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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\">",
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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": "2019-10-26T21:44:55.753611",
"gwas_harmonisation_command": "--json /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ebi_gwas_import/processed/EBI-a-GCST006366/EBI-a-GCST006366_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-GCST006366/EBI-a-GCST006366.vcf.gz -O z /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ebi_gwas_import/processed/EBI-a-GCST006366/EBI-a-GCST006366_data.vcf.gz; Date=Sat Oct 26 21:59:02 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-GCST006366/ebi-a-GCST006366.vcf.gz; Date=Sat May 9 20:39:39 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-GCST006366/EBI-a-GCST006366.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-GCST006366/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 22:18:32 2019
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ebi_gwas_import/processed/EBI-a-GCST006366/EBI-a-GCST006366.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 22:19:26 2019
Total time elapsed: 54.16s
{
"af_correlation": 0.9405,
"inflation_factor": 1.064,
"mean_EFFECT": -0.005,
"n": "-Inf",
"n_snps": 8131508,
"n_clumped_hits": 26,
"n_p_sig": 1355,
"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": 223064,
"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 | TRUE |
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 | 1.000000 | 3 | 59 | 0 | 8112224 | 0 | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
character | REF | 0 | 1.000000 | 1 | 1 | 0 | 4 | 0 | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
character | ALT | 0 | 1.000000 | 1 | 1 | 0 | 4 | 0 | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
logical | N | 8112305 | 0.000000 | NA | NA | NA | NA | NA | NaN | : | NA | NA | NA | NA | NA | NA | NA | NA |
numeric | CHROM | 0 | 1.000000 | NA | NA | NA | NA | NA | NA | NA | 8.669749e+00 | 5.762267e+00 | 1.0000 | 4.000000e+00 | 8.000000e+00 | 1.300000e+01 | 2.300000e+01 | ▇▅▅▂▂ |
numeric | POS | 0 | 1.000000 | NA | NA | NA | NA | NA | NA | NA | 7.850927e+07 | 5.643765e+07 | 828.0000 | 3.208020e+07 | 6.897003e+07 | 1.143215e+08 | 2.492223e+08 | ▇▆▅▂▁ |
numeric | EFFECT | 0 | 1.000000 | NA | NA | NA | NA | NA | NA | NA | -5.028500e-03 | 1.171836e+00 | -19.3235 | -4.738000e-01 | -2.000000e-03 | 4.681000e-01 | 1.890130e+01 | ▁▁▇▁▁ |
numeric | SE | 0 | 1.000000 | NA | NA | NA | NA | NA | NA | NA | 9.176636e-01 | 6.961161e-01 | 0.3681 | 4.398000e-01 | 6.128000e-01 | 1.135700e+00 | 5.820100e+00 | ▇▁▁▁▁ |
