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.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": "2019-10-26T21:45:36.977846",
    "gwas_harmonisation_command": "--json /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ebi_gwas_import/processed/EBI-a-GCST006909/EBI-a-GCST006909_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",
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    "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-GCST006909/EBI-a-GCST006909.vcf.gz -O z /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ebi_gwas_import/processed/EBI-a-GCST006909/EBI-a-GCST006909_data.vcf.gz; Date=Sat Oct 26 22:02:11 2019",
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    "bcftools_viewCommand": "view -h /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/ebi-a-GCST006909/ebi-a-GCST006909.vcf.gz; Date=Sun May 10 12:32:03 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-GCST006909/EBI-a-GCST006909.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-GCST006909/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 22:28:03 2019
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ebi_gwas_import/processed/EBI-a-GCST006909/EBI-a-GCST006909.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 22:28:56 2019
Total time elapsed: 53.38s

QC metrics

Metrics

Metrics

{
    "af_correlation": 0.9422,
    "inflation_factor": 1.1187,
    "mean_EFFECT": 0.0143,
    "n": "-Inf",
    "n_snps": 8280845,
    "n_clumped_hits": 0,
    "n_p_sig": 0,
    "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": 171153,
    "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 59 0 8263682 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 8263706 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 8.647773e+00 5.751692e+00 1.0000000 4.000000e+00 8.000000e+00 1.300000e+01 2.300000e+01 ▇▅▅▂▂
numeric POS 0 1.0000000 NA NA NA NA NA NA NA 7.858579e+07 5.643227e+07 828.0000000 3.218412e+07 6.901092e+07 1.144051e+08 2.492297e+08 ▇▆▅▂▁
numeric EFFECT 0 1.0000000 NA NA NA NA NA NA NA 1.434070e-02 6.862050e-02 -1.0428000 -1.960000e-02 6.900000e-03 3.750000e-02 8.987000e-01 ▁▁▇▁▁
numeric SE 0 1.0000000 NA NA NA NA NA NA NA 5.291910e-02 3.857330e-02 0.0206000 2.620000e-02 3.610000e-02 6.630000e-02 3.954000e-01 ▇▁▁▁▁
numeric PVAL 0 1.0000000 NA NA NA NA NA NA NA 4.819981e-01 2.930993e-01 0.0000001 2.242999e-01 4.756002e-01 7.359003e-01 9.998000e-01 ▇▇▇▇▇
numeric PVAL_ztest 0 1.0000000 NA NA NA NA NA NA NA 4.819974e-01 2.930989e-01 0.0000001 2.242693e-01 4.756536e-01 7.359178e-01 9.996928e-01 ▇▇▇▇▇
numeric AF 0 1.0000000 NA NA NA NA NA NA NA 2.549538e-01 2.594681e-01 0.0101000 4.320000e-02 1.510000e-01 4.018000e-01 9.899000e-01 ▇▂▂▁▁
numeric AF_reference 171153 0.9792886 NA NA NA NA NA NA NA 2.553455e-01 2.533464e-01 0.0000000 4.732430e-02 1.653350e-01 4.001600e-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 0.0158 0.0547 0.7733000 0.7726975 0.1199 0.1475640 NA
1 693731 rs12238997 A G 0.0157 0.0518 0.7614002 0.7618222 0.1265 0.1417730 NA
1 729679 rs4951859 C G -0.0200 0.0473 0.6729999 0.6724171 0.8337 0.6399760 NA
1 731718 rs142557973 T C 0.0137 0.0499 0.7839006 0.7836627 0.1316 0.1543530 NA
1 732809 rs12131618 T C 0.0657 0.0733 0.3701996 0.3700837 0.0715 0.0615016 NA
1 734349 rs141242758 T C 0.0201 0.0502 0.6889996 0.6888631 0.1298 0.1525560 NA
1 736289 rs79010578 T A 0.0391 0.0536 0.4657995 0.4657096 0.1371 0.1395770 NA
1 748878 rs143214544 G T -0.0479 0.0467 0.3053001 0.3050349 0.7791 0.6309900 NA
1 751756 rs143225517 T C -0.0094 0.0432 0.8272000 0.8277466 0.1394 0.2422120 NA
1 752566 rs3094315 G A -0.0161 0.0389 0.6797997 0.6789607 0.8335 0.7182510 NA
CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
22 51222052 rs2879915 G A 0.0178 0.0409 0.6642002 0.6634116 0.2649 0.2194490 NA
22 51224600 rs187908482 G A -0.0449 0.0577 0.4369996 0.4364730 0.1093 0.0387380 NA
22 51228910 rs145146472 G A -0.0093 0.0363 0.7971000 0.7977977 0.2861 0.2276360 NA
22 51229805 rs9616985 T C 0.0716 0.0572 0.2110999 0.2106616 0.0706 0.0730831 NA
22 51229855 rs144549712 G A 0.0802 0.0631 0.2034998 0.2037292 0.1348 0.1160140 NA
22 51233300 rs9616839 C T 0.0726 0.0443 0.1012001 0.1012495 0.3283 0.3146960 NA
22 51237063 rs3896457 T C 0.0093 0.0426 0.8278000 0.8271877 0.2706 0.2050720 NA
22 51238249 rs149733995 A C 0.0316 0.0780 0.6856998 0.6853833 0.0697 NA NA
23 46256106 rs12007097 G C -0.0434 0.0959 0.6505999 0.6508694 0.9742 0.6821190 NA
23 100784211 rs188350543 C A 0.0353 0.0319 0.2687002 0.2684742 0.7420 0.6498010 NA

