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/dev/ieu-a-import/processed/ieu-a-1229/ieu-a-1229.vcf.gz \
--ref-ld-chr /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/reference/eur_w_ld_chr/ \
--out /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ieu-a-import/processed/ieu-a-1229/ldsc.txt \
--w-ld-chr /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/reference/eur_w_ld_chr/ 

Beginning analysis at Tue Feb  4 12:56:15 2020
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ieu-a-import/processed/ieu-a-1229/ieu-a-1229.vcf.gz ...
Read summary statistics for 15240073 SNPs.
Reading reference panel LD Score from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/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 /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/reference/eur_w_ld_chr/[1-22] ...
Read regression weight LD Scores for 1290028 SNPs.
After merging with reference panel LD, 1218950 SNPs remain.
After merging with regression SNP LD, 1218950 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.0157 (0.0126)
Lambda GC: 1.0272
Mean Chi^2: 1.0335
Intercept: 1.02 (0.0064)
Ratio: 0.5967 (0.1915)
Analysis finished at Tue Feb  4 12:58:46 2020
Total time elapsed: 2.0m:31.78s

QC metrics

Metrics

Metrics

{
    "af_correlation": 0.9601,
    "inflation_factor": 1.0513,
    "mean_EFFECT": -0.5157,
    "n": 43907,
    "n_snps": 15240073,
    "n_clumped_hits": 8,
    "n_p_sig": 186,
    "n_mono": 0,
    "n_ns": 775455,
    "n_mac": 255269,
    "is_snpid_unique": false,
    "n_miss_EFFECT": 0,
    "n_miss_SE": 0,
    "n_miss_PVAL": 0,
    "n_miss_AF": 1334,
    "n_miss_AF_reference": 159611,
    "n_est": 42340.1555,
    "ratio_se_n": 0.982,
    "mean_diff": 0.5126,
    "ratio_diff": 4.7016,
    "sd_y_est1": 4.6724,
    "sd_y_est2": 4.5883,
    "r2_sum1": 0.1555,
    "r2_sum2": 0.0071,
    "r2_sum3": 0.0074,
    "r2_sum4": 0.0076,
    "ldsc_nsnp_merge_refpanel_ld": 1218950,
    "ldsc_nsnp_merge_regression_ld": 1218950,
    "ldsc_observed_scale_h2_beta": 0.0157,
    "ldsc_observed_scale_h2_se": 0.0126,
    "ldsc_intercept_beta": 1.02,
    "ldsc_intercept_se": 0.0064,
    "ldsc_lambda_gc": 1.0272,
    "ldsc_mean_chisq": 1.0335,
    "ldsc_ratio": 0.597
}

Flags

name value
af_correlation FALSE
inflation_factor FALSE
n FALSE
is_snpid_non_unique TRUE
mean_EFFECT_nonfinite FALSE
mean_EFFECT_05 TRUE
mean_EFFECT_01 TRUE
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 numeric.mean numeric.sd numeric.p0 numeric.p25 numeric.p50 numeric.p75 numeric.p100 numeric.hist
character ID 0 1.0000000 3 47 0 15240071 0 NA NA NA NA NA NA NA NA
character REF 0 1.0000000 1 101 0 37391 0 NA NA NA NA NA NA NA NA
character ALT 0 1.0000000 1 105 0 18040 0 NA NA NA NA NA NA NA NA
numeric CHROM 0 1.0000000 NA NA NA NA NA 8.898959e+00 6.257405e+00 1.0000e+00 4.000000e+00 7.000000e+00 1.400000e+01 2.400000e+01 ▇▆▂▃▂
numeric POS 0 1.0000000 NA NA NA NA NA 7.931397e+07 5.683333e+07 8.2800e+02 3.250930e+07 6.965052e+07 1.158400e+08 2.492402e+08 ▇▆▅▂▁
numeric EFFECT 0 1.0000000 NA NA NA NA NA -5.157247e-01 3.066232e+00 -2.0420e+01 -7.542000e-02 -1.696000e-03 6.288000e-02 2.042000e+01 ▁▁▇▁▁
numeric SE 0 1.0000000 NA NA NA NA NA 1.097431e+00 7.166866e+00 9.7100e-05 3.975000e-02 1.109000e-01 4.224000e-01 1.000000e+03 ▇▁▁▁▁
numeric PVAL 0 1.0000000 NA NA NA NA NA 4.927599e-01 2.886971e-01 0.0000e+00 2.419998e-01 4.891995e-01 7.418003e-01 1.000000e+00 ▇▇▇▇▇
numeric PVAL_ztest 0 1.0000000 NA NA NA NA NA 4.928251e-01 2.886675e-01 0.0000e+00 2.421394e-01 4.892363e-01 7.418078e-01 9.999999e-01 ▇▇▇▇▇
numeric AF 1334 0.9999125 NA NA NA NA NA 1.571079e-01 2.465365e-01 0.0000e+00 2.364000e-03 2.240000e-02 2.150000e-01 9.999840e-01 ▇▁▁▁▁
numeric AF_reference 159611 0.9895269 NA NA NA NA NA 1.568614e-01 2.338980e-01 0.0000e+00 2.995200e-03 3.434500e-02 2.204470e-01 1.000000e+00 ▇▁▁▁▁
numeric N 0 1.0000000 NA NA NA NA NA 4.390700e+04 0.000000e+00 4.3907e+04 4.390700e+04 4.390700e+04 4.390700e+04 4.390700e+04 ▁▁▇▁▁

