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-5610_1/ukb-d-5610_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-5610_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 16:56:57 2019
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ukb-d-import/processed/ukb-d-5610_1/ukb-d-5610_1.vcf.gz ...
Read summary statistics for 10212514 SNPs.
Dropped 7994 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, 1279468 SNPs remain.
After merging with regression SNP LD, 1279468 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.0129 (0.0134)
Lambda GC: 1.0197
Mean Chi^2: 1.0133
Intercept: 1.0052 (0.0058)
Ratio: 0.39 (0.4357)
Analysis finished at Mon Nov 25 16:58:18 2019
Total time elapsed: 1.0m:20.21s

QC metrics

Metrics

Metrics

{
    "af_correlation": 0.9427,
    "inflation_factor": 1.0143,
    "mean_EFFECT": -4.4352e-06,
    "n": 31494,
    "n_snps": 10212514,
    "n_clumped_hits": 0,
    "n_p_sig": 0,
    "n_mono": 0,
    "n_ns": 1095698,
    "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": 201191,
    "n_est": 31545.6766,
    "ratio_se_n": 1.0008,
    "mean_diff": -0,
    "ratio_diff": 28.3722,
    "sd_y_est1": 0.2287,
    "sd_y_est2": 0.2289,
    "r2_sum1": 0,
    "r2_sum2": 0,
    "r2_sum3": 0,
    "r2_sum4": 0,
    "ldsc_nsnp_merge_refpanel_ld": 1279468,
    "ldsc_nsnp_merge_regression_ld": 1279468,
    "ldsc_observed_scale_h2_beta": 0.0129,
    "ldsc_observed_scale_h2_se": 0.0134,
    "ldsc_intercept_beta": 1.0052,
    "ldsc_intercept_se": 0.0058,
    "ldsc_lambda_gc": 1.0197,
    "ldsc_mean_chisq": 1.0133,
    "ldsc_ratio": 0.391
}

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 10205080 0 NA NA NA NA NA NA NA NA
character REF 0 1.0000000 1 100 0 48885 0 NA NA NA NA NA NA NA NA
character ALT 0 1.0000000 1 342 0 30408 0 NA NA NA NA NA NA NA NA
numeric CHROM 0 1.0000000 NA NA NA NA NA 9.078777e+00 6.178319e+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 7.877139e+07 5.606214e+07 3.02000e+02 3.252678e+07 6.968552e+07 1.147212e+08 2.492297e+08 ▇▆▅▂▁
numeric EFFECT 0 1.0000000 NA NA NA NA NA -4.400000e-06 4.635100e-03 -4.28417e-02 -2.099700e-03 -2.740000e-05 2.036400e-03 5.251380e-02 ▁▁▇▁▁
numeric SE 0 1.0000000 NA NA NA NA NA 3.905300e-03 2.470900e-03 1.50040e-03 2.016200e-03 2.783000e-03 5.086100e-03 1.402170e-02 ▇▂▁▁▁
numeric PVAL 0 1.0000000 NA NA NA NA NA 4.982348e-01 2.892920e-01 6.00000e-07 2.468607e-01 4.969469e-01 7.492418e-01 1.000000e+00 ▇▇▇▇▇
numeric PVAL_ztest 0 1.0000000 NA NA NA NA NA 4.982297e-01 2.892951e-01 6.00000e-07 2.468520e-01 4.969419e-01 7.492402e-01 9.999999e-01 ▇▇▇▇▇
numeric AF 0 1.0000000 NA NA NA NA NA 2.497534e-01 2.628796e-01 7.20470e-03 3.500330e-02 1.423140e-01 3.990880e-01 9.927950e-01 ▇▂▂▁▁
numeric AF_reference 201191 0.9802996 NA NA NA NA NA 2.494949e-01 2.537528e-01 0.00000e+00 3.813900e-02 1.587460e-01 3.955670e-01 1.000000e+00 ▇▃▂▁▁
numeric N 0 1.0000000 NA NA NA NA NA 3.149400e+04 0.000000e+00 3.14940e+04 3.149400e+04 3.149400e+04 3.149400e+04 3.149400e+04 ▁▁▇▁▁

