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 /data/cromwell-executions/qc/3a55663b-79ca-4cb2-9a2b-30c31c59568b/call-ldsc/inputs/-261043455/ieu-b-4953.vcf.gz \
--ref-ld-chr /data/ref/eur_w_ld_chr/ \
--out /data/igd/ieu-b-4953/ldsc.txt \
--w-ld-chr /data/ref/eur_w_ld_chr/ 

Beginning analysis at Fri Mar  4 03:15:08 2022
Reading summary statistics from /data/cromwell-executions/qc/3a55663b-79ca-4cb2-9a2b-30c31c59568b/call-ldsc/inputs/-261043455/ieu-b-4953.vcf.gz ...
Read summary statistics for 6303340 SNPs.
Dropped 102828 SNPs with duplicated rs numbers.
Reading reference panel LD Score from /data/ref/eur_w_ld_chr/[1-22] ... (ldscore_fromlist)
Read reference panel LD Scores for 1290028 SNPs.
Removing partitioned LD Scores with zero variance.
Reading regression weight LD Score from /data/ref/eur_w_ld_chr/[1-22] ... (ldscore_fromlist)
Read regression weight LD Scores for 1290028 SNPs.
After merging with reference panel LD, 1029177 SNPs remain.
After merging with regression SNP LD, 1029177 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.0007 (0.0013)
Lambda GC: 1.0069
Mean Chi^2: 1.005
Intercept: 0.9991 (0.0074)
Ratio < 0 (usually indicates GC correction).
Analysis finished at Fri Mar  4 03:16:33 2022
Total time elapsed: 1.0m:24.81s

QC metrics

Metrics

Metrics

{
    "af_correlation": 0.901,
    "inflation_factor": 1,
    "mean_EFFECT": 7.2209e-08,
    "n": "-Inf",
    "n_snps": 6304034,
    "n_clumped_hits": 3,
    "n_p_sig": 89,
    "n_mono": 0,
    "n_ns": 828685,
    "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": 812877,
    "n_est": "NA",
    "ratio_se_n": "NA",
    "mean_diff": "NaN",
    "ratio_diff": "NaN",
    "sd_y_est1": "NaN",
    "sd_y_est2": "NA",
    "r2_sum1": 0,
    "r2_sum2": 0,
    "r2_sum3": 0,
    "r2_sum4": 0,
    "ldsc_nsnp_merge_refpanel_ld": 1029177,
    "ldsc_nsnp_merge_regression_ld": 1029177,
    "ldsc_observed_scale_h2_beta": 0.0007,
    "ldsc_observed_scale_h2_se": 0.0013,
    "ldsc_intercept_beta": 0.9991,
    "ldsc_intercept_se": 0.0074,
    "ldsc_lambda_gc": 1.0069,
    "ldsc_mean_chisq": 1.005,
    "ldsc_ratio": -0.18
}

Flags

name value
af_correlation FALSE
inflation_factor FALSE
n TRUE
is_snpid_non_unique TRUE
mean_EFFECT_nonfinite FALSE
mean_EFFECT_05 FALSE
mean_EFFECT_01 FALSE
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 logical.mean logical.count numeric.mean numeric.sd numeric.p0 numeric.p25 numeric.p50 numeric.p75 numeric.p100 numeric.hist
character ID 455 0.9999278 3 58 0 6289014 0 NA NA NA NA NA NA NA NA NA NA
character REF 0 1.0000000 1 83 0 10960 0 NA NA NA NA NA NA NA NA NA NA
character ALT 0 1.0000000 1 662 0 44872 0 NA NA NA NA NA NA NA NA NA NA
logical N 6304034 0.0000000 NA NA NA NA NA NaN : NA NA NA NA NA NA NA NA
numeric CHROM 0 1.0000000 NA NA NA NA NA NA NA 8.906962e+00 5.999295e+00 1.0000000 4.000000e+00 8.000000e+00 1.300000e+01 2.300000e+01 ▇▅▅▂▂
numeric POS 0 1.0000000 NA NA NA NA NA NA NA 7.834261e+07 5.653798e+07 302.0000000 3.179891e+07 6.868538e+07 1.144565e+08 2.492405e+08 ▇▆▅▂▁
numeric EFFECT 0 1.0000000 NA NA NA NA NA NA NA 1.000000e-07 6.380000e-05 -0.0005559 -4.110000e-05 -3.000000e-07 4.070000e-05 6.464000e-04 ▁▁▇▁▁
numeric SE 0 1.0000000 NA NA NA NA NA NA NA 6.220000e-05 1.310000e-05 0.0000405 5.140000e-05 5.770000e-05 7.040000e-05 1.800000e-04 ▇▃▁▁▁
numeric PVAL 0 1.0000000 NA NA NA NA NA NA NA 4.982228e-01 2.889093e-01 0.0000000 2.500000e-01 5.000000e-01 7.499995e-01 1.000000e+00 ▇▇▇▇▇
numeric PVAL_ztest 0 1.0000000 NA NA NA NA NA NA NA 4.982240e-01 2.888834e-01 0.0000000 2.474015e-01 4.973618e-01 7.480035e-01 9.999999e-01 ▇▇▇▇▇
numeric AF 0 1.0000000 NA NA NA NA NA NA NA 3.957610e-01 2.489469e-01 0.0744050 1.735700e-01 3.418195e-01 5.912500e-01 9.255950e-01 ▇▅▃▃▂
numeric AF_reference 812877 0.8710545 NA NA NA NA NA NA NA 3.587831e-01 2.319499e-01 0.0000000 1.661340e-01 3.085060e-01 5.229630e-01 1.000000e+00 ▇▇▅▃▁

