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-1127/ieu-a-1127.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-1127/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 08:55:57 2020
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ieu-a-import/processed/ieu-a-1127/ieu-a-1127.vcf.gz ...
Read summary statistics for 10179906 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, 1220210 SNPs remain.
After merging with regression SNP LD, 1220210 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.1353 (0.0123)
Lambda GC: 1.275
Mean Chi^2: 1.5319
Intercept: 1.075 (0.0111)
Ratio: 0.141 (0.0208)
Analysis finished at Wed Feb  5 08:57:34 2020
Total time elapsed: 1.0m:37.07s

QC metrics

Metrics

Metrics

{
    "af_correlation": 0.9512,
    "inflation_factor": 1.2085,
    "mean_EFFECT": -0.002,
    "n": 175475,
    "n_snps": 10179906,
    "n_clumped_hits": 108,
    "n_p_sig": 11599,
    "n_mono": 0,
    "n_ns": 620054,
    "n_mac": 0,
    "is_snpid_unique": false,
    "n_miss_EFFECT": 0,
    "n_miss_SE": 0,
    "n_miss_PVAL": 0,
    "n_miss_AF": 0,
    "n_miss_AF_reference": 131535,
    "n_est": 175935.0911,
    "ratio_se_n": 1.0013,
    "mean_diff": 0.0018,
    "ratio_diff": 2.5773,
    "sd_y_est1": 2.321,
    "sd_y_est2": 2.3241,
    "r2_sum1": 0.2745,
    "r2_sum2": 0.051,
    "r2_sum3": 0.0508,
    "r2_sum4": 0.057,
    "ldsc_nsnp_merge_refpanel_ld": 1220210,
    "ldsc_nsnp_merge_regression_ld": 1220210,
    "ldsc_observed_scale_h2_beta": 0.1353,
    "ldsc_observed_scale_h2_se": 0.0123,
    "ldsc_intercept_beta": 1.075,
    "ldsc_intercept_se": 0.0111,
    "ldsc_lambda_gc": 1.275,
    "ldsc_mean_chisq": 1.5319,
    "ldsc_ratio": 0.141
}

Flags

name value
af_correlation FALSE
inflation_factor TRUE
n FALSE
is_snpid_non_unique TRUE
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 1.000000 3 47 0 10179904 0 NA NA NA NA NA NA NA NA
character REF 0 1.000000 1 99 0 30504 0 NA NA NA NA NA NA NA NA
character ALT 0 1.000000 1 103 0 16155 0 NA NA NA NA NA NA NA NA
numeric CHROM 0 1.000000 NA NA NA NA NA 8.958341e+00 6.304093e+00 1.00000e+00 4.000000e+00 7.000000e+00 1.400000e+01 2.400000e+01 ▇▆▂▃▂
numeric POS 0 1.000000 NA NA NA NA NA 7.911777e+07 5.683111e+07 8.28000e+02 3.228412e+07 6.944297e+07 1.156280e+08 2.492385e+08 ▇▆▅▂▁
numeric EFFECT 0 1.000000 NA NA NA NA NA -1.980900e-03 2.679057e+00 -8.51528e+03 -1.140000e-02 -1.000000e-04 1.090000e-02 2.655000e+00 ▁▁▁▁▇
numeric SE 0 1.000000 NA NA NA NA NA 2.992480e-02 1.691162e+01 7.20000e-03 8.800000e-03 1.340000e-02 2.930000e-02 5.378630e+04 ▇▁▁▁▁
numeric PVAL 0 1.000000 NA NA NA NA NA 4.682382e-01 2.983315e-01 0.00000e+00 2.010000e-01 4.584004e-01 7.268001e-01 1.000000e+00 ▇▆▆▆▆
numeric PVAL_ztest 0 1.000000 NA NA NA NA NA 4.682415e-01 2.983383e-01 0.00000e+00 2.010210e-01 4.584635e-01 7.267572e-01 1.000000e+00 ▇▆▆▆▆
numeric AF 0 1.000000 NA NA NA NA NA 2.293849e-01 2.637829e-01 1.00000e-03 2.260000e-02 1.095000e-01 3.651000e-01 9.990000e-01 ▇▂▁▁▁
numeric AF_reference 131535 0.987079 NA NA NA NA NA 2.273079e-01 2.511891e-01 1.99700e-04 2.436100e-02 1.261980e-01 3.578270e-01 9.996010e-01 ▇▂▂▁▁
numeric N 0 1.000000 NA NA NA NA NA 1.754750e+05 0.000000e+00 1.75475e+05 1.754750e+05 1.754750e+05 1.754750e+05 1.754750e+05 ▁▁▇▁▁

