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-1/ieu-a-1.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-1/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 09:21:13 2020
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ieu-a-import/processed/ieu-a-1/ieu-a-1.vcf.gz ...
Read summary statistics for 2631751 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, 1187168 SNPs remain.
After merging with regression SNP LD, 1187168 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.1464 (0.0234)
Lambda GC: 1.0674
Mean Chi^2: 1.0913
Intercept: 1.0136 (0.0073)
Ratio: 0.1492 (0.0799)
Analysis finished at Wed Feb  5 09:21:47 2020
Total time elapsed: 33.87s

QC metrics

Metrics

Metrics

{
    "af_correlation": 0.0402,
    "inflation_factor": 1.0005,
    "mean_EFFECT": -0.0001,
    "n": 29347,
    "n_snps": 2631751,
    "n_clumped_hits": 14,
    "n_p_sig": 236,
    "n_mono": 0,
    "n_ns": 0,
    "n_mac": 13,
    "is_snpid_unique": true,
    "n_miss_EFFECT": 0,
    "n_miss_SE": 0,
    "n_miss_PVAL": 0,
    "n_miss_AF": 32176,
    "n_miss_AF_reference": 26109,
    "n_est": 27338.4081,
    "ratio_se_n": 0.9652,
    "mean_diff": -0.0001,
    "ratio_diff": 2.3288,
    "sd_y_est1": 0.5623,
    "sd_y_est2": 0.5427,
    "r2_sum1": 0.0147,
    "r2_sum2": 0.0465,
    "r2_sum3": 0.0499,
    "r2_sum4": 0.0422,
    "ldsc_nsnp_merge_refpanel_ld": 1187168,
    "ldsc_nsnp_merge_regression_ld": 1187168,
    "ldsc_observed_scale_h2_beta": 0.1464,
    "ldsc_observed_scale_h2_se": 0.0234,
    "ldsc_intercept_beta": 1.0136,
    "ldsc_intercept_se": 0.0073,
    "ldsc_lambda_gc": 1.0674,
    "ldsc_mean_chisq": 1.0913,
    "ldsc_ratio": 0.149
}

Flags

name value
af_correlation TRUE
inflation_factor FALSE
n FALSE
is_snpid_non_unique FALSE
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 numeric.mean numeric.sd numeric.p0 numeric.p25 numeric.p50 numeric.p75 numeric.p100 numeric.hist
character ID 0 1.0000000 3 42 0 2631751 0 NA NA NA NA NA NA NA NA
character REF 0 1.0000000 1 1 0 4 0 NA NA NA NA NA NA NA NA
character ALT 0 1.0000000 1 1 0 4 0 NA NA NA NA NA NA NA NA
numeric CHROM 0 1.0000000 NA NA NA NA NA 8.960980e+00 6.029486e+00 1.000000 4.000000e+00 8.000000e+00 1.300000e+01 2.40000e+01 ▇▆▃▃▂
numeric POS 0 1.0000000 NA NA NA NA NA 7.871800e+07 5.554483e+07 6888.000000 3.246140e+07 7.032897e+07 1.145722e+08 2.49219e+08 ▇▆▅▂▁
numeric EFFECT 0 1.0000000 NA NA NA NA NA -1.437000e-04 3.395795e-01 -244.590000 -4.629000e-03 -6.000000e-05 4.480000e-03 3.64787e+02 ▁▁▇▁▁
numeric SE 0 1.0000000 NA NA NA NA NA 3.875747e+08 6.287497e+11 0.004232 4.767000e-03 5.749000e-03 8.610000e-03 1.02000e+15 ▇▁▁▁▁
numeric PVAL 0 1.0000000 NA NA NA NA NA 4.999477e-01 2.887214e-01 0.000000 2.506303e-01 4.998895e-01 7.499287e-01 1.00000e+00 ▇▇▇▇▇
numeric PVAL_ztest 0 1.0000000 NA NA NA NA NA 4.901489e-01 2.912515e-01 0.000000 2.361297e-01 4.865459e-01 7.423657e-01 1.00000e+00 ▇▇▇▇▇
numeric AF 32176 0.9877739 NA NA NA NA NA 4.920352e-01 3.143317e-01 0.004000 2.000000e-01 4.900000e-01 7.833000e-01 9.96000e-01 ▇▆▅▆▇
numeric AF_reference 26109 0.9900792 NA NA NA NA NA 3.578115e-01 2.581876e-01 0.000000 1.405750e-01 2.941290e-01 5.429310e-01 1.00000e+00 ▇▆▃▃▂
numeric N 0 1.0000000 NA NA NA NA NA 2.631103e+04 6.830495e+03 74.000000 2.711700e+04 2.928900e+04 2.933700e+04 2.93470e+04 ▁▁▁▁▇

