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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": "2019-10-26T21:45:23.654489",
"gwas_harmonisation_command": "--json /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ebi_gwas_import/processed/EBI-a-GCST006906/EBI-a-GCST006906_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-GCST006906/EBI-a-GCST006906.vcf.gz -O z /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ebi_gwas_import/processed/EBI-a-GCST006906/EBI-a-GCST006906_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-GCST006906/ebi-a-GCST006906.vcf.gz; Date=Sun May 10 09:16:56 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-GCST006906/EBI-a-GCST006906.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-GCST006906/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 22:23:30 2019
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ebi_gwas_import/processed/EBI-a-GCST006906/EBI-a-GCST006906.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 22:24:23 2019
Total time elapsed: 53.31s
{
"af_correlation": 0.9421,
"inflation_factor": 1.1036,
"mean_EFFECT": 0.0016,
"n": "-Inf",
"n_snps": 8211693,
"n_clumped_hits": 8,
"n_p_sig": 360,
"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": 161464,
"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 | 59 | 0 | 8194659 | 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 | 8194682 | 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 | 8.647544e+00 | 5.752013e+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 | 7.860068e+07 | 5.643171e+07 | 828.0000 | 3.219437e+07 | 6.903521e+07 | 1.144321e+08 | 2.492297e+08 | ▇▆▅▂▁ |
numeric | EFFECT | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 1.627700e-03 | 2.566370e-02 | -0.3705 | -1.000000e-02 | 1.100000e-03 | 1.240000e-02 | 3.701000e-01 | ▁▁▇▁▁ |
numeric | SE | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 2.065610e-02 | 1.463230e-02 | 0.0081 | 1.050000e-02 | 1.430000e-02 | 2.570000e-02 | 1.266000e-01 | ▇▂▁▁▁ |
numeric | PVAL | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 4.836583e-01 | 2.924032e-01 | 0.0000 | 2.263002e-01 | 4.786003e-01 | 7.369992e-01 | 9.996000e-01 | ▇▇▇▇▇ |
numeric | PVAL_ztest | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 4.836548e-01 | 2.924016e-01 | 0.0000 | 2.262789e-01 | 4.785670e-01 | 7.367695e-01 | 9.991908e-01 | ▇▇▇▇▇ |
numeric | AF | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 2.563176e-01 | 2.592875e-01 | 0.0101 | 4.440000e-02 | 1.529000e-01 | 4.038000e-01 | 9.897000e-01 | ▇▂▂▁▁ |
numeric | AF_reference | 161464 | 0.9802965 | NA | NA | NA | NA | NA | NA | NA | 2.562651e-01 | 2.531419e-01 | 0.0000 | 4.832270e-02 | 1.667330e-01 | 4.013580e-01 | 1.000000e+00 | ▇▃▂▁▁ |
CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
---|---|---|---|---|---|---|---|---|---|---|---|
1 | 662622 | rs61769339 | G | A | -0.0095 | 0.0244 | 0.6981006 | 0.6970215 | 0.1264 | 0.1475640 | NA |
1 | 693731 | rs12238997 | A | G | -0.0123 | 0.0236 | 0.6021005 | 0.6022369 | 0.1317 | 0.1417730 | NA |
1 | 729679 | rs4951859 | C | G | 0.0024 | 0.0197 | 0.9037000 | 0.9030357 | 0.8336 | 0.6399760 | NA |
1 | 731718 | rs142557973 | T | C | -0.0007 | 0.0217 | 0.9749001 | 0.9742663 | 0.1367 | 0.1543530 | NA |
