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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    "FORMAT.1": "<ID=SE,Number=A,Type=Float,Description=\"Standard error of effect size estimate\">",
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    "gwas_harmonisation_command": "--out /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/ukbiobank/vcf_09_19b/bgzip_vcf/data.batch_4123.vcf.gz --id UKB-b:5463 --data /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/ukbiobank/raw-output/data.batch_4123.txt.gz --cohort_controls 146181 --ref /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/ukbiobank/human_g1k_v37.fasta --json /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/ukbiobank/ukb_gwas.json; 1.1.1",
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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/public/UKB-b-5463/UKB-b-5463_data.vcf.gz \
--ref-ld-chr ../reference/eur_w_ld_chr/ \
--out /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-5463/ldsc.txt \
--w-ld-chr ../reference/eur_w_ld_chr/ 

Beginning analysis at Thu Oct 17 14:45:22 2019
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-5463/UKB-b-5463_data.vcf.gz ...
Read summary statistics for 9301603 SNPs.
Dropped 10287 SNPs with duplicated rs numbers.
Reading reference panel LD Score from ../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 ../reference/eur_w_ld_chr/[1-22] ...
Read regression weight LD Scores for 1290028 SNPs.
After merging with reference panel LD, 1287944 SNPs remain.
After merging with regression SNP LD, 1287944 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.2898 (0.0261)
Lambda GC: 1.4249
Mean Chi^2: 1.9732
Intercept: 1.0998 (0.0135)
Ratio: 0.1026 (0.0139)
Analysis finished at Thu Oct 17 14:46:49 2019
Total time elapsed: 1.0m:27.53s

QC metrics

Metrics

Metrics

{
    "af_correlation": 0.9487,
    "inflation_factor": 1.3107,
    "mean_EFFECT": 0,
    "n": "-Inf",
    "n_snps": 9851866,
    "n_clumped_hits": 222,
    "n_p_sig": 27293,
    "n_mono": 0,
    "n_ns": 0,
    "n_mac": 0,
    "is_snpid_unique": true,
    "n_miss_EFFECT": 0,
    "n_miss_SE": 0,
    "n_miss_PVAL": 0,
    "n_miss_AF": 0,
    "n_miss_AF_reference": 111616,
    "n_est": "NA",
    "ratio_se_n": "NA",
    "mean_diff": "NaN",
    "ratio_diff": "NaN",
    "sd_y_est1": "NaN",
    "sd_y_est2": "NA",
    "r2_sum1": 0,
    "r2_sum2": 0,
    "r2_sum3": 0,
    "r2_sum4": 0,
    "ldsc_nsnp_merge_refpanel_ld": 1287944,
    "ldsc_nsnp_merge_regression_ld": 1287944,
    "ldsc_observed_scale_h2_beta": 0.2898,
    "ldsc_observed_scale_h2_se": 0.0261,
    "ldsc_intercept_beta": 1.0998,
    "ldsc_intercept_se": 0.0135,
    "ldsc_lambda_gc": 1.4249,
    "ldsc_mean_chisq": 1.9732,
    "ldsc_ratio": 0.1025
}
 

