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": "2019-10-27T07:29:31.463790",
"gwas_harmonisation_command": "--json /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ebi_gwas_import/processed/EBI-a-GCST005813/EBI-a-GCST005813_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-GCST005813/EBI-a-GCST005813.vcf.gz -O z /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ebi_gwas_import/processed/EBI-a-GCST005813/EBI-a-GCST005813_data.vcf.gz; Date=Sun Oct 27 07:53:44 2019",
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"bcftools_viewCommand": "view -h /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/ebi-a-GCST005813/ebi-a-GCST005813.vcf.gz; Date=Sun May 10 02:32:50 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-GCST005813/EBI-a-GCST005813.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-GCST005813/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-GCST005813/EBI-a-GCST005813.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:45.54sQC metrics
Metrics
Metrics
{
"af_correlation": 0.9556,
"inflation_factor": 0.9756,
"mean_EFFECT": 0.0002,
"n": "-Inf",
"n_snps": 15708688,
"n_clumped_hits": 0,
"n_p_sig": 0,
"n_mono": 0,
"n_ns": 1401577,
"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": 483923,
"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 | 15685671 | 0 | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| character | REF | 0 | 1.0000000 | 1 | 84 | 0 | 67071 | 0 | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| character | ALT | 0 | 1.0000000 | 1 | 63 | 0 | 34365 | 0 | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| logical | N | 15686243 | 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 | 8.775803e+00 | 5.809619e+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 | 7.835128e+07 | 5.621760e+07 | 56.0000000 | 3.223216e+07 | 6.884561e+07 | 1.137672e+08 | 2.492397e+08 | ▇▆▅▂▁ |
| numeric | EFFECT | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 1.731000e-04 | 1.792872e-01 | -8.0568000 | -4.451560e-02 | 7.627000e-04 | 4.794520e-02 | 2.767780e+00 | ▁▁▁▇▁ |
| numeric | SE | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 1.391291e-01 | 1.455969e-01 | 0.0233171 | 3.108170e-02 | 7.511100e-02 | 2.269740e-01 | 2.154020e+01 | ▇▁▁▁▁ |
| numeric | PVAL | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 5.032930e-01 | 2.893966e-01 | 0.0000001 | 2.524539e-01 | 5.052845e-01 | 7.546768e-01 | 1.000000e+00 | ▇▇▇▇▇ |
| numeric | PVAL_ztest | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 5.040525e-01 | 2.887858e-01 | 0.0000000 | 2.541786e-01 | 5.058884e-01 | 7.547509e-01 | 1.000000e+00 | ▇▇▇▇▇ |
| numeric | AF | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 1.628316e-01 | 2.453467e-01 | 0.0010000 | 3.540200e-03 | 2.880830e-02 | 2.318885e-01 | 9.989990e-01 | ▇▁▁▁▁ |
| numeric | AF_reference | 483923 | 0.9691498 | NA | NA | NA | NA | NA | NA | NA | 1.659792e-01 | 2.382690e-01 | 0.0000000 | 1.996800e-03 | 4.113420e-02 | 2.470050e-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 | -0.0231460 | 0.0341378 | 0.4974736 | 0.4977611 | 0.3996350 | 0.4253190 | NA |
| 1 | 10352 | rs555500075 | T | TA | 0.0154176 | 0.0355675 | 0.6648030 | 0.6646702 | 0.3890130 | 0.4375000 | NA |
| 1 | 10616 | rs376342519 | CCGCCGTTGCAAAGGCGCGCCG | C | 0.0245851 | 0.2451740 | 0.9186141 | 0.9201251 | 0.9951320 | 0.9930110 | NA |
| 1 | 11012 | rs544419019 | C | G | -0.0170739 | 0.0603968 | 0.7769302 | 0.7774103 | 0.0851744 | 0.0880591 | NA |
| 1 | 13110 | rs540538026 | G | A | 0.0191410 | 0.0778137 | 0.8061879 | 0.8056939 | 0.0604375 | 0.0267572 | NA |
