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\">",
    "FORMAT.5": "<ID=NC,Number=A,Type=Float,Description=\"Number of cases used to estimate genetic effect\">",
    "FORMAT.6": "<ID=SE,Number=A,Type=Float,Description=\"Standard error of effect size estimate\">",
    "FORMAT.7": "<ID=SI,Number=A,Type=Float,Description=\"Accuracy score of summary data imputation\">",
    "FORMAT.8": "<ID=SS,Number=A,Type=Float,Description=\"Sample size used to estimate genetic effect\">",
    "INFO": "<ID=AF,Number=A,Type=Float,Description=\"Allele Frequency\">",
    "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.\">",
    "INFO.2": "<ID=SwappedAlleles,Number=0,Type=Flag,Description=\"The REF and the ALT alleles have been swapped in liftover due to changes in the reference. It is possible that not all INFO annotations reflect this swap, and in the genotypes, only the GT, PL, and AD fields have been modified. You should check the TAGS_TO_REVERSE parameter that was used during the LiftOver to be sure.\">",
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    "META.5": "<ID=TotalVariants,Number=1,Type=Integer,Description=\"Total number of variants in input\">",
    "META.6": "<ID=VariantsNotHarmonised,Number=1,Type=Integer,Description=\"Total number of variants that could not be harmonised\">",
    "META.7": "<ID=VariantsNotRead,Number=1,Type=Integer,Description=\"Number of variants that could not be read\">",
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    "file_date": "2019-10-27T20:49:14.463111",
    "gwas_harmonisation_command": "--json /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ebi_gwas_import/processed/EBI-a-GCST006368/EBI-a-GCST006368_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-GCST006368/EBI-a-GCST006368.vcf.gz -O z /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ebi_gwas_import/processed/EBI-a-GCST006368/EBI-a-GCST006368_data.vcf.gz; Date=Sun Oct 27 21:30:43 2019",
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    "bcftools_viewCommand": "view -h /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/ebi-a-GCST006368/ebi-a-GCST006368.vcf.gz; Date=Sun May 10 23:20:28 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-GCST006368/EBI-a-GCST006368.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-GCST006368/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 Sun Oct 27 21:58:13 2019
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ebi_gwas_import/processed/EBI-a-GCST006368/EBI-a-GCST006368.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 Sun Oct 27 22:01:12 2019
Total time elapsed: 2.0m:58.42s

QC metrics

Metrics

Metrics

{
    "af_correlation": -0.0176,
    "inflation_factor": 1.0966,
    "mean_EFFECT": 0.0014,
    "n": "-Inf",
    "n_snps": 27364851,
    "n_clumped_hits": 152,
    "n_p_sig": 10178,
    "n_mono": 0,
    "n_ns": 1106123,
    "n_mac": 0,
    "is_snpid_unique": false,
    "n_miss_EFFECT": 0,
    "n_miss_SE": 0,
    "n_miss_PVAL": 0,
    "n_miss_AF": 53369,
    "n_miss_AF_reference": 1101219,
    "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 1.0000000 3 59 0 27154140 0 NA NA NA NA NA NA NA NA NA NA
character REF 0 1.0000000 1 951 0 36465 0 NA NA NA NA NA NA NA NA NA NA
character ALT 0 1.0000000 1 42 0 21341 0 NA NA NA NA NA NA NA NA NA NA
logical N 27155471 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 8.749657e+00 5.894119e+00 1.00000 4.000000e+00 8.000000e+00 1.300000e+01 2.400000e+01 ▇▆▃▃▁
numeric POS 0 1.0000000 NA NA NA NA NA NA NA 7.897502e+07 5.602317e+07 56.00000 3.294395e+07 6.988115e+07 1.147142e+08 2.492395e+08 ▇▆▅▂▁
numeric EFFECT 0 1.0000000 NA NA NA NA NA NA NA 1.440400e-03 1.000624e-01 -2.10000 -1.950000e-02 3.080000e-04 2.320000e-02 2.590000e+00 ▁▁▇▁▁
numeric SE 0 1.0000000 NA NA NA NA NA NA NA 6.799740e-02 7.158000e-02 0.00244 7.530000e-03 4.670000e-02 1.020000e-01 2.000000e+00 ▇▁▁▁▁
numeric PVAL 0 1.0000000 NA NA NA NA NA NA NA 4.854419e-01 2.944103e-01 0.00000 2.300001e-01 4.799997e-01 7.400005e-01 1.000000e+00 ▇▇▇▇▇
numeric PVAL_ztest 0 1.0000000 NA NA NA NA NA NA NA 4.854425e-01 2.943853e-01 0.00000 2.271583e-01 4.821986e-01 7.408646e-01 1.000000e+00 ▇▇▇▇▇
numeric AF 53369 0.9980347 NA NA NA NA NA NA NA 5.265588e-01 3.305125e-01 0.00010 1.506000e-01 6.911000e-01 7.167000e-01 9.999000e-01 ▅▁▁▇▂
numeric AF_reference 1101219 0.9594476 NA NA NA NA NA NA NA 9.768710e-02 2.012937e-01 0.00000 1.996800e-03 8.386600e-03 6.589460e-02 1.000000e+00 ▇▁▁▁▁

