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-5959/ukb-d-5959.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-5959/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 17:19:26 2019
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ukb-d-import/processed/ukb-d-5959/ukb-d-5959.vcf.gz ...
Read summary statistics for 9787768 SNPs.
Dropped 7429 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, 1275880 SNPs remain.
After merging with regression SNP LD, 1275880 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: -0.123 (0.1853)
Lambda GC: 0.9997
Mean Chi^2: 1.0006
Intercept: 1.0055 (0.0053)
Ratio: 8.8869 (8.6153)
Analysis finished at Mon Nov 25 17:21:25 2019
Total time elapsed: 1.0m:58.36s

QC metrics

Metrics

Metrics

{
    "af_correlation": 0.9403,
    "inflation_factor": 0.9988,
    "mean_EFFECT": -0.0001,
    "n": 2005,
    "n_snps": 9787768,
    "n_clumped_hits": 0,
    "n_p_sig": 0,
    "n_mono": 0,
    "n_ns": 1069367,
    "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": 194545,
    "n_est": 2028.1301,
    "ratio_se_n": 1.0058,
    "mean_diff": -0.0002,
    "ratio_diff": 9.0512,
    "sd_y_est1": 0.4725,
    "sd_y_est2": 0.4753,
    "r2_sum1": 0,
    "r2_sum2": 0,
    "r2_sum3": 0,
    "r2_sum4": 0,
    "ldsc_nsnp_merge_refpanel_ld": 1275880,
    "ldsc_nsnp_merge_regression_ld": 1275880,
    "ldsc_observed_scale_h2_beta": "NA",
    "ldsc_observed_scale_h2_se": "NA",
    "ldsc_intercept_beta": 1.0055,
    "ldsc_intercept_se": 0.0053,
    "ldsc_lambda_gc": 0.9997,
    "ldsc_mean_chisq": 1.0006,
    "ldsc_ratio": 9.1667
}

Flags

name value
af_correlation FALSE
inflation_factor FALSE
n TRUE
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 TRUE
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 9780890 0 NA NA NA NA NA NA NA NA
character REF 0 1.0000000 1 100 0 47414 0 NA NA NA NA NA NA NA NA
character ALT 0 1.0000000 1 342 0 29829 0 NA NA NA NA NA NA NA NA
numeric CHROM 0 1.0000000 NA NA NA NA NA 9.079620e+00 6.176302e+00 1.0000000 4.000000e+00 8.000000e+00 1.300000e+01 2.300000e+01 ▇▅▅▂▂
numeric POS 0 1.0000000 NA NA NA NA NA 7.873515e+07 5.610155e+07 302.0000000 3.244271e+07 6.962536e+07 1.147284e+08 2.492297e+08 ▇▆▅▂▁
numeric EFFECT 0 1.0000000 NA NA NA NA NA -1.325000e-04 3.417560e-02 -0.3870920 -1.615800e-02 -5.290000e-05 1.612150e-02 3.125900e-01 ▁▁▇▁▁
numeric SE 0 1.0000000 NA NA NA NA NA 2.965300e-02 1.730870e-02 0.0105881 1.639480e-02 2.197460e-02 3.807940e-02 1.002580e-01 ▇▂▂▁▁
numeric PVAL 0 1.0000000 NA NA NA NA NA 5.003377e-01 2.885581e-01 0.0000001 2.500852e-01 5.002545e-01 7.505662e-01 1.000000e+00 ▇▇▇▇▇
numeric PVAL_ztest 0 1.0000000 NA NA NA NA NA 5.002572e-01 2.886066e-01 0.0000001 2.499453e-01 5.001769e-01 7.505323e-01 9.999999e-01 ▇▇▇▇▇
numeric AF 0 1.0000000 NA NA NA NA NA 2.595235e-01 2.629238e-01 0.0092944 4.234810e-02 1.566080e-01 4.134660e-01 9.907060e-01 ▇▂▂▁▁
numeric AF_reference 194545 0.9801237 NA NA NA NA NA 2.590008e-01 2.537288e-01 0.0000000 4.772360e-02 1.719250e-01 4.089460e-01 1.000000e+00 ▇▃▂▁▁
numeric N 0 1.0000000 NA NA NA NA NA 2.005000e+03 0.000000e+00 2005.0000000 2.005000e+03 2.005000e+03 2.005000e+03 2.005000e+03 ▁▁▇▁▁

