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-7596/UKB-b-7596_data.vcf.gz \
--ref-ld-chr ../reference/eur_w_ld_chr/ \
--out /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-7596/ldsc.txt \
--w-ld-chr ../reference/eur_w_ld_chr/ 

Beginning analysis at Thu Oct 17 14:40:44 2019
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-7596/UKB-b-7596_data.vcf.gz ...
Read summary statistics for 8993776 SNPs.
Dropped 8680 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, 1287187 SNPs remain.
After merging with regression SNP LD, 1287187 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.0036 (0.0049)
Lambda GC: 1.017
Mean Chi^2: 1.0213
Intercept: 1.0145 (0.0059)
Ratio: 0.6779 (0.2776)
Analysis finished at Thu Oct 17 14:42:19 2019
Total time elapsed: 1.0m:35.04s

QC metrics

Metrics

Metrics

{
    "af_correlation": 0.9478,
    "inflation_factor": 1,
    "mean_EFFECT": -0.0001,
    "n": "-Inf",
    "n_snps": 9851866,
    "n_clumped_hits": 0,
    "n_p_sig": 0,
    "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": 92908,
    "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": 1287187,
    "ldsc_nsnp_merge_regression_ld": 1287187,
    "ldsc_observed_scale_h2_beta": 0.0036,
    "ldsc_observed_scale_h2_se": 0.0049,
    "ldsc_intercept_beta": 1.0145,
    "ldsc_intercept_se": 0.0059,
    "ldsc_lambda_gc": 1.017,
    "ldsc_mean_chisq": 1.0213,
    "ldsc_ratio": 0.6808
}

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 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 8985135 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 8993776 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 8.643392e+00 5.758311e+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 7.878744e+07 5.634103e+07 828.0000000 3.242790e+07 6.934861e+07 1.145459e+08 2.492385e+08 ▇▆▅▂▁
numeric EFFECT 0 1.0000000 NA NA NA NA NA NA NA -7.370000e-05 9.730700e-03 -0.1224730 -3.798600e-03 -1.930000e-05 3.723000e-03 1.151830e-01 ▁▁▇▁▁
numeric SE 0 1.0000000 NA NA NA NA NA NA NA 7.790300e-03 5.691500e-03 0.0028415 3.385400e-03 5.176300e-03 1.068230e-02 6.581570e-02 ▇▁▁▁▁
numeric PVAL 0 1.0000000 NA NA NA NA NA NA NA 4.974097e-01 2.895947e-01 0.0000002 2.500000e-01 5.000000e-01 7.499995e-01 1.000000e+00 ▇▇▇▇▇
numeric PVAL_ztest 0 1.0000000 NA NA NA NA NA NA NA 4.974124e-01 2.895677e-01 0.0000002 2.462596e-01 4.969172e-01 7.479029e-01 9.999999e-01 ▇▇▇▇▇
numeric AF 0 1.0000000 NA NA NA NA NA NA NA 2.205249e-01 2.585740e-01 0.0036460 2.066900e-02 1.019340e-01 3.478320e-01 9.963540e-01 ▇▂▁▁▁
numeric AF_reference 92908 0.9896697 NA NA NA NA NA NA NA 2.208105e-01 2.504823e-01 0.0000000 1.797120e-02 1.194090e-01 3.460460e-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 0.0121206 0.0052466 0.0210000 0.0208786 0.623641 0.7821490 NA
1 54676 rs2462492 C T -0.0004223 0.0052116 0.9400001 0.9354137 0.398977 NA NA
1 86028 rs114608975 T C -0.0100348 0.0082650 0.2200002 0.2246951 0.104065 0.0277556 NA
1 91536 rs6702460 G T 0.0027219 0.0051208 0.5999997 0.5950465 0.455685 0.4207270 NA
1 234313 rs8179466 C T 0.0220423 0.0100255 0.0280001 0.0279047 0.074834 NA NA
1 534192 rs6680723 C T 0.0034368 0.0058614 0.5600000 0.5576458 0.240593 NA NA
1 546697 rs12025928 A G -0.0020020 0.0072660 0.7800007 0.7829090 0.912843 NA NA
1 693731 rs12238997 A G 0.0017940 0.0048730 0.7099994 0.7127538 0.117831 0.1417730 NA
1 705882 rs72631875 G A -0.0007851 0.0071391 0.9100000 0.9124344 0.067561 0.0315495 NA
1 706368 rs55727773 A G 0.0033395 0.0036135 0.3599996 0.3553864 0.514323 0.2751600 NA
CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
22 51219006 rs28729663 G A 0.0016181 0.0043739 0.7099994 0.7114158 0.137178 0.2052720 NA
22 51219387 rs9616832 T C 0.0110783 0.0056991 0.0519996 0.0519105 0.072666 0.0654952 NA
22 51219704 rs147475742 G A 0.0142336 0.0075835 0.0610000 0.0605285 0.041778 0.0473243 NA
22 51221190 rs369304721 G A 0.0130755 0.0076268 0.0860003 0.0864542 0.049109 NA NA
22 51221731 rs115055839 T C 0.0113789 0.0057007 0.0460002 0.0459266 0.072193 0.0625000 NA
22 51222100 rs114553188 G T -0.0117118 0.0066732 0.0790005 0.0792521 0.054410 0.0880591 NA
22 51223637 rs375798137 G A -0.0123504 0.0067082 0.0659994 0.0656084 0.054024 0.0788738 NA
22 51229805 rs9616985 T C 0.0114272 0.0057213 0.0460002 0.0457917 0.072053 0.0730831 NA
22 51232488 rs376461333 A G -0.0203246 0.0135095 0.1299999 0.1324611 0.019996 NA NA
22 51237063 rs3896457 T C 0.0036595 0.0034778 0.2900000 0.2926786 0.298510 0.2050720 NA