numeric | PVAL | 0 | 1.000000 | NA | NA | NA | NA | NA | NA | NA | 4.895691e-01 | 2.921834e-01 | 0.0000 | 2.340998e-01 | 4.865999e-01 | 7.430996e-01 | 1.000000e+00 | ▇▇▇▇▇ |
numeric | PVAL_ztest | 0 | 1.000000 | NA | NA | NA | NA | NA | NA | NA | 4.895691e-01 | 2.921834e-01 | 0.0000 | 2.340755e-01 | 4.866395e-01 | 7.430650e-01 | 9.999821e-01 | ▇▇▇▇▇ |
numeric | AF | 0 | 1.000000 | NA | NA | NA | NA | NA | NA | NA | 2.605156e-01 | 2.603576e-01 | 0.0101 | 4.740000e-02 | 1.577000e-01 | 4.092000e-01 | 9.897000e-01 | ▇▂▂▁▁ |
numeric | AF_reference | 223064 | 0.972503 | NA | NA | NA | NA | NA | NA | NA | 2.628727e-01 | 2.545406e-01 | 0.0000 | 5.451280e-02 | 1.741210e-01 | 4.101440e-01 | 1.000000e+00 | ▇▃▂▁▁ |
CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
---|---|---|---|---|---|---|---|---|---|---|---|
1 | 73841 | rs143773730 | C | T | -0.4405 | 1.3915 | 0.7516004 | 0.7515738 | 0.2357 | NA | NA |
1 | 84002 | rs28850140 | G | A | 3.2619 | 1.8846 | 0.0834795 | 0.0834842 | 0.1110 | NA | NA |
1 | 162463 | rs143399298 | T | C | 1.3128 | 1.9597 | 0.5029004 | 0.5029225 | 0.0973 | NA | NA |
1 | 240789 | rs71222827 | T | G | 5.2838 | 3.6298 | 0.1455000 | 0.1454832 | 0.0216 | NA | NA |
1 | 662622 | rs61769339 | G | A | 1.0394 | 1.8237 | 0.5686997 | 0.5687182 | 0.0991 | 0.1475640 | NA |
1 | 693731 | rs12238997 | A | G | -0.7765 | 1.6622 | 0.6403995 | 0.6403912 | 0.1164 | 0.1417730 | NA |
1 | 704637 | rs142559957 | G | A | 0.3447 | 2.6454 | 0.8963000 | 0.8963278 | 0.0521 | 0.0473243 | NA |
1 | 705882 | rs72631875 | G | A | 1.5150 | 2.2135 | 0.4936999 | 0.4936996 | 0.0620 | 0.0315495 | NA |
1 | 706368 | rs55727773 | A | G | 0.8985 | 1.1460 | 0.4330998 | 0.4330217 | 0.3967 | 0.2751600 | NA |
1 | 722670 | rs116030099 | T | C | -0.6590 | 1.9990 | 0.7416995 | 0.7416532 | 0.0920 | 0.0413339 | NA |
CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
---|---|---|---|---|---|---|---|---|---|---|---|
22 | 51224718 | rs189454695 | T | G | -0.9212 | 1.3675 | 0.5006002 | 0.5005415 | 0.1523 | NA | NA |
22 | 51228910 | rs145146472 | G | A | -0.0450 | 0.9522 | 0.9623000 | 0.9623068 | 0.2801 | 0.2276360 | NA |
22 | 51229805 | rs9616985 | T | C | -1.5667 | 1.5346 | 0.3073003 | 0.3072935 | 0.0806 | 0.0730831 | NA |
22 | 51229855 | rs144549712 | G | A | -0.1331 | 1.4605 | 0.9274000 | 0.9273868 | 0.1045 | 0.1160140 | NA |
22 | 51233300 | rs9616839 | C | T | 0.0911 | 0.9590 | 0.9243001 | 0.9243190 | 0.3031 | 0.3146960 | NA |
22 | 51237063 | rs3896457 | T | C | 0.2797 | 1.0031 | 0.7803995 | 0.7803710 | 0.2552 | 0.2050720 | NA |
