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-9039/UKB-b-9039_data.vcf.gz \
--ref-ld-chr ../reference/eur_w_ld_chr/ \
--out /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-9039/ldsc.txt \
--w-ld-chr ../reference/eur_w_ld_chr/ 

Beginning analysis at Thu Oct 17 14:42:17 2019
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-9039/UKB-b-9039_data.vcf.gz ...
Read summary statistics for 4218400 SNPs.
Dropped 859 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, 992468 SNPs remain.
After merging with regression SNP LD, 992468 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.0007 (0.0011)
Lambda GC: 1.026
Mean Chi^2: 1.0249
Intercept: 1.0175 (0.008)
Ratio: 0.704 (0.3205)
Analysis finished at Thu Oct 17 14:43:38 2019
Total time elapsed: 1.0m:21.25s

QC metrics

Metrics

Metrics

{
    "af_correlation": 0.8836,
    "inflation_factor": 1.0475,
    "mean_EFFECT": -6.6415e-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": 34661,
    "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": 992468,
    "ldsc_nsnp_merge_regression_ld": 992468,
    "ldsc_observed_scale_h2_beta": 0.0007,
    "ldsc_observed_scale_h2_se": 0.0011,
    "ldsc_intercept_beta": 1.0175,
    "ldsc_intercept_se": 0.008,
    "ldsc_lambda_gc": 1.026,
    "ldsc_mean_chisq": 1.0249,
    "ldsc_ratio": 0.7028
}

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 3 58 0 4217546 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 4218400 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 8.654229e+00 5.765148e+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 7.859663e+07 5.673722e+07 828.0000000 3.167387e+07 6.896527e+07 1.146780e+08 2.492385e+08 ▇▆▅▂▁
numeric EFFECT 0 1.0000000 NA NA NA NA NA NA NA -7.000000e-07 2.148000e-04 -0.0013729 -1.415000e-04 -1.500000e-06 1.401000e-04 1.228400e-03 ▁▁▇▂▁
numeric SE 0 1.0000000 NA NA NA NA NA NA NA 2.094000e-04 3.220000e-05 0.0001694 1.816000e-04 1.987000e-04 2.312000e-04 6.197000e-04 ▇▁▁▁▁
numeric PVAL 0 1.0000000 NA NA NA NA NA NA NA 4.955450e-01 2.899073e-01 0.0000010 2.399999e-01 4.899999e-01 7.499995e-01 1.000000e+00 ▇▇▇▇▇
numeric PVAL_ztest 0 1.0000000 NA NA NA NA NA NA NA 4.955453e-01 2.898808e-01 0.0000010 2.435206e-01 4.937862e-01 7.467028e-01 9.999986e-01 ▇▇▇▇▇
numeric AF 0 1.0000000 NA NA NA NA NA NA NA 3.848884e-01 2.193454e-01 0.1051370 1.941520e-01 3.330210e-01 5.454810e-01 8.948620e-01 ▇▅▃▂▂
numeric AF_reference 34661 0.9917834 NA NA NA NA NA NA NA 3.749680e-01 2.213840e-01 0.0000000 1.926920e-01 3.308710e-01 5.335460e-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 -0.0001009 0.0003118 0.7499995 0.7461803 0.623763 0.782149 NA
1 54676 rs2462492 C T -0.0001724 0.0003089 0.5800000 0.5769185 0.400401 NA NA
1 91536 rs6702460 G T -0.0000479 0.0003042 0.8700001 0.8749569 0.456851 0.420727 NA
1 534192 rs6680723 C T 0.0002377 0.0003475 0.4899999 0.4939844 0.240960 NA NA
1 693731 rs12238997 A G -0.0001018 0.0002912 0.7300002 0.7267148 0.116325 0.141773 NA
1 706368 rs55727773 A G -0.0001634 0.0002157 0.4500005 0.4487233 0.515650 0.275160 NA
1 729679 rs4951859 C G 0.0000305 0.0002524 0.9000000 0.9038309 0.843212 0.639976 NA
1 731718 rs142557973 T C -0.0001232 0.0002762 0.6600001 0.6556098 0.122307 0.154353 NA
1 734349 rs141242758 T C -0.0000940 0.0002763 0.7300002 0.7337099 0.121549 0.152556 NA
1 736289 rs79010578 T A -0.0002512 0.0002724 0.3599996 0.3563826 0.132330 0.139577 NA
CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
22 51198027 rs34939255 A G 0.0001798 0.0002151 0.4000000 0.4032921 0.254557 0.0984425 NA
22 51208537 rs72619593 G A 0.0000491 0.0002875 0.8600001 0.8644803 0.120739 0.1142170 NA
22 51210289 rs112565862 C T -0.0003139 0.0002864 0.2700001 0.2730377 0.129955 0.1018370 NA
22 51211106 rs9628250 T C 0.0001395 0.0002133 0.5099998 0.5131347 0.271547 0.1671330 NA
22 51211392 rs3888396 T C -0.0003402 0.0002838 0.2300001 0.2306740 0.132635 0.1641370 NA
22 51212875 rs2238837 A C -0.0000908 0.0002026 0.6499995 0.6541110 0.331455 0.3724040 NA
22 51213613 rs34726907 C T 0.0004530 0.0002670 0.0899995 0.0897450 0.127816 0.1727240 NA
22 51216564 rs9616970 T C 0.0004307 0.0002658 0.1100001 0.1052310 0.128330 0.1563500 NA
22 51219006 rs28729663 G A 0.0004150 0.0002602 0.1100001 0.1106858 0.137953 0.2052720 NA
22 51237063 rs3896457 T C -0.0001267 0.0002074 0.5400003 0.5413691 0.297971 0.2050720 NA

