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-20417/ukb-d-20417.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-20417/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 17:16:28 2019
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ukb-d-import/processed/ukb-d-20417/ukb-d-20417.vcf.gz ...
Read summary statistics for 13540399 SNPs.
Dropped 12655 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, 1283494 SNPs remain.
After merging with regression SNP LD, 1283494 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.0733 (0.0152)
Lambda GC: 1.0472
Mean Chi^2: 1.0423
Intercept: 0.9943 (0.0064)
Ratio < 0 (usually indicates GC correction).
Analysis finished at Mon Nov 25 17:18:43 2019
Total time elapsed: 2.0m:14.88s

QC metrics

Metrics

Metrics

{
    "af_correlation": 0.952,
    "inflation_factor": 1.0267,
    "mean_EFFECT": -0,
    "n": 33301,
    "n_snps": 13540399,
    "n_clumped_hits": 1,
    "n_p_sig": 1,
    "n_mono": 0,
    "n_ns": 1250194,
    "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": 557247,
    "n_est": 33408.6697,
    "ratio_se_n": 1.0016,
    "mean_diff": -0,
    "ratio_diff": 422.3806,
    "sd_y_est1": 0.4832,
    "sd_y_est2": 0.484,
    "r2_sum1": 0.0002,
    "r2_sum2": 0.001,
    "r2_sum3": 0.001,
    "r2_sum4": 0.0009,
    "ldsc_nsnp_merge_refpanel_ld": 1283494,
    "ldsc_nsnp_merge_regression_ld": 1283494,
    "ldsc_observed_scale_h2_beta": 0.0733,
    "ldsc_observed_scale_h2_se": 0.0152,
    "ldsc_intercept_beta": 0.9943,
    "ldsc_intercept_se": 0.0064,
    "ldsc_lambda_gc": 1.0472,
    "ldsc_mean_chisq": 1.0423,
    "ldsc_ratio": -0.1348
}

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 13528408 0 NA NA NA NA NA NA NA NA
character REF 0 1.0000000 1 100 0 57002 0 NA NA NA NA NA NA NA NA
character ALT 0 1.0000000 1 342 0 33311 0 NA NA NA NA NA NA NA NA
numeric CHROM 0 1.0000000 NA NA NA NA NA 9.051608e+00 6.185107e+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 7.902330e+07 5.591489e+07 3.02000e+02 3.292461e+07 7.013994e+07 1.148560e+08 2.492309e+08 ▇▆▅▂▁
numeric EFFECT 0 1.0000000 NA NA NA NA NA -3.190000e-05 2.168400e-02 -2.47832e-01 -5.857600e-03 -1.300000e-05 5.788000e-03 2.750820e-01 ▁▁▇▁▁
numeric SE 0 1.0000000 NA NA NA NA NA 1.559700e-02 1.501240e-02 3.18030e-03 4.473000e-03 8.205700e-03 2.237220e-02 8.330150e-02 ▇▂▁▁▁
numeric PVAL 0 1.0000000 NA NA NA NA NA 4.957915e-01 2.896767e-01 0.00000e+00 2.442890e-01 4.943232e-01 7.466843e-01 1.000000e+00 ▇▇▇▇▇
numeric PVAL_ztest 0 1.0000000 NA NA NA NA NA 4.957867e-01 2.896796e-01 0.00000e+00 2.442810e-01 4.943186e-01 7.466824e-01 9.999999e-01 ▇▇▇▇▇
numeric AF 0 1.0000000 NA NA NA NA NA 1.914162e-01 2.545537e-01 1.00000e-03 7.592900e-03 6.070670e-02 2.965850e-01 9.990000e-01 ▇▂▁▁▁
numeric AF_reference 557247 0.9588456 NA NA NA NA NA 1.967825e-01 2.472010e-01 0.00000e+00 5.790700e-03 8.486420e-02 3.089060e-01 1.000000e+00 ▇▂▁▁▁
numeric N 0 1.0000000 NA NA NA NA NA 3.330100e+04 0.000000e+00 3.33010e+04 3.330100e+04 3.330100e+04 3.330100e+04 3.330100e+04 ▁▁▇▁▁

