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-20429/ukb-d-20429.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-20429/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 17:15:45 2019
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ukb-d-import/processed/ukb-d-20429/ukb-d-20429.vcf.gz ...
Read summary statistics for 13541411 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, 1283490 SNPs remain.
After merging with regression SNP LD, 1283490 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.0406 (0.012)
Lambda GC: 1.0315
Mean Chi^2: 1.0349
Intercept: 1.0079 (0.0054)
Ratio: 0.2263 (0.1534)
Analysis finished at Mon Nov 25 17:18:30 2019
Total time elapsed: 2.0m:45.34s

QC metrics

Metrics

Metrics

{
    "af_correlation": 0.952,
    "inflation_factor": 1.0267,
    "mean_EFFECT": -0,
    "n": 34121,
    "n_snps": 13541411,
    "n_clumped_hits": 0,
    "n_p_sig": 0,
    "n_mono": 0,
    "n_ns": 1250260,
    "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": 557494,
    "n_est": 34227.2136,
    "ratio_se_n": 1.0016,
    "mean_diff": -0,
    "ratio_diff": 257.4433,
    "sd_y_est1": 0.448,
    "sd_y_est2": 0.4487,
    "r2_sum1": 0,
    "r2_sum2": 0,
    "r2_sum3": 0,
    "r2_sum4": 0,
    "ldsc_nsnp_merge_refpanel_ld": 1283490,
    "ldsc_nsnp_merge_regression_ld": 1283490,
    "ldsc_observed_scale_h2_beta": 0.0406,
    "ldsc_observed_scale_h2_se": 0.012,
    "ldsc_intercept_beta": 1.0079,
    "ldsc_intercept_se": 0.0054,
    "ldsc_lambda_gc": 1.0315,
    "ldsc_mean_chisq": 1.0349,
    "ldsc_ratio": 0.2264
}

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 13529420 0 NA NA NA NA NA NA NA NA
character REF 0 1.0000000 1 100 0 57008 0 NA NA NA NA NA NA NA NA
character ALT 0 1.0000000 1 342 0 33312 0 NA NA NA NA NA NA NA NA
numeric CHROM 0 1.0000000 NA NA NA NA NA 9.051544e+00 6.185061e+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 7.902406e+07 5.591640e+07 3.02000e+02 3.292431e+07 7.013750e+07 1.148591e+08 2.492309e+08 ▇▆▅▂▁
numeric EFFECT 0 1.0000000 NA NA NA NA NA -3.940000e-05 1.991480e-02 -2.69654e-01 -5.320700e-03 -4.000000e-07 5.340500e-03 2.240660e-01 ▁▁▇▁▁
numeric SE 0 1.0000000 NA NA NA NA NA 1.428730e-02 1.375250e-02 2.91480e-03 4.096800e-03 7.516700e-03 2.049700e-02 7.833850e-02 ▇▂▁▁▁
numeric PVAL 0 1.0000000 NA NA NA NA NA 4.961041e-01 2.897085e-01 2.00000e-07 2.443622e-01 4.943414e-01 7.472054e-01 1.000000e+00 ▇▇▇▇▇
numeric PVAL_ztest 0 1.0000000 NA NA NA NA NA 4.960994e-01 2.897113e-01 2.00000e-07 2.443535e-01 4.943364e-01 7.472025e-01 1.000000e+00 ▇▇▇▇▇
numeric AF 0 1.0000000 NA NA NA NA NA 1.914050e-01 2.545546e-01 1.00000e-03 7.590000e-03 6.072560e-02 2.965570e-01 9.990000e-01 ▇▂▁▁▁
numeric AF_reference 557494 0.9588304 NA NA NA NA NA 1.967741e-01 2.472015e-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 3.412100e+04 0.000000e+00 3.41210e+04 3.412100e+04 3.412100e+04 3.412100e+04 3.412100e+04 ▁▁▇▁▁

