Summary

Summary {data-width=650}

Manhattan plot

manhattan_plot

QQ plot

qq_plot

AF plot

af_plot

P-Z plot

pz_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\">",
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    "FORMAT.3": "<ID=ID,Number=1,Type=String,Description=\"Study variant identifier\">",
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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.\">",
    "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.7": "<ID=VariantsNotRead,Number=1,Type=Integer,Description=\"Number of variants that could not be read\">",
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    "file_date": "2019-10-26T21:45:39.309452",
    "gwas_harmonisation_command": "--json /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ebi_gwas_import/processed/EBI-a-GCST005344/EBI-a-GCST005344_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-GCST005344/EBI-a-GCST005344.vcf.gz -O z /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ebi_gwas_import/processed/EBI-a-GCST005344/EBI-a-GCST005344_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-GCST005344/ebi-a-GCST005344.vcf.gz; Date=Thu May  7 12:50:58 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-GCST005344/EBI-a-GCST005344.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-GCST005344/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 22:27:38 2019
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ebi_gwas_import/processed/EBI-a-GCST005344/EBI-a-GCST005344.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 22:28:33 2019
Total time elapsed: 55.2s

QC metrics

Metrics

Metrics

{
    "af_correlation": 0.9545,
    "inflation_factor": 1.0117,
    "mean_EFFECT": 0.0003,
    "n": "-Inf",
    "n_snps": 8509502,
    "n_clumped_hits": 1,
    "n_p_sig": 9,
    "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": 189598,
    "n_est": "NA",
    "ratio_se_n": "NA",
    "mean_diff": "NaN",
    "ratio_diff": "NaN",
    "sd_y_est1": "NA",
    "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 8493320 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 8493325 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 8.612887e+00 5.735247e+00 1.0000 4.000000e+00 8.000000e+00 1.300000e+01 2.200000e+01 <U+2587><U+2585><U+2585><U+2582><U+2582>
numeric POS 0 1.0000000 NA NA NA NA NA NA NA 7.884666e+07 5.622317e+07 828.0000 3.258340e+07 6.946792e+07 1.144321e+08 2.492297e+08 <U+2587><U+2586><U+2585><U+2582><U+2581>
numeric EFFECT 0 1.0000000 NA NA NA NA NA NA NA 2.558000e-04 6.666710e-02 -0.9589 -2.680000e-02 1.000000e-04 2.710000e-02 8.979000e-01 <U+2581><U+2581><U+2587><U+2581><U+2581>
numeric SE 0 1.0000000 NA NA NA NA NA NA NA 5.338380e-02 3.911830e-02 0.0202 2.590000e-02 3.620000e-02 6.670000e-02 2.825000e-01 <U+2587><U+2582><U+2581><U+2581><U+2581>
numeric PVAL 0 1.0000000 NA NA NA NA NA NA NA 4.978097e-01 2.890665e-01 0.0000 2.466000e-01 4.974999e-01 7.484004e-01 9.998000e-01 <U+2587><U+2587><U+2587><U+2587><U+2587>
numeric PVAL_ztest 0 1.0000000 NA NA NA NA NA NA NA 4.978095e-01 2.890661e-01 0.0000 2.465901e-01 4.975034e-01 7.484566e-01 9.996602e-01 <U+2587><U+2587><U+2587><U+2587><U+2587>
numeric AF 0 1.0000000 NA NA NA NA NA NA NA 2.490877e-01 2.567016e-01 0.0051 4.260000e-02 1.444000e-01 3.907000e-01 9.945000e-01 <U+2587><U+2582><U+2582><U+2581><U+2581>
numeric AF_reference 189598 0.9776768 NA NA NA NA NA NA NA 2.495838e-01 2.538970e-01 0.0000 4.193290e-02 1.565500e-01 3.915730e-01 1.000000e+00 <U+2587><U+2583><U+2582><U+2581><U+2581>

