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-7992/UKB-b-7992_data.vcf.gz \
--ref-ld-chr ../reference/eur_w_ld_chr/ \
--out /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-7992/ldsc.txt \
--w-ld-chr ../reference/eur_w_ld_chr/ 

Beginning analysis at Thu Oct 17 14:41:05 2019
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-7992/UKB-b-7992_data.vcf.gz ...
Read summary statistics for 9851866 SNPs.
Dropped 14738 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, 1289166 SNPs remain.
After merging with regression SNP LD, 1289166 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.1291 (0.0046)
Lambda GC: 1.8057
Mean Chi^2: 2.2684
Intercept: 1.1228 (0.0146)
Ratio: 0.0968 (0.0115)
Analysis finished at Thu Oct 17 14:42:52 2019
Total time elapsed: 1.0m:46.9s

QC metrics

Metrics

Metrics

{
    "af_correlation": 0.9499,
    "inflation_factor": 1.4921,
    "mean_EFFECT": -0,
    "n": "-Inf",
    "n_snps": 9851866,
    "n_clumped_hits": 263,
    "n_p_sig": 32713,
    "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": 184849,
    "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": 1289166,
    "ldsc_nsnp_merge_regression_ld": 1289166,
    "ldsc_observed_scale_h2_beta": 0.1291,
    "ldsc_observed_scale_h2_se": 0.0046,
    "ldsc_intercept_beta": 1.1228,
    "ldsc_intercept_se": 0.0146,
    "ldsc_lambda_gc": 1.8057,
    "ldsc_mean_chisq": 2.2684,
    "ldsc_ratio": 0.0968
}

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 9837196 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 9851866 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 8.622825e+00 5.748290e+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 7.886027e+07 5.628334e+07 828.0000000 3.259061e+07 6.948835e+07 1.145912e+08 2.492385e+08 ▇▆▅▂▁
numeric EFFECT 0 1.0000000 NA NA NA NA NA NA NA -2.830000e-05 1.067800e-02 -0.1696960 -3.801900e-03 -3.000000e-06 3.759100e-03 1.582790e-01 ▁▁▇▁▁
numeric SE 0 1.0000000 NA NA NA NA NA NA NA 7.128300e-03 6.739300e-03 0.0019952 2.443400e-03 4.097000e-03 9.452000e-03 1.048210e-01 ▇▁▁▁▁
numeric PVAL 0 1.0000000 NA NA NA NA NA NA NA 4.317446e-01 3.063676e-01 0.0000000 1.499999e-01 4.100001e-01 6.999999e-01 1.000000e+00 ▇▅▅▅▅
numeric PVAL_ztest 0 1.0000000 NA NA NA NA NA NA NA 4.317451e-01 3.063440e-01 0.0000000 1.492703e-01 4.056981e-01 6.968797e-01 9.999999e-01 ▇▅▅▅▅
numeric AF 0 1.0000000 NA NA NA NA NA NA NA 2.035090e-01 2.568554e-01 0.0009400 1.317300e-02 7.792100e-02 3.164490e-01 9.990220e-01 ▇▂▁▁▁
numeric AF_reference 184849 0.9812372 NA NA NA NA NA NA NA 2.068392e-01 2.482924e-01 0.0000000 1.198080e-02 9.984030e-02 3.202880e-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 -0.0032477 0.0036709 0.3800004 0.3763159 0.623964 0.7821490 NA
1 54676 rs2462492 C T 0.0057167 0.0036347 0.1199999 0.1157650 0.400339 NA NA
1 86028 rs114608975 T C 0.0104748 0.0058196 0.0719996 0.0718732 0.103469 0.0277556 NA
1 91536 rs6702460 G T 0.0040375 0.0035795 0.2599998 0.2593377 0.456860 0.4207270 NA
1 234313 rs8179466 C T -0.0017145 0.0070561 0.8100000 0.8080169 0.074567 NA NA
1 534192 rs6680723 C T -0.0038311 0.0040903 0.3500000 0.3489486 0.240920 NA NA
1 546697 rs12025928 A G -0.0059826 0.0050957 0.2399999 0.2403697 0.913351 NA NA
1 693731 rs12238997 A G -0.0013499 0.0034214 0.6899999 0.6931844 0.116609 0.1417730 NA
1 705882 rs72631875 G A 0.0091156 0.0050179 0.0690001 0.0692778 0.067340 0.0315495 NA
1 706368 rs55727773 A G 0.0049962 0.0025378 0.0490004 0.0489870 0.515645 0.2751600 NA
CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
22 51219704 rs147475742 G A 0.0020923 0.0053486 0.6999999 0.6956660 0.041823 0.0473243 NA
22 51219766 rs182321900 C T 0.0111884 0.0247879 0.6499995 0.6517262 0.001950 NA NA
22 51220146 rs868950473 C T 0.0107128 0.0245523 0.6600001 0.6626004 0.001999 NA NA
22 51221190 rs369304721 G A -0.0020647 0.0053424 0.6999999 0.6991537 0.049531 NA NA
22 51221731 rs115055839 T C -0.0004984 0.0039942 0.9000000 0.9007064 0.072972 0.0625000 NA
22 51222100 rs114553188 G T 0.0014929 0.0046877 0.7499995 0.7501324 0.054572 0.0880591 NA
22 51223637 rs375798137 G A 0.0013695 0.0047103 0.7700005 0.7712430 0.054202 0.0788738 NA
22 51229805 rs9616985 T C -0.0004657 0.0040083 0.9100000 0.9075067 0.072823 0.0730831 NA
22 51232488 rs376461333 A G -0.0005504 0.0094156 0.9500000 0.9533839 0.020095 NA NA
22 51237063 rs3896457 T C 0.0039160 0.0024473 0.1100001 0.1095730 0.297841 0.2050720 NA

