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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    "FORMAT.1": "<ID=ES,Number=A,Type=Float,Description=\"Effect size estimate relative to the alternative allele\">",
    "FORMAT.2": "<ID=EZ,Number=A,Type=Float,Description=\"Z-score provided if it was used to derive the EFFECT and SE fields\">",
    "FORMAT.3": "<ID=ID,Number=1,Type=String,Description=\"Study variant identifier\">",
    "FORMAT.4": "<ID=LP,Number=A,Type=Float,Description=\"-log10 p-value for effect estimate\">",
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    "FORMAT.8": "<ID=SS,Number=A,Type=Float,Description=\"Sample size used to estimate genetic effect\">",
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    "INFO.1": "<ID=ReverseComplementedAlleles,Number=0,Type=Flag,Description=\"The REF and the ALT alleles have been reverse complemented in liftover since the mapping from the previous reference to the current one was on the negative strand.\">",
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    "file_date": "2019-10-26T21:44:18.208367",
    "gwas_harmonisation_command": "--json /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ebi_gwas_import/processed/EBI-a-GCST005840/EBI-a-GCST005840_data.json --ref /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/QC/genomes/hg38/hg38.fa; 1.1.1",
    "reference": "file:/mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/QC/genomes/b37/human_g1k_v37.fasta",
    "bcftools_annotateVersion": "1.9-74-g6af271c+htslib-1.9-64-g226b4a8",
    "bcftools_annotateCommand": "annotate -a /mnt/storage/home/gh13047/mr-eve/vcf-reference-datasets/dbsnp/dbsnp.v153.b37.vcf.gz -c ID -o /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ebi_gwas_import/processed/EBI-a-GCST005840/EBI-a-GCST005840.vcf.gz -O z /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ebi_gwas_import/processed/EBI-a-GCST005840/EBI-a-GCST005840_data.vcf.gz; Date=Sat Oct 26 21:58:28 2019",
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    "bcftools_viewCommand": "view -h /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/ebi-a-GCST005840/ebi-a-GCST005840.vcf.gz; Date=Sat May  9 22:31:38 2020"
}

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/ebi_gwas_import/processed/EBI-a-GCST005840/EBI-a-GCST005840.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/ebi_gwas_import/processed/EBI-a-GCST005840/ldsc.txt \
--snplist /data/ref/snplist.gz \
--w-ld-chr /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/reference/eur_w_ld_chr/ 

Beginning analysis at Sat Oct 26 22:24:56 2019
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ebi_gwas_import/processed/EBI-a-GCST005840/EBI-a-GCST005840.vcf.gz ...
and extracting SNPs specified in /data/ref/snplist.gz ...
Traceback (most recent call last):
  File "./ldsc/ldsc.py", line 647, in <module>
    sumstats.estimate_h2(args, log)
  File "/mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ebi_gwas_import/igd-hpc-pipeline/resources/gwas_processing/ldsc/ldscore/sumstats.py", line 330, in estimate_h2
    args, log, args.h2)
  File "/mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ebi_gwas_import/igd-hpc-pipeline/resources/gwas_processing/ldsc/ldscore/sumstats.py", line 246, in _read_ld_sumstats
    sumstats = _read_sumstats(args, log, fh, alleles=alleles, dropna=dropna)
  File "/mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ebi_gwas_import/igd-hpc-pipeline/resources/gwas_processing/ldsc/ldscore/sumstats.py", line 165, in _read_sumstats
    sumstats = ps.sumstats(fh, alleles=alleles, dropna=dropna, slh=args.snplist)
  File "/mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ebi_gwas_import/igd-hpc-pipeline/resources/gwas_processing/ldsc/ldscore/parse.py", line 85, in sumstats
    x = read_vcf(fh, alleles, slh)
  File "/mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ebi_gwas_import/igd-hpc-pipeline/resources/gwas_processing/ldsc/ldscore/parse.py", line 161, in read_vcf
    with gzip.open(slh) as f:
  File "/mnt/storage/home/gh13047/mr-eve/conda/ldsc/lib/python2.7/gzip.py", line 34, in open
    return GzipFile(filename, mode, compresslevel)
  File "/mnt/storage/home/gh13047/mr-eve/conda/ldsc/lib/python2.7/gzip.py", line 94, in __init__
    fileobj = self.myfileobj = __builtin__.open(filename, mode or 'rb')
IOError: [Errno 2] No such file or directory: '/data/ref/snplist.gz'

