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-20421/ukb-d-20421.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-20421/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 17:18:50 2019
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ukb-d-import/processed/ukb-d-20421/ukb-d-20421.vcf.gz ...
Read summary statistics for 13570570 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: 0.0559 (0.0047)
Lambda GC: 1.0966
Mean Chi^2: 1.1145
Intercept: 0.9924 (0.0063)
Ratio < 0 (usually indicates GC correction).
Analysis finished at Mon Nov 25 17:21:39 2019
Total time elapsed: 2.0m:49.46s

QC metrics

Metrics

Metrics

{
    "af_correlation": 0.9521,
    "inflation_factor": 1.065,
    "mean_EFFECT": 1.6357e-06,
    "n": 110315,
    "n_snps": 13570570,
    "n_clumped_hits": 0,
    "n_p_sig": 0,
    "n_mono": 0,
    "n_ns": 1251338,
    "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": 564326,
    "n_est": 110737.3812,
    "ratio_se_n": 1.0019,
    "mean_diff": 1.3085e-06,
    "ratio_diff": 1.7068,
    "sd_y_est1": 0.4399,
    "sd_y_est2": 0.4408,
    "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": 0.0559,
    "ldsc_observed_scale_h2_se": 0.0047,
    "ldsc_intercept_beta": 0.9924,
    "ldsc_intercept_se": 0.0063,
    "ldsc_lambda_gc": 1.0966,
    "ldsc_mean_chisq": 1.1145,
    "ldsc_ratio": -0.0664
}

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 13558541 0 NA NA NA NA NA NA NA NA
character REF 0 1.0000000 1 100 0 57056 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 9.051384e+00 6.185058e+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 7.902537e+07 5.591619e+07 3.02000e+02 3.292818e+07 7.013942e+07 1.148592e+08 2.492309e+08 ▇▆▅▂▁
numeric EFFECT 0 1.0000000 NA NA NA NA NA 1.600000e-06 1.098290e-02 -1.30432e-01 -3.014400e-03 -1.800000e-06 2.987400e-03 1.361940e-01 ▁▁▇▁▁
numeric SE 0 1.0000000 NA NA NA NA NA 7.846800e-03 7.563600e-03 1.54660e-03 2.240000e-03 4.121900e-03 1.126510e-02 3.784560e-02 ▇▂▁▁▁
numeric PVAL 0 1.0000000 NA NA NA NA NA 4.894726e-01 2.920536e-01 1.00000e-07 2.337082e-01 4.863938e-01 7.427968e-01 1.000000e+00 ▇▇▇▇▇
numeric PVAL_ztest 0 1.0000000 NA NA NA NA NA 4.894712e-01 2.920545e-01 1.00000e-07 2.337048e-01 4.863928e-01 7.427959e-01 1.000000e+00 ▇▇▇▇▇
numeric AF 0 1.0000000 NA NA NA NA NA 1.910105e-01 2.544528e-01 1.00000e-03 7.486300e-03 6.028590e-02 2.957080e-01 9.989990e-01 ▇▂▁▁▁
numeric AF_reference 564326 0.9584155 NA NA NA NA NA 1.964816e-01 2.471311e-01 0.00000e+00 5.790700e-03 8.446490e-02 3.083440e-01 1.000000e+00 ▇▂▁▁▁
numeric N 0 1.0000000 NA NA NA NA NA 1.103150e+05 0.000000e+00 1.10315e+05 1.103150e+05 1.103150e+05 1.103150e+05 1.103150e+05 ▁▁▇▁▁

