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-9942/UKB-b-9942_data.vcf.gz \
--ref-ld-chr ../reference/eur_w_ld_chr/ \
--out /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-9942/ldsc.txt \
--w-ld-chr ../reference/eur_w_ld_chr/ 

Beginning analysis at Thu Oct 17 14:43:08 2019
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-9942/UKB-b-9942_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: 0.0166 (0.0018)
Lambda GC: 1.308
Mean Chi^2: 1.3288
Intercept: 1.1801 (0.0083)
Ratio: 0.5479 (0.0253)
Analysis finished at Thu Oct 17 14:45:01 2019
Total time elapsed: 1.0m:52.42s

QC metrics

Metrics

Metrics

{
    "af_correlation": 0.9499,
    "inflation_factor": 1.2544,
    "mean_EFFECT": 0.0004,
    "n": "-Inf",
    "n_snps": 9851866,
    "n_clumped_hits": 8,
    "n_p_sig": 241,
    "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": 0.0166,
    "ldsc_observed_scale_h2_se": 0.0018,
    "ldsc_intercept_beta": 1.1801,
    "ldsc_intercept_se": 0.0083,
    "ldsc_lambda_gc": 1.308,
    "ldsc_mean_chisq": 1.3288,
    "ldsc_ratio": 0.5477
}

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 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 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 3.539000e-04 1.065600e-02 -0.1801910 -3.130500e-03 8.480000e-05 3.403000e-03 1.683280e-01 ▁▁▇▁▁
numeric SE 0 1.0000000 NA NA NA NA NA NA NA 7.057100e-03 6.680600e-03 0.0019749 2.417300e-03 4.053500e-03 9.353100e-03 1.038480e-01 ▇▁▁▁▁
numeric PVAL 0 1.0000000 NA NA NA NA NA NA NA 4.621149e-01 2.982307e-01 0.0000000 1.900002e-01 4.500005e-01 7.199992e-01 1.000000e+00 ▇▆▆▆▆
numeric PVAL_ztest 0 1.0000000 NA NA NA NA NA NA NA 4.621173e-01 2.982066e-01 0.0000000 1.944760e-01 4.471921e-01 7.210214e-01 9.999999e-01 ▇▆▆▆▆
numeric AF 0 1.0000000 NA NA NA NA NA NA NA 2.035075e-01 2.568621e-01 0.0009790 1.316800e-02 7.791200e-02 3.164550e-01 9.990120e-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 -0.0024123 0.0036319 0.5099998 0.5065549 0.623756 0.7821490 NA
1 54676 rs2462492 C T 0.0010561 0.0035988 0.7700005 0.7691675 0.400407 NA NA
1 86028 rs114608975 T C 0.0098809 0.0057542 0.0860003 0.0859459 0.103555 0.0277556 NA
1 91536 rs6702460 G T 0.0005817 0.0035428 0.8700001 0.8695833 0.456805 0.4207270 NA
1 234313 rs8179466 C T -0.0034035 0.0069832 0.6300007 0.6259817 0.074538 NA NA
1 534192 rs6680723 C T 0.0000055 0.0040466 1.0000000 0.9989140 0.240997 NA NA
1 546697 rs12025928 A G 0.0114949 0.0050508 0.0230001 0.0228546 0.913520 NA NA
1 693731 rs12238997 A G 0.0060707 0.0033904 0.0729995 0.0733670 0.116381 0.1417730 NA
1 705882 rs72631875 G A 0.0013061 0.0049726 0.7899998 0.7928167 0.067232 0.0315495 NA
1 706368 rs55727773 A G -0.0042099 0.0025128 0.0940005 0.0938575 0.515569 0.2751600 NA
CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
22 51219704 rs147475742 G A 0.0017653 0.0052787 0.7400005 0.7380626 0.041920 0.0473243 NA
22 51219766 rs182321900 C T 0.0390393 0.0246109 0.1100001 0.1126802 0.001934 NA NA
22 51220146 rs868950473 C T 0.0413930 0.0243847 0.0899995 0.0896024 0.001981 NA NA
22 51221190 rs369304721 G A 0.0045549 0.0052708 0.3900004 0.3874939 0.049688 NA NA
22 51221731 rs115055839 T C 0.0034046 0.0039407 0.3900004 0.3876115 0.073200 0.0625000 NA
22 51222100 rs114553188 G T 0.0013025 0.0046384 0.7800007 0.7788574 0.054461 0.0880591 NA
22 51223637 rs375798137 G A 0.0010933 0.0046607 0.8100000 0.8145421 0.054091 0.0788738 NA
22 51229805 rs9616985 T C 0.0030212 0.0039550 0.4400003 0.4449340 0.073035 0.0730831 NA
22 51232488 rs376461333 A G -0.0018473 0.0093149 0.8400000 0.8427961 0.020045 NA NA
22 51237063 rs3896457 T C -0.0033789 0.0024182 0.1600000 0.1623329 0.297983 0.2050720 NA