Head and tail

CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
1 692794 rs530212009 CA C 0.0120919 0.0258151 0.6395463 0.6394956 0.1155130 0.1894970 2005
1 693731 rs12238997 A G 0.0070241 0.0246453 0.7756664 0.7756376 0.1149510 0.1417730 2005
1 707522 rs371890604 G C -0.0034666 0.0278165 0.9008330 0.9008205 0.0987922 0.1293930 2005
1 717587 rs144155419 G A 0.0364518 0.0677771 0.5907626 0.5907021 0.0155415 0.0045926 2005
1 730087 rs148120343 T C 0.0122219 0.0342104 0.7209398 0.7208995 0.0574632 0.0127796 2005
1 731718 rs142557973 T C 0.0048479 0.0231646 0.8342500 0.8342282 0.1235510 0.1543530 2005
1 732032 rs61770163 A C 0.0157940 0.0251217 0.5296171 0.5295458 0.1217010 0.1555510 2005
1 734349 rs141242758 T C 0.0056883 0.0231823 0.8061941 0.8061683 0.1225460 0.1525560 2005
1 749963 rs529266287 T TAA -0.0209466 0.0231186 0.3650211 0.3649096 0.8682720 0.7641770 2005
1 751343 rs28544273 T A 0.0206934 0.0226044 0.3600626 0.3599507 0.1255470 0.2426120 2005
CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
23 154923311 rs141127553 C T 0.0403219 0.0246572 0.1021459 0.1019863 0.0506313 0.0309934 2005
23 154923374 rs111332691 T A -0.0328383 0.0260669 0.2078998 0.2077523 0.0433915 0.0116556 2005
23 154925045 rs509981 C T 0.0189230 0.0124005 0.1271730 0.1270131 0.2421640 0.3634440 2005
23 154925895 rs538470 C T 0.0262861 0.0126906 0.0384592 0.0383303 0.2378550 0.3634440 2005
23 154927581 rs644138 G A 0.0253784 0.0116947 0.0301203 0.0300010 0.2934940 0.4635760 2005
23 154929412 rs557132 C T 0.0189325 0.0124010 0.1269980 0.1268378 0.2421540 0.3568210 2005
23 154929637 rs35185538 CT C 0.0191092 0.0129469 0.1401109 0.1399527 0.2273100 0.3011920 2005
23 154929952 rs4012982 CAA C 0.0185609 0.0130714 0.1557780 0.1556186 0.2337130 0.3165560 2005
23 154930230 rs781880 A G 0.0190018 0.0124025 0.1256591 0.1254992 0.2422410 0.3618540 2005
23 154930487 rs781879 T A 0.0105854 0.0409072 0.7958421 0.7958157 0.0210748 0.1263580 2005

