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-22604_4/ukb-d-22604_4.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-22604_4/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 16:37:15 2019
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ukb-d-import/processed/ukb-d-22604_4/ukb-d-22604_4.vcf.gz ...
Read summary statistics for 13563393 SNPs.
Dropped 12678 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, 1283500 SNPs remain.
After merging with regression SNP LD, 1283500 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.028 (0.0075)
Lambda GC: 1.0308
Mean Chi^2: 1.048
Intercept: 1.0045 (0.0074)
Ratio: 0.0944 (0.1546)
Analysis finished at Mon Nov 25 16:39:57 2019
Total time elapsed: 2.0m:42.21s

QC metrics

Metrics

Metrics

{
    "af_correlation": 0.9521,
    "inflation_factor": 1.0204,
    "mean_EFFECT": -0,
    "n": 75177,
    "n_snps": 13563393,
    "n_clumped_hits": 0,
    "n_p_sig": 0,
    "n_mono": 0,
    "n_ns": 1251060,
    "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": 562172,
    "n_est": 75447.5709,
    "ratio_se_n": 1.0018,
    "mean_diff": -0,
    "ratio_diff": 17.2376,
    "sd_y_est1": 0.4759,
    "sd_y_est2": 0.4767,
    "r2_sum1": 0,
    "r2_sum2": 0,
    "r2_sum3": 0,
    "r2_sum4": 0,
    "ldsc_nsnp_merge_refpanel_ld": 1283500,
    "ldsc_nsnp_merge_regression_ld": 1283500,
    "ldsc_observed_scale_h2_beta": 0.028,
    "ldsc_observed_scale_h2_se": 0.0075,
    "ldsc_intercept_beta": 1.0045,
    "ldsc_intercept_se": 0.0074,
    "ldsc_lambda_gc": 1.0308,
    "ldsc_mean_chisq": 1.048,
    "ldsc_ratio": 0.0937
}

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 13551378 0 NA NA NA NA NA NA NA NA
character REF 0 1.0000000 1 100 0 57038 0 NA NA NA NA NA NA NA NA
character ALT 0 1.0000000 1 342 0 33329 0 NA NA NA NA NA NA NA NA
numeric CHROM 0 1.0000000 NA NA NA NA NA 9.051500e+00 6.185025e+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 7.902521e+07 5.591715e+07 3.02000e+02 3.292786e+07 7.013476e+07 1.148632e+08 2.492309e+08 ▇▆▅▂▁
numeric EFFECT 0 1.0000000 NA NA NA NA NA -2.310000e-05 1.428620e-02 -1.60282e-01 -3.845200e-03 -7.200000e-06 3.808200e-03 1.741140e-01 ▁▁▇▁▁
numeric SE 0 1.0000000 NA NA NA NA NA 1.026630e-02 9.891700e-03 2.03950e-03 2.934600e-03 5.395700e-03 1.473830e-02 4.989430e-02 ▇▂▁▁▁
numeric PVAL 0 1.0000000 NA NA NA NA NA 4.964497e-01 2.902629e-01 1.00000e-07 2.436571e-01 4.956636e-01 7.481953e-01 1.000000e+00 ▇▇▇▇▇
numeric PVAL_ztest 0 1.0000000 NA NA NA NA NA 4.964476e-01 2.902641e-01 1.00000e-07 2.436536e-01 4.956616e-01 7.481946e-01 1.000000e+00 ▇▇▇▇▇
numeric AF 0 1.0000000 NA NA NA NA NA 1.911163e-01 2.544894e-01 1.00000e-03 7.513700e-03 6.035730e-02 2.958730e-01 9.989990e-01 ▇▂▁▁▁
numeric AF_reference 562172 0.9585523 NA NA NA NA NA 1.965590e-01 2.471553e-01 0.00000e+00 5.790700e-03 8.446490e-02 3.085060e-01 1.000000e+00 ▇▂▁▁▁
numeric N 0 1.0000000 NA NA NA NA NA 7.517700e+04 0.000000e+00 7.51770e+04 7.517700e+04 7.517700e+04 7.517700e+04 7.517700e+04 ▁▁▇▁▁