Head and tail

CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
1 234313 rs8179466 C T -0.007704 0.033632 0.8242064 0.8188164 NA NA 1861
1 568752 rs9326624 T C -0.002433 0.027559 0.9317556 0.9296515 NA NA 4021
1 569604 rs9645429 G A 0.004973 0.038512 0.9003451 0.8972559 NA 0.0075879 3926
1 721290 rs12565286 G C 0.015027 0.021281 0.4935294 0.4801118 0.06780 0.0371406 10293
1 723819 rs11804171 T A 0.014968 0.021201 0.4936226 0.4801854 0.03704 0.1345850 10293
1 723891 rs2977670 G C -0.008751 0.024673 0.7309236 0.7228299 0.92857 0.7799520 8657
1 724300 rs12069907 C T -0.010130 0.033759 0.7710845 0.7641252 NA 0.0734824 2317
1 726481 rs3131980 T G -0.046957 0.035431 0.1987385 0.1850689 NA NA 3890
1 750235 rs12138618 G A 0.000387 0.030431 0.9901569 0.9898533 0.05833 NA 6434
1 752566 rs3094315 G A -0.011113 0.007589 0.1556500 0.1430966 0.84480 0.7182510 19921
CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
23 154916845 rs669237 G T -0.008766 0.011924 0.4759617 0.4622445 0.17780 0.4166890 2718
23 154925045 rs509981 C T -0.008644 0.011985 0.4843430 0.4707650 0.18890 0.3634440 2718
23 154927581 rs644138 G A -0.011340 0.012029 0.3606517 0.3458232 0.26670 0.4635760 2718
23 154929412 rs557132 C T -0.000245 0.008396 0.9774150 0.9767206 0.17780 0.3568210 5141
23 154977448 rs306897 G A 0.007772 0.054676 0.8903525 0.8869643 0.03333 0.1162140 2718
23 155004636 rs17653586 G T 0.046030 0.045167 0.3230487 0.3081522 0.09400 0.0565096 1616
23 155092794 rs6567787 C T -0.016300 0.030273 0.6016238 0.5902777 0.23000 0.3057110 1613
23 155217992 rs5983854 C A 0.011590 0.029727 0.7054123 0.6966244 NA 0.5880590 1615
24 3803578 rs400901 T C 0.016031 0.033695 0.6445714 0.6342397 0.40000 NA 2718
24 4030586 rs2557668 G A -0.003638 0.013695 0.7966985 0.7905131 0.76670 NA 2718