Head and tail

CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
1 10177 rs1264289758 AC A -0.0000836 0.0000735 0.2599998 0.2553373 0.601331 NA NA
1 10352 rs1557426776 TA T 0.0000738 0.0000757 0.3300000 0.3295112 0.607014 NA NA
1 11008 rs575272151 C G 0.0005100 0.0001258 0.0000500 0.0000505 0.086213 0.0880591 NA
1 11012 rs544419019 C G 0.0005100 0.0001258 0.0000500 0.0000505 0.086213 0.0880591 NA
1 13116 rs62635286 T G 0.0000210 0.0000990 0.8300000 0.8324311 0.189421 0.0970447 NA
1 13118 rs200579949 A G 0.0000210 0.0000990 0.8300000 0.8324311 0.189421 0.0970447 NA
1 13273 rs531730856 G C -0.0001359 0.0001161 0.2399999 0.2415394 0.133926 0.0950479 NA
1 14464 rs546169444 A T -0.0000732 0.0001054 0.4899999 0.4874930 0.157049 0.0958466 NA
1 14599 rs531646671 T A 0.0000378 0.0000961 0.6899999 0.6944203 0.191575 0.1475640 NA
1 14604 rs541940975 A G 0.0000378 0.0000961 0.6899999 0.6944203 0.191575 0.1475640 NA
CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
23 154901936 rs697727 A G -4.14e-05 4.71e-05 0.3800004 0.3794573 0.751485 0.643179 NA
23 154901964 rs697726 G A -4.52e-05 4.97e-05 0.3599996 0.3627703 0.347461 0.117616 NA
23 154902105 rs696316 G T -4.13e-05 4.71e-05 0.3800004 0.3800696 0.751438 0.636026 NA
23 154902889 rs697725 A T -4.08e-05 4.70e-05 0.3900004 0.3858051 0.751109 0.584106 NA
23 154903118 rs479770 G A -4.14e-05 4.71e-05 0.3800004 0.3792247 0.751528 0.643444 NA
23 154903224 rs480725 A T -4.14e-05 4.71e-05 0.3800004 0.3791796 0.751531 0.643444 NA
23 154903937 rs674707 G A -4.14e-05 4.71e-05 0.3800004 0.3790258 0.751541 0.643444 NA
23 154909055 rs473529 C G 6.74e-05 4.43e-05 0.1299999 0.1282716 0.305136 0.463046 NA
23 154918266 rs642043 C T 7.09e-05 4.45e-05 0.1100001 0.1109726 0.303001 0.478675 NA
23 154927581 rs644138 G A 7.10e-05 4.45e-05 0.1100001 0.1103096 0.302873 0.463576 NA