Head and tail

CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
1 692794 rs530212009 CA C 0.0053924 0.0042903 0.2087988 0.2087947 0.1115640 0.1894970 75177
1 693731 rs12238997 A G 0.0064646 0.0040621 0.1115080 0.1115042 0.1164770 0.1417730 75177
1 707522 rs371890604 G C 0.0054779 0.0045655 0.2302062 0.2302030 0.0977849 0.1293930 75177
1 717587 rs144155419 G A 0.0196194 0.0108325 0.0701197 0.0701160 0.0159063 0.0045926 75177
1 723329 rs189787166 A T -0.0184443 0.0317645 0.5614732 0.5614712 0.0017753 0.0003994 75177
1 730087 rs148120343 T C 0.0052989 0.0056324 0.3468199 0.3468165 0.0569733 0.0127796 75177
1 731718 rs142557973 T C 0.0059006 0.0038534 0.1257060 0.1257017 0.1223380 0.1543530 75177
1 732032 rs61770163 A C 0.0064741 0.0041123 0.1154181 0.1154133 0.1218660 0.1555510 75177
1 734349 rs141242758 T C 0.0060785 0.0038557 0.1149100 0.1149063 0.1216090 0.1525560 75177
1 740284 rs61770167 C T -0.0148879 0.0174641 0.3939481 0.3939444 0.0058807 0.0023962 75177
CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
23 154923311 rs141127553 C T 0.0035607 0.0045659 0.4354828 0.4354812 0.0546566 0.0309934 75177
23 154923374 rs111332691 T A 0.0020560 0.0049227 0.6761966 0.6761961 0.0450404 0.0116556 75177
23 154925045 rs509981 C T -0.0002543 0.0023814 0.9149600 0.9149604 0.2443920 0.3634440 75177
23 154925895 rs538470 C T -0.0002418 0.0024344 0.9208869 0.9208867 0.2408890 0.3634440 75177
23 154927581 rs644138 G A 0.0006389 0.0022425 0.7757200 0.7757184 0.2994310 0.4635760 75177
23 154929412 rs557132 C T -0.0002738 0.0023819 0.9084859 0.9084863 0.2442760 0.3568210 75177
23 154929637 rs35185538 CT C -0.0004172 0.0024868 0.8667521 0.8667517 0.2287170 0.3011920 75177
23 154929952 rs4012982 CAA C -0.0002800 0.0025063 0.9110380 0.9110380 0.2382650 0.3165560 75177
23 154930230 rs781880 A G -0.0002121 0.0023813 0.9290351 0.9290344 0.2447030 0.3618540 75177
23 154930487 rs781879 T A 0.0048067 0.0080914 0.5524780 0.5524762 0.0195950 0.1263580 75177