| 1 | 13116 | rs62635286 | T | G | -0.0227974 | 0.0468826 | 0.6260269 | 0.6267788 | 0.1917100 | 0.0970447 | NA |
| 1 | 13118 | rs200579949 | A | G | -0.0227974 | 0.0468826 | 0.6260269 | 0.6267788 | 0.1917100 | 0.0970447 | NA |
| 1 | 13273 | rs531730856 | G | C | 0.0134217 | 0.0534788 | 0.8021170 | 0.8018355 | 0.1345350 | 0.0950479 | NA |
| 1 | 13453 | rs568927457 | T | C | 0.1507010 | 0.2024370 | 0.4668776 | 0.4566139 | 0.0062203 | 0.0007987 | NA |
| 1 | 13483 | rs554760071 | G | C | 0.0559249 | 0.2300840 | 0.8096330 | 0.8079566 | 0.0053287 | 0.0019968 | NA |
| CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 22 | 51238328 | rs553081191 | A | C | 0.3440990 | 0.3058980 | 0.2768299 | 0.2606393 | 0.0016618 | 0.0005990 | NA |
| 22 | 51238364 | rs564490465 | C | G | -0.3632540 | 0.3136070 | 0.2127340 | 0.2467377 | 0.0054168 | 0.0005990 | NA |
| 22 | 51238394 | rs149712012 | C | T | 0.0790594 | 0.2673650 | 0.7697576 | 0.7674604 | 0.0032768 | 0.0033946 | NA |
| 22 | 51239281 | rs8138215 | G | C | -0.0184085 | 0.3579240 | 0.9584861 | 0.9589818 | 0.0016602 | 0.0111821 | NA |
| 22 | 51239296 | rs8137179 | T | C | -0.0184085 | 0.3579240 | 0.9584861 | 0.9589818 | 0.0016602 | 0.0111821 | NA |
| 22 | 51239304 | rs8142977 | C | T | -0.0184085 | 0.3579240 | 0.9584861 | 0.9589818 | 0.0016602 | 0.0111821 | NA |
| 22 | 51239586 | rs535432390 | T | G | 0.0949074 | 0.3807490 | 0.8054801 | 0.8031558 | 0.0016185 | 0.0001997 | NA |
| 22 | 51239794 | rs561893765 | C | A | 0.1117880 | 0.3496950 | 0.7518635 | 0.7492163 | 0.0017412 | 0.0299521 | NA |
| 22 | 51240820 | rs202228854 | C | T | 0.0918302 | 0.0938577 | 0.3327791 | 0.3278774 | 0.0255524 | 0.1267970 | NA |
| 22 | 51244237 | rs575160859 | C | T | -0.2743750 | 0.1684150 | 0.0880096 | 0.1032791 | 0.0135512 | 0.0037939 | NA |
bcf preview
1 10177 rs367896724 A AC . PASS AF=0.399635 ES:SE:LP:AF:ID -0.023146:0.0341378:0.30323:0.399635:rs367896724
1 10352 rs555500075 T TA . PASS AF=0.389013 ES:SE:LP:AF:ID 0.0154176:0.0355675:0.177307:0.389013:rs555500075
1 10616 rs376342519 CCGCCGTTGCAAAGGCGCGCCG C . PASS AF=0.995132 ES:SE:LP:AF:ID 0.0245851:0.245174:0.0368669:0.995132:rs376342519
1 11012 rs544419019 C G . PASS AF=0.0851744 ES:SE:LP:AF:ID -0.0170739:0.0603968:0.109618:0.0851744:rs544419019
1 13110 rs540538026 G A . PASS AF=0.0604375 ES:SE:LP:AF:ID 0.019141:0.0778137:0.0935637:0.0604375:rs540538026
1 13116 rs62635286 T G . PASS AF=0.19171 ES:SE:LP:AF:ID -0.0227974:0.0468826:0.203407:0.19171:rs62635286
1 13118 rs62028691 A G . PASS AF=0.19171 ES:SE:LP:AF:ID -0.0227974:0.0468826:0.203407:0.19171:rs62028691
1 13273 rs531730856 G C . PASS AF=0.134535 ES:SE:LP:AF:ID 0.0134217:0.0534788:0.0957623:0.134535:rs531730856
1 13453 rs568927457 T C . PASS AF=0.00622027 ES:SE:LP:AF:ID 0.150701:0.202437:0.330797:0.00622027:rs568927457
1 13483 rs554760071 G C . PASS AF=0.00532871 ES:SE:LP:AF:ID 0.0559249:0.230084:0.0917118:0.00532871:rs554760071
1 14464 rs546169444 A T . PASS AF=0.156623 ES:SE:LP:AF:ID 0.0192506:0.0487592:0.158929:0.156623:rs546169444
1 14599 rs707680 T A . PASS AF=0.192469 ES:SE:LP:AF:ID -0.00662367:0.0445582:0.0546506:0.192469:rs707680
1 14604 rs541940975 A G . PASS AF=0.192469 ES:SE:LP:AF:ID -0.00662367:0.0445582:0.0546506:0.192469:rs541940975
1 14930 rs6682385 A G . PASS AF=0.468833 ES:SE:LP:AF:ID -0.0221274:0.0351832:0.276326:0.468833:rs6682385
1 14933 rs199856693 G A . PASS AF=0.0488092 ES:SE:LP:AF:ID -0.0556905:0.0842101:0.296575:0.0488092:rs199856693
1 15211 rs3982632 T G . PASS AF=0.745164 ES:SE:LP:AF:ID -0.0784273:0.0394913:1.3178:0.745164:rs3982632
1 15245 rs576044687 C T . PASS AF=0.00111968 ES:SE:LP:AF:ID 0.179293:0.451121:0.157496:0.00111968:rs576044687