Head and tail

CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
1 10616 rs376342519 CCGCCGTTGCAAAGGCGCGCCG C -0.04973 0.20220 0.8057001 0.8057251 0.991000 0.9930110 43907
1 14933 rs199856693 G A -0.09456 0.13610 0.4870999 0.4871911 0.047970 0.0283546 43907
1 15774 rs374029747 G A 0.47860 0.29650 0.1065001 0.1064916 0.006579 0.0119808 43907
1 16949 rs199745162 A C -0.42380 0.18530 0.0221901 0.0221899 0.016750 0.0139776 43907
1 51479 rs116400033 T A -0.05150 0.05733 0.3689997 0.3690213 0.232100 0.1281950 43907
1 52185 rs201374420 TTAA T 0.49710 0.74780 0.5061998 0.5062105 0.005882 0.0053914 43907
1 54353 rs140052487 C A -0.30050 0.78270 0.7011001 0.7010322 0.001339 0.0089856 43907
1 54490 rs141149254 G A -0.08068 0.06437 0.2099999 0.2100678 0.166100 0.0960463 43907
1 55164 rs3091274 C A -0.14370 0.18350 0.4335997 0.4335647 0.980700 0.9233230 43907
1 55326 rs3107975 T C -0.16110 0.40190 0.6884002 0.6885335 0.028260 0.0459265 43907
CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
23 154925045 rs509981 C T -0.018720 0.03688 0.6116993 0.6117394 0.250000 0.3634440 43907
23 154925895 rs538470 C T -0.009090 0.03809 0.8114000 0.8113806 0.252700 0.3634440 43907
23 154926376 rs116490668 C T -0.165500 0.61920 0.7891999 0.7892533 0.001859 0.0349669 43907
23 154927185 rs185685661 T C -0.032500 0.06419 0.6126000 0.6126395 0.139300 0.1796030 43907
23 154927199 rs645904 C T -0.017960 0.03691 0.6264999 0.6265496 0.248000 0.3674170 43907
23 154927581 rs644138 G A -0.004021 0.03599 0.9110000 0.9110411 0.299900 0.4635760 43907
23 154929412 rs557132 C T -0.015760 0.03695 0.6695993 0.6697273 0.250400 0.3568210 43907
23 154929952 rs4012982 CAA C -0.016310 0.03698 0.6592999 0.6591774 0.250900 0.3165560 43907
23 154930230 rs781880 A G -0.018080 0.03717 0.6267004 0.6266738 0.249000 0.3618540 43907
24 13537468 rs7203107 A G 0.149600 0.20160 0.4578002 0.4580489 0.985590 NA 43907

