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"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\">",
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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": "2019-10-26T21:49:20.746333",
"gwas_harmonisation_command": "--json /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ebi_gwas_import/processed/EBI-a-GCST006358/EBI-a-GCST006358_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-GCST006358/EBI-a-GCST006358.vcf.gz -O z /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ebi_gwas_import/processed/EBI-a-GCST006358/EBI-a-GCST006358_data.vcf.gz; Date=Sat Oct 26 22:00:05 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-GCST006358/ebi-a-GCST006358.vcf.gz; Date=Sun May 10 07:58:29 2020"
}
*********************************************************************
* 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-GCST006358/EBI-a-GCST006358.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-GCST006358/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 22:22:50 2019
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ebi_gwas_import/processed/EBI-a-GCST006358/EBI-a-GCST006358.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 22:23:25 2019
Total time elapsed: 34.85s
{
"af_correlation": 0.9164,
"inflation_factor": 1.0045,
"mean_EFFECT": -0.0001,
"n": "-Inf",
"n_snps": 5278042,
"n_clumped_hits": 0,
"n_p_sig": 0,
"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": 35252,
"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"
}
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 |
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 SNPsn_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:
A, C, G or T
.< 0
or > 1
.<= 0
or = Infinity
).< 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.
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.
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.
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.
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
> 0.5ldsc_intercept_beta
: ldsc_intercept_beta
> 1.5n_clumped_hits
: n_clumped_hits
> 1000r2_sum<*>
: r2_sum<*>
> 0.5Plots
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 | 5265316 | 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 | 5265346 | 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 | 8.638495e+00 | 5.738675e+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 | 7.879344e+07 | 5.645854e+07 | 828.0000000 | 3.228537e+07 | 6.932693e+07 | 1.146312e+08 | 2.492385e+08 | ▇▆▅▂▁ |
numeric | EFFECT | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | -7.640000e-05 | 3.791880e-02 | -0.2586050 | -2.370650e-02 | -1.162000e-04 | 2.333590e-02 | 2.811720e-01 | ▁▁▇▁▁ |
numeric | SE | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 3.650900e-02 | 9.637800e-03 | 0.0251986 | 2.849460e-02 | 3.290910e-02 | 4.235320e-02 | 6.624440e-02 | ▇▃▂▂▁ |
