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-2134/UKB-b-2134_data.vcf.gz \
--ref-ld-chr ../reference/eur_w_ld_chr/ \
--out /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-2134/ldsc.txt \
--w-ld-chr ../reference/eur_w_ld_chr/ 

Beginning analysis at Thu Oct 17 14:42:18 2019
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-2134/UKB-b-2134_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: 0.0875 (0.0032)
Lambda GC: 1.575
Mean Chi^2: 1.7931
Intercept: 1.0531 (0.01)
Ratio: 0.0669 (0.0126)
Analysis finished at Thu Oct 17 14:44:10 2019
Total time elapsed: 1.0m:51.68s

QC metrics

Metrics

Metrics

{
    "af_correlation": 0.9499,
    "inflation_factor": 1.369,
    "mean_EFFECT": 0,
    "n": "-Inf",
    "n_snps": 9851866,
    "n_clumped_hits": 101,
    "n_p_sig": 7263,
    "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": 0.0875,
    "ldsc_observed_scale_h2_se": 0.0032,
    "ldsc_intercept_beta": 1.0531,
    "ldsc_intercept_se": 0.01,
    "ldsc_lambda_gc": 1.575,
    "ldsc_mean_chisq": 1.7931,
    "ldsc_ratio": 0.067
}

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 1.780000e-05 1.352380e-02 -0.1947020 -4.676700e-03 -1.580000e-05 4.658800e-03 3.114390e-01 ▁▇▂▁▁
numeric SE 0 1.0000000 NA NA NA NA NA NA NA 9.291200e-03 8.802200e-03 0.0026001 3.181500e-03 5.335300e-03 1.231030e-02 1.365330e-01 ▇▁▁▁▁
numeric PVAL 0 1.0000000 NA NA NA NA NA NA NA 4.465817e-01 3.028027e-01 0.0000000 1.700000e-01 4.299995e-01 7.099994e-01 1.000000e+00 ▇▆▆▅▅
numeric PVAL_ztest 0 1.0000000 NA NA NA NA NA NA NA 4.465831e-01 3.027795e-01 0.0000000 1.709303e-01 4.271658e-01 7.087889e-01 9.999998e-01 ▇▆▅▅▅
numeric AF 0 1.0000000 NA NA NA NA NA NA NA 2.035067e-01 2.568663e-01 0.0009510 1.316700e-02 7.790500e-02 3.164410e-01 9.990400e-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 -0.0092439 0.0047781 0.0530005 0.0530353 0.623870 0.7821490 NA
1 54676 rs2462492 C T 0.0026727 0.0047345 0.5700002 0.5724073 0.400419 NA NA
1 86028 rs114608975 T C -0.0056439 0.0075635 0.4600002 0.4555485 0.103590 0.0277556 NA
1 91536 rs6702460 G T -0.0043433 0.0046598 0.3500000 0.3512966 0.456878 0.4207270 NA
1 234313 rs8179466 C T -0.0047497 0.0091856 0.6100002 0.6051003 0.074547 NA NA
1 534192 rs6680723 C T 0.0002776 0.0053299 0.9599999 0.9584641 0.240710 NA NA
1 546697 rs12025928 A G 0.0039051 0.0066349 0.5600000 0.5561459 0.913371 NA NA
1 693731 rs12238997 A G 0.0046150 0.0044636 0.2999998 0.3011666 0.116324 0.1417730 NA
1 705882 rs72631875 G A -0.0016051 0.0065346 0.8100000 0.8059738 0.067345 0.0315495 NA
1 706368 rs55727773 A G 0.0005897 0.0033054 0.8600001 0.8584037 0.515865 0.2751600 NA
CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
22 51219704 rs147475742 G A -0.0062598 0.0069420 0.3700002 0.3671982 0.042027 0.0473243 NA
22 51219766 rs182321900 C T 0.0034870 0.0321797 0.9100000 0.9137104 0.001956 NA NA
22 51220146 rs868950473 C T 0.0111986 0.0318537 0.7300002 0.7251656 0.002008 NA NA
22 51221190 rs369304721 G A -0.0005594 0.0069288 0.9400001 0.9356579 0.049845 NA NA
22 51221731 rs115055839 T C -0.0034987 0.0051829 0.5000000 0.4996411 0.073381 0.0625000 NA
22 51222100 rs114553188 G T -0.0000023 0.0061025 1.0000000 0.9997018 0.054497 0.0880591 NA
22 51223637 rs375798137 G A -0.0002634 0.0061322 0.9699999 0.9657411 0.054128 0.0788738 NA
22 51229805 rs9616985 T C -0.0038264 0.0052021 0.4600002 0.4620013 0.073211 0.0730831 NA
22 51232488 rs376461333 A G -0.0001550 0.0122364 0.9900000 0.9898910 0.020104 NA NA
22 51237063 rs3896457 T C 0.0002011 0.0031844 0.9500000 0.9496413 0.298048 0.2050720 NA

