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-1011/ieu-a-1011.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-1011/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 16:56:18 2020
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ieu-a-import/processed/ieu-a-1011/ieu-a-1011.vcf.gz ...
Read summary statistics for 7524386 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, 1275293 SNPs remain.
After merging with regression SNP LD, 1275293 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.1623 (0.006)
Lambda GC: 1.2365
Mean Chi^2: 1.4639
Intercept: 0.9535 (0.0083)
Ratio < 0 (usually indicates GC correction).
Analysis finished at Tue Feb  4 16:57:34 2020
Total time elapsed: 1.0m:15.78s

QC metrics

Metrics

Metrics

{
    "af_correlation": 0.9386,
    "inflation_factor": 1.2422,
    "mean_EFFECT": -0.0001,
    "n": 162028,
    "n_snps": 7524386,
    "n_clumped_hits": 22,
    "n_p_sig": 1490,
    "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": 82012,
    "n_est": 151545.1154,
    "ratio_se_n": 0.9671,
    "mean_diff": 7.637e-07,
    "ratio_diff": 0.2873,
    "sd_y_est1": 0.9984,
    "sd_y_est2": 0.9656,
    "r2_sum1": 0.0049,
    "r2_sum2": 0.0049,
    "r2_sum3": 0.0052,
    "r2_sum4": 0.0059,
    "ldsc_nsnp_merge_refpanel_ld": 1275293,
    "ldsc_nsnp_merge_regression_ld": 1275293,
    "ldsc_observed_scale_h2_beta": 0.1623,
    "ldsc_observed_scale_h2_se": 0.006,
    "ldsc_intercept_beta": 0.9535,
    "ldsc_intercept_se": 0.0083,
    "ldsc_lambda_gc": 1.2365,
    "ldsc_mean_chisq": 1.4639,
    "ldsc_ratio": -0.1002
}

Flags

name value
af_correlation FALSE
inflation_factor TRUE
n FALSE
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 numeric.mean numeric.sd numeric.p0 numeric.p25 numeric.p50 numeric.p75 numeric.p100 numeric.hist
character ID 0 1.0000000 3 58 0 7524386 0 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
character ALT 0 1.0000000 1 1 0 4 0 NA NA NA NA NA NA NA NA
numeric CHROM 0 1.0000000 NA NA NA NA NA 8.635889e+00 5.749463e+00 1.00000e+00 4.000000e+00 8.000000e+00 1.300000e+01 2.300000e+01 ▇▅▅▂▂
numeric POS 0 1.0000000 NA NA NA NA NA 7.897922e+07 5.633915e+07 8.28000e+02 3.264932e+07 6.968504e+07 1.147327e+08 2.492223e+08 ▇▆▅▂▁
numeric EFFECT 0 1.0000000 NA NA NA NA NA -5.320000e-05 8.160900e-03 -9.90000e-02 -4.000000e-03 0.000000e+00 4.000000e-03 1.010000e-01 ▁▁▇▁▁
numeric SE 0 1.0000000 NA NA NA NA NA 6.546900e-03 4.180000e-03 3.00000e-03 4.000000e-03 5.000000e-03 8.000000e-03 3.600000e-02 ▇▂▁▁▁
numeric PVAL 0 1.0000000 NA NA NA NA NA 4.642702e-01 2.985285e-01 0.00000e+00 1.966002e-01 4.522005e-01 7.226001e-01 1.000000e+00 ▇▆▆▆▆
numeric PVAL_ztest 0 1.0000000 NA NA NA NA NA 4.624693e-01 3.036134e-01 0.00000e+00 1.824224e-01 4.532547e-01 7.388827e-01 1.000000e+00 ▇▆▆▆▆
numeric AF 0 1.0000000 NA NA NA NA NA 2.669879e-01 2.602480e-01 1.11900e-02 5.224000e-02 1.698000e-01 4.216000e-01 9.888100e-01 ▇▃▂▁▁
numeric AF_reference 82012 0.9891005 NA NA NA NA NA 2.675116e-01 2.525242e-01 1.99700e-04 5.990420e-02 1.821090e-01 4.175320e-01 1.000000e+00 ▇▃▂▂▁
numeric N 0 1.0000000 NA NA NA NA NA 1.620280e+05 0.000000e+00 1.62028e+05 1.620280e+05 1.620280e+05 1.620280e+05 1.620280e+05 ▁▁▇▁▁