Head and tail

CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
1 692794 rs530212009 CA C -0.0028039 0.0031900 0.3794268 0.3794208 0.1116860 0.1894970 31494
1 693731 rs12238997 A G -0.0014288 0.0030157 0.6356470 0.6356421 0.1175430 0.1417730 31494
1 707522 rs371890604 G C -0.0026597 0.0033928 0.4330938 0.4330883 0.0978470 0.1293930 31494
1 717587 rs144155419 G A 0.0028711 0.0080926 0.7227548 0.7227512 0.0158964 0.0045926 31494
1 730087 rs148120343 T C -0.0035765 0.0041848 0.3927580 0.3927520 0.0574672 0.0127796 31494
1 731718 rs142557973 T C -0.0020989 0.0028570 0.4625631 0.4625579 0.1232790 0.1543530 31494
1 732032 rs61770163 A C -0.0012964 0.0030422 0.6700111 0.6700083 0.1228850 0.1555510 31494
1 734349 rs141242758 T C -0.0021722 0.0028598 0.4475237 0.4475180 0.1224210 0.1525560 31494
1 749963 rs529266287 T TAA 0.0015219 0.0028209 0.5895369 0.5895335 0.8686160 0.7641770 31494
1 751343 rs28544273 T A -0.0014860 0.0027966 0.5951754 0.5951705 0.1237510 0.2426120 31494
CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
23 154923311 rs141127553 C T 0.0048370 0.0033148 0.1445120 0.1445019 0.0562109 0.0309934 31494
23 154923374 rs111332691 T A -0.0028375 0.0036485 0.4367360 0.4367307 0.0442783 0.0116556 31494
23 154925045 rs509981 C T 0.0004845 0.0017593 0.7830112 0.7830095 0.2440420 0.3634440 31494
23 154925895 rs538470 C T 0.0004926 0.0017991 0.7842454 0.7842450 0.2407340 0.3634440 31494
23 154927581 rs644138 G A 0.0016042 0.0016499 0.3309131 0.3309066 0.3007300 0.4635760 31494
23 154929412 rs557132 C T 0.0004447 0.0017600 0.8005390 0.8005373 0.2439040 0.3568210 31494
23 154929637 rs35185538 CT C -0.0002025 0.0018338 0.9120589 0.9120587 0.2286140 0.3011920 31494
23 154929952 rs4012982 CAA C -0.0007053 0.0018514 0.7032375 0.7032348 0.2378770 0.3165560 31494
23 154930230 rs781880 A G 0.0003388 0.0017596 0.8473140 0.8473127 0.2443960 0.3618540 31494
23 154930487 rs781879 T A 0.0013602 0.0062474 0.8276429 0.8276417 0.0182666 0.1263580 31494