Head and tail

CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
1 692794 rs530212009 CA C 0.0026065 0.0032687 0.4252125 0.4252094 0.1115450 0.1894970 110315
1 693731 rs12238997 A G 0.0040630 0.0030938 0.1890989 0.1890968 0.1165790 0.1417730 110315
1 707522 rs371890604 G C 0.0040675 0.0034741 0.2416752 0.2416732 0.0981382 0.1293930 110315
1 717587 rs144155419 G A 0.0130407 0.0082845 0.1154660 0.1154629 0.0158338 0.0045926 110315
1 723329 rs189787166 A T 0.0182063 0.0242444 0.4526859 0.4526835 0.0017712 0.0003994 110315
1 730087 rs148120343 T C 0.0020819 0.0043105 0.6291091 0.6291083 0.0567366 0.0127796 110315
1 731718 rs142557973 T C 0.0043476 0.0029347 0.1384931 0.1384900 0.1225070 0.1543530 110315
1 732032 rs61770163 A C 0.0043052 0.0031282 0.1687489 0.1687461 0.1220920 0.1555510 110315
1 734349 rs141242758 T C 0.0042122 0.0029364 0.1514311 0.1514284 0.1217620 0.1525560 110315
1 740284 rs61770167 C T 0.0024790 0.0134596 0.8538711 0.8538704 0.0057997 0.0023962 110315
CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
23 154923311 rs141127553 C T 0.0034190 0.0034318 0.3191273 0.3191246 0.0555842 0.0309934 110315
23 154923374 rs111332691 T A -0.0060146 0.0037339 0.1072289 0.1072259 0.0450437 0.0116556 110315
23 154925045 rs509981 C T 0.0018781 0.0018037 0.2977831 0.2977812 0.2447920 0.3634440 110315
23 154925895 rs538470 C T 0.0019361 0.0018443 0.2938123 0.2938112 0.2412630 0.3634440 110315
23 154927581 rs644138 G A 0.0025953 0.0016966 0.1260840 0.1260812 0.3007250 0.4635760 110315
23 154929412 rs557132 C T 0.0019003 0.0018041 0.2921837 0.2921826 0.2446840 0.3568210 110315
23 154929637 rs35185538 CT C 0.0015156 0.0018852 0.4214170 0.4214149 0.2288870 0.3011920 110315
23 154929952 rs4012982 CAA C 0.0019026 0.0018988 0.3163559 0.3163532 0.2387440 0.3165560 110315
23 154930230 rs781880 A G 0.0018041 0.0018035 0.3171451 0.3171415 0.2451250 0.3618540 110315
23 154930487 rs781879 T A 0.0133813 0.0060874 0.0279364 0.0279338 0.0199238 0.1263580 110315

