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/public/UKB-b-20415/UKB-b-20415_data.vcf.gz \
--ref-ld-chr ../reference/eur_w_ld_chr/ \
--out /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-20415/ldsc.txt \
--w-ld-chr ../reference/eur_w_ld_chr/ 

Beginning analysis at Thu Oct 17 14:42:09 2019
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-20415/UKB-b-20415_data.vcf.gz ...
Read summary statistics for 2345204 SNPs.
Dropped 259 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, 596044 SNPs remain.
After merging with regression SNP LD, 596044 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.0001 (0.0012)
Lambda GC: 1.0128
Mean Chi^2: 1.0157
Intercept: 1.0143 (0.0092)
Ratio: 0.9113 (0.5868)
Analysis finished at Thu Oct 17 14:42:43 2019
Total time elapsed: 34.49s

QC metrics

Metrics

Metrics

{
    "af_correlation": 0.7487,
    "inflation_factor": 1,
    "mean_EFFECT": -4.8949e-07,
    "n": "-Inf",
    "n_snps": 9851866,
    "n_clumped_hits": 0,
    "n_p_sig": 0,
    "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": 18565,
    "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": 596044,
    "ldsc_nsnp_merge_regression_ld": 596044,
    "ldsc_observed_scale_h2_beta": 0.0001,
    "ldsc_observed_scale_h2_se": 0.0012,
    "ldsc_intercept_beta": 1.0143,
    "ldsc_intercept_se": 0.0092,
    "ldsc_lambda_gc": 1.0128,
    "ldsc_mean_chisq": 1.0157,
    "ldsc_ratio": 0.9108
}
 

Flags

name value
af_correlation FALSE
inflation_factor FALSE
n TRUE
is_snpid_non_unique FALSE
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 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 4 58 0 2344947 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 2345204 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 8.650115e+00 5.768895e+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 7.862184e+07 5.666330e+07 5687.0000000 3.173826e+07 6.904854e+07 1.147860e+08 2.491722e+08 ▇▆▅▂▁
numeric EFFECT 0 1.0000000 NA NA NA NA NA NA NA -5.000000e-07 1.219000e-04 -0.0006197 -8.220000e-05 -3.000000e-07 8.150000e-05 6.055000e-04 ▁▂▇▂▁
numeric SE 0 1.0000000 NA NA NA NA NA NA NA 1.211000e-04 5.900000e-06 0.0001107 1.162000e-04 1.195000e-04 1.251000e-04 2.397000e-04 ▇▁▁▁▁
numeric PVAL 0 1.0000000 NA NA NA NA NA NA NA 4.984819e-01 2.902029e-01 0.0000003 2.399999e-01 5.000000e-01 7.499995e-01 1.000000e+00 ▇▇▇▇▇
numeric PVAL_ztest 0 1.0000000 NA NA NA NA NA NA NA 4.984768e-01 2.901787e-01 0.0000003 2.449159e-01 4.981186e-01 7.509622e-01 1.000000e+00 ▇▇▇▇▇
numeric AF 0 1.0000000 NA NA NA NA NA NA NA 4.586430e-01 1.437800e-01 0.2475250 3.320700e-01 4.387830e-01 5.747652e-01 7.524750e-01 ▇▆▅▅▃
numeric AF_reference 18565 0.9920838 NA NA NA NA NA NA NA 4.396744e-01 1.715498e-01 0.0001997 3.053120e-01 4.261180e-01 5.648960e-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 0.0000335 0.0002037 0.8700001 0.8694920 0.623763 0.7821490 NA
1 54676 rs2462492 C T -0.0001795 0.0002018 0.3700002 0.3736755 0.400401 NA NA
1 91536 rs6702460 G T -0.0000182 0.0001987 0.9299999 0.9271945 0.456851 0.4207270 NA
1 706368 rs55727773 A G 0.0001233 0.0001409 0.3800004 0.3815836 0.515650 0.2751600 NA
1 763394 rs369924889 G A 0.0000626 0.0001652 0.6999999 0.7049004 0.706753 0.6176120 NA
1 776546 rs12124819 A G -0.0000240 0.0001506 0.8700001 0.8735101 0.265390 0.0756789 NA
1 814495 rs74461805 C A 0.0001517 0.0001932 0.4299995 0.4321718 0.340397 NA NA
1 830181 rs28444699 A G 0.0001919 0.0001292 0.1400000 0.1375669 0.697259 0.6912940 NA
1 831489 rs4970385 C T 0.0002621 0.0001269 0.0389996 0.0389202 0.705403 0.6491610 NA
1 831909 rs9697642 C T 0.0002614 0.0001269 0.0389996 0.0394102 0.705448 0.6485620 NA
CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
22 51180501 rs5770999 T C 0.0000486 0.0001326 0.7099994 0.7139502 0.713658 0.6369810 NA
22 51181919 rs9616825 G C 0.0000496 0.0001319 0.7099994 0.7068339 0.695471 0.6194090 NA
22 51182485 rs6009961 A G 0.0000590 0.0001330 0.6600001 0.6574139 0.715505 0.6383790 NA
22 51186143 rs2879914 T C 0.0000518 0.0001233 0.6700003 0.6742929 0.381826 0.2733630 NA
22 51186228 rs3865766 C T -0.0000214 0.0001202 0.8600001 0.8588804 0.451063 0.4532750 NA
22 51197266 rs61290853 A G -0.0000479 0.0001241 0.6999999 0.6994086 0.386333 0.4229230 NA
22 51198027 rs34939255 A G 0.0001291 0.0001405 0.3599996 0.3582110 0.254557 0.0984425 NA
22 51211106 rs9628250 T C 0.0001488 0.0001393 0.2900000 0.2853606 0.271547 0.1671330 NA
22 51212875 rs2238837 A C 0.0000674 0.0001324 0.6100002 0.6107579 0.331455 0.3724040 NA
22 51237063 rs3896457 T C 0.0000176 0.0001355 0.9000000 0.8967194 0.297971 0.2050720 NA