bcf preview

1   10616   rs376342519 CCGCCGTTGCAAAGGCGCGCCG  C   .   PASS    AF=0.991    ES:SE:LP:AF:SS:ID   -0.04973:0.2022:0.0938266:0.991:43907:rs376342519
1   14933   rs199856693 G   A   .   PASS    AF=0.04797  ES:SE:LP:AF:SS:ID   -0.09456:0.1361:0.312382:0.04797:43907:rs199856693
1   15774   rs374029747 G   A   .   PASS    AF=0.006579 ES:SE:LP:AF:SS:ID   0.4786:0.2965:0.97265:0.006579:43907:rs374029747
1   16949   rs199745162 A   C   .   PASS    AF=0.01675  ES:SE:LP:AF:SS:ID   -0.4238:0.1853:1.65384:0.01675:43907:rs199745162
1   51479   rs116400033 T   A   .   PASS    AF=0.2321   ES:SE:LP:AF:SS:ID   -0.0515:0.05733:0.432974:0.2321:43907:rs116400033
1   52185   rs201374420 TTAA    T   .   PASS    AF=0.005882 ES:SE:LP:AF:SS:ID   0.4971:0.7478:0.295678:0.005882:43907:rs201374420
1   54353   rs140052487 C   A   .   PASS    AF=0.001339 ES:SE:LP:AF:SS:ID   -0.3005:0.7827:0.15422:0.001339:43907:rs140052487
1   54490   rs141149254 G   A   .   PASS    AF=0.1661   ES:SE:LP:AF:SS:ID   -0.08068:0.06437:0.677781:0.1661:43907:rs141149254
1   55164   rs3091274   C   A   .   PASS    AF=0.9807   ES:SE:LP:AF:SS:ID   -0.1437:0.1835:0.362911:0.9807:43907:rs3091274
1   55326   rs3107975   T   C   .   PASS    AF=0.02826  ES:SE:LP:AF:SS:ID   -0.1611:0.4019:0.162159:0.02826:43907:rs3107975
1   55545   rs28396308  C   T   .   PASS    AF=0.2248   ES:SE:LP:AF:SS:ID   0.06142:0.06178:0.494714:0.2248:43907:rs28396308
1   57183   rs368339209 A   G   .   PASS    AF=0.0007041    ES:SE:LP:AF:SS:ID   -0.8129:1.203:0.301551:0.0007041:43907:rs368339209
1   57292   rs201418760 C   T   .   PASS    AF=0.02393  ES:SE:LP:AF:SS:ID   0.1674:0.1734:0.475734:0.02393:43907:rs201418760
1   58814   rs114420996 G   A   .   PASS    AF=0.1003   ES:SE:LP:AF:SS:ID   0.1483:0.0867:1.05958:0.1003:43907:rs114420996
1   61543   rs201849102 T   C   .   PASS    AF=0.0003079    ES:SE:LP:AF:SS:ID   -12.83:9.933:0.706416:0.0003079:43907:rs201849102
1   61743   rs184286948 G   C   .   PASS    AF=0.009155 ES:SE:LP:AF:SS:ID   0.2652:0.2518:0.53432:0.009155:43907:rs184286948
1   61920   rs62637820  G   A   .   PASS    AF=0.02945  ES:SE:LP:AF:SS:ID   0.01224:0.1527:0.0286778:0.02945:43907:rs62637820
1   63093   rs200092917 G   A   .   PASS    AF=0.0207   ES:SE:LP:AF:SS:ID   0.2207:0.1854:0.630784:0.0207:43907:rs200092917
1   64649   rs181431124 A   C   .   PASS    AF=0.02715  ES:SE:LP:AF:SS:ID   0.07804:0.1653:0.195997:0.02715:43907:rs181431124
1   66219   rs181028663 A   T   .   PASS    AF=0.01624  ES:SE:LP:AF:SS:ID   0.05858:0.2003:0.113566:0.01624:43907:rs181028663
1   68082   rs367789441 T   C   .   PASS    AF=0.06526  ES:SE:LP:AF:SS:ID   0.06696:0.09715:0.309184:0.06526:43907:rs367789441
1   68596   rs372212855 T   G   .   PASS    AF=0.003797 ES:SE:LP:AF:SS:ID   -0.3655:0.3828:0.469032:0.003797:43907:rs372212855
1   69428   rs140739101 T   G   .   PASS    AF=0.04215  ES:SE:LP:AF:SS:ID   -0.06063:0.1238:0.204607:0.04215:43907:rs140739101
1   69534   rs190717287 T   C   .   PASS    AF=0.0003164    ES:SE:LP:AF:SS:ID   0.07667:1.261:0.0215912:0.0003164:43907:rs190717287
1   69761   rs200505207 A   T   .   PASS    AF=0.06821  ES:SE:LP:AF:SS:ID   0.03179:0.09492:0.13212:0.06821:43907:rs200505207