Head and tail

CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
1 10616 rs376342519 CCGCCGTTGCAAAGGCGCGCCG C -0.0437 0.0645 0.4983001 0.4980765 0.9925 0.9930110 175475
1 14933 rs199856693 G A -0.0064 0.0334 0.8473000 0.8480424 0.0399 0.0283546 175475
1 15774 rs374029747 G A -0.2087 0.1051 0.0470100 0.0470635 0.0069 0.0119808 175475
1 16949 rs199745162 A C -0.0275 0.0580 0.6348995 0.6354016 0.0195 0.0139776 175475
1 51479 rs116400033 T A -0.0007 0.0150 0.9627001 0.9627789 0.2300 0.1281950 175475
1 52185 rs201374420 TTAA T -0.1028 0.1135 0.3654004 0.3650804 0.0066 0.0053914 175475
1 54490 rs141149254 G A -0.0051 0.0169 0.7632995 0.7628235 0.1678 0.0960463 175475
1 55164 rs3091274 C A 0.0805 0.0486 0.0978205 0.0976452 0.9808 0.9233230 175475
1 55326 rs3107975 T C 0.0310 0.0436 0.4773995 0.4770786 0.0247 0.0459265 175475
1 55545 rs28396308 C T -0.0130 0.0197 0.5106002 0.5093190 0.2298 0.2392170 175475
CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
23 154925045 rs509981 C T 0.0018 0.0089 0.8376001 0.8397235 0.2387 0.3634440 175475
23 154925895 rs538470 C T 0.0027 0.0089 0.7603998 0.7616073 0.2463 0.3634440 175475
23 154927185 rs185685661 T C 0.0051 0.0168 0.7602002 0.7614544 0.1114 0.1796030 175475
23 154927199 rs645904 C T 0.0022 0.0089 0.8092000 0.8047604 0.2396 0.3674170 175475
23 154927581 rs644138 G A 0.0029 0.0086 0.7363003 0.7359591 0.2878 0.4635760 175475
23 154928151 rs144607509 C T -0.0141 0.0615 0.8181000 0.8186604 0.0215 0.0084768 175475
23 154929412 rs557132 C T 0.0018 0.0089 0.8370999 0.8397235 0.2382 0.3568210 175475
23 154929952 rs4012982 CAA C 0.0076 0.0131 0.5603998 0.5618117 0.1986 0.3165560 175475
23 154930230 rs781880 A G 0.0018 0.0089 0.8421001 0.8397235 0.2380 0.3618540 175475
24 13537468 rs7203107 A G 0.0429 0.0547 0.4322002 0.4328771 0.9873 NA 175475

