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-1231/ieu-a-1231.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-1231/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 09:31:15 2020
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ieu-a-import/processed/ieu-a-1231/ieu-a-1231.vcf.gz ...
Read summary statistics for 15474559 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, 1218951 SNPs remain.
After merging with regression SNP LD, 1218951 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.0309 (0.0116)
Lambda GC: 1.029
Mean Chi^2: 1.0355
Intercept: 1.0096 (0.0066)
Ratio: 0.2688 (0.1865)
Analysis finished at Wed Feb  5 09:33:46 2020
Total time elapsed: 2.0m:31.8s

QC metrics

Metrics

Metrics

{
    "af_correlation": 0.9603,
    "inflation_factor": 1.0378,
    "mean_EFFECT": -0.7292,
    "n": 43507,
    "n_snps": 15474559,
    "n_clumped_hits": 6,
    "n_p_sig": 194,
    "n_mono": 0,
    "n_ns": 780195,
    "n_mac": 302162,
    "is_snpid_unique": false,
    "n_miss_EFFECT": 0,
    "n_miss_SE": 0,
    "n_miss_PVAL": 0,
    "n_miss_AF": 1471,
    "n_miss_AF_reference": 161101,
    "n_est": 41940.2575,
    "ratio_se_n": 0.9818,
    "mean_diff": 0.7259,
    "ratio_diff": 4.9156,
    "sd_y_est1": 4.9005,
    "sd_y_est2": 4.8115,
    "r2_sum1": 0.1736,
    "r2_sum2": 0.0072,
    "r2_sum3": 0.0075,
    "r2_sum4": 0.008,
    "ldsc_nsnp_merge_refpanel_ld": 1218951,
    "ldsc_nsnp_merge_regression_ld": 1218951,
    "ldsc_observed_scale_h2_beta": 0.0309,
    "ldsc_observed_scale_h2_se": 0.0116,
    "ldsc_intercept_beta": 1.0096,
    "ldsc_intercept_se": 0.0066,
    "ldsc_lambda_gc": 1.029,
    "ldsc_mean_chisq": 1.0355,
    "ldsc_ratio": 0.2704
}

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 15474557 0 NA NA NA NA NA NA NA NA
character REF 0 1.0000000 1 101 0 37571 0 NA NA NA NA NA NA NA NA
character ALT 0 1.0000000 1 105 0 18054 0 NA NA NA NA NA NA NA NA
numeric CHROM 0 1.0000000 NA NA NA NA NA 8.892507e+00 6.252512e+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 7.931341e+07 5.682786e+07 5.6000e+01 3.251421e+07 6.964105e+07 1.158363e+08 2.492402e+08 ▇▆▅▂▁
numeric EFFECT 0 1.0000000 NA NA NA NA NA -7.292033e-01 3.643806e+00 -2.0380e+01 -8.238000e-02 -1.334000e-03 6.809000e-02 2.037000e+01 ▁▁▇▁▁
numeric SE 0 1.0000000 NA NA NA NA NA 1.763965e+00 1.016326e+01 1.7860e-03 4.201000e-02 1.210000e-01 4.745000e-01 1.000000e+03 ▇▁▁▁▁
numeric PVAL 0 1.0000000 NA NA NA NA NA 4.940519e-01 2.890415e-01 0.0000e+00 2.422998e-01 4.919999e-01 7.440001e-01 1.000000e+00 ▇▇▇▇▇
numeric PVAL_ztest 0 1.0000000 NA NA NA NA NA 4.941238e-01 2.890130e-01 0.0000e+00 2.423954e-01 4.921045e-01 7.440083e-01 9.999998e-01 ▇▇▇▇▇
numeric AF 1471 0.9999049 NA NA NA NA NA 1.547536e-01 2.454409e-01 0.0000e+00 2.115000e-03 2.076000e-02 2.093000e-01 9.999880e-01 ▇▁▁▁▁
numeric AF_reference 161101 0.9895893 NA NA NA NA NA 1.545122e-01 2.329114e-01 0.0000e+00 2.595800e-03 3.194890e-02 2.152560e-01 1.000000e+00 ▇▁▁▁▁
numeric N 0 1.0000000 NA NA NA NA NA 4.350700e+04 0.000000e+00 4.3507e+04 4.350700e+04 4.350700e+04 4.350700e+04 4.350700e+04 ▁▁▇▁▁