bcf preview

1   49298   rs10399793  T   C   .   PASS    AF=0.623763 ES:SE:LP:AF:ID  3.34672e-05:0.000203691:0.0604807:0.623763:rs10399793
1   54676   rs2462492   C   T   .   PASS    AF=0.400401 ES:SE:LP:AF:ID  -0.000179517:0.000201793:0.431798:0.400401:rs2462492
1   91536   rs6702460   G   T   .   PASS    AF=0.456851 ES:SE:LP:AF:ID  -1.81556e-05:0.000198693:0.0315171:0.456851:rs6702460
1   706368  rs12029736  A   G   .   PASS    AF=0.51565  ES:SE:LP:AF:ID  0.000123278:0.000140892:0.420216:0.51565:rs12029736
1   763394  rs3115847   G   A   .   PASS    AF=0.706753 ES:SE:LP:AF:ID  6.25567e-05:0.000165182:0.154902:0.706753:rs3115847
1   776546  rs12124819  A   G   .   PASS    AF=0.26539  ES:SE:LP:AF:ID  -2.39748e-05:0.000150594:0.0604807:0.26539:rs12124819
1   814495  rs74461805  C   A   .   PASS    AF=0.340397 ES:SE:LP:AF:ID  0.000151747:0.00019319:0.366532:0.340397:rs74461805
1   830181  rs28444699  A   G   .   PASS    AF=0.697259 ES:SE:LP:AF:ID  0.000191925:0.00012925:0.853872:0.697259:rs28444699
1   831489  rs4970385   C   T   .   PASS    AF=0.705403 ES:SE:LP:AF:ID  0.000262077:0.000126912:1.40894:0.705403:rs4970385
1   831909  rs9697642   C   T   .   PASS    AF=0.705448 ES:SE:LP:AF:ID  0.000261415:0.000126908:1.40894:0.705448:rs9697642
1   832066  rs9697380   G   C   .   PASS    AF=0.705634 ES:SE:LP:AF:ID  0.000260347:0.000126913:1.39794:0.705634:rs9697380
1   832318  rs4500250   C   A   .   PASS    AF=0.705662 ES:SE:LP:AF:ID  0.000259721:0.000126927:1.38722:0.705662:rs4500250
1   832398  rs4553118   T   C   .   PASS    AF=0.730134 ES:SE:LP:AF:ID  0.000195936:0.000130385:0.886057:0.730134:rs4553118
1   832918  rs28765502  T   C   .   PASS    AF=0.294371 ES:SE:LP:AF:ID  -0.000259528:0.000126921:1.38722:0.294371:rs28765502
1   836896  rs28705752  T   C   .   PASS    AF=0.269503 ES:SE:LP:AF:ID  -0.000156023:0.000129379:0.638272:0.269503:rs28705752
1   839103  rs28562941  A   G   .   PASS    AF=0.27001  ES:SE:LP:AF:ID  -0.000141191:0.00012947:0.552842:0.27001:rs28562941
1   840753  rs4970382   T   C   .   PASS    AF=0.400106 ES:SE:LP:AF:ID  -7.34154e-05:0.000117066:0.275724:0.400106:rs4970382
1   843405  rs11516185  A   G   .   PASS    AF=0.362599 ES:SE:LP:AF:ID  -7.07288e-05:0.000145324:0.200659:0.362599:rs11516185
1   850218  rs6664536   T   A   .   PASS    AF=0.590333 ES:SE:LP:AF:ID  0.000253121:0.000116723:1.52288:0.590333:rs6664536
1   850371  rs6679046   G   T   .   PASS    AF=0.603726 ES:SE:LP:AF:ID  0.000251095:0.000117378:1.49485:0.603726:rs6679046
1   850780  rs6657440   C   T   .   PASS    AF=0.603944 ES:SE:LP:AF:ID  0.00024404:0.000117361:1.42022:0.603944:rs6657440
1   852037  rs4970463   G   A   .   PASS    AF=0.589688 ES:SE:LP:AF:ID  0.000249299:0.000116912:1.48149:0.589688:rs4970463
1   852063  rs28436996  G   A   .   PASS    AF=0.589667 ES:SE:LP:AF:ID  0.000246994:0.00011686:1.45593:0.589667:rs28436996
1   852875  rs13303369  C   T   .   PASS    AF=0.607674 ES:SE:LP:AF:ID  0.000253833:0.000117624:1.50864:0.607674:rs13303369
1   853954  rs1806509   C   A   .   PASS    AF=0.607833 ES:SE:LP:AF:ID  0.000251927:0.00011764:1.49485:0.607833:rs1806509