Flags

name value
af_correlation FALSE
inflation_factor TRUE
n TRUE
is_snpid_non_unique FALSE
mean_EFFECT_nonfinite FALSE
mean_EFFECT_05 FALSE
mean_EFFECT_01 FALSE
mean_chisq TRUE
n_p_sig TRUE
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 logical.mean logical.count numeric.mean numeric.sd numeric.p0 numeric.p25 numeric.p50 numeric.p75 numeric.p100 numeric.hist
character ID 0 1.0000000 3 58 0 9291368 0 NA NA NA NA NA NA NA NA NA NA
character REF 0 1.0000000 1 1 0 4 0 NA NA NA NA NA NA NA NA NA NA
character ALT 0 1.0000000 1 1 0 4 0 NA NA NA NA NA NA NA NA NA NA
logical N 9301603 0.0000000 NA NA NA NA NA NaN : NA NA NA NA NA NA NA NA
numeric CHROM 0 1.0000000 NA NA NA NA NA NA NA 8.635414e+00 5.754177e+00 1.0000000 4.000000e+00 8.000000e+00 1.300000e+01 2.200000e+01 ▇▅▃▂▂
numeric POS 0 1.0000000 NA NA NA NA NA NA NA 7.880933e+07 5.630798e+07 828.0000000 3.250012e+07 6.939138e+07 1.145406e+08 2.492385e+08 ▇▆▅▂▁
numeric EFFECT 0 1.0000000 NA NA NA NA NA NA NA 2.710000e-05 1.373700e-02 -0.2110810 -5.336500e-03 8.000000e-07 5.334200e-03 3.747450e-01 ▁▇▁▁▁
numeric SE 0 1.0000000 NA NA NA NA NA NA NA 9.868600e-03 7.777900e-03 0.0033075 3.988300e-03 6.296700e-03 1.353000e-02 8.288560e-02 ▇▁▁▁▁
numeric PVAL 0 1.0000000 NA NA NA NA NA NA NA 4.548956e-01 3.022084e-01 0.0000000 1.800002e-01 4.400003e-01 7.199992e-01 1.000000e+00 ▇▆▆▅▆
numeric PVAL_ztest 0 1.0000000 NA NA NA NA NA NA NA 4.548977e-01 3.021840e-01 0.0000000 1.818809e-01 4.397750e-01 7.168630e-01 9.999999e-01 ▇▆▆▅▅
numeric AF 0 1.0000000 NA NA NA NA NA NA NA 2.138884e-01 2.578303e-01 0.0023950 1.754800e-02 9.266700e-02 3.358620e-01 9.976050e-01 ▇▂▁▁▁
numeric AF_reference 111616 0.9880003 NA NA NA NA NA NA NA 2.148840e-01 2.496222e-01 0.0000000 1.477640e-02 1.110220e-01 3.356630e-01 1.000000e+00 ▇▂▁▁▁

Head and tail

CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
1 49298 rs200943160 T C -0.0033694 0.0061062 0.5800000 0.5810828 0.623875 0.7821490 NA
1 54676 rs2462492 C T -0.0021805 0.0060615 0.7199992 0.7190496 0.399273 NA NA
1 86028 rs114608975 T C -0.0024815 0.0096597 0.8000000 0.7972653 0.103774 0.0277556 NA
1 91536 rs6702460 G T 0.0003641 0.0059718 0.9500000 0.9513881 0.456146 0.4207270 NA
1 234313 rs8179466 C T 0.0034886 0.0118022 0.7700005 0.7675427 0.074421 NA NA
1 534192 rs6680723 C T 0.0097564 0.0068218 0.1499999 0.1526646 0.241222 NA NA
1 546697 rs12025928 A G 0.0218638 0.0084671 0.0098001 0.0098168 0.913003 NA NA
1 693731 rs12238997 A G 0.0020525 0.0056956 0.7199992 0.7185708 0.116800 0.1417730 NA
1 705882 rs72631875 G A -0.0105321 0.0083137 0.2099999 0.2052126 0.067758 0.0315495 NA
1 706368 rs55727773 A G -0.0057310 0.0042137 0.1700000 0.1738002 0.515059 0.2751600 NA
CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
22 51219006 rs28729663 G A -0.0006727 0.0051233 0.9000000 0.8955414 0.137270 0.2052720 NA
22 51219387 rs9616832 T C -0.0022570 0.0066579 0.7300002 0.7346137 0.072947 0.0654952 NA
22 51219704 rs147475742 G A -0.0090528 0.0088863 0.3100002 0.3083275 0.041767 0.0473243 NA
22 51221190 rs369304721 G A -0.0098781 0.0089081 0.2700001 0.2674799 0.049245 NA NA
22 51221731 rs115055839 T C -0.0018695 0.0066629 0.7800007 0.7790297 0.072428 0.0625000 NA
22 51222100 rs114553188 G T -0.0042006 0.0078143 0.5900000 0.5908850 0.054388 0.0880591 NA
22 51223637 rs375798137 G A -0.0040504 0.0078549 0.6100002 0.6060979 0.053994 0.0788738 NA
22 51229805 rs9616985 T C -0.0019489 0.0066870 0.7700005 0.7707164 0.072295 0.0730831 NA
22 51232488 rs376461333 A G 0.0037686 0.0156637 0.8100000 0.8098689 0.020175 NA NA
22 51237063 rs3896457 T C 0.0014319 0.0040710 0.7300002 0.7250436 0.297608 0.2050720 NA

