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/ukb-d-import/processed/ukb-d-20113_101/ukb-d-20113_101.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/ukb-d-import/processed/ukb-d-20113_101/ldsc.txt \
--w-ld-chr /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/reference/eur_w_ld_chr/ 

Beginning analysis at Mon Nov 25 14:58:40 2019
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ukb-d-import/processed/ukb-d-20113_101/ukb-d-20113_101.vcf.gz ...
Read summary statistics for 10615672 SNPs.
Dropped 8555 SNPs with duplicated rs numbers.
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, 1280901 SNPs remain.
After merging with regression SNP LD, 1280901 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.1093 (0.1627)
Lambda GC: 1.0057
Mean Chi^2: 1.0013
Intercept: 0.995 (0.0067)
Ratio < 0 (usually indicates GC correction).
Analysis finished at Mon Nov 25 15:00:24 2019
Total time elapsed: 1.0m:43.98s

QC metrics

Metrics

Metrics

{
    "af_correlation": 0.9444,
    "inflation_factor": 1.009,
    "mean_EFFECT": 0.0001,
    "n": 2906,
    "n_snps": 10615672,
    "n_clumped_hits": 0,
    "n_p_sig": 0,
    "n_mono": 0,
    "n_ns": 1117793,
    "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": 210007,
    "n_est": 2923.8697,
    "ratio_se_n": 1.0031,
    "mean_diff": 0.0001,
    "ratio_diff": 150.7571,
    "sd_y_est1": 0.4438,
    "sd_y_est2": 0.4452,
    "r2_sum1": 0,
    "r2_sum2": 0,
    "r2_sum3": 0,
    "r2_sum4": 0,
    "ldsc_nsnp_merge_refpanel_ld": 1280901,
    "ldsc_nsnp_merge_regression_ld": 1280901,
    "ldsc_observed_scale_h2_beta": 0.1093,
    "ldsc_observed_scale_h2_se": 0.1627,
    "ldsc_intercept_beta": 0.995,
    "ldsc_intercept_se": 0.0067,
    "ldsc_lambda_gc": 1.0057,
    "ldsc_mean_chisq": 1.0013,
    "ldsc_ratio": -3.8462
}

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 numeric.mean numeric.sd numeric.p0 numeric.p25 numeric.p50 numeric.p75 numeric.p100 numeric.hist
character ID 0 1.0000000 3 94 0 10607687 0 NA NA NA NA NA NA NA NA
character REF 0 1.0000000 1 100 0 50025 0 NA NA NA NA NA NA NA NA
character ALT 0 1.0000000 1 342 0 30863 0 NA NA NA NA NA NA NA NA
numeric CHROM 0 1.0000000 NA NA NA NA NA 9.076150e+00 6.179502e+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 7.879405e+07 5.604673e+07 302.0000000 3.256518e+07 6.973983e+07 1.147298e+08 2.492297e+08 ▇▆▅▂▁
numeric EFFECT 0 1.0000000 NA NA NA NA NA 9.280000e-05 3.252490e-02 -0.3930350 -1.343050e-02 1.859000e-04 1.387740e-02 2.894050e-01 ▁▁▇▂▁
numeric SE 0 1.0000000 NA NA NA NA NA 2.686680e-02 1.827500e-02 0.0095328 1.298460e-02 1.843840e-02 3.548330e-02 1.014580e-01 ▇▂▁▁▁
numeric PVAL 0 1.0000000 NA NA NA NA NA 4.992829e-01 2.883609e-01 0.0000002 2.501762e-01 4.980799e-01 7.491555e-01 1.000000e+00 ▇▇▇▇▇
numeric PVAL_ztest 0 1.0000000 NA NA NA NA NA 4.992276e-01 2.883941e-01 0.0000002 2.500805e-01 4.980257e-01 7.491317e-01 1.000000e+00 ▇▇▇▇▇
numeric AF 0 1.0000000 NA NA NA NA NA 2.409905e-01 2.624736e-01 0.0056745 2.917220e-02 1.299230e-01 3.858330e-01 9.943250e-01 ▇▂▂▁▁
numeric AF_reference 210007 0.9802173 NA NA NA NA NA 2.409291e-01 2.534337e-01 0.0000000 2.975240e-02 1.467650e-01 3.829870e-01 1.000000e+00 ▇▂▂▁▁
numeric N 0 1.0000000 NA NA NA NA NA 2.906000e+03 0.000000e+00 2906.0000000 2.906000e+03 2.906000e+03 2.906000e+03 2.906000e+03 ▁▁▇▁▁

