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-1126/ieu-a-1126.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-1126/ldsc.txt \
--w-ld-chr /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/reference/eur_w_ld_chr/ 

Beginning analysis at Tue Feb  4 18:17:17 2020
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ieu-a-import/processed/ieu-a-1126/ieu-a-1126.vcf.gz ...
Read summary statistics for 10180512 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: 0.1322 (0.0106)
Lambda GC: 1.3571
Mean Chi^2: 1.6734
Intercept: 1.0964 (0.0122)
Ratio: 0.1431 (0.0181)
Analysis finished at Tue Feb  4 18:18:54 2020
Total time elapsed: 1.0m:37.73s

QC metrics

Metrics

Metrics

{
    "af_correlation": 0.9512,
    "inflation_factor": 1.2571,
    "mean_EFFECT": -0.0009,
    "n": 228951,
    "n_snps": 10180512,
    "n_clumped_hits": 142,
    "n_p_sig": 17295,
    "n_mono": 0,
    "n_ns": 620101,
    "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": 131548,
    "n_est": 228106.0071,
    "ratio_se_n": 0.9982,
    "mean_diff": 0.0007,
    "ratio_diff": 3.5106,
    "sd_y_est1": 2.2368,
    "sd_y_est2": 2.2327,
    "r2_sum1": 0.2542,
    "r2_sum2": 0.0508,
    "r2_sum3": 0.051,
    "r2_sum4": 0.0574,
    "ldsc_nsnp_merge_refpanel_ld": 1220210,
    "ldsc_nsnp_merge_regression_ld": 1220210,
    "ldsc_observed_scale_h2_beta": 0.1322,
    "ldsc_observed_scale_h2_se": 0.0106,
    "ldsc_intercept_beta": 1.0964,
    "ldsc_intercept_se": 0.0122,
    "ldsc_lambda_gc": 1.3571,
    "ldsc_mean_chisq": 1.6734,
    "ldsc_ratio": 0.1432
}

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 1.0000000 3 47 0 10180510 0 NA NA NA NA NA NA NA NA
character REF 0 1.0000000 1 99 0 30504 0 NA NA NA NA NA NA NA NA
character ALT 0 1.0000000 1 103 0 16155 0 NA NA NA NA NA NA NA NA
numeric CHROM 0 1.0000000 NA NA NA NA NA 8.958683e+00 6.304344e+00 1.00000e+00 4.000000e+00 7.000000e+00 1.400000e+01 2.400000e+01 ▇▆▂▃▂
numeric POS 0 1.0000000 NA NA NA NA NA 7.911736e+07 5.683088e+07 8.28000e+02 3.228392e+07 6.944248e+07 1.156271e+08 2.492385e+08 ▇▆▅▂▁
numeric EFFECT 0 1.0000000 NA NA NA NA NA -9.421000e-04 2.425550e-01 -7.54979e+02 -9.900000e-03 -2.000000e-04 9.300000e-03 1.267500e+00 ▁▁▁▁▇
numeric SE 0 1.0000000 NA NA NA NA NA 1.953940e-02 1.104919e+00 6.10000e-03 7.400000e-03 1.130000e-02 2.470000e-02 3.510620e+03 ▇▁▁▁▁
numeric PVAL 0 1.0000000 NA NA NA NA NA 4.617769e-01 2.999376e-01 0.00000e+00 1.927001e-01 4.495003e-01 7.218999e-01 1.000000e+00 ▇▆▆▆▆
numeric PVAL_ztest 0 1.0000000 NA NA NA NA NA 4.617802e-01 2.999465e-01 0.00000e+00 1.927006e-01 4.493364e-01 7.218913e-01 1.000000e+00 ▇▆▆▆▆
numeric AF 0 1.0000000 NA NA NA NA NA 2.292229e-01 2.639198e-01 5.10000e-03 2.190000e-02 1.095000e-01 3.652000e-01 9.949000e-01 ▇▂▁▁▁
numeric AF_reference 131548 0.9870784 NA NA NA NA NA 2.273020e-01 2.511925e-01 1.99700e-04 2.436100e-02 1.261980e-01 3.578270e-01 9.996010e-01 ▇▂▂▁▁
numeric N 0 1.0000000 NA NA NA NA NA 2.289510e+05 0.000000e+00 2.28951e+05 2.289510e+05 2.289510e+05 2.289510e+05 2.289510e+05 ▁▁▇▁▁

