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-20079_1/ukb-d-20079_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-20079_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 16:43:01 2019
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ukb-d-import/processed/ukb-d-20079_1/ukb-d-20079_1.vcf.gz ...
Read summary statistics for 12887939 SNPs.
Dropped 11696 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, 1283357 SNPs remain.
After merging with regression SNP LD, 1283357 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.0035 (0.0078)
Lambda GC: 1.0045
Mean Chi^2: 0.9993
Intercept: 0.9957 (0.0056)
Ratio: NA (mean chi^2 < 1)
Analysis finished at Mon Nov 25 16:45:08 2019
Total time elapsed: 2.0m:7.08s

QC metrics

Metrics

Metrics

{
    "af_correlation": 0.951,
    "inflation_factor": 1.0041,
    "mean_EFFECT": -1.9608e-06,
    "n": 51427,
    "n_snps": 12887939,
    "n_clumped_hits": 0,
    "n_p_sig": 0,
    "n_mono": 0,
    "n_ns": 1224247,
    "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": 408241,
    "n_est": 51641.0562,
    "ratio_se_n": 1.0021,
    "mean_diff": -1.2682e-06,
    "ratio_diff": 0.5928,
    "sd_y_est1": 0.3645,
    "sd_y_est2": 0.3653,
    "r2_sum1": 0,
    "r2_sum2": 0,
    "r2_sum3": 0,
    "r2_sum4": 0,
    "ldsc_nsnp_merge_refpanel_ld": 1283357,
    "ldsc_nsnp_merge_regression_ld": 1283357,
    "ldsc_observed_scale_h2_beta": 0.0035,
    "ldsc_observed_scale_h2_se": 0.0078,
    "ldsc_intercept_beta": 0.9957,
    "ldsc_intercept_se": 0.0056,
    "ldsc_lambda_gc": 1.0045,
    "ldsc_mean_chisq": 0.9993,
    "ldsc_ratio": 6.1429
}

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 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 12876892 0 NA NA NA NA NA NA NA NA
character REF 0 1.0000000 1 100 0 55570 0 NA NA NA NA NA NA NA NA
character ALT 0 1.0000000 1 342 0 32867 0 NA NA NA NA NA NA NA NA
numeric CHROM 0 1.0000000 NA NA NA NA NA 9.059403e+00 6.185834e+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 7.897314e+07 5.594381e+07 3.02000e+02 3.282590e+07 7.004258e+07 1.148240e+08 2.492309e+08 ▇▆▅▂▁
numeric EFFECT 0 1.0000000 NA NA NA NA NA -2.000000e-06 1.113360e-02 -1.27129e-01 -3.314900e-03 -2.730000e-05 3.251900e-03 1.562320e-01 ▁▁▇▁▁
numeric SE 0 1.0000000 NA NA NA NA NA 8.246900e-03 7.483000e-03 1.87150e-03 2.670800e-03 4.598400e-03 1.166490e-02 4.222270e-02 ▇▂▁▁▁
numeric PVAL 0 1.0000000 NA NA NA NA NA 4.996099e-01 2.885843e-01 1.00000e-07 2.495313e-01 4.991315e-01 7.494696e-01 1.000000e+00 ▇▇▇▇▇
numeric PVAL_ztest 0 1.0000000 NA NA NA NA NA 4.996068e-01 2.885861e-01 1.00000e-07 2.495256e-01 4.991275e-01 7.494688e-01 9.999999e-01 ▇▇▇▇▇
numeric AF 0 1.0000000 NA NA NA NA NA 2.006105e-01 2.566921e-01 1.55450e-03 1.021150e-02 7.290590e-02 3.147210e-01 9.984450e-01 ▇▂▁▁▁
numeric AF_reference 408241 0.9683238 NA NA NA NA NA 2.039347e-01 2.487330e-01 0.00000e+00 7.587900e-03 9.484820e-02 3.222840e-01 1.000000e+00 ▇▂▁▁▁
numeric N 0 1.0000000 NA NA NA NA NA 5.142700e+04 0.000000e+00 5.14270e+04 5.142700e+04 5.142700e+04 5.142700e+04 5.142700e+04 ▁▁▇▁▁

