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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    "FORMAT.1": "<ID=SE,Number=A,Type=Float,Description=\"Standard error of effect size estimate\">",
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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-19206/UKB-b-19206_data.vcf.gz \
--ref-ld-chr ../reference/eur_w_ld_chr/ \
--out /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-19206/ldsc.txt \
--w-ld-chr ../reference/eur_w_ld_chr/ 

Beginning analysis at Thu Oct 17 14:41:09 2019
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-19206/UKB-b-19206_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: 0.011 (0.0013)
Lambda GC: 1.1046
Mean Chi^2: 1.1108
Intercept: 1.0106 (0.0069)
Ratio: 0.0953 (0.0622)
Analysis finished at Thu Oct 17 14:43:00 2019
Total time elapsed: 1.0m:50.74s

QC metrics

Metrics

Metrics

{
    "af_correlation": 0.9499,
    "inflation_factor": 1.0966,
    "mean_EFFECT": -0,
    "n": "-Inf",
    "n_snps": 9851866,
    "n_clumped_hits": 2,
    "n_p_sig": 6,
    "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": 0.011,
    "ldsc_observed_scale_h2_se": 0.0013,
    "ldsc_intercept_beta": 1.0106,
    "ldsc_intercept_se": 0.0069,
    "ldsc_lambda_gc": 1.1046,
    "ldsc_mean_chisq": 1.1108,
    "ldsc_ratio": 0.0957
}

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 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 -3.150000e-05 5.332000e-03 -0.0783686 -1.637600e-03 -4.200000e-06 1.617600e-03 8.412510e-02 ▁▁▇▁▁
numeric SE 0 1.0000000 NA NA NA NA NA NA NA 3.826600e-03 3.621800e-03 0.0010707 1.310800e-03 2.198100e-03 5.071900e-03 5.629010e-02 ▇▁▁▁▁
numeric PVAL 0 1.0000000 NA NA NA NA NA NA NA 4.884620e-01 2.916903e-01 0.0000000 2.300001e-01 4.799997e-01 7.400005e-01 1.000000e+00 ▇▇▇▇▇
numeric PVAL_ztest 0 1.0000000 NA NA NA NA NA NA NA 4.884632e-01 2.916637e-01 0.0000000 2.331822e-01 4.844007e-01 7.409371e-01 9.999999e-01 ▇▇▇▇▇
numeric AF 0 1.0000000 NA NA NA NA NA NA NA 2.035077e-01 2.568614e-01 0.0009920 1.317000e-02 7.791500e-02 3.164530e-01 9.990020e-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 -0.0001888 0.0019703 0.9199999 0.9236777 0.623761 0.7821490 NA
1 54676 rs2462492 C T 0.0010920 0.0019520 0.5800000 0.5758545 0.400409 NA NA
1 86028 rs114608975 T C 0.0004539 0.0031207 0.8800001 0.8843672 0.103556 0.0277556 NA
1 91536 rs6702460 G T 0.0005980 0.0019220 0.7600007 0.7557056 0.456850 0.4207270 NA
1 234313 rs8179466 C T -0.0003294 0.0037899 0.9299999 0.9307289 0.074500 NA NA
1 534192 rs6680723 C T -0.0018325 0.0021954 0.4000000 0.4038812 0.240950 NA NA
1 546697 rs12025928 A G 0.0005380 0.0027386 0.8400000 0.8442637 0.913463 NA NA
1 693731 rs12238997 A G -0.0005247 0.0018400 0.7800007 0.7755128 0.116301 0.1417730 NA
1 705882 rs72631875 G A -0.0002532 0.0026960 0.9299999 0.9251728 0.067289 0.0315495 NA
1 706368 rs55727773 A G 0.0031334 0.0013628 0.0210000 0.0214945 0.515661 0.2751600 NA
CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
22 51219704 rs147475742 G A 0.0019322 0.0028596 0.5000000 0.4992456 0.041960 0.0473243 NA
22 51219766 rs182321900 C T -0.0052719 0.0133231 0.6899999 0.6923281 0.001938 NA NA
22 51220146 rs868950473 C T -0.0076206 0.0131974 0.5600000 0.5636457 0.001986 NA NA
22 51221190 rs369304721 G A 0.0009103 0.0028550 0.7499995 0.7498415 0.049736 NA NA
22 51221731 rs115055839 T C 0.0001519 0.0021353 0.9400001 0.9432775 0.073245 0.0625000 NA
22 51222100 rs114553188 G T 0.0006669 0.0025142 0.7899998 0.7908076 0.054460 0.0880591 NA
22 51223637 rs375798137 G A 0.0006277 0.0025264 0.8000000 0.8037817 0.054089 0.0788738 NA
22 51229805 rs9616985 T C 0.0003241 0.0021431 0.8800001 0.8797886 0.073080 0.0730831 NA
22 51232488 rs376461333 A G -0.0003248 0.0050488 0.9500000 0.9487064 0.020043 NA NA
22 51237063 rs3896457 T C 0.0010737 0.0013109 0.4100001 0.4127404 0.297934 0.2050720 NA

