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-16499/UKB-b-16499_data.vcf.gz \
--ref-ld-chr ../reference/eur_w_ld_chr/ \
--out /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-16499/ldsc.txt \
--w-ld-chr ../reference/eur_w_ld_chr/ 

Beginning analysis at Thu Oct 17 14:45:05 2019
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-16499/UKB-b-16499_data.vcf.gz ...
Read summary statistics for 7312040 SNPs.
Dropped 4808 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, 1272088 SNPs remain.
After merging with regression SNP LD, 1272088 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.0213 (0.0019)
Lambda GC: 1.1902
Mean Chi^2: 1.2375
Intercept: 1.0375 (0.0081)
Ratio: 0.1577 (0.034)
Analysis finished at Thu Oct 17 14:46:25 2019
Total time elapsed: 1.0m:19.68s

QC metrics

Metrics

Metrics

{
    "af_correlation": 0.9384,
    "inflation_factor": 1.1474,
    "mean_EFFECT": -4.3923e-06,
    "n": "-Inf",
    "n_snps": 9851866,
    "n_clumped_hits": 34,
    "n_p_sig": 4231,
    "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": 67569,
    "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": 1272088,
    "ldsc_nsnp_merge_regression_ld": 1272088,
    "ldsc_observed_scale_h2_beta": 0.0213,
    "ldsc_observed_scale_h2_se": 0.0019,
    "ldsc_intercept_beta": 1.0375,
    "ldsc_intercept_se": 0.0081,
    "ldsc_lambda_gc": 1.1902,
    "ldsc_mean_chisq": 1.2375,
    "ldsc_ratio": 0.1579
}

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 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 7307254 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 7312040 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 8.664138e+00 5.764032e+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 7.863143e+07 5.644681e+07 828.0000000 3.216339e+07 6.905241e+07 1.145138e+08 2.492385e+08 ▇▆▅▂▁
numeric EFFECT 0 1.0000000 NA NA NA NA NA NA NA -4.400000e-06 1.062200e-03 -0.0119547 -5.534000e-04 -3.800000e-06 5.460000e-04 1.545030e-02 ▁▁▇▁▁
numeric SE 0 1.0000000 NA NA NA NA NA NA NA 8.848000e-04 4.501000e-04 0.0004624 5.261000e-04 6.930000e-04 1.127800e-03 5.014500e-03 ▇▂▁▁▁
numeric PVAL 0 1.0000000 NA NA NA NA NA NA NA 4.747512e-01 2.957197e-01 0.0000000 2.099999e-01 4.700002e-01 7.300002e-01 1.000000e+00 ▇▇▇▆▆
numeric PVAL_ztest 0 1.0000000 NA NA NA NA NA NA NA 4.747547e-01 2.956952e-01 0.0000000 2.127133e-01 4.658863e-01 7.309617e-01 9.999998e-01 ▇▇▆▆▆
numeric AF 0 1.0000000 NA NA NA NA NA NA NA 2.658375e-01 2.605329e-01 0.0134070 5.100900e-02 1.652890e-01 4.185560e-01 9.865930e-01 ▇▂▂▁▁
numeric AF_reference 67569 0.9907592 NA NA NA NA NA NA NA 2.644888e-01 2.524191e-01 0.0000000 5.730830e-02 1.783150e-01 4.121410e-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 0.0004868 0.0008508 0.5700002 0.5672282 0.623763 0.7821490 NA
1 54676 rs2462492 C T -0.0001624 0.0008429 0.8499999 0.8471763 0.400401 NA NA
1 86028 rs114608975 T C -0.0020934 0.0013476 0.1199999 0.1203092 0.103556 0.0277556 NA
1 91536 rs6702460 G T 0.0010544 0.0008299 0.2000000 0.2038995 0.456851 0.4207270 NA
1 234313 rs8179466 C T 0.0047396 0.0016364 0.0038000 0.0037752 0.074508 NA NA
1 534192 rs6680723 C T -0.0015710 0.0009480 0.0969996 0.0974678 0.240960 NA NA
1 546697 rs12025928 A G -0.0002349 0.0011827 0.8400000 0.8425428 0.913473 NA NA
1 693731 rs12238997 A G -0.0006037 0.0007945 0.4500005 0.4473479 0.116325 0.1417730 NA
1 705882 rs72631875 G A -0.0012304 0.0011642 0.2900000 0.2905817 0.067285 0.0315495 NA
1 706368 rs55727773 A G -0.0000887 0.0005885 0.8800001 0.8801644 0.515650 0.2751600 NA
CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
22 51219006 rs28729663 G A -0.0002400 0.0007101 0.7400005 0.7354098 0.137953 0.2052720 NA
22 51219387 rs9616832 T C 0.0000098 0.0009217 0.9900000 0.9915456 0.073747 0.0654952 NA
22 51219704 rs147475742 G A -0.0004019 0.0012351 0.7400005 0.7448805 0.041955 0.0473243 NA
22 51221190 rs369304721 G A -0.0002489 0.0012331 0.8400000 0.8400240 0.049731 NA NA
22 51221731 rs115055839 T C 0.0000392 0.0009223 0.9699999 0.9660545 0.073238 0.0625000 NA
22 51222100 rs114553188 G T -0.0012230 0.0010858 0.2599998 0.2600260 0.054459 0.0880591 NA
22 51223637 rs375798137 G A -0.0011600 0.0010911 0.2900000 0.2876767 0.054088 0.0788738 NA
22 51229805 rs9616985 T C 0.0000040 0.0009256 1.0000000 0.9965624 0.073073 0.0730831 NA
22 51232488 rs376461333 A G -0.0024716 0.0021805 0.2599998 0.2570078 0.020043 NA NA
22 51237063 rs3896457 T C -0.0004896 0.0005661 0.3900004 0.3871696 0.297971 0.2050720 NA