1 | 732809 | rs12131618 | T | C | 0.0365 | 0.0297 | 0.2192002 | 0.2190882 | 0.0770 | 0.0615016 | NA |
1 | 734349 | rs141242758 | T | C | 0.0006 | 0.0202 | 0.9768001 | 0.9763039 | 0.1336 | 0.1525560 | NA |
1 | 736289 | rs79010578 | T | A | 0.0005 | 0.0211 | 0.9829000 | 0.9810946 | 0.1426 | 0.1395770 | NA |
1 | 751756 | rs143225517 | T | C | -0.0037 | 0.0181 | 0.8373000 | 0.8380254 | 0.1451 | 0.2422120 | NA |
1 | 752566 | rs3094315 | G | A | 0.0115 | 0.0155 | 0.4587996 | 0.4581264 | 0.8287 | 0.7182510 | NA |
1 | 752721 | rs3131972 | A | G | 0.0082 | 0.0155 | 0.5964994 | 0.5967831 | 0.8153 | 0.6533550 | NA |
CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
---|---|---|---|---|---|---|---|---|---|---|---|
22 | 51221731 | rs115055839 | T | C | 0.0110 | 0.0263 | 0.6740995 | 0.6757636 | 0.0678 | 0.0625000 | NA |
22 | 51222052 | rs2879915 | G | A | 0.0248 | 0.0176 | 0.1583999 | 0.1588083 | 0.2782 | 0.2194490 | NA |
22 | 51224600 | rs187908482 | G | A | -0.0471 | 0.0252 | 0.0623706 | 0.0616162 | 0.1061 | 0.0387380 | NA |
22 | 51228910 | rs145146472 | G | A | 0.0056 | 0.0156 | 0.7212005 | 0.7196143 | 0.3023 | 0.2276360 | NA |
22 | 51229805 | rs9616985 | T | C | 0.0059 | 0.0258 | 0.8203000 | 0.8191160 | 0.0690 | 0.0730831 | NA |
22 | 51233300 | rs9616839 | C | T | 0.0334 | 0.0205 | 0.1028000 | 0.1032562 | 0.3300 | 0.3146960 | NA |
22 | 51237063 | rs3896457 | T | C | 0.0207 | 0.0206 | 0.3156000 | 0.3149670 | 0.2785 | 0.2050720 | NA |
22 | 51238249 | rs149733995 | A | C | 0.0128 | 0.0390 | 0.7424001 | 0.7427566 | 0.0704 | NA | NA |
23 | 46256106 | rs12007097 | G | C | -0.0445 | 0.0406 | 0.2737001 | 0.2730529 | 0.9728 | 0.6821190 | NA |
23 | 100784211 | rs188350543 | C | A | -0.0029 | 0.0138 | 0.8342000 | 0.8335546 | 0.7431 | 0.6498010 | NA |
1 662622 rs61769339 G A . PASS AF=0.1264 ES:SE:LP:AF:ID -0.0095:0.0244:0.156082:0.1264:rs61769339
1 693731 rs12238997 A G . PASS AF=0.1317 ES:SE:LP:AF:ID -0.0123:0.0236:0.220331:0.1317:rs12238997
1 729679 rs4951859 C G . PASS AF=0.8336 ES:SE:LP:AF:ID 0.0024:0.0197:0.0439757:0.8336:rs4951859
1 731718 rs58276399 T C . PASS AF=0.1367 ES:SE:LP:AF:ID -0.0007:0.0217:0.0110399:0.1367:rs58276399
1 732809 rs12131618 T C . PASS AF=0.077 ES:SE:LP:AF:ID 0.0365:0.0297:0.659159:0.077:rs12131618
1 734349 rs141242758 T C . PASS AF=0.1336 ES:SE:LP:AF:ID 0.0006:0.0202:0.0101943:0.1336:rs141242758
1 736289 rs79010578 T A . PASS AF=0.1426 ES:SE:LP:AF:ID 0.0005:0.0211:0.00749066:0.1426:rs79010578
1 751756 rs28527770 T C . PASS AF=0.1451 ES:SE:LP:AF:ID -0.0037:0.0181:0.0771189:0.1451:rs28527770
1 752566 rs3094315 G A . PASS AF=0.8287 ES:SE:LP:AF:ID 0.0115:0.0155:0.338377:0.8287:rs3094315
1 752721 rs3131972 A G . PASS AF=0.8153 ES:SE:LP:AF:ID 0.0082:0.0155:0.22439:0.8153:rs3131972
1 752894 rs3131971 T C . PASS AF=0.8152 ES:SE:LP:AF:ID 0.012:0.0171:0.318487:0.8152:rs3131971
1 753405 rs3115860 C A . PASS AF=0.8478 ES:SE:LP:AF:ID 0.0088:0.0175:0.210419:0.8478:rs3115860
1 753474 rs2073814 C G . PASS AF=0.8132 ES:SE:LP:AF:ID 0.0085:0.017:0.209152:0.8132:rs2073814
1 753541 rs2073813 G A . PASS AF=0.1481 ES:SE:LP:AF:ID -0.0054:0.0171:0.122801:0.1481:rs2073813
1 754182 rs3131969 A G . PASS AF=0.8497 ES:SE:LP:AF:ID 0.0027:0.0172:0.0586874:0.8497:rs3131969
1 754192 rs3131968 A G . PASS AF=0.8497 ES:SE:LP:AF:ID 0.0036:0.0171:0.0779496:0.8497:rs3131968