bcf preview

1   10177   rs1264289758    AC  A   .   PASS    AF=0.601331 ES:SE:LP:AF:ID  -8.36061e-05:7.35011e-05:0.585027:0.601331:rs1264289758
1   10352   rs1557426776    TA  T   .   PASS    AF=0.607014 ES:SE:LP:AF:ID  7.38221e-05:7.57073e-05:0.481486:0.607014:rs1557426776
1   11008   rs575272151 C   G   .   PASS    AF=0.086213 ES:SE:LP:AF:ID  0.000509998:0.000125821:4.30103:0.086213:rs575272151
1   11012   rs544419019 C   G   .   PASS    AF=0.086213 ES:SE:LP:AF:ID  0.000509998:0.000125821:4.30103:0.086213:rs544419019
1   13116   rs62635286  T   G   .   PASS    AF=0.189421 ES:SE:LP:AF:ID  2.09513e-05:9.90209e-05:0.0809219:0.189421:rs62635286
1   13118   rs62028691  A   G   .   PASS    AF=0.189421 ES:SE:LP:AF:ID  2.09513e-05:9.90209e-05:0.0809219:0.189421:rs62028691
1   13273   rs531730856 G   C   .   PASS    AF=0.133926 ES:SE:LP:AF:ID  -0.000135948:0.000116081:0.619789:0.133926:rs531730856
1   14464   rs546169444 A   T   .   PASS    AF=0.157049 ES:SE:LP:AF:ID  -7.31912e-05:0.000105417:0.309804:0.157049:rs546169444
1   14599   rs707680    T   A   .   PASS    AF=0.191575 ES:SE:LP:AF:ID  3.77532e-05:9.60975e-05:0.161151:0.191575:rs707680
1   14604   rs1418508701    A   G   .   PASS    AF=0.191575 ES:SE:LP:AF:ID  3.77532e-05:9.60975e-05:0.161151:0.191575:rs1418508701
1   14930   rs6682385   A   G   .   PASS    AF=0.474005 ES:SE:LP:AF:ID  2.78648e-05:7.45473e-05:0.148742:0.474005:rs6682385
1   15211   rs3982632   T   G   .   PASS    AF=0.741409 ES:SE:LP:AF:ID  -0.000115129:8.62042e-05:0.744727:0.741409:rs3982632
1   15820   rs1316988498    G   T   .   PASS    AF=0.27521  ES:SE:LP:AF:ID  -7.88565e-05:8.83993e-05:0.431798:0.27521:rs1316988498
1   15903   rs557514207 GC  G   .   PASS    AF=0.581028 ES:SE:LP:AF:ID  3.03658e-05:7.28876e-05:0.167491:0.581028:rs557514207
1   30923   rs1165072081    G   T   .   PASS    AF=0.910278 ES:SE:LP:AF:ID  -8.37531e-05:0.000137622:0.267606:0.910278:rs1165072081
1   49298   rs10399793  T   C   .   PASS    AF=0.62365  ES:SE:LP:AF:ID  0.000179089:8.74531e-05:1.38722:0.62365:rs10399793
1   49554   rs539322794 A   G   .   PASS    AF=0.092968 ES:SE:LP:AF:ID  -3.89822e-05:0.000134509:0.113509:0.092968:rs539322794
1   51479   rs116400033 T   A   .   PASS    AF=0.213491 ES:SE:LP:AF:ID  -2.24702e-05:9.34845e-05:0.091515:0.213491:rs116400033
1   54490   rs141149254 G   A   .   PASS    AF=0.154529 ES:SE:LP:AF:ID  -1.36016e-05:0.000105039:0.0457575:0.154529:rs141149254
1   54676   rs2462492   C   T   .   PASS    AF=0.400424 ES:SE:LP:AF:ID  2.33442e-05:8.66327e-05:0.102373:0.400424:rs2462492
1   54712   rs573184866 TTTTC   T   .   PASS    AF=0.41485  ES:SE:LP:AF:ID  6.46116e-05:6.84808e-05:0.455932:0.41485:rs573184866
1   54716   rs1166278911    C   T   .   PASS    AF=0.417219 ES:SE:LP:AF:ID  -7.41552e-05:7.90882e-05:0.455932:0.417219:rs1166278911
1   55545   rs28396308  C   T   .   PASS    AF=0.253874 ES:SE:LP:AF:ID  9.29722e-05:8.89694e-05:0.522879:0.253874:rs28396308
1   58814   rs114420996 G   A   .   PASS    AF=0.090041 ES:SE:LP:AF:ID  0.000180262:0.000135484:0.744727:0.090041:rs114420996
1   59040   rs62637815  T   C   .   PASS    AF=0.088875 ES:SE:LP:AF:ID  9.91548e-05:0.000136003:0.327902:0.088875:rs62637815