bcf preview

1   49298   rs10399793  T   C   .   PASS    AF=0.623875 ES:SE:LP:AF:ID  -0.00336943:0.00610621:0.236572:0.623875:rs10399793
1   54676   rs2462492   C   T   .   PASS    AF=0.399273 ES:SE:LP:AF:ID  -0.00218051:0.00606153:0.142668:0.399273:rs2462492
1   86028   rs114608975 T   C   .   PASS    AF=0.103774 ES:SE:LP:AF:ID  -0.00248147:0.00965974:0.09691:0.103774:rs114608975
1   91536   rs6702460   G   T   .   PASS    AF=0.456146 ES:SE:LP:AF:ID  0.000364062:0.00597178:0.0222764:0.456146:rs6702460
1   234313  rs8179466   C   T   .   PASS    AF=0.074421 ES:SE:LP:AF:ID  0.00348862:0.0118022:0.113509:0.074421:rs8179466
1   534192  rs6680723   C   T   .   PASS    AF=0.241222 ES:SE:LP:AF:ID  0.00975642:0.0068218:0.823909:0.241222:rs6680723
1   546697  rs12025928  A   G   .   PASS    AF=0.913003 ES:SE:LP:AF:ID  0.0218638:0.00846707:2.00877:0.913003:rs12025928
1   693731  rs12238997  A   G   .   PASS    AF=0.1168   ES:SE:LP:AF:ID  0.00205251:0.00569557:0.142668:0.1168:rs12238997
1   705882  rs72631875  G   A   .   PASS    AF=0.067758 ES:SE:LP:AF:ID  -0.0105321:0.00831368:0.677781:0.067758:rs72631875
1   706368  rs12029736  A   G   .   PASS    AF=0.515059 ES:SE:LP:AF:ID  -0.005731:0.00421368:0.769551:0.515059:rs12029736
1   714596  rs149887893 T   C   .   PASS    AF=0.033495 ES:SE:LP:AF:ID  -0.00828042:0.0105404:0.366532:0.033495:rs149887893
1   715265  rs12184267  C   T   .   PASS    AF=0.037201 ES:SE:LP:AF:ID  -0.00916567:0.00956994:0.468521:0.037201:rs12184267
1   715367  rs12184277  A   G   .   PASS    AF=0.037328 ES:SE:LP:AF:ID  -0.00989003:0.00953224:0.522879:0.037328:rs12184277
1   717485  rs12184279  C   A   .   PASS    AF=0.036981 ES:SE:LP:AF:ID  -0.0104817:0.00960524:0.552842:0.036981:rs12184279
1   717587  rs144155419 G   A   .   PASS    AF=0.016371 ES:SE:LP:AF:ID  0.000431284:0.0149807:0.00877392:0.016371:rs144155419
1   720381  rs116801199 G   T   .   PASS    AF=0.03756  ES:SE:LP:AF:ID  -0.00953118:0.00949512:0.49485:0.03756:rs116801199
1   721290  rs12565286  G   C   .   PASS    AF=0.037651 ES:SE:LP:AF:ID  -0.0093157:0.00946532:0.481486:0.037651:rs12565286
1   722670  rs116030099 T   C   .   PASS    AF=0.101703 ES:SE:LP:AF:ID  0.0138709:0.00693566:1.33724:0.101703:rs116030099
1   723891  rs2977670   G   C   .   PASS    AF=0.9584   ES:SE:LP:AF:ID  0.00743133:0.0091317:0.376751:0.9584:rs2977670
1   724849  rs12126395  C   A   .   PASS    AF=0.031736 ES:SE:LP:AF:ID  -0.0127801:0.0166623:0.356547:0.031736:rs12126395
1   725060  rs865924913 A   T   .   PASS    AF=0.052666 ES:SE:LP:AF:ID  -0.0175867:0.0134681:0.721246:0.052666:rs865924913
1   726794  rs28454925  C   G   .   PASS    AF=0.037137 ES:SE:LP:AF:ID  -0.00861221:0.00952975:0.431798:0.037137:rs28454925
1   729632  rs116720794 C   T   .   PASS    AF=0.037451 ES:SE:LP:AF:ID  -0.00994452:0.00944643:0.537602:0.037451:rs116720794
1   729679  rs4951859   C   G   .   PASS    AF=0.842155 ES:SE:LP:AF:ID  0.00128297:0.00492851:0.102373:0.842155:rs4951859
1   730087  rs148120343 T   C   .   PASS    AF=0.05605  ES:SE:LP:AF:ID  -0.000767146:0.00800375:0.0362122:0.05605:rs148120343