Analysis finished at Sat Oct 26 22:25:48 2019
Total time elapsed: 51.43s

QC metrics

Metrics

Metrics

{
    "af_correlation": 0.9701,
    "inflation_factor": 1.1036,
    "mean_EFFECT": 0.0097,
    "n": "-Inf",
    "n_snps": 7992739,
    "n_clumped_hits": 4,
    "n_p_sig": 73,
    "n_mono": 0,
    "n_ns": 0,
    "n_mac": 0,
    "is_snpid_unique": false,
    "n_miss_EFFECT": 0,
    "n_miss_SE": 0,
    "n_miss_PVAL": 0,
    "n_miss_AF": 0,
    "n_miss_AF_reference": 148748,
    "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": "NA",
    "ldsc_nsnp_merge_regression_ld": "NA",
    "ldsc_observed_scale_h2_beta": "NA",
    "ldsc_observed_scale_h2_se": "NA",
    "ldsc_intercept_beta": "NA",
    "ldsc_intercept_se": "NA",
    "ldsc_lambda_gc": "NA",
    "ldsc_mean_chisq": "NA",
    "ldsc_ratio": "NA"
}

Flags

name value
af_correlation FALSE
inflation_factor FALSE
n TRUE
is_snpid_non_unique TRUE
mean_EFFECT_nonfinite FALSE
mean_EFFECT_05 FALSE
mean_EFFECT_01 FALSE
mean_chisq TRUE
n_p_sig FALSE
miss_EFFECT FALSE
miss_SE FALSE
miss_PVAL FALSE
ldsc_ratio TRUE
ldsc_intercept_beta TRUE
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 7975865 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 7975887 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 8.650431e+00 5.749033e+00 1.0000 4.000000e+00 8.000000e+00 1.300000e+01 2.300000e+01 ▇▅▅▂▂
numeric POS 0 1.0000000 NA NA NA NA NA NA NA 7.865799e+07 5.646290e+07 828.0000 3.219433e+07 6.912551e+07 1.145187e+08 2.492297e+08 ▇▆▅▂▁
numeric EFFECT 0 1.0000000 NA NA NA NA NA NA NA 9.653200e-03 5.617250e-02 -0.9038 -1.810000e-02 4.700000e-03 2.990000e-02 7.145000e-01 ▁▁▇▁▁
numeric SE 0 1.0000000 NA NA NA NA NA NA NA 4.388740e-02 3.110480e-02 0.0186 2.320000e-02 3.050000e-02 5.180000e-02 2.852000e-01 ▇▁▁▁▁
numeric PVAL 0 1.0000000 NA NA NA NA NA NA NA 4.840105e-01 2.923595e-01 0.0000 2.270001e-01 4.786003e-01 7.370993e-01 9.997000e-01 ▇▇▇▇▇
numeric PVAL_ztest 0 1.0000000 NA NA NA NA NA NA NA 4.840098e-01 2.923592e-01 0.0000 2.269916e-01 4.786223e-01 7.370470e-01 9.996270e-01 ▇▇▇▇▇
numeric AF 0 1.0000000 NA NA NA NA NA NA NA 2.781168e-01 2.408003e-01 0.0101 7.890000e-02 2.022000e-01 4.220000e-01 9.897000e-01 ▇▃▂▂▁
numeric AF_reference 148748 0.9813503 NA NA NA NA NA NA NA 2.633431e-01 2.526627e-01 0.0000 5.690890e-02 1.753190e-01 4.103430e-01 1.000000e+00 ▇▃▂▁▁