bcf preview

1   49298   rs10399793  T   C   .   PASS    AF=0.623756 ES:SE:LP:AF:ID  -0.00241233:0.00363187:0.29243:0.623756:rs10399793
1   54676   rs2462492   C   T   .   PASS    AF=0.400407 ES:SE:LP:AF:ID  0.00105613:0.00359884:0.113509:0.400407:rs2462492
1   86028   rs114608975 T   C   .   PASS    AF=0.103555 ES:SE:LP:AF:ID  0.00988094:0.00575416:1.0655:0.103555:rs114608975
1   91536   rs6702460   G   T   .   PASS    AF=0.456805 ES:SE:LP:AF:ID  0.000581686:0.00354281:0.0604807:0.456805:rs6702460
1   234313  rs8179466   C   T   .   PASS    AF=0.074538 ES:SE:LP:AF:ID  -0.00340353:0.00698317:0.200659:0.074538:rs8179466
1   534192  rs6680723   C   T   .   PASS    AF=0.240997 ES:SE:LP:AF:ID  5.50759e-06:0.00404656:-0:0.240997:rs6680723
1   546697  rs12025928  A   G   .   PASS    AF=0.91352  ES:SE:LP:AF:ID  0.0114949:0.0050508:1.63827:0.91352:rs12025928
1   693731  rs12238997  A   G   .   PASS    AF=0.116381 ES:SE:LP:AF:ID  0.00607074:0.00339045:1.13668:0.116381:rs12238997
1   705882  rs72631875  G   A   .   PASS    AF=0.067232 ES:SE:LP:AF:ID  0.00130609:0.00497265:0.102373:0.067232:rs72631875
1   706368  rs12029736  A   G   .   PASS    AF=0.515569 ES:SE:LP:AF:ID  -0.00420994:0.00251281:1.02687:0.515569:rs12029736
1   714596  rs149887893 T   C   .   PASS    AF=0.033    ES:SE:LP:AF:ID  0.010365:0.00633408:1:0.033:rs149887893
1   715265  rs12184267  C   T   .   PASS    AF=0.036611 ES:SE:LP:AF:ID  0.00907089:0.00575372:0.958607:0.036611:rs12184267
1   715367  rs12184277  A   G   .   PASS    AF=0.036726 ES:SE:LP:AF:ID  0.00880097:0.00573201:0.920819:0.036726:rs12184277
1   717485  rs12184279  C   A   .   PASS    AF=0.036422 ES:SE:LP:AF:ID  0.00818102:0.0057736:0.79588:0.036422:rs12184279
1   717587  rs144155419 G   A   .   PASS    AF=0.01643  ES:SE:LP:AF:ID  -0.0017603:0.00888044:0.0757207:0.01643:rs144155419
1   720381  rs116801199 G   T   .   PASS    AF=0.036964 ES:SE:LP:AF:ID  0.00868587:0.00570937:0.886057:0.036964:rs116801199
1   721290  rs12565286  G   C   .   PASS    AF=0.037061 ES:SE:LP:AF:ID  0.0081042:0.00568982:0.823909:0.037061:rs12565286
1   722670  rs116030099 T   C   .   PASS    AF=0.101221 ES:SE:LP:AF:ID  -0.00805212:0.00414494:1.284:0.101221:rs116030099
1   723891  rs2977670   G   C   .   PASS    AF=0.959116 ES:SE:LP:AF:ID  -0.0112883:0.00548823:1.39794:0.959116:rs2977670
1   724849  rs12126395  C   A   .   PASS    AF=0.031451 ES:SE:LP:AF:ID  -0.0132383:0.00995774:0.744727:0.031451:rs12126395
1   725060  rs865924913 A   T   .   PASS    AF=0.053252 ES:SE:LP:AF:ID  -0.0105345:0.00792517:0.744727:0.053252:rs865924913
1   726794  rs28454925  C   G   .   PASS    AF=0.036579 ES:SE:LP:AF:ID  0.00865111:0.00572674:0.886057:0.036579:rs28454925
1   729632  rs116720794 C   T   .   PASS    AF=0.0369   ES:SE:LP:AF:ID  0.00879108:0.00567426:0.920819:0.0369:rs116720794
1   729679  rs4951859   C   G   .   PASS    AF=0.843173 ES:SE:LP:AF:ID  -0.00718441:0.0029386:1.85387:0.843173:rs4951859
1   730087  rs148120343 T   C   .   PASS    AF=0.055948 ES:SE:LP:AF:ID  0.00455181:0.00475708:0.468521:0.055948:rs148120343