numeric | PVAL | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 4.991635e-01 | 2.890274e-01 | 0.0000001 | 2.492294e-01 | 4.990344e-01 | 7.489210e-01 | 1.000000e+00 | ▇▇▇▇▇ |
numeric | PVAL_ztest | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 4.990021e-01 | 2.891242e-01 | 0.0000001 | 2.489507e-01 | 4.988757e-01 | 7.488524e-01 | 1.000000e+00 | ▇▇▇▇▇ |
numeric | AF | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 3.367567e-01 | 2.455678e-01 | 0.0500527 | 1.262580e-01 | 2.655940e-01 | 5.045270e-01 | 9.499470e-01 | ▇▃▂▂▂ |
numeric | AF_reference | 35252 | 0.9933049 | NA | NA | NA | NA | NA | NA | NA | 3.319970e-01 | 2.396594e-01 | 0.0001997 | 1.343850e-01 | 2.693690e-01 | 4.936100e-01 | 9.998000e-01 | ▇▆▃▂▁ |
CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
---|---|---|---|---|---|---|---|---|---|---|---|
1 | 729679 | rs4951859 | C | G | -0.0220384 | 0.0386636 | 0.5688045 | 0.5686751 | 0.852616 | 0.639976 | NA |
1 | 731718 | rs142557973 | T | C | 0.0102407 | 0.0434871 | 0.8138789 | 0.8138298 | 0.105634 | 0.154353 | NA |
1 | 734349 | rs141242758 | T | C | 0.0186230 | 0.0442747 | 0.6741212 | 0.6740297 | 0.103119 | 0.152556 | NA |
1 | 736289 | rs79010578 | T | A | 0.0443115 | 0.0420134 | 0.2918213 | 0.2915629 | 0.121227 | 0.139577 | NA |
1 | 752566 | rs3094315 | G | A | -0.0162810 | 0.0391272 | 0.6774247 | 0.6773336 | 0.860161 | 0.718251 | NA |
1 | 752721 | rs3131972 | A | G | -0.0162810 | 0.0391272 | 0.6774247 | 0.6773336 | 0.860161 | 0.653355 | NA |
1 | 753405 | rs3115860 | C | A | -0.0152836 | 0.0421508 | 0.7169865 | 0.7169087 | 0.886318 | 0.751797 | NA |
1 | 753541 | rs2073813 | G | A | 0.0198878 | 0.0429120 | 0.6431407 | 0.6430379 | 0.110161 | 0.301917 | NA |
1 | 754182 | rs3131969 | A | G | -0.0140347 | 0.0421003 | 0.7389295 | 0.7388600 | 0.885815 | 0.678514 | NA |
1 | 754192 | rs3131968 | A | G | -0.0140347 | 0.0421003 | 0.7389295 | 0.7388600 | 0.885815 | 0.678514 | NA |
CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
---|---|---|---|---|---|---|---|---|---|---|---|
22 | 51217954 | rs9616974 | G | A | 0.0613591 | 0.0529438 | 0.2467579 | 0.2464775 | 0.0729376 | 0.0621006 | NA |
22 | 51218224 | rs9616975 | C | A | 0.0613591 | 0.0529438 | 0.2467579 | 0.2464775 | 0.0729376 | 0.0619010 | NA |
22 | 51218377 | rs2519461 | G | C | 0.0588576 | 0.0528063 | 0.2652962 | 0.2650243 | 0.0734406 | 0.0826677 | NA |
22 | 51219006 | rs28729663 | G | A | 0.0337548 | 0.0391471 | 0.3887577 | 0.3885470 | 0.1423540 | 0.2052720 | NA |
22 | 51219387 | rs9616832 | T | C | 0.0613591 | 0.0529438 | 0.2467579 | 0.2464775 | 0.0729376 | 0.0654952 | NA |
22 | 51221731 | rs115055839 | T | C | 0.0613591 | 0.0529438 | 0.2467579 | 0.2464775 | 0.0729376 | 0.0625000 | NA |
22 | 51222100 | rs114553188 | G | T | 0.0245164 | 0.0578302 | 0.6717041 | 0.6716113 | 0.0588531 | 0.0880591 | NA |