Head and tail

CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
1 752566 rs3094315 G A -0.005 0.006 0.3980998 0.4046568 0.8451 0.718251 162028
1 752721 rs3131972 A G -0.005 0.006 0.4045004 0.4046568 0.8414 0.653355 162028
1 753474 rs2073814 C G -0.005 0.006 0.4199001 0.4046568 0.8358 0.611422 162028
1 753541 rs2073813 G A 0.004 0.006 0.5137999 0.5049851 0.1213 0.301917 162028
1 754182 rs3131969 A G -0.004 0.006 0.5071997 0.5049851 0.8787 0.678514 162028
1 754192 rs3131968 A G -0.004 0.006 0.4944997 0.5049851 0.8787 0.678514 162028
1 754503 rs3115859 G A -0.004 0.006 0.4994005 0.5049851 0.8414 0.663938 162028
1 755890 rs3115858 A T -0.007 0.006 0.2656000 0.2433450 0.8713 0.751398 162028
1 757640 rs3115853 G A -0.005 0.006 0.4243000 0.4046568 0.8787 0.640176 162028
1 757734 rs4951929 C T -0.005 0.006 0.4070999 0.4046568 0.8787 0.748203 162028
CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
22 51194679 rs6009965 T C 0.001 0.004 0.7977999 0.8025873 0.41230 0.4758390 162028
22 51196164 rs8136603 A T -0.017 0.008 0.0461105 0.0335866 0.05410 0.1427720 162028
22 51196922 rs181629058 G A -0.011 0.013 0.4180998 0.3974669 0.02612 0.0087859 162028
22 51197602 rs187225588 T A -0.020 0.009 0.0218499 0.0262683 0.05597 0.0175719 162028
22 51198027 rs34939255 A G 0.001 0.005 0.9030999 0.8414806 0.23510 0.0984425 162028
22 51198569 rs142671391 G C -0.008 0.010 0.4482002 0.4237108 0.04104 0.1110220 162028
22 51198868 rs185017671 T C 0.021 0.020 0.2938001 0.2937181 0.01119 0.0045926 162028
22 51198998 rs117815989 C A 0.021 0.020 0.2925998 0.2937181 0.01119 0.0045926 162028
22 51208568 rs148425445 G T -0.015 0.008 0.0722703 0.0607927 0.05410 0.1160140 162028
23 100784211 rs188350543 C A 0.001 0.004 0.8774999 0.8025873 0.72200 0.6498010 162028

