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-20415/ukb-d-20415.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-20415/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 17:19:55 2019
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ukb-d-import/processed/ukb-d-20415/ukb-d-20415.vcf.gz ...
Read summary statistics for 9575722 SNPs.
Dropped 7140 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, 1273709 SNPs remain.
After merging with regression SNP LD, 1273709 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: -0.0383 (0.1648)
Lambda GC: 1.0057
Mean Chi^2: 1.002
Intercept: 1.0041 (0.0064)
Ratio: 2.0151 (3.1098)
Analysis finished at Mon Nov 25 17:21:30 2019
Total time elapsed: 1.0m:34.43s

QC metrics

Metrics

Metrics

{
    "af_correlation": 0.9391,
    "inflation_factor": 1.0139,
    "mean_EFFECT": -0.0002,
    "n": 2739,
    "n_snps": 9575722,
    "n_clumped_hits": 0,
    "n_p_sig": 0,
    "n_mono": 0,
    "n_ns": 1055671,
    "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": 191180,
    "n_est": 2755.7877,
    "ratio_se_n": 1.0031,
    "mean_diff": -0.0002,
    "ratio_diff": 81.8382,
    "sd_y_est1": 0.4978,
    "sd_y_est2": 0.4993,
    "r2_sum1": 0,
    "r2_sum2": 0,
    "r2_sum3": 0,
    "r2_sum4": 0,
    "ldsc_nsnp_merge_refpanel_ld": 1273709,
    "ldsc_nsnp_merge_regression_ld": 1273709,
    "ldsc_observed_scale_h2_beta": "NA",
    "ldsc_observed_scale_h2_se": "NA",
    "ldsc_intercept_beta": 1.0041,
    "ldsc_intercept_se": 0.0064,
    "ldsc_lambda_gc": 1.0057,
    "ldsc_mean_chisq": 1.002,
    "ldsc_ratio": 2.05
}

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 9569123 0 NA NA NA NA NA NA NA NA
character REF 0 1.0000000 1 98 0 46664 0 NA NA NA NA NA NA NA NA
character ALT 0 1.0000000 1 342 0 29539 0 NA NA NA NA NA NA NA NA
numeric CHROM 0 1.0000000 NA NA NA NA NA 9.078677e+00 6.174720e+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 7.873478e+07 5.612192e+07 302.0000000 3.242596e+07 6.961939e+07 1.147494e+08 2.492297e+08 ▇▆▅▂▁
numeric EFFECT 0 1.0000000 NA NA NA NA NA -1.855000e-04 2.969170e-02 -0.3186170 -1.455640e-02 -1.332000e-04 1.423080e-02 2.732510e-01 ▁▁▇▁▁
numeric SE 0 1.0000000 NA NA NA NA NA 2.579210e-02 1.436530e-02 0.0105496 1.470480e-02 1.947040e-02 3.286320e-02 8.217510e-02 ▇▂▂▁▁
numeric PVAL 0 1.0000000 NA NA NA NA NA 4.981182e-01 2.890560e-01 0.0000010 2.470398e-01 4.970327e-01 7.484573e-01 9.999990e-01 ▇▇▇▇▇
numeric PVAL_ztest 0 1.0000000 NA NA NA NA NA 4.980593e-01 2.890914e-01 0.0000010 2.469382e-01 4.969749e-01 7.484321e-01 9.999993e-01 ▇▇▇▇▇
numeric AF 0 1.0000000 NA NA NA NA NA 2.646320e-01 2.628048e-01 0.0105577 4.657420e-02 1.637750e-01 4.208590e-01 9.894420e-01 ▇▂▂▁▁
numeric AF_reference 191180 0.9800349 NA NA NA NA NA 2.640165e-01 2.536044e-01 0.0000000 5.311500e-02 1.785140e-01 4.159350e-01 1.000000e+00 ▇▃▂▁▁
numeric N 0 1.0000000 NA NA NA NA NA 2.739000e+03 0.000000e+00 2739.0000000 2.739000e+03 2.739000e+03 2.739000e+03 2.739000e+03 ▁▁▇▁▁