Head and tail

CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
1 10616 rs376342519 CCGCCGTTGCAAAGGCGCGCCG C 0.20420 0.23940 0.3938003 0.3936783 0.991000 0.9930110 43507
1 14933 rs199856693 G A 0.22700 0.13500 0.0925508 0.0926694 0.047970 0.0283546 43507
1 15774 rs374029747 G A 0.16350 0.34650 0.6371006 0.6370257 0.006579 0.0119808 43507
1 16949 rs199745162 A C -0.18250 0.19450 0.3481000 0.3480885 0.016750 0.0139776 43507
1 51479 rs116400033 T A 0.13540 0.05893 0.0216202 0.0215822 0.232100 0.1281950 43507
1 52185 rs201374420 TTAA T 1.08900 1.88100 0.5627001 0.5626247 0.005882 0.0053914 43507
1 54353 rs140052487 C A -3.10600 1.32600 0.0191999 0.0191610 0.001339 0.0089856 43507
1 54490 rs141149254 G A 0.10550 0.06609 0.1103001 0.1104200 0.166100 0.0960463 43507
1 55164 rs3091274 C A 0.03015 0.20080 0.8806000 0.8806467 0.980700 0.9233230 43507
1 55326 rs3107975 T C 0.14270 0.37340 0.7023992 0.7023398 0.028260 0.0459265 43507
CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
23 154925895 rs538470 C T -0.09348 0.04144 0.0240802 0.0240837 0.252700 0.3634440 43507
23 154926376 rs116490668 C T -2.67500 1.01000 0.0081100 0.0080846 0.001859 0.0349669 43507
23 154926843 rs192521690 T C 0.52940 0.51450 0.3035002 0.3034984 0.002532 0.0007947 43507
23 154927185 rs185685661 T C -0.11290 0.06981 0.1057000 0.1058250 0.139300 0.1796030 43507
23 154927199 rs645904 C T -0.08822 0.04006 0.0276503 0.0276514 0.248000 0.3674170 43507
23 154927581 rs644138 G A -0.07539 0.03893 0.0527995 0.0528000 0.299900 0.4635760 43507
23 154929412 rs557132 C T -0.08548 0.04009 0.0329800 0.0329902 0.250400 0.3568210 43507
23 154929952 rs4012982 CAA C -0.08807 0.04013 0.0282001 0.0281910 0.250900 0.3165560 43507
23 154930230 rs781880 A G -0.08723 0.04033 0.0305499 0.0305484 0.249000 0.3618540 43507
24 13537468 rs7203107 A G -0.06493 0.21520 0.7629007 0.7628660 0.985590 NA 43507