bcf preview

1   49298   rs10399793  T   C   .   PASS    AF=0.623964 ES:SE:LP:AF:ID  -0.00324768:0.00367092:0.420216:0.623964:rs10399793
1   54676   rs2462492   C   T   .   PASS    AF=0.400339 ES:SE:LP:AF:ID  0.00571669:0.00363472:0.920819:0.400339:rs2462492
1   86028   rs114608975 T   C   .   PASS    AF=0.103469 ES:SE:LP:AF:ID  0.0104748:0.00581959:1.14267:0.103469:rs114608975
1   91536   rs6702460   G   T   .   PASS    AF=0.45686  ES:SE:LP:AF:ID  0.00403748:0.00357946:0.585027:0.45686:rs6702460
1   234313  rs8179466   C   T   .   PASS    AF=0.074567 ES:SE:LP:AF:ID  -0.00171453:0.00705611:0.091515:0.074567:rs8179466
1   534192  rs6680723   C   T   .   PASS    AF=0.24092  ES:SE:LP:AF:ID  -0.0038311:0.0040903:0.455932:0.24092:rs6680723
1   546697  rs12025928  A   G   .   PASS    AF=0.913351 ES:SE:LP:AF:ID  -0.00598265:0.00509568:0.619789:0.913351:rs12025928
1   693731  rs12238997  A   G   .   PASS    AF=0.116609 ES:SE:LP:AF:ID  -0.00134987:0.0034214:0.161151:0.116609:rs12238997
1   705882  rs72631875  G   A   .   PASS    AF=0.06734  ES:SE:LP:AF:ID  0.00911559:0.00501793:1.16115:0.06734:rs72631875
1   706368  rs12029736  A   G   .   PASS    AF=0.515645 ES:SE:LP:AF:ID  0.00499616:0.00253779:1.3098:0.515645:rs12029736
1   714596  rs149887893 T   C   .   PASS    AF=0.033052 ES:SE:LP:AF:ID  -0.0056406:0.006393:0.420216:0.033052:rs149887893
1   715265  rs12184267  C   T   .   PASS    AF=0.036674 ES:SE:LP:AF:ID  -0.00485031:0.00580658:0.39794:0.036674:rs12184267
1   715367  rs12184277  A   G   .   PASS    AF=0.036796 ES:SE:LP:AF:ID  -0.00487129:0.00578383:0.39794:0.036796:rs12184277
1   717485  rs12184279  C   A   .   PASS    AF=0.036492 ES:SE:LP:AF:ID  -0.0048795:0.00582581:0.39794:0.036492:rs12184279
1   717587  rs144155419 G   A   .   PASS    AF=0.016423 ES:SE:LP:AF:ID  0.000292984:0.00897473:0.0132283:0.016423:rs144155419
1   720381  rs116801199 G   T   .   PASS    AF=0.037034 ES:SE:LP:AF:ID  -0.0051361:0.00576127:0.431798:0.037034:rs116801199
1   721290  rs12565286  G   C   .   PASS    AF=0.037127 ES:SE:LP:AF:ID  -0.00460164:0.00574194:0.376751:0.037127:rs12565286
1   722670  rs116030099 T   C   .   PASS    AF=0.101398 ES:SE:LP:AF:ID  -0.00200691:0.00418236:0.200659:0.101398:rs116030099
1   723891  rs2977670   G   C   .   PASS    AF=0.958985 ES:SE:LP:AF:ID  0.00437377:0.00553466:0.366532:0.958985:rs2977670
1   724849  rs12126395  C   A   .   PASS    AF=0.031554 ES:SE:LP:AF:ID  -0.0029536:0.0100297:0.113509:0.031554:rs12126395
1   725060  rs865924913 A   T   .   PASS    AF=0.053101 ES:SE:LP:AF:ID  0.00614739:0.00802638:0.356547:0.053101:rs865924913
1   726794  rs28454925  C   G   .   PASS    AF=0.036653 ES:SE:LP:AF:ID  -0.00512387:0.00577807:0.420216:0.036653:rs28454925
1   729632  rs116720794 C   T   .   PASS    AF=0.036969 ES:SE:LP:AF:ID  -0.00537771:0.00572584:0.455932:0.036969:rs116720794
1   729679  rs4951859   C   G   .   PASS    AF=0.842837 ES:SE:LP:AF:ID  0.00399784:0.0029656:0.744727:0.842837:rs4951859
1   730087  rs148120343 T   C   .   PASS    AF=0.056026 ES:SE:LP:AF:ID  0.000414838:0.00480297:0.0315171:0.056026:rs148120343