Head and tail

CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
1 692794 rs530212009 CA C 0.0045240 0.0065173 0.4875914 0.4875857 0.1120450 0.1894970 33301
1 693731 rs12238997 A G 0.0055557 0.0061635 0.3673880 0.3673815 0.1170350 0.1417730 33301
1 707522 rs371890604 G C 0.0063821 0.0069180 0.3562558 0.3562491 0.0988912 0.1293930 33301
1 717587 rs144155419 G A -0.0115570 0.0161815 0.4751011 0.4750969 0.0164251 0.0045926 33301
1 723329 rs189787166 A T -0.0876876 0.0486394 0.0714266 0.0714180 0.0017850 0.0003994 33301
1 730087 rs148120343 T C 0.0050161 0.0085731 0.5584856 0.5584820 0.0568824 0.0127796 33301
1 731718 rs142557973 T C 0.0045602 0.0058405 0.4349386 0.4349328 0.1236040 0.1543530 33301
1 732032 rs61770163 A C 0.0030284 0.0062279 0.6267827 0.6267792 0.1232590 0.1555510 33301
1 734349 rs141242758 T C 0.0047953 0.0058453 0.4120150 0.4120104 0.1228030 0.1525560 33301
1 740284 rs61770167 C T 0.0278813 0.0271110 0.3037631 0.3037557 0.0057074 0.0023962 33301
CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
23 154923311 rs141127553 C T 0.0026292 0.0069662 0.7058623 0.7058592 0.0568733 0.0309934 33301
23 154923374 rs111332691 T A -0.0050459 0.0077992 0.5176557 0.5176509 0.0440677 0.0116556 33301
23 154925045 rs509981 C T -0.0065211 0.0037248 0.0800037 0.0799942 0.2433040 0.3634440 33301
23 154925895 rs538470 C T -0.0056682 0.0038098 0.1368211 0.1368123 0.2396350 0.3634440 33301
23 154927581 rs644138 G A -0.0052367 0.0034929 0.1338191 0.1338092 0.3006350 0.4635760 33301
23 154929412 rs557132 C T -0.0065506 0.0037260 0.0787426 0.0787327 0.2431280 0.3568210 33301
23 154929637 rs35185538 CT C -0.0088520 0.0038915 0.0229303 0.0229240 0.2276660 0.3011920 33301
23 154929952 rs4012982 CAA C -0.0078446 0.0039263 0.0457267 0.0457188 0.2373240 0.3165560 33301
23 154930230 rs781880 A G -0.0065077 0.0037256 0.0806863 0.0806777 0.2434050 0.3618540 33301
23 154930487 rs781879 T A -0.0099711 0.0122539 0.4158187 0.4158126 0.0204248 0.1263580 33301

