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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"file_date": "2019-10-27T07:29:29.669615",
"gwas_harmonisation_command": "--json /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ebi_gwas_import/processed/EBI-a-GCST005814/EBI-a-GCST005814_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-GCST005814/EBI-a-GCST005814.vcf.gz -O z /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ebi_gwas_import/processed/EBI-a-GCST005814/EBI-a-GCST005814_data.vcf.gz; Date=Sun Oct 27 07:53:44 2019",
"bcftools_viewVersion": "1.9-74-g6af271c+htslib-1.9-64-g226b4a8",
"bcftools_viewCommand": "view -h /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/ebi-a-GCST005814/ebi-a-GCST005814.vcf.gz; Date=Sat May 9 18:40:39 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-GCST005814/EBI-a-GCST005814.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-GCST005814/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 08:19:30 2019
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ebi_gwas_import/processed/EBI-a-GCST005814/EBI-a-GCST005814.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 08:21:16 2019
Total time elapsed: 1.0m:45.68sQC metrics
Metrics
Metrics
{
"af_correlation": 0.9558,
"inflation_factor": 1.0118,
"mean_EFFECT": 0.0002,
"n": "-Inf",
"n_snps": 15845509,
"n_clumped_hits": 0,
"n_p_sig": 0,
"n_mono": 0,
"n_ns": 1406404,
"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": 499732,
"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 betweenAFandAF_reference.inflation_factor(lambda): Genomic inflation factor.mean_EFFECT: Mean ofEFFECTsize.n: Maximum value of reported sample size across all SNPs, \(n\).n_clumped_hits: Number of clumped hits.n_snps: Number of SNPsn_p_sig: Number of SNPs with pvalue below5e-8.n_mono: Number of monomorphic (MAF == 1orMAF == 0) SNPs.n_ns: Number of SNPs with nonsense values:- alleles other than
A, C, G or T. - P-values
< 0or> 1. - negative or infinite standard errors (
<= 0or= Infinity). - infinite beta estimates or allele frequencies
< 0or> 1.
- alleles other than
n_mac: Number of cases whereMAC(\(2 \times N \times MAF\)) is less than6.is_snpid_unique:trueif the combination ofIDREFALTis unique and therefore no duplication in snpid.n_miss_<*>: Number ofNAobservations 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 expectratio_se_nto 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 ofdiffand the mean ofdiff2(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<*>:r2statistics under various assumptions1: \(r^2 = \sum_j{\frac{2 \times \beta_j^2 \times {MAF}_j \times (1 - {MAF}_j)}{\texttt{var1}}}\), \(\texttt{var1} = 1\).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: NOTis_snpid_unique.mean_EFFECT_nonfinite:mean(EFFECT)isNA,NaN, orInf.mean_EFFECT_05:abs(mean(EFFECT))> 0.5.mean_EFFECT_01:abs(mean(EFFECT))> 0.1.mean_chisq:ldsc_mean_chisq> 1.3 orldsc_mean_chisq< 0.7.n_p_sig:n_p_sig> 1000.miss_<*>:n_miss_<*>/n_snps> 0.01.ldsc_ratio:ldsc_ratio> 0.5ldsc_intercept_beta:ldsc_intercept_beta> 1.5n_clumped_hits:n_clumped_hits> 1000r2_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 | 15822547 | 0 | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| character | REF | 0 | 1.0000000 | 1 | 84 | 0 | 67564 | 0 | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| character | ALT | 0 | 1.0000000 | 1 | 63 | 0 | 34409 | 0 | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| logical | N | 15823122 | 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 | 8.780161e+00 | 5.811123e+00 | 1.0000000 | 4.000000e+00 | 8.000000e+00 | 1.300000e+01 | 2.200000e+01 | ▇▅▅▃▂ |