bcf preview

1   692794  rs530212009 CA  C   .   PASS    AF=0.111564 ES:SE:LP:AF:SS:ID   0.00539237:0.00429026:0.680272:0.111564:75177:1_692794_CA_C
1   693731  rs12238997  A   G   .   PASS    AF=0.116477 ES:SE:LP:AF:SS:ID   0.00646464:0.00406206:0.952694:0.116477:75177:rs12238997
1   707522  rs371890604 G   C   .   PASS    AF=0.0977849    ES:SE:LP:AF:SS:ID   0.0054779:0.00456554:0.637883:0.0977849:75177:rs371890604
1   717587  rs144155419 G   A   .   PASS    AF=0.0159063    ES:SE:LP:AF:SS:ID   0.0196194:0.0108325:1.15416:0.0159063:75177:rs144155419
1   723329  rs189787166 A   T   .   PASS    AF=0.00177526   ES:SE:LP:AF:SS:ID   -0.0184443:0.0317645:0.250671:0.00177526:75177:rs189787166
1   730087  rs148120343 T   C   .   PASS    AF=0.0569733    ES:SE:LP:AF:SS:ID   0.00529889:0.00563243:0.459896:0.0569733:75177:rs148120343
1   731718  rs58276399  T   C   .   PASS    AF=0.122338 ES:SE:LP:AF:SS:ID   0.00590055:0.00385336:0.900644:0.122338:75177:rs58276399
1   732032  rs61770163  A   C   .   PASS    AF=0.121866 ES:SE:LP:AF:SS:ID   0.00647408:0.0041123:0.937726:0.121866:75177:rs61770163
1   734349  rs141242758 T   C   .   PASS    AF=0.121609 ES:SE:LP:AF:SS:ID   0.00607852:0.00385566:0.939642:0.121609:75177:rs141242758
1   740284  rs61770167  C   T   .   PASS    AF=0.00588068   ES:SE:LP:AF:SS:ID   -0.0148879:0.0174641:0.404561:0.00588068:75177:rs61770167
1   742813  rs112573343 C   T   .   PASS    AF=0.00180846   ES:SE:LP:AF:SS:ID   -0.0218398:0.0340155:0.283296:0.00180846:75177:rs112573343
1   749963  rs529266287 T   TAA .   PASS    AF=0.868816 ES:SE:LP:AF:SS:ID   -0.00399147:0.0037937:0.533515:0.868816:75177:rs529266287
1   750230  rs190826124 G   C   .   PASS    AF=0.00165878   ES:SE:LP:AF:SS:ID   -0.0144445:0.0328834:0.180146:0.00165878:75177:rs190826124
1   751343  rs28544273  T   A   .   PASS    AF=0.123758 ES:SE:LP:AF:SS:ID   0.0037234:0.00376126:0.491862:0.123758:75177:rs28544273
1   751488  rs200141114 G   GA  .   PASS    AF=0.143056 ES:SE:LP:AF:SS:ID   0.00367916:0.00372663:0.490102:0.143056:75177:rs200141114
1   751756  rs28527770  T   C   .   PASS    AF=0.123902 ES:SE:LP:AF:SS:ID   0.00374357:0.00375567:0.49638:0.123902:75177:rs28527770
1   753405  rs3115860   C   A   .   PASS    AF=0.869912 ES:SE:LP:AF:SS:ID   -0.00539185:0.00365955:0.851836:0.869912:75177:rs3115860
1   753425  rs3131970   T   C   .   PASS    AF=0.874529 ES:SE:LP:AF:SS:ID   -0.00348443:0.00371876:0.457463:0.874529:75177:rs3131970
1   753541  rs2073813   G   A   .   PASS    AF=0.129553 ES:SE:LP:AF:SS:ID   0.00534087:0.00367124:0.836445:0.129553:75177:rs2073813
1   754105  rs12184325  C   T   .   PASS    AF=0.0360084    ES:SE:LP:AF:SS:ID   0.00673258:0.00668653:0.503081:0.0360084:75177:rs12184325
1   754182  rs3131969   A   G   .   PASS    AF=0.869552 ES:SE:LP:AF:SS:ID   -0.00543874:0.00365662:0.86353:0.869552:75177:rs3131969
1   754192  rs3131968   A   G   .   PASS    AF=0.869633 ES:SE:LP:AF:SS:ID   -0.00535556:0.00365799:0.844124:0.869633:75177:rs3131968
1   754334  rs3131967   T   C   .   PASS    AF=0.869547 ES:SE:LP:AF:SS:ID   -0.00544798:0.00365647:0.865695:0.869547:75177:rs3131967
1   754433  rs150578204 G   A   .   PASS    AF=0.00528791   ES:SE:LP:AF:SS:ID   -0.0166953:0.0183507:0.440169:0.00528791:75177:rs150578204
1   754458  rs142682604 G   T   .   PASS    AF=0.00525393   ES:SE:LP:AF:SS:ID   -0.0170403:0.0183969:0.450612:0.00525393:75177:rs142682604