bcf preview

1   692794  rs530212009 CA  C   .   PASS    AF=0.115513 ES:SE:LP:AF:SS:ID   0.0120919:0.0258151:0.194128:0.115513:2005:1_692794_CA_C
1   693731  rs12238997  A   G   .   PASS    AF=0.114951 ES:SE:LP:AF:SS:ID   0.00702412:0.0246453:0.110325:0.114951:2005:rs12238997
1   707522  rs371890604 G   C   .   PASS    AF=0.0987922    ES:SE:LP:AF:SS:ID   -0.00346663:0.0278165:0.0453557:0.0987922:2005:rs371890604
1   717587  rs144155419 G   A   .   PASS    AF=0.0155415    ES:SE:LP:AF:SS:ID   0.0364518:0.0677771:0.228587:0.0155415:2005:rs144155419
1   730087  rs148120343 T   C   .   PASS    AF=0.0574632    ES:SE:LP:AF:SS:ID   0.0122219:0.0342104:0.142101:0.0574632:2005:rs148120343
1   731718  rs58276399  T   C   .   PASS    AF=0.123551 ES:SE:LP:AF:SS:ID   0.00484793:0.0231646:0.0787038:0.123551:2005:rs58276399
1   732032  rs61770163  A   C   .   PASS    AF=0.121701 ES:SE:LP:AF:SS:ID   0.015794:0.0251217:0.276038:0.121701:2005:rs61770163
1   734349  rs141242758 T   C   .   PASS    AF=0.122546 ES:SE:LP:AF:SS:ID   0.00568829:0.0231823:0.0935604:0.122546:2005:rs141242758
1   749963  rs529266287 T   TAA .   PASS    AF=0.868272 ES:SE:LP:AF:SS:ID   -0.0209466:0.0231186:0.437682:0.868272:2005:rs529266287
1   751343  rs28544273  T   A   .   PASS    AF=0.125547 ES:SE:LP:AF:SS:ID   0.0206934:0.0226044:0.443622:0.125547:2005:rs28544273
1   751488  rs200141114 G   GA  .   PASS    AF=0.146141 ES:SE:LP:AF:SS:ID   0.00637925:0.0222499:0.111054:0.146141:2005:rs200141114
1   751756  rs28527770  T   C   .   PASS    AF=0.125696 ES:SE:LP:AF:SS:ID   0.0204003:0.0225445:0.436953:0.125696:2005:rs28527770
1   753405  rs3115860   C   A   .   PASS    AF=0.866026 ES:SE:LP:AF:SS:ID   -0.0112853:0.0218409:0.217944:0.866026:2005:rs3115860
1   753425  rs3131970   T   C   .   PASS    AF=0.873295 ES:SE:LP:AF:SS:ID   -0.0176737:0.0222875:0.368677:0.873295:2005:rs3131970
1   753541  rs2073813   G   A   .   PASS    AF=0.133433 ES:SE:LP:AF:SS:ID   0.0137674:0.021903:0.275963:0.133433:2005:rs2073813
1   754105  rs12184325  C   T   .   PASS    AF=0.0411471    ES:SE:LP:AF:SS:ID   -0.0424132:0.0383385:0.570668:0.0411471:2005:rs12184325
1   754182  rs3131969   A   G   .   PASS    AF=0.865542 ES:SE:LP:AF:SS:ID   -0.0118175:0.0218241:0.230452:0.865542:2005:rs3131969
1   754192  rs3131968   A   G   .   PASS    AF=0.866049 ES:SE:LP:AF:SS:ID   -0.0126348:0.0218467:0.249413:0.866049:2005:rs3131968
1   754334  rs3131967   T   C   .   PASS    AF=0.865546 ES:SE:LP:AF:SS:ID   -0.0118833:0.0218233:0.231998:0.865546:2005:rs3131967
1   755890  rs3115858   A   T   .   PASS    AF=0.865556 ES:SE:LP:AF:SS:ID   -0.0111189:0.021801:0.214601:0.865556:2005:rs3115858
1   756434  rs61768170  G   C   .   PASS    AF=0.130214 ES:SE:LP:AF:SS:ID   0.0160521:0.0223486:0.32543:0.130214:2005:rs61768170
1   756604  rs3131962   A   G   .   PASS    AF=0.865087 ES:SE:LP:AF:SS:ID   -0.0115349:0.0217523:0.224772:0.865087:2005:rs3131962
1   757640  rs3115853   G   A   .   PASS    AF=0.864422 ES:SE:LP:AF:SS:ID   -0.0123049:0.02175:0.242883:0.864422:2005:rs3115853
1   757734  rs4951929   C   T   .   PASS    AF=0.865075 ES:SE:LP:AF:SS:ID   -0.0115908:0.0217522:0.226073:0.865075:2005:rs4951929
1   757936  rs4951862   C   A   .   PASS    AF=0.865084 ES:SE:LP:AF:SS:ID   -0.0115812:0.0217544:0.225823:0.865084:2005:rs4951862