bcf preview

1   49298   rs10399793  T   C   .   PASS    AF=0.62387  ES:SE:LP:AF:ID  -0.00924391:0.00477812:1.27572:0.62387:rs10399793
1   54676   rs2462492   C   T   .   PASS    AF=0.400419 ES:SE:LP:AF:ID  0.00267266:0.00473448:0.244125:0.400419:rs2462492
1   86028   rs114608975 T   C   .   PASS    AF=0.10359  ES:SE:LP:AF:ID  -0.00564389:0.00756354:0.337242:0.10359:rs114608975
1   91536   rs6702460   G   T   .   PASS    AF=0.456878 ES:SE:LP:AF:ID  -0.00434334:0.00465985:0.455932:0.456878:rs6702460
1   234313  rs8179466   C   T   .   PASS    AF=0.074547 ES:SE:LP:AF:ID  -0.0047497:0.00918562:0.21467:0.074547:rs8179466
1   534192  rs6680723   C   T   .   PASS    AF=0.24071  ES:SE:LP:AF:ID  0.000277586:0.00532988:0.0177288:0.24071:rs6680723
1   546697  rs12025928  A   G   .   PASS    AF=0.913371 ES:SE:LP:AF:ID  0.00390513:0.00663488:0.251812:0.913371:rs12025928
1   693731  rs12238997  A   G   .   PASS    AF=0.116324 ES:SE:LP:AF:ID  0.00461502:0.00446355:0.522879:0.116324:rs12238997
1   705882  rs72631875  G   A   .   PASS    AF=0.067345 ES:SE:LP:AF:ID  -0.00160506:0.00653464:0.091515:0.067345:rs72631875
1   706368  rs12029736  A   G   .   PASS    AF=0.515865 ES:SE:LP:AF:ID  0.000589714:0.00330545:0.0655015:0.515865:rs12029736
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1   715265  rs12184267  C   T   .   PASS    AF=0.036585 ES:SE:LP:AF:ID  6.34295e-05:0.00757395:0.00436481:0.036585:rs12184267
1   715367  rs12184277  A   G   .   PASS    AF=0.036705 ES:SE:LP:AF:ID  -0.000301894:0.00754469:0.0132283:0.036705:rs12184277
1   717485  rs12184279  C   A   .   PASS    AF=0.036401 ES:SE:LP:AF:ID  0.000535229:0.0075995:0.0268721:0.036401:rs12184279
1   717587  rs144155419 G   A   .   PASS    AF=0.01638  ES:SE:LP:AF:ID  -0.00308959:0.0117067:0.102373:0.01638:rs144155419
1   720381  rs116801199 G   T   .   PASS    AF=0.03694  ES:SE:LP:AF:ID  1.82317e-05:0.00751531:-0:0.03694:rs116801199
1   721290  rs12565286  G   C   .   PASS    AF=0.037033 ES:SE:LP:AF:ID  -0.000112195:0.00749025:0.00436481:0.037033:rs12565286
1   722670  rs116030099 T   C   .   PASS    AF=0.101332 ES:SE:LP:AF:ID  0.00263754:0.0054505:0.200659:0.101332:rs116030099
1   723891  rs2977670   G   C   .   PASS    AF=0.959153 ES:SE:LP:AF:ID  0.00180548:0.0072265:0.09691:0.959153:rs2977670
1   724849  rs12126395  C   A   .   PASS    AF=0.031499 ES:SE:LP:AF:ID  -0.00387035:0.0130798:0.113509:0.031499:rs12126395
1   725060  rs865924913 A   T   .   PASS    AF=0.053251 ES:SE:LP:AF:ID  -0.00129796:0.0104209:0.0457575:0.053251:rs865924913
1   726794  rs28454925  C   G   .   PASS    AF=0.036546 ES:SE:LP:AF:ID  -0.000244142:0.00753869:0.0132283:0.036546:rs28454925
1   729632  rs116720794 C   T   .   PASS    AF=0.036873 ES:SE:LP:AF:ID  0.000913255:0.00746883:0.0457575:0.036873:rs116720794
1   729679  rs4951859   C   G   .   PASS    AF=0.843287 ES:SE:LP:AF:ID  -0.00179175:0.0038694:0.19382:0.843287:rs4951859
1   730087  rs148120343 T   C   .   PASS    AF=0.055812 ES:SE:LP:AF:ID  0.0073351:0.00626682:0.619789:0.055812:rs148120343
