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": "2019-10-26T21:53:57.062874",
    "gwas_harmonisation_command": "--json /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ebi_gwas_import/processed/EBI-a-GCST005413/EBI-a-GCST005413_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-GCST005413/EBI-a-GCST005413.vcf.gz -O z /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ebi_gwas_import/processed/EBI-a-GCST005413/EBI-a-GCST005413_data.vcf.gz; Date=Sat Oct 26 22:19:31 2019",
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    "bcftools_viewCommand": "view -h /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/ebi-a-GCST005413/ebi-a-GCST005413.vcf.gz; Date=Sun May 10 03:14:23 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-GCST005413/EBI-a-GCST005413.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-GCST005413/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 22:44:18 2019
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ebi_gwas_import/processed/EBI-a-GCST005413/EBI-a-GCST005413.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 22:45:51 2019
Total time elapsed: 1.0m:32.74s

QC metrics

Metrics

Metrics

{
    "af_correlation": 0.0939,
    "inflation_factor": 0.9696,
    "mean_EFFECT": 0.0052,
    "n": "-Inf",
    "n_snps": 14277791,
    "n_clumped_hits": 16,
    "n_p_sig": 1437,
    "n_mono": 0,
    "n_ns": 964607,
    "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": 1169703,
    "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 TRUE
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 TRUE
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 1.000000 3 59 0 14260288 0 NA NA NA NA NA NA NA NA NA NA
character REF 0 1.000000 1 951 0 42688 0 NA NA NA NA NA NA NA NA NA NA
character ALT 0 1.000000 1 43 0 25888 0 NA NA NA NA NA NA NA NA NA NA
logical N 14260316 0.000000 NA NA NA NA NA NaN : NA NA NA NA NA NA NA NA
numeric CHROM 0 1.000000 NA NA NA NA NA NA NA 8.572234e+00 5.721590e+00 1.0000 4.000000e+00 8.000000e+00 1.300000e+01 2.200000e+01 ▇▅▃▂▂
numeric POS 0 1.000000 NA NA NA NA NA NA NA 7.928099e+07 5.622108e+07 302.0000 3.293080e+07 7.016421e+07 1.149000e+08 2.492303e+08 ▇▆▅▂▁
numeric EFFECT 0 1.000000 NA NA NA NA NA NA NA 5.193000e-03 2.408410e-01 -10.3203 -2.900000e-02 1.900000e-03 3.700000e-02 8.563800e+00 ▁▁▇▁▁
numeric SE 0 1.000000 NA NA NA NA NA NA NA 1.554142e-01 2.672652e-01 0.0155 2.090000e-02 4.990000e-02 1.717000e-01 1.769860e+01 ▇▁▁▁▁
numeric PVAL 0 1.000000 NA NA NA NA NA NA NA 5.038564e-01 2.895532e-01 0.0000 2.541002e-01 5.065998e-01 7.550992e-01 1.000000e+00 ▇▇▇▇▇
numeric PVAL_ztest 0 1.000000 NA NA NA NA NA NA NA 5.038561e-01 2.895529e-01 0.0000 2.541167e-01 5.065033e-01 7.549914e-01 9.999550e-01 ▇▇▇▇▇
numeric AF 0 1.000000 NA NA NA NA NA NA NA 4.466408e-01 4.111992e-01 0.0010 1.810000e-02 3.420000e-01 9.317000e-01 9.990000e-01 ▇▂▁▂▆
numeric AF_reference 1169703 0.917975 NA NA NA NA NA NA NA 1.746858e-01 2.408390e-01 0.0000 4.393000e-03 5.630990e-02 2.573880e-01 1.000000e+00 ▇▂▁▁▁

Head and tail

CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
1 720468 rs187315357 G A 0.2877 0.6980 0.6802006 0.6802092 0.0042 0.0039936 NA
1 721290 rs12565286 G C -0.0929 0.1478 0.5295000 0.5296423 0.0316 0.0371406 NA
1 723891 rs2977670 G C 0.1483 0.1269 0.2426001 0.2425500 0.0420 0.7799520 NA
1 724321 rs753164112 TGAGTG T 0.5606 1.2404 0.6512999 0.6513043 0.0013 NA NA
1 724324 rs28692873 G A -0.1067 0.0927 0.2501002 0.2497220 0.0399 0.0359425 NA
1 724621 rs552249494 CAAATG C -0.1613 0.1531 0.2918999 0.2920845 0.9698 NA NA
1 725389 rs375619475 C T -0.1062 0.0946 0.2615002 0.2615983 0.0386 0.0363419 NA
1 726794 rs28454925 C G -0.1121 0.1495 0.4529998 0.4533554 0.9692 0.0279553 NA
1 729632 rs116720794 C T -0.0960 0.1470 0.5137005 0.5137168 0.0318 0.0099840 NA
1 729679 rs4951859 C G 0.0317 0.0410 0.4396995 0.4394213 0.8313 0.6399760 NA
CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
22 51225002 rs184911728 A G 0.9416 0.9025 0.2968001 0.2967982 0.9950 0.0027955 NA
22 51226620 rs189416433 T A 0.7473 0.8772 0.3943002 0.3942612 0.0034 0.0033946 NA
22 51228910 rs145146472 G A 0.0251 0.0423 0.5538995 0.5529265 0.3125 0.2276360 NA
22 51229805 rs9616985 T C 0.0329 0.0837 0.6944005 0.6942674 0.9306 0.0730831 NA
22 51229855 rs144549712 G A 0.0424 0.1234 0.7313007 0.7311486 0.1445 0.1160140 NA
22 51233300 rs9616839 C T 0.0207 0.0410 0.6139995 0.6136445 0.3755 0.3146960 NA
22 51236013 rs200507571 A AT -0.0067 0.0497 0.8926999 0.8927630 0.7634 0.1487620 NA
22 51237063 rs3896457 T C 0.0159 0.0425 0.7074993 0.7083168 0.6862 0.2050720 NA
22 51238249 rs149733995 A C 0.0203 0.0893 0.8198000 0.8201721 0.9280 NA NA
22 51243297 rs2905159 A T 0.2818 0.2444 0.2489001 0.2488990 0.9682 NA NA