bcf preview

1   10616   rs376342519 CCGCCGTTGCAAAGGCGCGCCG  C   .   PASS    AF=0.991    ES:SE:LP:AF:SS:ID   0.2042:0.2394:0.404724:0.991:43507:rs376342519
1   14933   rs199856693 G   A   .   PASS    AF=0.04797  ES:SE:LP:AF:SS:ID   0.227:0.135:1.03362:0.04797:43507:rs199856693
1   15774   rs374029747 G   A   .   PASS    AF=0.006579 ES:SE:LP:AF:SS:ID   0.1635:0.3465:0.195792:0.006579:43507:rs374029747
1   16949   rs199745162 A   C   .   PASS    AF=0.01675  ES:SE:LP:AF:SS:ID   -0.1825:0.1945:0.458296:0.01675:43507:rs199745162
1   51479   rs116400033 T   A   .   PASS    AF=0.2321   ES:SE:LP:AF:SS:ID   0.1354:0.05893:1.66514:0.2321:43507:rs116400033
1   52185   rs201374420 TTAA    T   .   PASS    AF=0.005882 ES:SE:LP:AF:SS:ID   1.089:1.881:0.249723:0.005882:43507:rs201374420
1   54353   rs140052487 C   A   .   PASS    AF=0.001339 ES:SE:LP:AF:SS:ID   -3.106:1.326:1.7167:0.001339:43507:rs140052487
1   54490   rs141149254 G   A   .   PASS    AF=0.1661   ES:SE:LP:AF:SS:ID   0.1055:0.06609:0.957424:0.1661:43507:rs141149254
1   55164   rs3091274   C   A   .   PASS    AF=0.9807   ES:SE:LP:AF:SS:ID   0.03015:0.2008:0.0552213:0.9807:43507:rs3091274
1   55326   rs3107975   T   C   .   PASS    AF=0.02826  ES:SE:LP:AF:SS:ID   0.1427:0.3734:0.153416:0.02826:43507:rs3107975
1   55545   rs28396308  C   T   .   PASS    AF=0.2248   ES:SE:LP:AF:SS:ID   -0.08563:0.06663:0.701584:0.2248:43507:rs28396308
1   57183   rs368339209 A   G   .   PASS    AF=0.0007041    ES:SE:LP:AF:SS:ID   -2.965:1.966:0.881074:0.0007041:43507:rs368339209
1   57292   rs201418760 C   T   .   PASS    AF=0.02393  ES:SE:LP:AF:SS:ID   0.3839:0.1736:1.56831:0.02393:43507:rs201418760
1   58814   rs114420996 G   A   .   PASS    AF=0.1003   ES:SE:LP:AF:SS:ID   -0.1837:0.09714:1.23203:0.1003:43507:rs114420996
1   61543   rs201849102 T   C   .   PASS    AF=0.0003079    ES:SE:LP:AF:SS:ID   -2.118:3.07:0.309538:0.0003079:43507:rs201849102
1   61743   rs184286948 G   C   .   PASS    AF=0.009155 ES:SE:LP:AF:SS:ID   -0.3941:0.3372:0.615288:0.009155:43507:rs184286948
1   61920   rs62637820  G   A   .   PASS    AF=0.02945  ES:SE:LP:AF:SS:ID   -0.1412:0.167:0.400226:0.02945:43507:rs62637820
1   63093   rs200092917 G   A   .   PASS    AF=0.0207   ES:SE:LP:AF:SS:ID   -0.1852:0.2186:0.401319:0.0207:43507:rs200092917
1   64649   rs181431124 A   C   .   PASS    AF=0.02715  ES:SE:LP:AF:SS:ID   -0.03743:0.1786:0.078834:0.02715:43507:rs181431124
1   66219   rs181028663 A   T   .   PASS    AF=0.01624  ES:SE:LP:AF:SS:ID   -0.06382:0.2244:0.110082:0.01624:43507:rs181028663
1   68082   rs367789441 T   C   .   PASS    AF=0.06526  ES:SE:LP:AF:SS:ID   0.03214:0.1034:0.121593:0.06526:43507:rs367789441
1   68596   rs372212855 T   G   .   PASS    AF=0.003797 ES:SE:LP:AF:SS:ID   -0.4358:0.429:0.509199:0.003797:43507:rs372212855
1   69428   rs140739101 T   G   .   PASS    AF=0.04215  ES:SE:LP:AF:SS:ID   0.06591:0.1277:0.217742:0.04215:43507:rs140739101
1   69534   rs190717287 T   C   .   PASS    AF=0.0003164    ES:SE:LP:AF:SS:ID   0.6108:1.117:0.233141:0.0003164:43507:rs190717287
1   69761   rs200505207 A   T   .   PASS    AF=0.06821  ES:SE:LP:AF:SS:ID   0.05411:0.1001:0.229958:0.06821:43507:rs200505207