bcf preview

1   10616   rs376342519 CCGCCGTTGCAAAGGCGCGCCG  C   .   PASS    AF=0.9925   ES:SE:LP:AF:SS:ID   -0.0437:0.0645:0.302509:0.9925:175475:rs376342519
1   14933   rs199856693 G   A   .   PASS    AF=0.0399   ES:SE:LP:AF:SS:ID   -0.0064:0.0334:0.0719628:0.0399:175475:rs199856693
1   15774   rs374029747 G   A   .   PASS    AF=0.0069   ES:SE:LP:AF:SS:ID   -0.2087:0.1051:1.32781:0.0069:175475:rs374029747
1   16949   rs199745162 A   C   .   PASS    AF=0.0195   ES:SE:LP:AF:SS:ID   -0.0275:0.058:0.197295:0.0195:175475:rs199745162
1   51479   rs116400033 T   A   .   PASS    AF=0.23 ES:SE:LP:AF:SS:ID   -0.0007:0.015:0.016509:0.23:175475:rs116400033
1   52185   rs201374420 TTAA    T   .   PASS    AF=0.0066   ES:SE:LP:AF:SS:ID   -0.1028:0.1135:0.437231:0.0066:175475:rs201374420
1   54490   rs141149254 G   A   .   PASS    AF=0.1678   ES:SE:LP:AF:SS:ID   -0.0051:0.0169:0.117305:0.1678:175475:rs141149254
1   55164   rs3091274   C   A   .   PASS    AF=0.9808   ES:SE:LP:AF:SS:ID   0.0805:0.0486:1.00957:0.9808:175475:rs3091274
1   55326   rs3107975   T   C   .   PASS    AF=0.0247   ES:SE:LP:AF:SS:ID   0.031:0.0436:0.321118:0.0247:175475:rs3107975
1   55545   rs28396308  C   T   .   PASS    AF=0.2298   ES:SE:LP:AF:SS:ID   -0.013:0.0197:0.291919:0.2298:175475:rs28396308
1   57292   rs201418760 C   T   .   PASS    AF=0.0242   ES:SE:LP:AF:SS:ID   0.023:0.0437:0.222428:0.0242:175475:rs201418760
1   58814   rs114420996 G   A   .   PASS    AF=0.0949   ES:SE:LP:AF:SS:ID   -0.0094:0.0284:0.130006:0.0949:175475:rs114420996
1   61743   rs184286948 G   C   .   PASS    AF=0.0087   ES:SE:LP:AF:SS:ID   -0.064:0.0727:0.421475:0.0087:175475:rs184286948
1   61920   rs62637820  G   A   .   PASS    AF=0.0281   ES:SE:LP:AF:SS:ID   0.0238:0.0488:0.203703:0.0281:175475:rs62637820
1   63093   rs200092917 G   A   .   PASS    AF=0.023    ES:SE:LP:AF:SS:ID   0.0034:0.0447:0.0271494:0.023:175475:rs200092917
1   64649   rs181431124 A   C   .   PASS    AF=0.024    ES:SE:LP:AF:SS:ID   0.0429:0.0535:0.37366:0.024:175475:rs181431124
1   66219   rs181028663 A   T   .   PASS    AF=0.015    ES:SE:LP:AF:SS:ID   -0.0835:0.0682:0.655804:0.015:175475:rs181028663
1   68082   rs367789441 T   C   .   PASS    AF=0.0738   ES:SE:LP:AF:SS:ID   -0.0083:0.0244:0.13389:0.0738:175475:rs367789441
1   69428   rs140739101 T   G   .   PASS    AF=0.0421   ES:SE:LP:AF:SS:ID   0.0035:0.0306:0.0416273:0.0421:175475:rs140739101
1   69761   rs200505207 A   T   .   PASS    AF=0.0782   ES:SE:LP:AF:SS:ID   -0.0117:0.0239:0.205582:0.0782:175475:rs200505207
1   69897   rs200676709 T   C   .   PASS    AF=0.7546   ES:SE:LP:AF:SS:ID   0.0187:0.015:0.67469:0.7546:175475:rs200676709
1   72297   rs200651397 G   GTAT    .   PASS    AF=0.0055   ES:SE:LP:AF:SS:ID   0.1044:0.115:0.439257:0.0055:175475:rs200651397
1   74790   rs13328700  C   G   .   PASS    AF=0.0319   ES:SE:LP:AF:SS:ID   0.0481:0.0395:0.649946:0.0319:175475:rs13328700
1   74792   rs13328684  G   A   .   PASS    AF=0.0319   ES:SE:LP:AF:SS:ID   0.0481:0.0395:0.649946:0.0319:175475:rs13328684
1   76854   rs367666799 A   G   .   PASS    AF=0.0632   ES:SE:LP:AF:SS:ID   -0.0195:0.0263:0.337525:0.0632:175475:rs367666799
