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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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"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.1": "<ID=StudyType,Number=1,Type=String,Description=\"Type of GWAS study [Continuous or CaseControl]\">",
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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": "2019-10-26T21:44:00.518953",
"gwas_harmonisation_command": "--json /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ebi_gwas_import/processed/EBI-a-GCST005838/EBI-a-GCST005838_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-GCST005838/EBI-a-GCST005838.vcf.gz -O z /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ebi_gwas_import/processed/EBI-a-GCST005838/EBI-a-GCST005838_data.vcf.gz; Date=Sat Oct 26 21:58:00 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-GCST005838/ebi-a-GCST005838.vcf.gz; Date=Sat May 9 13:10:20 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-GCST005838/EBI-a-GCST005838.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-GCST005838/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 22:22:19 2019
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ebi_gwas_import/processed/EBI-a-GCST005838/EBI-a-GCST005838.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 22:23:08 2019
Total time elapsed: 48.83s
{
"af_correlation": 0.9692,
"inflation_factor": 1.135,
"mean_EFFECT": 0.0013,
"n": "-Inf",
"n_snps": 7633440,
"n_clumped_hits": 17,
"n_p_sig": 438,
"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": 125211,
"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 | 7617511 | 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 | 7617521 | 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 | 8.627578e+00 | 5.741298e+00 | 1.0000 | 4.000000e+00 | 8.000000e+00 | 1.300000e+01 | 2.300000e+01 | ▇▅▅▂▂ |
numeric | POS | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 7.878162e+07 | 5.641072e+07 | 828.0000 | 3.235365e+07 | 6.933596e+07 | 1.145717e+08 | 2.492297e+08 | ▇▆▅▂▁ |
numeric | EFFECT | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 1.346400e-03 | 1.800680e-02 | -0.2192 | -8.100000e-03 | 9.000000e-04 | 1.010000e-02 | 2.002000e-01 | ▁▁▇▁▁ |
numeric | SE | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 1.508240e-02 | 8.506600e-03 | 0.0071 | 9.000000e-03 | 1.150000e-02 | 1.820000e-02 | 8.680000e-02 | ▇▁▁▁▁ |
numeric | PVAL | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 4.789053e-01 | 2.933922e-01 | 0.0000 | 2.195002e-01 | 4.724001e-01 | 7.334002e-01 | 9.993000e-01 | ▇▇▇▆▆ |
numeric | PVAL_ztest | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 4.789023e-01 | 2.933893e-01 | 0.0000 | 2.194935e-01 | 4.722950e-01 | 7.333340e-01 | 9.986545e-01 | ▇▇▇▆▆ |
numeric | AF | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 2.860331e-01 | 2.399532e-01 | 0.0105 | 9.000000e-02 | 2.103000e-01 | 4.304000e-01 | 9.884000e-01 | ▇▃▂▂▁ |
numeric | AF_reference | 125211 | 0.9835628 | NA | NA | NA | NA | NA | NA | NA | 2.727042e-01 | 2.519959e-01 | 0.0000 | 6.709270e-02 | 1.871010e-01 | 4.225240e-01 | 1.000000e+00 | ▇▃▂▂▁ |
CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
---|---|---|---|---|---|---|---|---|---|---|---|
1 | 729679 | rs4951859 | C | G | -0.0123 | 0.0177 | 0.4859001 | 0.4871084 | 0.7665 | 0.639976 | NA |
