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-20486/ukb-d-20486.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-20486/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 17:08:04 2019
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ukb-d-import/processed/ukb-d-20486/ukb-d-20486.vcf.gz ...
Read summary statistics for 11386517 SNPs.
Dropped 9628 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, 1282470 SNPs remain.
After merging with regression SNP LD, 1282470 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.036 (0.0257)
Lambda GC: 1.0154
Mean Chi^2: 1.0159
Intercept: 1.0036 (0.0063)
Ratio: 0.2244 (0.3954)
Analysis finished at Mon Nov 25 17:09:56 2019
Total time elapsed: 1.0m:52.29s

QC metrics

Metrics

Metrics

{
    "af_correlation": 0.9472,
    "inflation_factor": 1.0152,
    "mean_EFFECT": -0,
    "n": 17244,
    "n_snps": 11386517,
    "n_clumped_hits": 0,
    "n_p_sig": 0,
    "n_mono": 0,
    "n_ns": 1156522,
    "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": 237592,
    "n_est": 17276.6032,
    "ratio_se_n": 1.0009,
    "mean_diff": -0,
    "ratio_diff": 36.0396,
    "sd_y_est1": 0.3991,
    "sd_y_est2": 0.3994,
    "r2_sum1": 0,
    "r2_sum2": 0,
    "r2_sum3": 0,
    "r2_sum4": 0,
    "ldsc_nsnp_merge_refpanel_ld": 1282470,
    "ldsc_nsnp_merge_regression_ld": 1282470,
    "ldsc_observed_scale_h2_beta": 0.036,
    "ldsc_observed_scale_h2_se": 0.0257,
    "ldsc_intercept_beta": 1.0036,
    "ldsc_intercept_se": 0.0063,
    "ldsc_lambda_gc": 1.0154,
    "ldsc_mean_chisq": 1.0159,
    "ldsc_ratio": 0.2264
}

Flags

name value
af_correlation FALSE
inflation_factor FALSE
n FALSE
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 11377488 0 NA NA NA NA NA NA NA NA
character REF 0 1.0000000 1 100 0 52011 0 NA NA NA NA NA NA NA NA
character ALT 0 1.0000000 1 342 0 31629 0 NA NA NA NA NA NA NA NA
numeric CHROM 0 1.0000000 NA NA NA NA NA 9.073479e+00 6.183323e+00 1.00000e+00 4.000000e+00 8.000000e+00 1.300000e+01 2.300000e+01 ▇▅▅▂▂
numeric POS 0 1.0000000 NA NA NA NA NA 7.883824e+07 5.600146e+07 3.02000e+02 3.262823e+07 6.983662e+07 1.147306e+08 2.492309e+08 ▇▆▅▂▁
numeric EFFECT 0 1.0000000 NA NA NA NA NA -2.520000e-05 1.450600e-02 -1.43836e-01 -5.499000e-03 -5.630000e-05 5.354200e-03 1.839330e-01 ▁▁▇▁▁
numeric SE 0 1.0000000 NA NA NA NA NA 1.149710e-02 8.788500e-03 3.66300e-03 4.870700e-03 7.340800e-03 1.558160e-02 5.262360e-02 ▇▂▁▁▁
numeric PVAL 0 1.0000000 NA NA NA NA NA 4.977882e-01 2.891860e-01 4.00000e-07 2.469932e-01 4.967581e-01 7.481592e-01 1.000000e+00 ▇▇▇▇▇
numeric PVAL_ztest 0 1.0000000 NA NA NA NA NA 4.977789e-01 2.891916e-01 3.00000e-07 2.469767e-01 4.967484e-01 7.481558e-01 1.000000e+00 ▇▇▇▇▇
numeric AF 0 1.0000000 NA NA NA NA NA 2.256198e-01 2.609786e-01 3.63590e-03 2.038340e-02 1.080030e-01 3.606500e-01 9.963640e-01 ▇▂▁▁▁
numeric AF_reference 237592 0.9791339 NA NA NA NA NA 2.261874e-01 2.521910e-01 0.00000e+00 1.797120e-02 1.261980e-01 3.602240e-01 1.000000e+00 ▇▂▂▁▁
numeric N 0 1.0000000 NA NA NA NA NA 1.724400e+04 0.000000e+00 1.72440e+04 1.724400e+04 1.724400e+04 1.724400e+04 1.724400e+04 ▁▁▇▁▁