bcf preview

1   234313  rs8179466   C   T   .   PASS    .   ES:SE:LP:SS:ID  -0.007704:0.033632:0.083964:1861:rs8179466
1   568752  rs9326624   T   C   .   PASS    .   ES:SE:LP:SS:ID  -0.002433:0.027559:0.030698:4021:rs9326624
1   569604  rs9645429   G   A   .   PASS    .   ES:SE:LP:SS:ID  0.004973:0.038512:0.045591:3926:rs9645429
1   721290  rs12565286  G   C   .   PASS    AF=0.0678   ES:SE:LP:AF:SS:ID   0.015027:0.021281:0.306687:0.0678:10293:rs12565286
1   723819  rs11804171  T   A   .   PASS    AF=0.03704  ES:SE:LP:AF:SS:ID   0.014968:0.021201:0.306605:0.03704:10293:rs11804171
1   723891  rs2977670   G   C   .   PASS    AF=0.92857  ES:SE:LP:AF:SS:ID   -0.008751:0.024673:0.136128:0.92857:8657:rs2977670
1   724300  rs12069907  C   T   .   PASS    .   ES:SE:LP:SS:ID  -0.01013:0.033759:0.112898:2317:rs12069907
1   726481  rs3131980   T   G   .   PASS    .   ES:SE:LP:SS:ID  -0.046957:0.035431:0.701718:3890:rs3131980
1   750235  rs12138618  G   A   .   PASS    AF=0.05833  ES:SE:LP:AF:SS:ID   0.000387:0.030431:0.00429598:0.05833:6434:rs12138618
1   752566  rs3094315   G   A   .   PASS    AF=0.8448   ES:SE:LP:AF:SS:ID   -0.011113:0.007589:0.807851:0.8448:19921:rs3094315
1   753405  rs3115860   C   A   .   PASS    AF=0.862    ES:SE:LP:AF:SS:ID   0.009442:0.035945:0.097486:0.862:1914:rs3115860
1   754192  rs3131968   A   G   .   PASS    AF=0.875    ES:SE:LP:AF:SS:ID   -0.003026:0.012097:0.092411:0.875:10992:rs3131968
1   754334  rs3131967   T   C   .   PASS    AF=0.879    ES:SE:LP:AF:SS:ID   0.015096:0.057604:0.097235:0.879:1213:rs3131967
1   761147  rs3115850   T   C   .   PASS    AF=0.856    ES:SE:LP:AF:SS:ID   0.004564:0.035975:0.044755:0.856:1873:rs3115850
1   768448  rs12562034  G   A   .   PASS    AF=0.09167  ES:SE:LP:AF:SS:ID   0.017872:0.015462:0.581082:0.09167:7663:rs12562034
1   775659  rs2905035   A   G   .   PASS    AF=0.875    ES:SE:LP:AF:SS:ID   -0.014218:0.008636:0.957116:0.875:19653:rs2905035
1   776546  rs12124819  A   G   .   PASS    AF=0.3417   ES:SE:LP:AF:SS:ID   0.010223:0.012766:0.359042:0.3417:4633:rs12124819
1   777122  rs2980319   A   T   .   PASS    AF=0.875    ES:SE:LP:AF:SS:ID   -0.014025:0.008636:0.938028:0.875:19653:rs2980319
1   779322  rs4040617   A   G   .   PASS    AF=0.125    ES:SE:LP:AF:SS:ID   0.012851:0.008632:0.827187:0.125:19647:rs4040617
1   780785  rs2977612   T   A   .   PASS    AF=0.8661   ES:SE:LP:AF:SS:ID   -0.013478:0.008671:0.88023:0.8661:19651:rs2977612
1   784023  rs17160939  A   G   .   PASS    AF=0.008475 ES:SE:LP:AF:SS:ID   -0.146404:0.106732:0.736422:0.008475:1229:rs17160939
1   785050  rs2905062   G   A   .   PASS    AF=0.8558   ES:SE:LP:AF:SS:ID   -0.011378:0.008657:0.693601:0.8558:19649:rs2905062
1   785989  rs2980300   T   C   .   PASS    AF=0.8729   ES:SE:LP:AF:SS:ID   -0.009672:0.008399:0.578196:0.8729:19580:rs2980300
1   793947  rs2519031   A   G   .   PASS    AF=0.093    ES:SE:LP:AF:SS:ID   -0.00105:0.041566:0.008578:0.093:1864:rs2519031
1   798026  rs4951864   C   T   .   PASS    AF=0.9  ES:SE:LP:AF:SS:ID   -0.019079:0.021211:0.41667:0.9:7406:rs4951864