bcf preview

1   49298   rs10399793  T   C   .   PASS    AF=0.623641 ES:SE:LP:AF:ID  0.0121206:0.00524662:1.67778:0.623641:rs10399793
1   54676   rs2462492   C   T   .   PASS    AF=0.398977 ES:SE:LP:AF:ID  -0.000422322:0.00521157:0.0268721:0.398977:rs2462492
1   86028   rs114608975 T   C   .   PASS    AF=0.104065 ES:SE:LP:AF:ID  -0.0100348:0.00826496:0.657577:0.104065:rs114608975
1   91536   rs6702460   G   T   .   PASS    AF=0.455685 ES:SE:LP:AF:ID  0.00272187:0.00512075:0.221849:0.455685:rs6702460
1   234313  rs8179466   C   T   .   PASS    AF=0.074834 ES:SE:LP:AF:ID  0.0220423:0.0100255:1.55284:0.074834:rs8179466
1   534192  rs6680723   C   T   .   PASS    AF=0.240593 ES:SE:LP:AF:ID  0.00343679:0.00586141:0.251812:0.240593:rs6680723
1   546697  rs12025928  A   G   .   PASS    AF=0.912843 ES:SE:LP:AF:ID  -0.00200201:0.00726603:0.107905:0.912843:rs12025928
1   693731  rs12238997  A   G   .   PASS    AF=0.117831 ES:SE:LP:AF:ID  0.00179403:0.00487296:0.148742:0.117831:rs12238997
1   705882  rs72631875  G   A   .   PASS    AF=0.067561 ES:SE:LP:AF:ID  -0.000785077:0.00713911:0.0409586:0.067561:rs72631875
1   706368  rs12029736  A   G   .   PASS    AF=0.514323 ES:SE:LP:AF:ID  0.00333954:0.00361347:0.443698:0.514323:rs12029736
1   714596  rs149887893 T   C   .   PASS    AF=0.033622 ES:SE:LP:AF:ID  0.0119586:0.00902624:0.721246:0.033622:rs149887893
1   715265  rs12184267  C   T   .   PASS    AF=0.037269 ES:SE:LP:AF:ID  0.0141025:0.0082094:1.0655:0.037269:rs12184267
1   715367  rs12184277  A   G   .   PASS    AF=0.03736  ES:SE:LP:AF:ID  0.0145502:0.008182:1.12494:0.03736:rs12184277
1   717485  rs12184279  C   A   .   PASS    AF=0.037059 ES:SE:LP:AF:ID  0.0153117:0.00823812:1.20066:0.037059:rs12184279
1   717587  rs144155419 G   A   .   PASS    AF=0.016714 ES:SE:LP:AF:ID  0.0221885:0.0127087:1.09151:0.016714:rs144155419
1   720381  rs116801199 G   T   .   PASS    AF=0.037618 ES:SE:LP:AF:ID  0.0142624:0.00814722:1.09691:0.037618:rs116801199
1   721290  rs12565286  G   C   .   PASS    AF=0.037715 ES:SE:LP:AF:ID  0.013427:0.00812067:1.00877:0.037715:rs12565286
1   722670  rs116030099 T   C   .   PASS    AF=0.101108 ES:SE:LP:AF:ID  -0.00228826:0.00598181:0.154902:0.101108:rs116030099
1   723891  rs2977670   G   C   .   PASS    AF=0.958088 ES:SE:LP:AF:ID  -0.0157394:0.00781142:1.35655:0.958088:rs2977670
1   724849  rs12126395  C   A   .   PASS    AF=0.031875 ES:SE:LP:AF:ID  -0.00803406:0.0142395:0.244125:0.031875:rs12126395
1   725060  rs865924913 A   T   .   PASS    AF=0.052626 ES:SE:LP:AF:ID  0.0104733:0.0115218:0.443698:0.052626:rs865924913
1   726794  rs28454925  C   G   .   PASS    AF=0.03719  ES:SE:LP:AF:ID  0.0144297:0.00817571:1.10791:0.03719:rs28454925
1   729632  rs116720794 C   T   .   PASS    AF=0.037503 ES:SE:LP:AF:ID  0.0146542:0.00810643:1.14874:0.037503:rs116720794
1   729679  rs4951859   C   G   .   PASS    AF=0.840885 ES:SE:LP:AF:ID  -0.00545471:0.00422168:0.69897:0.840885:rs4951859
1   730087  rs148120343 T   C   .   PASS    AF=0.056136 ES:SE:LP:AF:ID  0.00449262:0.00687073:0.29243:0.056136:rs148120343