bcf preview

1   49298   rs10399793  T   C   .   PASS    AF=0.623763 ES:SE:LP:AF:ID  0.000486776:0.000850801:0.244125:0.623763:rs10399793
1   54676   rs2462492   C   T   .   PASS    AF=0.400401 ES:SE:LP:AF:ID  -0.000162441:0.000842875:0.0705811:0.400401:rs2462492
1   86028   rs114608975 T   C   .   PASS    AF=0.103556 ES:SE:LP:AF:ID  -0.00209345:0.00134759:0.920819:0.103556:rs114608975
1   91536   rs6702460   G   T   .   PASS    AF=0.456851 ES:SE:LP:AF:ID  0.00105444:0.000829928:0.69897:0.456851:rs6702460
1   234313  rs8179466   C   T   .   PASS    AF=0.074508 ES:SE:LP:AF:ID  0.00473958:0.00163639:2.42022:0.074508:rs8179466
1   534192  rs6680723   C   T   .   PASS    AF=0.24096  ES:SE:LP:AF:ID  -0.00157105:0.000947983:1.01323:0.24096:rs6680723
1   546697  rs12025928  A   G   .   PASS    AF=0.913473 ES:SE:LP:AF:ID  -0.000234926:0.00118266:0.0757207:0.913473:rs12025928
1   693731  rs12238997  A   G   .   PASS    AF=0.116325 ES:SE:LP:AF:ID  -0.000603664:0.000794458:0.346787:0.116325:rs12238997
1   705882  rs72631875  G   A   .   PASS    AF=0.067285 ES:SE:LP:AF:ID  -0.00123037:0.00116419:0.537602:0.067285:rs72631875
1   706368  rs12029736  A   G   .   PASS    AF=0.51565  ES:SE:LP:AF:ID  -8.87221e-05:0.000588496:0.0555173:0.51565:rs12029736
1   714596  rs149887893 T   C   .   PASS    AF=0.033004 ES:SE:LP:AF:ID  0.00159804:0.00148364:0.552842:0.033004:rs149887893
1   715265  rs12184267  C   T   .   PASS    AF=0.036621 ES:SE:LP:AF:ID  0.00125906:0.00134762:0.455932:0.036621:rs12184267
1   715367  rs12184277  A   G   .   PASS    AF=0.036737 ES:SE:LP:AF:ID  0.00127295:0.00134252:0.468521:0.036737:rs12184277
1   717485  rs12184279  C   A   .   PASS    AF=0.036437 ES:SE:LP:AF:ID  0.00130341:0.0013522:0.468521:0.036437:rs12184279
1   717587  rs144155419 G   A   .   PASS    AF=0.016407 ES:SE:LP:AF:ID  0.00134316:0.00208201:0.283997:0.016407:rs144155419
1   720381  rs116801199 G   T   .   PASS    AF=0.036976 ES:SE:LP:AF:ID  0.00122321:0.00133722:0.443698:0.036976:rs116801199
1   721290  rs12565286  G   C   .   PASS    AF=0.037072 ES:SE:LP:AF:ID  0.00119479:0.00133264:0.431798:0.037072:rs12565286
1   722670  rs116030099 T   C   .   PASS    AF=0.101199 ES:SE:LP:AF:ID  0.00072828:0.000970981:0.346787:0.101199:rs116030099
1   723891  rs2977670   G   C   .   PASS    AF=0.959096 ES:SE:LP:AF:ID  -0.00122303:0.0012853:0.468521:0.959096:rs2977670
1   724849  rs12126395  C   A   .   PASS    AF=0.031451 ES:SE:LP:AF:ID  0.00221329:0.0023332:0.468521:0.031451:rs12126395
1   725060  rs865924913 A   T   .   PASS    AF=0.053254 ES:SE:LP:AF:ID  -0.000810324:0.00185617:0.180456:0.053254:rs865924913
1   726794  rs28454925  C   G   .   PASS    AF=0.03659  ES:SE:LP:AF:ID  0.00123013:0.00134127:0.443698:0.03659:rs28454925
1   729632  rs116720794 C   T   .   PASS    AF=0.036907 ES:SE:LP:AF:ID  0.00124224:0.00132906:0.455932:0.036907:rs116720794
1   729679  rs4951859   C   G   .   PASS    AF=0.843212 ES:SE:LP:AF:ID  0.000304253:0.000688499:0.180456:0.843212:rs4951859
1   730087  rs148120343 T   C   .   PASS    AF=0.055911 ES:SE:LP:AF:ID  -0.000132094:0.00111479:0.0409586:0.055911:rs148120343