Head and tail

CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
1 662622 rs61769339 G A 0.0585 0.0571 0.3059997 0.3055905 0.1423 0.1475640 NA
1 693731 rs12238997 A G 0.0425 0.0526 0.4197000 0.4190993 0.1453 0.1417730 NA
1 729679 rs4951859 C G -0.0339 0.0488 0.4869003 0.4872608 0.7638 0.6399760 NA
1 731718 rs142557973 T C 0.0687 0.0498 0.1681001 0.1677351 0.1527 0.1543530 NA
1 732809 rs12131618 T C 0.0508 0.0764 0.5064995 0.5061007 0.0725 0.0615016 NA
1 734349 rs141242758 T C 0.0707 0.0500 0.1574001 0.1573619 0.1505 0.1525560 NA
1 736289 rs79010578 T A 0.0497 0.0540 0.3565997 0.3573792 0.1477 0.1395770 NA
1 751756 rs143225517 T C 0.0253 0.0342 0.4590997 0.4594419 0.1842 0.2422120 NA
1 752566 rs3094315 G A -0.0101 0.0307 0.7424001 0.7421631 0.7951 0.7182510 NA
1 752721 rs3131972 A G -0.0143 0.0313 0.6469996 0.6477652 0.7444 0.6533550 NA
CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
22 51221731 rs115055839 T C 0.0027 0.0618 0.9651000 0.9651521 0.0726 0.0625000 NA
22 51222052 rs2879915 G A 0.0299 0.0406 0.4624002 0.4614549 0.2625 0.2194490 NA
22 51224600 rs187908482 G A -0.0779 0.0620 0.2094002 0.2089523 0.1075 0.0387380 NA
22 51228910 rs145146472 G A -0.0136 0.0383 0.7218999 0.7225211 0.2805 0.2276360 NA
22 51229805 rs9616985 T C -0.0262 0.0608 0.6663003 0.6665258 0.0776 0.0730831 NA
22 51229855 rs144549712 G A 0.0636 0.0632 0.3140003 0.3142573 0.1320 0.1160140 NA
22 51233300 rs9616839 C T 0.0163 0.0423 0.6999999 0.6999835 0.3244 0.3146960 NA
22 51237063 rs3896457 T C -0.0101 0.0449 0.8211999 0.8220226 0.2655 0.2050720 NA
23 46256106 rs12007097 G C -0.0052 0.1047 0.9604001 0.9603888 0.9721 0.6821190 NA
23 100784211 rs188350543 C A 0.0110 0.0290 0.7048002 0.7044574 0.7409 0.6498010 NA

