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-20546_1/ukb-d-20546_1.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-20546_1/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 16:33:13 2019
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ukb-d-import/processed/ukb-d-20546_1/ukb-d-20546_1.vcf.gz ...
Read summary statistics for 11698434 SNPs.
Dropped 10037 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, 1282812 SNPs remain.
After merging with regression SNP LD, 1282812 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.0086 (0.0038)
Lambda GC: 1.0218
Mean Chi^2: 1.0165
Intercept: 0.9962 (0.0064)
Ratio < 0 (usually indicates GC correction).
Analysis finished at Mon Nov 25 16:35:07 2019
Total time elapsed: 1.0m:54.12s

QC metrics

Metrics

Metrics

{
    "af_correlation": 0.9482,
    "inflation_factor": 1.0139,
    "mean_EFFECT": 2.9576e-06,
    "n": 117763,
    "n_snps": 11698434,
    "n_clumped_hits": 1,
    "n_p_sig": 7,
    "n_mono": 0,
    "n_ns": 1170895,
    "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": 257040,
    "n_est": 118052.484,
    "ratio_se_n": 1.0012,
    "mean_diff": 0,
    "ratio_diff": 520.0893,
    "sd_y_est1": 0.1834,
    "sd_y_est2": 0.1837,
    "r2_sum1": 0,
    "r2_sum2": 0.0003,
    "r2_sum3": 0.0003,
    "r2_sum4": 0.0003,
    "ldsc_nsnp_merge_refpanel_ld": 1282812,
    "ldsc_nsnp_merge_regression_ld": 1282812,
    "ldsc_observed_scale_h2_beta": 0.0086,
    "ldsc_observed_scale_h2_se": 0.0038,
    "ldsc_intercept_beta": 0.9962,
    "ldsc_intercept_se": 0.0064,
    "ldsc_lambda_gc": 1.0218,
    "ldsc_mean_chisq": 1.0165,
    "ldsc_ratio": -0.2303
}

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 11689010 0 NA NA NA NA NA NA NA NA
character REF 0 1.0000000 1 100 0 52701 0 NA NA NA NA NA NA NA NA
character ALT 0 1.0000000 1 342 0 31899 0 NA NA NA NA NA NA NA NA
numeric CHROM 0 1.0000000 NA NA NA NA NA 9.072097e+00 6.184318e+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 7.886482e+07 5.598707e+07 3.02000e+02 3.266634e+07 6.988431e+07 1.147310e+08 2.492309e+08 ▇▆▅▂▁
numeric EFFECT 0 1.0000000 NA NA NA NA NA 3.000000e-06 2.756000e-03 -2.71922e-02 -9.942000e-04 -8.500000e-06 9.688000e-04 3.535340e-02 ▁▁▇▁▁
numeric SE 0 1.0000000 NA NA NA NA NA 2.151800e-03 1.714200e-03 6.26500e-04 8.633000e-04 1.335500e-03 2.942600e-03 1.049980e-02 ▇▂▁▁▁
numeric PVAL 0 1.0000000 NA NA NA NA NA 4.979142e-01 2.887141e-01 0.00000e+00 2.477781e-01 4.970339e-01 7.475702e-01 1.000000e+00 ▇▇▇▇▇
numeric PVAL_ztest 0 1.0000000 NA NA NA NA NA 4.979129e-01 2.887149e-01 0.00000e+00 2.477757e-01 4.970328e-01 7.475702e-01 1.000000e+00 ▇▇▇▇▇
numeric AF 0 1.0000000 NA NA NA NA NA 2.199280e-01 2.602139e-01 3.04060e-03 1.765580e-02 9.992600e-02 3.507670e-01 9.969590e-01 ▇▂▁▁▁
numeric AF_reference 257040 0.9780278 NA NA NA NA NA 2.208462e-01 2.515609e-01 0.00000e+00 1.457670e-02 1.188100e-01 3.514380e-01 1.000000e+00 ▇▂▂▁▁
numeric N 0 1.0000000 NA NA NA NA NA 1.177630e+05 0.000000e+00 1.17763e+05 1.177630e+05 1.177630e+05 1.177630e+05 1.177630e+05 ▁▁▇▁▁

