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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": "2019-10-27T07:19:15.773191",
"gwas_harmonisation_command": "--json /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ebi_gwas_import/processed/EBI-a-GCST005218/EBI-a-GCST005218_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-GCST005218/EBI-a-GCST005218.vcf.gz -O z /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ebi_gwas_import/processed/EBI-a-GCST005218/EBI-a-GCST005218_data.vcf.gz; Date=Sun Oct 27 07:23:25 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-GCST005218/ebi-a-GCST005218.vcf.gz; Date=Sun May 10 03:10:08 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-GCST005218/EBI-a-GCST005218.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-GCST005218/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 07:45:45 2019
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ebi_gwas_import/processed/EBI-a-GCST005218/EBI-a-GCST005218.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 07:46:01 2019
Total time elapsed: 15.44s
{
"af_correlation": -0.3898,
"inflation_factor": 1.0221,
"mean_EFFECT": 0.0001,
"n": "-Inf",
"n_snps": 2428482,
"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": 1931,
"n_miss_AF_reference": 19083,
"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 | TRUE |
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 | 42 | 0 | 2422204 | 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 | 2422206 | 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 | 8.589827e+00 | 5.657306e+00 | 1.0000e+00 | 4.000000e+00 | 8.000000e+00 | 1.200000e+01 | 2.300000e+01 | ▇▅▅▂▂ |
numeric | POS | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 7.884510e+07 | 5.567461e+07 | 1.1523e+04 | 3.268025e+07 | 7.029970e+07 | 1.143323e+08 | 2.492190e+08 | ▇▇▅▂▁ |
numeric | EFFECT | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 1.337000e-04 | 3.948210e-02 | -7.7000e-01 | -2.100000e-02 | -5.800000e-05 | 2.100000e-02 | 7.400000e-01 | ▁▁▇▁▁ |
numeric | SE | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 3.451530e-02 | 1.877240e-02 | 2.1000e-02 | 2.300000e-02 | 2.800000e-02 | 3.700000e-02 | 4.300000e-01 | ▇▁▁▁▁ |
numeric | PVAL | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 4.968015e-01 | 2.891248e-01 | 6.0000e-07 | 2.458018e-01 | 4.952973e-01 | 7.469835e-01 | 9.999900e-01 | ▇▇▇▇▇ |
numeric | PVAL_ztest | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 4.968273e-01 | 2.891771e-01 | 6.0000e-07 | 2.451696e-01 | 4.953539e-01 | 7.469018e-01 | 9.999914e-01 | ▇▇▇▇▇ |
numeric | AF | 1931 | 0.9992028 | NA | NA | NA | NA | NA | NA | NA | 5.696657e-01 | 2.989613e-01 | 4.0000e-03 | 3.080000e-01 | 6.060000e-01 | 8.500000e-01 | 9.960000e-01 | ▅▅▅▅▇ |
numeric | AF_reference | 19083 | 0.9921216 | NA | NA | NA | NA | NA | NA | NA | 3.627056e-01 | 2.543931e-01 | 1.9970e-04 | 1.489620e-01 | 3.015180e-01 | 5.461260e-01 | 1.000000e+00 | ▇▆▅▃▂ |
CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
---|---|---|---|---|---|---|---|---|---|---|---|
1 | 721290 | rs12565286 | G | C | -0.110 | 0.073 | 0.1465210 | 0.1318493 | 0.968 | 0.0371406 | NA |
1 | 723819 | rs11804171 | T | A | -0.110 | 0.073 | 0.1442139 | 0.1318493 | 0.963 | 0.1345850 | NA |