Head and tail

CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
1 692794 rs530212009 CA C 0.0074084 0.0075347 0.3255090 0.3254951 0.1106940 0.1894970 17244
1 693731 rs12238997 A G 0.0048137 0.0070919 0.4972995 0.4972903 0.1162750 0.1417730 17244
1 707522 rs371890604 G C 0.0114037 0.0079751 0.1527591 0.1527399 0.0990443 0.1293930 17244
1 717587 rs144155419 G A -0.0280993 0.0193007 0.1454481 0.1454287 0.0153008 0.0045926 17244
1 730087 rs148120343 T C 0.0168424 0.0098463 0.0871867 0.0871681 0.0575816 0.0127796 17244
1 731718 rs142557973 T C 0.0066523 0.0067166 0.3219860 0.3219721 0.1226400 0.1543530 17244
1 732032 rs61770163 A C 0.0100121 0.0071949 0.1640748 0.1640583 0.1219050 0.1555510 17244
1 734349 rs141242758 T C 0.0071186 0.0067180 0.2893277 0.2893135 0.1220170 0.1525560 17244
1 740284 rs61770167 C T 0.0245874 0.0318206 0.4397178 0.4397070 0.0055061 0.0023962 17244
1 749963 rs529266287 T TAA -0.0043264 0.0066408 0.5147460 0.5147377 0.8691130 0.7641770 17244
CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
23 154923311 rs141127553 C T 0.0264494 0.0082398 0.0013300 0.0013276 0.0546676 0.0309934 17244
23 154923374 rs111332691 T A -0.0111053 0.0091835 0.2265740 0.2265584 0.0426815 0.0116556 17244
23 154925045 rs509981 C T -0.0000086 0.0042472 0.9983910 0.9983907 0.2502950 0.3634440 17244
23 154925895 rs538470 C T -0.0001049 0.0043370 0.9806960 0.9806956 0.2469020 0.3634440 17244
23 154927581 rs644138 G A 0.0064214 0.0040086 0.1091941 0.1091758 0.3054640 0.4635760 17244
23 154929412 rs557132 C T -0.0002368 0.0042488 0.9555519 0.9555515 0.2501480 0.3568210 17244
23 154929637 rs35185538 CT C 0.0011240 0.0044324 0.7998250 0.7998223 0.2336280 0.3011920 17244
23 154929952 rs4012982 CAA C 0.0014553 0.0044810 0.7453513 0.7453469 0.2432900 0.3165560 17244
23 154930230 rs781880 A G 0.0000189 0.0042486 0.9964490 0.9964485 0.2506840 0.3618540 17244
23 154930487 rs781879 T A 0.0202356 0.0144001 0.1599680 0.1599499 0.0202463 0.1263580 17244