1   731718  rs58276399  T   C   .   PASS    AF=0.122245 ES:SE:LP:AF:ID  0.00173557:0.00423541:0.167491:0.122245:rs58276399
1   732989  rs369030935 C   T   .   PASS    AF=0.025721 ES:SE:LP:AF:ID  0.00492845:0.0104047:0.19382:0.025721:rs369030935
1   734349  rs141242758 T   C   .   PASS    AF=0.121493 ES:SE:LP:AF:ID  0.00190288:0.00423713:0.187087:0.121493:rs141242758
1   736289  rs79010578  T   A   .   PASS    AF=0.132305 ES:SE:LP:AF:ID  0.00247943:0.0041747:0.259637:0.132305:rs79010578
1   736689  rs181876450 T   C   .   PASS    AF=0.011085 ES:SE:LP:AF:ID  0.0179432:0.0152048:0.619789:0.011085:rs181876450
1   740284  rs61770167  C   T   .   PASS    AF=0.005728 ES:SE:LP:AF:ID  -0.0322801:0.0195359:1.00877:0.005728:rs61770167
1   742813  rs112573343 C   T   .   PASS    AF=0.002276 ES:SE:LP:AF:ID  0.0202468:0.0328219:0.267606:0.002276:rs112573343
1   746189  rs139221807 A   G   .   PASS    AF=0.001006 ES:SE:LP:AF:ID  -0.151289:0.0548694:2.23657:0.001006:rs139221807
1   752478  rs146277091 G   A   .   PASS    AF=0.036776 ES:SE:LP:AF:ID  0.000148439:0.00739446:0.00877392:0.036776:rs146277091
1   752566  rs3094315   G   A   .   PASS    AF=0.838997 ES:SE:LP:AF:ID  -0.00100696:0.00374652:0.102373:0.838997:rs3094315
1   752721  rs3131972   A   G   .   PASS    AF=0.838626 ES:SE:LP:AF:ID  -0.0011283:0.00374259:0.119186:0.838626:rs3131972
1   753405  rs3115860   C   A   .   PASS    AF=0.869821 ES:SE:LP:AF:ID  -7.6459e-05:0.00401581:0.00877392:0.869821:rs3115860
1   753541  rs2073813   G   A   .   PASS    AF=0.129813 ES:SE:LP:AF:ID  -0.000139655:0.0040243:0.0132283:0.129813:rs2073813
1   754063  rs12184312  G   T   .   PASS    AF=0.037291 ES:SE:LP:AF:ID  0.00123981:0.00726858:0.0655015:0.037291:rs12184312
1   754105  rs12184325  C   T   .   PASS    AF=0.037536 ES:SE:LP:AF:ID  0.000844931:0.00722228:0.0409586:0.037536:rs12184325
1   754182  rs3131969   A   G   .   PASS    AF=0.869158 ES:SE:LP:AF:ID  -3.87758e-05:0.00400792:0.00436481:0.869158:rs3131969
1   754192  rs3131968   A   G   .   PASS    AF=0.869258 ES:SE:LP:AF:ID  -0.000114446:0.00400957:0.00877392:0.869258:rs3131968
1   754211  rs12184313  G   A   .   PASS    AF=0.037493 ES:SE:LP:AF:ID  0.000932905:0.00725407:0.0457575:0.037493:rs12184313
1   754334  rs3131967   T   C   .   PASS    AF=0.86916  ES:SE:LP:AF:ID  -6.32376e-05:0.00400785:0.00436481:0.86916:rs3131967
1   754433  rs150578204 G   A   .   PASS    AF=0.005156 ES:SE:LP:AF:ID  0.000487981:0.0205049:0.00877392:0.005156:rs150578204
1   754458  rs142682604 G   T   .   PASS    AF=0.005123 ES:SE:LP:AF:ID  0.000688146:0.0205564:0.0132283:0.005123:rs142682604
1   754503  rs3115859   G   A   .   PASS    AF=0.838079 ES:SE:LP:AF:ID  -0.0010642:0.00373208:0.107905:0.838079:rs3115859
1   754629  rs10454459  A   G   .   PASS    AF=0.037506 ES:SE:LP:AF:ID  0.0010697:0.00726422:0.0555173:0.037506:rs10454459
1   754964  rs3131966   C   T   .   PASS    AF=0.838708 ES:SE:LP:AF:ID  -0.00088637:0.00374255:0.091515:0.838708:rs3131966
1   755240  rs181660517 T   G   .   PASS    AF=0.013764 ES:SE:LP:AF:ID  -0.014083:0.0130573:0.552842:0.013764:rs181660517