Head and tail

CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
1 692794 rs530212009 CA C -0.0012083 0.0059659 0.8395029 0.8395026 0.1123980 0.1894970 34121
1 693731 rs12238997 A G -0.0004207 0.0056380 0.9405240 0.9405235 0.1174050 0.1417730 34121
1 707522 rs371890604 G C 0.0006039 0.0063337 0.9240441 0.9240435 0.0989295 0.1293930 34121
1 717587 rs144155419 G A -0.0083770 0.0148278 0.5721106 0.5721076 0.0164591 0.0045926 34121
1 723329 rs189787166 A T 0.0508256 0.0443122 0.2513941 0.2513862 0.0017923 0.0003994 34121
1 730087 rs148120343 T C -0.0001511 0.0078595 0.9846640 0.9846641 0.0567763 0.0127796 34121
1 731718 rs142557973 T C 0.0004458 0.0053459 0.9335361 0.9335350 0.1238690 0.1543530 34121
1 732032 rs61770163 A C -0.0029507 0.0056986 0.6046040 0.6046003 0.1233770 0.1555510 34121
1 734349 rs141242758 T C 0.0005077 0.0053498 0.9243940 0.9243940 0.1230790 0.1525560 34121
1 740284 rs61770167 C T 0.0187184 0.0250304 0.4545713 0.4545647 0.0056319 0.0023962 34121
CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
23 154923311 rs141127553 C T -0.0045069 0.0064348 0.4836865 0.4836820 0.0561995 0.0309934 34121
23 154923374 rs111332691 T A -0.0144699 0.0071641 0.0434140 0.0434063 0.0438000 0.0116556 34121
23 154925045 rs509981 C T -0.0000520 0.0034174 0.9878660 0.9878654 0.2427590 0.3634440 34121
23 154925895 rs538470 C T 0.0008878 0.0034946 0.7994599 0.7994589 0.2392390 0.3634440 34121
23 154927581 rs644138 G A -0.0011351 0.0032058 0.7232742 0.7232725 0.2994080 0.4635760 34121
23 154929412 rs557132 C T 0.0001433 0.0034185 0.9665611 0.9665611 0.2425870 0.3568210 34121
23 154929637 rs35185538 CT C 0.0002214 0.0035675 0.9505140 0.9505136 0.2272000 0.3011920 34121
23 154929952 rs4012982 CAA C -0.0001270 0.0036014 0.9718761 0.9718761 0.2368280 0.3165560 34121
23 154930230 rs781880 A G 0.0005732 0.0034179 0.8668269 0.8668262 0.2429060 0.3618540 34121
23 154930487 rs781879 T A -0.0085449 0.0114126 0.4540273 0.4540224 0.0199736 0.1263580 34121

