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-9667/UKB-b-9667_data.vcf.gz \
--ref-ld-chr ../reference/eur_w_ld_chr/ \
--out /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-9667/ldsc.txt \
--w-ld-chr ../reference/eur_w_ld_chr/ 

Beginning analysis at Thu Oct 17 14:42:56 2019
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-9667/UKB-b-9667_data.vcf.gz ...
Read summary statistics for 8338738 SNPs.
Dropped 6797 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, 1284580 SNPs remain.
After merging with regression SNP LD, 1284580 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.0338 (0.0018)
Lambda GC: 1.3137
Mean Chi^2: 1.3556
Intercept: 1.054 (0.0082)
Ratio: 0.1519 (0.0231)
Analysis finished at Thu Oct 17 14:44:42 2019
Total time elapsed: 1.0m:46.07s

QC metrics

Metrics

Metrics

{
    "af_correlation": 0.9448,
    "inflation_factor": 1.2544,
    "mean_EFFECT": 0,
    "n": "-Inf",
    "n_snps": 9851866,
    "n_clumped_hits": 10,
    "n_p_sig": 196,
    "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": 78568,
    "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": 1284580,
    "ldsc_nsnp_merge_regression_ld": 1284580,
    "ldsc_observed_scale_h2_beta": 0.0338,
    "ldsc_observed_scale_h2_se": 0.0018,
    "ldsc_intercept_beta": 1.054,
    "ldsc_intercept_se": 0.0082,
    "ldsc_lambda_gc": 1.3137,
    "ldsc_mean_chisq": 1.3556,
    "ldsc_ratio": 0.1519
}