Head and tail

CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
1 10616 rs376342519 CCGCCGTTGCAAAGGCGCGCCG C 0.0001 0.0578 0.9987000 0.9986196 0.9925 0.9930110 228951
1 14933 rs199856693 G A 0.0125 0.0282 0.6575004 0.6575759 0.0397 0.0283546 228951
1 15774 rs374029747 G A -0.2633 0.0925 0.0044470 0.0044205 0.0070 0.0119808 228951
1 16949 rs199745162 A C -0.0060 0.0495 0.9033000 0.9035230 0.0191 0.0139776 228951
1 51479 rs116400033 T A -0.0101 0.0127 0.4242003 0.4264532 0.2298 0.1281950 228951
1 52185 rs201374420 TTAA T -0.0370 0.0958 0.6991993 0.6993328 0.0065 0.0053914 228951
1 54490 rs141149254 G A -0.0214 0.0143 0.1350001 0.1345225 0.1672 0.0960463 228951
1 55164 rs3091274 C A 0.0691 0.0417 0.0976090 0.0975044 0.9807 0.9233230 228951
1 55326 rs3107975 T C 0.0248 0.0376 0.5094998 0.5095269 0.0248 0.0459265 228951
1 55545 rs28396308 C T -0.0096 0.0166 0.5639999 0.5630526 0.2303 0.2392170 228951
CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
23 154925045 rs509981 C T -0.0012 0.0077 0.8798001 0.8761559 0.2388 0.3634440 228951
23 154925895 rs538470 C T -0.0004 0.0077 0.9594000 0.9585701 0.2463 0.3634440 228951
23 154927185 rs185685661 T C 0.0065 0.0145 0.6552002 0.6539541 0.1118 0.1796030 228951
23 154927199 rs645904 C T -0.0008 0.0077 0.9157000 0.9172518 0.2398 0.3674170 228951
23 154927581 rs644138 G A 0.0007 0.0074 0.9255000 0.9246368 0.2880 0.4635760 228951
23 154928151 rs144607509 C T -0.0269 0.0552 0.6261004 0.6260324 0.0215 0.0084768 228951
23 154929412 rs557132 C T -0.0010 0.0077 0.8918001 0.8966692 0.2383 0.3568210 228951
23 154929952 rs4012982 CAA C 0.0039 0.0112 0.7276005 0.7276793 0.2007 0.3165560 228951
23 154930230 rs781880 A G -0.0012 0.0077 0.8801000 0.8761559 0.2382 0.3618540 228951
24 13537468 rs7203107 A G -0.0021 0.0459 0.9632001 0.9635082 0.9868 NA 228951