Head and tail

CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
1 10583 rs58108140 G A -0.02050 0.01010 0.0420001 0.0423867 0.6338 NA NA
1 10611 rs189107123 C G -0.03280 0.08760 0.7099994 0.7080850 0.9351 NA NA
1 10711 rs1434325972 A G -0.03850 0.03920 0.3300000 0.3260295 0.2811 NA NA
1 10880 rs1351904884 G A 0.25500 0.09340 0.0063000 0.0063297 0.0014 NA NA
1 13624 rs1304990809 C G 0.00307 0.00737 0.6800001 0.6770050 0.5692 NA NA
1 13957 rs77270114 TC T 0.04630 0.09940 0.6400000 0.6413624 0.9366 NA NA
1 14971 rs1238549125 C T 0.11400 0.14400 0.4299995 0.4285551 0.0304 NA NA
1 15340 rs1477171760 G A 0.01070 0.05060 0.8300000 0.8325264 0.7207 NA NA
1 15761 rs1269189092 A G 0.00122 0.00739 0.8700001 0.8688748 0.6033 NA NA
1 15811 rs1359290710 T C -0.00451 0.00771 0.5600000 0.5585782 0.4418 NA NA
CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
24 21936138 rs2032609 C T 0.039700 0.06370 0.5300002 0.5331308 0.0212 NA NA
24 22003770 rs9786678 A G -0.029600 0.01610 0.0659994 0.0659874 0.4793 0.6975 NA
24 22100087 rs17250275 T C 0.005390 0.00731 0.4600002 0.4609119 0.1710 0.0397 NA
24 22513726 rs3906451 A C -0.000303 0.00869 0.9699999 0.9721853 0.0983 NA NA
24 22601068 rs9785928 C T 0.001300 0.00579 0.8200001 0.8223488 0.4260 0.7575 NA
24 22746786 rs17323322 T C 0.005580 0.03110 0.8600001 0.8576070 0.0965 0.0268 NA
24 22749853 rs13447352 A C -0.000425 0.01040 0.9699999 0.9674032 0.0709 0.0616 NA
24 22918577 rs16980548 C T -0.005770 0.01060 0.5800000 0.5862078 0.0807 0.2612 NA
24 23443971 rs17842518 G T 0.003980 0.01210 0.7400005 0.7422119 0.0585 0.2612 NA
24 23984056 rs1276034 A G -0.021900 0.01580 0.1700000 0.1657237 0.5916 0.8248 NA