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 FALSE
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 1.000000 3 58 0 8331971 0 NA NA NA NA NA NA NA NA NA NA
character REF 0 1.000000 1 1 0 4 0 NA NA NA NA NA NA NA NA NA NA
character ALT 0 1.000000 1 1 0 4 0 NA NA NA NA NA NA NA NA NA NA
logical N 8338738 0.000000 NA NA NA NA NA NaN : NA NA NA NA NA NA NA NA
numeric CHROM 0 1.000000 NA NA NA NA NA NA NA 8.654535e+00 5.762179e+00 1.0000000 4.000000e+00 8.000000e+00 1.300000e+01 2.200000e+01 ▇▅▅▂▂
numeric POS 0 1.000000 NA NA NA NA NA NA NA 7.874117e+07 5.638504e+07 828.0000000 3.233594e+07 6.923676e+07 1.145498e+08 2.492385e+08 ▇▆▅▂▁
numeric EFFECT 0 1.000000 NA NA NA NA NA NA NA 3.730000e-05 1.936400e-03 -0.0172868 -8.669000e-04 2.040000e-05 9.203000e-04 1.938170e-02 ▁▁▇▁▁
numeric SE 0 1.000000 NA NA NA NA NA NA NA 1.523500e-03 9.847000e-04 0.0006441 7.529000e-04 1.080600e-03 2.035000e-03 1.006940e-02 ▇▂▁▁▁
numeric PVAL 0 1.000000 NA NA NA NA NA NA NA 4.641819e-01 2.980487e-01 0.0000000 2.000000e-01 4.500005e-01 7.199992e-01 1.000000e+00 ▇▆▆▆▆
numeric PVAL_ztest 0 1.000000 NA NA NA NA NA NA NA 4.641816e-01 2.980233e-01 0.0000000 1.975815e-01 4.506366e-01 7.221870e-01 9.999999e-01 ▇▆▆▆▆
numeric AF 0 1.000000 NA NA NA NA NA NA NA 2.363798e-01 2.601719e-01 0.0065400 2.952800e-02 1.239730e-01 3.743380e-01 9.934600e-01 ▇▂▂▁▁
numeric AF_reference 78568 0.990578 NA NA NA NA NA NA NA 2.358991e-01 2.520693e-01 0.0000000 2.915340e-02 1.399760e-01 3.708070e-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 -0.0006488 0.0011850 0.5800000 0.5840272 0.623799 0.7821490 NA
1 54676 rs2462492 C T 0.0005732 0.0011738 0.6300007 0.6253165 0.400435 NA NA
1 86028 rs114608975 T C 0.0017925 0.0018770 0.3400001 0.3395950 0.103546 0.0277556 NA
1 91536 rs6702460 G T 0.0004017 0.0011559 0.7300002 0.7281775 0.456844 0.4207270 NA
1 234313 rs8179466 C T -0.0006957 0.0022792 0.7600007 0.7601679 0.074511 NA NA
1 534192 rs6680723 C T -0.0000982 0.0013204 0.9400001 0.9407199 0.240982 NA NA
1 546697 rs12025928 A G -0.0001071 0.0016474 0.9500000 0.9481411 0.913490 NA NA
1 693731 rs12238997 A G 0.0016094 0.0011061 0.1499999 0.1456727 0.116360 0.1417730 NA
1 705882 rs72631875 G A -0.0026774 0.0016217 0.0990011 0.0987353 0.067257 0.0315495 NA
1 706368 rs55727773 A G -0.0008322 0.0008197 0.3100002 0.3099523 0.515625 0.2751600 NA
CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
22 51219006 rs28729663 G A -0.0004618 0.0009892 0.6400000 0.6406190 0.137940 0.2052720 NA
22 51219387 rs9616832 T C -0.0008974 0.0012842 0.4799997 0.4846488 0.073713 0.0654952 NA
22 51219704 rs147475742 G A -0.0009756 0.0017206 0.5700002 0.5706902 0.041941 0.0473243 NA
22 51221190 rs369304721 G A -0.0008046 0.0017180 0.6400000 0.6395546 0.049706 NA NA
22 51221731 rs115055839 T C -0.0008427 0.0012850 0.5099998 0.5119448 0.073202 0.0625000 NA
22 51222100 rs114553188 G T -0.0007022 0.0015122 0.6400000 0.6424168 0.054476 0.0880591 NA
22 51223637 rs375798137 G A -0.0006789 0.0015195 0.6600001 0.6550117 0.054106 0.0788738 NA
22 51229805 rs9616985 T C -0.0007610 0.0012896 0.5600000 0.5551446 0.073038 0.0730831 NA
22 51232488 rs376461333 A G -0.0020822 0.0030369 0.4899999 0.4929555 0.020043 NA NA
22 51237063 rs3896457 T C 0.0006947 0.0007886 0.3800004 0.3783613 0.297924 0.2050720 NA