1 754334 rs3131967 T C . PASS AF=0.8416 ES:SE:LP:AF:ID -0.0016:0.0176:0.0335297:0.8416:rs3131967
1 754503 rs3115859 G A . PASS AF=0.8242 ES:SE:LP:AF:ID 0.0065:0.0164:0.160333:0.8242:rs3115859
1 754964 rs3131966 C T . PASS AF=0.8166 ES:SE:LP:AF:ID 0.0061:0.0165:0.146606:0.8166:rs3131966
1 755775 rs3131965 A G . PASS AF=0.795 ES:SE:LP:AF:ID 0.0066:0.0192:0.135489:0.795:rs3131965
1 755890 rs3115858 A T . PASS AF=0.8482 ES:SE:LP:AF:ID 0.0106:0.0169:0.277284:0.8482:rs3115858
1 756604 rs3131962 A G . PASS AF=0.8387 ES:SE:LP:AF:ID 0.0122:0.017:0.326242:0.8387:rs3131962
1 756912 rs6699990 A G . PASS AF=0.0294 ES:SE:LP:AF:ID 0.0687:0.0555:0.66615:0.0294:rs6699990
1 757640 rs3115853 G A . PASS AF=0.8478 ES:SE:LP:AF:ID 0.0086:0.0175:0.205094:0.8478:rs3115853
1 757734 rs4951929 C T . PASS AF=0.8528 ES:SE:LP:AF:ID 0.0074:0.017:0.178486:0.8528:rs4951929
1 757936 rs4951862 C A . PASS AF=0.8501 ES:SE:LP:AF:ID 0.0071:0.0169:0.17031:0.8501:rs4951862
1 758144 rs3131956 A G . PASS AF=0.8395 ES:SE:LP:AF:ID 0.0064:0.0164:0.157204:0.8395:rs3131956
1 758626 rs3131954 C T . PASS AF=0.8517 ES:SE:LP:AF:ID 0.0119:0.0172:0.310425:0.8517:rs3131954
1 759700 rs3115852 T C . PASS AF=0.8076 ES:SE:LP:AF:ID 0.0107:0.0217:0.205721:0.8076:rs3115852
1 759837 rs3115851 T A . PASS AF=0.8528 ES:SE:LP:AF:ID 0.0098:0.0185:0.22388:0.8528:rs3115851
1 760912 rs1048488 C T . PASS AF=0.8175 ES:SE:LP:AF:ID 0.0174:0.0173:0.501689:0.8175:rs1048488
1 761147 rs3115850 T C . PASS AF=0.818 ES:SE:LP:AF:ID 0.0064:0.0169:0.151749:0.818:rs3115850
1 761732 rs2286139 C T . PASS AF=0.8347 ES:SE:LP:AF:ID -0.0047:0.0179:0.100015:0.8347:rs2286139
1 761752 rs1057213 C T . PASS AF=0.8524 ES:SE:LP:AF:ID 0.0136:0.0193:0.318307:0.8524:rs1057213
1 762273 rs3115849 G A . PASS AF=0.8403 ES:SE:LP:AF:ID 0.0045:0.0188:0.0909256:0.8403:rs3115849
1 762472 rs145493205 C T . PASS AF=0.1068 ES:SE:LP:AF:ID -0.0008:0.0359:0.00735813:0.1068:rs145493205
1 762485 rs12095200 C A . PASS AF=0.1149 ES:SE:LP:AF:ID -0.0224:0.0247:0.437945:0.1149:rs12095200
1 762589 rs3115848 G C . PASS AF=0.8351 ES:SE:LP:AF:ID 0.0034:0.0197:0.063235:0.8351:rs3115848
1 762592 rs3131950 C G . PASS AF=0.8337 ES:SE:LP:AF:ID 0.0038:0.0197:0.0729891:0.8337:rs3131950
1 762601 rs3131949 T C . PASS AF=0.8345 ES:SE:LP:AF:ID 0.0003:0.0196:0.00594694:0.8345:rs3131949
1 762632 rs3131948 T A . PASS AF=0.8357 ES:SE:LP:AF:ID 0.0071:0.0196:0.143452:0.8357:rs3131948
1 764191 rs7515915 T G . PASS AF=0.1448 ES:SE:LP:AF:ID -0.0066:0.019:0.13763:0.1448:rs7515915
1 766007 rs61768174 A C . PASS AF=0.127 ES:SE:LP:AF:ID 0.0002:0.0194:0.00291956:0.127:rs61768174
1 768253 rs2977608 A C . PASS AF=0.742 ES:SE:LP:AF:ID -0.0095:0.0142:0.298691:0.742:rs2977608
1 768448 rs12562034 G A . PASS AF=0.1032 ES:SE:LP:AF:ID 0.0041:0.0178:0.0885228:0.1032:rs12562034
1 769223 rs60320384 C G . PASS AF=0.1426 ES:SE:LP:AF:ID -0.0054:0.0181:0.116055:0.1426:rs60320384
1 769963 rs7518545 G A . PASS AF=0.0988 ES:SE:LP:AF:ID 0.0075:0.0199:0.150888:0.0988:rs7518545
1 771823 rs2977605 T C . PASS AF=0.8543 ES:SE:LP:AF:ID 0.0043:0.0178:0.0930188:0.8543:rs2977605
1 771967 rs59066358 G A . PASS AF=0.1443 ES:SE:LP:AF:ID -0.0049:0.0178:0.105296:0.1443:rs59066358
1 772755 rs2905039 A C . PASS AF=0.8543 ES:SE:LP:AF:ID 0.004:0.0178:0.0857626:0.8543:rs2905039