1 | 723891 | rs2977670 | G | C | 0.130 | 0.085 | 0.1231530 | 0.1261624 | 0.071 | 0.7799520 | NA |
1 | 750235 | rs12138618 | G | A | -0.140 | 0.110 | 0.2008968 | 0.2031148 | 0.942 | NA | NA |
1 | 752566 | rs3094315 | G | A | 0.034 | 0.029 | 0.2283779 | 0.2410310 | 0.835 | 0.7182510 | NA |
1 | 754192 | rs3131968 | A | G | 0.040 | 0.047 | 0.3993852 | 0.3947339 | 0.875 | 0.6785140 | NA |
1 | 768448 | rs12562034 | G | A | -0.097 | 0.061 | 0.1123650 | 0.1117979 | 0.102 | 0.1918930 | NA |
1 | 775659 | rs2905035 | A | G | 0.026 | 0.033 | 0.4298501 | 0.4307676 | 0.875 | 0.7450080 | NA |
1 | 777122 | rs2980319 | A | T | 0.026 | 0.033 | 0.4327838 | 0.4307676 | 0.866 | 0.7472040 | NA |
1 | 779322 | rs4040617 | A | G | -0.025 | 0.033 | 0.4507586 | 0.4487050 | 0.133 | 0.2264380 | NA |
CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
---|---|---|---|---|---|---|---|---|---|---|---|
22 | 51178090 | rs2285395 | G | A | 0.047 | 0.045 | 0.2990047 | 0.2962798 | 0.934 | 0.0666933 | NA |
22 | 51183017 | rs58651371 | C | T | 0.022 | 0.058 | 0.7010694 | 0.7044574 | 0.733 | 0.4137380 | NA |
22 | 51196164 | rs8136603 | A | T | 0.044 | 0.056 | 0.4252614 | 0.4320349 | 0.925 | 0.1427720 | NA |
22 | 51211392 | rs3888396 | T | C | 0.033 | 0.098 | 0.7346576 | 0.7363169 | 0.894 | 0.1641370 | NA |
22 | 51212875 | rs2238837 | A | C | -0.044 | 0.036 | 0.2155952 | 0.2216236 | 0.615 | 0.3724040 | NA |
22 | 51216564 | rs9616970 | T | C | 0.022 | 0.049 | 0.6536948 | 0.6534464 | 0.850 | 0.1563500 | NA |
22 | 51217134 | rs117417021 | A | G | -0.041 | 0.037 | 0.2647872 | 0.2678151 | 0.558 | 0.2671730 | NA |
22 | 51223637 | rs375798137 | G | A | 0.060 | 0.056 | 0.2807573 | 0.2839768 | 0.933 | 0.0788738 | NA |
22 | 51229805 | rs9616985 | T | C | -0.016 | 0.100 | 0.8786510 | 0.8728811 | 0.908 | 0.0730831 | NA |
23 | 118495837 | rs12882977 | G | A | 0.056 | 0.022 | 0.0121899 | 0.0109136 | 0.491 | 0.2307280 | NA |
1 721290 rs12565286 G C . PASS AF=0.968 ES:SE:LP:AF:ID -0.11:0.073:0.8341:0.968:rs12565286
1 723819 rs11804171 T A . PASS AF=0.963 ES:SE:LP:AF:ID -0.11:0.073:0.840993:0.963:rs11804171
1 723891 rs2977670 G C . PASS AF=0.071 ES:SE:LP:AF:ID 0.13:0.085:0.909555:0.071:rs2977670
1 750235 rs12138618 G A . PASS AF=0.942 ES:SE:LP:AF:ID -0.14:0.11:0.697027:0.942:rs12138618
1 752566 rs3094315 G A . PASS AF=0.835 ES:SE:LP:AF:ID 0.034:0.029:0.641346:0.835:rs3094315
1 754192 rs3131968 A G . PASS AF=0.875 ES:SE:LP:AF:ID 0.04:0.047:0.398608:0.875:rs3131968
1 768448 rs12562034 G A . PASS AF=0.102 ES:SE:LP:AF:ID -0.097:0.061:0.949369:0.102:rs12562034
1 775659 rs2905035 A G . PASS AF=0.875 ES:SE:LP:AF:ID 0.026:0.033:0.366683:0.875:rs2905035
1 777122 rs2980319 A T . PASS AF=0.866 ES:SE:LP:AF:ID 0.026:0.033:0.363729:0.866:rs2980319
1 779322 rs4040617 A G . PASS AF=0.133 ES:SE:LP:AF:ID -0.025:0.033:0.346056:0.133:rs4040617
1 780785 rs2977612 T A . PASS AF=0.866 ES:SE:LP:AF:ID 0.024:0.033:0.331931:0.866:rs2977612
1 785050 rs2905062 G A . PASS AF=0.856 ES:SE:LP:AF:ID 0.023:0.033:0.308363:0.856:rs2905062
1 785989 rs2980300 T C . PASS AF=0.868 ES:SE:LP:AF:ID 0.023:0.033:0.306086:0.868:rs2980300
1 798026 rs4951864 C T . PASS AF=0.1 ES:SE:LP:AF:ID 0.1:0.063:0.966685:0.1:rs4951864
1 798801 rs12132517 G A . PASS AF=0.892 ES:SE:LP:AF:ID -0.1:0.064:0.94038:0.892:rs12132517