Head and tail

CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
1 751756 rs143225517 T C 0.0555 0.0385 0.1496001 0.1494270 0.1471 0.242212 NA
1 752566 rs3094315 G A -0.0576 0.0336 0.0862601 0.0864763 0.8140 0.718251 NA
1 752721 rs3131972 A G -0.0696 0.0349 0.0464002 0.0461226 0.7584 0.653355 NA
1 752894 rs3131971 T C -0.0617 0.0376 0.1014000 0.1008062 0.7989 0.753195 NA
1 753405 rs3115860 C A -0.0639 0.0370 0.0843199 0.0841628 0.8300 0.751797 NA
1 753474 rs2073814 C G -0.0721 0.0378 0.0568002 0.0564679 0.7201 0.611422 NA
1 753541 rs2073813 G A 0.0824 0.0416 0.0477595 0.0476172 0.2041 0.301917 NA
1 754182 rs3131969 A G -0.0807 0.0401 0.0443404 0.0441705 0.7827 0.678514 NA
1 754192 rs3131968 A G -0.0802 0.0401 0.0454601 0.0455003 0.7824 0.678514 NA
1 754334 rs3131967 T C -0.0787 0.0401 0.0497600 0.0496934 0.7671 0.684305 NA
CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
22 51221731 rs115055839 T C 0.0881 0.0683 0.1968000 0.1970862 0.0791 0.0625000 NA
22 51222052 rs2879915 G A 0.0534 0.0475 0.2608002 0.2609237 0.2345 0.2194490 NA
22 51222100 rs114553188 G T -0.1761 0.0810 0.0295999 0.0296996 0.0515 0.0880591 NA
22 51222766 rs139240849 G A -0.1789 0.0961 0.0626902 0.0626591 0.0426 0.0321486 NA
22 51224600 rs187908482 G A -0.0921 0.0751 0.2205002 0.2200614 0.0978 0.0387380 NA
22 51228910 rs145146472 G A 0.0286 0.0451 0.5262996 0.5259853 0.2580 0.2276360 NA
22 51229805 rs9616985 T C 0.0628 0.0689 0.3618004 0.3620499 0.0790 0.0730831 NA
22 51229855 rs144549712 G A -0.0200 0.0624 0.7480007 0.7485796 0.1138 0.1160140 NA
22 51233300 rs9616839 C T 0.0361 0.0436 0.4082996 0.4076809 0.3196 0.3146960 NA
22 51237063 rs3896457 T C 0.0489 0.0468 0.2956998 0.2960822 0.2450 0.2050720 NA