bcf preview

1   10616   rs376342519 CCGCCGTTGCAAAGGCGCGCCG  C   .   PASS    AF=0.9925   ES:SE:LP:AF:SS:ID   0.0001:0.0578:0.00056495:0.9925:228951:rs376342519
1   14933   rs199856693 G   A   .   PASS    AF=0.0397   ES:SE:LP:AF:SS:ID   0.0125:0.0282:0.182104:0.0397:228951:rs199856693
1   15774   rs374029747 G   A   .   PASS    AF=0.007    ES:SE:LP:AF:SS:ID   -0.2633:0.0925:2.35193:0.007:228951:rs374029747
1   16949   rs199745162 A   C   .   PASS    AF=0.0191   ES:SE:LP:AF:SS:ID   -0.006:0.0495:0.044168:0.0191:228951:rs199745162
1   51479   rs116400033 T   A   .   PASS    AF=0.2298   ES:SE:LP:AF:SS:ID   -0.0101:0.0127:0.372429:0.2298:228951:rs116400033
1   52185   rs201374420 TTAA    T   .   PASS    AF=0.0065   ES:SE:LP:AF:SS:ID   -0.037:0.0958:0.155399:0.0065:228951:rs201374420
1   54490   rs141149254 G   A   .   PASS    AF=0.1672   ES:SE:LP:AF:SS:ID   -0.0214:0.0143:0.869666:0.1672:228951:rs141149254
1   55164   rs3091274   C   A   .   PASS    AF=0.9807   ES:SE:LP:AF:SS:ID   0.0691:0.0417:1.01051:0.9807:228951:rs3091274
1   55326   rs3107975   T   C   .   PASS    AF=0.0248   ES:SE:LP:AF:SS:ID   0.0248:0.0376:0.292856:0.0248:228951:rs3107975
1   55545   rs28396308  C   T   .   PASS    AF=0.2303   ES:SE:LP:AF:SS:ID   -0.0096:0.0166:0.248721:0.2303:228951:rs28396308
1   57292   rs201418760 C   T   .   PASS    AF=0.0242   ES:SE:LP:AF:SS:ID   0.0215:0.0376:0.245728:0.0242:228951:rs201418760
1   58814   rs114420996 G   A   .   PASS    AF=0.0949   ES:SE:LP:AF:SS:ID   -0.023:0.0241:0.467628:0.0949:228951:rs114420996
1   61743   rs184286948 G   C   .   PASS    AF=0.0087   ES:SE:LP:AF:SS:ID   -0.0664:0.0633:0.5318:0.0087:228951:rs184286948
1   61920   rs62637820  G   A   .   PASS    AF=0.0279   ES:SE:LP:AF:SS:ID   0.0184:0.0413:0.182699:0.0279:228951:rs62637820
1   63093   rs200092917 G   A   .   PASS    AF=0.023    ES:SE:LP:AF:SS:ID   0.0256:0.038:0.300943:0.023:228951:rs200092917
1   64649   rs181431124 A   C   .   PASS    AF=0.0241   ES:SE:LP:AF:SS:ID   0.0333:0.0449:0.338566:0.0241:228951:rs181431124
1   66219   rs181028663 A   T   .   PASS    AF=0.0152   ES:SE:LP:AF:SS:ID   -0.0812:0.0567:0.818728:0.0152:228951:rs181028663
1   68082   rs367789441 T   C   .   PASS    AF=0.0729   ES:SE:LP:AF:SS:ID   0.0149:0.0207:0.327348:0.0729:228951:rs367789441
1   69428   rs140739101 T   G   .   PASS    AF=0.042    ES:SE:LP:AF:SS:ID   -0.0067:0.0258:0.0988688:0.042:228951:rs140739101
1   69761   rs200505207 A   T   .   PASS    AF=0.0772   ES:SE:LP:AF:SS:ID   0.0093:0.0203:0.190575:0.0772:228951:rs200505207
1   69897   rs200676709 T   C   .   PASS    AF=0.7544   ES:SE:LP:AF:SS:ID   0.0141:0.0126:0.57741:0.7544:228951:rs200676709
1   72297   rs200651397 G   GTAT    .   PASS    AF=0.0055   ES:SE:LP:AF:SS:ID   0.1332:0.1018:0.719422:0.0055:228951:rs200651397
1   74790   rs13328700  C   G   .   PASS    AF=0.0316   ES:SE:LP:AF:SS:ID   0.0409:0.0341:0.637706:0.0316:228951:rs13328700
1   74792   rs13328684  G   A   .   PASS    AF=0.0316   ES:SE:LP:AF:SS:ID   0.0409:0.0341:0.637706:0.0316:228951:rs13328684
1   76854   rs367666799 A   G   .   PASS    AF=0.063    ES:SE:LP:AF:SS:ID   0.0062:0.0222:0.107571:0.063:228951:rs367666799
