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/ieu-a-import/processed/ieu-a-1123/ieu-a-1123.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/ieu-a-import/processed/ieu-a-1123/ldsc.txt \
--w-ld-chr /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/reference/eur_w_ld_chr/ 

Beginning analysis at Wed Feb  5 08:27:52 2020
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ieu-a-import/processed/ieu-a-1123/ieu-a-1123.vcf.gz ...
Read summary statistics for 15448819 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, 1218946 SNPs remain.
After merging with regression SNP LD, 1218946 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.0332 (0.0108)
Lambda GC: 1.0291
Mean Chi^2: 1.033
Intercept: 1.0059 (0.0065)
Ratio: 0.18 (0.1955)
Analysis finished at Wed Feb  5 08:30:21 2020
Total time elapsed: 2.0m:29.56s

QC metrics

Metrics

Metrics

{
    "af_correlation": 0.9603,
    "inflation_factor": 1.0388,
    "mean_EFFECT": -1.0272,
    "n": 42358,
    "n_snps": 15448819,
    "n_clumped_hits": 3,
    "n_p_sig": 61,
    "n_mono": 0,
    "n_ns": 779736,
    "n_mac": 302038,
    "is_snpid_unique": false,
    "n_miss_EFFECT": 0,
    "n_miss_SE": 0,
    "n_miss_PVAL": 0,
    "n_miss_AF": 1266,
    "n_miss_AF_reference": 160955,
    "n_est": 40785.9939,
    "ratio_se_n": 0.9813,
    "mean_diff": 1.0215,
    "ratio_diff": 6.449,
    "sd_y_est1": 6.3686,
    "sd_y_est2": 6.2493,
    "r2_sum1": 0.0862,
    "r2_sum2": 0.0021,
    "r2_sum3": 0.0022,
    "r2_sum4": 0.0025,
    "ldsc_nsnp_merge_refpanel_ld": 1218946,
    "ldsc_nsnp_merge_regression_ld": 1218946,
    "ldsc_observed_scale_h2_beta": 0.0332,
    "ldsc_observed_scale_h2_se": 0.0108,
    "ldsc_intercept_beta": 1.0059,
    "ldsc_intercept_se": 0.0065,
    "ldsc_lambda_gc": 1.0291,
    "ldsc_mean_chisq": 1.033,
    "ldsc_ratio": 0.1788
}

Flags

name value
af_correlation FALSE
inflation_factor FALSE
n FALSE
is_snpid_non_unique TRUE
mean_EFFECT_nonfinite FALSE
mean_EFFECT_05 TRUE
mean_EFFECT_01 TRUE
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 numeric.mean numeric.sd numeric.p0 numeric.p25 numeric.p50 numeric.p75 numeric.p100 numeric.hist
character ID 0 1.0000000 3 47 0 15448817 0 NA NA NA NA NA NA NA NA
character REF 0 1.0000000 1 101 0 37547 0 NA NA NA NA NA NA NA NA
character ALT 0 1.0000000 1 105 0 18055 0 NA NA NA NA NA NA NA NA
numeric CHROM 0 1.0000000 NA NA NA NA NA 8.892523e+00 6.252719e+00 1.0000e+00 4.000000e+00 7.000000e+00 1.400000e+01 2.400000e+01 ▇▆▂▃▂
numeric POS 0 1.0000000 NA NA NA NA NA 7.931533e+07 5.682943e+07 5.6000e+01 3.251308e+07 6.964479e+07 1.158420e+08 2.492402e+08 ▇▆▅▂▁
numeric EFFECT 0 1.0000000 NA NA NA NA NA -1.027220e+00 4.288595e+00 -2.0390e+01 -1.153000e-01 -3.185000e-03 8.659000e-02 2.042000e+01 ▁▁▇▁▁
numeric SE 0 1.0000000 NA NA NA NA NA 2.309321e+00 1.104609e+01 6.9380e-04 5.531000e-02 1.588000e-01 6.295000e-01 1.000000e+03 ▇▁▁▁▁
numeric PVAL 0 1.0000000 NA NA NA NA NA 4.937827e-01 2.883951e-01 0.0000e+00 2.435000e-01 4.918005e-01 7.422992e-01 1.000000e+00 ▇▇▇▇▇
numeric PVAL_ztest 0 1.0000000 NA NA NA NA NA 4.938810e-01 2.883609e-01 0.0000e+00 2.436904e-01 4.918968e-01 7.423521e-01 1.000000e+00 ▇▇▇▇▇
numeric AF 1266 0.9999181 NA NA NA NA NA 1.549907e-01 2.455523e-01 0.0000e+00 2.134000e-03 2.092000e-02 2.098000e-01 9.999840e-01 ▇▁▁▁▁
numeric AF_reference 160955 0.9895814 NA NA NA NA NA 1.547524e-01 2.330127e-01 0.0000e+00 2.649000e-03 3.214860e-02 2.158550e-01 1.000000e+00 ▇▁▁▁▁
numeric N 0 1.0000000 NA NA NA NA NA 4.235800e+04 0.000000e+00 4.2358e+04 4.235800e+04 4.235800e+04 4.235800e+04 4.235800e+04 ▁▁▇▁▁