Head and tail

CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
1 692794 rs530212009 CA C -0.0011645 0.0241902 0.9616101 0.9616059 0.1102920 0.1894970 2739
1 693731 rs12238997 A G -0.0162261 0.0222385 0.4656719 0.4656102 0.1205690 0.1417730 2739
1 707522 rs371890604 G C 0.0114469 0.0250623 0.6478956 0.6478595 0.1021880 0.1293930 2739
1 717587 rs144155419 G A -0.0894438 0.0620155 0.1493379 0.1492230 0.0146855 0.0045926 2739
1 730087 rs148120343 T C -0.0119514 0.0315472 0.7048343 0.7048053 0.0575335 0.0127796 2739
1 731718 rs142557973 T C -0.0143444 0.0211196 0.4970694 0.4970121 0.1258300 0.1543530 2739
1 732032 rs61770163 A C -0.0063657 0.0225913 0.7781369 0.7781158 0.1251570 0.1555510 2739
1 734349 rs141242758 T C -0.0134754 0.0211147 0.5233979 0.5233435 0.1252480 0.1525560 2739
1 749963 rs529266287 T TAA 0.0039196 0.0208686 0.8510291 0.8510151 0.8649530 0.7641770 2739
1 751343 rs28544273 T A 0.0022173 0.0207964 0.9150990 0.9150917 0.1266640 0.2426120 2739
CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
23 154923311 rs141127553 C T -0.0238058 0.0231215 0.3032941 0.3031998 0.0576287 0.0309934 2739
23 154923374 rs111332691 T A -0.0019682 0.0262556 0.9402510 0.9402450 0.0427163 0.0116556 2739
23 154925045 rs509981 C T 0.0170945 0.0124516 0.1699042 0.1697910 0.2438620 0.3634440 2739
23 154925895 rs538470 C T 0.0219781 0.0126834 0.0832415 0.0831270 0.2403750 0.3634440 2739
23 154927581 rs644138 G A 0.0095738 0.0116599 0.4116669 0.4115959 0.3018530 0.4635760 2739
23 154929412 rs557132 C T 0.0173126 0.0124521 0.1645391 0.1644269 0.2437230 0.3568210 2739
23 154929637 rs35185538 CT C 0.0221843 0.0129918 0.0878314 0.0877177 0.2296120 0.3011920 2739
23 154929952 rs4012982 CAA C 0.0237849 0.0131047 0.0696354 0.0695254 0.2382030 0.3165560 2739
23 154930230 rs781880 A G 0.0199009 0.0124527 0.1101349 0.1100164 0.2436970 0.3618540 2739
23 154930487 rs781879 T A 0.0251895 0.0422593 0.5511782 0.5511285 0.0207038 0.1263580 2739