1   82163   rs139113303 G   A   .   PASS    AF=0.0624   ES:SE:LP:AF:SS:ID   0.0043:0.0222:0.072681:0.0624:228951:rs139113303
1   82609   rs149189449 C   G   .   PASS    AF=0.0631   ES:SE:LP:AF:SS:ID   0.0007:0.022:0.0117979:0.0631:228951:rs149189449
1   83514   rs201754587 C   T   .   PASS    AF=0.3416   ES:SE:LP:AF:SS:ID   0.018:0.0115:0.927383:0.3416:228951:rs201754587
1   84139   rs183605470 A   T   .   PASS    AF=0.0217   ES:SE:LP:AF:SS:ID   0.0248:0.0408:0.265841:0.0217:228951:rs183605470
1   86028   rs114608975 T   C   .   PASS    AF=0.0444   ES:SE:LP:AF:SS:ID   -0.002:0.0263:0.0278435:0.0444:228951:rs114608975
1   86065   rs116504101 G   C   .   PASS    AF=0.0649   ES:SE:LP:AF:SS:ID   0.0064:0.0217:0.11413:0.0649:228951:rs116504101
1   86331   rs115209712 A   G   .   PASS    AF=0.1038   ES:SE:LP:AF:SS:ID   0.001:0.0233:0.0147532:0.1038:228951:rs115209712
1   87021   rs188486692 T   C   .   PASS    AF=0.0086   ES:SE:LP:AF:SS:ID   0.0737:0.0611:0.641684:0.0086:228951:rs188486692
1   87360   rs180907504 C   T   .   PASS    AF=0.0246   ES:SE:LP:AF:SS:ID   -0.0297:0.0359:0.38934:0.0246:228951:rs180907504
1   87409   rs139490478 C   T   .   PASS    AF=0.066    ES:SE:LP:AF:SS:ID   0.006:0.0216:0.106849:0.066:228951:rs139490478
1   88169   rs940550    C   T   .   PASS    AF=0.2114   ES:SE:LP:AF:SS:ID   -0.0319:0.0128:1.89688:0.2114:228951:rs940550
1   88172   rs940551    G   A   .   PASS    AF=0.0716   ES:SE:LP:AF:SS:ID   0.0109:0.0209:0.219611:0.0716:228951:rs940551
1   88177   rs143215837 G   C   .   PASS    AF=0.0708   ES:SE:LP:AF:SS:ID   0.0128:0.021:0.265921:0.0708:228951:rs143215837
1   88188   rs148331237 C   A   .   PASS    AF=0.0073   ES:SE:LP:AF:SS:ID   -0.0136:0.064:0.0799811:0.0073:228951:rs148331237
1   88236   rs186918018 C   T   .   PASS    AF=0.0139   ES:SE:LP:AF:SS:ID   -0.0231:0.062:0.14917:0.0139:228951:rs186918018
1   88316   rs113759966 G   A   .   PASS    AF=0.0708   ES:SE:LP:AF:SS:ID   0.0066:0.021:0.122283:0.0708:228951:rs113759966
1   88338   rs55700207  G   A   .   PASS    AF=0.083    ES:SE:LP:AF:SS:ID   0.0115:0.0261:0.17993:0.083:228951:rs55700207
1   88710   rs186575039 C   G   .   PASS    AF=0.0659   ES:SE:LP:AF:SS:ID   0.0059:0.0216:0.105629:0.0659:228951:rs186575039
1   89599   rs375955515 A   T   .   PASS    AF=0.0659   ES:SE:LP:AF:SS:ID   0.0059:0.0216:0.105629:0.0659:228951:rs375955515
1   89946   rs138808727 A   T   .   PASS    AF=0.2283   ES:SE:LP:AF:SS:ID   -0.0141:0.0127:0.575772:0.2283:228951:rs138808727
1   91190   rs143856811 G   A   .   PASS    AF=0.0667   ES:SE:LP:AF:SS:ID   0.0023:0.0216:0.0389113:0.0667:228951:rs143856811
1   91421   rs28619159  T   C   .   PASS    AF=0.0122   ES:SE:LP:AF:SS:ID   -0.0951:0.0475:1.34323:0.0122:228951:rs28619159
1   91515   rs376723915 A   C   .   PASS    AF=0.5556   ES:SE:LP:AF:SS:ID   0.0047:0.0109:0.17633:0.5556:228951:rs376723915
1   92633   rs149776517 C   T   .   PASS    AF=0.0319   ES:SE:LP:AF:SS:ID   -0.0504:0.0303:1.01692:0.0319:228951:rs149776517
1   92858   rs147061536 G   T   .   PASS    AF=0.2349   ES:SE:LP:AF:SS:ID   -0.0167:0.0126:0.734946:0.2349:228951:rs147061536