bcf preview

1   692794  rs530212009 CA  C   .   PASS    AF=0.111686 ES:SE:LP:AF:SS:ID   -0.00280393:0.00319004:0.420872:0.111686:31494:1_692794_CA_C
1   693731  rs12238997  A   G   .   PASS    AF=0.117543 ES:SE:LP:AF:SS:ID   -0.00142885:0.00301572:0.196784:0.117543:31494:rs12238997
1   707522  rs371890604 G   C   .   PASS    AF=0.097847 ES:SE:LP:AF:SS:ID   -0.0026597:0.00339283:0.363418:0.097847:31494:rs371890604
1   717587  rs144155419 G   A   .   PASS    AF=0.0158964    ES:SE:LP:AF:SS:ID   0.00287111:0.00809255:0.141009:0.0158964:31494:rs144155419
1   730087  rs148120343 T   C   .   PASS    AF=0.0574672    ES:SE:LP:AF:SS:ID   -0.00357646:0.00418477:0.405875:0.0574672:31494:rs148120343
1   731718  rs58276399  T   C   .   PASS    AF=0.123279 ES:SE:LP:AF:SS:ID   -0.0020989:0.00285704:0.334829:0.123279:31494:rs58276399
1   732032  rs61770163  A   C   .   PASS    AF=0.122885 ES:SE:LP:AF:SS:ID   -0.00129638:0.00304217:0.173918:0.122885:31494:rs61770163
1   734349  rs141242758 T   C   .   PASS    AF=0.122421 ES:SE:LP:AF:SS:ID   -0.00217215:0.00285975:0.349184:0.122421:31494:rs141242758
1   749963  rs529266287 T   TAA .   PASS    AF=0.868616 ES:SE:LP:AF:SS:ID   0.00152191:0.0028209:0.229489:0.868616:31494:rs529266287
1   751343  rs28544273  T   A   .   PASS    AF=0.123751 ES:SE:LP:AF:SS:ID   -0.00148597:0.00279655:0.225355:0.123751:31494:rs28544273
1   751488  rs200141114 G   GA  .   PASS    AF=0.142984 ES:SE:LP:AF:SS:ID   -0.00103908:0.00277636:0.149835:0.142984:31494:rs200141114
1   751756  rs28527770  T   C   .   PASS    AF=0.12384  ES:SE:LP:AF:SS:ID   -0.00141641:0.00279246:0.213249:0.12384:31494:rs28527770
1   753405  rs3115860   C   A   .   PASS    AF=0.869898 ES:SE:LP:AF:SS:ID   0.00138981:0.00271973:0.215135:0.869898:31494:rs3115860
1   753425  rs3131970   T   C   .   PASS    AF=0.874802 ES:SE:LP:AF:SS:ID   0.00154751:0.00276652:0.239642:0.874802:31494:rs3131970
1   753541  rs2073813   G   A   .   PASS    AF=0.129805 ES:SE:LP:AF:SS:ID   -0.00185346:0.00272533:0.30412:0.129805:31494:rs2073813
1   754105  rs12184325  C   T   .   PASS    AF=0.0363244    ES:SE:LP:AF:SS:ID   0.00215692:0.0049504:0.178451:0.0363244:31494:rs12184325
1   754182  rs3131969   A   G   .   PASS    AF=0.869435 ES:SE:LP:AF:SS:ID   0.00154242:0.0027167:0.243969:0.869435:31494:rs3131969
1   754192  rs3131968   A   G   .   PASS    AF=0.869579 ES:SE:LP:AF:SS:ID   0.00147523:0.00271924:0.231017:0.869579:31494:rs3131968
1   754334  rs3131967   T   C   .   PASS    AF=0.869431 ES:SE:LP:AF:SS:ID   0.00154648:0.00271661:0.244753:0.869431:31494:rs3131967
1   755890  rs3115858   A   T   .   PASS    AF=0.869571 ES:SE:LP:AF:SS:ID   0.00128892:0.00271147:0.197544:0.869571:31494:rs3115858
1   756434  rs61768170  G   C   .   PASS    AF=0.126925 ES:SE:LP:AF:SS:ID   -0.00152327:0.00276895:0.2349:0.126925:31494:rs61768170
1   756604  rs3131962   A   G   .   PASS    AF=0.869197 ES:SE:LP:AF:SS:ID   0.00137499:0.0027057:0.213724:0.869197:31494:rs3131962
1   757640  rs3115853   G   A   .   PASS    AF=0.868317 ES:SE:LP:AF:SS:ID   0.0010713:0.00270187:0.160059:0.868317:31494:rs3115853
1   757734  rs4951929   C   T   .   PASS    AF=0.869302 ES:SE:LP:AF:SS:ID   0.00133335:0.00270719:0.205963:0.869302:31494:rs4951929
1   757936  rs4951862   C   A   .   PASS    AF=0.869309 ES:SE:LP:AF:SS:ID   0.00133068:0.00270738:0.20546:0.869309:31494:rs4951862
