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-M13_JOINTOTH/ukb-d-M13_JOINTOTH.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-M13_JOINTOTH/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 14:54:19 2019
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ukb-d-import/processed/ukb-d-M13_JOINTOTH/ukb-d-M13_JOINTOTH.vcf.gz ...
Read summary statistics for 12861422 SNPs.
Dropped 11661 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, 1283340 SNPs remain.
After merging with regression SNP LD, 1283340 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.0045 (0.0013)
Lambda GC: 1.0418
Mean Chi^2: 1.0453
Intercept: 1.0128 (0.0061)
Ratio: 0.2814 (0.1343)
Analysis finished at Mon Nov 25 14:56:13 2019
Total time elapsed: 1.0m:54.61s

QC metrics

Metrics

Metrics

{
    "af_correlation": 0.9509,
    "inflation_factor": 1.0314,
    "mean_EFFECT": 9.3258e-06,
    "n": 361194,
    "n_snps": 12861422,
    "n_clumped_hits": 0,
    "n_p_sig": 0,
    "n_mono": 0,
    "n_ns": 1222908,
    "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": 404442,
    "n_est": 362300.1249,
    "ratio_se_n": 1.0015,
    "mean_diff": 0.0001,
    "ratio_diff": 1825.6509,
    "sd_y_est1": 0.1472,
    "sd_y_est2": 0.1474,
    "r2_sum1": 0,
    "r2_sum2": 0,
    "r2_sum3": 0,
    "r2_sum4": 0,
    "ldsc_nsnp_merge_refpanel_ld": 1283340,
    "ldsc_nsnp_merge_regression_ld": 1283340,
    "ldsc_observed_scale_h2_beta": 0.0045,
    "ldsc_observed_scale_h2_se": 0.0013,
    "ldsc_intercept_beta": 1.0128,
    "ldsc_intercept_se": 0.0061,
    "ldsc_lambda_gc": 1.0418,
    "ldsc_mean_chisq": 1.0453,
    "ldsc_ratio": 0.2826
}

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 12850411 0 NA NA NA NA NA NA NA NA
character REF 0 1.0000000 1 100 0 55470 0 NA NA NA NA NA NA NA NA
character ALT 0 1.0000000 1 342 0 32849 0 NA NA NA NA NA NA NA NA
numeric CHROM 0 1.0000000 NA NA NA NA NA 9.060206e+00 6.185858e+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 7.896663e+07 5.593907e+07 3.02000e+02 3.282584e+07 7.003969e+07 1.148072e+08 2.492309e+08 ▇▆▅▂▁
numeric EFFECT 0 1.0000000 NA NA NA NA NA 9.300000e-06 1.692500e-03 -1.83046e-02 -5.107000e-04 -1.500000e-06 5.074000e-04 2.460380e-02 ▁▁▇▁▁
numeric SE 0 1.0000000 NA NA NA NA NA 1.249400e-03 1.131000e-03 2.84800e-04 4.066000e-04 6.982000e-04 1.766300e-03 6.096500e-03 ▇▂▁▁▁
numeric PVAL 0 1.0000000 NA NA NA NA NA 4.948857e-01 2.903172e-01 1.00000e-07 2.421253e-01 4.933385e-01 7.465244e-01 1.000000e+00 ▇▇▇▇▇
numeric PVAL_ztest 0 1.0000000 NA NA NA NA NA 4.948853e-01 2.903175e-01 1.00000e-07 2.421250e-01 4.933373e-01 7.465252e-01 9.999997e-01 ▇▇▇▇▇
numeric AF 0 1.0000000 NA NA NA NA NA 2.009812e-01 2.567646e-01 1.57370e-03 1.032620e-02 7.339570e-02 3.155150e-01 9.984260e-01 ▇▂▁▁▁
numeric AF_reference 404442 0.9685539 NA NA NA NA NA 2.042329e-01 2.487957e-01 0.00000e+00 7.587900e-03 9.524760e-02 3.228830e-01 1.000000e+00 ▇▂▁▁▁
numeric N 0 1.0000000 NA NA NA NA NA 3.611940e+05 0.000000e+00 3.61194e+05 3.611940e+05 3.611940e+05 3.611940e+05 3.611940e+05 ▁▁▇▁▁