bcf preview

1   692794  rs530212009 CA  C   .   PASS    AF=0.111545 ES:SE:LP:AF:SS:ID   0.00260649:0.00326867:0.371394:0.111545:110315:1_692794_CA_C
1   693731  rs12238997  A   G   .   PASS    AF=0.116579 ES:SE:LP:AF:SS:ID   0.00406299:0.00309383:0.723311:0.116579:110315:rs12238997
1   707522  rs371890604 G   C   .   PASS    AF=0.0981382    ES:SE:LP:AF:SS:ID   0.00406754:0.00347411:0.616768:0.0981382:110315:rs371890604
1   717587  rs144155419 G   A   .   PASS    AF=0.0158338    ES:SE:LP:AF:SS:ID   0.0130407:0.00828451:0.937546:0.0158338:110315:rs144155419
1   723329  rs189787166 A   T   .   PASS    AF=0.00177118   ES:SE:LP:AF:SS:ID   0.0182063:0.0242444:0.344203:0.00177118:110315:rs189787166
1   730087  rs148120343 T   C   .   PASS    AF=0.0567366    ES:SE:LP:AF:SS:ID   0.00208191:0.00431053:0.201274:0.0567366:110315:rs148120343
1   731718  rs58276399  T   C   .   PASS    AF=0.122507 ES:SE:LP:AF:SS:ID   0.00434759:0.00293471:0.858572:0.122507:110315:rs58276399
1   732032  rs61770163  A   C   .   PASS    AF=0.122092 ES:SE:LP:AF:SS:ID   0.00430518:0.00312821:0.772759:0.122092:110315:rs61770163
1   734349  rs141242758 T   C   .   PASS    AF=0.121762 ES:SE:LP:AF:SS:ID   0.00421225:0.00293638:0.819785:0.121762:110315:rs141242758
1   740284  rs61770167  C   T   .   PASS    AF=0.00579968   ES:SE:LP:AF:SS:ID   0.00247902:0.0134596:0.0686077:0.00579968:110315:rs61770167
1   742813  rs112573343 C   T   .   PASS    AF=0.00183738   ES:SE:LP:AF:SS:ID   0.0226998:0.0256799:0.423979:0.00183738:110315:rs112573343
1   749963  rs529266287 T   TAA .   PASS    AF=0.869037 ES:SE:LP:AF:SS:ID   -0.0047015:0.00289269:0.982545:0.869037:110315:rs529266287
1   750230  rs190826124 G   C   .   PASS    AF=0.0015767    ES:SE:LP:AF:SS:ID   0.00684707:0.0257773:0.102082:0.0015767:110315:rs190826124
1   751343  rs28544273  T   A   .   PASS    AF=0.12361  ES:SE:LP:AF:SS:ID   0.00504774:0.00286571:1.10697:0.12361:110315:rs28544273
1   751488  rs200141114 G   GA  .   PASS    AF=0.143212 ES:SE:LP:AF:SS:ID   0.00546219:0.0028345:1.26779:0.143212:110315:rs200141114
1   751756  rs28527770  T   C   .   PASS    AF=0.123731 ES:SE:LP:AF:SS:ID   0.00493142:0.00286174:1.07134:0.123731:110315:rs28527770
1   753405  rs3115860   C   A   .   PASS    AF=0.869876 ES:SE:LP:AF:SS:ID   -0.0046564:0.00278694:1.02335:0.869876:110315:rs3115860
1   753425  rs3131970   T   C   .   PASS    AF=0.874679 ES:SE:LP:AF:SS:ID   -0.00443634:0.00283385:0.930062:0.874679:110315:rs3131970
1   753541  rs2073813   G   A   .   PASS    AF=0.129569 ES:SE:LP:AF:SS:ID   0.00500459:0.002795:1.13449:0.129569:110315:rs2073813
1   754105  rs12184325  C   T   .   PASS    AF=0.0365317    ES:SE:LP:AF:SS:ID   0.00620693:0.00507022:0.65584:0.0365317:110315:rs12184325
1   754182  rs3131969   A   G   .   PASS    AF=0.869476 ES:SE:LP:AF:SS:ID   -0.00475233:0.00278439:1.05618:0.869476:110315:rs3131969
1   754192  rs3131968   A   G   .   PASS    AF=0.869538 ES:SE:LP:AF:SS:ID   -0.00485243:0.00278516:1.08901:0.869538:110315:rs3131968
1   754334  rs3131967   T   C   .   PASS    AF=0.869475 ES:SE:LP:AF:SS:ID   -0.00477525:0.00278432:1.06379:0.869475:110315:rs3131967
1   754433  rs150578204 G   A   .   PASS    AF=0.00516206   ES:SE:LP:AF:SS:ID   0.00756712:0.0141606:0.226887:0.00516206:110315:rs150578204
1   754458  rs142682604 G   T   .   PASS    AF=0.00513057   ES:SE:LP:AF:SS:ID   0.00787101:0.014191:0.237219:0.00513057:110315:rs142682604