1   755435  rs184270342 T   G   .   PASS    AF=0.00558736   ES:SE:LP:AF:SS:ID   0.0315739:0.0180901:1.09192:0.00558736:75177:rs184270342
1   755890  rs3115858   A   T   .   PASS    AF=0.869525 ES:SE:LP:AF:SS:ID   -0.00567413:0.00364862:0.921123:0.869525:75177:rs3115858
1   756434  rs61768170  G   C   .   PASS    AF=0.126948 ES:SE:LP:AF:SS:ID   0.00504395:0.00372604:0.754895:0.126948:75177:rs61768170
1   756604  rs3131962   A   G   .   PASS    AF=0.869049 ES:SE:LP:AF:SS:ID   -0.00591268:0.00363937:0.981957:0.869049:75177:rs3131962
1   757640  rs3115853   G   A   .   PASS    AF=0.868472 ES:SE:LP:AF:SS:ID   -0.00552611:0.00363765:0.89032:0.868472:75177:rs3115853
1   757734  rs4951929   C   T   .   PASS    AF=0.869198 ES:SE:LP:AF:SS:ID   -0.0057084:0.00364259:0.931484:0.869198:75177:rs4951929
1   757936  rs4951862   C   A   .   PASS    AF=0.869203 ES:SE:LP:AF:SS:ID   -0.00570736:0.00364283:0.931143:0.869203:75177:rs4951862
1   758144  rs3131956   A   G   .   PASS    AF=0.869206 ES:SE:LP:AF:SS:ID   -0.00571217:0.00364287:0.932275:0.869206:75177:rs3131956
1   758626  rs3131954   C   T   .   PASS    AF=0.869689 ES:SE:LP:AF:SS:ID   -0.00566616:0.00365231:0.91789:0.869689:75177:rs3131954
1   759293  rs10157329  T   A   .   PASS    AF=0.0991701    ES:SE:LP:AF:SS:ID   0.00167201:0.00424944:0.158656:0.0991701:75177:rs10157329
1   759600  rs545998451 AGT A   .   PASS    AF=0.00642849   ES:SE:LP:AF:SS:ID   0.0286171:0.0164575:1.08584:0.00642849:75177:1_759600_AGT_A
1   759837  rs3115851   T   A   .   PASS    AF=0.873648 ES:SE:LP:AF:SS:ID   -0.00471471:0.00370586:0.691873:0.873648:75177:rs3115851
1   761732  rs2286139   C   T   .   PASS    AF=0.863065 ES:SE:LP:AF:SS:ID   -0.00613391:0.00363645:1.03788:0.863065:75177:rs2286139
1   761752  rs1057213   C   T   .   PASS    AF=0.868456 ES:SE:LP:AF:SS:ID   -0.00528527:0.00367123:0.82399:0.868456:75177:rs1057213
1   762273  rs3115849   G   A   .   PASS    AF=0.865365 ES:SE:LP:AF:SS:ID   -0.00533467:0.00367254:0.834628:0.865365:75177:rs3115849
1   762485  rs12095200  C   A   .   PASS    AF=0.0995942    ES:SE:LP:AF:SS:ID   0.00585673:0.00439471:0.738399:0.0995942:75177:rs12095200
1   762589  rs3115848   G   C   .   PASS    AF=0.870659 ES:SE:LP:AF:SS:ID   -0.00510713:0.00371406:0.771828:0.870659:75177:rs3115848
1   762592  rs3131950   C   G   .   PASS    AF=0.870659 ES:SE:LP:AF:SS:ID   -0.00510735:0.00371406:0.771874:0.870659:75177:rs3131950
1   762601  rs3131949   T   C   .   PASS    AF=0.870656 ES:SE:LP:AF:SS:ID   -0.00510607:0.00371408:0.771597:0.870656:75177:rs3131949
1   762632  rs3131948   T   A   .   PASS    AF=0.871036 ES:SE:LP:AF:SS:ID   -0.00491149:0.0037159:0.729892:0.871036:75177:rs3131948
1   764191  rs7515915   T   G   .   PASS    AF=0.126586 ES:SE:LP:AF:SS:ID   0.00455483:0.00372004:0.655993:0.126586:75177:rs7515915
1   766007  rs61768174  A   C   .   PASS    AF=0.10597  ES:SE:LP:AF:SS:ID   0.00473661:0.00404411:0.61707:0.10597:75177:rs61768174
1   766105  rs2519015   T   A   .   PASS    AF=0.854336 ES:SE:LP:AF:SS:ID   -0.0048362:0.00363548:0.736527:0.854336:75177:rs2519015
1   767393  rs538667473 A   C   .   PASS    AF=0.00168869   ES:SE:LP:AF:SS:ID   -0.019124:0.0318394:0.261155:0.00168869:75177:rs538667473
1   768116  rs376645387 A   AGTTTT  .   PASS    AF=0.839618 ES:SE:LP:AF:SS:ID   0.00133864:0.00359122:0.14915:0.839618:75177:rs376645387