bcf preview

1   49298   rs10399793  T   C   .   PASS    AF=0.623761 ES:SE:LP:AF:ID  -0.000188759:0.0019703:0.0362122:0.623761:rs10399793
1   54676   rs2462492   C   T   .   PASS    AF=0.400409 ES:SE:LP:AF:ID  0.00109203:0.00195197:0.236572:0.400409:rs2462492
1   86028   rs114608975 T   C   .   PASS    AF=0.103556 ES:SE:LP:AF:ID  0.000453863:0.00312072:0.0555173:0.103556:rs114608975
1   91536   rs6702460   G   T   .   PASS    AF=0.45685  ES:SE:LP:AF:ID  0.000597973:0.00192197:0.119186:0.45685:rs6702460
1   234313  rs8179466   C   T   .   PASS    AF=0.0745   ES:SE:LP:AF:ID  -0.000329447:0.00378989:0.0315171:0.0745:rs8179466
1   534192  rs6680723   C   T   .   PASS    AF=0.24095  ES:SE:LP:AF:ID  -0.00183248:0.00219535:0.39794:0.24095:rs6680723
1   546697  rs12025928  A   G   .   PASS    AF=0.913463 ES:SE:LP:AF:ID  0.000537972:0.00273857:0.0757207:0.913463:rs12025928
1   693731  rs12238997  A   G   .   PASS    AF=0.116301 ES:SE:LP:AF:ID  -0.000524707:0.00183997:0.107905:0.116301:rs12238997
1   705882  rs72631875  G   A   .   PASS    AF=0.067289 ES:SE:LP:AF:ID  -0.000253206:0.00269598:0.0315171:0.067289:rs72631875
1   706368  rs12029736  A   G   .   PASS    AF=0.515661 ES:SE:LP:AF:ID  0.00313342:0.00136284:1.67778:0.515661:rs12029736
1   714596  rs149887893 T   C   .   PASS    AF=0.033    ES:SE:LP:AF:ID  -0.00896719:0.00343602:2.04096:0.033:rs149887893
1   715265  rs12184267  C   T   .   PASS    AF=0.036616 ES:SE:LP:AF:ID  -0.00801041:0.00312103:2:0.036616:rs12184267
1   715367  rs12184277  A   G   .   PASS    AF=0.036733 ES:SE:LP:AF:ID  -0.00779823:0.00310916:1.92082:0.036733:rs12184277
1   717485  rs12184279  C   A   .   PASS    AF=0.03643  ES:SE:LP:AF:ID  -0.00788372:0.00313167:1.92082:0.03643:rs12184279
1   717587  rs144155419 G   A   .   PASS    AF=0.016401 ES:SE:LP:AF:ID  -0.00484946:0.00482278:0.508638:0.016401:rs144155419
1   720381  rs116801199 G   T   .   PASS    AF=0.036969 ES:SE:LP:AF:ID  -0.00782176:0.00309698:1.92082:0.036969:rs116801199
1   721290  rs12565286  G   C   .   PASS    AF=0.037066 ES:SE:LP:AF:ID  -0.00789478:0.00308635:1.95861:0.037066:rs12565286
1   722670  rs116030099 T   C   .   PASS    AF=0.101195 ES:SE:LP:AF:ID  -0.0025743:0.00224859:0.60206:0.101195:rs116030099
1   723891  rs2977670   G   C   .   PASS    AF=0.959103 ES:SE:LP:AF:ID  0.00777325:0.00297681:2.04576:0.959103:rs2977670
1   724849  rs12126395  C   A   .   PASS    AF=0.03145  ES:SE:LP:AF:ID  -0.00255007:0.00540325:0.19382:0.03145:rs12126395
1   725060  rs865924913 A   T   .   PASS    AF=0.053253 ES:SE:LP:AF:ID  0.00574635:0.00429866:0.744727:0.053253:rs865924913
1   726794  rs28454925  C   G   .   PASS    AF=0.036586 ES:SE:LP:AF:ID  -0.00817531:0.00310625:2.07058:0.036586:rs28454925
1   729632  rs116720794 C   T   .   PASS    AF=0.036901 ES:SE:LP:AF:ID  -0.00783316:0.00307801:1.95861:0.036901:rs116720794
1   729679  rs4951859   C   G   .   PASS    AF=0.843239 ES:SE:LP:AF:ID  0.00319885:0.00159452:1.34679:0.843239:rs4951859
1   730087  rs148120343 T   C   .   PASS    AF=0.055905 ES:SE:LP:AF:ID  -0.00186494:0.0025817:0.327902:0.055905:rs148120343