bcf preview

1   10583   rs58108140  G   A   .   PASS    AF=0.6338   ES:SE:LP:AF:ID  -0.0205:0.0101:1.37675:0.6338:rs58108140
1   10611   rs189107123 C   G   .   PASS    AF=0.9351   ES:SE:LP:AF:ID  -0.0328:0.0876:0.148742:0.9351:rs189107123
1   10711   rs1434325972    A   G   .   PASS    AF=0.2811   ES:SE:LP:AF:ID  -0.0385:0.0392:0.481486:0.2811:rs1434325972
1   10880   rs1351904884    G   A   .   PASS    AF=0.0014   ES:SE:LP:AF:ID  0.255:0.0934:2.20066:0.0014:rs1351904884
1   13624   rs1304990809    C   G   .   PASS    AF=0.5692   ES:SE:LP:AF:ID  0.00307:0.00737:0.167491:0.5692:rs1304990809
1   13957   rs77270114  TC  T   .   PASS    AF=0.9366   ES:SE:LP:AF:ID  0.0463:0.0994:0.19382:0.9366:rs201747181
1   14971   rs1238549125    C   T   .   PASS    AF=0.0304   ES:SE:LP:AF:ID  0.114:0.144:0.366532:0.0304:rs1238549125
1   15340   rs1477171760    G   A   .   PASS    AF=0.7207   ES:SE:LP:AF:ID  0.0107:0.0506:0.0809219:0.7207:rs1477171760
1   15761   rs1269189092    A   G   .   PASS    AF=0.6033   ES:SE:LP:AF:ID  0.00122:0.00739:0.0604807:0.6033:rs1269189092
1   15811   rs1359290710    T   C   .   PASS    AF=0.4418   ES:SE:LP:AF:ID  -0.00451:0.00771:0.251812:0.4418:rs1359290710
1   15850   rs575961614 G   A   .   PASS    AF=0.9402   ES:SE:LP:AF:ID  -0.0549:0.0883:0.275724:0.9402:rs575961614
1   15893   rs555382915 T   C   .   PASS    AF=0.389    ES:SE:LP:AF:ID  -0.00312:0.00777:0.161151:0.389:rs555382915
1   16016   rs1438306001    G   A   .   PASS    AF=0.9868   ES:SE:LP:AF:ID  0.0641:0.331:0.0705811:0.9868:rs1438306001
1   16296   rs1196752759    G   A   .   PASS    AF=0.9849   ES:SE:LP:AF:ID  0.417:0.254:1:0.9849:rs1196752759
1   16876   rs1309054513    C   T   .   PASS    AF=0.6609   ES:SE:LP:AF:ID  -0.00168:0.012:0.05061:0.6609:rs1309054513
1   17661   rs1199908028    G   A   .   PASS    AF=0.0014   ES:SE:LP:AF:ID  0.0172:0.109:0.0604807:0.0014:rs1199908028
1   30923   rs806731    G   T   .   PASS    AF=0.2787   ES:SE:LP:AF:ID  0.00287:0.0219:0.0457575:0.2787:rs806731
1   46402   rs1553121056    C   CTGT    .   PASS    AF=0.9573   ES:SE:LP:AF:ID  0.159:0.151:0.537602:0.9573:rs199681827
1   47190   rs200430748 G   GA  .   PASS    AF=0.9241   ES:SE:LP:AF:ID  -0.0144:0.0836:0.0655015:0.9241:rs200430748
1   47869   rs1169148240    G   A   .   PASS    AF=0.4086   ES:SE:LP:AF:ID  -0.0178:0.00878:1.36653:0.4086:rs1169148240
1   51479   rs116400033 T   A   .   PASS    AF=0.6418   ES:SE:LP:AF:ID  -0.0257:0.0104:1.88606:0.6418:rs116400033
1   51954   rs185832753 G   C   .   PASS    AF=0.0008   ES:SE:LP:AF:ID  0.0475:0.151:0.124939:0.0008:rs185832753
1   52144   rs190291950 T   A   .   PASS    AF=0.9436   ES:SE:LP:AF:ID  0.0261:0.113:0.0861861:0.9436:rs190291950
1   52185   rs201374420 TTAA    T   .   PASS    AF=0.7171   ES:SE:LP:AF:ID  -0.0677:0.0595:0.585027:0.7171:rs201374420
1   52238   rs2691277   T   G   .   PASS    AF=0.1273   ES:SE:LP:AF:ID  -0.0189:0.0257:0.337242:0.1273:rs2691277