bcf preview

1   49298   rs10399793  T   C   .   PASS    AF=0.623763 ES:SE:LP:AF:ID  -0.000100938:0.000311845:0.124939:0.623763:rs10399793
1   54676   rs2462492   C   T   .   PASS    AF=0.400401 ES:SE:LP:AF:ID  -0.000172355:0.00030894:0.236572:0.400401:rs2462492
1   91536   rs6702460   G   T   .   PASS    AF=0.456851 ES:SE:LP:AF:ID  -4.78696e-05:0.000304194:0.0604807:0.456851:rs6702460
1   534192  rs6680723   C   T   .   PASS    AF=0.24096  ES:SE:LP:AF:ID  0.000237661:0.000347465:0.309804:0.24096:rs6680723
1   693731  rs12238997  A   G   .   PASS    AF=0.116325 ES:SE:LP:AF:ID  -0.000101772:0.000291194:0.136677:0.116325:rs12238997
1   706368  rs12029736  A   G   .   PASS    AF=0.51565  ES:SE:LP:AF:ID  -0.000163404:0.000215702:0.346787:0.51565:rs12029736
1   729679  rs4951859   C   G   .   PASS    AF=0.843212 ES:SE:LP:AF:ID  3.04905e-05:0.000252356:0.0457575:0.843212:rs4951859
1   731718  rs58276399  T   C   .   PASS    AF=0.122307 ES:SE:LP:AF:ID  -0.000123192:0.000276226:0.180456:0.122307:rs58276399
1   734349  rs141242758 T   C   .   PASS    AF=0.121549 ES:SE:LP:AF:ID  -9.40101e-05:0.000276342:0.136677:0.121549:rs141242758
1   736289  rs79010578  T   A   .   PASS    AF=0.13233  ES:SE:LP:AF:ID  -0.000251194:0.000272362:0.443698:0.13233:rs79010578
1   752566  rs3094315   G   A   .   PASS    AF=0.838951 ES:SE:LP:AF:ID  4.85506e-05:0.000244389:0.0757207:0.838951:rs3094315
1   752721  rs3131972   A   G   .   PASS    AF=0.83858  ES:SE:LP:AF:ID  5.50616e-05:0.000244126:0.0861861:0.83858:rs3131972
1   753405  rs3115860   C   A   .   PASS    AF=0.869781 ES:SE:LP:AF:ID  0.000111427:0.000261957:0.173925:0.869781:rs3115860
1   753541  rs2073813   G   A   .   PASS    AF=0.129871 ES:SE:LP:AF:ID  -7.84405e-05:0.000262493:0.113509:0.129871:rs2073813
1   754182  rs3131969   A   G   .   PASS    AF=0.869123 ES:SE:LP:AF:ID  0.000103907:0.000261444:0.161151:0.869123:rs3131969
1   754192  rs3131968   A   G   .   PASS    AF=0.869221 ES:SE:LP:AF:ID  9.70175e-05:0.000261548:0.148742:0.869221:rs3131968
1   754334  rs3131967   T   C   .   PASS    AF=0.869126 ES:SE:LP:AF:ID  0.000103224:0.000261439:0.161151:0.869126:rs3131967
1   754503  rs3115859   G   A   .   PASS    AF=0.838033 ES:SE:LP:AF:ID  9.53376e-06:0.000243449:0.0132283:0.838033:rs3115859
1   754964  rs3131966   C   T   .   PASS    AF=0.838664 ES:SE:LP:AF:ID  8.3776e-06:0.000244133:0.0132283:0.838664:rs3131966
1   755775  rs3131965   A   G   .   PASS    AF=0.839777 ES:SE:LP:AF:ID  2.54608e-05:0.000247435:0.0362122:0.839777:rs3131965
1   755890  rs3115858   A   T   .   PASS    AF=0.869405 ES:SE:LP:AF:ID  0.0001163:0.000261137:0.180456:0.869405:rs3115858
1   756604  rs3131962   A   G   .   PASS    AF=0.868952 ES:SE:LP:AF:ID  8.99024e-05:0.00026048:0.136677:0.868952:rs3131962
1   757640  rs3115853   G   A   .   PASS    AF=0.867905 ES:SE:LP:AF:ID  9.92117e-05:0.00025998:0.154902:0.867905:rs3115853
1   757734  rs4951929   C   T   .   PASS    AF=0.869095 ES:SE:LP:AF:ID  0.000104555:0.000260693:0.161151:0.869095:rs4951929
1   757936  rs4951862   C   A   .   PASS    AF=0.869104 ES:SE:LP:AF:ID  0.000104763:0.000260713:0.161151:0.869104:rs4951862