bcf preview

1   692794  rs530212009 CA  C   .   PASS    AF=0.112045 ES:SE:LP:AF:SS:ID   0.00452403:0.00651733:0.311944:0.112045:33301:1_692794_CA_C
1   693731  rs12238997  A   G   .   PASS    AF=0.117035 ES:SE:LP:AF:SS:ID   0.00555572:0.00616351:0.434875:0.117035:33301:rs12238997
1   707522  rs371890604 G   C   .   PASS    AF=0.0988912    ES:SE:LP:AF:SS:ID   0.00638214:0.00691804:0.448238:0.0988912:33301:rs371890604
1   717587  rs144155419 G   A   .   PASS    AF=0.0164251    ES:SE:LP:AF:SS:ID   -0.011557:0.0161815:0.323214:0.0164251:33301:rs144155419
1   723329  rs189787166 A   T   .   PASS    AF=0.00178497   ES:SE:LP:AF:SS:ID   -0.0876876:0.0486394:1.14614:0.00178497:33301:rs189787166
1   730087  rs148120343 T   C   .   PASS    AF=0.0568824    ES:SE:LP:AF:SS:ID   0.00501609:0.00857308:0.252988:0.0568824:33301:rs148120343
1   731718  rs58276399  T   C   .   PASS    AF=0.123604 ES:SE:LP:AF:SS:ID   0.00456016:0.00584053:0.361572:0.123604:33301:rs58276399
1   732032  rs61770163  A   C   .   PASS    AF=0.123259 ES:SE:LP:AF:SS:ID   0.00302843:0.00622794:0.202883:0.123259:33301:rs61770163
1   734349  rs141242758 T   C   .   PASS    AF=0.122803 ES:SE:LP:AF:SS:ID   0.00479528:0.00584533:0.385087:0.122803:33301:rs141242758
1   740284  rs61770167  C   T   .   PASS    AF=0.00570736   ES:SE:LP:AF:SS:ID   0.0278813:0.027111:0.517465:0.00570736:33301:rs61770167
1   742813  rs112573343 C   T   .   PASS    AF=0.00198345   ES:SE:LP:AF:SS:ID   0.0744:0.048768:0.895783:0.00198345:33301:rs112573343
1   749963  rs529266287 T   TAA .   PASS    AF=0.867535 ES:SE:LP:AF:SS:ID   0.000587074:0.00573773:0.0369185:0.867535:33301:rs529266287
1   750230  rs190826124 G   C   .   PASS    AF=0.00147726   ES:SE:LP:AF:SS:ID   0.00593991:0.053476:0.0402162:0.00147726:33301:rs190826124
1   751343  rs28544273  T   A   .   PASS    AF=0.124951 ES:SE:LP:AF:SS:ID   0.000578575:0.00569409:0.0366528:0.124951:33301:rs28544273
1   751488  rs200141114 G   GA  .   PASS    AF=0.144956 ES:SE:LP:AF:SS:ID   -0.00132571:0.00563274:0.0894119:0.144956:33301:rs200141114
1   751756  rs28527770  T   C   .   PASS    AF=0.125026 ES:SE:LP:AF:SS:ID   0.000726031:0.00568658:0.0465269:0.125026:33301:rs28527770
1   753405  rs3115860   C   A   .   PASS    AF=0.868482 ES:SE:LP:AF:SS:ID   -0.00260425:0.00554687:0.194692:0.868482:33301:rs3115860
1   753425  rs3131970   T   C   .   PASS    AF=0.873333 ES:SE:LP:AF:SS:ID   -0.000668769:0.00563326:0.043112:0.873333:33301:rs3131970
1   753541  rs2073813   G   A   .   PASS    AF=0.13099  ES:SE:LP:AF:SS:ID   0.00279131:0.00555901:0.210713:0.13099:33301:rs2073813
1   754105  rs12184325  C   T   .   PASS    AF=0.0360199    ES:SE:LP:AF:SS:ID   0.00718748:0.0101972:0.317935:0.0360199:33301:rs12184325
1   754182  rs3131969   A   G   .   PASS    AF=0.868029 ES:SE:LP:AF:SS:ID   -0.0030074:0.00553883:0.231247:0.868029:33301:rs3131969
1   754192  rs3131968   A   G   .   PASS    AF=0.868077 ES:SE:LP:AF:SS:ID   -0.00317482:0.0055397:0.24674:0.868077:33301:rs3131968
1   754334  rs3131967   T   C   .   PASS    AF=0.868022 ES:SE:LP:AF:SS:ID   -0.00302435:0.00553858:0.232819:0.868022:33301:rs3131967
1   754433  rs150578204 G   A   .   PASS    AF=0.00541955   ES:SE:LP:AF:SS:ID   0.00108977:0.027497:0.013951:0.00541955:33301:rs150578204
1   754458  rs142682604 G   T   .   PASS    AF=0.00539447   ES:SE:LP:AF:SS:ID   0.00119748:0.0275508:0.0153233:0.00539447:33301:rs142682604