1   755435  rs184270342 T   G   .   PASS    AF=0.00568282   ES:SE:LP:AF:SS:ID   0.00196749:0.0137252:0.0525589:0.00568282:110315:rs184270342
1   755890  rs3115858   A   T   .   PASS    AF=0.869554 ES:SE:LP:AF:SS:ID   -0.00453536:0.00277922:0.9884:0.869554:110315:rs3115858
1   756434  rs61768170  G   C   .   PASS    AF=0.126859 ES:SE:LP:AF:SS:ID   0.00505239:0.00283708:1.12528:0.126859:110315:rs61768170
1   756604  rs3131962   A   G   .   PASS    AF=0.869075 ES:SE:LP:AF:SS:ID   -0.00449417:0.00277201:0.978964:0.869075:110315:rs3131962
1   757640  rs3115853   G   A   .   PASS    AF=0.868479 ES:SE:LP:AF:SS:ID   -0.00470865:0.00277101:1.04928:0.868479:110315:rs3115853
1   757734  rs4951929   C   T   .   PASS    AF=0.86926  ES:SE:LP:AF:SS:ID   -0.00464418:0.00277467:1.02605:0.86926:110315:rs4951929
1   757936  rs4951862   C   A   .   PASS    AF=0.869267 ES:SE:LP:AF:SS:ID   -0.00464504:0.00277487:1.02622:0.869267:110315:rs4951862
1   758144  rs3131956   A   G   .   PASS    AF=0.869269 ES:SE:LP:AF:SS:ID   -0.00464347:0.00277488:1.02571:0.869269:110315:rs3131956
1   758626  rs3131954   C   T   .   PASS    AF=0.869708 ES:SE:LP:AF:SS:ID   -0.00461782:0.002782:1.0135:0.869708:110315:rs3131954
1   759293  rs10157329  T   A   .   PASS    AF=0.0993073    ES:SE:LP:AF:SS:ID   0.00450915:0.00323807:0.785787:0.0993073:110315:rs10157329
1   759600  rs545998451 AGT A   .   PASS    AF=0.00653761   ES:SE:LP:AF:SS:ID   0.00976108:0.0124534:0.363358:0.00653761:110315:1_759600_AGT_A
1   759837  rs3115851   T   A   .   PASS    AF=0.873759 ES:SE:LP:AF:SS:ID   -0.00464112:0.00282481:0.998314:0.873759:110315:rs3115851
1   761732  rs2286139   C   T   .   PASS    AF=0.863076 ES:SE:LP:AF:SS:ID   -0.00579511:0.0027702:1.43835:0.863076:110315:rs2286139
1   761752  rs1057213   C   T   .   PASS    AF=0.868427 ES:SE:LP:AF:SS:ID   -0.00418719:0.00279664:0.871798:0.868427:110315:rs1057213
1   762273  rs3115849   G   A   .   PASS    AF=0.865441 ES:SE:LP:AF:SS:ID   -0.00458691:0.00279687:0.995657:0.865441:110315:rs3115849
1   762485  rs12095200  C   A   .   PASS    AF=0.0997287    ES:SE:LP:AF:SS:ID   0.00664719:0.00334115:1.33115:0.0997287:110315:rs12095200
1   762589  rs3115848   G   C   .   PASS    AF=0.870756 ES:SE:LP:AF:SS:ID   -0.00468813:0.00283029:1.01037:0.870756:110315:rs3115848
1   762592  rs3131950   C   G   .   PASS    AF=0.870756 ES:SE:LP:AF:SS:ID   -0.00468779:0.00283029:1.01026:0.870756:110315:rs3131950
1   762601  rs3131949   T   C   .   PASS    AF=0.870755 ES:SE:LP:AF:SS:ID   -0.00469298:0.0028303:1.0119:0.870755:110315:rs3131949
1   762632  rs3131948   T   A   .   PASS    AF=0.871074 ES:SE:LP:AF:SS:ID   -0.00456867:0.00283154:0.97208:0.871074:110315:rs3131948
1   764191  rs7515915   T   G   .   PASS    AF=0.12645  ES:SE:LP:AF:SS:ID   0.00474254:0.00283414:1.02568:0.12645:110315:rs7515915
1   766007  rs61768174  A   C   .   PASS    AF=0.10609  ES:SE:LP:AF:SS:ID   0.00365877:0.00308204:0.628598:0.10609:110315:rs61768174
1   766105  rs2519015   T   A   .   PASS    AF=0.854445 ES:SE:LP:AF:SS:ID   -0.00472791:0.0027694:1.05656:0.854445:110315:rs2519015
1   767393  rs538667473 A   C   .   PASS    AF=0.00168366   ES:SE:LP:AF:SS:ID   0.0191017:0.0243562:0.363625:0.00168366:110315:rs538667473
1   768116  rs376645387 A   AGTTTT  .   PASS    AF=0.839013 ES:SE:LP:AF:SS:ID   -0.00475506:0.00274001:1.08265:0.839013:110315:rs376645387