Summary

Summary {data-width=650}

Manhattan plot

manhattan_plot

QQ plot

qq_plot

AF plot

af_plot

P-Z plot

pz_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-4063/UKB-b-4063_data.vcf.gz \
--ref-ld-chr ../reference/eur_w_ld_chr/ \
--out /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-4063/ldsc.txt \
--w-ld-chr ../reference/eur_w_ld_chr/ 

Beginning analysis at Thu Oct 17 14:43:57 2019
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-4063/UKB-b-4063_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: 0.0553 (0.0021)
Lambda GC: 1.4449
Mean Chi^2: 1.547
Intercept: 1.0489 (0.01)
Ratio: 0.0894 (0.0183)
Analysis finished at Thu Oct 17 14:45:44 2019
Total time elapsed: 1.0m:46.72s

QC metrics

Metrics

Metrics

{
    "af_correlation": 0.9499,
    "inflation_factor": 1.3107,
    "mean_EFFECT": -0,
    "n": "-Inf",
    "n_snps": 9851866,
    "n_clumped_hits": 41,
    "n_p_sig": 3765,
    "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": "NA",
    "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": 0.0553,
    "ldsc_observed_scale_h2_se": 0.0021,
    "ldsc_intercept_beta": 1.0489,
    "ldsc_intercept_se": 0.01,
    "ldsc_lambda_gc": 1.4449,
    "ldsc_mean_chisq": 1.547,
    "ldsc_ratio": 0.0894
}

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 <U+2587><U+2585><U+2583><U+2582><U+2582>
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 <U+2587><U+2586><U+2585><U+2582><U+2581>
numeric EFFECT 0 1.0000000 NA NA NA NA NA NA NA -1.640000e-05 8.446600e-03 -0.1451650 -2.820400e-03 -1.000000e-06 2.824400e-03 1.295090e-01 <U+2581><U+2581><U+2587><U+2581><U+2581>
numeric SE 0 1.0000000 NA NA NA NA NA NA NA 5.883600e-03 5.568400e-03 0.0016467 2.015600e-03 3.379900e-03 7.798700e-03 8.654820e-02 <U+2587><U+2581><U+2581><U+2581><U+2581>
numeric PVAL 0 1.0000000 NA NA NA NA NA NA NA 4.573067e-01 3.002441e-01 0.0000000 1.900002e-01 4.400003e-01 7.199992e-01 1.000000e+00 <U+2587><U+2586><U+2586><U+2585><U+2586>
numeric PVAL_ztest 0 1.0000000 NA NA NA NA NA NA NA 4.573091e-01 3.002189e-01 0.0000000 1.864996e-01 4.423030e-01 7.169921e-01 1.000000e+00 <U+2587><U+2586><U+2586><U+2586><U+2586>
numeric AF 0 1.0000000 NA NA NA NA NA NA NA 2.035078e-01 2.568609e-01 0.0009970 1.316900e-02 7.791400e-02 3.164530e-01 9.990010e-01 <U+2587><U+2582><U+2581><U+2581><U+2581>
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 <U+2587><U+2582><U+2581><U+2581><U+2581>

Head and tail

CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
1 49298 rs200943160 T C -0.0004278 0.0030286 0.8900000 0.8876640 0.623763 0.7821490 NA
1 54676 rs2462492 C T 0.0005404 0.0030004 0.8600001 0.8570576 0.400401 NA NA
1 86028 rs114608975 T C -0.0031846 0.0047970 0.5099998 0.5067803 0.103556 0.0277556 NA
1 91536 rs6702460 G T 0.0008212 0.0029543 0.7800007 0.7810442 0.456851 0.4207270 NA
1 234313 rs8179466 C T 0.0079262 0.0058251 0.1700000 0.1736036 0.074508 NA NA
1 534192 rs6680723 C T -0.0030089 0.0033745 0.3700002 0.3725756 0.240960 NA NA
1 546697 rs12025928 A G -0.0042335 0.0042099 0.3100002 0.3146064 0.913473 NA NA
1 693731 rs12238997 A G 0.0008630 0.0028280 0.7600007 0.7602437 0.116325 0.1417730 NA
1 705882 rs72631875 G A 0.0038605 0.0041442 0.3500000 0.3515668 0.067285 0.0315495 NA
1 706368 rs55727773 A G -0.0004595 0.0020949 0.8300000 0.8263997 0.515650 0.2751600 NA
CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
22 51219704 rs147475742 G A 0.0036165 0.0043993 0.4100001 0.4110382 0.041955 0.0473243 NA
22 51219766 rs182321900 C T 0.0112232 0.0204974 0.5800000 0.5840060 0.001937 NA NA
22 51220146 rs868950473 C T 0.0069174 0.0203041 0.7300002 0.7333360 0.001986 NA NA
22 51221190 rs369304721 G A 0.0008825 0.0043922 0.8400000 0.8407611 0.049731 NA NA
22 51221731 rs115055839 T C 0.0023385 0.0032850 0.4799997 0.4765509 0.073238 0.0625000 NA
22 51222100 rs114553188 G T 0.0056699 0.0038676 0.1400000 0.1426457 0.054459 0.0880591 NA
22 51223637 rs375798137 G A 0.0056408 0.0038863 0.1499999 0.1466493 0.054088 0.0788738 NA
22 51229805 rs9616985 T C 0.0021943 0.0032969 0.5099998 0.5056927 0.073073 0.0730831 NA
22 51232488 rs376461333 A G 0.0159587 0.0077668 0.0400000 0.0399040 0.020043 NA NA
22 51237063 rs3896457 T C 0.0040542 0.0020164 0.0439997 0.0443732 0.297971 0.2050720 NA