bcf preview

1   692794  rs530212009 CA  C   .   PASS    AF=0.110694 ES:SE:LP:AF:SS:ID   0.00740835:0.00753472:0.487437:0.110694:17244:1_692794_CA_C
1   693731  rs12238997  A   G   .   PASS    AF=0.116275 ES:SE:LP:AF:SS:ID   0.00481368:0.00709188:0.303382:0.116275:17244:rs12238997
1   707522  rs371890604 G   C   .   PASS    AF=0.0990443    ES:SE:LP:AF:SS:ID   0.0114037:0.00797506:0.815993:0.0990443:17244:rs371890604
1   717587  rs144155419 G   A   .   PASS    AF=0.0153008    ES:SE:LP:AF:SS:ID   -0.0280993:0.0193007:0.837292:0.0153008:17244:rs144155419
1   730087  rs148120343 T   C   .   PASS    AF=0.0575816    ES:SE:LP:AF:SS:ID   0.0168424:0.00984631:1.05955:0.0575816:17244:rs148120343
1   731718  rs58276399  T   C   .   PASS    AF=0.12264  ES:SE:LP:AF:SS:ID   0.00665226:0.00671665:0.492163:0.12264:17244:rs58276399
1   732032  rs61770163  A   C   .   PASS    AF=0.121905 ES:SE:LP:AF:SS:ID   0.0100121:0.00719492:0.784958:0.121905:17244:rs61770163
1   734349  rs141242758 T   C   .   PASS    AF=0.122017 ES:SE:LP:AF:SS:ID   0.00711864:0.00671805:0.53861:0.122017:17244:rs141242758
1   740284  rs61770167  C   T   .   PASS    AF=0.00550609   ES:SE:LP:AF:SS:ID   0.0245874:0.0318206:0.356826:0.00550609:17244:rs61770167
1   749963  rs529266287 T   TAA .   PASS    AF=0.869113 ES:SE:LP:AF:SS:ID   -0.00432637:0.00664085:0.288407:0.869113:17244:rs529266287
1   751343  rs28544273  T   A   .   PASS    AF=0.123645 ES:SE:LP:AF:SS:ID   0.00355419:0.00656911:0.230266:0.123645:17244:rs28544273
1   751488  rs200141114 G   GA  .   PASS    AF=0.143294 ES:SE:LP:AF:SS:ID   0.00475265:0.0064887:0.333572:0.143294:17244:rs200141114
1   751756  rs28527770  T   C   .   PASS    AF=0.123755 ES:SE:LP:AF:SS:ID   0.00356463:0.00655955:0.231478:0.123755:17244:rs28527770
1   753405  rs3115860   C   A   .   PASS    AF=0.869529 ES:SE:LP:AF:SS:ID   -0.00410256:0.00637571:0.284055:0.869529:17244:rs3115860
1   753425  rs3131970   T   C   .   PASS    AF=0.874238 ES:SE:LP:AF:SS:ID   -0.00210862:0.00648135:0.127884:0.874238:17244:rs3131970
1   753541  rs2073813   G   A   .   PASS    AF=0.129823 ES:SE:LP:AF:SS:ID   0.00459517:0.00639813:0.32547:0.129823:17244:rs2073813
1   754105  rs12184325  C   T   .   PASS    AF=0.0369114    ES:SE:LP:AF:SS:ID   0.0120643:0.0115768:0.526694:0.0369114:17244:rs12184325
1   754182  rs3131969   A   G   .   PASS    AF=0.869091 ES:SE:LP:AF:SS:ID   -0.00377351:0.00636931:0.256839:0.869091:17244:rs3131969
1   754192  rs3131968   A   G   .   PASS    AF=0.869183 ES:SE:LP:AF:SS:ID   -0.00388533:0.00637108:0.266019:0.869183:17244:rs3131968
1   754334  rs3131967   T   C   .   PASS    AF=0.86911  ES:SE:LP:AF:SS:ID   -0.00379767:0.00636926:0.258836:0.86911:17244:rs3131967
1   754433  rs150578204 G   A   .   PASS    AF=0.00503068   ES:SE:LP:AF:SS:ID   -0.0404849:0.0329206:0.659955:0.00503068:17244:rs150578204
1   754458  rs142682604 G   T   .   PASS    AF=0.00499043   ES:SE:LP:AF:SS:ID   -0.0397735:0.0330113:0.641532:0.00499043:17244:rs142682604
1   755435  rs184270342 T   G   .   PASS    AF=0.00578206   ES:SE:LP:AF:SS:ID   0.0513391:0.0311084:1.00483:0.00578206:17244:rs184270342
1   755890  rs3115858   A   T   .   PASS    AF=0.869232 ES:SE:LP:AF:SS:ID   -0.00462089:0.00635763:0.330364:0.869232:17244:rs3115858
1   756434  rs61768170  G   C   .   PASS    AF=0.126892 ES:SE:LP:AF:SS:ID   0.00416955:0.00649927:0.283012:0.126892:17244:rs61768170