bcf preview

1   720468  rs187315357 G   A   .   PASS    AF=0.0042   ES:SE:LP:AF:ID  0.2877:0.698:0.167363:0.0042:rs187315357
1   721290  rs12565286  G   C   .   PASS    AF=0.0316   ES:SE:LP:AF:ID  -0.0929:0.1478:0.276134:0.0316:rs12565286
1   723891  rs2977670   G   C   .   PASS    AF=0.042    ES:SE:LP:AF:ID  0.1483:0.1269:0.615109:0.042:rs2977670
1   724321  rs753164112 TGAGTG  T   .   PASS    AF=0.0013   ES:SE:LP:AF:ID  0.5606:1.2404:0.186219:0.0013:rs753164112
1   724324  rs28692873  G   A   .   PASS    AF=0.0399   ES:SE:LP:AF:ID  -0.1067:0.0927:0.601886:0.0399:rs28692873
1   724621  rs552249494 CAAATG  C   .   PASS    AF=0.9698   ES:SE:LP:AF:ID  -0.1613:0.1531:0.534766:0.9698:rs552249494
1   725389  rs375619475 C   T   .   PASS    AF=0.0386   ES:SE:LP:AF:ID  -0.1062:0.0946:0.582528:0.0386:rs375619475
1   726794  rs28454925  C   G   .   PASS    AF=0.9692   ES:SE:LP:AF:ID  -0.1121:0.1495:0.343902:0.9692:rs28454925
1   729632  rs116720794 C   T   .   PASS    AF=0.0318   ES:SE:LP:AF:ID  -0.096:0.147:0.28929:0.0318:rs116720794
1   729679  rs4951859   C   G   .   PASS    AF=0.8313   ES:SE:LP:AF:ID  0.0317:0.041:0.356844:0.8313:rs4951859
1   731718  rs58276399  T   C   .   PASS    AF=0.8687   ES:SE:LP:AF:ID  0.0215:0.0262:0.385841:0.8687:rs58276399
1   736289  rs79010578  T   A   .   PASS    AF=0.1421   ES:SE:LP:AF:ID  -0.0456:0.0454:0.501689:0.1421:rs79010578
1   736736  rs10454457  A   G   .   PASS    AF=0.9613   ES:SE:LP:AF:ID  -0.1056:0.0921:0.599289:0.9613:rs10454457
1   745642  rs200097270 AC  A   .   PASS    AF=0.0379   ES:SE:LP:AF:ID  0.0127:0.1292:0.0354575:0.0379:rs200097270
1   746727  rs144595511 G   A   .   PASS    AF=0.0375   ES:SE:LP:AF:ID  0.0309:0.1301:0.0902301:0.0375:rs144595511
1   747966  rs189811062 G   A   .   PASS    AF=0.0123   ES:SE:LP:AF:ID  -0.0077:0.4241:0.00634337:0.0123:rs189811062
1   749963  rs529266287 T   TAA .   PASS    AF=0.8623   ES:SE:LP:AF:ID  -0.0076:0.0242:0.123263:0.8623:rs529266287
1   751456  rs141709959 T   C   .   PASS    AF=0.9603   ES:SE:LP:AF:ID  -0.0671:0.1215:0.235899:0.9603:rs141709959
1   751756  rs28527770  T   C   .   PASS    AF=0.8637   ES:SE:LP:AF:ID  -0.0264:0.0434:0.2652:0.8637:rs28527770
1   752307  rs201062411 AT  A   .   PASS    AF=0.0397   ES:SE:LP:AF:ID  -0.1165:0.0872:0.740884:0.0397:rs201062411
1   752478  rs146277091 G   A   .   PASS    AF=0.0411   ES:SE:LP:AF:ID  -0.1198:0.0866:0.778064:0.0411:rs146277091
1   752566  rs3094315   G   A   .   PASS    AF=0.1696   ES:SE:LP:AF:ID  -0.0023:0.0234:0.0350336:0.1696:rs3094315
1   752593  rs372531941 T   G   .   PASS    AF=0.9613   ES:SE:LP:AF:ID  -0.1491:0.0909:0.996109:0.9613:rs372531941
1   752617  rs149886465 C   A   .   PASS    AF=0.0423   ES:SE:LP:AF:ID  -0.0998:0.0837:0.633017:0.0423:rs149886465
1   752721  rs3131972   A   G   .   PASS    AF=0.8248   ES:SE:LP:AF:ID  -0.0026:0.0231:0.0411018:0.8248:rs3131972