| numeric | POS | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 7.834935e+07 | 5.621134e+07 | 56.0000000 | 3.221807e+07 | 6.886592e+07 | 1.137585e+08 | 2.492397e+08 | ▇▆▅▂▁ |
| numeric | EFFECT | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 2.112000e-04 | 1.230546e-01 | -3.1015600 | -3.102950e-02 | 4.071000e-04 | 3.260680e-02 | 1.546230e+00 | ▁▁▁▇▁ |
| numeric | SE | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 9.408740e-02 | 8.899250e-02 | 0.0156008 | 2.081050e-02 | 5.144880e-02 | 1.556490e-01 | 3.424710e+00 | ▇▁▁▁▁ |
| numeric | PVAL | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 4.975645e-01 | 2.902673e-01 | 0.0000001 | 2.451997e-01 | 4.974827e-01 | 7.492918e-01 | 1.000000e+00 | ▇▇▇▇▇ |
| numeric | PVAL_ztest | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 4.979069e-01 | 2.899888e-01 | 0.0000000 | 2.459602e-01 | 4.977435e-01 | 7.493241e-01 | 9.999997e-01 | ▇▇▇▇▇ |
| numeric | AF | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 1.610020e-01 | 2.445968e-01 | 0.0010000 | 3.353000e-03 | 2.708630e-02 | 2.275328e-01 | 9.989990e-01 | ▇▁▁▁▁ |
| numeric | AF_reference | 499732 | 0.9684176 | NA | NA | NA | NA | NA | NA | NA | 1.643113e-01 | 2.376135e-01 | 0.0000000 | 1.797100e-03 | 3.893770e-02 | 2.432110e-01 | 1.000000e+00 | ▇▂▁▁▁ |
Head and tail
| CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 | 10177 | rs367896724 | A | AC | 0.0330172 | 0.0227753 | 0.1474450 | 0.1471441 | 0.4002910 | 0.4253190 | NA |
| 1 | 10352 | rs555500075 | T | TA | -0.0061089 | 0.0237825 | 0.7972461 | 0.7972824 | 0.3899790 | 0.4375000 | NA |
| 1 | 10616 | rs376342519 | CCGCCGTTGCAAAGGCGCGCCG | C | 0.0412707 | 0.1632260 | 0.7992400 | 0.8003888 | 0.9952020 | 0.9930110 | NA |
| 1 | 11012 | rs544419019 | C | G | -0.0139639 | 0.0397072 | 0.7246178 | 0.7250845 | 0.0860688 | 0.0880591 | NA |
| 1 | 13110 | rs540538026 | G | A | -0.0083903 | 0.0519603 | 0.8715751 | 0.8717197 | 0.0603408 | 0.0267572 | NA |
| 1 | 13116 | rs62635286 | T | G | -0.0197650 | 0.0313566 | 0.5276962 | 0.5284788 | 0.1908160 | 0.0970447 | NA |
| 1 | 13118 | rs200579949 | A | G | -0.0197650 | 0.0313566 | 0.5276962 | 0.5284788 | 0.1908160 | 0.0970447 | NA |
| 1 | 13273 | rs531730856 | G | C | 0.0014148 | 0.0355778 | 0.9685430 | 0.9682792 | 0.1351740 | 0.0950479 | NA |
| 1 | 13453 | rs568927457 | T | C | 0.0744772 | 0.1373210 | 0.5919868 | 0.5875716 | 0.0064214 | 0.0007987 | NA |
| 1 | 13483 | rs554760071 | G | C | 0.2057090 | 0.1486580 | 0.1793911 | 0.1664278 | 0.0050558 | 0.0019968 | NA |
| CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 22 | 51238328 | rs553081191 | A | C | 0.0772697 | 0.2063800 | 0.7107158 | 0.7081030 | 0.0019638 | 0.0005990 | NA |
| 22 | 51238364 | rs564490465 | C | G | -0.0557506 | 0.1706080 | 0.7416193 | 0.7438373 | 0.0054368 | 0.0005990 | NA |