Head and tail

CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
1 692794 rs530212009 CA C -0.0009507 0.0006066 0.1170351 0.1170343 0.1106400 0.1894970 361194
1 693731 rs12238997 A G -0.0002034 0.0005731 0.7226833 0.7226824 0.1158300 0.1417730 361194
1 707522 rs371890604 G C -0.0003524 0.0006443 0.5844078 0.5844075 0.0973034 0.1293930 361194
1 717587 rs144155419 G A -0.0005235 0.0015375 0.7334626 0.7334619 0.0156880 0.0045926 361194
1 723329 rs189787166 A T -0.0040822 0.0045362 0.3681603 0.3681593 0.0017336 0.0003994 361194
1 730087 rs148120343 T C -0.0006621 0.0007984 0.4069687 0.4069687 0.0564602 0.0127796 361194
1 731718 rs142557973 T C -0.0004472 0.0005436 0.4106313 0.4106309 0.1217380 0.1543530 361194
1 732032 rs61770163 A C -0.0004324 0.0005798 0.4557587 0.4557581 0.1211710 0.1555510 361194
1 734349 rs141242758 T C -0.0004590 0.0005438 0.3986704 0.3986699 0.1209650 0.1525560 361194
1 740284 rs61770167 C T 0.0012037 0.0024881 0.6285285 0.6285286 0.0057851 0.0023962 361194
CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
23 154923311 rs141127553 C T -0.0000581 0.0006280 0.9262950 0.9262950 0.0561667 0.0309934 361194
23 154923374 rs111332691 T A 0.0004492 0.0006901 0.5151314 0.5151304 0.0447862 0.0116556 361194
23 154925045 rs509981 C T 0.0005915 0.0003321 0.0748531 0.0748513 0.2456060 0.3634440 361194
23 154925895 rs538470 C T 0.0006005 0.0003397 0.0770850 0.0770847 0.2419150 0.3634440 361194
23 154927581 rs644138 G A 0.0004983 0.0003123 0.1105549 0.1105548 0.3021620 0.4635760 361194
23 154929412 rs557132 C T 0.0005868 0.0003322 0.0772859 0.0772853 0.2454590 0.3568210 361194
23 154929637 rs35185538 CT C 0.0004295 0.0003467 0.2153828 0.2153816 0.2296970 0.3011920 361194
23 154929952 rs4012982 CAA C 0.0005974 0.0003493 0.0872730 0.0872720 0.2394250 0.3165560 361194
23 154930230 rs781880 A G 0.0005783 0.0003321 0.0816112 0.0816104 0.2458690 0.3618540 361194
23 154930487 rs781879 T A -0.0026547 0.0011393 0.0197970 0.0197970 0.0195623 0.1263580 361194