Head and tail

CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
1 692794 rs530212009 CA C -0.0002040 0.0013178 0.8769540 0.8769529 0.1116950 0.1894970 117763
1 693731 rs12238997 A G 0.0000899 0.0012480 0.9425600 0.9425598 0.1167150 0.1417730 117763
1 707522 rs371890604 G C 0.0007197 0.0014002 0.6072619 0.6072612 0.0983485 0.1293930 117763
1 717587 rs144155419 G A 0.0021209 0.0033554 0.5273185 0.5273170 0.0157583 0.0045926 117763
1 730087 rs148120343 T C -0.0005086 0.0017367 0.7696300 0.7696287 0.0568966 0.0127796 117763
1 731718 rs142557973 T C 0.0001614 0.0011840 0.8915410 0.8915405 0.1226470 0.1543530 117763
1 732032 rs61770163 A C 0.0005061 0.0012620 0.6884303 0.6884301 0.1222350 0.1555510 117763
1 734349 rs141242758 T C 0.0002020 0.0011847 0.8646340 0.8646337 0.1219010 0.1525560 117763
1 740284 rs61770167 C T 0.0057384 0.0054066 0.2885227 0.2885210 0.0058608 0.0023962 117763
1 749963 rs529266287 T TAA 0.0000435 0.0011672 0.9702740 0.9702737 0.8690130 0.7641770 117763
CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
23 154923311 rs141127553 C T -0.0013265 0.0013922 0.3406928 0.3406911 0.0554823 0.0309934 117763
23 154923374 rs111332691 T A -0.0019069 0.0015180 0.2090528 0.2090511 0.0447339 0.0116556 117763
23 154925045 rs509981 C T -0.0006301 0.0007307 0.3885214 0.3885195 0.2447530 0.3634440 117763
23 154925895 rs538470 C T -0.0007566 0.0007472 0.3112247 0.3112234 0.2411730 0.3634440 117763
23 154927581 rs644138 G A -0.0008832 0.0006875 0.1989198 0.1989178 0.3005980 0.4635760 117763
23 154929412 rs557132 C T -0.0006154 0.0007309 0.3997551 0.3997538 0.2446280 0.3568210 117763
23 154929637 rs35185538 CT C -0.0006931 0.0007635 0.3639712 0.3639687 0.2288620 0.3011920 117763
23 154929952 rs4012982 CAA C -0.0007973 0.0007692 0.2999722 0.2999702 0.2387120 0.3165560 117763
23 154930230 rs781880 A G -0.0006863 0.0007307 0.3475874 0.3475853 0.2450460 0.3618540 117763
23 154930487 rs781879 T A -0.0009796 0.0024838 0.6932789 0.6932788 0.0196777 0.1263580 117763