1   752796  rs148649543 C   T   .   PASS    AF=0.0476   ES:SE:LP:AF:ID  -0.0673:0.1046:0.28383:0.0476:rs148649543
1   752894  rs3131971   T   C   .   PASS    AF=0.83 ES:SE:LP:AF:ID  0.0515:0.0386:0.739929:0.83:rs3131971
1   753405  rs3115860   C   A   .   PASS    AF=0.1286   ES:SE:LP:AF:ID  -0.0048:0.0259:0.0682879:0.1286:rs3115860
1   753474  rs2073814   C   G   .   PASS    AF=0.8149   ES:SE:LP:AF:ID  0.0548:0.0374:0.84436:0.8149:rs2073814
1   753541  rs2073813   G   A   .   PASS    AF=0.1424   ES:SE:LP:AF:ID  0.005:0.0232:0.0813407:0.1424:rs2073813
1   754063  rs12184312  G   T   .   PASS    AF=0.0434   ES:SE:LP:AF:ID  -0.1191:0.0858:0.782253:0.0434:rs12184312
1   754105  rs12184325  C   T   .   PASS    AF=0.0371   ES:SE:LP:AF:ID  -0.1036:0.0913:0.59159:0.0371:rs12184325
1   754121  rs12184335  T   G   .   PASS    AF=0.962    ES:SE:LP:AF:ID  -0.034:0.1296:0.100727:0.962:rs12184335
1   754182  rs3131969   A   G   .   PASS    AF=0.8596   ES:SE:LP:AF:ID  -0.0066:0.0231:0.110362:0.8596:rs3131969
1   754192  rs3131968   A   G   .   PASS    AF=0.8594   ES:SE:LP:AF:ID  -0.0064:0.0231:0.106294:0.8594:rs3131968
1   754211  rs12184313  G   A   .   PASS    AF=0.042    ES:SE:LP:AF:ID  -0.1069:0.0885:0.643592:0.042:rs12184313
1   754334  rs3131967   T   C   .   PASS    AF=0.8595   ES:SE:LP:AF:ID  -0.0068:0.0232:0.114582:0.8595:rs3131967
1   754503  rs3115859   G   A   .   PASS    AF=0.1678   ES:SE:LP:AF:ID  -0.001:0.023:0.0157428:0.1678:rs3115859
1   754629  rs10454459  A   G   .   PASS    AF=0.9579   ES:SE:LP:AF:ID  -0.0882:0.0864:0.512862:0.9579:rs10454459
1   754671  rs10454460  A   G   .   PASS    AF=0.9625   ES:SE:LP:AF:ID  -0.1066:0.0944:0.587036:0.9625:rs10454460
1   754954  rs10454454  G   A   .   PASS    AF=0.0479   ES:SE:LP:AF:ID  -0.046:0.1059:0.177897:0.0479:rs10454454
1   754964  rs3131966   C   T   .   PASS    AF=0.1666   ES:SE:LP:AF:ID  -0.0006:0.0236:0.00833099:0.1666:rs3131966
1   755240  rs181660517 T   G   .   PASS    AF=0.9878   ES:SE:LP:AF:ID  -0.0788:0.4271:0.0687456:0.9878:rs181660517
1   755364  rs150361407 G   C   .   PASS    AF=0.0488   ES:SE:LP:AF:ID  -0.0442:0.1067:0.168322:0.0488:rs150361407
1   755609  rs188739018 T   C   .   PASS    AF=0.9513   ES:SE:LP:AF:ID  -0.0549:0.1052:0.220476:0.9513:rs188739018
1   755775  rs3131965   A   G   .   PASS    AF=0.8084   ES:SE:LP:AF:ID  0.0513:0.0387:0.732828:0.8084:rs3131965
1   755887  rs3131964   C   G   .   PASS    AF=0.9982   ES:SE:LP:AF:ID  0.0612:0.2457:0.0951763:0.9982:rs3131964
1   755890  rs3115858   A   T   .   PASS    AF=0.8612   ES:SE:LP:AF:ID  -0.0094:0.0236:0.161592:0.8612:rs3115858
1   756604  rs3131962   A   G   .   PASS    AF=0.839    ES:SE:LP:AF:ID  0.0238:0.0411:0.249569:0.839:rs3131962
1   757640  rs3115853   G   A   .   PASS    AF=0.1414   ES:SE:LP:AF:ID  -0.0079:0.0235:0.13324:0.1414:rs3115853