bcf preview

1   692794  rs530212009 CA  C   .   PASS    AF=0.11064  ES:SE:LP:AF:SS:ID   -0.000950682:0.000606556:0.931684:0.11064:361194:1_692794_CA_C
1   693731  rs12238997  A   G   .   PASS    AF=0.11583  ES:SE:LP:AF:SS:ID   -0.000203388:0.000573124:0.141052:0.11583:361194:rs12238997
1   707522  rs371890604 G   C   .   PASS    AF=0.0973034    ES:SE:LP:AF:SS:ID   -0.00035241:0.000644309:0.233284:0.0973034:361194:rs371890604
1   717587  rs144155419 G   A   .   PASS    AF=0.015688 ES:SE:LP:AF:SS:ID   -0.000523549:0.00153748:0.134622:0.015688:361194:rs144155419
1   723329  rs189787166 A   T   .   PASS    AF=0.00173363   ES:SE:LP:AF:SS:ID   -0.00408222:0.00453617:0.433963:0.00173363:361194:rs189787166
1   730087  rs148120343 T   C   .   PASS    AF=0.0564602    ES:SE:LP:AF:SS:ID   -0.000662095:0.000798436:0.390439:0.0564602:361194:rs148120343
1   731718  rs58276399  T   C   .   PASS    AF=0.121738 ES:SE:LP:AF:SS:ID   -0.000447225:0.000543551:0.386548:0.121738:361194:rs58276399
1   732032  rs61770163  A   C   .   PASS    AF=0.121171 ES:SE:LP:AF:SS:ID   -0.000432446:0.000579803:0.341265:0.121171:361194:rs61770163
1   734349  rs141242758 T   C   .   PASS    AF=0.120965 ES:SE:LP:AF:SS:ID   -0.000459003:0.000543843:0.399386:0.120965:361194:rs141242758
1   740284  rs61770167  C   T   .   PASS    AF=0.00578512   ES:SE:LP:AF:SS:ID   0.00120374:0.0024881:0.201675:0.00578512:361194:rs61770167
1   742813  rs112573343 C   T   .   PASS    AF=0.00187787   ES:SE:LP:AF:SS:ID   -0.00222695:0.00469901:0.196844:0.00187787:361194:rs112573343
1   749963  rs529266287 T   TAA .   PASS    AF=0.869742 ES:SE:LP:AF:SS:ID   0.000292091:0.000536144:0.232182:0.869742:361194:rs529266287
1   751343  rs28544273  T   A   .   PASS    AF=0.122916 ES:SE:LP:AF:SS:ID   -0.000360514:0.00053098:0.303501:0.122916:361194:rs28544273
1   751488  rs200141114 G   GA  .   PASS    AF=0.142712 ES:SE:LP:AF:SS:ID   -0.000213854:0.000524845:0.165154:0.142712:361194:rs200141114
1   751756  rs28527770  T   C   .   PASS    AF=0.123031 ES:SE:LP:AF:SS:ID   -0.000353761:0.000530241:0.296998:0.123031:361194:rs28527770
1   753405  rs3115860   C   A   .   PASS    AF=0.87089  ES:SE:LP:AF:SS:ID   0.000471619:0.000516702:0.442042:0.87089:361194:rs3115860
1   753425  rs3131970   T   C   .   PASS    AF=0.875472 ES:SE:LP:AF:SS:ID   0.000315559:0.000525265:0.26122:0.875472:361194:rs3131970
1   753541  rs2073813   G   A   .   PASS    AF=0.128631 ES:SE:LP:AF:SS:ID   -0.000509858:0.000517997:0.48815:0.128631:361194:rs2073813
1   754105  rs12184325  C   T   .   PASS    AF=0.0363613    ES:SE:LP:AF:SS:ID   4.98573e-05:0.000939768:0.018775:0.0363613:361194:rs12184325
1   754182  rs3131969   A   G   .   PASS    AF=0.870484 ES:SE:LP:AF:SS:ID   0.000511105:0.000516165:0.492038:0.870484:361194:rs3131969
1   754192  rs3131968   A   G   .   PASS    AF=0.870589 ES:SE:LP:AF:SS:ID   0.000529292:0.0005164:0.515159:0.870589:361194:rs3131968
1   754334  rs3131967   T   C   .   PASS    AF=0.870481 ES:SE:LP:AF:SS:ID   0.000496799:0.000516145:0.473932:0.870481:361194:rs3131967
1   754433  rs150578204 G   A   .   PASS    AF=0.00504367   ES:SE:LP:AF:SS:ID   0.00147787:0.00264981:0.238801:0.00504367:361194:rs150578204
1   754458  rs142682604 G   T   .   PASS    AF=0.00501064   ES:SE:LP:AF:SS:ID   0.00142289:0.0026569:0.227478:0.00501064:361194:rs142682604
1   755435  rs184270342 T   G   .   PASS    AF=0.00558665   ES:SE:LP:AF:SS:ID   4.23811e-05:0.0025664:0.0057603:0.00558665:361194:rs184270342