| 22 | 51238394 | rs149712012 | C | T | -0.0752156 | 0.1925180 | 0.6929422 | 0.6960235 | 0.0032410 | 0.0033946 | NA |
| 22 | 51239281 | rs8138215 | G | C | 0.3428130 | 0.2345770 | 0.1590699 | 0.1439032 | 0.0014421 | 0.0111821 | NA |
| 22 | 51239296 | rs8137179 | T | C | 0.3428130 | 0.2345770 | 0.1590699 | 0.1439032 | 0.0014421 | 0.0111821 | NA |
| 22 | 51239304 | rs8142977 | C | T | 0.3428130 | 0.2345770 | 0.1590699 | 0.1439032 | 0.0014421 | 0.0111821 | NA |
| 22 | 51239586 | rs535432390 | T | G | -0.0440915 | 0.2722640 | 0.8704940 | 0.8713500 | 0.0016666 | 0.0001997 | NA |
| 22 | 51239794 | rs561893765 | C | A | 0.0413402 | 0.2678070 | 0.8779490 | 0.8773214 | 0.0016502 | 0.0299521 | NA |
| 22 | 51240820 | rs202228854 | C | T | 0.0299869 | 0.0640009 | 0.6405204 | 0.6393994 | 0.0253118 | 0.1267970 | NA |
| 22 | 51244237 | rs575160859 | C | T | -0.0743978 | 0.1026370 | 0.4634523 | 0.4685359 | 0.0133565 | 0.0037939 | NA |
bcf preview
1 10177 rs367896724 A AC . PASS AF=0.400291 ES:SE:LP:AF:ID 0.0330172:0.0227753:0.83137:0.400291:rs367896724
1 10352 rs555500075 T TA . PASS AF=0.389979 ES:SE:LP:AF:ID -0.00610891:0.0237825:0.0984076:0.389979:rs555500075
1 10616 rs376342519 CCGCCGTTGCAAAGGCGCGCCG C . PASS AF=0.995202 ES:SE:LP:AF:ID 0.0412707:0.163226:0.0973228:0.995202:rs376342519
1 11012 rs544419019 C G . PASS AF=0.0860688 ES:SE:LP:AF:ID -0.0139639:0.0397072:0.139891:0.0860688:rs544419019
1 13110 rs540538026 G A . PASS AF=0.0603408 ES:SE:LP:AF:ID -0.00839026:0.0519603:0.0596952:0.0603408:rs540538026
1 13116 rs62635286 T G . PASS AF=0.190816 ES:SE:LP:AF:ID -0.019765:0.0313566:0.277616:0.190816:rs62635286
1 13118 rs62028691 A G . PASS AF=0.190816 ES:SE:LP:AF:ID -0.019765:0.0313566:0.277616:0.190816:rs62028691
1 13273 rs531730856 G C . PASS AF=0.135174 ES:SE:LP:AF:ID 0.00141481:0.0355778:0.0138811:0.135174:rs531730856
1 13453 rs568927457 T C . PASS AF=0.00642143 ES:SE:LP:AF:ID 0.0744772:0.137321:0.227688:0.00642143:rs568927457
1 13483 rs554760071 G C . PASS AF=0.00505578 ES:SE:LP:AF:ID 0.205709:0.148658:0.746199:0.00505578:rs554760071
1 14464 rs546169444 A T . PASS AF=0.156319 ES:SE:LP:AF:ID 0.0162729:0.0324938:0.209657:0.156319:rs546169444
1 14599 rs707680 T A . PASS AF=0.193149 ES:SE:LP:AF:ID 0.00838762:0.0297102:0.109095:0.193149:rs707680
1 14604 rs541940975 A G . PASS AF=0.193149 ES:SE:LP:AF:ID 0.00838762:0.0297102:0.109095:0.193149:rs541940975
1 14930 rs6682385 A G . PASS AF=0.470982 ES:SE:LP:AF:ID -0.028865:0.0233718:0.664275:0.470982:rs6682385
1 14933 rs199856693 G A . PASS AF=0.0484044 ES:SE:LP:AF:ID -0.0631586:0.0563913:0.587598:0.0484044:rs199856693
1 15211 rs3982632 T G . PASS AF=0.743901 ES:SE:LP:AF:ID -0.0609878:0.0264551:1.66459:0.743901:rs3982632
1 15245 rs576044687 C T . PASS AF=0.00109757 ES:SE:LP:AF:ID 0.606314:0.275199:1.43879:0.00109757:rs576044687
1 15644 rs564003018 G A . PASS AF=0.00349563 ES:SE:LP:AF:ID -0.06764:0.211314:0.127086:0.00349563:rs564003018
1 15820 rs2691315 G T . PASS AF=0.26972 ES:SE:LP:AF:ID 0.0118851:0.0274181:0.177234:0.26972:rs2691315
1 15903 rs557514207 G GC . PASS AF=0.407127 ES:SE:LP:AF:ID -0.00896893:0.022836:0.158371:0.407127:rs557514207
1 16142 rs548165136 G A . PASS AF=0.00302653 ES:SE:LP:AF:ID -0.303093:0.24275:0.718355:0.00302653:rs548165136