1   854777  rs13303019  A   G   .   PASS    AF=0.610318 ES:SE:LP:AF:ID  0.000247227:0.000117755:1.4437:0.610318:rs13303019
1   854978  rs13303057  A   C   .   PASS    AF=0.603286 ES:SE:LP:AF:ID  0.000251575:0.000117407:1.49485:0.603286:rs13303057
1   855075  rs6673914   C   G   .   PASS    AF=0.610338 ES:SE:LP:AF:ID  0.000249622:0.000117757:1.46852:0.610338:rs6673914
1   856099  rs28534711  T   G   .   PASS    AF=0.389935 ES:SE:LP:AF:ID  -0.000252916:0.00011778:1.49485:0.389935:rs28534711
1   856108  rs28742275  A   G   .   PASS    AF=0.389918 ES:SE:LP:AF:ID  -0.000253064:0.000117786:1.49485:0.389918:rs28742275
1   856476  rs4040605   A   G   .   PASS    AF=0.350351 ES:SE:LP:AF:ID  -0.000268156:0.000121:1.56864:0.350351:rs4040605
1   866893  rs2880024   T   C   .   PASS    AF=0.610554 ES:SE:LP:AF:ID  0.000182508:0.000118419:0.920819:0.610554:rs2880024
1   868418  rs28546443  C   T   .   PASS    AF=0.297865 ES:SE:LP:AF:ID  -8.79895e-05:0.000130109:0.30103:0.297865:rs28546443
1   870645  rs28576697  T   C   .   PASS    AF=0.291287 ES:SE:LP:AF:ID  -0.000328718:0.000129072:1.95861:0.291287:rs28576697
1   871334  rs4072383   G   T   .   PASS    AF=0.720619 ES:SE:LP:AF:ID  0.000314411:0.000128273:1.85387:0.720619:rs4072383
1   872352  rs1806780   G   C   .   PASS    AF=0.267526 ES:SE:LP:AF:ID  -0.000350106:0.000130012:2.14874:0.267526:rs1806780
1   873558  rs1110052   G   T   .   PASS    AF=0.715253 ES:SE:LP:AF:ID  0.000284265:0.000127254:1.60206:0.715253:rs1110052
1   875770  rs4970379   A   G   .   PASS    AF=0.600084 ES:SE:LP:AF:ID  0.000188542:0.000119403:0.958607:0.600084:rs4970379
1   881627  rs2272757   G   A   .   PASS    AF=0.65239  ES:SE:LP:AF:ID  0.000206024:0.000120618:1.05552:0.65239:rs2272757
1   891059  rs13303065  C   T   .   PASS    AF=0.652428 ES:SE:LP:AF:ID  0.000205641:0.000120599:1.05552:0.652428:rs13303065
1   891945  rs13303106  A   G   .   PASS    AF=0.65249  ES:SE:LP:AF:ID  0.000205559:0.000120739:1.05061:0.65249:rs13303106
1   900505  rs28705211  G   C   .   PASS    AF=0.271766 ES:SE:LP:AF:ID  -0.000282951:0.000130528:1.52288:0.271766:rs28705211
1   903245  rs28690976  A   G   .   PASS    AF=0.566937 ES:SE:LP:AF:ID  0.000139101:0.000119921:0.60206:0.566937:rs28690976
1   909073  rs3892467   C   T   .   PASS    AF=0.386683 ES:SE:LP:AF:ID  7.58524e-05:0.000119595:0.275724:0.386683:rs3892467
1   909238  rs3829740   G   C   .   PASS    AF=0.571412 ES:SE:LP:AF:ID  4.2584e-05:0.000115824:0.148742:0.571412:rs3829740
1   910394  rs28477686  C   T   .   PASS    AF=0.324456 ES:SE:LP:AF:ID  -7.2931e-05:0.000125541:0.251812:0.324456:rs28477686
1   912049  rs7367995   T   C   .   PASS    AF=0.58525  ES:SE:LP:AF:ID  7.11106e-05:0.000116998:0.267606:0.58525:rs7367995
1   913889  rs2340596   G   A   .   PASS    AF=0.599213 ES:SE:LP:AF:ID  3.35977e-05:0.000117188:0.113509:0.599213:rs2340596
1   914333  rs13302979  C   G   .   PASS    AF=0.602521 ES:SE:LP:AF:ID  4.42257e-05:0.000117544:0.148742:0.602521:rs13302979
1   914852  rs13303368  G   C   .   PASS    AF=0.600078 ES:SE:LP:AF:ID  3.72483e-05:0.000117318:0.124939:0.600078:rs13303368