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-20529/ukb-d-20529.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-20529/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 17:17:24 2019
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ukb-d-import/processed/ukb-d-20529/ukb-d-20529.vcf.gz ...
Read summary statistics for 13571615 SNPs.
Dropped 12693 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, 1283502 SNPs remain.
After merging with regression SNP LD, 1283502 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.0273 (0.0046)
Lambda GC: 1.068
Mean Chi^2: 1.0698
Intercept: 1.0052 (0.0068)
Ratio: 0.074 (0.0975)
Analysis finished at Mon Nov 25 17:19:26 2019
Total time elapsed: 2.0m:2.27s

QC metrics

Metrics

Metrics

{
    "af_correlation": 0.9521,
    "inflation_factor": 1.0506,
    "mean_EFFECT": 7.2786e-06,
    "n": 117846,
    "n_snps": 13571615,
    "n_clumped_hits": 0,
    "n_p_sig": 0,
    "n_mono": 0,
    "n_ns": 1251349,
    "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": 564619,
    "n_est": 118273.185,
    "ratio_se_n": 1.0018,
    "mean_diff": 0,
    "ratio_diff": 7.1691,
    "sd_y_est1": 0.383,
    "sd_y_est2": 0.3837,
    "r2_sum1": 0,
    "r2_sum2": 0,
    "r2_sum3": 0,
    "r2_sum4": 0,
    "ldsc_nsnp_merge_refpanel_ld": 1283502,
    "ldsc_nsnp_merge_regression_ld": 1283502,
    "ldsc_observed_scale_h2_beta": 0.0273,
    "ldsc_observed_scale_h2_se": 0.0046,
    "ldsc_intercept_beta": 1.0052,
    "ldsc_intercept_se": 0.0068,
    "ldsc_lambda_gc": 1.068,
    "ldsc_mean_chisq": 1.0698,
    "ldsc_ratio": 0.0745
}

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 13559586 0 NA NA NA NA NA NA NA NA
character REF 0 1.0000000 1 100 0 57059 0 NA NA NA NA NA NA NA NA
character ALT 0 1.0000000 1 342 0 33331 0 NA NA NA NA NA NA NA NA
numeric CHROM 0 1.0000000 NA NA NA NA NA 9.051440e+00 6.185077e+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 7.902483e+07 5.591557e+07 3.02000e+02 3.292808e+07 7.013894e+07 1.148580e+08 2.492309e+08 ▇▆▅▂▁
numeric EFFECT 0 1.0000000 NA NA NA NA NA 7.300000e-06 9.227500e-03 -1.19413e-01 -2.514500e-03 -4.000000e-07 2.491200e-03 1.301130e-01 ▁▁▇▁▁
numeric SE 0 1.0000000 NA NA NA NA NA 6.610900e-03 6.372400e-03 1.30640e-03 1.886800e-03 3.472400e-03 9.492400e-03 3.179650e-02 ▇▂▁▁▁
numeric PVAL 0 1.0000000 NA NA NA NA NA 4.922292e-01 2.909131e-01 2.00000e-07 2.379978e-01 4.893448e-01 7.443291e-01 1.000000e+00 ▇▇▇▇▇
numeric PVAL_ztest 0 1.0000000 NA NA NA NA NA 4.922278e-01 2.909139e-01 2.00000e-07 2.379956e-01 4.893441e-01 7.443288e-01 9.999998e-01 ▇▇▇▇▇
numeric AF 0 1.0000000 NA NA NA NA NA 1.909966e-01 2.544487e-01 1.00000e-03 7.483300e-03 6.026440e-02 2.956710e-01 9.990000e-01 ▇▂▁▁▁
numeric AF_reference 564619 0.9583971 NA NA NA NA NA 1.964722e-01 2.471286e-01 0.00000e+00 5.790700e-03 8.446490e-02 3.083070e-01 1.000000e+00 ▇▂▁▁▁
numeric N 0 1.0000000 NA NA NA NA NA 1.178460e+05 0.000000e+00 1.17846e+05 1.178460e+05 1.178460e+05 1.178460e+05 1.178460e+05 ▁▁▇▁▁