Head and tail

CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
1 692794 rs530212009 CA C -0.0237890 0.0206686 0.2498377 0.2497434 0.1111720 0.1894970 2906
1 693731 rs12238997 A G -0.0195892 0.0192432 0.3087742 0.3086873 0.1160680 0.1417730 2906
1 707522 rs371890604 G C -0.0167652 0.0213509 0.4323884 0.4323233 0.0980237 0.1293930 2906
1 717587 rs144155419 G A -0.0024157 0.0516802 0.9627209 0.9627180 0.0161674 0.0045926 2906
1 730087 rs148120343 T C -0.0373428 0.0264189 0.1576210 0.1575123 0.0576893 0.0127796 2906
1 731718 rs142557973 T C -0.0178183 0.0182676 0.3294413 0.3293596 0.1223740 0.1543530 2906
1 732032 rs61770163 A C -0.0119356 0.0194629 0.5397604 0.5397118 0.1219650 0.1555510 2906
1 734349 rs141242758 T C -0.0161912 0.0182737 0.3756721 0.3755968 0.1215630 0.1525560 2906
1 740284 rs61770167 C T -0.0310840 0.0828513 0.7075547 0.7075280 0.0060187 0.0023962 2906
1 749963 rs529266287 T TAA 0.0153893 0.0179751 0.3919882 0.3919173 0.8703350 0.7641770 2906
CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
23 154923311 rs141127553 C T -0.0044543 0.0199652 0.8234700 0.8234548 0.0623281 0.0309934 2906
23 154923374 rs111332691 T A -0.0345558 0.0235134 0.1417741 0.1416643 0.0443909 0.0116556 2906
23 154925045 rs509981 C T 0.0150637 0.0113552 0.1847481 0.1846442 0.2412490 0.3634440 2906
23 154925895 rs538470 C T 0.0168582 0.0116150 0.1467719 0.1466640 0.2369750 0.3634440 2906
23 154927581 rs644138 G A 0.0118942 0.0105676 0.2604582 0.2603625 0.3037750 0.4635760 2906
23 154929412 rs557132 C T 0.0147306 0.0113642 0.1950011 0.1948968 0.2409490 0.3568210 2906
23 154929637 rs35185538 CT C 0.0041243 0.0118388 0.7275888 0.7275625 0.2270290 0.3011920 2906
23 154929952 rs4012982 CAA C 0.0159593 0.0119215 0.1807769 0.1806687 0.2344250 0.3165560 2906
23 154930230 rs781880 A G 0.0151876 0.0113696 0.1817180 0.1816121 0.2405400 0.3618540 2906
23 154930487 rs781879 T A 0.0064274 0.0408659 0.8750350 0.8750238 0.0193886 0.1263580 2906