1 798959 rs11240777 G A . PASS AF=0.219 ES:SE:LP:AF:ID -0.046:0.039:0.622872:0.219:rs11240777
1 962210 rs3128126 A G . PASS AF=0.575 ES:SE:LP:AF:ID -0.0013:0.051:0.00916541:0.575:rs3128126
1 990380 rs3121561 C T . PASS AF=0.267 ES:SE:LP:AF:ID -0.028:0.045:0.272409:0.267:rs3121561
1 998501 rs3813193 G C . PASS AF=0.85 ES:SE:LP:AF:ID -0.037:0.038:0.470203:0.85:rs3813193
1 1003629 rs4075116 C T . PASS AF=0.734 ES:SE:LP:AF:ID 0.00022:0.025:0.00306825:0.734:rs4075116
1 1005806 rs3934834 C T . PASS AF=0.124 ES:SE:LP:AF:ID -0.039:0.038:0.521744:0.124:rs3934834
1 1017170 rs3766193 C G . PASS AF=0.431 ES:SE:LP:AF:ID 0.0079:0.028:0.111208:0.431:rs3766193
1 1017197 rs3766192 C T . PASS AF=0.429 ES:SE:LP:AF:ID 0.019:0.025:0.339539:0.429:rs3766192
1 1017587 rs3766191 C T . PASS AF=0.124 ES:SE:LP:AF:ID -0.035:0.039:0.435628:0.124:rs3766191
1 1018562 rs9442371 C T . PASS AF=0.408 ES:SE:LP:AF:ID 0.019:0.025:0.344697:0.408:rs9442371
1 1018704 rs9442372 A G . PASS AF=0.412 ES:SE:LP:AF:ID 0.019:0.025:0.361948:0.412:rs9442372
1 1021346 rs10907177 A G . PASS AF=0.137 ES:SE:LP:AF:ID -0.036:0.041:0.421087:0.137:rs10907177
1 1021415 rs3737728 A G . PASS AF=0.265 ES:SE:LP:AF:ID 0.0086:0.028:0.119926:0.265:rs3737728
1 1021583 rs10907178 A C . PASS AF=0.113 ES:SE:LP:AF:ID -0.036:0.041:0.420453:0.113:rs10907178
1 1021695 rs9442398 A G . PASS AF=0.274 ES:SE:LP:AF:ID 0.0038:0.028:0.0485454:0.274:rs9442398
1 1022037 rs6701114 C T . PASS AF=0.433 ES:SE:LP:AF:ID 0.018:0.03:0.262908:0.433:rs6701114
1 1025301 rs9442400 T C . PASS AF=0.053 ES:SE:LP:AF:ID -0.15:0.14:0.549175:0.053:rs9442400
1 1026707 rs4074137 C A . PASS AF=0.6 ES:SE:LP:AF:ID 0.025:0.038:0.289768:0.6:rs4074137
1 1030565 rs6687776 C T . PASS AF=0.133 ES:SE:LP:AF:ID -0.1:0.045:1.65716:0.133:rs6687776
1 1031540 rs9651273 A G . PASS AF=0.283 ES:SE:LP:AF:ID -0.031:0.036:0.40537:0.283:rs9651273
1 1036959 rs11579015 T C . PASS AF=0.95 ES:SE:LP:AF:ID -0.042:0.068:0.271932:0.95:rs11579015
1 1040026 rs6671356 T C . PASS AF=0.885 ES:SE:LP:AF:ID -0.058:0.059:0.481759:0.885:rs6671356
1 1046164 rs6666280 C T . PASS AF=0.067 ES:SE:LP:AF:ID -0.055:0.059:0.452257:0.067:rs6666280
1 1048955 rs4970405 A G . PASS AF=0.088 ES:SE:LP:AF:ID -0.038:0.068:0.241022:0.088:rs4970405
1 1049950 rs12726255 A G . PASS AF=0.115 ES:SE:LP:AF:ID -0.034:0.055:0.270266:0.115:rs12726255
1 1053452 rs4970409 G A . PASS AF=0.907 ES:SE:LP:AF:ID -0.013:0.064:0.0773155:0.907:rs4970409
1 1060235 rs7540009 G A . PASS AF=0.983 ES:SE:LP:AF:ID -0.025:0.089:0.109077:0.983:rs7540009
1 1060608 rs17160824 G A . PASS AF=0.903 ES:SE:LP:AF:ID -0.018:0.065:0.104985:0.903:rs17160824
1 1061115 rs17160826 T C . PASS AF=0.945 ES:SE:LP:AF:ID -0.017:0.065:0.097606:0.945:rs17160826
1 1061152 rs12748370 T C . PASS AF=0.95 ES:SE:LP:AF:ID -0.018:0.065:0.105375:0.95:rs12748370
1 1061166 rs11807848 T C . PASS AF=0.611 ES:SE:LP:AF:ID 0.035:0.035:0.497604:0.611:rs11807848
1 1062015 rs9659914 C T . PASS AF=0.017 ES:SE:LP:AF:ID -0.026:0.091:0.111678:0.017:rs9659914
1 1062638 rs9442373 C A . PASS AF=0.575 ES:SE:LP:AF:ID 0.02:0.035:0.257106:0.575:rs9442373
1 1064535 rs6682475 G C . PASS AF=0.246 ES:SE:LP:AF:ID 0.11:0.052:1.3914:0.246:rs6682475
1 1064979 rs2298217 C T . PASS AF=0.115 ES:SE:LP:AF:ID -0.088:0.05:1.10682:0.115:rs2298217