1   755435  rs184270342 T   G   .   PASS    AF=0.00593116   ES:SE:LP:AF:SS:ID   -0.00574768:0.0266719:0.0812454:0.00593116:33301:rs184270342
1   755890  rs3115858   A   T   .   PASS    AF=0.868181 ES:SE:LP:AF:SS:ID   -0.00283176:0.00553204:0.215572:0.868181:33301:rs3115858
1   756434  rs61768170  G   C   .   PASS    AF=0.128245 ES:SE:LP:AF:SS:ID   0.00231314:0.00563859:0.166446:0.128245:33301:rs61768170
1   756604  rs3131962   A   G   .   PASS    AF=0.867662 ES:SE:LP:AF:SS:ID   -0.00293175:0.00551679:0.22539:0.867662:33301:rs3131962
1   757640  rs3115853   G   A   .   PASS    AF=0.86709  ES:SE:LP:AF:SS:ID   -0.00283495:0.005512:0.21679:0.86709:33301:rs3115853
1   757734  rs4951929   C   T   .   PASS    AF=0.867857 ES:SE:LP:AF:SS:ID   -0.00287869:0.00552252:0.220269:0.867857:33301:rs4951929
1   757936  rs4951862   C   A   .   PASS    AF=0.867865 ES:SE:LP:AF:SS:ID   -0.00287703:0.00552289:0.220101:0.867865:33301:rs4951862
1   758144  rs3131956   A   G   .   PASS    AF=0.867867 ES:SE:LP:AF:SS:ID   -0.00288263:0.00552289:0.22061:0.867867:33301:rs3131956
1   758626  rs3131954   C   T   .   PASS    AF=0.86832  ES:SE:LP:AF:SS:ID   -0.00288375:0.00553713:0.220037:0.86832:33301:rs3131954
1   759293  rs10157329  T   A   .   PASS    AF=0.100321 ES:SE:LP:AF:SS:ID   0.00363232:0.00643012:0.242489:0.100321:33301:rs10157329
1   759600  rs545998451 AGT A   .   PASS    AF=0.00679459   ES:SE:LP:AF:SS:ID   0.000838875:0.0243847:0.0120849:0.00679459:33301:1_759600_AGT_A
1   759837  rs3115851   T   A   .   PASS    AF=0.872418 ES:SE:LP:AF:SS:ID   -0.000806974:0.00561733:0.0526781:0.872418:33301:rs3115851
1   761732  rs2286139   C   T   .   PASS    AF=0.861593 ES:SE:LP:AF:SS:ID   -0.00369544:0.00550534:0.299237:0.861593:33301:rs2286139
1   761752  rs1057213   C   T   .   PASS    AF=0.867193 ES:SE:LP:AF:SS:ID   -0.00184234:0.00556795:0.130337:0.867193:33301:rs1057213
1   762273  rs3115849   G   A   .   PASS    AF=0.864161 ES:SE:LP:AF:SS:ID   -0.00239412:0.00556533:0.175832:0.864161:33301:rs3115849
1   762485  rs12095200  C   A   .   PASS    AF=0.100732 ES:SE:LP:AF:SS:ID   -0.00258531:0.00664391:0.156651:0.100732:33301:rs12095200
1   762589  rs3115848   G   C   .   PASS    AF=0.869281 ES:SE:LP:AF:SS:ID   -0.000912501:0.00562346:0.0599335:0.869281:33301:rs3115848
1   762592  rs3131950   C   G   .   PASS    AF=0.869281 ES:SE:LP:AF:SS:ID   -0.000912956:0.00562346:0.0599654:0.869281:33301:rs3131950
1   762601  rs3131949   T   C   .   PASS    AF=0.869278 ES:SE:LP:AF:SS:ID   -0.000915717:0.00562346:0.0601579:0.869278:33301:rs3131949
1   762632  rs3131948   T   A   .   PASS    AF=0.869668 ES:SE:LP:AF:SS:ID   -0.00109449:0.00562721:0.0727395:0.869668:33301:rs3131948
1   764191  rs7515915   T   G   .   PASS    AF=0.127744 ES:SE:LP:AF:SS:ID   0.00153803:0.00563527:0.105181:0.127744:33301:rs7515915
1   766007  rs61768174  A   C   .   PASS    AF=0.106505 ES:SE:LP:AF:SS:ID   0.00478872:0.00615018:0.360311:0.106505:33301:rs61768174
1   766105  rs2519015   T   A   .   PASS    AF=0.853132 ES:SE:LP:AF:SS:ID   -0.00145129:0.00550138:0.101312:0.853132:33301:rs2519015
1   767393  rs538667473 A   C   .   PASS    AF=0.00168958   ES:SE:LP:AF:SS:ID   -0.0946046:0.0489717:1.27254:0.00168958:33301:rs538667473
1   768116  rs376645387 A   AGTTTT  .   PASS    AF=0.837861 ES:SE:LP:AF:SS:ID   -0.00320098:0.00546728:0.253187:0.837861:33301:rs376645387