bcf preview

1   692794  rs530212009 CA  C   .   PASS    AF=0.112398 ES:SE:LP:AF:SS:ID   -0.00120828:0.00596594:0.0759778:0.112398:34121:1_692794_CA_C
1   693731  rs12238997  A   G   .   PASS    AF=0.117405 ES:SE:LP:AF:SS:ID   -0.000420658:0.00563795:0.0266301:0.117405:34121:rs12238997
1   707522  rs371890604 G   C   .   PASS    AF=0.0989295    ES:SE:LP:AF:SS:ID   0.000603868:0.00633373:0.0343073:0.0989295:34121:rs371890604
1   717587  rs144155419 G   A   .   PASS    AF=0.0164591    ES:SE:LP:AF:SS:ID   -0.00837697:0.0148278:0.24252:0.0164591:34121:rs144155419
1   723329  rs189787166 A   T   .   PASS    AF=0.0017923    ES:SE:LP:AF:SS:ID   0.0508256:0.0443122:0.599645:0.0017923:34121:rs189787166
1   730087  rs148120343 T   C   .   PASS    AF=0.0567763    ES:SE:LP:AF:SS:ID   -0.000151074:0.00785949:0.00671194:0.0567763:34121:rs148120343
1   731718  rs58276399  T   C   .   PASS    AF=0.123869 ES:SE:LP:AF:SS:ID   0.000445838:0.0053459:0.0298689:0.123869:34121:rs58276399
1   732032  rs61770163  A   C   .   PASS    AF=0.123377 ES:SE:LP:AF:SS:ID   -0.00295071:0.00569859:0.218529:0.123377:34121:rs61770163
1   734349  rs141242758 T   C   .   PASS    AF=0.123079 ES:SE:LP:AF:SS:ID   0.000507695:0.00534977:0.0341429:0.123079:34121:rs141242758
1   740284  rs61770167  C   T   .   PASS    AF=0.00563186   ES:SE:LP:AF:SS:ID   0.0187184:0.0250304:0.342398:0.00563186:34121:rs61770167
1   742813  rs112573343 C   T   .   PASS    AF=0.00196877   ES:SE:LP:AF:SS:ID   0.0423951:0.0449752:0.461081:0.00196877:34121:rs112573343
1   749963  rs529266287 T   TAA .   PASS    AF=0.867281 ES:SE:LP:AF:SS:ID   0.00107099:0.00525553:0.0764845:0.867281:34121:rs529266287
1   750230  rs190826124 G   C   .   PASS    AF=0.00146181   ES:SE:LP:AF:SS:ID   0.00246462:0.0493587:0.0176492:0.00146181:34121:rs190826124
1   751343  rs28544273  T   A   .   PASS    AF=0.125218 ES:SE:LP:AF:SS:ID   -0.0021336:0.00521178:0.166048:0.125218:34121:rs28544273
1   751488  rs200141114 G   GA  .   PASS    AF=0.144984 ES:SE:LP:AF:SS:ID   -0.00120398:0.00515843:0.0886021:0.144984:34121:rs200141114
1   751756  rs28527770  T   C   .   PASS    AF=0.1253   ES:SE:LP:AF:SS:ID   -0.00207803:0.00520488:0.161331:0.1253:34121:rs28527770
1   753405  rs3115860   C   A   .   PASS    AF=0.868123 ES:SE:LP:AF:SS:ID   -0.000542674:0.00507642:0.0386416:0.868123:34121:rs3115860
1   753425  rs3131970   T   C   .   PASS    AF=0.87307  ES:SE:LP:AF:SS:ID   0.00160687:0.00515624:0.121869:0.87307:34121:rs3131970
1   753541  rs2073813   G   A   .   PASS    AF=0.131359 ES:SE:LP:AF:SS:ID   -0.00024349:0.00508722:0.0169035:0.131359:34121:rs2073813
1   754105  rs12184325  C   T   .   PASS    AF=0.0366197    ES:SE:LP:AF:SS:ID   0.0189071:0.00926761:1.38358:0.0366197:34121:rs12184325
1   754182  rs3131969   A   G   .   PASS    AF=0.867671 ES:SE:LP:AF:SS:ID   -0.000387708:0.00506906:0.0273187:0.867671:34121:rs3131969
1   754192  rs3131968   A   G   .   PASS    AF=0.867734 ES:SE:LP:AF:SS:ID   -0.000503755:0.00507005:0.0358092:0.867734:34121:rs3131968
1   754334  rs3131967   T   C   .   PASS    AF=0.867664 ES:SE:LP:AF:SS:ID   -0.000399341:0.00506882:0.0281654:0.867664:34121:rs3131967
1   754433  rs150578204 G   A   .   PASS    AF=0.00548745   ES:SE:LP:AF:SS:ID   -0.0141421:0.0250282:0.242569:0.00548745:34121:rs150578204
1   754458  rs142682604 G   T   .   PASS    AF=0.00546067   ES:SE:LP:AF:SS:ID   -0.0143465:0.0250808:0.246173:0.00546067:34121:rs142682604