bcf preview

1   692794  rs530212009 CA  C   .   PASS    AF=0.111172 ES:SE:LP:AF:SS:ID   -0.023789:0.0206686:0.602342:0.111172:2906:1_692794_CA_C
1   693731  rs12238997  A   G   .   PASS    AF=0.116068 ES:SE:LP:AF:SS:ID   -0.0195892:0.0192432:0.510359:0.116068:2906:rs12238997
1   707522  rs371890604 G   C   .   PASS    AF=0.0980237    ES:SE:LP:AF:SS:ID   -0.0167652:0.0213509:0.364126:0.0980237:2906:rs371890604
1   717587  rs144155419 G   A   .   PASS    AF=0.0161674    ES:SE:LP:AF:SS:ID   -0.00241569:0.0516802:0.0164996:0.0161674:2906:rs144155419
1   730087  rs148120343 T   C   .   PASS    AF=0.0576893    ES:SE:LP:AF:SS:ID   -0.0373428:0.0264189:0.802386:0.0576893:2906:rs148120343
1   731718  rs58276399  T   C   .   PASS    AF=0.122374 ES:SE:LP:AF:SS:ID   -0.0178183:0.0182676:0.482222:0.122374:2906:rs58276399
1   732032  rs61770163  A   C   .   PASS    AF=0.121965 ES:SE:LP:AF:SS:ID   -0.0119356:0.0194629:0.267799:0.121965:2906:rs61770163
1   734349  rs141242758 T   C   .   PASS    AF=0.121563 ES:SE:LP:AF:SS:ID   -0.0161912:0.0182737:0.425191:0.121563:2906:rs141242758
1   740284  rs61770167  C   T   .   PASS    AF=0.00601865   ES:SE:LP:AF:SS:ID   -0.031084:0.0828513:0.15024:0.00601865:2906:rs61770167
1   749963  rs529266287 T   TAA .   PASS    AF=0.870335 ES:SE:LP:AF:SS:ID   0.0153893:0.0179751:0.406727:0.870335:2906:rs529266287
1   751343  rs28544273  T   A   .   PASS    AF=0.124143 ES:SE:LP:AF:SS:ID   -0.0145723:0.0177504:0.385375:0.124143:2906:rs28544273
1   751488  rs200141114 G   GA  .   PASS    AF=0.144138 ES:SE:LP:AF:SS:ID   -0.0107558:0.0175601:0.267407:0.144138:2906:rs200141114
1   751756  rs28527770  T   C   .   PASS    AF=0.124249 ES:SE:LP:AF:SS:ID   -0.0145087:0.017723:0.383984:0.124249:2906:rs28527770
1   753405  rs3115860   C   A   .   PASS    AF=0.870459 ES:SE:LP:AF:SS:ID   0.0163273:0.0172816:0.462372:0.870459:2906:rs3115860
1   753425  rs3131970   T   C   .   PASS    AF=0.873999 ES:SE:LP:AF:SS:ID   0.01238:0.0175393:0.318448:0.873999:2906:rs3131970
1   753541  rs2073813   G   A   .   PASS    AF=0.128905 ES:SE:LP:AF:SS:ID   -0.0149037:0.0173414:0.408741:0.128905:2906:rs2073813
1   754105  rs12184325  C   T   .   PASS    AF=0.0352719    ES:SE:LP:AF:SS:ID   0.0202705:0.0320513:0.278065:0.0352719:2906:rs12184325
1   754182  rs3131969   A   G   .   PASS    AF=0.870125 ES:SE:LP:AF:SS:ID   0.0160262:0.0172758:0.451418:0.870125:2906:rs3131969
1   754192  rs3131968   A   G   .   PASS    AF=0.870468 ES:SE:LP:AF:SS:ID   0.0168363:0.0173159:0.480197:0.870468:2906:rs3131968
1   754334  rs3131967   T   C   .   PASS    AF=0.870284 ES:SE:LP:AF:SS:ID   0.0164146:0.0172814:0.465629:0.870284:2906:rs3131967
1   754433  rs150578204 G   A   .   PASS    AF=0.00603754   ES:SE:LP:AF:SS:ID   0.0717476:0.0796457:0.434445:0.00603754:2906:rs150578204
1   754458  rs142682604 G   T   .   PASS    AF=0.00599503   ES:SE:LP:AF:SS:ID   0.0710132:0.0799745:0.426382:0.00599503:2906:rs142682604
1   755435  rs184270342 T   G   .   PASS    AF=0.00629934   ES:SE:LP:AF:SS:ID   0.00941401:0.0807845:0.0422783:0.00629934:2906:rs184270342
1   755890  rs3115858   A   T   .   PASS    AF=0.869891 ES:SE:LP:AF:SS:ID   0.0157415:0.0172215:0.442779:0.869891:2906:rs3115858
1   756434  rs61768170  G   C   .   PASS    AF=0.126799 ES:SE:LP:AF:SS:ID   -0.0158598:0.0175664:0.435712:0.126799:2906:rs61768170