bcf preview

1   692794  rs530212009 CA  C   .   PASS    AF=0.111695 ES:SE:LP:AF:SS:ID   -0.000204039:0.0013178:0.0570232:0.111695:117763:1_692794_CA_C
1   693731  rs12238997  A   G   .   PASS    AF=0.116715 ES:SE:LP:AF:SS:ID   8.99184e-05:0.00124795:0.025691:0.116715:117763:rs12238997
1   707522  rs371890604 G   C   .   PASS    AF=0.0983485    ES:SE:LP:AF:SS:ID   0.000719674:0.00140018:0.216624:0.0983485:117763:rs371890604
1   717587  rs144155419 G   A   .   PASS    AF=0.0157583    ES:SE:LP:AF:SS:ID   0.00212094:0.00335535:0.277927:0.0157583:117763:rs144155419
1   730087  rs148120343 T   C   .   PASS    AF=0.0568966    ES:SE:LP:AF:SS:ID   -0.000508608:0.00173669:0.113718:0.0568966:117763:rs148120343
1   731718  rs58276399  T   C   .   PASS    AF=0.122647 ES:SE:LP:AF:SS:ID   0.00016145:0.00118404:0.0498587:0.122647:117763:rs58276399
1   732032  rs61770163  A   C   .   PASS    AF=0.122235 ES:SE:LP:AF:SS:ID   0.000506053:0.00126202:0.16214:0.122235:117763:rs61770163
1   734349  rs141242758 T   C   .   PASS    AF=0.121901 ES:SE:LP:AF:SS:ID   0.000201961:0.00118467:0.0631677:0.121901:117763:rs141242758
1   740284  rs61770167  C   T   .   PASS    AF=0.00586084   ES:SE:LP:AF:SS:ID   0.00573838:0.00540657:0.53982:0.00586084:117763:rs61770167
1   749963  rs529266287 T   TAA .   PASS    AF=0.869013 ES:SE:LP:AF:SS:ID   4.34968e-05:0.00116723:0.0131056:0.869013:117763:rs529266287
1   751343  rs28544273  T   A   .   PASS    AF=0.123679 ES:SE:LP:AF:SS:ID   -0.000184853:0.00115657:0.0589778:0.123679:117763:rs28544273
1   751488  rs200141114 G   GA  .   PASS    AF=0.143308 ES:SE:LP:AF:SS:ID   3.94039e-05:0.00114388:0.0121015:0.143308:117763:rs200141114
1   751756  rs28527770  T   C   .   PASS    AF=0.123801 ES:SE:LP:AF:SS:ID   -0.000214062:0.00115497:0.0690698:0.123801:117763:rs28527770
1   753405  rs3115860   C   A   .   PASS    AF=0.869786 ES:SE:LP:AF:SS:ID   7.62248e-05:0.00112474:0.0241236:0.869786:117763:rs3115860
1   753425  rs3131970   T   C   .   PASS    AF=0.874576 ES:SE:LP:AF:SS:ID   4.73894e-05:0.00114369:0.0145964:0.874576:117763:rs3131970
1   753541  rs2073813   G   A   .   PASS    AF=0.129674 ES:SE:LP:AF:SS:ID   -0.000116404:0.00112789:0.0372515:0.129674:117763:rs2073813
1   754105  rs12184325  C   T   .   PASS    AF=0.0365183    ES:SE:LP:AF:SS:ID   0.00389998:0.00204834:1.24476:0.0365183:117763:rs12184325
1   754182  rs3131969   A   G   .   PASS    AF=0.869381 ES:SE:LP:AF:SS:ID   8.15277e-05:0.00112368:0.0258749:0.869381:117763:rs3131969
1   754192  rs3131968   A   G   .   PASS    AF=0.869453 ES:SE:LP:AF:SS:ID   9.90116e-05:0.0011241:0.0316049:0.869453:117763:rs3131968
1   754334  rs3131967   T   C   .   PASS    AF=0.869381 ES:SE:LP:AF:SS:ID   8.34795e-05:0.00112365:0.0265133:0.869381:117763:rs3131967
1   754433  rs150578204 G   A   .   PASS    AF=0.00512144   ES:SE:LP:AF:SS:ID   -0.00567503:0.00574538:0.490428:0.00512144:117763:rs150578204
1   754458  rs142682604 G   T   .   PASS    AF=0.00509053   ES:SE:LP:AF:SS:ID   -0.00611467:0.005758:0.540211:0.00509053:117763:rs142682604
1   755435  rs184270342 T   G   .   PASS    AF=0.00568601   ES:SE:LP:AF:SS:ID   -0.00326834:0.00553836:0.255624:0.00568601:117763:rs184270342
1   755890  rs3115858   A   T   .   PASS    AF=0.869452 ES:SE:LP:AF:SS:ID   6.7091e-06:0.00112157:0.00207785:0.869452:117763:rs3115858
1   756434  rs61768170  G   C   .   PASS    AF=0.126951 ES:SE:LP:AF:SS:ID   -0.000139799:0.00114491:0.0444008:0.126951:117763:rs61768170