bcf preview

1   662622  rs61769339  G   A   .   PASS    AF=0.1423   ES:SE:LP:AF:ID  0.0585:0.0571:0.514279:0.1423:rs61769339
1   693731  rs12238997  A   G   .   PASS    AF=0.1453   ES:SE:LP:AF:ID  0.0425:0.0526:0.377061:0.1453:rs12238997
1   729679  rs4951859   C   G   .   PASS    AF=0.7638   ES:SE:LP:AF:ID  -0.0339:0.0488:0.31256:0.7638:rs4951859
1   731718  rs58276399  T   C   .   PASS    AF=0.1527   ES:SE:LP:AF:ID  0.0687:0.0498:0.774432:0.1527:rs58276399
1   732809  rs12131618  T   C   .   PASS    AF=0.0725   ES:SE:LP:AF:ID  0.0508:0.0764:0.295421:0.0725:rs12131618
1   734349  rs141242758 T   C   .   PASS    AF=0.1505   ES:SE:LP:AF:ID  0.0707:0.05:0.802995:0.1505:rs141242758
1   736289  rs79010578  T   A   .   PASS    AF=0.1477   ES:SE:LP:AF:ID  0.0497:0.054:0.447819:0.1477:rs79010578
1   751756  rs28527770  T   C   .   PASS    AF=0.1842   ES:SE:LP:AF:ID  0.0253:0.0342:0.338093:0.1842:rs28527770
1   752566  rs3094315   G   A   .   PASS    AF=0.7951   ES:SE:LP:AF:ID  -0.0101:0.0307:0.129362:0.7951:rs3094315
1   752721  rs3131972   A   G   .   PASS    AF=0.7444   ES:SE:LP:AF:ID  -0.0143:0.0313:0.189096:0.7444:rs3131972
1   752894  rs3131971   T   C   .   PASS    AF=0.7944   ES:SE:LP:AF:ID  -0.0166:0.0323:0.216025:0.7944:rs3131971
1   753405  rs3115860   C   A   .   PASS    AF=0.8109   ES:SE:LP:AF:ID  -0.0318:0.033:0.473144:0.8109:rs3115860
1   753474  rs2073814   C   G   .   PASS    AF=0.7393   ES:SE:LP:AF:ID  -0.0331:0.0377:0.420559:0.7393:rs2073814
1   753541  rs2073813   G   A   .   PASS    AF=0.229    ES:SE:LP:AF:ID  0.0674:0.0389:1.08124:0.229:rs2073813
1   754182  rs3131969   A   G   .   PASS    AF=0.763    ES:SE:LP:AF:ID  -0.0757:0.0389:1.28887:0.763:rs3131969
1   754192  rs3131968   A   G   .   PASS    AF=0.7625   ES:SE:LP:AF:ID  -0.0761:0.0389:1.29456:0.7625:rs3131968
1   754334  rs3131967   T   C   .   PASS    AF=0.7555   ES:SE:LP:AF:ID  -0.0644:0.0393:0.992679:0.7555:rs3131967
1   754503  rs3115859   G   A   .   PASS    AF=0.7487   ES:SE:LP:AF:ID  -0.0257:0.033:0.360613:0.7487:rs3115859
1   754964  rs3131966   C   T   .   PASS    AF=0.7395   ES:SE:LP:AF:ID  -0.0325:0.0381:0.404835:0.7395:rs3131966
1   755775  rs3131965   A   G   .   PASS    AF=0.781    ES:SE:LP:AF:ID  -0.0067:0.0362:0.0687456:0.781:rs3131965
1   755890  rs3115858   A   T   .   PASS    AF=0.8067   ES:SE:LP:AF:ID  -0.0328:0.0338:0.479124:0.8067:rs3115858
1   756604  rs3131962   A   G   .   PASS    AF=0.7959   ES:SE:LP:AF:ID  -0.0349:0.0345:0.507519:0.7959:rs3131962
1   757640  rs3115853   G   A   .   PASS    AF=0.7556   ES:SE:LP:AF:ID  -0.0508:0.0397:0.698102:0.7556:rs3115853
1   757734  rs4951929   C   T   .   PASS    AF=0.807    ES:SE:LP:AF:ID  -0.039:0.0346:0.586868:0.807:rs4951929
1   757936  rs4951862   C   A   .   PASS    AF=0.8054   ES:SE:LP:AF:ID  -0.035:0.0347:0.505567:0.8054:rs4951862