bcf preview

1   692794  rs530212009 CA  C   .   PASS    AF=0.110292 ES:SE:LP:AF:SS:ID   -0.00116448:0.0241902:0.017001:0.110292:2739:1_692794_CA_C
1   693731  rs12238997  A   G   .   PASS    AF=0.120569 ES:SE:LP:AF:SS:ID   -0.0162261:0.0222385:0.33192:0.120569:2739:rs12238997
1   707522  rs371890604 G   C   .   PASS    AF=0.102188 ES:SE:LP:AF:SS:ID   0.0114469:0.0250623:0.188495:0.102188:2739:rs371890604
1   717587  rs144155419 G   A   .   PASS    AF=0.0146855    ES:SE:LP:AF:SS:ID   -0.0894438:0.0620155:0.82583:0.0146855:2739:rs144155419
1   730087  rs148120343 T   C   .   PASS    AF=0.0575335    ES:SE:LP:AF:SS:ID   -0.0119514:0.0315472:0.151913:0.0575335:2739:rs148120343
1   731718  rs58276399  T   C   .   PASS    AF=0.12583  ES:SE:LP:AF:SS:ID   -0.0143444:0.0211196:0.303583:0.12583:2739:rs58276399
1   732032  rs61770163  A   C   .   PASS    AF=0.125157 ES:SE:LP:AF:SS:ID   -0.00636567:0.0225913:0.108944:0.125157:2739:rs61770163
1   734349  rs141242758 T   C   .   PASS    AF=0.125248 ES:SE:LP:AF:SS:ID   -0.0134754:0.0211147:0.281168:0.125248:2739:rs141242758
1   749963  rs529266287 T   TAA .   PASS    AF=0.864953 ES:SE:LP:AF:SS:ID   0.00391961:0.0208686:0.0700556:0.864953:2739:rs529266287
1   751343  rs28544273  T   A   .   PASS    AF=0.126664 ES:SE:LP:AF:SS:ID   0.00221728:0.0207964:0.0385319:0.126664:2739:rs28544273
1   751488  rs200141114 G   GA  .   PASS    AF=0.146679 ES:SE:LP:AF:SS:ID   -0.0155433:0.0204224:0.350015:0.146679:2739:rs200141114
1   751756  rs28527770  T   C   .   PASS    AF=0.126652 ES:SE:LP:AF:SS:ID   0.00259537:0.0207824:0.045456:0.126652:2739:rs28527770
1   753405  rs3115860   C   A   .   PASS    AF=0.865863 ES:SE:LP:AF:SS:ID   0.00366272:0.020116:0.0677632:0.865863:2739:rs3115860
1   753425  rs3131970   T   C   .   PASS    AF=0.871417 ES:SE:LP:AF:SS:ID   -0.00460435:0.0205465:0.084758:0.871417:2739:rs3131970
1   753541  rs2073813   G   A   .   PASS    AF=0.134061 ES:SE:LP:AF:SS:ID   -0.00758158:0.020133:0.150876:0.134061:2739:rs2073813
1   754105  rs12184325  C   T   .   PASS    AF=0.0363271    ES:SE:LP:AF:SS:ID   -0.00737464:0.0366054:0.0755388:0.0363271:2739:rs12184325
1   754182  rs3131969   A   G   .   PASS    AF=0.865197 ES:SE:LP:AF:SS:ID   0.00510206:0.0200957:0.0971261:0.865197:2739:rs3131969
1   754192  rs3131968   A   G   .   PASS    AF=0.865189 ES:SE:LP:AF:SS:ID   0.00505868:0.0200964:0.0962179:0.865189:2739:rs3131968
1   754334  rs3131967   T   C   .   PASS    AF=0.865189 ES:SE:LP:AF:SS:ID   0.00510624:0.0200957:0.0972136:0.865189:2739:rs3131967
1   755890  rs3115858   A   T   .   PASS    AF=0.865299 ES:SE:LP:AF:SS:ID   0.00377166:0.0200354:0.0702261:0.865299:2739:rs3115858
1   756434  rs61768170  G   C   .   PASS    AF=0.131344 ES:SE:LP:AF:SS:ID   -0.00453592:0.020434:0.0838899:0.131344:2739:rs61768170
1   756604  rs3131962   A   G   .   PASS    AF=0.864732 ES:SE:LP:AF:SS:ID   0.00185636:0.0199582:0.0334354:0.864732:2739:rs3131962
1   757640  rs3115853   G   A   .   PASS    AF=0.864239 ES:SE:LP:AF:SS:ID   0.00513307:0.0200015:0.0982802:0.864239:2739:rs3115853
1   757734  rs4951929   C   T   .   PASS    AF=0.864909 ES:SE:LP:AF:SS:ID   0.00272278:0.0199985:0.0497749:0.864909:2739:rs4951929
1   757936  rs4951862   C   A   .   PASS    AF=0.86491  ES:SE:LP:AF:SS:ID   0.00271685:0.0199989:0.0496595:0.86491:2739:rs4951862