bcf preview

1   49298   rs10399793  T   C   .   PASS    AF=0.623763 ES:SE:LP:AF:ID  -0.000427822:0.0030286:0.05061:0.623763:rs10399793
1   54676   rs2462492   C   T   .   PASS    AF=0.400401 ES:SE:LP:AF:ID  0.000540433:0.00300039:0.0655015:0.400401:rs2462492
1   86028   rs114608975 T   C   .   PASS    AF=0.103556 ES:SE:LP:AF:ID  -0.00318456:0.00479704:0.29243:0.103556:rs114608975
1   91536   rs6702460   G   T   .   PASS    AF=0.456851 ES:SE:LP:AF:ID  0.000821173:0.0029543:0.107905:0.456851:rs6702460
1   234313  rs8179466   C   T   .   PASS    AF=0.074508 ES:SE:LP:AF:ID  0.00792625:0.00582506:0.769551:0.074508:rs8179466
1   534192  rs6680723   C   T   .   PASS    AF=0.24096  ES:SE:LP:AF:ID  -0.00300894:0.00337454:0.431798:0.24096:rs6680723
1   546697  rs12025928  A   G   .   PASS    AF=0.913473 ES:SE:LP:AF:ID  -0.00423352:0.00420993:0.508638:0.913473:rs12025928
1   693731  rs12238997  A   G   .   PASS    AF=0.116325 ES:SE:LP:AF:ID  0.000863007:0.00282804:0.119186:0.116325:rs12238997
1   705882  rs72631875  G   A   .   PASS    AF=0.067285 ES:SE:LP:AF:ID  0.00386052:0.00414417:0.455932:0.067285:rs72631875
1   706368  rs12029736  A   G   .   PASS    AF=0.51565  ES:SE:LP:AF:ID  -0.000459452:0.00209488:0.0809219:0.51565:rs12029736
1   714596  rs149887893 T   C   .   PASS    AF=0.033004 ES:SE:LP:AF:ID  -0.00644676:0.00528134:0.657577:0.033004:rs149887893
1   715265  rs12184267  C   T   .   PASS    AF=0.036621 ES:SE:LP:AF:ID  -0.00597679:0.00479714:0.677781:0.036621:rs12184267
1   715367  rs12184277  A   G   .   PASS    AF=0.036737 ES:SE:LP:AF:ID  -0.00592003:0.00477899:0.657577:0.036737:rs12184277
1   717485  rs12184279  C   A   .   PASS    AF=0.036437 ES:SE:LP:AF:ID  -0.00655464:0.00481343:0.769551:0.036437:rs12184279
1   717587  rs144155419 G   A   .   PASS    AF=0.016407 ES:SE:LP:AF:ID  0.0132248:0.00741135:1.13077:0.016407:rs144155419
1   720381  rs116801199 G   T   .   PASS    AF=0.036976 ES:SE:LP:AF:ID  -0.00589473:0.00476012:0.657577:0.036976:rs116801199
1   721290  rs12565286  G   C   .   PASS    AF=0.037072 ES:SE:LP:AF:ID  -0.00632451:0.00474381:0.744727:0.037072:rs12565286
1   722670  rs116030099 T   C   .   PASS    AF=0.101199 ES:SE:LP:AF:ID  0.00135529:0.00345641:0.161151:0.101199:rs116030099
1   723891  rs2977670   G   C   .   PASS    AF=0.959096 ES:SE:LP:AF:ID  0.00668662:0.00457531:0.853872:0.959096:rs2977670
1   724849  rs12126395  C   A   .   PASS    AF=0.031451 ES:SE:LP:AF:ID  0.0046923:0.00830551:0.244125:0.031451:rs12126395
1   725060  rs865924913 A   T   .   PASS    AF=0.053254 ES:SE:LP:AF:ID  -0.0113485:0.00660741:1.0655:0.053254:rs865924913
1   726794  rs28454925  C   G   .   PASS    AF=0.03659  ES:SE:LP:AF:ID  -0.00659944:0.00477452:0.769551:0.03659:rs28454925
1   729632  rs116720794 C   T   .   PASS    AF=0.036907 ES:SE:LP:AF:ID  -0.00585004:0.00473105:0.657577:0.036907:rs116720794
1   729679  rs4951859   C   G   .   PASS    AF=0.843212 ES:SE:LP:AF:ID  0.00115985:0.00245086:0.19382:0.843212:rs4951859
1   730087  rs148120343 T   C   .   PASS    AF=0.055911 ES:SE:LP:AF:ID  -0.00168838:0.00396832:0.173925:0.055911:rs148120343
