF=0.00692766   ES:SE:LP:AF:SS:ID   0.0149795:0.0102897:0.837262:0.00692766:154702:rs12562811
1   769223  rs60320384  C   G   .   PASS    AF=0.128651 ES:SE:LP:AF:SS:ID   0.000269703:0.0025473:0.0382567:0.128651:154702:rs60320384
1   769224  rs141644775 G   A   .   PASS    AF=0.00143239   ES:SE:LP:AF:SS:ID   -0.0082079:0.0234309:0.138996:0.00143239:154702:rs141644775
1   770181  rs146076599 A   G   .   PASS    AF=0.00907328   ES:SE:LP:AF:SS:ID   0.0049932:0.00966427:0.217965:0.00907328:154702:rs146076599
1   770377  rs112563271 A   T   .   PASS    AF=0.00692321   ES:SE:LP:AF:SS:ID   0.0156403:0.0103375:0.885096:0.00692321:154702:rs112563271
1   771823  rs2977605   T   C   .   PASS    AF=0.869934 ES:SE:LP:AF:SS:ID   -0.000448328:0.00253588:0.0656682:0.869934:154702:rs2977605
1   771967  rs59066358  G   A   .   PASS    AF=0.128709 ES:SE:LP:AF:SS:ID   0.000215026:0.00254645:0.0302552:0.128709:154702:rs59066358
1   772755  rs2905039   A   C   .   PASS    AF=0.870112 ES:SE:LP:AF:SS:ID   -0.000513558:0.00253615:0.0759638:0.870112:154702:rs2905039
1   774736  rs28830877  A   C   .   PASS    AF=0.998797 ES:SE:LP:AF:SS:ID   -0.0330512:0.0262653:0.681386:0.998797:154702:rs28830877
1   776556  rs151160018 C   T   .   PASS    AF=0.00851871   ES:SE:LP:AF:SS:ID   0.00973966:0.0094994:0.515377:0.00851871:154702:rs151160018
1   777122  rs2980319   A   T   .   PASS    AF=0.871122 ES:SE:LP:AF:SS:ID   9.58742e-06:0.00254067:0.00130963:0.871122:154702:rs2980319
1   777232  rs112618790 C   T   .   PASS    AF=0.0961319    ES:SE:LP:AF:SS:ID   -0.0012315:0.00292564:0.171466:0.0961319:154702:rs112618790
1   778745  rs1055606   A   G   .   PASS    AF=0.127871 ES:SE:LP:AF:SS:ID   -0.000285124:0.0025492:0.0405083:0.127871:154702:rs1055606
1   779322  rs4040617   A   G   .   PASS    AF=0.127984 ES:SE:LP:AF:SS:ID   -0.000299334:0.00254565:0.0426825:0.127984:154702:rs4040617
1   780785  rs2977612   T   A   .   PASS    AF=0.870455 ES:SE:LP:AF:SS:ID   0.000223611:0.00253565:0.0316441:0.870455:154702:rs2977612
1   781367  rs149821290 A   C   .   PASS    AF=0.00989772   ES:SE:LP:AF:SS:ID   0.0101154:0.00893558:0.589019:0.00989772:154702:rs149821290
1   781845  rs61768199  A   G   .   PASS    AF=0.1044   ES:SE:LP:AF:SS:ID   9.47153e-05:0.00285401:0.0116524:0.1044:154702:rs61768199
1   782721  rs185280546 G   A   .   PASS    AF=0.0143713    ES:SE:LP:AF:SS:ID   -0.00453409:0.00771916:0.254185:0.0143713:154702:rs185280546
1   782981  rs6594026   C   T   .   PASS    AF=0.128338 ES:SE:LP:AF:SS:ID   -0.000350877:0.00254641:0.0504129:0.128338:154702:rs6594026
1   783193  rs145767270 G   C   .   PASS    AF=0.0143639    ES:SE:LP:AF:SS:ID   -0.00562925:0.00775349:0.329918:0.0143639:154702:rs145767270
1   783194  rs138555831 G   T   .   PASS    AF=0.0143713    ES:SE:LP:AF:SS:ID   -0.00563317:0.00775235:0.330267:0.0143713:154702:rs138555831
1   783711  rs184266993 G   A   .   PASS    AF=0.00541372   ES:SE:LP:AF:SS:ID   0.00773422:0.0123705:0.274227:0.00541372:154702:rs184266993
1   785050  rs2905062   G   A   .   PASS    AF=0.87014  ES:SE:LP:AF:SS:ID   0.000220278:0.00253651:0.0311455:0.87014:154702:rs2905062
1   785989  rs2980300   T   C   .   PASS    AF=0.87009  ES:SE:LP:AF:SS:ID   0.000239767:0.00253831:0.0339785:0.87009:154702:rs2980300