1   60351   rs62637817  A   G   .   PASS    AF=0.081027 ES:SE:LP:AF:ID  0.000149056:0.000141076:0.537602:0.081027:rs62637817
1   62777   rs3844233   A   T   .   PASS    AF=0.438473 ES:SE:LP:AF:ID  -0.000110931:7.51925e-05:0.853872:0.438473:rs3844233
1   63268   rs28664618  T   C   .   PASS    AF=0.382116 ES:SE:LP:AF:ID  4.35846e-05:8.08233e-05:0.229148:0.382116:rs28664618
1   63671   rs80011619  G   A   .   PASS    AF=0.15885  ES:SE:LP:AF:ID  0.000142306:0.000102897:0.769551:0.15885:rs80011619
1   63735   rs61158452  C   CCTA    .   PASS    AF=0.683973 ES:SE:LP:AF:ID  -1.10288e-05:8.01093e-05:0.05061:0.683973:rs61158452
1   64931   rs62639104  G   A   .   PASS    AF=0.079632 ES:SE:LP:AF:ID  6.57473e-05:0.000142797:0.187087:0.079632:rs62639104
1   69897   rs200676709 T   C   .   PASS    AF=0.751159 ES:SE:LP:AF:ID  6.74803e-05:9.07365e-05:0.337242:0.751159:rs200676709
1   76838   rs563953605 T   G   .   PASS    AF=0.077201 ES:SE:LP:AF:ID  -2.29854e-05:0.000145521:0.0604807:0.077201:rs563953605
1   76854   rs367666799 A   G   .   PASS    AF=0.07745  ES:SE:LP:AF:ID  5.33906e-05:0.000140536:0.154902:0.07745:rs367666799
1   77866   rs563593912 C   T   .   PASS    AF=0.077004 ES:SE:LP:AF:ID  -2.13978e-05:0.000145559:0.0555173:0.077004:rs563593912
1   77874   rs62641297  G   A   .   PASS    AF=0.077004 ES:SE:LP:AF:ID  -2.13978e-05:0.000145559:0.0555173:0.077004:rs62641297
1   82163   rs139113303 G   A   .   PASS    AF=0.07541  ES:SE:LP:AF:ID  7.89264e-05:0.000142311:0.236572:0.07541:rs139113303
1   82609   rs149189449 C   G   .   PASS    AF=0.075437 ES:SE:LP:AF:ID  8.06581e-05:0.000142282:0.244125:0.075437:rs149189449
1   83514   rs201754587 C   T   .   PASS    AF=0.352687 ES:SE:LP:AF:ID  -2.16706e-05:8.14657e-05:0.102373:0.352687:rs201754587
1   86028   rs114608975 T   C   .   PASS    AF=0.103486 ES:SE:LP:AF:ID  -0.000198057:0.000138581:0.823909:0.103486:rs114608975
1   86065   rs116504101 G   C   .   PASS    AF=0.0761   ES:SE:LP:AF:ID  6.49965e-05:0.000142702:0.187087:0.0761:rs116504101
1   86331   rs115209712 A   G   .   PASS    AF=0.109614 ES:SE:LP:AF:ID  -3.94988e-05:0.000125522:0.124939:0.109614:rs115209712
1   87409   rs139490478 C   T   .   PASS    AF=0.076696 ES:SE:LP:AF:ID  5.68709e-05:0.00014224:0.161151:0.076696:rs139490478
1   88169   rs940550    C   T   .   PASS    AF=0.208366 ES:SE:LP:AF:ID  4.9567e-05:9.26197e-05:0.229148:0.208366:rs940550
1   88338   rs55700207  G   A   .   PASS    AF=0.08007  ES:SE:LP:AF:ID  1.98816e-05:0.000143277:0.05061:0.08007:rs55700207
1   88710   rs186575039 C   G   .   PASS    AF=0.07666  ES:SE:LP:AF:ID  5.68638e-05:0.000142245:0.161151:0.07666:rs186575039
1   89599   rs375955515 A   T   .   PASS    AF=0.07666  ES:SE:LP:AF:ID  5.68638e-05:0.000142245:0.161151:0.07666:rs375955515
1   89946   rs138808727 A   T   .   PASS    AF=0.214666 ES:SE:LP:AF:ID  -9.94074e-06:9.51612e-05:0.0362122:0.214666:rs138808727
1   91190   rs143856811 G   A   .   PASS    AF=0.078488 ES:SE:LP:AF:ID  3.70062e-05:0.000139485:0.102373:0.078488:rs143856811
1   91515   rs376723915 A   C   .   PASS    AF=0.55857  ES:SE:LP:AF:ID  -3.45847e-05:7.70519e-05:0.187087:0.55857:rs376723915