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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": "2019-10-27T07:18:45.137238",
"gwas_harmonisation_command": "--json /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ebi_gwas_import/processed/EBI-a-GCST006327/EBI-a-GCST006327_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-GCST006327/EBI-a-GCST006327.vcf.gz -O z /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ebi_gwas_import/processed/EBI-a-GCST006327/EBI-a-GCST006327_data.vcf.gz; Date=Sun Oct 27 07:22:24 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-GCST006327/ebi-a-GCST006327.vcf.gz; Date=Sun May 10 10:32:31 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-GCST006327/EBI-a-GCST006327.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-GCST006327/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 07:44:55 2019
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ebi_gwas_import/processed/EBI-a-GCST006327/EBI-a-GCST006327.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 07:45:10 2019
Total time elapsed: 14.96s
{
"af_correlation": 0.063,
"inflation_factor": 1.0269,
"mean_EFFECT": 0.0017,
"n": "-Inf",
"n_snps": 2300350,
"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": 17107,
"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 | 1.000000 | 3 | 42 | 0 | 2294380 | 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 | 2294385 | 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 | 8.564093e+00 | 5.642393e+00 | 1.0000e+00 | 4.000000e+00 | 8.000000e+00 | 1.200000e+01 | 2.300000e+01 | ▇▅▅▂▂ |
numeric | POS | 0 | 1.000000 | NA | NA | NA | NA | NA | NA | NA | 7.890105e+07 | 5.560741e+07 | 2.9443e+04 | 3.278665e+07 | 7.037362e+07 | 1.142781e+08 | 2.492107e+08 | ▇▇▅▂▁ |
numeric | EFFECT | 0 | 1.000000 | NA | NA | NA | NA | NA | NA | NA | 1.696000e-03 | 1.453078e-01 | -1.6487e+00 | -8.370000e-02 | 1.100000e-03 | 8.650000e-02 | 1.401000e+00 | ▁▁▇▁▁ |
numeric | SE | 0 | 1.000000 | NA | NA | NA | NA | NA | NA | NA | 1.348567e-01 | 5.042010e-02 | 8.8100e-02 | 1.003000e-01 | 1.153000e-01 | 1.498000e-01 | 7.432000e-01 | ▇▁▁▁▁ |
numeric | PVAL | 0 | 1.000000 | NA | NA | NA | NA | NA | NA | NA | 4.963038e-01 | 2.897469e-01 | 2.1000e-06 | 2.443999e-01 | 4.943004e-01 | 7.480007e-01 | 9.999000e-01 | ▇▇▇▇▇ |
numeric | PVAL_ztest | 0 | 1.000000 | NA | NA | NA | NA | NA | NA | NA | 4.963039e-01 | 2.897470e-01 | 2.1000e-06 | 2.444371e-01 | 4.943531e-01 | 7.480081e-01 | 9.997979e-01 | ▇▇▇▇▇ |
numeric | AF | 0 | 1.000000 | NA | NA | NA | NA | NA | NA | NA | 4.909007e-01 | 2.969036e-01 | 1.0000e-02 | 2.170000e-01 | 4.830000e-01 | 7.650000e-01 | 9.900000e-01 | ▇▆▆▆▇ |
numeric | AF_reference | 17107 | 0.992544 | NA | NA | NA | NA | NA | NA | NA | 3.708058e-01 | 2.491832e-01 | 1.9970e-04 | 1.615420e-01 | 3.142970e-01 | 5.521170e-01 | 1.000000e+00 | ▇▇▅▃▂ |
CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
---|---|---|---|---|---|---|---|---|---|---|---|
1 | 990380 | rs3121561 | C | T | 0.0480 | 0.1644 | 0.7703002 | 0.7703089 | 0.267 | 0.343450 | NA |
1 | 998501 | rs3813193 | G | C | 0.0350 | 0.1552 | 0.8217000 | 0.8215783 | 0.150 | 0.206669 | NA |
1 | 1005806 | rs3934834 | C | T | -0.0170 | 0.1541 | 0.9119999 | 0.9121572 | 0.119 | 0.223442 | NA |