1   756604  rs3131962   A   G   .   PASS    AF=0.86958  ES:SE:LP:AF:SS:ID   0.0154494:0.0171731:0.433689:0.86958:2906:rs3131962
1   757640  rs3115853   G   A   .   PASS    AF=0.868956 ES:SE:LP:AF:SS:ID   0.0158362:0.0171616:0.448299:0.868956:2906:rs3115853
1   757734  rs4951929   C   T   .   PASS    AF=0.869689 ES:SE:LP:AF:SS:ID   0.0157028:0.0171995:0.442097:0.869689:2906:rs4951929
1   757936  rs4951862   C   A   .   PASS    AF=0.869718 ES:SE:LP:AF:SS:ID   0.0158216:0.0172038:0.446324:0.869718:2906:rs4951862
1   758144  rs3131956   A   G   .   PASS    AF=0.86973  ES:SE:LP:AF:SS:ID   0.0157944:0.0172039:0.445317:0.86973:2906:rs3131956
1   758626  rs3131954   C   T   .   PASS    AF=0.869985 ES:SE:LP:AF:SS:ID   0.0159661:0.0172384:0.450479:0.869985:2906:rs3131954
1   759293  rs10157329  T   A   .   PASS    AF=0.0984312    ES:SE:LP:AF:SS:ID   -0.0173836:0.0200086:0.41451:0.0984312:2906:rs10157329
1   759600  rs545998451 AGT A   .   PASS    AF=0.00695653   ES:SE:LP:AF:SS:ID   -0.0195368:0.0753194:0.0994384:0.00695653:2906:1_759600_AGT_A
1   759837  rs3115851   T   A   .   PASS    AF=0.873799 ES:SE:LP:AF:SS:ID   0.0129506:0.0175072:0.337691:0.873799:2906:rs3115851
1   761732  rs2286139   C   T   .   PASS    AF=0.862638 ES:SE:LP:AF:SS:ID   0.0175484:0.0171557:0.513647:0.862638:2906:rs2286139
1   761752  rs1057213   C   T   .   PASS    AF=0.867936 ES:SE:LP:AF:SS:ID   0.0160186:0.0173375:0.449036:0.867936:2906:rs1057213
1   762273  rs3115849   G   A   .   PASS    AF=0.865277 ES:SE:LP:AF:SS:ID   0.0147996:0.0173074:0.406088:0.865277:2906:rs3115849
1   762485  rs12095200  C   A   .   PASS    AF=0.0981553    ES:SE:LP:AF:SS:ID   -0.0102967:0.0211404:0.203252:0.0981553:2906:rs12095200
1   762589  rs3115848   G   C   .   PASS    AF=0.87099  ES:SE:LP:AF:SS:ID   0.0135398:0.0175663:0.35566:0.87099:2906:rs3115848
1   762592  rs3131950   C   G   .   PASS    AF=0.870988 ES:SE:LP:AF:SS:ID   0.0135364:0.0175661:0.355554:0.870988:2906:rs3131950
1   762601  rs3131949   T   C   .   PASS    AF=0.870986 ES:SE:LP:AF:SS:ID   0.0135302:0.0175662:0.355344:0.870986:2906:rs3131949
1   762632  rs3131948   T   A   .   PASS    AF=0.871237 ES:SE:LP:AF:SS:ID   0.0129822:0.0175635:0.337365:0.871237:2906:rs3131948
1   764191  rs7515915   T   G   .   PASS    AF=0.126611 ES:SE:LP:AF:SS:ID   -0.0139654:0.0175598:0.370082:0.126611:2906:rs7515915
1   766007  rs61768174  A   C   .   PASS    AF=0.105187 ES:SE:LP:AF:SS:ID   -0.0200103:0.019143:0.528754:0.105187:2906:rs61768174
1   766105  rs2519015   T   A   .   PASS    AF=0.854691 ES:SE:LP:AF:SS:ID   0.0165241:0.0172238:0.471791:0.854691:2906:rs2519015
1   768116  rs376645387 A   AGTTTT  .   PASS    AF=0.833478 ES:SE:LP:AF:SS:ID   -0.0188328:0.0168717:0.577716:0.833478:2906:rs376645387
1   768253  rs2977608   A   C   .   PASS    AF=0.757857 ES:SE:LP:AF:SS:ID   -0.00401914:0.0135111:0.115698:0.757857:2906:rs2977608
1   768448  rs12562034  G   A   .   PASS    AF=0.110289 ES:SE:LP:AF:SS:ID   0.0286297:0.0187333:0.897731:0.110289:2906:rs12562034
1   769138  rs59306077  CAT C   .   PASS    AF=0.130107 ES:SE:LP:AF:SS:ID   -0.0160633:0.0172987:0.452003:0.130107:2906:rs762168062
1   769223  rs60320384  C   G   .   PASS    AF=0.129238 ES:SE:LP:AF:SS:ID   -0.0148568:0.017314:0.407915:0.129238:2906:rs60320384