1   731718  rs58276399  T   C   .   PASS    AF=0.122282 ES:SE:LP:AF:ID  -0.001133:0.00174537:0.283997:0.122282:rs58276399
1   732989  rs369030935 C   T   .   PASS    AF=0.025718 ES:SE:LP:AF:ID  0.00927982:0.00429247:1.50864:0.025718:rs369030935
1   734349  rs141242758 T   C   .   PASS    AF=0.121524 ES:SE:LP:AF:ID  -0.00114293:0.00174611:0.29243:0.121524:rs141242758
1   736289  rs79010578  T   A   .   PASS    AF=0.132312 ES:SE:LP:AF:ID  -0.00308174:0.0017209:1.13668:0.132312:rs79010578
1   736689  rs181876450 T   C   .   PASS    AF=0.011138 ES:SE:LP:AF:ID  0.00108499:0.00625587:0.0655015:0.011138:rs181876450
1   740284  rs61770167  C   T   .   PASS    AF=0.005695 ES:SE:LP:AF:ID  0.0115075:0.00807991:0.823909:0.005695:rs61770167
1   742813  rs112573343 C   T   .   PASS    AF=0.002272 ES:SE:LP:AF:ID  -0.0226149:0.0135717:1.01773:0.002272:rs112573343
1   746189  rs139221807 A   G   .   PASS    AF=0.001029 ES:SE:LP:AF:ID  0.00173829:0.0222385:0.0268721:0.001029:rs139221807
1   752478  rs146277091 G   A   .   PASS    AF=0.036817 ES:SE:LP:AF:ID  -0.00792642:0.00304687:2.03152:0.036817:rs146277091
1   752566  rs3094315   G   A   .   PASS    AF=0.83898  ES:SE:LP:AF:ID  0.00361764:0.00154419:1.72125:0.83898:rs3094315
1   752721  rs3131972   A   G   .   PASS    AF=0.838611 ES:SE:LP:AF:ID  0.00347126:0.00154253:1.61979:0.838611:rs3131972
1   753405  rs3115860   C   A   .   PASS    AF=0.869809 ES:SE:LP:AF:ID  0.00185792:0.00165524:0.585027:0.869809:rs3115860
1   753541  rs2073813   G   A   .   PASS    AF=0.129838 ES:SE:LP:AF:ID  -0.0013266:0.00165865:0.376751:0.129838:rs2073813
1   754063  rs12184312  G   T   .   PASS    AF=0.037328 ES:SE:LP:AF:ID  -0.00795631:0.0029952:2.10237:0.037328:rs12184312
1   754105  rs12184325  C   T   .   PASS    AF=0.037572 ES:SE:LP:AF:ID  -0.00776875:0.00297631:2.04576:0.037572:rs12184325
1   754182  rs3131969   A   G   .   PASS    AF=0.869154 ES:SE:LP:AF:ID  0.00163476:0.00165201:0.49485:0.869154:rs3131969
1   754192  rs3131968   A   G   .   PASS    AF=0.869252 ES:SE:LP:AF:ID  0.00156518:0.00165266:0.468521:0.869252:rs3131968
1   754211  rs12184313  G   A   .   PASS    AF=0.037528 ES:SE:LP:AF:ID  -0.00792059:0.00298924:2.09152:0.037528:rs12184313
1   754334  rs3131967   T   C   .   PASS    AF=0.869156 ES:SE:LP:AF:ID  0.00163917:0.00165197:0.49485:0.869156:rs3131967
1   754433  rs150578204 G   A   .   PASS    AF=0.005119 ES:SE:LP:AF:ID  -0.00687932:0.00848377:0.376751:0.005119:rs150578204
1   754458  rs142682604 G   T   .   PASS    AF=0.005085 ES:SE:LP:AF:ID  -0.00703673:0.00850599:0.387216:0.005085:rs142682604
1   754503  rs3115859   G   A   .   PASS    AF=0.838064 ES:SE:LP:AF:ID  0.00341571:0.00153825:1.58503:0.838064:rs3115859
1   754629  rs10454459  A   G   .   PASS    AF=0.037541 ES:SE:LP:AF:ID  -0.00811572:0.00299346:2.17393:0.037541:rs10454459
1   754964  rs3131966   C   T   .   PASS    AF=0.838695 ES:SE:LP:AF:ID  0.00342968:0.00154258:1.58503:0.838695:rs3131966
1   755240  rs181660517 T   G   .   PASS    AF=0.013769 ES:SE:LP:AF:ID  0.00116771:0.005385:0.0809219:0.013769:rs181660517