1 15644 rs564003018 G A . PASS AF=0.00352363 ES:SE:LP:AF:ID -0.127738:0.343484:0.15274:0.00352363:rs564003018
1 15820 rs2691315 G T . PASS AF=0.269952 ES:SE:LP:AF:ID 0.00911644:0.0411964:0.0835629:0.269952:rs2691315
1 15903 rs557514207 G GC . PASS AF=0.408394 ES:SE:LP:AF:ID -0.0321944:0.0344588:0.456289:0.408394:rs557514207
1 16142 rs548165136 G A . PASS AF=0.00316947 ES:SE:LP:AF:ID -0.781255:0.467698:1.28556:0.00316947:rs548165136
1 16949 rs199745162 A C . PASS AF=0.0212029 ES:SE:LP:AF:ID -0.264499:0.134269:1.39646:0.0212029:rs199745162
1 18643 rs564023708 G A . PASS AF=0.00646843 ES:SE:LP:AF:ID 0.092219:0.211269:0.176363:0.00646843:rs564023708
1 18849 rs533090414 C G . PASS AF=0.975614 ES:SE:LP:AF:ID 0.0450602:0.107271:0.172334:0.975614:rs533090414
1 30923 rs806731 G T . PASS AF=0.905678 ES:SE:LP:AF:ID -0.059831:0.0608948:0.48235:0.905678:rs806731
1 46285 rs545414834 ATAT A . PASS AF=0.00170547 ES:SE:LP:AF:ID 0.0982012:0.371655:0.100264:0.00170547:rs545414834
1 47159 rs540662756 T C . PASS AF=0.06535 ES:SE:LP:AF:ID 0.041656:0.073115:0.24341:0.06535:rs540662756
1 49298 rs10399793 T C . PASS AF=0.838704 ES:SE:LP:AF:ID -0.0471602:0.0486028:0.476182:0.838704:rs10399793
1 49318 rs536836601 A G . PASS AF=0.00164614 ES:SE:LP:AF:ID -0.98877:0.772926:0.968297:0.00164614:rs536836601
1 49343 rs553572247 T C . PASS AF=0.00207547 ES:SE:LP:AF:ID 0.173255:0.354344:0.199376:0.00207547:rs553572247
1 49554 rs539322794 A G . PASS AF=0.0976815 ES:SE:LP:AF:ID 0.0731799:0.0594769:0.652865:0.0976815:rs539322794
1 51047 rs559500163 A T . PASS AF=0.00154544 ES:SE:LP:AF:ID 0.262382:0.442286:0.247359:0.00154544:rs559500163
1 51049 rs528344458 A C . PASS AF=0.00154544 ES:SE:LP:AF:ID 0.262382:0.442286:0.247359:0.00154544:rs528344458
1 51050 rs551668143 A T . PASS AF=0.00154544 ES:SE:LP:AF:ID 0.262382:0.442286:0.247359:0.00154544:rs551668143
1 51053 rs565211799 G T . PASS AF=0.00154544 ES:SE:LP:AF:ID 0.262382:0.442286:0.247359:0.00154544:rs565211799
1 51479 rs116400033 T A . PASS AF=0.211829 ES:SE:LP:AF:ID 0.00695218:0.043223:0.0593396:0.211829:rs116400033
1 51762 rs559190862 A G . PASS AF=0.00877642 ES:SE:LP:AF:ID -0.0130748:0.191282:0.0243904:0.00877642:rs559190862
1 51765 rs575564077 C G . PASS AF=0.00852885 ES:SE:LP:AF:ID 0.0113715:0.190988:0.021037:0.00852885:rs575564077
1 52238 rs2691277 T G . PASS AF=0.978018 ES:SE:LP:AF:ID -0.0270419:0.127943:0.0792273:0.978018:rs2691277
1 54353 rs140052487 C A . PASS AF=0.00202393 ES:SE:LP:AF:ID -0.595492:0.426851:0.919056:0.00202393:rs140052487
1 54354 rs569165477 C T . PASS AF=0.0022264 ES:SE:LP:AF:ID 0.166645:0.316013:0.216444:0.0022264:rs569165477
1 54490 rs141149254 G A . PASS AF=0.153224 ES:SE:LP:AF:ID 0.0044358:0.048532:0.0326566:0.153224:rs141149254
1 54591 rs561234294 A G . PASS AF=0.00219184 ES:SE:LP:AF:ID 0.0364425:0.36224:0.0353228:0.00219184:rs561234294
1 54716 rs569128616 C T . PASS AF=0.425742 ES:SE:LP:AF:ID 0.0653385:0.0365058:1.13197:0.425742:rs569128616
1 54945 rs569799965 C A . PASS AF=0.00567239 ES:SE:LP:AF:ID 0.0844384:0.232035:0.143319:0.00567239:rs569799965
1 55164 rs3091274 C A . PASS AF=0.982863 ES:SE:LP:AF:ID 0.0569029:0.145367:0.159275:0.982863:rs3091274
1 55249 rs200769871 C CTATGG . PASS AF=0.00855796 ES:SE:LP:AF:ID 0.153659:0.175933:0.407821:0.00855796:rs200769871
1 55326 rs3107975 T C . PASS AF=0.0157572 ES:SE:LP:AF:ID -0.104053:0.155477:0.304202:0.0157572:rs3107975
1 55405 rs372455836 C T . PASS AF=0.00504956 ES:SE:LP:AF:ID 0.227682:0.236687:0.451426:0.00504956:rs372455836
1 55427 rs183189405 T C . PASS AF=0.00166061 ES:SE:LP:AF:ID 0.188231:0.445758:0.166937:0.00166061:rs183189405