bcf preview

1   662622  rs61769339  G   A   .   PASS    AF=0.1199   ES:SE:LP:AF:ID  0.0158:0.0547:0.111652:0.1199:rs61769339
1   693731  rs12238997  A   G   .   PASS    AF=0.1265   ES:SE:LP:AF:ID  0.0157:0.0518:0.118387:0.1265:rs12238997
1   729679  rs4951859   C   G   .   PASS    AF=0.8337   ES:SE:LP:AF:ID  -0.02:0.0473:0.171985:0.8337:rs4951859
1   731718  rs58276399  T   C   .   PASS    AF=0.1316   ES:SE:LP:AF:ID  0.0137:0.0499:0.105739:0.1316:rs58276399
1   732809  rs12131618  T   C   .   PASS    AF=0.0715   ES:SE:LP:AF:ID  0.0657:0.0733:0.431564:0.0715:rs12131618
1   734349  rs141242758 T   C   .   PASS    AF=0.1298   ES:SE:LP:AF:ID  0.0201:0.0502:0.161781:0.1298:rs141242758
1   736289  rs79010578  T   A   .   PASS    AF=0.1371   ES:SE:LP:AF:ID  0.0391:0.0536:0.331801:0.1371:rs79010578
1   748878  rs2519043   G   T   .   PASS    AF=0.7791   ES:SE:LP:AF:ID  -0.0479:0.0467:0.515273:0.7791:rs2519043
1   751756  rs28527770  T   C   .   PASS    AF=0.1394   ES:SE:LP:AF:ID  -0.0094:0.0432:0.0823895:0.1394:rs28527770
1   752566  rs3094315   G   A   .   PASS    AF=0.8335   ES:SE:LP:AF:ID  -0.0161:0.0389:0.167619:0.8335:rs3094315
1   752721  rs3131972   A   G   .   PASS    AF=0.8171   ES:SE:LP:AF:ID  -0.0213:0.039:0.232547:0.8171:rs3131972
1   752894  rs3131971   T   C   .   PASS    AF=0.8209   ES:SE:LP:AF:ID  -0.0136:0.0407:0.131708:0.8209:rs3131971
1   753405  rs3115860   C   A   .   PASS    AF=0.8544   ES:SE:LP:AF:ID  -0.0072:0.0419:0.063788:0.8544:rs3115860
1   753474  rs2073814   C   G   .   PASS    AF=0.8182   ES:SE:LP:AF:ID  -0.0141:0.0406:0.137928:0.8182:rs2073814
1   753541  rs2073813   G   A   .   PASS    AF=0.146    ES:SE:LP:AF:ID  0.0125:0.0432:0.11227:0.146:rs2073813
1   754182  rs3131969   A   G   .   PASS    AF=0.8521   ES:SE:LP:AF:ID  0.0038:0.0431:0.0313303:0.8521:rs3131969
1   754192  rs3131968   A   G   .   PASS    AF=0.852    ES:SE:LP:AF:ID  0.0029:0.043:0.0236959:0.852:rs3131968
1   754334  rs3131967   T   C   .   PASS    AF=0.8397   ES:SE:LP:AF:ID  -0.0048:0.0432:0.040577:0.8397:rs3131967
1   754503  rs3115859   G   A   .   PASS    AF=0.827    ES:SE:LP:AF:ID  -0.0154:0.0412:0.150089:0.827:rs3115859
1   754964  rs3131966   C   T   .   PASS    AF=0.8158   ES:SE:LP:AF:ID  -0.0207:0.0415:0.209504:0.8158:rs3131966
1   755775  rs3131965   A   G   .   PASS    AF=0.7966   ES:SE:LP:AF:ID  -0.0206:0.0474:0.177897:0.7966:rs3131965
1   755890  rs3115858   A   T   .   PASS    AF=0.852    ES:SE:LP:AF:ID  -0.0036:0.0424:0.0305375:0.852:rs3115858
1   756604  rs3131962   A   G   .   PASS    AF=0.842    ES:SE:LP:AF:ID  0.0035:0.043:0.0293278:0.842:rs3131962
1   756912  rs6699990   A   G   .   PASS    AF=0.0291   ES:SE:LP:AF:ID  -0.0892:0.1339:0.296537:0.0291:rs6699990
1   757640  rs3115853   G   A   .   PASS    AF=0.8514   ES:SE:LP:AF:ID  -0.0049:0.0436:0.0405293:0.8514:rs3115853