1   53215   rs1361133293    G   A   .   PASS    AF=0.6091   ES:SE:LP:AF:ID  0.00377:0.00779:0.200659:0.6091:rs1361133293
1   53234   rs199502715 CAT C   .   PASS    AF=0.9526   ES:SE:LP:AF:ID  -0.017:0.117:0.0555173:0.9526:rs199502715
1   54353   rs140052487 C   A   .   PASS    AF=0.9505   ES:SE:LP:AF:ID  -0.0542:0.178:0.119186:0.9505:rs140052487
1   54421   rs146477069 A   G   .   PASS    AF=0.895    ES:SE:LP:AF:ID  0.0856:0.0447:1.25181:0.895:rs146477069
1   54490   rs141149254 G   A   .   PASS    AF=0.6602   ES:SE:LP:AF:ID  -0.0267:0.0117:1.65758:0.6602:rs141149254
1   54676   rs2462492   C   T   .   PASS    AF=0.6474   ES:SE:LP:AF:ID  0.0273:0.0108:1.92082:0.6474:rs2462492
1   54753   rs143174675 T   G   .   PASS    AF=0.6884   ES:SE:LP:AF:ID  0.0739:0.0219:3.12494:0.6884:rs143174675
1   55164   rs3091274   C   A   .   PASS    AF=0.1206   ES:SE:LP:AF:ID  -0.03:0.0271:0.568636:0.1206:rs3091274
1   55249   rs200769871 C   CTATGG  .   PASS    AF=0.9137   ES:SE:LP:AF:ID  0.118:0.0494:1.76955:0.9137:rs200769871
1   55299   rs10399749  C   T   .   PASS    AF=0.7881   ES:SE:LP:AF:ID  0.0366:0.0234:0.920819:0.7881:rs10399749
1   55326   rs3107975   T   C   .   PASS    AF=0.9306   ES:SE:LP:AF:ID  -0.0323:0.054:0.259637:0.9306:rs3107975
1   55367   rs190850374 G   A   .   PASS    AF=0.0047   ES:SE:LP:AF:ID  -0.156:0.174:0.431798:0.0047:rs190850374
1   55394   rs2949420   T   A   .   PASS    AF=0.7108   ES:SE:LP:AF:ID  0.0701:0.0334:1.4437:0.7108:rs2949420
1   55416   rs193242050 G   A   .   PASS    AF=0.9571   ES:SE:LP:AF:ID  -0.0248:0.116:0.0809219:0.9571:rs193242050
1   55850   rs191890754 C   G   .   PASS    AF=0.7395   ES:SE:LP:AF:ID  -0.131:0.0469:2.284:0.7395:rs191890754
1   55852   rs184233019 G   C   .   PASS    AF=0.7216   ES:SE:LP:AF:ID  0.0828:0.0575:0.823909:0.7216:rs184233019
1   56644   rs143342222 A   C   .   PASS    AF=0.9869   ES:SE:LP:AF:ID  -0.115:0.267:0.173925:0.9869:rs143342222
1   57321   rs1244179854    G   A   .   PASS    AF=0.635    ES:SE:LP:AF:ID  0.0107:0.0103:0.522879:0.635:rs1244179854
1   57952   rs2691334   A   C   .   PASS    AF=0.1317   ES:SE:LP:AF:ID  -0.0207:0.029:0.318759:0.1317:rs2691334
1   58814   rs114420996 G   A   .   PASS    AF=0.8441   ES:SE:LP:AF:ID  -0.0178:0.0293:0.267606:0.8441:rs114420996
1   59040   rs62637815  T   C   .   PASS    AF=0.8896   ES:SE:LP:AF:ID  -0.01:0.0462:0.0809219:0.8896:rs62637815
1   61424   rs1189968251    C   T   .   PASS    AF=0.0007   ES:SE:LP:AF:ID  0.217:0.132:1:0.0007:rs1189968251
1   61442   rs2531261   A   G   .   PASS    AF=0.0916   ES:SE:LP:AF:ID  -0.00702:0.0394:0.0655015:0.0916:rs2531261
1   61462   rs56992750  T   A   .   PASS    AF=0.917    ES:SE:LP:AF:ID  0.0357:0.0487:0.337242:0.917:rs56992750
1   61743   rs184286948 G   C   .   PASS    AF=0.0036   ES:SE:LP:AF:ID  -0.0986:0.21:0.19382:0.0036:rs184286948