Head and tail

CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
1 692794 rs530212009 CA C 0.0015669 0.0027474 0.5684693 0.5684674 0.1117140 0.1894970 117846
1 693731 rs12238997 A G 0.0003344 0.0026018 0.8977400 0.8977399 0.1167340 0.1417730 117846
1 707522 rs371890604 G C 0.0013192 0.0029192 0.6513524 0.6513520 0.0983555 0.1293930 117846
1 717587 rs144155419 G A -0.0066293 0.0069964 0.3433697 0.3433681 0.0157568 0.0045926 117846
1 723329 rs189787166 A T 0.0198872 0.0203998 0.3296272 0.3296236 0.0017763 0.0003994 117846
1 730087 rs148120343 T C 0.0031305 0.0036189 0.3870152 0.3870134 0.0569585 0.0127796 117846
1 731718 rs142557973 T C 0.0004639 0.0024685 0.8509270 0.8509271 0.1226720 0.1543530 117846
1 732032 rs61770163 A C 0.0007780 0.0026310 0.7674428 0.7674423 0.1222720 0.1555510 117846
1 734349 rs141242758 T C 0.0007376 0.0024698 0.7652142 0.7652138 0.1219270 0.1525560 117846
1 740284 rs61770167 C T -0.0038107 0.0112765 0.7354125 0.7354118 0.0058572 0.0023962 117846
CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
23 154923311 rs141127553 C T -0.0039583 0.0029030 0.1727241 0.1727211 0.0554834 0.0309934 117846
23 154923374 rs111332691 T A -0.0071742 0.0031622 0.0232873 0.0232854 0.0448297 0.0116556 117846
23 154925045 rs509981 C T 0.0004371 0.0015235 0.7742033 0.7742029 0.2447640 0.3634440 117846
23 154925895 rs538470 C T 0.0003473 0.0015579 0.8236050 0.8236052 0.2411900 0.3634440 117846
23 154927581 rs644138 G A -0.0004313 0.0014336 0.7635140 0.7635137 0.3006100 0.4635760 117846
23 154929412 rs557132 C T 0.0004486 0.0015239 0.7684595 0.7684579 0.2446390 0.3568210 117846
23 154929637 rs35185538 CT C 0.0009100 0.0015918 0.5675616 0.5675598 0.2289160 0.3011920 117846
23 154929952 rs4012982 CAA C 0.0006160 0.0016038 0.7008983 0.7008983 0.2387080 0.3165560 117846
23 154930230 rs781880 A G 0.0004129 0.0015235 0.7863755 0.7863746 0.2450620 0.3618540 117846
23 154930487 rs781879 T A -0.0013567 0.0051798 0.7933814 0.7933798 0.0196685 0.1263580 117846