Head and tail

CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
1 692794 rs530212009 CA C 0.0031373 0.0039576 0.4279352 0.4279317 0.1121000 0.1894970 51427
1 693731 rs12238997 A G 0.0032966 0.0037608 0.3807238 0.3807193 0.1168090 0.1417730 51427
1 707522 rs371890604 G C 0.0012796 0.0042180 0.7616194 0.7616176 0.0982930 0.1293930 51427
1 717587 rs144155419 G A 0.0026965 0.0101972 0.7914455 0.7914460 0.0154808 0.0045926 51427
1 723329 rs189787166 A T 0.0162756 0.0289816 0.5744021 0.5743996 0.0017973 0.0003994 51427
1 730087 rs148120343 T C 0.0041241 0.0052373 0.4310285 0.4310260 0.0570822 0.0127796 51427
1 731718 rs142557973 T C 0.0033605 0.0035738 0.3470627 0.3470597 0.1225210 0.1543530 51427
1 732032 rs61770163 A C 0.0023830 0.0038097 0.5316466 0.5316446 0.1216510 0.1555510 51427
1 734349 rs141242758 T C 0.0030106 0.0035758 0.3998269 0.3998237 0.1217650 0.1525560 51427
1 740284 rs61770167 C T 0.0236056 0.0156268 0.1309001 0.1308944 0.0062329 0.0023962 51427
CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
23 154923311 rs141127553 C T -0.0014002 0.0042046 0.7391218 0.7391202 0.0542488 0.0309934 51427
23 154923374 rs111332691 T A -0.0021788 0.0045546 0.6323813 0.6323798 0.0445389 0.0116556 51427
23 154925045 rs509981 C T 0.0044972 0.0021894 0.0399761 0.0399708 0.2434190 0.3634440 51427
23 154925895 rs538470 C T 0.0046471 0.0022365 0.0377320 0.0377275 0.2401390 0.3634440 51427
23 154927581 rs644138 G A 0.0038475 0.0020594 0.0617362 0.0617306 0.2981050 0.4635760 51427
23 154929412 rs557132 C T 0.0045317 0.0021902 0.0385452 0.0385403 0.2432580 0.3568210 51427
23 154929637 rs35185538 CT C 0.0032028 0.0022821 0.1605029 0.1604970 0.2278210 0.3011920 51427
23 154929952 rs4012982 CAA C 0.0045680 0.0023044 0.0474504 0.0474443 0.2374290 0.3165560 51427
23 154930230 rs781880 A G 0.0043879 0.0021892 0.0450433 0.0450381 0.2438260 0.3618540 51427
23 154930487 rs781879 T A 0.0043197 0.0076130 0.5704374 0.5704347 0.0189843 0.1263580 51427