1   798801  rs12132517  G   A   .   PASS    AF=0.1083   ES:SE:LP:AF:SS:ID   0.022855:0.021509:0.518767:0.1083:6434:rs12132517
1   798959  rs11240777  G   A   .   PASS    AF=0.1667   ES:SE:LP:AF:SS:ID   0.02801:0.015109:1.14113:0.1667:9850:rs11240777
1   846808  rs4475691   C   T   .   PASS    AF=0.142    ES:SE:LP:AF:SS:ID   0.022949:0.033678:0.293461:0.142:1915:rs4475691
1   888659  rs3748597   T   C   .   PASS    AF=0.93333  ES:SE:LP:AF:SS:ID   0.011685:0.064292:0.065453:0.93333:1914:rs3748597
1   900505  rs28705211  G   C   .   PASS    .   ES:SE:LP:SS:ID  0.062621:0.030196:1.35303:1915:rs28705211
1   918384  rs13303118  G   T   .   PASS    AF=0.628    ES:SE:LP:AF:SS:ID   -0.014736:0.027409:0.220284:0.628:1913:rs13303118
1   928836  rs9777703   C   T   .   PASS    AF=0.973    ES:SE:LP:AF:SS:ID   0.029885:0.075654:0.153842:0.973:1915:rs9777703
1   943468  rs3121567   T   C   .   PASS    AF=0.973    ES:SE:LP:AF:SS:ID   0.020388:0.077225:0.098023:0.973:1914:rs3121567
1   949608  rs1921  G   A   .   PASS    .   ES:SE:LP:SS:ID  0.02497:0.016713:0.831457:2188:rs1921
1   962210  rs3128126   A   G   .   PASS    AF=0.425    ES:SE:LP:AF:SS:ID   0.052617:0.013324:3.88706:0.425:7142:rs3128126
1   990380  rs3121561   C   T   .   PASS    AF=0.2667   ES:SE:LP:AF:SS:ID   0.038288:0.009802:3.81417:0.2667:13156:rs3121561
1   998501  rs3813193   G   C   .   PASS    AF=0.85 ES:SE:LP:AF:SS:ID   0.028902:0.009188:2.63918:0.85:14180:rs3813193
1   1003629 rs4075116   C   T   .   PASS    AF=0.2627   ES:SE:LP:AF:SS:ID   -0.012817:0.005413:1.66346:0.2627:28689:rs4075116
1   1005806 rs3934834   C   T   .   PASS    AF=0.1186   ES:SE:LP:AF:SS:ID   0.02632:0.008914:2.37575:0.1186:14331:rs3934834
1   1017170 rs3766193   C   G   .   PASS    AF=0.431    ES:SE:LP:AF:SS:ID   -0.02304:0.005902:3.81051:0.431:28171:rs3766193
1   1017197 rs3766192   C   T   .   PASS    AF=0.4237   ES:SE:LP:AF:SS:ID   -0.022615:0.005566:4.08407:0.4237:28811:rs3766192
1   1017587 rs3766191   C   T   .   PASS    AF=0.09649  ES:SE:LP:AF:SS:ID   0.023905:0.009258:1.9098:0.09649:14193:rs3766191
1   1018562 rs9442371   C   T   .   PASS    AF=0.4083   ES:SE:LP:AF:SS:ID   -0.021748:0.005439:3.97224:0.4083:28981:rs9442371
1   1018704 rs9442372   A   G   .   PASS    AF=0.3983   ES:SE:LP:AF:SS:ID   -0.021753:0.005445:3.96537:0.3983:28988:rs9442372
1   1021346 rs10907177  A   G   .   PASS    AF=0.1271   ES:SE:LP:AF:SS:ID   0.024277:0.009551:1.86233:0.1271:14127:rs10907177
1   1021415 rs3737728   A   G   .   PASS    AF=0.2833   ES:SE:LP:AF:SS:ID   -0.009863:0.00537:1.12516:0.2833:29346:rs3737728
1   1021583 rs10907178  A   C   .   PASS    AF=0.1132   ES:SE:LP:AF:SS:ID   0.025591:0.009726:1.96851:0.1132:14097:rs10907178
1   1021695 rs9442398   A   G   .   PASS    AF=0.275    ES:SE:LP:AF:SS:ID   -0.012133:0.005602:1.44689:0.275:29121:rs9442398
1   1022037 rs6701114   C   T   .   PASS    AF=0.4333   ES:SE:LP:AF:SS:ID   -0.017584:0.00613:2.26574:0.4333:27175:rs6701114
1   1025301 rs9442400   T   C   .   PASS    AF=0.94737  ES:SE:LP:AF:SS:ID   0.008571:0.060448:0.050304:0.94737:4940:rs9442400