bcf preview

1   49298   rs10399793  T   C   .   PASS    AF=0.623799 ES:SE:LP:AF:ID  -0.000648774:0.00118495:0.236572:0.623799:rs10399793
1   54676   rs2462492   C   T   .   PASS    AF=0.400435 ES:SE:LP:AF:ID  0.000573206:0.00117381:0.200659:0.400435:rs2462492
1   86028   rs114608975 T   C   .   PASS    AF=0.103546 ES:SE:LP:AF:ID  0.00179249:0.00187702:0.468521:0.103546:rs114608975
1   91536   rs6702460   G   T   .   PASS    AF=0.456844 ES:SE:LP:AF:ID  0.000401734:0.0011559:0.136677:0.456844:rs6702460
1   234313  rs8179466   C   T   .   PASS    AF=0.074511 ES:SE:LP:AF:ID  -0.000695734:0.00227915:0.119186:0.074511:rs8179466
1   534192  rs6680723   C   T   .   PASS    AF=0.240982 ES:SE:LP:AF:ID  -9.81894e-05:0.00132037:0.0268721:0.240982:rs6680723
1   546697  rs12025928  A   G   .   PASS    AF=0.91349  ES:SE:LP:AF:ID  -0.000107149:0.0016474:0.0222764:0.91349:rs12025928
1   693731  rs12238997  A   G   .   PASS    AF=0.11636  ES:SE:LP:AF:ID  0.00160942:0.00110614:0.823909:0.11636:rs12238997
1   705882  rs72631875  G   A   .   PASS    AF=0.067257 ES:SE:LP:AF:ID  -0.00267742:0.00162168:1.00436:0.067257:rs72631875
1   706368  rs12029736  A   G   .   PASS    AF=0.515625 ES:SE:LP:AF:ID  -0.000832225:0.000819666:0.508638:0.515625:rs12029736
1   714596  rs149887893 T   C   .   PASS    AF=0.032997 ES:SE:LP:AF:ID  0.00176454:0.00206658:0.408935:0.032997:rs149887893
1   715265  rs12184267  C   T   .   PASS    AF=0.036611 ES:SE:LP:AF:ID  0.00203128:0.00187718:0.552842:0.036611:rs12184267
1   715367  rs12184277  A   G   .   PASS    AF=0.036726 ES:SE:LP:AF:ID  0.0019937:0.00187011:0.537602:0.036726:rs12184277
1   717485  rs12184279  C   A   .   PASS    AF=0.036428 ES:SE:LP:AF:ID  0.00215162:0.0018835:0.60206:0.036428:rs12184279
1   717587  rs144155419 G   A   .   PASS    AF=0.016395 ES:SE:LP:AF:ID  -0.00154751:0.00290084:0.229148:0.016395:rs144155419
1   720381  rs116801199 G   T   .   PASS    AF=0.036967 ES:SE:LP:AF:ID  0.00213112:0.00186263:0.60206:0.036967:rs116801199
1   721290  rs12565286  G   C   .   PASS    AF=0.037066 ES:SE:LP:AF:ID  0.00220261:0.00185621:0.619789:0.037066:rs12565286
1   722670  rs116030099 T   C   .   PASS    AF=0.101202 ES:SE:LP:AF:ID  -0.000227321:0.00135224:0.0604807:0.101202:rs116030099
1   723891  rs2977670   G   C   .   PASS    AF=0.959115 ES:SE:LP:AF:ID  -0.00233064:0.00179051:0.721246:0.959115:rs2977670
1   724849  rs12126395  C   A   .   PASS    AF=0.031442 ES:SE:LP:AF:ID  -0.00316092:0.00325022:0.481486:0.031442:rs12126395
1   725060  rs865924913 A   T   .   PASS    AF=0.053274 ES:SE:LP:AF:ID  -0.00293067:0.0025837:0.585027:0.053274:rs865924913
1   726794  rs28454925  C   G   .   PASS    AF=0.036581 ES:SE:LP:AF:ID  0.00201336:0.0018683:0.552842:0.036581:rs28454925
1   729632  rs116720794 C   T   .   PASS    AF=0.036898 ES:SE:LP:AF:ID  0.00200928:0.00185123:0.552842:0.036898:rs116720794
1   729679  rs4951859   C   G   .   PASS    AF=0.8432   ES:SE:LP:AF:ID  -0.00189032:0.000958755:1.3098:0.8432:rs4951859
1   730087  rs148120343 T   C   .   PASS    AF=0.055952 ES:SE:LP:AF:ID  0.00293407:0.00155191:1.22915:0.055952:rs148120343