bcf preview

1   692794  rs530212009 CA  C   .   PASS    AF=0.1121   ES:SE:LP:AF:SS:ID   0.0031373:0.00395756:0.368622:0.1121:51427:1_692794_CA_C
1   693731  rs12238997  A   G   .   PASS    AF=0.116809 ES:SE:LP:AF:SS:ID   0.00329662:0.00376081:0.41939:0.116809:51427:rs12238997
1   707522  rs371890604 G   C   .   PASS    AF=0.098293 ES:SE:LP:AF:SS:ID   0.00127957:0.00421803:0.118262:0.098293:51427:rs371890604
1   717587  rs144155419 G   A   .   PASS    AF=0.0154808    ES:SE:LP:AF:SS:ID   0.00269648:0.0101972:0.101579:0.0154808:51427:rs144155419
1   723329  rs189787166 A   T   .   PASS    AF=0.00179726   ES:SE:LP:AF:SS:ID   0.0162756:0.0289816:0.240784:0.00179726:51427:rs189787166
1   730087  rs148120343 T   C   .   PASS    AF=0.0570822    ES:SE:LP:AF:SS:ID   0.00412406:0.00523732:0.365494:0.0570822:51427:rs148120343
1   731718  rs58276399  T   C   .   PASS    AF=0.122521 ES:SE:LP:AF:SS:ID   0.0033605:0.00357383:0.459592:0.122521:51427:rs58276399
1   732032  rs61770163  A   C   .   PASS    AF=0.121651 ES:SE:LP:AF:SS:ID   0.00238297:0.00380972:0.274377:0.121651:51427:rs61770163
1   734349  rs141242758 T   C   .   PASS    AF=0.121765 ES:SE:LP:AF:SS:ID   0.00301057:0.00357577:0.398128:0.121765:51427:rs141242758
1   740284  rs61770167  C   T   .   PASS    AF=0.0062329    ES:SE:LP:AF:SS:ID   0.0236056:0.0156268:0.88306:0.0062329:51427:rs61770167
1   742813  rs112573343 C   T   .   PASS    AF=0.00176649   ES:SE:LP:AF:SS:ID   0.025215:0.032473:0.35906:0.00176649:51427:rs112573343
1   749963  rs529266287 T   TAA .   PASS    AF=0.868613 ES:SE:LP:AF:SS:ID   -0.0016241:0.00352004:0.190761:0.868613:51427:rs529266287
1   750230  rs190826124 G   C   .   PASS    AF=0.00158492   ES:SE:LP:AF:SS:ID   0.0221271:0.0315842:0.315538:0.00158492:51427:rs190826124
1   751343  rs28544273  T   A   .   PASS    AF=0.123957 ES:SE:LP:AF:SS:ID   0.00214442:0.00348709:0.268746:0.123957:51427:rs28544273
1   751488  rs200141114 G   GA  .   PASS    AF=0.143385 ES:SE:LP:AF:SS:ID   0.000789176:0.00345974:0.0864155:0.143385:51427:rs200141114
1   751756  rs28527770  T   C   .   PASS    AF=0.124126 ES:SE:LP:AF:SS:ID   0.00215745:0.0034813:0.271288:0.124126:51427:rs28527770
1   753405  rs3115860   C   A   .   PASS    AF=0.869933 ES:SE:LP:AF:SS:ID   -0.0020323:0.00339285:0.260285:0.869933:51427:rs3115860
1   753425  rs3131970   T   C   .   PASS    AF=0.874426 ES:SE:LP:AF:SS:ID   -0.0025808:0.00344679:0.342937:0.874426:51427:rs3131970
1   753541  rs2073813   G   A   .   PASS    AF=0.129659 ES:SE:LP:AF:SS:ID   0.00144403:0.00340122:0.173176:0.129659:51427:rs2073813
1   754105  rs12184325  C   T   .   PASS    AF=0.0369164    ES:SE:LP:AF:SS:ID   -0.00246371:0.00612605:0.162689:0.0369164:51427:rs12184325
1   754182  rs3131969   A   G   .   PASS    AF=0.869554 ES:SE:LP:AF:SS:ID   -0.00180436:0.00338969:0.225836:0.869554:51427:rs3131969
1   754192  rs3131968   A   G   .   PASS    AF=0.869648 ES:SE:LP:AF:SS:ID   -0.00177499:0.00339145:0.221329:0.869648:51427:rs3131968
1   754334  rs3131967   T   C   .   PASS    AF=0.86957  ES:SE:LP:AF:SS:ID   -0.00184315:0.00338969:0.231648:0.86957:51427:rs3131967
1   754433  rs150578204 G   A   .   PASS    AF=0.00531261   ES:SE:LP:AF:SS:ID   0.00299456:0.0169893:0.0654566:0.00531261:51427:rs150578204
1   754458  rs142682604 G   T   .   PASS    AF=0.00527727   ES:SE:LP:AF:SS:ID   0.00315999:0.0170339:0.0691385:0.00527727:51427:rs142682604