22 | 51238249 | rs149733995 | A | C | -0.3400 | 1.5533 | 0.8266999 | 0.8267367 | 0.0860 | NA | NA |
22 | 51243297 | rs2905159 | A | T | 0.2618 | 1.4368 | 0.8553999 | 0.8554176 | 0.1361 | NA | NA |
23 | 46256106 | rs12007097 | G | C | 0.4607 | 1.8266 | 0.8009000 | 0.8008732 | 0.9689 | 0.6821190 | NA |
23 | 100784211 | rs188350543 | C | A | -0.8295 | 0.8025 | 0.3012999 | 0.3013022 | 0.7579 | 0.6498010 | NA |
1 73841 rs143773730 C T . PASS AF=0.2357 ES:SE:LP:AF:ID -0.4405:1.3915:0.124013:0.2357:rs143773730
1 84002 rs28850140 G A . PASS AF=0.111 ES:SE:LP:AF:ID 3.2619:1.8846:1.07842:0.111:rs28850140
1 162463 rs143399298 T C . PASS AF=0.0973 ES:SE:LP:AF:ID 1.3128:1.9597:0.298518:0.0973:rs143399298
1 240789 rs71222827 T G . PASS AF=0.0216 ES:SE:LP:AF:ID 5.2838:3.6298:0.837137:0.0216:rs71222827
1 662622 rs61769339 G A . PASS AF=0.0991 ES:SE:LP:AF:ID 1.0394:1.8237:0.245117:0.0991:rs61769339
1 693731 rs12238997 A G . PASS AF=0.1164 ES:SE:LP:AF:ID -0.7765:1.6622:0.193549:0.1164:rs12238997
1 704637 rs142559957 G A . PASS AF=0.0521 ES:SE:LP:AF:ID 0.3447:2.6454:0.0475466:0.0521:rs142559957
1 705882 rs72631875 G A . PASS AF=0.062 ES:SE:LP:AF:ID 1.515:2.2135:0.306537:0.062:rs72631875
1 706368 rs12029736 A G . PASS AF=0.3967 ES:SE:LP:AF:ID 0.8985:1.146:0.363412:0.3967:rs12029736
1 722670 rs116030099 T C . PASS AF=0.092 ES:SE:LP:AF:ID -0.659:1.999:0.129772:0.092:rs116030099
1 729679 rs4951859 C G . PASS AF=0.8085 ES:SE:LP:AF:ID -0.1991:1.2469:0.058936:0.8085:rs4951859
1 731718 rs58276399 T C . PASS AF=0.1289 ES:SE:LP:AF:ID 0.2995:1.4585:0.0771189:0.1289:rs58276399
1 732801 rs144022023 A G . PASS AF=0.0319 ES:SE:LP:AF:ID -1.2156:3.2271:0.150949:0.0319:rs144022023
1 734349 rs141242758 T C . PASS AF=0.1244 ES:SE:LP:AF:ID 0.0725:1.4856:0.0172314:0.1244:rs141242758
1 734462 rs12564807 G A . PASS AF=0.7586 ES:SE:LP:AF:ID 0.3638:1.3697:0.102043:0.7586:rs12564807
1 736289 rs79010578 T A . PASS AF=0.1338 ES:SE:LP:AF:ID -0.1567:1.4581:0.0388638:0.1338:rs79010578
1 739210 rs2427917 A G . PASS AF=0.8155 ES:SE:LP:AF:ID 0.2698:1.4905:0.0673233:0.8155:rs2427917
1 741579 rs3115865 T C . PASS AF=0.949 ES:SE:LP:AF:ID -2.578:2.5974:0.49363:0.949:rs3115865
1 748141 rs2427893 G A . PASS AF=0.0359 ES:SE:LP:AF:ID 1.1062:3.037:0.145269:0.0359:rs2427893
1 748878 rs2519043 G T . PASS AF=0.7397 ES:SE:LP:AF:ID -0.166:1.1321:0.0537934:0.7397:rs2519043
1 750055 rs11240771 T C . PASS AF=0.0887 ES:SE:LP:AF:ID 4.0494:2.0294:1.33724:0.0887:rs11240771
1 751756 rs28527770 T C . PASS AF=0.1448 ES:SE:LP:AF:ID -0.796:0.8524:0.455436:0.1448:rs28527770
1 752566 rs3094315 G A . PASS AF=0.8285 ES:SE:LP:AF:ID -0.0578:0.6455:0.0321246:0.8285:rs3094315