bcf preview

1   752566  rs3094315   G   A   .   PASS    AF=0.8451   ES:SE:LP:AF:SS:ID   -0.005:0.006:0.400008:0.8451:162028:rs3094315
1   752721  rs3131972   A   G   .   PASS    AF=0.8414   ES:SE:LP:AF:SS:ID   -0.005:0.006:0.393081:0.8414:162028:rs3131972
1   753474  rs2073814   C   G   .   PASS    AF=0.8358   ES:SE:LP:AF:SS:ID   -0.005:0.006:0.376854:0.8358:162028:rs2073814
1   753541  rs2073813   G   A   .   PASS    AF=0.1213   ES:SE:LP:AF:SS:ID   0.004:0.006:0.289206:0.1213:162028:rs2073813
1   754182  rs3131969   A   G   .   PASS    AF=0.8787   ES:SE:LP:AF:SS:ID   -0.004:0.006:0.294821:0.8787:162028:rs3131969
1   754192  rs3131968   A   G   .   PASS    AF=0.8787   ES:SE:LP:AF:SS:ID   -0.004:0.006:0.305834:0.8787:162028:rs3131968
1   754503  rs3115859   G   A   .   PASS    AF=0.8414   ES:SE:LP:AF:SS:ID   -0.004:0.006:0.301551:0.8414:162028:rs3115859
1   755890  rs3115858   A   T   .   PASS    AF=0.8713   ES:SE:LP:AF:SS:ID   -0.007:0.006:0.575772:0.8713:162028:rs3115858
1   757640  rs3115853   G   A   .   PASS    AF=0.8787   ES:SE:LP:AF:SS:ID   -0.005:0.006:0.372327:0.8787:162028:rs3115853
1   757734  rs4951929   C   T   .   PASS    AF=0.8787   ES:SE:LP:AF:SS:ID   -0.005:0.006:0.390299:0.8787:162028:rs4951929
1   757936  rs4951862   C   A   .   PASS    AF=0.8769   ES:SE:LP:AF:SS:ID   -0.005:0.006:0.375924:0.8769:162028:rs4951862
1   758144  rs3131956   A   G   .   PASS    AF=0.8489   ES:SE:LP:AF:SS:ID   -0.005:0.006:0.417482:0.8489:162028:rs3131956
1   758626  rs3131954   C   T   .   PASS    AF=0.8731   ES:SE:LP:AF:SS:ID   -0.005:0.007:0.335076:0.8731:162028:rs3131954
1   768253  rs2977608   A   C   .   PASS    AF=0.7761   ES:SE:LP:AF:SS:ID   -0.005:0.005:0.510182:0.7761:162028:rs2977608
1   768448  rs12562034  G   A   .   PASS    AF=0.08769  ES:SE:LP:AF:SS:ID   0.003:0.007:0.173536:0.08769:162028:rs12562034
1   769963  rs7518545   G   A   .   PASS    AF=0.08582  ES:SE:LP:AF:SS:ID   0.005:0.007:0.307241:0.08582:162028:rs7518545
1   771823  rs2977605   T   C   .   PASS    AF=0.875    ES:SE:LP:AF:SS:ID   -0.005:0.007:0.34756:0.875:162028:rs2977605
1   772755  rs2905039   A   C   .   PASS    AF=0.8769   ES:SE:LP:AF:SS:ID   -0.005:0.007:0.326795:0.8769:162028:rs2905039
1   775181  rs61768182  A   G   .   PASS    AF=0.1213   ES:SE:LP:AF:SS:ID   0.01:0.006:0.985479:0.1213:162028:rs61768182
1   777122  rs2980319   A   T   .   PASS    AF=0.8806   ES:SE:LP:AF:SS:ID   -0.008:0.006:0.768785:0.8806:162028:rs2980319
1   778745  rs1055606   A   G   .   PASS    AF=0.1175   ES:SE:LP:AF:SS:ID   0.01:0.006:1.06651:0.1175:162028:rs1055606
1   779322  rs4040617   A   G   .   PASS    AF=0.1175   ES:SE:LP:AF:SS:ID   0.01:0.006:0.996109:0.1175:162028:rs4040617
1   780785  rs2977612   T   A   .   PASS    AF=0.8787   ES:SE:LP:AF:SS:ID   -0.007:0.006:0.713544:0.8787:162028:rs2977612
1   781845  rs61768199  A   G   .   PASS    AF=0.09328  ES:SE:LP:AF:SS:ID   0.012:0.007:1.07119:0.09328:162028:rs61768199
1   783318  rs6686696   A   G   .   PASS    AF=0.1101   ES:SE:LP:AF:SS:ID   0.009:0.006:0.929593:0.1101:162028:rs6686696