1   755890  rs3115858   A   T   .   PASS    AF=0.870563 ES:SE:LP:AF:SS:ID   0.000502173:0.000515237:0.481832:0.870563:361194:rs3115858
1   756434  rs61768170  G   C   .   PASS    AF=0.125985 ES:SE:LP:AF:SS:ID   -0.000394504:0.000525731:0.343883:0.125985:361194:rs61768170
1   756604  rs3131962   A   G   .   PASS    AF=0.870127 ES:SE:LP:AF:SS:ID   0.000466729:0.000513997:0.439067:0.870127:361194:rs3131962
1   757640  rs3115853   G   A   .   PASS    AF=0.869414 ES:SE:LP:AF:SS:ID   0.000467135:0.000513529:0.440089:0.869414:361194:rs3115853
1   757734  rs4951929   C   T   .   PASS    AF=0.870281 ES:SE:LP:AF:SS:ID   0.000455038:0.00051444:0.424339:0.870281:361194:rs4951929
1   757936  rs4951862   C   A   .   PASS    AF=0.870287 ES:SE:LP:AF:SS:ID   0.000454517:0.000514476:0.423669:0.870287:361194:rs4951862
1   758144  rs3131956   A   G   .   PASS    AF=0.870295 ES:SE:LP:AF:SS:ID   0.000459625:0.000514492:0.429846:0.870295:361194:rs3131956
1   758626  rs3131954   C   T   .   PASS    AF=0.870739 ES:SE:LP:AF:SS:ID   0.000504267:0.000515802:0.48379:0.870739:361194:rs3131954
1   759293  rs10157329  T   A   .   PASS    AF=0.0988442    ES:SE:LP:AF:SS:ID   -0.000487919:0.000599394:0.381289:0.0988442:361194:rs10157329
1   759600  rs545998451 AGT A   .   PASS    AF=0.00647588   ES:SE:LP:AF:SS:ID   -0.000792895:0.00231849:0.135275:0.00647588:361194:1_759600_AGT_A
1   759837  rs3115851   T   A   .   PASS    AF=0.874635 ES:SE:LP:AF:SS:ID   0.000391894:0.00052349:0.34286:0.874635:361194:rs3115851
1   761732  rs2286139   C   T   .   PASS    AF=0.864027 ES:SE:LP:AF:SS:ID   0.000525759:0.000513359:0.514615:0.864027:361194:rs2286139
1   761752  rs1057213   C   T   .   PASS    AF=0.869425 ES:SE:LP:AF:SS:ID   0.000432673:0.000518343:0.393753:0.869425:361194:rs1057213
1   762273  rs3115849   G   A   .   PASS    AF=0.866371 ES:SE:LP:AF:SS:ID   0.000465226:0.000518448:0.432343:0.866371:361194:rs3115849
1   762485  rs12095200  C   A   .   PASS    AF=0.0987831    ES:SE:LP:AF:SS:ID   -0.000427825:0.00062068:0.309233:0.0987831:361194:rs12095200
1   762589  rs3115848   G   C   .   PASS    AF=0.871556 ES:SE:LP:AF:SS:ID   0.000411891:0.000524355:0.364367:0.871556:361194:rs3115848
1   762592  rs3131950   C   G   .   PASS    AF=0.871556 ES:SE:LP:AF:SS:ID   0.000411902:0.000524355:0.364378:0.871556:361194:rs3131950
1   762601  rs3131949   T   C   .   PASS    AF=0.871555 ES:SE:LP:AF:SS:ID   0.000411362:0.000524365:0.363764:0.871555:361194:rs3131949
1   762632  rs3131948   T   A   .   PASS    AF=0.871929 ES:SE:LP:AF:SS:ID   0.000387408:0.000524664:0.336981:0.871929:361194:rs3131948
1   764191  rs7515915   T   G   .   PASS    AF=0.125562 ES:SE:LP:AF:SS:ID   -0.000427107:0.000525078:0.380928:0.125562:361194:rs7515915
1   766007  rs61768174  A   C   .   PASS    AF=0.105428 ES:SE:LP:AF:SS:ID   -0.00053696:0.000571619:0.458991:0.105428:361194:rs61768174
1   766105  rs2519015   T   A   .   PASS    AF=0.855376 ES:SE:LP:AF:SS:ID   0.000398998:0.000513167:0.359666:0.855376:361194:rs2519015
1   767393  rs538667473 A   C   .   PASS    AF=0.00165444   ES:SE:LP:AF:SS:ID   -0.00437918:0.00454592:0.474455:0.00165444:361194:rs538667473
1   768116  rs376645387 A   AGTTTT  .   PASS    AF=0.838358 ES:SE:LP:AF:SS:ID   -0.000127793:0.000505562:0.0966696:0.838358:361194:rs376645387
1   768253  rs2977608   A   C   .   PASS    AF=0.763351 ES:SE:LP:AF:SS:ID   7.91736e-06:0.000406882:0.00679531:0.763351:361194:rs2977608