1   731718  rs58276399  T   C   .   PASS    AF=0.122754 ES:SE:LP:AF:ID  0.00205795:0.0054048:0.154902:0.122754:rs58276399
1   732989  rs369030935 C   T   .   PASS    AF=0.025715 ES:SE:LP:AF:ID  -0.00814387:0.0132939:0.267606:0.025715:rs369030935
1   734349  rs141242758 T   C   .   PASS    AF=0.121972 ES:SE:LP:AF:ID  0.00177559:0.00540752:0.130768:0.121972:rs141242758
1   736289  rs79010578  T   A   .   PASS    AF=0.1332   ES:SE:LP:AF:ID  -0.00217897:0.00531888:0.167491:0.1332:rs79010578
1   736689  rs181876450 T   C   .   PASS    AF=0.011254 ES:SE:LP:AF:ID  -0.000637156:0.0192543:0.0132283:0.011254:rs181876450
1   740284  rs61770167  C   T   .   PASS    AF=0.005812 ES:SE:LP:AF:ID  0.0319278:0.0246935:0.69897:0.005812:rs61770167
1   752478  rs146277091 G   A   .   PASS    AF=0.037392 ES:SE:LP:AF:ID  -0.00874013:0.00935011:0.455932:0.037392:rs146277091
1   752566  rs3094315   G   A   .   PASS    AF=0.837809 ES:SE:LP:AF:ID  -0.000635737:0.00477067:0.05061:0.837809:rs3094315
1   752721  rs3131972   A   G   .   PASS    AF=0.837421 ES:SE:LP:AF:ID  -0.000971828:0.00476494:0.0757207:0.837421:rs3131972
1   753405  rs3115860   C   A   .   PASS    AF=0.86908  ES:SE:LP:AF:ID  -0.0047486:0.00511576:0.455932:0.86908:rs3115860
1   753541  rs2073813   G   A   .   PASS    AF=0.130618 ES:SE:LP:AF:ID  0.00539361:0.00512572:0.537602:0.130618:rs2073813
1   754063  rs12184312  G   T   .   PASS    AF=0.037886 ES:SE:LP:AF:ID  -0.00718927:0.00919677:0.366532:0.037886:rs12184312
1   754105  rs12184325  C   T   .   PASS    AF=0.038144 ES:SE:LP:AF:ID  -0.00648594:0.00913774:0.318759:0.038144:rs12184325
1   754182  rs3131969   A   G   .   PASS    AF=0.86841  ES:SE:LP:AF:ID  -0.00515454:0.00510534:0.508638:0.86841:rs3131969
1   754192  rs3131968   A   G   .   PASS    AF=0.868512 ES:SE:LP:AF:ID  -0.00529853:0.00510732:0.522879:0.868512:rs3131968
1   754211  rs12184313  G   A   .   PASS    AF=0.038068 ES:SE:LP:AF:ID  -0.00703986:0.00917841:0.356547:0.038068:rs12184313
1   754334  rs3131967   T   C   .   PASS    AF=0.868403 ES:SE:LP:AF:ID  -0.00502622:0.005105:0.49485:0.868403:rs3131967
1   754433  rs150578204 G   A   .   PASS    AF=0.005179 ES:SE:LP:AF:ID  0.0367989:0.0261407:0.79588:0.005179:rs150578204
1   754458  rs142682604 G   T   .   PASS    AF=0.00515  ES:SE:LP:AF:ID  0.0366088:0.0261964:0.79588:0.00515:rs142682604
1   754503  rs3115859   G   A   .   PASS    AF=0.836917 ES:SE:LP:AF:ID  -0.0012111:0.00475298:0.09691:0.836917:rs3115859
1   754629  rs10454459  A   G   .   PASS    AF=0.038078 ES:SE:LP:AF:ID  -0.00674046:0.00919114:0.337242:0.038078:rs10454459
1   754964  rs3131966   C   T   .   PASS    AF=0.837555 ES:SE:LP:AF:ID  -0.00113559:0.00476633:0.091515:0.837555:rs3131966
1   755240  rs181660517 T   G   .   PASS    AF=0.013277 ES:SE:LP:AF:ID  0.0114786:0.0170268:0.30103:0.013277:rs181660517
1   755435  rs184270342 T   G   .   PASS    AF=0.005467 ES:SE:LP:AF:ID  0.00264035:0.0258597:0.0362122:0.005467:rs184270342
1   755775  rs3131965   A   G   .   PASS    AF=0.838791 ES:SE:LP:AF:ID  -0.00133751:0.004832:0.107905:0.838791:rs3131965