1 752721 rs3131972 A G . PASS AF=0.7866 ES:SE:LP:AF:ID 0.1807:0.7145:0.0967472:0.7866:rs3131972
1 752894 rs3131971 T C . PASS AF=0.7932 ES:SE:LP:AF:ID 0.0955:0.7607:0.0457092:0.7932:rs3131971
1 753405 rs3115860 C A . PASS AF=0.8361 ES:SE:LP:AF:ID 0.7219:0.8514:0.401757:0.8361:rs3115860
1 753474 rs2073814 C G . PASS AF=0.7523 ES:SE:LP:AF:ID 0.0933:0.7625:0.0445047:0.7523:rs2073814
1 753541 rs2073813 G A . PASS AF=0.1915 ES:SE:LP:AF:ID -0.1844:0.84:0.0828623:0.1915:rs2073813
1 753849 rs58324164 G T . PASS AF=0.1714 ES:SE:LP:AF:ID 1.095:1.5001:0.332174:0.1714:rs58324164
1 754182 rs3131969 A G . PASS AF=0.8019 ES:SE:LP:AF:ID 0.0462:0.8167:0.0200421:0.8019:rs3131969
1 754192 rs3131968 A G . PASS AF=0.8013 ES:SE:LP:AF:ID 0.0676:0.8196:0.0295137:0.8013:rs3131968
1 754334 rs3131967 T C . PASS AF=0.7833 ES:SE:LP:AF:ID -0.3015:0.8155:0.147764:0.7833:rs3131967
1 754503 rs3115859 G A . PASS AF=0.7859 ES:SE:LP:AF:ID 0.0542:0.764:0.0252581:0.7859:rs3115859
1 754964 rs3131966 C T . PASS AF=0.7637 ES:SE:LP:AF:ID -0.0918:0.7872:0.042297:0.7637:rs3131966
1 755775 rs3131965 A G . PASS AF=0.7746 ES:SE:LP:AF:ID 0.3689:0.7697:0.19942:0.7746:rs3131965
1 755890 rs3115858 A T . PASS AF=0.8317 ES:SE:LP:AF:ID 0.3129:0.8187:0.153477:0.8317:rs3115858
1 756604 rs3131962 A G . PASS AF=0.8093 ES:SE:LP:AF:ID 0.7991:0.7993:0.498256:0.8093:rs3131962
1 757640 rs3115853 G A . PASS AF=0.7954 ES:SE:LP:AF:ID 0.2774:0.8696:0.125112:0.7954:rs3115853
1 757734 rs4951929 C T . PASS AF=0.8397 ES:SE:LP:AF:ID 0.3374:0.8203:0.166917:0.8397:rs4951929
1 757936 rs4951862 C A . PASS AF=0.8385 ES:SE:LP:AF:ID 0.3721:0.8225:0.186419:0.8385:rs4951862
1 758048 rs3131957 A G . PASS AF=0.1127 ES:SE:LP:AF:ID 0.5508:1.7704:0.121651:0.1127:rs3131957
1 758144 rs3131956 A G . PASS AF=0.8233 ES:SE:LP:AF:ID 0.3328:0.7869:0.172372:0.8233:rs3131956
1 758626 rs3131954 C T . PASS AF=0.8375 ES:SE:LP:AF:ID 0.3867:0.8419:0.189767:0.8375:rs3131954
1 759700 rs3115852 T C . PASS AF=0.7935 ES:SE:LP:AF:ID 1.0538:0.8782:0.637895:0.7935:rs3115852
1 759837 rs3115851 T A . PASS AF=0.8429 ES:SE:LP:AF:ID 0.8227:0.9358:0.421017:0.8429:rs3115851
1 760912 rs1048488 C T . PASS AF=0.7883 ES:SE:LP:AF:ID 0.2423:0.7987:0.118273:0.7883:rs1048488
1 761147 rs3115850 T C . PASS AF=0.7933 ES:SE:LP:AF:ID 0.1507:0.7999:0.0702746:0.7933:rs3115850
1 761732 rs2286139 C T . PASS AF=0.7882 ES:SE:LP:AF:ID -0.3101:0.988:0.122859:0.7882:rs2286139
1 761752 rs1057213 C T . PASS AF=0.8308 ES:SE:LP:AF:ID 0.6179:0.8587:0.326242:0.8308:rs1057213
1 762273 rs3115849 G A . PASS AF=0.818 ES:SE:LP:AF:ID 0.9274:1.0443:0.426548:0.818:rs3115849