1 | 1017170 | rs3766193 | C | G | -0.0572 | 0.1173 | 0.6256998 | 0.6258059 | 0.569 | 0.575479 | NA |
1 | 1017197 | rs3766192 | C | T | -0.0399 | 0.1126 | 0.7230994 | 0.7230753 | 0.424 | 0.511182 | NA |
1 | 1017587 | rs3766191 | C | T | 0.0119 | 0.1574 | 0.9400001 | 0.9397345 | 0.096 | 0.171126 | NA |
1 | 1018562 | rs9442371 | C | T | -0.0039 | 0.1112 | 0.9722000 | 0.9720224 | 0.408 | 0.530152 | NA |
1 | 1018704 | rs9442372 | A | G | -0.0020 | 0.1110 | 0.9855000 | 0.9856245 | 0.602 | 0.611022 | NA |
1 | 1021346 | rs10907177 | A | G | 0.0044 | 0.1552 | 0.9775000 | 0.9773826 | 0.873 | 0.178914 | NA |
1 | 1021415 | rs3737728 | A | G | -0.0881 | 0.1106 | 0.4255004 | 0.4257042 | 0.717 | 0.812700 | NA |
CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
---|---|---|---|---|---|---|---|---|---|---|---|
22 | 51140316 | rs739365 | C | T | -0.0029 | 0.1058 | 0.9785000 | 0.9781326 | 0.333 | 0.4363020 | NA |
22 | 51146139 | rs5770992 | A | G | -0.0310 | 0.1516 | 0.8380000 | 0.8379741 | 0.836 | 0.1136180 | NA |
22 | 51146439 | rs6010060 | A | G | -0.1059 | 0.1900 | 0.5774003 | 0.5772757 | 0.915 | 0.0551118 | NA |
22 | 51147015 | rs2040487 | A | G | 0.0033 | 0.1072 | 0.9757000 | 0.9754421 | 0.575 | 0.4556710 | NA |
22 | 51150473 | rs5770820 | G | A | -0.1105 | 0.1256 | 0.3786997 | 0.3789801 | 0.190 | 0.2462060 | NA |
22 | 51151350 | rs6009951 | C | T | -0.1310 | 0.1084 | 0.2270001 | 0.2268600 | 0.387 | 0.5559110 | NA |
22 | 51151724 | rs6010061 | C | T | -0.1108 | 0.1085 | 0.3071001 | 0.3071606 | 0.381 | 0.6098240 | NA |
22 | 51162059 | rs10451 | G | A | 0.0935 | 0.1354 | 0.4898002 | 0.4898506 | 0.285 | 0.3865810 | NA |
22 | 51171497 | rs2301584 | G | A | 0.1938 | 0.2085 | 0.3524999 | 0.3526319 | 0.164 | 0.2533950 | NA |
23 | 118495837 | rs12882977 | G | A | 0.0901 | 0.0944 | 0.3400001 | 0.3398563 | 0.491 | 0.2307280 | NA |
1 990380 rs3121561 C T . PASS AF=0.267 ES:SE:LP:AF:ID 0.048:0.1644:0.11334:0.267:rs3121561
1 998501 rs3813193 G C . PASS AF=0.15 ES:SE:LP:AF:ID 0.035:0.1552:0.0852867:0.15:rs3813193
1 1005806 rs3934834 C T . PASS AF=0.119 ES:SE:LP:AF:ID -0.017:0.1541:0.0400052:0.119:rs3934834
1 1017170 rs3766193 C G . PASS AF=0.569 ES:SE:LP:AF:ID -0.0572:0.1173:0.203634:0.569:rs3766193
1 1017197 rs3766192 C T . PASS AF=0.424 ES:SE:LP:AF:ID -0.0399:0.1126:0.140802:0.424:rs3766192
1 1017587 rs3766191 C T . PASS AF=0.096 ES:SE:LP:AF:ID 0.0119:0.1574:0.0268721:0.096:rs3766191
1 1018562 rs9442371 C T . PASS AF=0.408 ES:SE:LP:AF:ID -0.0039:0.1112:0.0122444:0.408:rs9442371
1 1018704 rs9442372 A G . PASS AF=0.602 ES:SE:LP:AF:ID -0.002:0.111:0.00634337:0.602:rs9442372
1 1021346 rs10907177 A G . PASS AF=0.873 ES:SE:LP:AF:ID 0.0044:0.1552:0.00988323:0.873:rs10907177
1 1021415 rs3737728 A G . PASS AF=0.717 ES:SE:LP:AF:ID -0.0881:0.1106:0.3711:0.717:rs3737728
1 1021583 rs10907178 A C . PASS AF=0.887 ES:SE:LP:AF:ID 0.0024:0.1569:0.00537495:0.887:rs10907178
1 1021695 rs9442398 A G . PASS AF=0.725 ES:SE:LP:AF:ID -0.0348:0.1118:0.121593:0.725:rs9442398
1 1022037 rs6701114 C T . PASS AF=0.433 ES:SE:LP:AF:ID -0.0168:0.1158:0.0530567:0.433:rs6701114
1 1026707 rs4074137 C A . PASS AF=0.4 ES:SE:LP:AF:ID 0.0475:0.1191:0.160899:0.4:rs4074137
1 1030565 rs6687776 C T . PASS AF=0.083 ES:SE:LP:AF:ID -0.2962:0.1441:1.39914:0.083:rs6687776