1   757734  rs4951929   C   T   .   PASS    AF=0.8578   ES:SE:LP:AF:ID  -0.0018:0.0436:0.0143939:0.8578:rs4951929
1   757936  rs4951862   C   A   .   PASS    AF=0.8553   ES:SE:LP:AF:ID  0.0068:0.0436:0.0573472:0.8553:rs4951862
1   758144  rs3131956   A   G   .   PASS    AF=0.8429   ES:SE:LP:AF:ID  0.0077:0.0422:0.0684404:0.8429:rs3131956
1   758626  rs3131954   C   T   .   PASS    AF=0.8575   ES:SE:LP:AF:ID  0.0061:0.0438:0.0508052:0.8575:rs3131954
1   759700  rs3115852   T   C   .   PASS    AF=0.8178   ES:SE:LP:AF:ID  -0.0057:0.0487:0.0426801:0.8178:rs3115852
1   759837  rs3115851   T   A   .   PASS    AF=0.8597   ES:SE:LP:AF:ID  -0.015:0.0448:0.132238:0.8597:rs3115851
1   760912  rs1048488   C   T   .   PASS    AF=0.817    ES:SE:LP:AF:ID  -0.0099:0.0435:0.0861332:0.817:rs1048488
1   761147  rs3115850   T   C   .   PASS    AF=0.8183   ES:SE:LP:AF:ID  -0.0279:0.0427:0.290391:0.8183:rs3115850
1   761732  rs2286139   C   T   .   PASS    AF=0.8303   ES:SE:LP:AF:ID  -0.0167:0.0441:0.151811:0.8303:rs2286139
1   761752  rs1057213   C   T   .   PASS    AF=0.8589   ES:SE:LP:AF:ID  -0.0046:0.0454:0.0364483:0.8589:rs1057213
1   762273  rs3115849   G   A   .   PASS    AF=0.8463   ES:SE:LP:AF:ID  -0.0295:0.0442:0.296795:0.8463:rs3115849
1   762472  rs145493205 C   T   .   PASS    AF=0.1031   ES:SE:LP:AF:ID  0.0167:0.0722:0.0875122:0.1031:rs145493205
1   762485  rs12095200  C   A   .   PASS    AF=0.1094   ES:SE:LP:AF:ID  0.0341:0.0565:0.263205:0.1094:rs12095200
1   762589  rs3115848   G   C   .   PASS    AF=0.8388   ES:SE:LP:AF:ID  -0.0252:0.0447:0.241239:0.8388:rs3115848
1   762592  rs3131950   C   G   .   PASS    AF=0.8377   ES:SE:LP:AF:ID  -0.0314:0.0447:0.315873:0.8377:rs3131950
1   762601  rs3131949   T   C   .   PASS    AF=0.8378   ES:SE:LP:AF:ID  -0.0332:0.0452:0.334888:0.8378:rs3131949
1   762632  rs3131948   T   A   .   PASS    AF=0.8378   ES:SE:LP:AF:ID  -0.0251:0.0449:0.239427:0.8378:rs3131948
1   764191  rs7515915   T   G   .   PASS    AF=0.1395   ES:SE:LP:AF:ID  0.0076:0.0451:0.0622314:0.1395:rs7515915
1   766007  rs61768174  A   C   .   PASS    AF=0.1226   ES:SE:LP:AF:ID  0.0213:0.0492:0.176787:0.1226:rs61768174
1   768253  rs2977608   A   C   .   PASS    AF=0.7455   ES:SE:LP:AF:ID  -0.0026:0.0346:0.0270108:0.7455:rs2977608
1   768448  rs12562034  G   A   .   PASS    AF=0.102    ES:SE:LP:AF:ID  -0.0212:0.0456:0.192736:0.102:rs12562034
1   769223  rs60320384  C   G   .   PASS    AF=0.1383   ES:SE:LP:AF:ID  0.0198:0.0459:0.176135:0.1383:rs60320384
1   769963  rs7518545   G   A   .   PASS    AF=0.0988   ES:SE:LP:AF:ID  -0.0024:0.0477:0.0174574:0.0988:rs7518545
1   771823  rs2977605   T   C   .   PASS    AF=0.8587   ES:SE:LP:AF:ID  -0.0131:0.0449:0.113453:0.8587:rs2977605
1   771967  rs59066358  G   A   .   PASS    AF=0.1402   ES:SE:LP:AF:ID  0.005:0.0452:0.0397195:0.1402:rs59066358