Head and tail

CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
1 10616 rs376342519 CCGCCGTTGCAAAGGCGCGCCG C 0.28000 0.32830 0.3936996 0.3937267 0.991000 0.9930110 42358
1 14933 rs199856693 G A 0.35270 0.17200 0.0403404 0.0403077 0.047970 0.0283546 42358
1 15774 rs374029747 G A -0.37130 0.49890 0.4567999 0.4567329 0.006579 0.0119808 42358
1 16949 rs199745162 A C -0.31030 0.26090 0.2342001 0.2343041 0.016750 0.0139776 42358
1 51479 rs116400033 T A 0.12530 0.07780 0.1073999 0.1072801 0.232100 0.1281950 42358
1 52185 rs201374420 TTAA T 1.08900 1.88100 0.5627001 0.5626247 0.005882 0.0053914 42358
1 54353 rs140052487 C A -4.76100 2.45000 0.0519398 0.0519841 0.001339 0.0089856 42358
1 54490 rs141149254 G A 0.02623 0.08831 0.7663991 0.7664498 0.166100 0.0960463 42358
1 55164 rs3091274 C A -0.09709 0.25860 0.7073999 0.7073298 0.980700 0.9233230 42358
1 55326 rs3107975 T C 0.41930 0.51180 0.4126996 0.4126350 0.028260 0.0459265 42358
CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
23 154925895 rs538470 C T -0.10190 0.05473 0.0626498 0.0626218 0.252700 0.3634440 42358
23 154926376 rs116490668 C T -2.48400 1.28700 0.0535797 0.0535982 0.001859 0.0349669 42358
23 154926843 rs192521690 T C 1.18200 0.55870 0.0344001 0.0343767 0.002532 0.0007947 42358
23 154927185 rs185685661 T C -0.13430 0.09219 0.1450999 0.1451788 0.139300 0.1796030 42358
23 154927199 rs645904 C T -0.09040 0.05281 0.0869601 0.0869341 0.248000 0.3674170 42358
23 154927581 rs644138 G A -0.05429 0.05113 0.2883002 0.2883250 0.299900 0.4635760 42358
23 154929412 rs557132 C T -0.08721 0.05284 0.0988394 0.0988501 0.250400 0.3568210 42358
23 154929952 rs4012982 CAA C -0.09005 0.05290 0.0887095 0.0887051 0.250900 0.3165560 42358
23 154930230 rs781880 A G -0.08933 0.05316 0.0928710 0.0928798 0.249000 0.3618540 42358
24 13537468 rs7203107 A G -0.07663 0.30300 0.8003000 0.8003422 0.985590 NA 42358