1   758144  rs3131956   A   G   .   PASS    AF=0.864913 ES:SE:LP:AF:SS:ID   0.00273979:0.0199991:0.0501008:0.864913:2739:rs3131956
1   758626  rs3131954   C   T   .   PASS    AF=0.865362 ES:SE:LP:AF:SS:ID   0.00372032:0.0200463:0.0691615:0.865362:2739:rs3131954
1   759293  rs10157329  T   A   .   PASS    AF=0.105152 ES:SE:LP:AF:SS:ID   0.0201275:0.0231289:0.415385:0.105152:2739:rs10157329
1   759837  rs3115851   T   A   .   PASS    AF=0.869939 ES:SE:LP:AF:SS:ID   0.00131411:0.0204401:0.022851:0.869939:2739:rs3115851
1   761732  rs2286139   C   T   .   PASS    AF=0.858635 ES:SE:LP:AF:SS:ID   0.00362736:0.0199669:0.0675993:0.858635:2739:rs2286139
1   761752  rs1057213   C   T   .   PASS    AF=0.864851 ES:SE:LP:AF:SS:ID   0.00350107:0.020212:0.0642444:0.864851:2739:rs1057213
1   762273  rs3115849   G   A   .   PASS    AF=0.860555 ES:SE:LP:AF:SS:ID   0.00298655:0.0201647:0.054399:0.860555:2739:rs3115849
1   762485  rs12095200  C   A   .   PASS    AF=0.104688 ES:SE:LP:AF:SS:ID   -0.000478929:0.0236455:0.00707464:0.104688:2739:rs12095200
1   762589  rs3115848   G   C   .   PASS    AF=0.866536 ES:SE:LP:AF:SS:ID   0.00335672:0.0205084:0.0604812:0.866536:2739:rs3115848
1   762592  rs3131950   C   G   .   PASS    AF=0.866536 ES:SE:LP:AF:SS:ID   0.00335672:0.0205084:0.0604812:0.866536:2739:rs3131950
1   762601  rs3131949   T   C   .   PASS    AF=0.866533 ES:SE:LP:AF:SS:ID   0.00335659:0.0205084:0.0604788:0.866533:2739:rs3131949
1   762632  rs3131948   T   A   .   PASS    AF=0.86668  ES:SE:LP:AF:SS:ID   0.00291615:0.0205038:0.052119:0.86668:2739:rs3131948
1   764191  rs7515915   T   G   .   PASS    AF=0.130605 ES:SE:LP:AF:SS:ID   -0.00467956:0.0204459:0.0867251:0.130605:2739:rs7515915
1   766007  rs61768174  A   C   .   PASS    AF=0.112153 ES:SE:LP:AF:SS:ID   0.00748332:0.0219454:0.134818:0.112153:2739:rs61768174
1   766105  rs2519015   T   A   .   PASS    AF=0.84957  ES:SE:LP:AF:SS:ID   0.0080412:0.0200437:0.162212:0.84957:2739:rs2519015
1   768116  rs376645387 A   AGTTTT  .   PASS    AF=0.845636 ES:SE:LP:AF:SS:ID   0.0429589:0.0202075:1.47363:0.845636:2739:rs376645387
1   768253  rs2977608   A   C   .   PASS    AF=0.762467 ES:SE:LP:AF:SS:ID   0.0133012:0.0160334:0.390574:0.762467:2739:rs2977608
1   768448  rs12562034  G   A   .   PASS    AF=0.101497 ES:SE:LP:AF:SS:ID   -0.0199362:0.0222999:0.43016:0.101497:2739:rs12562034
1   769138  rs59306077  CAT C   .   PASS    AF=0.134919 ES:SE:LP:AF:SS:ID   -0.00689245:0.0200696:0.135903:0.134919:2739:rs762168062
1   769223  rs60320384  C   G   .   PASS    AF=0.134234 ES:SE:LP:AF:SS:ID   -0.0059164:0.0200841:0.114449:0.134234:2739:rs60320384
1   769963  rs7518545   G   A   .   PASS    AF=0.101203 ES:SE:LP:AF:SS:ID   -0.0200357:0.0224178:0.429997:0.101203:2739:rs7518545
1   770886  rs371458725 G   A   .   PASS    AF=0.0999921    ES:SE:LP:AF:SS:ID   -0.0225421:0.0226929:0.494004:0.0999921:2739:rs371458725
1   771410  rs2519006   C   T   .   PASS    AF=0.823542 ES:SE:LP:AF:SS:ID   0.00774582:0.0194721:0.160638:0.823542:2739:rs2519006
1   771823  rs2977605   T   C   .   PASS    AF=0.864453 ES:SE:LP:AF:SS:ID   0.00202056:0.0200024:0.036427:0.864453:2739:rs2977605
1   771967  rs59066358  G   A   .   PASS    AF=0.134331 ES:SE:LP:AF:SS:ID   -0.00586387:0.0200635:0.113449:0.134331:2739:rs59066358