1   731718  rs58276399  T   C   .   PASS    AF=0.122307 ES:SE:LP:AF:ID  0.00113509:0.00268268:0.173925:0.122307:rs58276399
1   732989  rs369030935 C   T   .   PASS    AF=0.025713 ES:SE:LP:AF:ID  0.00768305:0.00659882:0.619789:0.025713:rs369030935
1   734349  rs141242758 T   C   .   PASS    AF=0.121549 ES:SE:LP:AF:ID  0.00127926:0.0026838:0.200659:0.121549:rs141242758
1   736289  rs79010578  T   A   .   PASS    AF=0.13233  ES:SE:LP:AF:ID  -0.00326681:0.00264515:0.657577:0.13233:rs79010578
1   736689  rs181876450 T   C   .   PASS    AF=0.011134 ES:SE:LP:AF:ID  -0.0141723:0.00961762:0.853872:0.011134:rs181876450
1   740284  rs61770167  C   T   .   PASS    AF=0.005697 ES:SE:LP:AF:ID  0.00282393:0.0124174:0.0861861:0.005697:rs61770167
1   742813  rs112573343 C   T   .   PASS    AF=0.002269 ES:SE:LP:AF:ID  -0.0277004:0.0208764:0.744727:0.002269:rs112573343
1   746189  rs139221807 A   G   .   PASS    AF=0.00103  ES:SE:LP:AF:ID  -0.00604516:0.0341761:0.0655015:0.00103:rs139221807
1   752478  rs146277091 G   A   .   PASS    AF=0.036821 ES:SE:LP:AF:ID  -0.00606913:0.00468321:0.721246:0.036821:rs146277091
1   752566  rs3094315   G   A   .   PASS    AF=0.838951 ES:SE:LP:AF:ID  0.000468729:0.00237348:0.0757207:0.838951:rs3094315
1   752721  rs3131972   A   G   .   PASS    AF=0.83858  ES:SE:LP:AF:ID  0.000434847:0.00237093:0.0705811:0.83858:rs3131972
1   753405  rs3115860   C   A   .   PASS    AF=0.869781 ES:SE:LP:AF:ID  -0.00168332:0.0025441:0.29243:0.869781:rs3115860
1   753541  rs2073813   G   A   .   PASS    AF=0.129871 ES:SE:LP:AF:ID  0.00173959:0.00254931:0.30103:0.129871:rs2073813
1   754063  rs12184312  G   T   .   PASS    AF=0.037332 ES:SE:LP:AF:ID  -0.00622679:0.0046038:0.744727:0.037332:rs12184312
1   754105  rs12184325  C   T   .   PASS    AF=0.037576 ES:SE:LP:AF:ID  -0.00576309:0.0045747:0.677781:0.037576:rs12184325
1   754182  rs3131969   A   G   .   PASS    AF=0.869123 ES:SE:LP:AF:ID  -0.00170978:0.00253912:0.30103:0.869123:rs3131969
1   754192  rs3131968   A   G   .   PASS    AF=0.869221 ES:SE:LP:AF:ID  -0.00171792:0.00254012:0.30103:0.869221:rs3131968
1   754211  rs12184313  G   A   .   PASS    AF=0.037534 ES:SE:LP:AF:ID  -0.00620142:0.0045945:0.744727:0.037534:rs12184313
1   754334  rs3131967   T   C   .   PASS    AF=0.869126 ES:SE:LP:AF:ID  -0.00171208:0.00253907:0.30103:0.869126:rs3131967
1   754433  rs150578204 G   A   .   PASS    AF=0.005122 ES:SE:LP:AF:ID  2.74941e-05:0.0130367:-0:0.005122:rs150578204
1   754458  rs142682604 G   T   .   PASS    AF=0.005088 ES:SE:LP:AF:ID  -0.000242886:0.0130709:0.00436481:0.005088:rs142682604
1   754503  rs3115859   G   A   .   PASS    AF=0.838033 ES:SE:LP:AF:ID  0.000548551:0.00236435:0.0861861:0.838033:rs3115859
1   754629  rs10454459  A   G   .   PASS    AF=0.037547 ES:SE:LP:AF:ID  -0.00630948:0.00460099:0.769551:0.037547:rs10454459
1   754964  rs3131966   C   T   .   PASS    AF=0.838664 ES:SE:LP:AF:ID  0.000507158:0.00237099:0.0809219:0.838664:rs3131966
1   755240  rs181660517 T   G   .   PASS    AF=0.013773 ES:SE:LP:AF:ID  0.00276148:0.00827626:0.130768:0.013773:rs181660517