1   755435  rs184270342 T   G   .   PASS    AF=0.0057746    ES:SE:LP:AF:SS:ID   -0.00864895:0.0166134:0.219937:0.0057746:51427:rs184270342
1   755890  rs3115858   A   T   .   PASS    AF=0.869706 ES:SE:LP:AF:SS:ID   -0.00217098:0.00338457:0.28296:0.869706:51427:rs3115858
1   756434  rs61768170  G   C   .   PASS    AF=0.12702  ES:SE:LP:AF:SS:ID   0.001948:0.00345189:0.242199:0.12702:51427:rs61768170
1   756604  rs3131962   A   G   .   PASS    AF=0.869213 ES:SE:LP:AF:SS:ID   -0.00222192:0.00337567:0.292088:0.869213:51427:rs3131962
1   757640  rs3115853   G   A   .   PASS    AF=0.868449 ES:SE:LP:AF:SS:ID   -0.00200427:0.0033724:0.257821:0.868449:51427:rs3115853
1   757734  rs4951929   C   T   .   PASS    AF=0.869419 ES:SE:LP:AF:SS:ID   -0.00220262:0.00337939:0.288576:0.869419:51427:rs4951929
1   757936  rs4951862   C   A   .   PASS    AF=0.869426 ES:SE:LP:AF:SS:ID   -0.00220613:0.00337961:0.289119:0.869426:51427:rs4951862
1   758144  rs3131956   A   G   .   PASS    AF=0.869437 ES:SE:LP:AF:SS:ID   -0.00214076:0.00337977:0.278624:0.869437:51427:rs3131956
1   758626  rs3131954   C   T   .   PASS    AF=0.869848 ES:SE:LP:AF:SS:ID   -0.00225389:0.00338766:0.295981:0.869848:51427:rs3131954
1   759293  rs10157329  T   A   .   PASS    AF=0.0999077    ES:SE:LP:AF:SS:ID   0.00289019:0.00392853:0.335433:0.0999077:51427:rs10157329
1   759600  rs545998451 AGT A   .   PASS    AF=0.00659027   ES:SE:LP:AF:SS:ID   -0.0178684:0.0150896:0.626432:0.00659027:51427:1_759600_AGT_A
1   759837  rs3115851   T   A   .   PASS    AF=0.87358  ES:SE:LP:AF:SS:ID   -0.00235678:0.0034366:0.307285:0.87358:51427:rs3115851
1   761732  rs2286139   C   T   .   PASS    AF=0.86295  ES:SE:LP:AF:SS:ID   -0.00182198:0.00337149:0.229946:0.86295:51427:rs2286139
1   761752  rs1057213   C   T   .   PASS    AF=0.868667 ES:SE:LP:AF:SS:ID   -0.00231071:0.00340456:0.303361:0.868667:51427:rs1057213
1   762273  rs3115849   G   A   .   PASS    AF=0.8652   ES:SE:LP:AF:SS:ID   -0.002228:0.00340305:0.290171:0.8652:51427:rs3115849
1   762485  rs12095200  C   A   .   PASS    AF=0.0992889    ES:SE:LP:AF:SS:ID   0.0011433:0.00408425:0.108165:0.0992889:51427:rs12095200
1   762589  rs3115848   G   C   .   PASS    AF=0.870459 ES:SE:LP:AF:SS:ID   -0.00233494:0.0034413:0.303247:0.870459:51427:rs3115848
1   762592  rs3131950   C   G   .   PASS    AF=0.870459 ES:SE:LP:AF:SS:ID   -0.00233489:0.0034413:0.303238:0.870459:51427:rs3131950
1   762601  rs3131949   T   C   .   PASS    AF=0.870456 ES:SE:LP:AF:SS:ID   -0.00233527:0.00344132:0.303299:0.870456:51427:rs3131949
1   762632  rs3131948   T   A   .   PASS    AF=0.870829 ES:SE:LP:AF:SS:ID   -0.00254454:0.00344327:0.337321:0.870829:51427:rs3131948
1   764191  rs7515915   T   G   .   PASS    AF=0.126636 ES:SE:LP:AF:SS:ID   0.00189416:0.00344712:0.234577:0.126636:51427:rs7515915
1   766007  rs61768174  A   C   .   PASS    AF=0.106247 ES:SE:LP:AF:SS:ID   0.00189393:0.00375397:0.2119:0.106247:51427:rs61768174
1   766105  rs2519015   T   A   .   PASS    AF=0.854084 ES:SE:LP:AF:SS:ID   -0.00172475:0.00337114:0.215441:0.854084:51427:rs2519015
1   767393  rs538667473 A   C   .   PASS    AF=0.00168817   ES:SE:LP:AF:SS:ID   0.0162649:0.0292373:0.23807:0.00168817:51427:rs538667473
1   768116  rs376645387 A   AGTTTT  .   PASS    AF=0.836377 ES:SE:LP:AF:SS:ID   -0.00123893:0.00330149:0.150295:0.836377:51427:rs376645387