1 1030633 rs6678318 G A . PASS AF=0.086 ES:SE:LP:AF:ID -0.2681:0.1696:0.943095:0.086:rs6678318
1 1036959 rs11579015 T C . PASS AF=0.95 ES:SE:LP:AF:ID -0.1079:0.177:0.265921:0.95:rs11579015
1 1040026 rs6671356 T C . PASS AF=0.925 ES:SE:LP:AF:ID -0.2685:0.156:1.06966:0.925:rs6671356
1 1046164 rs6666280 C T . PASS AF=0.067 ES:SE:LP:AF:ID -0.2551:0.1535:1.01484:0.067:rs6666280
1 1048955 rs4970405 A G . PASS AF=0.948 ES:SE:LP:AF:ID -0.1248:0.1732:0.326887:0.948:rs4970405
1 1049950 rs12726255 A G . PASS AF=0.933 ES:SE:LP:AF:ID -0.2603:0.149:1.09345:0.933:rs12726255
1 1053452 rs4970409 G A . PASS AF=0.05 ES:SE:LP:AF:ID -0.1441:0.1719:0.395882:0.05:rs4970409
1 1060174 rs7548798 C T . PASS AF=0.398 ES:SE:LP:AF:ID 0.0061:0.1462:0.0147532:0.398:rs7548798
1 1060608 rs17160824 G A . PASS AF=0.058 ES:SE:LP:AF:ID -0.1055:0.1751:0.262172:0.058:rs17160824
1 1061115 rs17160826 T C . PASS AF=0.945 ES:SE:LP:AF:ID -0.1458:0.1754:0.391474:0.945:rs17160826
1 1061152 rs12748370 T C . PASS AF=0.95 ES:SE:LP:AF:ID -0.1472:0.1756:0.395882:0.95:rs12748370
1 1061166 rs11807848 T C . PASS AF=0.588 ES:SE:LP:AF:ID -0.1309:0.117:0.579384:0.588:rs11807848
1 1062638 rs9442373 C A . PASS AF=0.448 ES:SE:LP:AF:ID 0.131:0.1157:0.589391:0.448:rs9442373
1 1064535 rs6682475 G C . PASS AF=0.246 ES:SE:LP:AF:ID 0.3187:0.1613:1.31758:0.246:rs6682475
1 1066403 rs10907182 T C . PASS AF=0.675 ES:SE:LP:AF:ID 0.1332:0.135:0.489723:0.675:rs10907182
1 1079198 rs11260603 T C . PASS AF=0.776 ES:SE:LP:AF:ID 0.0769:0.1928:0.161151:0.776:rs11260603
1 1087683 rs9442380 T C . PASS AF=0.912 ES:SE:LP:AF:ID 0.0251:0.1849:0.0496351:0.912:rs9442380
1 1119858 rs1320565 C T . PASS AF=0.092 ES:SE:LP:AF:ID -0.4367:0.2205:1.32221:0.092:rs1320565
1 1121014 rs3813204 G A . PASS AF=0.112 ES:SE:LP:AF:ID -0.052:0.2058:0.0966387:0.112:rs3813204
1 1121794 rs11260549 G A . PASS AF=0.125 ES:SE:LP:AF:ID -0.084:0.1668:0.211549:0.125:rs11260549
1 1124663 rs6684820 G A . PASS AF=0.267 ES:SE:LP:AF:ID -0.2417:0.1275:1.23612:0.267:rs6684820
1 1125553 rs10907174 A T . PASS AF=0.775 ES:SE:LP:AF:ID -0.1211:0.1399:0.412626:0.775:rs10907174
1 1129672 rs11260554 G T . PASS AF=0.125 ES:SE:LP:AF:ID -0.0773:0.1668:0.191654:0.125:rs11260554
1 1130727 rs10907175 A C . PASS AF=0.9 ES:SE:LP:AF:ID -0.1098:0.1725:0.280337:0.9:rs10907175
1 1135242 rs9729550 A C . PASS AF=0.725 ES:SE:LP:AF:ID -0.2313:0.1271:1.16197:0.725:rs9729550
1 1138913 rs3819001 T C . PASS AF=0.957 ES:SE:LP:AF:ID -0.754:0.2641:2.36623:0.957:rs3819001
1 1140435 rs1815606 G T . PASS AF=0.31 ES:SE:LP:AF:ID -0.0496:0.1487:0.131532:0.31:rs1815606
1 1143657 rs3753348 C G . PASS AF=0.967 ES:SE:LP:AF:ID -0.7271:0.2861:1.95782:0.967:rs3753348
1 1152631 rs11721 C A . PASS AF=0.083 ES:SE:LP:AF:ID -0.211:0.189:0.577903:0.083:rs11721
1 1156131 rs2887286 T C . PASS AF=0.817 ES:SE:LP:AF:ID 0.0499:0.1298:0.154406:0.817:rs2887286
1 1158277 rs3813199 G A . PASS AF=0.1 ES:SE:LP:AF:ID 0.1918:0.1666:0.602755:0.1:rs3813199
1 1162435 rs3766186 C A . PASS AF=0.1 ES:SE:LP:AF:ID 0.1893:0.1666:0.592099:0.1:rs3766186
1 1163804 rs7515488 C T . PASS AF=0.15 ES:SE:LP:AF:ID -0.0342:0.1512:0.0856039:0.15:rs7515488
1 1165310 rs11260562 G A . PASS AF=0.052 ES:SE:LP:AF:ID -0.5742:0.2548:1.61529:0.052:rs11260562
1 1176597 rs6675798 T C . PASS AF=0.892 ES:SE:LP:AF:ID -0.1569:0.1811:0.41285:0.892:rs6675798