22 | 51223637 | rs375798137 | G | A | 0.0207562 | 0.0576324 | 0.7188131 | 0.7187364 | 0.0593561 | 0.0788738 | NA |
22 | 51229805 | rs9616985 | T | C | 0.0624923 | 0.0530900 | 0.2394391 | 0.2391551 | 0.0724346 | 0.0730831 | NA |
22 | 51237063 | rs3896457 | T | C | 0.0094006 | 0.0295157 | 0.7501774 | 0.7501101 | 0.2756540 | 0.2050720 | NA |
1 729679 rs4951859 C G . PASS AF=0.852616 ES:SE:LP:AF:ID -0.0220384:0.0386636:0.245037:0.852616:rs4951859
1 731718 rs58276399 T C . PASS AF=0.105634 ES:SE:LP:AF:ID 0.0102407:0.0434871:0.0894402:0.105634:rs58276399
1 734349 rs141242758 T C . PASS AF=0.103119 ES:SE:LP:AF:ID 0.018623:0.0442747:0.171262:0.103119:rs141242758
1 736289 rs79010578 T A . PASS AF=0.121227 ES:SE:LP:AF:ID 0.0443115:0.0420134:0.534883:0.121227:rs79010578
1 752566 rs3094315 G A . PASS AF=0.860161 ES:SE:LP:AF:ID -0.016281:0.0391272:0.169139:0.860161:rs3094315
1 752721 rs3131972 A G . PASS AF=0.860161 ES:SE:LP:AF:ID -0.016281:0.0391272:0.169139:0.860161:rs3131972
1 753405 rs3115860 C A . PASS AF=0.886318 ES:SE:LP:AF:ID -0.0152836:0.0421508:0.144489:0.886318:rs3115860
1 753541 rs2073813 G A . PASS AF=0.110161 ES:SE:LP:AF:ID 0.0198878:0.042912:0.191694:0.110161:rs2073813
1 754182 rs3131969 A G . PASS AF=0.885815 ES:SE:LP:AF:ID -0.0140347:0.0421003:0.131397:0.885815:rs3131969
1 754192 rs3131968 A G . PASS AF=0.885815 ES:SE:LP:AF:ID -0.0140347:0.0421003:0.131397:0.885815:rs3131968
1 754334 rs3131967 T C . PASS AF=0.886318 ES:SE:LP:AF:ID -0.0152836:0.0421508:0.144489:0.886318:rs3131967
1 754503 rs3115859 G A . PASS AF=0.86167 ES:SE:LP:AF:ID -0.0169708:0.0393523:0.176279:0.86167:rs3115859
1 754964 rs3131966 C T . PASS AF=0.86167 ES:SE:LP:AF:ID -0.0169708:0.0393523:0.176279:0.86167:rs3131966
1 755775 rs3131965 A G . PASS AF=0.864185 ES:SE:LP:AF:ID -0.0169161:0.039516:0.174778:0.864185:rs3131965
1 755890 rs3115858 A T . PASS AF=0.886318 ES:SE:LP:AF:ID -0.0152836:0.0421508:0.144489:0.886318:rs3115858
1 756604 rs3131962 A G . PASS AF=0.886318 ES:SE:LP:AF:ID -0.0152836:0.0421508:0.144489:0.886318:rs3131962
1 757640 rs3115853 G A . PASS AF=0.884306 ES:SE:LP:AF:ID -0.0174494:0.0416272:0.170584:0.884306:rs3115853
1 757734 rs4951929 C T . PASS AF=0.886318 ES:SE:LP:AF:ID -0.0152836:0.0421508:0.144489:0.886318:rs4951929
1 757936 rs4951862 C A . PASS AF=0.886318 ES:SE:LP:AF:ID -0.0152836:0.0421508:0.144489:0.886318:rs4951862
1 758144 rs3131956 A G . PASS AF=0.886318 ES:SE:LP:AF:ID -0.0152836:0.0421508:0.144489:0.886318:rs3131956
1 758626 rs3131954 C T . PASS AF=0.886318 ES:SE:LP:AF:ID -0.0152836:0.0421508:0.144489:0.886318:rs3131954
1 760912 rs1048488 C T . PASS AF=0.863682 ES:SE:LP:AF:ID -0.030817:0.0396306:0.359531:0.863682:rs1048488
1 761147 rs3115850 T C . PASS AF=0.863682 ES:SE:LP:AF:ID -0.030817:0.0396306:0.359531:0.863682:rs3115850