1   756604  rs3131962   A   G   .   PASS    AF=0.86897  ES:SE:LP:AF:SS:ID   4.21945e-05:0.00111862:0.0132681:0.86897:117763:rs3131962
1   757640  rs3115853   G   A   .   PASS    AF=0.868378 ES:SE:LP:AF:SS:ID   3.97158e-05:0.00111825:0.0124821:0.868378:117763:rs3115853
1   757734  rs4951929   C   T   .   PASS    AF=0.869162 ES:SE:LP:AF:SS:ID   1.2455e-05:0.00111973:0.00387157:0.869162:117763:rs4951929
1   757936  rs4951862   C   A   .   PASS    AF=0.869169 ES:SE:LP:AF:SS:ID   1.16384e-05:0.00111981:0.00361618:0.869169:117763:rs4951862
1   758144  rs3131956   A   G   .   PASS    AF=0.869171 ES:SE:LP:AF:SS:ID   1.08726e-05:0.00111982:0.00337758:0.869171:117763:rs3131956
1   758626  rs3131954   C   T   .   PASS    AF=0.869607 ES:SE:LP:AF:SS:ID   -8.19647e-06:0.00112269:0.00253716:0.869607:117763:rs3131954
1   759293  rs10157329  T   A   .   PASS    AF=0.0995777    ES:SE:LP:AF:SS:ID   0.000461553:0.00130513:0.140498:0.0995777:117763:rs10157329
1   759600  rs545998451 AGT A   .   PASS    AF=0.00654643   ES:SE:LP:AF:SS:ID   -0.000744428:0.00502743:0.0543911:0.00654643:117763:1_759600_AGT_A
1   759837  rs3115851   T   A   .   PASS    AF=0.873674 ES:SE:LP:AF:SS:ID   1.75199e-05:0.00113995:0.00535824:0.873674:117763:rs3115851
1   761732  rs2286139   C   T   .   PASS    AF=0.862966 ES:SE:LP:AF:SS:ID   -0.000231242:0.00111794:0.0777257:0.862966:117763:rs2286139
1   761752  rs1057213   C   T   .   PASS    AF=0.868361 ES:SE:LP:AF:SS:ID   0.000227079:0.00112869:0.0754354:0.868361:117763:rs1057213
1   762273  rs3115849   G   A   .   PASS    AF=0.865361 ES:SE:LP:AF:SS:ID   -6.94374e-05:0.00112884:0.0218419:0.865361:117763:rs3115849
1   762485  rs12095200  C   A   .   PASS    AF=0.0997465    ES:SE:LP:AF:SS:ID   4.2209e-06:0.00134897:0.00108579:0.0997465:117763:rs12095200
1   762589  rs3115848   G   C   .   PASS    AF=0.870665 ES:SE:LP:AF:SS:ID   -0.00012008:0.00114222:0.0379751:0.870665:117763:rs3115848
1   762592  rs3131950   C   G   .   PASS    AF=0.870665 ES:SE:LP:AF:SS:ID   -0.000120073:0.00114222:0.0379727:0.870665:117763:rs3131950
1   762601  rs3131949   T   C   .   PASS    AF=0.870663 ES:SE:LP:AF:SS:ID   -0.000121038:0.00114222:0.0382904:0.870663:117763:rs3131949
1   762632  rs3131948   T   A   .   PASS    AF=0.870985 ES:SE:LP:AF:SS:ID   -0.000106474:0.0011427:0.0335002:0.870985:117763:rs3131948
1   764191  rs7515915   T   G   .   PASS    AF=0.126537 ES:SE:LP:AF:SS:ID   -1.47134e-05:0.00114368:0.00448063:0.126537:117763:rs7515915
1   766007  rs61768174  A   C   .   PASS    AF=0.106315 ES:SE:LP:AF:SS:ID   -6.48423e-05:0.00124291:0.0184564:0.106315:117763:rs61768174
1   766105  rs2519015   T   A   .   PASS    AF=0.854401 ES:SE:LP:AF:SS:ID   0.000391108:0.00111767:0.13883:0.854401:117763:rs2519015
1   768116  rs376645387 A   AGTTTT  .   PASS    AF=0.839108 ES:SE:LP:AF:SS:ID   0.000395816:0.00110726:0.142223:0.839108:117763:rs376645387
1   768253  rs2977608   A   C   .   PASS    AF=0.763038 ES:SE:LP:AF:SS:ID   -9.34176e-05:0.000887509:0.0380235:0.763038:117763:rs2977608
1   768448  rs12562034  G   A   .   PASS    AF=0.105258 ES:SE:LP:AF:SS:ID   -1.46022e-05:0.00122782:0.0041407:0.105258:117763:rs12562034
1   768819  rs12562811  C   T   .   PASS    AF=0.00773328   ES:SE:LP:AF:SS:ID   -0.00337502:0.00453455:0.340367:0.00773328:117763:rs12562811
1   769138  rs59306077  CAT C   .   PASS    AF=0.129951 ES:SE:LP:AF:SS:ID   2.42859e-05:0.00112732:0.00752911:0.129951:117763:rs762168062