1   82163   rs139113303 G   A   .   PASS    AF=0.0626   ES:SE:LP:AF:SS:ID   -0.0218:0.0264:0.389233:0.0626:175475:rs139113303
1   82609   rs149189449 C   G   .   PASS    AF=0.0632   ES:SE:LP:AF:SS:ID   -0.0261:0.0262:0.495937:0.0632:175475:rs149189449
1   83514   rs201754587 C   T   .   PASS    AF=0.3404   ES:SE:LP:AF:SS:ID   0.0233:0.0137:1.05424:0.3404:175475:rs201754587
1   84139   rs183605470 A   T   .   PASS    AF=0.0215   ES:SE:LP:AF:SS:ID   0.06:0.0467:0.700711:0.0215:175475:rs183605470
1   86028   rs114608975 T   C   .   PASS    AF=0.0444   ES:SE:LP:AF:SS:ID   0.0077:0.0311:0.0939345:0.0444:175475:rs114608975
1   86065   rs116504101 G   C   .   PASS    AF=0.0651   ES:SE:LP:AF:SS:ID   -0.0126:0.0257:0.204607:0.0651:175475:rs116504101
1   86331   rs115209712 A   G   .   PASS    AF=0.1033   ES:SE:LP:AF:SS:ID   0.012:0.0279:0.176852:0.1033:175475:rs115209712
1   87021   rs188486692 T   C   .   PASS    AF=0.0086   ES:SE:LP:AF:SS:ID   0.0526:0.0708:0.339229:0.0086:175475:rs188486692
1   87360   rs180907504 C   T   .   PASS    AF=0.0246   ES:SE:LP:AF:SS:ID   -0.0458:0.0423:0.555487:0.0246:175475:rs180907504
1   87409   rs139490478 C   T   .   PASS    AF=0.0662   ES:SE:LP:AF:SS:ID   -0.0163:0.0256:0.28042:0.0662:175475:rs139490478
1   88169   rs940550    C   T   .   PASS    AF=0.211    ES:SE:LP:AF:SS:ID   -0.0408:0.0151:2.14831:0.211:175475:rs940550
1   88172   rs940551    G   A   .   PASS    AF=0.0724   ES:SE:LP:AF:SS:ID   -0.0134:0.0247:0.230844:0.0724:175475:rs940551
1   88177   rs143215837 G   C   .   PASS    AF=0.0717   ES:SE:LP:AF:SS:ID   -0.0109:0.0248:0.179799:0.0717:175475:rs143215837
1   88188   rs148331237 C   A   .   PASS    AF=0.0073   ES:SE:LP:AF:SS:ID   0.0189:0.0734:0.0985417:0.0073:175475:rs148331237
1   88236   rs186918018 C   T   .   PASS    AF=0.014    ES:SE:LP:AF:SS:ID   -0.0491:0.0762:0.284749:0.014:175475:rs186918018
1   88316   rs113759966 G   A   .   PASS    AF=0.0716   ES:SE:LP:AF:SS:ID   -0.0159:0.0248:0.284164:0.0716:175475:rs113759966
1   88338   rs55700207  G   A   .   PASS    AF=0.0832   ES:SE:LP:AF:SS:ID   0.0181:0.0308:0.255003:0.0832:175475:rs55700207
1   88710   rs186575039 C   G   .   PASS    AF=0.0661   ES:SE:LP:AF:SS:ID   -0.0162:0.0256:0.277695:0.0661:175475:rs186575039
1   89599   rs375955515 A   T   .   PASS    AF=0.0661   ES:SE:LP:AF:SS:ID   -0.0162:0.0256:0.277695:0.0661:175475:rs375955515
1   89946   rs138808727 A   T   .   PASS    AF=0.228    ES:SE:LP:AF:SS:ID   -0.0088:0.015:0.252821:0.228:175475:rs138808727
1   91190   rs143856811 G   A   .   PASS    AF=0.0668   ES:SE:LP:AF:SS:ID   -0.0205:0.0256:0.373249:0.0668:175475:rs143856811
1   91421   rs28619159  T   C   .   PASS    AF=0.0122   ES:SE:LP:AF:SS:ID   -0.0683:0.0543:0.681519:0.0122:175475:rs28619159
1   91515   rs376723915 A   C   .   PASS    AF=0.5556   ES:SE:LP:AF:SS:ID   0.0043:0.0129:0.130299:0.5556:175475:rs376723915
1   92633   rs149776517 C   T   .   PASS    AF=0.0318   ES:SE:LP:AF:SS:ID   -0.052:0.0362:0.823041:0.0318:175475:rs149776517
1   92858   rs147061536 G   T   .   PASS    AF=0.2346   ES:SE:LP:AF:SS:ID   -0.0107:0.0149:0.325414:0.2346:175475:rs147061536