1 16949 rs199745162 A C . PASS AF=0.0210214 ES:SE:LP:AF:ID -0.109648:0.0851009:0.72063:0.0210214:rs199745162
1 18643 rs564023708 G A . PASS AF=0.00653636 ES:SE:LP:AF:ID -0.206463:0.159945:0.738761:0.00653636:rs564023708
1 18849 rs533090414 C G . PASS AF=0.975397 ES:SE:LP:AF:ID 0.0251821:0.0702438:0.143258:0.975397:rs533090414
1 30923 rs806731 G T . PASS AF=0.905695 ES:SE:LP:AF:ID -0.057427:0.0407552:0.791035:0.905695:rs806731
1 46285 rs545414834 ATAT A . PASS AF=0.00172177 ES:SE:LP:AF:ID 0.0885768:0.241377:0.144957:0.00172177:rs545414834
1 47159 rs540662756 T C . PASS AF=0.0666481 ES:SE:LP:AF:ID 0.0105533:0.0481958:0.0825418:0.0666481:rs540662756
1 49298 rs10399793 T C . PASS AF=0.838344 ES:SE:LP:AF:ID -0.0179534:0.0325306:0.235314:0.838344:rs10399793
1 49318 rs536836601 A G . PASS AF=0.00160152 ES:SE:LP:AF:ID -0.433185:0.351734:0.737962:0.00160152:rs536836601
1 49343 rs553572247 T C . PASS AF=0.00209357 ES:SE:LP:AF:ID -0.300493:0.27761:0.587418:0.00209357:rs553572247
1 49554 rs539322794 A G . PASS AF=0.0979616 ES:SE:LP:AF:ID 0.0361957:0.0400362:0.434197:0.0979616:rs539322794
1 51047 rs559500163 A T . PASS AF=0.00167609 ES:SE:LP:AF:ID 0.188773:0.274649:0.300254:0.00167609:rs559500163
1 51049 rs528344458 A C . PASS AF=0.00167609 ES:SE:LP:AF:ID 0.188773:0.274649:0.300254:0.00167609:rs528344458
1 51050 rs551668143 A T . PASS AF=0.00167609 ES:SE:LP:AF:ID 0.188773:0.274649:0.300254:0.00167609:rs551668143
1 51053 rs565211799 G T . PASS AF=0.00167609 ES:SE:LP:AF:ID 0.188773:0.274649:0.300254:0.00167609:rs565211799
1 51479 rs116400033 T A . PASS AF=0.212447 ES:SE:LP:AF:ID 0.000427231:0.0288376:0.00500487:0.212447:rs116400033
1 51762 rs559190862 A G . PASS AF=0.00852669 ES:SE:LP:AF:ID -0.00717883:0.129752:0.0196607:0.00852669:rs559190862
1 51765 rs575564077 C G . PASS AF=0.00830926 ES:SE:LP:AF:ID 0.00518169:0.129814:0.0139972:0.00830926:rs575564077
1 54353 rs140052487 C A . PASS AF=0.0018896 ES:SE:LP:AF:ID -0.389947:0.270754:0.909537:0.0018896:rs140052487
1 54354 rs569165477 C T . PASS AF=0.00234266 ES:SE:LP:AF:ID 0.258111:0.191946:0.713137:0.00234266:rs569165477
1 54490 rs141149254 G A . PASS AF=0.153612 ES:SE:LP:AF:ID 0.00386623:0.0322832:0.0433687:0.153612:rs141149254
1 54591 rs561234294 A G . PASS AF=0.00231616 ES:SE:LP:AF:ID -0.0594872:0.239337:0.0957812:0.00231616:rs561234294
1 54716 rs569128616 C T . PASS AF=0.428019 ES:SE:LP:AF:ID 0.00615215:0.0244332:0.096245:0.428019:rs569128616
1 54945 rs569799965 C A . PASS AF=0.0060798 ES:SE:LP:AF:ID 0.0583421:0.148104:0.157394:0.0060798:rs569799965
1 55164 rs3091274 C A . PASS AF=0.982976 ES:SE:LP:AF:ID -0.0168616:0.0944917:0.0661504:0.982976:rs3091274
1 55249 rs200769871 C CTATGG . PASS AF=0.00899767 ES:SE:LP:AF:ID -0.123168:0.124875:0.499849:0.00899767:rs200769871
1 55326 rs3107975 T C . PASS AF=0.0157731 ES:SE:LP:AF:ID -0.0288779:0.100152:0.112313:0.0157731:rs3107975
1 55405 rs372455836 C T . PASS AF=0.00502769 ES:SE:LP:AF:ID 0.155286:0.163119:0.452053:0.00502769:rs372455836
1 55545 rs28396308 C T . PASS AF=0.26028 ES:SE:LP:AF:ID 0.00793308:0.0271769:0.113235:0.26028:rs28396308
1 56586 rs541979596 G A . PASS AF=0.00111198 ES:SE:LP:AF:ID -0.189388:0.367297:0.22489:0.00111198:rs541979596