1   69897   rs200676709 T   C   .   PASS    AF=0.7661   ES:SE:LP:AF:SS:ID   -0.02327:0.06099:0.153168:0.7661:43907:rs200676709
1   72297   rs200651397 G   GTAT    .   PASS    AF=0.006341 ES:SE:LP:AF:SS:ID   0.3439:0.3331:0.520137:0.006341:43907:rs200651397
1   74790   rs13328700  C   G   .   PASS    AF=0.03421  ES:SE:LP:AF:SS:ID   0.09762:0.1224:0.371407:0.03421:43907:rs13328700
1   74792   rs13328684  G   A   .   PASS    AF=0.03421  ES:SE:LP:AF:SS:ID   0.09762:0.1224:0.371407:0.03421:43907:rs13328684
1   76854   rs367666799 A   G   .   PASS    AF=0.06856  ES:SE:LP:AF:SS:ID   0.01097:0.09841:0.0403386:0.06856:43907:rs367666799
1   78942   rs372315362 C   G   .   PASS    AF=0.01116  ES:SE:LP:AF:SS:ID   2.963:1.602:1.19206:0.01116:43907:rs372315362
1   82163   rs139113303 G   A   .   PASS    AF=0.06791  ES:SE:LP:AF:SS:ID   0.01662:0.09905:0.0620811:0.06791:43907:rs139113303
1   82609   rs149189449 C   G   .   PASS    AF=0.06818  ES:SE:LP:AF:SS:ID   0.008549:0.1053:0.0290491:0.06818:43907:rs149189449
1   83514   rs201754587 C   T   .   PASS    AF=0.3501   ES:SE:LP:AF:SS:ID   0.09826:0.0561:1.09778:0.3501:43907:rs201754587
1   84139   rs183605470 A   T   .   PASS    AF=0.02132  ES:SE:LP:AF:SS:ID   0.3743:0.1923:1.2871:0.02132:43907:rs183605470
1   86028   rs114608975 T   C   .   PASS    AF=0.04742  ES:SE:LP:AF:SS:ID   0.1094:0.119:0.446117:0.04742:43907:rs114608975
1   86065   rs116504101 G   C   .   PASS    AF=0.06995  ES:SE:LP:AF:SS:ID   0.03255:0.09751:0.131591:0.06995:43907:rs116504101
1   86331   rs115209712 A   G   .   PASS    AF=0.1018   ES:SE:LP:AF:SS:ID   0.02711:0.08754:0.121019:0.1018:43907:rs115209712
1   87021   rs188486692 T   C   .   PASS    AF=0.00763  ES:SE:LP:AF:SS:ID   -0.2017:0.3029:0.296279:0.00763:43907:rs188486692
1   87360   rs180907504 C   T   .   PASS    AF=0.01853  ES:SE:LP:AF:SS:ID   0.1905:0.1726:0.56928:0.01853:43907:rs180907504
1   87409   rs139490478 C   T   .   PASS    AF=0.07088  ES:SE:LP:AF:SS:ID   0.02793:0.09669:0.111989:0.07088:43907:rs139490478
1   88169   rs940550    C   T   .   PASS    AF=0.2022   ES:SE:LP:AF:SS:ID   0.05539:0.05908:0.457797:0.2022:43907:rs940550
1   88172   rs940551    G   A   .   PASS    AF=0.06423  ES:SE:LP:AF:SS:ID   0.05216:0.09892:0.223371:0.06423:43907:rs940551
1   88177   rs143215837 G   C   .   PASS    AF=0.06377  ES:SE:LP:AF:SS:ID   0.07074:0.09918:0.322667:0.06377:43907:rs143215837
1   88188   rs148331237 C   A   .   PASS    AF=0.007142 ES:SE:LP:AF:SS:ID   0.01146:0.2826:0.0143041:0.007142:43907:rs148331237
1   88236   rs186918018 C   T   .   PASS    AF=0.01279  ES:SE:LP:AF:SS:ID   -0.3552:0.5178:0.307417:0.01279:43907:rs186918018
1   88316   rs113759966 G   A   .   PASS    AF=0.06376  ES:SE:LP:AF:SS:ID   0.08055:0.09928:0.37976:0.06376:43907:rs113759966
1   88338   rs55700207  G   A   .   PASS    AF=0.08209  ES:SE:LP:AF:SS:ID   0.156:0.09538:0.9914:0.08209:43907:rs55700207
1   88710   rs186575039 C   G   .   PASS    AF=0.07086  ES:SE:LP:AF:SS:ID   0.02813:0.09669:0.112889:0.07086:43907:rs186575039
1   89599   rs375955515 A   T   .   PASS    AF=0.07086  ES:SE:LP:AF:SS:ID   0.02813:0.09669:0.112889:0.07086:43907:rs375955515