1   731718  rs58276399  T   C   .   PASS    AF=0.123708 ES:SE:LP:AF:ID  0.00298955:0.0046276:0.283997:0.123708:rs58276399
1   732989  rs369030935 C   T   .   PASS    AF=0.025885 ES:SE:LP:AF:ID  -0.0035571:0.0113572:0.124939:0.025885:rs369030935
1   734349  rs141242758 T   C   .   PASS    AF=0.122907 ES:SE:LP:AF:ID  0.00268264:0.00462997:0.251812:0.122907:rs141242758
1   736289  rs79010578  T   A   .   PASS    AF=0.133739 ES:SE:LP:AF:ID  0.00344472:0.00456312:0.346787:0.133739:rs79010578
1   736689  rs181876450 T   C   .   PASS    AF=0.011242 ES:SE:LP:AF:ID  -0.00732294:0.0165438:0.180456:0.011242:rs181876450
1   740284  rs61770167  C   T   .   PASS    AF=0.00609  ES:SE:LP:AF:ID  0.0114839:0.0206756:0.236572:0.00609:rs61770167
1   752478  rs146277091 G   A   .   PASS    AF=0.037482 ES:SE:LP:AF:ID  0.0140945:0.00801629:1.10237:0.037482:rs146277091
1   752566  rs3094315   G   A   .   PASS    AF=0.836693 ES:SE:LP:AF:ID  -0.00807941:0.00408585:1.31876:0.836693:rs3094315
1   752721  rs3131972   A   G   .   PASS    AF=0.836262 ES:SE:LP:AF:ID  -0.00861278:0.00408127:1.45593:0.836262:rs3131972
1   753405  rs3115860   C   A   .   PASS    AF=0.868027 ES:SE:LP:AF:ID  -0.00620665:0.00437842:0.79588:0.868027:rs3115860
1   753541  rs2073813   G   A   .   PASS    AF=0.131634 ES:SE:LP:AF:ID  0.00631064:0.0043876:0.823909:0.131634:rs2073813
1   754063  rs12184312  G   T   .   PASS    AF=0.037923 ES:SE:LP:AF:ID  0.0121043:0.00789028:0.886057:0.037923:rs12184312
1   754105  rs12184325  C   T   .   PASS    AF=0.038169 ES:SE:LP:AF:ID  0.0117642:0.00784158:0.886057:0.038169:rs12184325
1   754182  rs3131969   A   G   .   PASS    AF=0.867327 ES:SE:LP:AF:ID  -0.00658283:0.00436962:0.886057:0.867327:rs3131969
1   754192  rs3131968   A   G   .   PASS    AF=0.867425 ES:SE:LP:AF:ID  -0.00656751:0.00437168:0.886057:0.867425:rs3131968
1   754211  rs12184313  G   A   .   PASS    AF=0.038117 ES:SE:LP:AF:ID  0.0123441:0.00787299:0.920819:0.038117:rs12184313
1   754334  rs3131967   T   C   .   PASS    AF=0.867325 ES:SE:LP:AF:ID  -0.00665421:0.00436934:0.886057:0.867325:rs3131967
1   754433  rs150578204 G   A   .   PASS    AF=0.005085 ES:SE:LP:AF:ID  0.0240149:0.022648:0.537602:0.005085:rs150578204
1   754458  rs142682604 G   T   .   PASS    AF=0.005052 ES:SE:LP:AF:ID  0.0238242:0.0227112:0.537602:0.005052:rs142682604
1   754503  rs3115859   G   A   .   PASS    AF=0.835803 ES:SE:LP:AF:ID  -0.00824957:0.00407252:1.36653:0.835803:rs3115859
1   754629  rs10454459  A   G   .   PASS    AF=0.038133 ES:SE:LP:AF:ID  0.0125876:0.00788378:0.958607:0.038133:rs10454459
1   754964  rs3131966   C   T   .   PASS    AF=0.836411 ES:SE:LP:AF:ID  -0.00789978:0.00408353:1.27572:0.836411:rs3131966
1   755240  rs181660517 T   G   .   PASS    AF=0.013157 ES:SE:LP:AF:ID  -0.00718868:0.0146684:0.207608:0.013157:rs181660517
1   755435  rs184270342 T   G   .   PASS    AF=0.005536 ES:SE:LP:AF:ID  -0.000903336:0.0220863:0.0132283:0.005536:rs184270342
1   755775  rs3131965   A   G   .   PASS    AF=0.837723 ES:SE:LP:AF:ID  -0.00804563:0.00413954:1.284:0.837723:rs3131965