1 761732 rs2286139 C T . PASS AF=0.881791 ES:SE:LP:AF:ID -0.0200059:0.0415283:0.200593:0.881791:rs2286139
1 766007 rs61768174 A C . PASS AF=0.0885312 ES:SE:LP:AF:ID 0.0287698:0.0464815:0.270761:0.0885312:rs61768174
1 768253 rs2977608 A C . PASS AF=0.776157 ES:SE:LP:AF:ID -0.025891:0.0329083:0.364908:0.776157:rs2977608
1 769223 rs60320384 C G . PASS AF=0.107646 ES:SE:LP:AF:ID 0.030774:0.043152:0.322467:0.107646:rs60320384
1 771823 rs2977605 T C . PASS AF=0.887324 ES:SE:LP:AF:ID -0.0206812:0.0421945:0.204715:0.887324:rs2977605
1 771967 rs59066358 G A . PASS AF=0.108652 ES:SE:LP:AF:ID 0.0325192:0.0430307:0.346789:0.108652:rs59066358
1 772755 rs2905039 A C . PASS AF=0.887324 ES:SE:LP:AF:ID -0.0206812:0.0421945:0.204715:0.887324:rs2905039
1 777122 rs2980319 A T . PASS AF=0.889336 ES:SE:LP:AF:ID -0.0180586:0.0424316:0.173604:0.889336:rs2980319
1 778745 rs1055606 A G . PASS AF=0.10664 ES:SE:LP:AF:ID 0.0299264:0.0432822:0.310282:0.10664:rs1055606
1 779322 rs4040617 A G . PASS AF=0.107143 ES:SE:LP:AF:ID 0.0266093:0.0432203:0.26901:0.107143:rs4040617
1 780785 rs2977612 T A . PASS AF=0.885815 ES:SE:LP:AF:ID -0.0089239:0.0414801:0.0810763:0.885815:rs2977612
1 781845 rs61768199 A G . PASS AF=0.0850101 ES:SE:LP:AF:ID 0.0342708:0.0476901:0.325553:0.0850101:rs61768199
1 785050 rs2905062 G A . PASS AF=0.885312 ES:SE:LP:AF:ID 0.00194598:0.0415749:0.0165194:0.885312:rs2905062
1 785989 rs2980300 T C . PASS AF=0.885312 ES:SE:LP:AF:ID 0.00194598:0.0415749:0.0165194:0.885312:rs2980300
1 787606 rs3863622 G T . PASS AF=0.10664 ES:SE:LP:AF:ID 0.0244545:0.0432813:0.242457:0.10664:rs3863622
1 787685 rs2905054 G T . PASS AF=0.881791 ES:SE:LP:AF:ID -0.00314925:0.0410218:0.0274167:0.881791:rs2905054
1 787844 rs2905053 C T . PASS AF=0.887324 ES:SE:LP:AF:ID -0.00836424:0.0419641:0.0746601:0.887324:rs2905053
1 790465 rs61768207 G A . PASS AF=0.084507 ES:SE:LP:AF:ID 0.0375443:0.0480665:0.361575:0.084507:rs61768207
1 791191 rs111818025 G A . PASS AF=0.10664 ES:SE:LP:AF:ID 0.0293544:0.0432775:0.302988:0.10664:rs111818025
1 791853 rs6684487 G A . PASS AF=0.0940644 ES:SE:LP:AF:ID 0.0476338:0.047514:0.49985:0.0940644:rs6684487
1 794332 rs12127425 G A . PASS AF=0.0870221 ES:SE:LP:AF:ID 0.0388271:0.0489492:0.368714:0.0870221:rs12127425
1 795222 rs12131377 C G . PASS AF=0.0855131 ES:SE:LP:AF:ID 0.0389522:0.0492726:0.367139:0.0855131:rs12131377
1 796100 rs12132398 C T . PASS AF=0.0865191 ES:SE:LP:AF:ID 0.0406785:0.0490759:0.390013:0.0865191:rs12132398
1 796375 rs12083781 T C . PASS AF=0.109155 ES:SE:LP:AF:ID 0.0442182:0.0424116:0.526672:0.109155:rs12083781
1 797281 rs76631953 G C . PASS AF=0.0860161 ES:SE:LP:AF:ID 0.0368896:0.0491709:0.343621:0.0860161:rs76631953
1 797325 rs111739932 T C . PASS AF=0.0860161 ES:SE:LP:AF:ID 0.0368896:0.0491709:0.343621:0.0860161:rs111739932
1 797440 rs58013264 T C . PASS AF=0.108652 ES:SE:LP:AF:ID 0.0402123:0.042468:0.463531:0.108652:rs58013264