1   731718  rs58276399  T   C   .   PASS    AF=0.122593 ES:SE:LP:AF:ID  -0.00263013:0.00324582:0.376751:0.122593:rs58276399
1   732989  rs369030935 C   T   .   PASS    AF=0.025653 ES:SE:LP:AF:ID  0.00538542:0.00800052:0.30103:0.025653:rs369030935
1   734349  rs141242758 T   C   .   PASS    AF=0.121836 ES:SE:LP:AF:ID  -0.00251577:0.0032472:0.356547:0.121836:rs141242758
1   736289  rs79010578  T   A   .   PASS    AF=0.132628 ES:SE:LP:AF:ID  -0.00367653:0.00320128:0.60206:0.132628:rs79010578
1   736689  rs181876450 T   C   .   PASS    AF=0.011113 ES:SE:LP:AF:ID  0.0167455:0.0116637:0.823909:0.011113:rs181876450
1   740284  rs61770167  C   T   .   PASS    AF=0.005767 ES:SE:LP:AF:ID  -0.0231453:0.0149389:0.920819:0.005767:rs61770167
1   742813  rs112573343 C   T   .   PASS    AF=0.00229  ES:SE:LP:AF:ID  0.00926641:0.0251656:0.148742:0.00229:rs112573343
1   746189  rs139221807 A   G   .   PASS    AF=0.001038 ES:SE:LP:AF:ID  -0.0500789:0.0412331:0.657577:0.001038:rs139221807
1   752478  rs146277091 G   A   .   PASS    AF=0.036891 ES:SE:LP:AF:ID  -0.00544188:0.00566738:0.468521:0.036891:rs146277091
1   752566  rs3094315   G   A   .   PASS    AF=0.83857  ES:SE:LP:AF:ID  0.00540327:0.00287212:1.22185:0.83857:rs3094315
1   752721  rs3131972   A   G   .   PASS    AF=0.838187 ES:SE:LP:AF:ID  0.00549261:0.00286894:1.25181:0.838187:rs3131972
1   753405  rs3115860   C   A   .   PASS    AF=0.869441 ES:SE:LP:AF:ID  0.00396528:0.00307779:0.69897:0.869441:rs3115860
1   753541  rs2073813   G   A   .   PASS    AF=0.13021  ES:SE:LP:AF:ID  -0.00402717:0.00308411:0.721246:0.13021:rs2073813
1   754063  rs12184312  G   T   .   PASS    AF=0.037398 ES:SE:LP:AF:ID  -0.00529874:0.00557139:0.468521:0.037398:rs12184312
1   754105  rs12184325  C   T   .   PASS    AF=0.037643 ES:SE:LP:AF:ID  -0.0052741:0.00553621:0.468521:0.037643:rs12184325
1   754182  rs3131969   A   G   .   PASS    AF=0.868765 ES:SE:LP:AF:ID  0.00397939:0.0030716:0.69897:0.868765:rs3131969
1   754192  rs3131968   A   G   .   PASS    AF=0.868866 ES:SE:LP:AF:ID  0.00396691:0.00307283:0.69897:0.868866:rs3131968
1   754211  rs12184313  G   A   .   PASS    AF=0.037601 ES:SE:LP:AF:ID  -0.00516874:0.00556021:0.455932:0.037601:rs12184313
1   754334  rs3131967   T   C   .   PASS    AF=0.868767 ES:SE:LP:AF:ID  0.00393611:0.0030715:0.69897:0.868767:rs3131967
1   754433  rs150578204 G   A   .   PASS    AF=0.005156 ES:SE:LP:AF:ID  -0.0421982:0.0157377:2.13668:0.005156:rs150578204
1   754458  rs142682604 G   T   .   PASS    AF=0.005122 ES:SE:LP:AF:ID  -0.0412975:0.0157785:2.05061:0.005122:rs142682604
1   754503  rs3115859   G   A   .   PASS    AF=0.837632 ES:SE:LP:AF:ID  0.00539872:0.00286085:1.22915:0.837632:rs3115859
1   754629  rs10454459  A   G   .   PASS    AF=0.037613 ES:SE:LP:AF:ID  -0.00563364:0.00556822:0.508638:0.037613:rs10454459
1   754964  rs3131966   C   T   .   PASS    AF=0.838264 ES:SE:LP:AF:ID  0.00550945:0.00286888:1.25964:0.838264:rs3131966
1   755240  rs181660517 T   G   .   PASS    AF=0.013667 ES:SE:LP:AF:ID  -2.885e-05:0.0100677:-0:0.013667:rs181660517