1   731718  rs58276399  T   C   .   PASS    AF=0.122336 ES:SE:LP:AF:ID  0.00173499:0.0010493:1.00877:0.122336:rs58276399
1   732989  rs369030935 C   T   .   PASS    AF=0.025701 ES:SE:LP:AF:ID  0.0026112:0.00258229:0.508638:0.025701:rs369030935
1   734349  rs141242758 T   C   .   PASS    AF=0.12158  ES:SE:LP:AF:ID  0.00176467:0.00104974:1.03152:0.12158:rs141242758
1   736289  rs79010578  T   A   .   PASS    AF=0.132365 ES:SE:LP:AF:ID  0.00168091:0.00103468:1:0.132365:rs79010578
1   736689  rs181876450 T   C   .   PASS    AF=0.011137 ES:SE:LP:AF:ID  -0.00141841:0.00376205:0.148742:0.011137:rs181876450
1   752478  rs146277091 G   A   .   PASS    AF=0.036812 ES:SE:LP:AF:ID  0.00204679:0.00183257:0.585027:0.036812:rs146277091
1   752566  rs3094315   G   A   .   PASS    AF=0.838931 ES:SE:LP:AF:ID  -0.00182874:0.000928514:1.3098:0.838931:rs3094315
1   752721  rs3131972   A   G   .   PASS    AF=0.838565 ES:SE:LP:AF:ID  -0.0017268:0.000927524:1.20066:0.838565:rs3131972
1   753405  rs3115860   C   A   .   PASS    AF=0.869755 ES:SE:LP:AF:ID  -0.00180336:0.000995233:1.1549:0.869755:rs3115860
1   753541  rs2073813   G   A   .   PASS    AF=0.129891 ES:SE:LP:AF:ID  0.00177443:0.00099727:1.12494:0.129891:rs2073813
1   754063  rs12184312  G   T   .   PASS    AF=0.037323 ES:SE:LP:AF:ID  0.00189581:0.00180149:0.537602:0.037323:rs12184312
1   754105  rs12184325  C   T   .   PASS    AF=0.037566 ES:SE:LP:AF:ID  0.00194244:0.00179011:0.552842:0.037566:rs12184325
1   754182  rs3131969   A   G   .   PASS    AF=0.869101 ES:SE:LP:AF:ID  -0.00177852:0.000993295:1.13668:0.869101:rs3131969
1   754192  rs3131968   A   G   .   PASS    AF=0.869199 ES:SE:LP:AF:ID  -0.00177411:0.00099369:1.13077:0.869199:rs3131968
1   754211  rs12184313  G   A   .   PASS    AF=0.037526 ES:SE:LP:AF:ID  0.00194057:0.00179782:0.552842:0.037526:rs12184313
1   754334  rs3131967   T   C   .   PASS    AF=0.869104 ES:SE:LP:AF:ID  -0.0017854:0.000993275:1.14267:0.869104:rs3131967
1   754503  rs3115859   G   A   .   PASS    AF=0.838014 ES:SE:LP:AF:ID  -0.00176107:0.00092493:1.24413:0.838014:rs3115859
1   754629  rs10454459  A   G   .   PASS    AF=0.037539 ES:SE:LP:AF:ID  0.00200313:0.00180035:0.568636:0.037539:rs10454459
1   754964  rs3131966   C   T   .   PASS    AF=0.838645 ES:SE:LP:AF:ID  -0.00180013:0.000927532:1.284:0.838645:rs3131966
1   755240  rs181660517 T   G   .   PASS    AF=0.013793 ES:SE:LP:AF:ID  0.00149664:0.00323576:0.19382:0.013793:rs181660517
1   755775  rs3131965   A   G   .   PASS    AF=0.839752 ES:SE:LP:AF:ID  -0.00195801:0.000940068:1.4318:0.839752:rs3131965
1   755890  rs3115858   A   T   .   PASS    AF=0.869378 ES:SE:LP:AF:ID  -0.00177857:0.000992113:1.13668:0.869378:rs3115858
1   756604  rs3131962   A   G   .   PASS    AF=0.868926 ES:SE:LP:AF:ID  -0.00174125:0.000989616:1.10791:0.868926:rs3131962
1   757640  rs3115853   G   A   .   PASS    AF=0.867883 ES:SE:LP:AF:ID  -0.00179536:0.000987723:1.16115:0.867883:rs3115853
1   757734  rs4951929   C   T   .   PASS    AF=0.869069 ES:SE:LP:AF:ID  -0.00173966:0.000990428:1.10237:0.869069:rs4951929