1   755435  rs184270342 T   G   .   PASS    AF=0.00587551   ES:SE:LP:AF:SS:ID   0.0242705:0.0245807:0.490174:0.00587551:34121:rs184270342
1   755890  rs3115858   A   T   .   PASS    AF=0.867792 ES:SE:LP:AF:SS:ID   -0.00063531:0.0050625:0.0456928:0.867792:34121:rs3115858
1   756434  rs61768170  G   C   .   PASS    AF=0.12857  ES:SE:LP:AF:SS:ID   4.154e-05:0.00516215:0.00279716:0.12857:34121:rs61768170
1   756604  rs3131962   A   G   .   PASS    AF=0.867296 ES:SE:LP:AF:SS:ID   -0.000740547:0.00504966:0.0538392:0.867296:34121:rs3131962
1   757640  rs3115853   G   A   .   PASS    AF=0.866756 ES:SE:LP:AF:SS:ID   -0.000786838:0.00504506:0.0574642:0.866756:34121:rs3115853
1   757734  rs4951929   C   T   .   PASS    AF=0.867477 ES:SE:LP:AF:SS:ID   -0.000694849:0.00505409:0.0502929:0.867477:34121:rs4951929
1   757936  rs4951862   C   A   .   PASS    AF=0.867483 ES:SE:LP:AF:SS:ID   -0.000692433:0.00505443:0.0501052:0.867483:34121:rs4951862
1   758144  rs3131956   A   G   .   PASS    AF=0.867486 ES:SE:LP:AF:SS:ID   -0.000693687:0.00505445:0.0502003:0.867486:34121:rs3131956
1   758626  rs3131954   C   T   .   PASS    AF=0.867928 ES:SE:LP:AF:SS:ID   -0.000789345:0.00506708:0.0573928:0.867928:34121:rs3131954
1   759293  rs10157329  T   A   .   PASS    AF=0.100435 ES:SE:LP:AF:SS:ID   0.00139511:0.00588524:0.0901141:0.100435:34121:rs10157329
1   759600  rs545998451 AGT A   .   PASS    AF=0.006831 ES:SE:LP:AF:SS:ID   0.0255843:0.0222447:0.601888:0.006831:34121:1_759600_AGT_A
1   759837  rs3115851   T   A   .   PASS    AF=0.872164 ES:SE:LP:AF:SS:ID   0.00048009:0.00514275:0.0335654:0.872164:34121:rs3115851
1   761732  rs2286139   C   T   .   PASS    AF=0.861082 ES:SE:LP:AF:SS:ID   -0.00188689:0.00503933:0.149915:0.861082:34121:rs2286139
1   761752  rs1057213   C   T   .   PASS    AF=0.866807 ES:SE:LP:AF:SS:ID   -0.000876594:0.00509606:0.0637739:0.866807:34121:rs1057213
1   762273  rs3115849   G   A   .   PASS    AF=0.863867 ES:SE:LP:AF:SS:ID   0.000209896:0.00509416:0.0145133:0.863867:34121:rs3115849
1   762485  rs12095200  C   A   .   PASS    AF=0.100838 ES:SE:LP:AF:SS:ID   -0.00232001:0.00608239:0.153115:0.100838:34121:rs12095200
1   762589  rs3115848   G   C   .   PASS    AF=0.869059 ES:SE:LP:AF:SS:ID   0.000662358:0.00514901:0.0468954:0.869059:34121:rs3115848
1   762592  rs3131950   C   G   .   PASS    AF=0.869059 ES:SE:LP:AF:SS:ID   0.000661103:0.005149:0.046802:0.869059:34121:rs3131950
1   762601  rs3131949   T   C   .   PASS    AF=0.869055 ES:SE:LP:AF:SS:ID   0.000663959:0.00514902:0.0470144:0.869055:34121:rs3131949
1   762632  rs3131948   T   A   .   PASS    AF=0.869459 ES:SE:LP:AF:SS:ID   0.000517029:0.00515223:0.0361805:0.869459:34121:rs3131948
1   764191  rs7515915   T   G   .   PASS    AF=0.128056 ES:SE:LP:AF:SS:ID   -0.000645558:0.00515887:0.0455563:0.128056:34121:rs7515915
1   766007  rs61768174  A   C   .   PASS    AF=0.106816 ES:SE:LP:AF:SS:ID   0.000917008:0.0056246:0.0602352:0.106816:34121:rs61768174
1   766105  rs2519015   T   A   .   PASS    AF=0.852792 ES:SE:LP:AF:SS:ID   0.00103606:0.00503706:0.0772559:0.852792:34121:rs2519015
1   767393  rs538667473 A   C   .   PASS    AF=0.00171023   ES:SE:LP:AF:SS:ID   0.049789:0.044518:0.579378:0.00171023:34121:rs538667473
1   768116  rs376645387 A   AGTTTT  .   PASS    AF=0.83734  ES:SE:LP:AF:SS:ID   -0.00303084:0.0050024:0.263922:0.83734:34121:rs376645387