1   69897   rs200676709 T   C   .   PASS    AF=0.7661   ES:SE:LP:AF:SS:ID   0.03599:0.06592:0.23277:0.7661:43507:rs200676709
1   72297   rs200651397 G   GTAT    .   PASS    AF=0.006341 ES:SE:LP:AF:SS:ID   -0.9492:0.4476:1.46903:0.006341:43507:rs200651397
1   74790   rs13328700  C   G   .   PASS    AF=0.03421  ES:SE:LP:AF:SS:ID   0.1009:0.1336:0.346595:0.03421:43507:rs13328700
1   74792   rs13328684  G   A   .   PASS    AF=0.03421  ES:SE:LP:AF:SS:ID   0.1009:0.1336:0.346595:0.03421:43507:rs13328684
1   76854   rs367666799 A   G   .   PASS    AF=0.06856  ES:SE:LP:AF:SS:ID   -0.04911:0.1117:0.18039:0.06856:43507:rs367666799
1   78942   rs372315362 C   G   .   PASS    AF=0.01116  ES:SE:LP:AF:SS:ID   -3.472:3.312:0.530915:0.01116:43507:rs372315362
1   80454   rs144226842 G   C   .   PASS    AF=0.0004404    ES:SE:LP:AF:SS:ID   -20.05:46.11:0.178028:0.0004404:43507:rs144226842
1   81590   rs202072409 AC  A   .   PASS    AF=0.004955 ES:SE:LP:AF:SS:ID   -2.178:5.523:0.159016:0.004955:43507:rs202072409
1   82163   rs139113303 G   A   .   PASS    AF=0.06791  ES:SE:LP:AF:SS:ID   -0.03923:0.1123:0.138585:0.06791:43507:rs139113303
1   82609   rs149189449 C   G   .   PASS    AF=0.06818  ES:SE:LP:AF:SS:ID   -0.03546:0.1119:0.124129:0.06818:43507:rs149189449
1   83514   rs201754587 C   T   .   PASS    AF=0.3501   ES:SE:LP:AF:SS:ID   0.05948:0.05966:0.496482:0.3501:43507:rs201754587
1   84139   rs183605470 A   T   .   PASS    AF=0.02132  ES:SE:LP:AF:SS:ID   -0.6666:0.2495:2.12182:0.02132:43507:rs183605470
1   86028   rs114608975 T   C   .   PASS    AF=0.04742  ES:SE:LP:AF:SS:ID   0.07329:0.1229:0.258927:0.04742:43507:rs114608975
1   86065   rs116504101 G   C   .   PASS    AF=0.06995  ES:SE:LP:AF:SS:ID   -0.0376:0.1115:0.133181:0.06995:43507:rs116504101
1   86331   rs115209712 A   G   .   PASS    AF=0.1018   ES:SE:LP:AF:SS:ID   -0.0436:0.09392:0.192127:0.1018:43507:rs115209712
1   87021   rs188486692 T   C   .   PASS    AF=0.00763  ES:SE:LP:AF:SS:ID   0.0993:0.2966:0.132061:0.00763:43507:rs188486692
1   87360   rs180907504 C   T   .   PASS    AF=0.01853  ES:SE:LP:AF:SS:ID   -0.103:0.193:0.226579:0.01853:43507:rs180907504
1   87409   rs139490478 C   T   .   PASS    AF=0.07088  ES:SE:LP:AF:SS:ID   -0.04341:0.1104:0.158453:0.07088:43507:rs139490478
1   88169   rs940550    C   T   .   PASS    AF=0.2022   ES:SE:LP:AF:SS:ID   -0.0198:0.06355:0.121823:0.2022:43507:rs940550
1   88172   rs940551    G   A   .   PASS    AF=0.06423  ES:SE:LP:AF:SS:ID   0.03454:0.1047:0.129947:0.06423:43507:rs940551
1   88177   rs143215837 G   C   .   PASS    AF=0.06377  ES:SE:LP:AF:SS:ID   0.03629:0.1053:0.136439:0.06377:43507:rs143215837
1   88188   rs148331237 C   A   .   PASS    AF=0.007142 ES:SE:LP:AF:SS:ID   -0.08224:0.2996:0.10585:0.007142:43507:rs148331237
1   88236   rs186918018 C   T   .   PASS    AF=0.01279  ES:SE:LP:AF:SS:ID   0.3509:0.4328:0.379239:0.01279:43507:rs186918018
1   88316   rs113759966 G   A   .   PASS    AF=0.06376  ES:SE:LP:AF:SS:ID   0.09221:0.09722:0.464833:0.06376:43507:rs113759966
1   88338   rs55700207  G   A   .   PASS    AF=0.08209  ES:SE:LP:AF:SS:ID   -0.3143:0.1097:2.38038:0.08209:43507:rs55700207