bcf preview

1   692794  rs530212009 CA  C   .   PASS    AF=0.111714 ES:SE:LP:AF:SS:ID   0.00156687:0.0027474:0.245293:0.111714:117846:1_692794_CA_C
1   693731  rs12238997  A   G   .   PASS    AF=0.116734 ES:SE:LP:AF:SS:ID   0.000334378:0.00260182:0.0468494:0.116734:117846:rs12238997
1   707522  rs371890604 G   C   .   PASS    AF=0.0983555    ES:SE:LP:AF:SS:ID   0.00131916:0.00291924:0.186184:0.0983555:117846:rs371890604
1   717587  rs144155419 G   A   .   PASS    AF=0.0157568    ES:SE:LP:AF:SS:ID   -0.00662928:0.00699637:0.464238:0.0157568:117846:rs144155419
1   723329  rs189787166 A   T   .   PASS    AF=0.0017763    ES:SE:LP:AF:SS:ID   0.0198872:0.0203998:0.481977:0.0017763:117846:rs189787166
1   730087  rs148120343 T   C   .   PASS    AF=0.0569585    ES:SE:LP:AF:SS:ID   0.00313049:0.00361887:0.412272:0.0569585:117846:rs148120343
1   731718  rs58276399  T   C   .   PASS    AF=0.122672 ES:SE:LP:AF:SS:ID   0.000463923:0.00246852:0.0701077:0.122672:117846:rs58276399
1   732032  rs61770163  A   C   .   PASS    AF=0.122272 ES:SE:LP:AF:SS:ID   0.000778045:0.002631:0.114954:0.122272:117846:rs61770163
1   734349  rs141242758 T   C   .   PASS    AF=0.121927 ES:SE:LP:AF:SS:ID   0.00073759:0.00246982:0.116217:0.121927:117846:rs141242758
1   740284  rs61770167  C   T   .   PASS    AF=0.00585723   ES:SE:LP:AF:SS:ID   -0.00381073:0.0112765:0.133469:0.00585723:117846:rs61770167
1   742813  rs112573343 C   T   .   PASS    AF=0.00183543   ES:SE:LP:AF:SS:ID   0.0115766:0.0216195:0.227438:0.00183543:117846:rs112573343
1   749963  rs529266287 T   TAA .   PASS    AF=0.869008 ES:SE:LP:AF:SS:ID   -0.00189581:0.00243364:0.360534:0.869008:117846:rs529266287
1   750230  rs190826124 G   C   .   PASS    AF=0.00158359   ES:SE:LP:AF:SS:ID   -0.0134621:0.0216583:0.272274:0.00158359:117846:rs190826124
1   751343  rs28544273  T   A   .   PASS    AF=0.123697 ES:SE:LP:AF:SS:ID   0.00169636:0.00241129:0.317185:0.123697:117846:rs28544273
1   751488  rs200141114 G   GA  .   PASS    AF=0.143328 ES:SE:LP:AF:SS:ID   0.00195149:0.00238495:0.383825:0.143328:117846:rs200141114
1   751756  rs28527770  T   C   .   PASS    AF=0.123818 ES:SE:LP:AF:SS:ID   0.00173238:0.00240795:0.326177:0.123818:117846:rs28527770
1   753405  rs3115860   C   A   .   PASS    AF=0.869762 ES:SE:LP:AF:SS:ID   -0.00208771:0.0023449:0.427947:0.869762:117846:rs3115860
1   753425  rs3131970   T   C   .   PASS    AF=0.874554 ES:SE:LP:AF:SS:ID   -0.0015088:0.0023844:0.278289:0.874554:117846:rs3131970
1   753541  rs2073813   G   A   .   PASS    AF=0.129696 ES:SE:LP:AF:SS:ID   0.0018875:0.00235147:0.374527:0.129696:117846:rs2073813
1   754105  rs12184325  C   T   .   PASS    AF=0.0365477    ES:SE:LP:AF:SS:ID   0.00833989:0.00426966:1.29424:0.0365477:117846:rs12184325
1   754182  rs3131969   A   G   .   PASS    AF=0.869356 ES:SE:LP:AF:SS:ID   -0.00203216:0.00234267:0.413757:0.869356:117846:rs3131969
1   754192  rs3131968   A   G   .   PASS    AF=0.869427 ES:SE:LP:AF:SS:ID   -0.00208249:0.00234354:0.426879:0.869427:117846:rs3131968
1   754334  rs3131967   T   C   .   PASS    AF=0.869355 ES:SE:LP:AF:SS:ID   -0.00205419:0.00234261:0.419587:0.869355:117846:rs3131967
1   754433  rs150578204 G   A   .   PASS    AF=0.00511836   ES:SE:LP:AF:SS:ID   0.0146075:0.0119812:0.652143:0.00511836:117846:rs150578204
1   754458  rs142682604 G   T   .   PASS    AF=0.00508746   ES:SE:LP:AF:SS:ID   0.0143794:0.0120076:0.636191:0.00508746:117846:rs142682604