1   758144  rs3131956   A   G   .   PASS    AF=0.869112 ES:SE:LP:AF:ID  0.00010458:0.000260719:0.161151:0.869112:rs3131956
1   758626  rs3131954   C   T   .   PASS    AF=0.869589 ES:SE:LP:AF:ID  0.000110777:0.000261435:0.173925:0.869589:rs3131954
1   760912  rs1048488   C   T   .   PASS    AF=0.838313 ES:SE:LP:AF:ID  9.68274e-07:0.000242987:-0:0.838313:rs1048488
1   761147  rs3115850   T   C   .   PASS    AF=0.838434 ES:SE:LP:AF:ID  -2.24862e-06:0.000243158:0.00436481:0.838434:rs3115850
1   761732  rs2286139   C   T   .   PASS    AF=0.862261 ES:SE:LP:AF:ID  9.03425e-05:0.000259776:0.136677:0.862261:rs2286139
1   763394  rs3115847   G   A   .   PASS    AF=0.706753 ES:SE:LP:AF:ID  4.81898e-06:0.00025289:0.00877392:0.706753:rs3115847
1   766007  rs61768174  A   C   .   PASS    AF=0.105142 ES:SE:LP:AF:ID  -0.000400773:0.000291327:0.769551:0.105142:rs61768174
1   768253  rs2977608   A   C   .   PASS    AF=0.761304 ES:SE:LP:AF:ID  7.78629e-05:0.000206403:0.148742:0.761304:rs2977608
1   768448  rs12562034  G   A   .   PASS    AF=0.106488 ES:SE:LP:AF:ID  1.2011e-05:0.000284487:0.0132283:0.106488:rs12562034
1   769223  rs60320384  C   G   .   PASS    AF=0.129576 ES:SE:LP:AF:ID  -7.41091e-05:0.000262337:0.107905:0.129576:rs60320384
1   771823  rs2977605   T   C   .   PASS    AF=0.868911 ES:SE:LP:AF:ID  0.000115907:0.000260936:0.180456:0.868911:rs2977605
1   771967  rs59066358  G   A   .   PASS    AF=0.129677 ES:SE:LP:AF:ID  -8.3629e-05:0.000262167:0.124939:0.129677:rs59066358
1   772755  rs2905039   A   C   .   PASS    AF=0.868921 ES:SE:LP:AF:ID  0.000115301:0.000260941:0.180456:0.868921:rs2905039
1   776546  rs12124819  A   G   .   PASS    AF=0.26539  ES:SE:LP:AF:ID  -0.000138474:0.000230556:0.259637:0.26539:rs12124819
1   777122  rs2980319   A   T   .   PASS    AF=0.870044 ES:SE:LP:AF:ID  4.84134e-05:0.000261473:0.0705811:0.870044:rs2980319
1   778745  rs1055606   A   G   .   PASS    AF=0.128576 ES:SE:LP:AF:ID  -2.56094e-05:0.000262505:0.0362122:0.128576:rs1055606
1   779322  rs4040617   A   G   .   PASS    AF=0.128873 ES:SE:LP:AF:ID  -2.97128e-05:0.00026206:0.0409586:0.128873:rs4040617
1   780785  rs2977612   T   A   .   PASS    AF=0.868786 ES:SE:LP:AF:ID  6.74868e-05:0.000260776:0.09691:0.868786:rs2977612
1   782981  rs6594026   C   T   .   PASS    AF=0.129513 ES:SE:LP:AF:ID  -2.23874e-05:0.000261975:0.0315171:0.129513:rs6594026
1   785050  rs2905062   G   A   .   PASS    AF=0.868539 ES:SE:LP:AF:ID  5.76062e-05:0.000260715:0.0809219:0.868539:rs2905062
1   785989  rs2980300   T   C   .   PASS    AF=0.86848  ES:SE:LP:AF:ID  6.59747e-05:0.000260877:0.09691:0.86848:rs2980300
1   787399  rs2905055   G   T   .   PASS    AF=0.86078  ES:SE:LP:AF:ID  5.1634e-05:0.000260698:0.0757207:0.86078:rs2905055
1   787606  rs3863622   G   T   .   PASS    AF=0.128461 ES:SE:LP:AF:ID  -4.76502e-05:0.000263387:0.0655015:0.128461:rs3863622
1   787685  rs2905054   G   T   .   PASS    AF=0.861493 ES:SE:LP:AF:ID  1.84536e-05:0.000260871:0.0268721:0.861493:rs2905054
1   787844  rs2905053   C   T   .   PASS    AF=0.869229 ES:SE:LP:AF:ID  6.32119e-05:0.000261831:0.091515:0.869229:rs2905053