1 | 731718 | rs142557973 | T | C | 0.0020 | 0.0197 | 0.9203000 | 0.9191354 | 0.1430 | 0.154353 | NA |
1 | 734349 | rs141242758 | T | C | 0.0017 | 0.0186 | 0.9275999 | 0.9271765 | 0.1388 | 0.152556 | NA |
1 | 736289 | rs79010578 | T | A | 0.0056 | 0.0196 | 0.7764992 | 0.7750970 | 0.1417 | 0.139577 | NA |
1 | 751756 | rs143225517 | T | C | -0.0026 | 0.0137 | 0.8483001 | 0.8494807 | 0.2060 | 0.242212 | NA |
1 | 752566 | rs3094315 | G | A | 0.0110 | 0.0120 | 0.3561000 | 0.3593173 | 0.7704 | 0.718251 | NA |
1 | 752721 | rs3131972 | A | G | 0.0076 | 0.0123 | 0.5377000 | 0.5366504 | 0.7337 | 0.653355 | NA |
1 | 752894 | rs3131971 | T | C | 0.0119 | 0.0131 | 0.3642999 | 0.3636685 | 0.7760 | 0.753195 | NA |
1 | 753405 | rs3115860 | C | A | 0.0101 | 0.0133 | 0.4470005 | 0.4476142 | 0.7880 | 0.751797 | NA |
1 | 753474 | rs2073814 | C | G | 0.0019 | 0.0146 | 0.8956000 | 0.8964580 | 0.7180 | 0.611422 | NA |
CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
---|---|---|---|---|---|---|---|---|---|---|---|
22 | 51216731 | rs5771014 | T | C | 0.0083 | 0.0132 | 0.5276999 | 0.5294879 | 0.3071 | 0.2593850 | NA |
22 | 51217954 | rs9616974 | G | A | -0.0048 | 0.0229 | 0.8347999 | 0.8339744 | 0.0719 | 0.0621006 | NA |
22 | 51218224 | rs9616975 | C | A | 0.0062 | 0.0240 | 0.7951001 | 0.7961497 | 0.0710 | 0.0619010 | NA |
22 | 51218377 | rs2519461 | G | C | 0.0105 | 0.0227 | 0.6442998 | 0.6436833 | 0.0919 | 0.0826677 | NA |
22 | 51219006 | rs28729663 | G | A | -0.0189 | 0.0164 | 0.2492998 | 0.2491407 | 0.1908 | 0.2052720 | NA |
22 | 51219387 | rs9616832 | T | C | 0.0064 | 0.0244 | 0.7928007 | 0.7930940 | 0.0726 | 0.0654952 | NA |
22 | 51219704 | rs147475742 | G | A | -0.0367 | 0.0293 | 0.2097998 | 0.2103660 | 0.0491 | 0.0473243 | NA |
22 | 51221731 | rs115055839 | T | C | 0.0061 | 0.0239 | 0.7972000 | 0.7985454 | 0.0720 | 0.0625000 | NA |
22 | 51229805 | rs9616985 | T | C | -0.0143 | 0.0231 | 0.5353995 | 0.5358850 | 0.0800 | 0.0730831 | NA |
23 | 100784211 | rs188350543 | C | A | -0.0017 | 0.0117 | 0.8832999 | 0.8844747 | 0.7392 | 0.6498010 | NA |
1 729679 rs4951859 C G . PASS AF=0.7665 ES:SE:LP:AF:ID -0.0123:0.0177:0.313453:0.7665:rs4951859
1 731718 rs58276399 T C . PASS AF=0.143 ES:SE:LP:AF:ID 0.002:0.0197:0.0360706:0.143:rs58276399
1 734349 rs141242758 T C . PASS AF=0.1388 ES:SE:LP:AF:ID 0.0017:0.0186:0.0326393:0.1388:rs141242758
1 736289 rs79010578 T A . PASS AF=0.1417 ES:SE:LP:AF:ID 0.0056:0.0196:0.109859:0.1417:rs79010578
1 751756 rs28527770 T C . PASS AF=0.206 ES:SE:LP:AF:ID -0.0026:0.0137:0.0714505:0.206:rs28527770
1 752566 rs3094315 G A . PASS AF=0.7704 ES:SE:LP:AF:ID 0.011:0.012:0.448428:0.7704:rs3094315
1 752721 rs3131972 A G . PASS AF=0.7337 ES:SE:LP:AF:ID 0.0076:0.0123:0.26946:0.7337:rs3131972
1 752894 rs3131971 T C . PASS AF=0.776 ES:SE:LP:AF:ID 0.0119:0.0131:0.438541:0.776:rs3131971
1 753405 rs3115860 C A . PASS AF=0.788 ES:SE:LP:AF:ID 0.0101:0.0133:0.349692:0.788:rs3115860
1 753474 rs2073814 C G . PASS AF=0.718 ES:SE:LP:AF:ID 0.0019:0.0146:0.0478859:0.718:rs2073814
1 753541 rs2073813 G A . PASS AF=0.2251 ES:SE:LP:AF:ID 0.0065:0.0146:0.182898:0.2251:rs2073813
1 754182 rs3131969 A G . PASS AF=0.7609 ES:SE:LP:AF:ID -0.0053:0.0147:0.143392:0.7609:rs3131969
1 754192 rs3131968 A G . PASS AF=0.7612 ES:SE:LP:AF:ID -0.0046:0.0146:0.124939:0.7612:rs3131968
1 754334 rs3131967 T C . PASS AF=0.7522 ES:SE:LP:AF:ID -0.0079:0.0149:0.225118:0.7522:rs3131967