bcf preview

1   751756  rs28527770  T   C   .   PASS    AF=0.1471   ES:SE:LP:AF:ID  0.0555:0.0385:0.825068:0.1471:rs28527770
1   752566  rs3094315   G   A   .   PASS    AF=0.814    ES:SE:LP:AF:ID  -0.0576:0.0336:1.06419:0.814:rs3094315
1   752721  rs3131972   A   G   .   PASS    AF=0.7584   ES:SE:LP:AF:ID  -0.0696:0.0349:1.33348:0.7584:rs3131972
1   752894  rs3131971   T   C   .   PASS    AF=0.7989   ES:SE:LP:AF:ID  -0.0617:0.0376:0.993962:0.7989:rs3131971
1   753405  rs3115860   C   A   .   PASS    AF=0.83 ES:SE:LP:AF:ID  -0.0639:0.037:1.07407:0.83:rs3115860
1   753474  rs2073814   C   G   .   PASS    AF=0.7201   ES:SE:LP:AF:ID  -0.0721:0.0378:1.24565:0.7201:rs2073814
1   753541  rs2073813   G   A   .   PASS    AF=0.2041   ES:SE:LP:AF:ID  0.0824:0.0416:1.32094:0.2041:rs2073813
1   754182  rs3131969   A   G   .   PASS    AF=0.7827   ES:SE:LP:AF:ID  -0.0807:0.0401:1.3532:0.7827:rs3131969
1   754192  rs3131968   A   G   .   PASS    AF=0.7824   ES:SE:LP:AF:ID  -0.0802:0.0401:1.34237:0.7824:rs3131968
1   754334  rs3131967   T   C   .   PASS    AF=0.7671   ES:SE:LP:AF:ID  -0.0787:0.0401:1.30312:0.7671:rs3131967
1   754503  rs3115859   G   A   .   PASS    AF=0.7594   ES:SE:LP:AF:ID  -0.0823:0.0386:1.48346:0.7594:rs3115859
1   754964  rs3131966   C   T   .   PASS    AF=0.7354   ES:SE:LP:AF:ID  -0.0767:0.0404:1.23837:0.7354:rs3131966
1   755775  rs3131965   A   G   .   PASS    AF=0.7711   ES:SE:LP:AF:ID  -0.0587:0.0398:0.851089:0.7711:rs3131965
1   755890  rs3115858   A   T   .   PASS    AF=0.8256   ES:SE:LP:AF:ID  -0.056:0.0401:0.788879:0.8256:rs3115858
1   756604  rs3131962   A   G   .   PASS    AF=0.8054   ES:SE:LP:AF:ID  -0.0536:0.0405:0.73002:0.8054:rs3131962
1   757640  rs3115853   G   A   .   PASS    AF=0.7654   ES:SE:LP:AF:ID  -0.0612:0.045:0.758952:0.7654:rs3115853
1   757734  rs4951929   C   T   .   PASS    AF=0.8278   ES:SE:LP:AF:ID  -0.0619:0.0414:0.870955:0.8278:rs4951929
1   757936  rs4951862   C   A   .   PASS    AF=0.8272   ES:SE:LP:AF:ID  -0.0618:0.0414:0.868702:0.8272:rs4951862
1   758144  rs3131956   A   G   .   PASS    AF=0.8098   ES:SE:LP:AF:ID  -0.0638:0.0407:0.932929:0.8098:rs3131956
1   758626  rs3131954   C   T   .   PASS    AF=0.8267   ES:SE:LP:AF:ID  -0.0633:0.042:0.881405:0.8267:rs3131954
1   759700  rs3115852   T   C   .   PASS    AF=0.7744   ES:SE:LP:AF:ID  -0.0705:0.0414:1.05453:0.7744:rs3115852
1   759837  rs3115851   T   A   .   PASS    AF=0.8292   ES:SE:LP:AF:ID  -0.065:0.0425:0.897909:0.8292:rs3115851
1   760912  rs1048488   C   T   .   PASS    AF=0.7686   ES:SE:LP:AF:ID  -0.067:0.042:0.957818:0.7686:rs1048488
1   761147  rs3115850   T   C   .   PASS    AF=0.7766   ES:SE:LP:AF:ID  -0.0681:0.0421:0.974285:0.7766:rs3115850
1   761752  rs1057213   C   T   .   PASS    AF=0.8169   ES:SE:LP:AF:ID  -0.0691:0.044:0.933301:0.8169:rs1057213
1   768448  rs12562034  G   A   .   PASS    AF=0.1104   ES:SE:LP:AF:ID  -0.007:0.0454:0.0569509:0.1104:rs12562034
1   768819  rs12562811  C   T   .   PASS    AF=0.0508   ES:SE:LP:AF:ID  -0.0289:0.1076:0.103364:0.0508:rs12562811
1   769963  rs7518545   G   A   .   PASS    AF=0.1089   ES:SE:LP:AF:ID  -0.0078:0.0488:0.0591848:0.1089:rs7518545
1   770377  rs112563271 A   T   .   PASS    AF=0.0445   ES:SE:LP:AF:ID  -0.0401:0.1214:0.13024:0.0445:rs112563271
1   845274  rs112856858 G   T   .   PASS    AF=0.2673   ES:SE:LP:AF:ID  0.0026:0.0385:0.0239712:0.2673:rs112856858
1   845635  rs117086422 C   T   .   PASS    AF=0.1662   ES:SE:LP:AF:ID  -0.0187:0.0453:0.167619:0.1662:rs117086422
1   845938  rs57760052  G   A   .   PASS    AF=0.271    ES:SE:LP:AF:ID  0.0183:0.0375:0.204398:0.271:rs57760052
1   846078  rs28612348  C   T   .   PASS    AF=0.1652   ES:SE:LP:AF:ID  -0.0171:0.0447:0.154096:0.1652:rs28612348
1   846398  rs58781670  G   A   .   PASS    AF=0.2636   ES:SE:LP:AF:ID  0.017:0.0376:0.186352:0.2636:rs58781670
1   846808  rs4475691   C   T   .   PASS    AF=0.2143   ES:SE:LP:AF:ID  -0.0102:0.0367:0.107794:0.2143:rs4475691
1   846864  rs950122    G   C   .   PASS    AF=0.1951   ES:SE:LP:AF:ID  -0.0165:0.0392:0.171598:0.1951:rs950122
1   847228  rs3905286   C   T   .   PASS    AF=0.2051   ES:SE:LP:AF:ID  -0.029:0.0395:0.334794:0.2051:rs3905286
1   847491  rs28407778  G   A   .   PASS    AF=0.2111   ES:SE:LP:AF:ID  -0.0247:0.0389:0.279675:0.2111:rs28407778
1   848090  rs4246505   G   A   .   PASS    AF=0.1736   ES:SE:LP:AF:ID  -0.0165:0.044:0.149721:0.1736:rs4246505
1   848445  rs4626817   G   A   .   PASS    AF=0.2123   ES:SE:LP:AF:ID  -0.0249:0.039:0.281415:0.2123:rs4626817
1   848456  rs11507767  A   G   .   PASS    AF=0.214    ES:SE:LP:AF:ID  -0.0231:0.0388:0.258927:0.214:rs11507767
1   848738  rs3829741   C   T   .   PASS    AF=0.1741   ES:SE:LP:AF:ID  -0.0176:0.044:0.161655:0.1741:rs3829741
1   850062  rs28723578  A   T   .   PASS    AF=0.2151   ES:SE:LP:AF:ID  -0.0195:0.039:0.209152:0.2151:rs28723578
1   850123  rs28622257  C   T   .   PASS    AF=0.1742   ES:SE:LP:AF:ID  -0.0164:0.0442:0.148191:0.1742:rs28622257
1   851190  rs28609852  G   A   .   PASS    AF=0.2145   ES:SE:LP:AF:ID  -0.0237:0.0395:0.260744:0.2145:rs28609852
1   851204  rs28552953  G   C   .   PASS    AF=0.2262   ES:SE:LP:AF:ID  -0.0312:0.0397:0.365221:0.2262:rs28552953
1   852664  rs28605311  C   T   .   PASS    AF=0.173    ES:SE:LP:AF:ID  -0.0218:0.0445:0.204259:0.173:rs28605311
1   852758  rs4970462   G   C   .   PASS    AF=0.1649   ES:SE:LP:AF:ID  -0.0328:0.046:0.322576:0.1649:rs4970462
1   853239  rs4970380   A   G   .   PASS    AF=0.1686   ES:SE:LP:AF:ID  -0.0317:0.0456:0.313185:0.1686:rs4970380
1   854250  rs7537756   A   G   .   PASS    AF=0.1976   ES:SE:LP:AF:ID  -0.0326:0.0434:0.344094:0.1976:rs7537756