1   758144  rs3131956   A   G   .   PASS    AF=0.869319 ES:SE:LP:AF:SS:ID   0.00132861:0.00270748:0.205073:0.869319:31494:rs3131956
1   758626  rs3131954   C   T   .   PASS    AF=0.869749 ES:SE:LP:AF:SS:ID   0.00126332:0.00271492:0.192666:0.869749:31494:rs3131954
1   759293  rs10157329  T   A   .   PASS    AF=0.0993643    ES:SE:LP:AF:SS:ID   -0.00243261:0.00316014:0.355131:0.0993643:31494:rs10157329
1   759837  rs3115851   T   A   .   PASS    AF=0.873989 ES:SE:LP:AF:SS:ID   0.00133394:0.00275826:0.201583:0.873989:31494:rs3115851
1   761732  rs2286139   C   T   .   PASS    AF=0.862883 ES:SE:LP:AF:SS:ID   0.00101957:0.00270056:0.151334:0.862883:31494:rs2286139
1   761752  rs1057213   C   T   .   PASS    AF=0.868517 ES:SE:LP:AF:SS:ID   0.00152293:0.00272893:0.238975:0.868517:31494:rs1057213
1   762273  rs3115849   G   A   .   PASS    AF=0.86524  ES:SE:LP:AF:SS:ID   0.00119587:0.00272798:0.17972:0.86524:31494:rs3115849
1   762485  rs12095200  C   A   .   PASS    AF=0.0996428    ES:SE:LP:AF:SS:ID   -0.000579554:0.00327536:0.0657268:0.0996428:31494:rs12095200
1   762589  rs3115848   G   C   .   PASS    AF=0.870703 ES:SE:LP:AF:SS:ID   0.00134369:0.00276179:0.203012:0.870703:31494:rs3115848
1   762592  rs3131950   C   G   .   PASS    AF=0.870703 ES:SE:LP:AF:SS:ID   0.00134366:0.00276179:0.203007:0.870703:31494:rs3131950
1   762601  rs3131949   T   C   .   PASS    AF=0.870699 ES:SE:LP:AF:SS:ID   0.00134429:0.0027618:0.203118:0.870699:31494:rs3131949
1   762632  rs3131948   T   A   .   PASS    AF=0.871086 ES:SE:LP:AF:SS:ID   0.00155748:0.00276304:0.241865:0.871086:31494:rs3131948
1   764191  rs7515915   T   G   .   PASS    AF=0.126451 ES:SE:LP:AF:SS:ID   -0.00142671:0.00276513:0.217611:0.126451:31494:rs7515915
1   766007  rs61768174  A   C   .   PASS    AF=0.106419 ES:SE:LP:AF:SS:ID   -0.00281101:0.00300593:0.456283:0.106419:31494:rs61768174
1   766105  rs2519015   T   A   .   PASS    AF=0.854426 ES:SE:LP:AF:SS:ID   0.00104971:0.0027028:0.156308:0.854426:31494:rs2519015
1   768116  rs376645387 A   AGTTTT  .   PASS    AF=0.838692 ES:SE:LP:AF:SS:ID   -0.00122148:0.00266724:0.189105:0.838692:31494:rs376645387
1   768253  rs2977608   A   C   .   PASS    AF=0.763349 ES:SE:LP:AF:SS:ID   0.00123888:0.00214642:0.24886:0.763349:31494:rs2977608
1   768448  rs12562034  G   A   .   PASS    AF=0.104925 ES:SE:LP:AF:SS:ID   -0.00129382:0.0029565:0.179361:0.104925:31494:rs12562034
1   768819  rs12562811  C   T   .   PASS    AF=0.00731736   ES:SE:LP:AF:SS:ID   -0.0132551:0.0112874:0.619295:0.00731736:31494:rs12562811
1   769138  rs59306077  CAT C   .   PASS    AF=0.12989  ES:SE:LP:AF:SS:ID   -0.00162269:0.00272388:0.258564:0.12989:31494:rs762168062
1   769223  rs60320384  C   G   .   PASS    AF=0.12956  ES:SE:LP:AF:SS:ID   -0.0017875:0.00272315:0.291099:0.12956:31494:rs60320384
1   769963  rs7518545   G   A   .   PASS    AF=0.104208 ES:SE:LP:AF:SS:ID   -0.00163828:0.00297984:0.234728:0.104208:31494:rs7518545
1   770181  rs146076599 A   G   .   PASS    AF=0.00978338   ES:SE:LP:AF:SS:ID   0.0086939:0.0100954:0.409884:0.00978338:31494:rs146076599
1   770377  rs112563271 A   T   .   PASS    AF=0.00731593   ES:SE:LP:AF:SS:ID   -0.0129729:0.0113487:0.596883:0.00731593:31494:rs112563271
1   770886  rs371458725 G   A   .   PASS    AF=0.103241 ES:SE:LP:AF:SS:ID   -0.00173441:0.00300427:0.248929:0.103241:31494:rs371458725