1 754503 rs3115859 G A . PASS AF=0.7454 ES:SE:LP:AF:ID 0.0078:0.0129:0.262251:0.7454:rs3115859
1 754964 rs3131966 C T . PASS AF=0.7385 ES:SE:LP:AF:ID -0.0001:0.0142:0.00200236:0.7385:rs3131966
1 755775 rs3131965 A G . PASS AF=0.7622 ES:SE:LP:AF:ID 0.0048:0.0145:0.13071:0.7622:rs3131965
1 755890 rs3115858 A T . PASS AF=0.7918 ES:SE:LP:AF:ID 0.0092:0.0132:0.313185:0.7918:rs3115858
1 756604 rs3131962 A G . PASS AF=0.7816 ES:SE:LP:AF:ID 0.0106:0.0132:0.374996:0.7816:rs3131962
1 757640 rs3115853 G A . PASS AF=0.7445 ES:SE:LP:AF:ID 0.0006:0.015:0.013273:0.7445:rs3115853
1 757734 rs4951929 C T . PASS AF=0.7939 ES:SE:LP:AF:ID 0.0075:0.0132:0.243668:0.7939:rs4951929
1 757936 rs4951862 C A . PASS AF=0.7927 ES:SE:LP:AF:ID 0.0076:0.0132:0.2498:0.7927:rs4951862
1 758144 rs3131956 A G . PASS AF=0.787 ES:SE:LP:AF:ID 0.0074:0.0128:0.247952:0.787:rs3131956
1 758626 rs3131954 C T . PASS AF=0.7943 ES:SE:LP:AF:ID 0.0095:0.0134:0.317945:0.7943:rs3131954
1 759700 rs3115852 T C . PASS AF=0.7655 ES:SE:LP:AF:ID 0.0062:0.0155:0.161655:0.7655:rs3115852
1 759837 rs3115851 T A . PASS AF=0.792 ES:SE:LP:AF:ID 0.0086:0.0141:0.266402:0.792:rs3115851
1 760912 rs1048488 C T . PASS AF=0.7632 ES:SE:LP:AF:ID 0.0154:0.0134:0.60415:0.7632:rs1048488
1 761147 rs3115850 T C . PASS AF=0.766 ES:SE:LP:AF:ID 0.0088:0.0132:0.298259:0.766:rs3115850
1 761732 rs2286139 C T . PASS AF=0.7287 ES:SE:LP:AF:ID -0.0104:0.0155:0.299037:0.7287:rs2286139
1 761752 rs1057213 C T . PASS AF=0.7874 ES:SE:LP:AF:ID 0.0135:0.0145:0.453704:0.7874:rs1057213
1 762273 rs3115849 G A . PASS AF=0.7795 ES:SE:LP:AF:ID 0.0101:0.0146:0.311491:0.7795:rs3115849
1 762589 rs3115848 G C . PASS AF=0.7736 ES:SE:LP:AF:ID 0.0062:0.015:0.168194:0.7736:rs3115848
1 762592 rs3131950 C G . PASS AF=0.7722 ES:SE:LP:AF:ID 0.0056:0.015:0.150458:0.7722:rs3131950
1 762601 rs3131949 T C . PASS AF=0.7717 ES:SE:LP:AF:ID 0.0035:0.0149:0.089429:0.7717:rs3131949
1 762632 rs3131948 T A . PASS AF=0.7776 ES:SE:LP:AF:ID 0.0095:0.015:0.279014:0.7776:rs3131948
1 764191 rs7515915 T G . PASS AF=0.1822 ES:SE:LP:AF:ID -0.0079:0.0148:0.225118:0.1822:rs7515915
1 766007 rs61768174 A C . PASS AF=0.1229 ES:SE:LP:AF:ID -0.0043:0.017:0.0975076:0.1229:rs61768174
1 768253 rs2977608 A C . PASS AF=0.6841 ES:SE:LP:AF:ID -0.0129:0.013:0.49174:0.6841:rs2977608
1 768448 rs12562034 G A . PASS AF=0.1268 ES:SE:LP:AF:ID 0.0146:0.0161:0.439854:0.1268:rs12562034
1 769223 rs60320384 C G . PASS AF=0.1614 ES:SE:LP:AF:ID -0.0067:0.0148:0.185886:0.1614:rs60320384
1 769963 rs7518545 G A . PASS AF=0.1228 ES:SE:LP:AF:ID 0.0224:0.0177:0.688882:0.1228:rs7518545
1 771823 rs2977605 T C . PASS AF=0.8036 ES:SE:LP:AF:ID 0.0082:0.0142:0.248028:0.8036:rs2977605
1 771967 rs59066358 G A . PASS AF=0.1734 ES:SE:LP:AF:ID -0.0096:0.0145:0.296021:0.1734:rs59066358
1 772755 rs2905039 A C . PASS AF=0.8071 ES:SE:LP:AF:ID 0.0088:0.0143:0.269379:0.8071:rs2905039
1 775181 rs61768182 A G . PASS AF=0.1821 ES:SE:LP:AF:ID -0.0098:0.015:0.291579:0.1821:rs61768182
1 777122 rs2980319 A T . PASS AF=0.7961 ES:SE:LP:AF:ID 0.0133:0.0141:0.459545:0.7961:rs2980319
1 777232 rs112618790 C T . PASS AF=0.079 ES:SE:LP:AF:ID 0.0056:0.0227:0.0938805:0.079:rs112618790
1 778745 rs1055606 A G . PASS AF=0.1726 ES:SE:LP:AF:ID -0.0113:0.0146:0.355758:0.1726:rs1055606
1 779322 rs4040617 A G . PASS AF=0.1801 ES:SE:LP:AF:ID -0.0092:0.0144:0.281581:0.1801:rs4040617
1 780785 rs2977612 T A . PASS AF=0.7671 ES:SE:LP:AF:ID -0.0101:0.0155:0.288108:0.7671:rs2977612