1   785050  rs2905062   G   A   .   PASS    AF=0.8806   ES:SE:LP:AF:SS:ID   -0.008:0.006:0.718058:0.8806:162028:rs2905062
1   786995  rs61768202  G   A   .   PASS    AF=0.1194   ES:SE:LP:AF:SS:ID   0.009:0.006:0.946154:0.1194:162028:rs61768202
1   787606  rs3863622   G   T   .   PASS    AF=0.1194   ES:SE:LP:AF:SS:ID   0.01:0.006:1.00485:0.1194:162028:rs3863622
1   787844  rs2905053   C   T   .   PASS    AF=0.8806   ES:SE:LP:AF:SS:ID   -0.008:0.006:0.751781:0.8806:162028:rs2905053
1   798400  rs10900604  A   G   .   PASS    AF=0.1978   ES:SE:LP:AF:SS:ID   -0.005:0.005:0.49853:0.1978:162028:rs10900604
1   798959  rs11240777  G   A   .   PASS    AF=0.2015   ES:SE:LP:AF:SS:ID   -0.006:0.005:0.552687:0.2015:162028:rs11240777
1   833927  rs28593608  T   C   .   PASS    AF=0.2127   ES:SE:LP:AF:SS:ID   -0.009:0.005:1.04499:0.2127:162028:rs28593608
1   834198  rs28385272  T   C   .   PASS    AF=0.2127   ES:SE:LP:AF:SS:ID   -0.009:0.005:1.00235:0.2127:162028:rs28385272
1   834928  rs4422949   A   G   .   PASS    AF=0.2146   ES:SE:LP:AF:SS:ID   -0.006:0.005:0.616364:0.2146:162028:rs4422949
1   834999  rs28570054  G   A   .   PASS    AF=0.2127   ES:SE:LP:AF:SS:ID   -0.007:0.005:0.718967:0.2127:162028:rs28570054
1   836529  rs28731045  C   G   .   PASS    AF=0.2146   ES:SE:LP:AF:SS:ID   -0.007:0.005:0.786482:0.2146:162028:rs28731045
1   836924  rs72890788  G   A   .   PASS    AF=0.2127   ES:SE:LP:AF:SS:ID   -0.007:0.005:0.846795:0.2127:162028:rs72890788
1   838387  rs4970384   T   C   .   PASS    AF=0.2164   ES:SE:LP:AF:SS:ID   -0.007:0.005:0.757956:0.2164:162028:rs4970384
1   838555  rs4970383   C   A   .   PASS    AF=0.2388   ES:SE:LP:AF:SS:ID   -0.004:0.005:0.39599:0.2388:162028:rs4970383
1   839538  rs142764718 G   A   .   PASS    AF=0.01119  ES:SE:LP:AF:SS:ID   -0.045:0.021:1.45161:0.01119:162028:rs142764718
1   841085  rs1574243   C   G   .   PASS    AF=0.2276   ES:SE:LP:AF:SS:ID   -0.003:0.005:0.289713:0.2276:162028:rs1574243
1   842013  rs7419119   T   G   .   PASS    AF=0.2146   ES:SE:LP:AF:SS:ID   -0.009:0.005:1.11053:0.2146:162028:rs7419119
1   842362  rs28540380  C   T   .   PASS    AF=0.222    ES:SE:LP:AF:SS:ID   -0.01:0.005:1.36191:0.222:162028:rs28540380
1   845274  rs112856858 G   T   .   PASS    AF=0.1959   ES:SE:LP:AF:SS:ID   -0.009:0.005:1.16368:0.1959:162028:rs112856858
1   845635  rs117086422 C   T   .   PASS    AF=0.1847   ES:SE:LP:AF:SS:ID   -0.013:0.005:2.0461:0.1847:162028:rs117086422
1   845938  rs57760052  G   A   .   PASS    AF=0.2034   ES:SE:LP:AF:SS:ID   -0.007:0.005:0.857611:0.2034:162028:rs57760052
1   846078  rs28612348  C   T   .   PASS    AF=0.1847   ES:SE:LP:AF:SS:ID   -0.015:0.005:2.51442:0.1847:162028:rs28612348
1   846398  rs58781670  G   A   .   PASS    AF=0.2015   ES:SE:LP:AF:SS:ID   -0.007:0.005:0.890421:0.2015:162028:rs58781670
1   846465  rs60454217  C   T   .   PASS    AF=0.01866  ES:SE:LP:AF:SS:ID   0.056:0.017:3.05178:0.01866:162028:rs60454217
1   846543  rs79396034  G   T   .   PASS    AF=0.01493  ES:SE:LP:AF:SS:ID   0.058:0.017:3.02803:0.01493:162028:rs79396034