bcf preview

1   10616   rs376342519 CCGCCGTTGCAAAGGCGCGCCG  C   .   PASS    AF=0.991    ES:SE:LP:AF:SS:ID   0.28:0.3283:0.404835:0.991:42358:rs376342519
1   14933   rs199856693 G   A   .   PASS    AF=0.04797  ES:SE:LP:AF:SS:ID   0.3527:0.172:1.39426:0.04797:42358:rs199856693
1   15774   rs374029747 G   A   .   PASS    AF=0.006579 ES:SE:LP:AF:SS:ID   -0.3713:0.4989:0.340274:0.006579:42358:rs374029747
1   16949   rs199745162 A   C   .   PASS    AF=0.01675  ES:SE:LP:AF:SS:ID   -0.3103:0.2609:0.630413:0.01675:42358:rs199745162
1   51479   rs116400033 T   A   .   PASS    AF=0.2321   ES:SE:LP:AF:SS:ID   0.1253:0.0778:0.968996:0.2321:42358:rs116400033
1   52185   rs201374420 TTAA    T   .   PASS    AF=0.005882 ES:SE:LP:AF:SS:ID   1.089:1.881:0.249723:0.005882:42358:rs201374420
1   54353   rs140052487 C   A   .   PASS    AF=0.001339 ES:SE:LP:AF:SS:ID   -4.761:2.45:1.2845:0.001339:42358:rs140052487
1   54490   rs141149254 G   A   .   PASS    AF=0.1661   ES:SE:LP:AF:SS:ID   0.02623:0.08831:0.115545:0.1661:42358:rs141149254
1   55164   rs3091274   C   A   .   PASS    AF=0.9807   ES:SE:LP:AF:SS:ID   -0.09709:0.2586:0.150335:0.9807:42358:rs3091274
1   55326   rs3107975   T   C   .   PASS    AF=0.02826  ES:SE:LP:AF:SS:ID   0.4193:0.5118:0.384366:0.02826:42358:rs3107975
1   55545   rs28396308  C   T   .   PASS    AF=0.2248   ES:SE:LP:AF:SS:ID   -0.1245:0.08674:0.820448:0.2248:42358:rs28396308
1   57183   rs368339209 A   G   .   PASS    AF=0.0007041    ES:SE:LP:AF:SS:ID   -10.63:5.506:1.27181:0.0007041:42358:rs368339209
1   57292   rs201418760 C   T   .   PASS    AF=0.02393  ES:SE:LP:AF:SS:ID   0.5589:0.225:1.88639:0.02393:42358:rs201418760
1   58814   rs114420996 G   A   .   PASS    AF=0.1003   ES:SE:LP:AF:SS:ID   -0.2003:0.126:0.950782:0.1003:42358:rs114420996
1   61543   rs201849102 T   C   .   PASS    AF=0.0003079    ES:SE:LP:AF:SS:ID   -9.867:9.686:0.510886:0.0003079:42358:rs201849102
1   61743   rs184286948 G   C   .   PASS    AF=0.009155 ES:SE:LP:AF:SS:ID   -0.5203:0.451:0.604499:0.009155:42358:rs184286948
1   61920   rs62637820  G   A   .   PASS    AF=0.02945  ES:SE:LP:AF:SS:ID   -0.4016:0.2279:1.10752:0.02945:42358:rs62637820
1   63093   rs200092917 G   A   .   PASS    AF=0.0207   ES:SE:LP:AF:SS:ID   -0.0713:0.2791:0.0978339:0.0207:42358:rs200092917
1   64649   rs181431124 A   C   .   PASS    AF=0.02715  ES:SE:LP:AF:SS:ID   -0.2457:0.2405:0.512862:0.02715:42358:rs181431124
1   66219   rs181028663 A   T   .   PASS    AF=0.01624  ES:SE:LP:AF:SS:ID   0.114:0.2811:0.164309:0.01624:42358:rs181028663
1   68082   rs367789441 T   C   .   PASS    AF=0.06526  ES:SE:LP:AF:SS:ID   -0.06815:0.1373:0.207819:0.06526:42358:rs367789441
1   68596   rs372212855 T   G   .   PASS    AF=0.003797 ES:SE:LP:AF:SS:ID   -0.1426:0.5311:0.103308:0.003797:42358:rs372212855
1   69428   rs140739101 T   G   .   PASS    AF=0.04215  ES:SE:LP:AF:SS:ID   0.169:0.1613:0.53062:0.04215:42358:rs140739101
1   69534   rs190717287 T   C   .   PASS    AF=0.0003164    ES:SE:LP:AF:SS:ID   -3.875:3.649:0.540306:0.0003164:42358:rs190717287
1   69761   rs200505207 A   T   .   PASS    AF=0.06821  ES:SE:LP:AF:SS:ID   -0.07658:0.1337:0.246494:0.06821:42358:rs200505207