1   758144  rs3131956   A   G   .   PASS    AF=0.865088 ES:SE:LP:AF:SS:ID   -0.011555:0.0217532:0.225228:0.865088:2005:rs3131956
1   758626  rs3131954   C   T   .   PASS    AF=0.865789 ES:SE:LP:AF:SS:ID   -0.0113397:0.0218305:0.219316:0.865789:2005:rs3131954
1   759293  rs10157329  T   A   .   PASS    AF=0.100276 ES:SE:LP:AF:SS:ID   0.00659565:0.0258333:0.0977218:0.100276:2005:rs10157329
1   759837  rs3115851   T   A   .   PASS    AF=0.87189  ES:SE:LP:AF:SS:ID   -0.020814:0.0222582:0.456124:0.87189:2005:rs3115851
1   761732  rs2286139   C   T   .   PASS    AF=0.858312 ES:SE:LP:AF:SS:ID   -0.0151131:0.0217862:0.311622:0.858312:2005:rs2286139
1   761752  rs1057213   C   T   .   PASS    AF=0.864432 ES:SE:LP:AF:SS:ID   -0.0138067:0.0219832:0.275692:0.864432:2005:rs1057213
1   762273  rs3115849   G   A   .   PASS    AF=0.8613   ES:SE:LP:AF:SS:ID   -0.0155495:0.0218549:0.321605:0.8613:2005:rs3115849
1   762485  rs12095200  C   A   .   PASS    AF=0.100094 ES:SE:LP:AF:SS:ID   0.0314549:0.0263896:0.631851:0.100094:2005:rs12095200
1   762589  rs3115848   G   C   .   PASS    AF=0.868851 ES:SE:LP:AF:SS:ID   -0.0194249:0.0221606:0.419263:0.868851:2005:rs3115848
1   762592  rs3131950   C   G   .   PASS    AF=0.868851 ES:SE:LP:AF:SS:ID   -0.0194249:0.0221606:0.419263:0.868851:2005:rs3131950
1   762601  rs3131949   T   C   .   PASS    AF=0.868847 ES:SE:LP:AF:SS:ID   -0.0194273:0.0221608:0.419324:0.868847:2005:rs3131949
1   762632  rs3131948   T   A   .   PASS    AF=0.869433 ES:SE:LP:AF:SS:ID   -0.018191:0.0222393:0.383549:0.869433:2005:rs3131948
1   764191  rs7515915   T   G   .   PASS    AF=0.129482 ES:SE:LP:AF:SS:ID   0.0191659:0.0222943:0.408854:0.129482:2005:rs7515915
1   766007  rs61768174  A   C   .   PASS    AF=0.108307 ES:SE:LP:AF:SS:ID   0.0115455:0.0244215:0.196246:0.108307:2005:rs61768174
1   766105  rs2519015   T   A   .   PASS    AF=0.849902 ES:SE:LP:AF:SS:ID   -0.00905953:0.0217765:0.16913:0.849902:2005:rs2519015
1   768116  rs376645387 A   AGTTTT  .   PASS    AF=0.825697 ES:SE:LP:AF:SS:ID   -0.00787242:0.0211136:0.149175:0.825697:2005:rs376645387
1   768253  rs2977608   A   C   .   PASS    AF=0.748001 ES:SE:LP:AF:SS:ID   0.00103184:0.0170965:0.0214178:0.748001:2005:rs2977608
1   768448  rs12562034  G   A   .   PASS    AF=0.11596  ES:SE:LP:AF:SS:ID   -0.0183534:0.0235481:0.360674:0.11596:2005:rs12562034
1   768819  rs12562811  C   T   .   PASS    AF=0.00997995   ES:SE:LP:AF:SS:ID   -0.0524363:0.0803017:0.289174:0.00997995:2005:rs12562811
1   769138  rs59306077  CAT C   .   PASS    AF=0.134151 ES:SE:LP:AF:SS:ID   0.0162949:0.0218892:0.340362:0.134151:2005:rs762168062
1   769223  rs60320384  C   G   .   PASS    AF=0.133746 ES:SE:LP:AF:SS:ID   0.0139472:0.0218864:0.280642:0.133746:2005:rs60320384
1   769963  rs7518545   G   A   .   PASS    AF=0.115258 ES:SE:LP:AF:SS:ID   -0.019404:0.0237195:0.383607:0.115258:2005:rs7518545
1   770377  rs112563271 A   T   .   PASS    AF=0.00972666   ES:SE:LP:AF:SS:ID   -0.0342168:0.0816648:0.170524:0.00972666:2005:rs112563271
1   770886  rs371458725 G   A   .   PASS    AF=0.114036 ES:SE:LP:AF:SS:ID   -0.0199525:0.023946:0.392742:0.114036:2005:rs371458725
1   771410  rs2519006   C   T   .   PASS    AF=0.82369  ES:SE:LP:AF:SS:ID   -0.012403:0.0212355:0.252403:0.82369:2005:rs2519006