1   731718  rs58276399  T   C   .   PASS    AF=0.12237  ES:SE:LP:AF:ID  0.00515214:0.00321611:0.958607:0.12237:rs58276399
1   732989  rs369030935 C   T   .   PASS    AF=0.025756 ES:SE:LP:AF:ID  0.00383126:0.00790673:0.200659:0.025756:rs369030935
1   734349  rs141242758 T   C   .   PASS    AF=0.121613 ES:SE:LP:AF:ID  0.00529863:0.00321742:1:0.121613:rs141242758
1   736289  rs79010578  T   A   .   PASS    AF=0.132352 ES:SE:LP:AF:ID  0.00773405:0.00317153:1.82391:0.132352:rs79010578
1   736689  rs181876450 T   C   .   PASS    AF=0.011107 ES:SE:LP:AF:ID  0.0146464:0.0115513:0.69897:0.011107:rs181876450
1   740284  rs61770167  C   T   .   PASS    AF=0.005704 ES:SE:LP:AF:ID  0.0108317:0.0148813:0.327902:0.005704:rs61770167
1   742813  rs112573343 C   T   .   PASS    AF=0.002262 ES:SE:LP:AF:ID  0.0260475:0.0250697:0.522879:0.002262:rs112573343
1   746189  rs139221807 A   G   .   PASS    AF=0.001028 ES:SE:LP:AF:ID  0.051728:0.0410432:0.677781:0.001028:rs139221807
1   752478  rs146277091 G   A   .   PASS    AF=0.036814 ES:SE:LP:AF:ID  0.00851678:0.00561689:0.886057:0.036814:rs146277091
1   752566  rs3094315   G   A   .   PASS    AF=0.838895 ES:SE:LP:AF:ID  -0.00823575:0.00284569:2.42022:0.838895:rs3094315
1   752721  rs3131972   A   G   .   PASS    AF=0.838528 ES:SE:LP:AF:ID  -0.00833586:0.00284266:2.46852:0.838528:rs3131972
1   753405  rs3115860   C   A   .   PASS    AF=0.869711 ES:SE:LP:AF:ID  -0.00687257:0.00304998:1.61979:0.869711:rs3115860
1   753541  rs2073813   G   A   .   PASS    AF=0.129936 ES:SE:LP:AF:ID  0.00711323:0.00305627:1.69897:0.129936:rs2073813
1   754063  rs12184312  G   T   .   PASS    AF=0.037328 ES:SE:LP:AF:ID  0.00767942:0.0055213:0.79588:0.037328:rs12184312
1   754105  rs12184325  C   T   .   PASS    AF=0.037572 ES:SE:LP:AF:ID  0.00748108:0.00548633:0.769551:0.037572:rs12184325
1   754182  rs3131969   A   G   .   PASS    AF=0.869056 ES:SE:LP:AF:ID  -0.00701143:0.00304407:1.67778:0.869056:rs3131969
1   754192  rs3131968   A   G   .   PASS    AF=0.869154 ES:SE:LP:AF:ID  -0.0068746:0.00304528:1.61979:0.869154:rs3131968
1   754211  rs12184313  G   A   .   PASS    AF=0.037531 ES:SE:LP:AF:ID  0.0077426:0.00551006:0.79588:0.037531:rs12184313
1   754334  rs3131967   T   C   .   PASS    AF=0.86906  ES:SE:LP:AF:ID  -0.00701043:0.00304402:1.67778:0.86906:rs3131967
1   754433  rs150578204 G   A   .   PASS    AF=0.005128 ES:SE:LP:AF:ID  0.0173203:0.0156229:0.568636:0.005128:rs150578204
1   754458  rs142682604 G   T   .   PASS    AF=0.005094 ES:SE:LP:AF:ID  0.0158324:0.0156642:0.508638:0.005094:rs142682604
1   754503  rs3115859   G   A   .   PASS    AF=0.837976 ES:SE:LP:AF:ID  -0.00808271:0.00283469:2.35655:0.837976:rs3115859
1   754629  rs10454459  A   G   .   PASS    AF=0.037544 ES:SE:LP:AF:ID  0.00773155:0.00551786:0.79588:0.037544:rs10454459
1   754964  rs3131966   C   T   .   PASS    AF=0.838606 ES:SE:LP:AF:ID  -0.00809173:0.00284264:2.35655:0.838606:rs3131966
1   755240  rs181660517 T   G   .   PASS    AF=0.013775 ES:SE:LP:AF:ID  -0.00891723:0.00992295:0.431798:0.013775:rs181660517