1   755435  rs184270342 T   G   .   PASS    AF=0.00568304   ES:SE:LP:AF:SS:ID   -0.0103132:0.0115548:0.429337:0.00568304:117846:rs184270342
1   755890  rs3115858   A   T   .   PASS    AF=0.869428 ES:SE:LP:AF:SS:ID   -0.00208988:0.00233828:0.430101:0.869428:117846:rs3115858
1   756434  rs61768170  G   C   .   PASS    AF=0.126969 ES:SE:LP:AF:SS:ID   0.00150691:0.00238697:0.277496:0.126969:117846:rs61768170
1   756604  rs3131962   A   G   .   PASS    AF=0.868948 ES:SE:LP:AF:SS:ID   -0.00203934:0.00233213:0.418082:0.868948:117846:rs3131962
1   757640  rs3115853   G   A   .   PASS    AF=0.868348 ES:SE:LP:AF:SS:ID   -0.00213405:0.00233124:0.443724:0.868348:117846:rs3115853
1   757734  rs4951929   C   T   .   PASS    AF=0.869137 ES:SE:LP:AF:SS:ID   -0.0021157:0.00233445:0.437967:0.869137:117846:rs4951929
1   757936  rs4951862   C   A   .   PASS    AF=0.869144 ES:SE:LP:AF:SS:ID   -0.00211836:0.00233462:0.438643:0.869144:117846:rs4951862
1   758144  rs3131956   A   G   .   PASS    AF=0.869147 ES:SE:LP:AF:SS:ID   -0.00211374:0.00233463:0.437394:0.869147:117846:rs3131956
1   758626  rs3131954   C   T   .   PASS    AF=0.869583 ES:SE:LP:AF:SS:ID   -0.00206685:0.00234062:0.423405:0.869583:117846:rs3131954
1   759293  rs10157329  T   A   .   PASS    AF=0.0995772    ES:SE:LP:AF:SS:ID   0.00200539:0.00272116:0.336162:0.0995772:117846:rs10157329
1   759600  rs545998451 AGT A   .   PASS    AF=0.00654335   ES:SE:LP:AF:SS:ID   -0.00670103:0.0104874:0.281624:0.00654335:117846:1_759600_AGT_A
1   759837  rs3115851   T   A   .   PASS    AF=0.873653 ES:SE:LP:AF:SS:ID   -0.00150074:0.00237661:0.277581:0.873653:117846:rs3115851
1   761732  rs2286139   C   T   .   PASS    AF=0.862926 ES:SE:LP:AF:SS:ID   -0.00227563:0.00233065:0.482976:0.862926:117846:rs2286139
1   761752  rs1057213   C   T   .   PASS    AF=0.86833  ES:SE:LP:AF:SS:ID   -0.00163624:0.00235312:0.312616:0.86833:117846:rs1057213
1   762273  rs3115849   G   A   .   PASS    AF=0.865344 ES:SE:LP:AF:SS:ID   -0.00221195:0.00235349:0.459306:0.865344:117846:rs3115849
1   762485  rs12095200  C   A   .   PASS    AF=0.0997611    ES:SE:LP:AF:SS:ID   0.00214158:0.00281241:0.350299:0.0997611:117846:rs12095200
1   762589  rs3115848   G   C   .   PASS    AF=0.870643 ES:SE:LP:AF:SS:ID   -0.00196417:0.00238133:0.387772:0.870643:117846:rs3115848
1   762592  rs3131950   C   G   .   PASS    AF=0.870643 ES:SE:LP:AF:SS:ID   -0.00196424:0.00238133:0.387791:0.870643:117846:rs3131950
1   762601  rs3131949   T   C   .   PASS    AF=0.870642 ES:SE:LP:AF:SS:ID   -0.00196846:0.00238133:0.388857:0.870642:117846:rs3131949
1   762632  rs3131948   T   A   .   PASS    AF=0.870964 ES:SE:LP:AF:SS:ID   -0.00194931:0.00238234:0.383812:0.870964:117846:rs3131948
1   764191  rs7515915   T   G   .   PASS    AF=0.126557 ES:SE:LP:AF:SS:ID   0.00147709:0.00238438:0.27116:0.126557:117846:rs7515915
1   766007  rs61768174  A   C   .   PASS    AF=0.10635  ES:SE:LP:AF:SS:ID   0.00232252:0.00259101:0.431736:0.10635:117846:rs61768174
1   766105  rs2519015   T   A   .   PASS    AF=0.854378 ES:SE:LP:AF:SS:ID   -0.00128809:0.00233008:0.236276:0.854378:117846:rs2519015
1   767393  rs538667473 A   C   .   PASS    AF=0.00168796   ES:SE:LP:AF:SS:ID   0.0214199:0.0204907:0.528906:0.00168796:117846:rs538667473
1   768116  rs376645387 A   AGTTTT  .   PASS    AF=0.83911  ES:SE:LP:AF:SS:ID   0.00233869:0.00230906:0.507041:0.83911:117846:rs376645387