1   758144  rs3131956   A   G   .   PASS    AF=0.799    ES:SE:LP:AF:ID  -0.0368:0.0336:0.56336:0.799:rs3131956
1   758626  rs3131954   C   T   .   PASS    AF=0.8072   ES:SE:LP:AF:ID  -0.0308:0.0351:0.420788:0.8072:rs3131954
1   759700  rs3115852   T   C   .   PASS    AF=0.7909   ES:SE:LP:AF:ID  0.0043:0.0368:0.0421055:0.7909:rs3115852
1   759837  rs3115851   T   A   .   PASS    AF=0.8078   ES:SE:LP:AF:ID  -0.0367:0.0352:0.526805:0.8078:rs3115851
1   760912  rs1048488   C   T   .   PASS    AF=0.7718   ES:SE:LP:AF:ID  -0.0057:0.0348:0.060331:0.7718:rs1048488
1   761147  rs3115850   T   C   .   PASS    AF=0.7744   ES:SE:LP:AF:ID  -0.0199:0.0343:0.250264:0.7744:rs3115850
1   761732  rs2286139   C   T   .   PASS    AF=0.7376   ES:SE:LP:AF:ID  -0.0605:0.0426:0.807433:0.7376:rs2286139
1   761752  rs1057213   C   T   .   PASS    AF=0.8033   ES:SE:LP:AF:ID  -0.0251:0.0364:0.309715:0.8033:rs1057213
1   762273  rs3115849   G   A   .   PASS    AF=0.7935   ES:SE:LP:AF:ID  -0.0398:0.0361:0.567351:0.7935:rs3115849
1   762472  rs145493205 C   T   .   PASS    AF=0.1141   ES:SE:LP:AF:ID  0.0159:0.0751:0.0797723:0.1141:rs145493205
1   762485  rs12095200  C   A   .   PASS    AF=0.1401   ES:SE:LP:AF:ID  0.09:0.0542:1.01233:0.1401:rs12095200
1   762589  rs3115848   G   C   .   PASS    AF=0.7877   ES:SE:LP:AF:ID  -0.0272:0.0364:0.343231:0.7877:rs3115848
1   762592  rs3131950   C   G   .   PASS    AF=0.7871   ES:SE:LP:AF:ID  -0.0293:0.0364:0.376337:0.7871:rs3131950
1   762601  rs3131949   T   C   .   PASS    AF=0.7849   ES:SE:LP:AF:ID  -0.0427:0.0366:0.612966:0.7849:rs3131949
1   762632  rs3131948   T   A   .   PASS    AF=0.7855   ES:SE:LP:AF:ID  -0.0334:0.0367:0.440932:0.7855:rs3131948
1   764191  rs7515915   T   G   .   PASS    AF=0.1786   ES:SE:LP:AF:ID  0.0407:0.037:0.566871:0.1786:rs7515915
1   766007  rs61768174  A   C   .   PASS    AF=0.1244   ES:SE:LP:AF:ID  0.0429:0.0446:0.473402:0.1244:rs61768174
1   768253  rs2977608   A   C   .   PASS    AF=0.6826   ES:SE:LP:AF:ID  0.0107:0.034:0.123551:0.6826:rs2977608
1   768448  rs12562034  G   A   .   PASS    AF=0.1357   ES:SE:LP:AF:ID  -0.0336:0.0404:0.391474:0.1357:rs12562034
1   769223  rs60320384  C   G   .   PASS    AF=0.1638   ES:SE:LP:AF:ID  0.036:0.0384:0.457922:0.1638:rs60320384
1   769963  rs7518545   G   A   .   PASS    AF=0.1294   ES:SE:LP:AF:ID  -0.0283:0.0427:0.294393:0.1294:rs7518545
1   771823  rs2977605   T   C   .   PASS    AF=0.8064   ES:SE:LP:AF:ID  -0.0433:0.0369:0.617983:0.8064:rs2977605
1   771967  rs59066358  G   A   .   PASS    AF=0.1747   ES:SE:LP:AF:ID  0.044:0.0379:0.608712:0.1747:rs59066358
1   772755  rs2905039   A   C   .   PASS    AF=0.8082   ES:SE:LP:AF:ID  -0.0426:0.0371:0.601366:0.8082:rs2905039
1   774874  rs28810152  A   C   .   PASS    AF=0.6721   ES:SE:LP:AF:ID  -0.0348:0.0486:0.324313:0.6721:rs28810152