1   69897   rs200676709 T   C   .   PASS    AF=0.7661   ES:SE:LP:AF:SS:ID   0.006396:0.08559:0.0266874:0.7661:42358:rs200676709
1   72297   rs200651397 G   GTAT    .   PASS    AF=0.006341 ES:SE:LP:AF:SS:ID   -0.7853:0.5625:0.788612:0.006341:42358:rs200651397
1   74790   rs13328700  C   G   .   PASS    AF=0.03421  ES:SE:LP:AF:SS:ID   0.1427:0.1728:0.388277:0.03421:42358:rs13328700
1   74792   rs13328684  G   A   .   PASS    AF=0.03421  ES:SE:LP:AF:SS:ID   0.1427:0.1728:0.388277:0.03421:42358:rs13328684
1   76854   rs367666799 A   G   .   PASS    AF=0.06856  ES:SE:LP:AF:SS:ID   -0.0275:0.1442:0.0712458:0.06856:42358:rs367666799
1   78942   rs372315362 C   G   .   PASS    AF=0.01116  ES:SE:LP:AF:SS:ID   -3.472:3.312:0.530915:0.01116:42358:rs372315362
1   80454   rs144226842 G   C   .   PASS    AF=0.0004404    ES:SE:LP:AF:SS:ID   -20.05:46.11:0.178028:0.0004404:42358:rs144226842
1   81590   rs202072409 AC  A   .   PASS    AF=0.004955 ES:SE:LP:AF:SS:ID   -2.178:5.523:0.159016:0.004955:42358:rs202072409
1   82163   rs139113303 G   A   .   PASS    AF=0.06791  ES:SE:LP:AF:SS:ID   -0.0171:0.1449:0.0428239:0.06791:42358:rs139113303
1   82609   rs149189449 C   G   .   PASS    AF=0.06818  ES:SE:LP:AF:SS:ID   -0.00912:0.1444:0.0224593:0.06818:42358:rs149189449
1   83514   rs201754587 C   T   .   PASS    AF=0.3501   ES:SE:LP:AF:SS:ID   0.05985:0.07732:0.357634:0.3501:42358:rs201754587
1   84139   rs183605470 A   T   .   PASS    AF=0.02132  ES:SE:LP:AF:SS:ID   -0.8462:0.3311:1.97469:0.02132:42358:rs183605470
1   86028   rs114608975 T   C   .   PASS    AF=0.04742  ES:SE:LP:AF:SS:ID   0.1391:0.1605:0.413413:0.04742:42358:rs114608975
1   86065   rs116504101 G   C   .   PASS    AF=0.06995  ES:SE:LP:AF:SS:ID   -0.03918:0.1445:0.104467:0.06995:42358:rs116504101
1   86331   rs115209712 A   G   .   PASS    AF=0.1018   ES:SE:LP:AF:SS:ID   0.05045:0.1193:0.172308:0.1018:42358:rs115209712
1   87021   rs188486692 T   C   .   PASS    AF=0.00763  ES:SE:LP:AF:SS:ID   0.3442:0.3698:0.453581:0.00763:42358:rs188486692
1   87360   rs180907504 C   T   .   PASS    AF=0.01853  ES:SE:LP:AF:SS:ID   -0.02265:0.2527:0.0321713:0.01853:42358:rs180907504
1   87409   rs139490478 C   T   .   PASS    AF=0.07088  ES:SE:LP:AF:SS:ID   -0.03322:0.1429:0.0882034:0.07088:42358:rs139490478
1   88169   rs940550    C   T   .   PASS    AF=0.2022   ES:SE:LP:AF:SS:ID   -0.0112:0.08254:0.0496351:0.2022:42358:rs940550
1   88172   rs940551    G   A   .   PASS    AF=0.06423  ES:SE:LP:AF:SS:ID   -0.07115:0.1394:0.214955:0.06423:42358:rs940551
1   88177   rs143215837 G   C   .   PASS    AF=0.06377  ES:SE:LP:AF:SS:ID   -0.07459:0.1402:0.225702:0.06377:42358:rs143215837
1   88188   rs148331237 C   A   .   PASS    AF=0.007142 ES:SE:LP:AF:SS:ID   -0.291:0.4134:0.317494:0.007142:42358:rs148331237
1   88236   rs186918018 C   T   .   PASS    AF=0.01279  ES:SE:LP:AF:SS:ID   0.1908:0.6481:0.114413:0.01279:42358:rs186918018
1   88316   rs113759966 G   A   .   PASS    AF=0.06376  ES:SE:LP:AF:SS:ID   -0.05208:0.1318:0.159455:0.06376:42358:rs113759966
1   88338   rs55700207  G   A   .   PASS    AF=0.08209  ES:SE:LP:AF:SS:ID   -0.5333:0.1472:3.53626:0.08209:42358:rs55700207