1   756604  rs3131962   A   G   .   PASS    AF=0.868824 ES:SE:LP:AF:SS:ID   -0.00477717:0.00634157:0.34556:0.868824:17244:rs3131962
1   757640  rs3115853   G   A   .   PASS    AF=0.868111 ES:SE:LP:AF:SS:ID   -0.00404914:0.00634147:0.281377:0.868111:17244:rs3115853
1   757734  rs4951929   C   T   .   PASS    AF=0.868979 ES:SE:LP:AF:SS:ID   -0.00466162:0.00634883:0.3346:0.868979:17244:rs4951929
1   757936  rs4951862   C   A   .   PASS    AF=0.868984 ES:SE:LP:AF:SS:ID   -0.0046622:0.00634931:0.334621:0.868984:17244:rs4951862
1   758144  rs3131956   A   G   .   PASS    AF=0.868986 ES:SE:LP:AF:SS:ID   -0.00466494:0.00634925:0.33487:0.868986:17244:rs3131956
1   758626  rs3131954   C   T   .   PASS    AF=0.869298 ES:SE:LP:AF:SS:ID   -0.00452342:0.0063615:0.321431:0.869298:17244:rs3131954
1   759293  rs10157329  T   A   .   PASS    AF=0.0999441    ES:SE:LP:AF:SS:ID   0.00740256:0.00742999:0.496054:0.0999441:17244:rs10157329
1   759600  rs545998451 AGT A   .   PASS    AF=0.0070258    ES:SE:LP:AF:SS:ID   0.0367999:0.0276787:0.735919:0.0070258:17244:1_759600_AGT_A
1   759837  rs3115851   T   A   .   PASS    AF=0.873309 ES:SE:LP:AF:SS:ID   -0.00175294:0.00646345:0.104448:0.873309:17244:rs3115851
1   761732  rs2286139   C   T   .   PASS    AF=0.862743 ES:SE:LP:AF:SS:ID   -0.00348124:0.00633414:0.234629:0.862743:17244:rs2286139
1   761752  rs1057213   C   T   .   PASS    AF=0.868186 ES:SE:LP:AF:SS:ID   -0.00298574:0.00639957:0.19326:0.868186:17244:rs1057213
1   762273  rs3115849   G   A   .   PASS    AF=0.865415 ES:SE:LP:AF:SS:ID   -0.00332614:0.00641387:0.218923:0.865415:17244:rs3115849
1   762485  rs12095200  C   A   .   PASS    AF=0.100462 ES:SE:LP:AF:SS:ID   0.0010658:0.00762924:0.0511471:0.100462:17244:rs12095200
1   762589  rs3115848   G   C   .   PASS    AF=0.870447 ES:SE:LP:AF:SS:ID   -0.00189803:0.00648158:0.113705:0.870447:17244:rs3115848
1   762592  rs3131950   C   G   .   PASS    AF=0.870447 ES:SE:LP:AF:SS:ID   -0.00189729:0.00648158:0.113656:0.870447:17244:rs3131950
1   762601  rs3131949   T   C   .   PASS    AF=0.870444 ES:SE:LP:AF:SS:ID   -0.00189666:0.0064816:0.113614:0.870444:17244:rs3131949
1   762632  rs3131948   T   A   .   PASS    AF=0.870674 ES:SE:LP:AF:SS:ID   -0.00163064:0.00648304:0.0961442:0.870674:17244:rs3131948
1   764191  rs7515915   T   G   .   PASS    AF=0.126652 ES:SE:LP:AF:SS:ID   0.00312899:0.0064916:0.200792:0.126652:17244:rs7515915
1   766007  rs61768174  A   C   .   PASS    AF=0.106661 ES:SE:LP:AF:SS:ID   0.0110481:0.0070581:0.929855:0.106661:17244:rs61768174
1   766105  rs2519015   T   A   .   PASS    AF=0.853385 ES:SE:LP:AF:SS:ID   -0.00338855:0.00631405:0.228042:0.853385:17244:rs2519015
1   768116  rs376645387 A   AGTTTT  .   PASS    AF=0.837287 ES:SE:LP:AF:SS:ID   -0.00944559:0.00626347:0.88087:0.837287:17244:rs376645387
1   768253  rs2977608   A   C   .   PASS    AF=0.760956 ES:SE:LP:AF:SS:ID   -0.0089661:0.00501796:1.13084:0.760956:17244:rs2977608
1   768448  rs12562034  G   A   .   PASS    AF=0.106907 ES:SE:LP:AF:SS:ID   0.0128561:0.00694024:1.19391:0.106907:17244:rs12562034
1   768819  rs12562811  C   T   .   PASS    AF=0.00808841   ES:SE:LP:AF:SS:ID   -0.00986727:0.0250987:0.158502:0.00808841:17244:rs12562811
1   769138  rs59306077  CAT C   .   PASS    AF=0.129933 ES:SE:LP:AF:SS:ID   0.00447762:0.00640335:0.314799:0.129933:17244:rs762168062