1   731718  rs58276399  T   C   .   PASS    AF=0.122307 ES:SE:LP:AF:ID  -0.000421407:0.000753622:0.236572:0.122307:rs58276399
1   732989  rs369030935 C   T   .   PASS    AF=0.025713 ES:SE:LP:AF:ID  -0.00158323:0.00185375:0.408935:0.025713:rs369030935
1   734349  rs141242758 T   C   .   PASS    AF=0.121549 ES:SE:LP:AF:ID  -0.000471115:0.000753939:0.275724:0.121549:rs141242758
1   736289  rs79010578  T   A   .   PASS    AF=0.13233  ES:SE:LP:AF:ID  -0.000411585:0.000743081:0.236572:0.13233:rs79010578
1   752478  rs146277091 G   A   .   PASS    AF=0.036821 ES:SE:LP:AF:ID  0.00112292:0.00131561:0.408935:0.036821:rs146277091
1   752566  rs3094315   G   A   .   PASS    AF=0.838951 ES:SE:LP:AF:ID  -4.62353e-05:0.000666763:0.0268721:0.838951:rs3094315
1   752721  rs3131972   A   G   .   PASS    AF=0.83858  ES:SE:LP:AF:ID  -2.30405e-06:0.000666046:-0:0.83858:rs3131972
1   753405  rs3115860   C   A   .   PASS    AF=0.869781 ES:SE:LP:AF:ID  1.87362e-05:0.000714693:0.00877392:0.869781:rs3115860
1   753541  rs2073813   G   A   .   PASS    AF=0.129871 ES:SE:LP:AF:ID  -0.000100201:0.000716156:0.05061:0.129871:rs2073813
1   754063  rs12184312  G   T   .   PASS    AF=0.037332 ES:SE:LP:AF:ID  0.00109113:0.00129331:0.39794:0.037332:rs12184312
1   754105  rs12184325  C   T   .   PASS    AF=0.037576 ES:SE:LP:AF:ID  0.00102511:0.00128513:0.366532:0.037576:rs12184325
1   754182  rs3131969   A   G   .   PASS    AF=0.869123 ES:SE:LP:AF:ID  8.1944e-05:0.000713294:0.0409586:0.869123:rs3131969
1   754192  rs3131968   A   G   .   PASS    AF=0.869221 ES:SE:LP:AF:ID  5.69515e-05:0.000713576:0.0268721:0.869221:rs3131968
1   754211  rs12184313  G   A   .   PASS    AF=0.037534 ES:SE:LP:AF:ID  0.00101598:0.00129069:0.366532:0.037534:rs12184313
1   754334  rs3131967   T   C   .   PASS    AF=0.869126 ES:SE:LP:AF:ID  7.99618e-05:0.000713279:0.0409586:0.869126:rs3131967
1   754503  rs3115859   G   A   .   PASS    AF=0.838033 ES:SE:LP:AF:ID  -1.39669e-06:0.000664196:-0:0.838033:rs3115859
1   754629  rs10454459  A   G   .   PASS    AF=0.037547 ES:SE:LP:AF:ID  0.00103471:0.00129252:0.376751:0.037547:rs10454459
1   754964  rs3131966   C   T   .   PASS    AF=0.838664 ES:SE:LP:AF:ID  -1.99956e-05:0.000666063:0.00877392:0.838664:rs3131966
1   755240  rs181660517 T   G   .   PASS    AF=0.013773 ES:SE:LP:AF:ID  0.00752997:0.00232498:2.92082:0.013773:rs181660517
1   755775  rs3131965   A   G   .   PASS    AF=0.839777 ES:SE:LP:AF:ID  -8.40912e-05:0.000675072:0.0457575:0.839777:rs3131965
1   755890  rs3115858   A   T   .   PASS    AF=0.869405 ES:SE:LP:AF:ID  3.24658e-05:0.000712454:0.0177288:0.869405:rs3115858
1   756604  rs3131962   A   G   .   PASS    AF=0.868952 ES:SE:LP:AF:ID  6.67076e-05:0.000710662:0.0315171:0.868952:rs3131962
1   757640  rs3115853   G   A   .   PASS    AF=0.867905 ES:SE:LP:AF:ID  8.41176e-05:0.0007093:0.0409586:0.867905:rs3115853
1   757734  rs4951929   C   T   .   PASS    AF=0.869095 ES:SE:LP:AF:ID  1.11091e-05:0.000711244:0.00436481:0.869095:rs4951929
1   757936  rs4951862   C   A   .   PASS    AF=0.869104 ES:SE:LP:AF:ID  1.53502e-05:0.000711298:0.00877392:0.869104:rs4951862