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"gwas_harmonisation_command": "--json /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ubm-a-import/processed/ubm-a-2913/ubm-a-2913_data.json --ref /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/QC/genomes/b37/human_g1k_v37.fasta; 1.1.1",
"file_date": "2020-02-08T05:14:06.890807",
"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/ubm-a-import/processed/ubm-a-2913/ubm-a-2913.vcf.gz -O z /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ubm-a-import/processed/ubm-a-2913/ubm-a-2913_data.vcf.gz; Date=Sat Feb 8 05:54:20 2020",
"bcftools_viewVersion": "1.9-74-g6af271c+htslib-1.9-64-g226b4a8",
"bcftools_viewCommand": "view -h /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/ubm-a-2913/ubm-a-2913.vcf.gz; Date=Sat May 9 20:54:51 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/ubm-a-import/processed/ubm-a-2913/ubm-a-2913.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/ubm-a-import/processed/ubm-a-2913/ldsc.txt \
--w-ld-chr /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/reference/eur_w_ld_chr/
Beginning analysis at Sat Feb 8 06:56:40 2020
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ubm-a-import/processed/ubm-a-2913/ubm-a-2913.vcf.gz ...
Read summary statistics for 11734353 SNPs.
Dropped 14445 SNPs with duplicated rs numbers.
Reading reference panel LD Score from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/reference/eur_w_ld_chr/[1-22] ...
Read reference panel LD Scores for 1290028 SNPs.
Removing partitioned LD Scores with zero variance.
Reading regression weight LD Score from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/reference/eur_w_ld_chr/[1-22] ...
Read regression weight LD Scores for 1290028 SNPs.
After merging with reference panel LD, 1288946 SNPs remain.
After merging with regression SNP LD, 1288946 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.1965 (0.0566)
Lambda GC: 1.028
Mean Chi^2: 1.0308
Intercept: 0.9999 (0.0063)
Ratio < 0 (usually indicates GC correction).
Analysis finished at Sat Feb 8 06:58:22 2020
Total time elapsed: 1.0m:42.21s
{
"af_correlation": 0.9541,
"inflation_factor": 0.9945,
"mean_EFFECT": -0.0001,
"n": "-Inf",
"n_snps": 11734353,
"n_clumped_hits": 0,
"n_p_sig": 0,
"n_mono": 0,
"n_ns": 0,
"n_mac": 0,
"is_snpid_unique": true,
"n_miss_EFFECT": 0,
"n_miss_SE": 0,
"n_miss_PVAL": 0,
"n_miss_AF": 0,
"n_miss_AF_reference": 433877,
"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": 1288946,
"ldsc_nsnp_merge_regression_ld": 1288946,
"ldsc_observed_scale_h2_beta": 0.1965,
"ldsc_observed_scale_h2_se": 0.0566,
"ldsc_intercept_beta": 0.9999,
"ldsc_intercept_se": 0.0063,
"ldsc_lambda_gc": 1.028,
"ldsc_mean_chisq": 1.0308,
"ldsc_ratio": -0.0032
}
name | value |
---|---|
name | value |
af_correlation | FALSE |
inflation_factor | FALSE |
n | TRUE |
is_snpid_non_unique | FALSE |
mean_EFFECT_nonfinite | FALSE |
mean_EFFECT_05 | FALSE |
mean_EFFECT_01 | FALSE |
mean_chisq | FALSE |
n_p_sig | FALSE |
miss_EFFECT | FALSE |
miss_SE | FALSE |
miss_PVAL | FALSE |
ldsc_ratio | FALSE |
ldsc_intercept_beta | FALSE |
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×N×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, ˆn.ratio_se_n
: ratio_se_n=√ˆn√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
: mean_diff=∑j^βstdj−βjn_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
: ratio_diff=|mean_diffmean_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
: r2=∑j2×β2j×MAFj×(1−MAFj)var1, var1=1.2
: r2=∑j2×β2j×MAFj×(1−MAFj)var2, var2=^sd1y2,3
: r2=∑j2×β2j×MAFj×(1−MAFj)var3, var3=^sd2y2,4
: r2=∑jFjFj+n−2, F=β2jse2j.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 χ2 statistics.ldsc_ratio
: ldsc_intercept_beta−1ldsc_mean_chisq−1, the proportion of the inflation in the mean χ2 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 h2 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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 64 | 0 | 11719943 | 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 | 11734353 | 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 | 8.650690e+00 | 5.767834e+00 | 1.0000000 | 4.000000e+00 | 8.000000e+00 | 1.300000e+01 | 2.200000e+01 | ▇▅▃▂▂ |
numeric | POS | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 7.882237e+07 | 5.627455e+07 | 173.0000000 | 3.258219e+07 | 6.943117e+07 | 1.145037e+08 | 2.492385e+08 | ▇▆▅▂▁ |
numeric | EFFECT | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | -6.090000e-05 | 8.520330e-02 | -1.7707000 | -2.200000e-02 | 0.000000e+00 | 2.230000e-02 | 1.372100e+00 | ▁▁▇▁▁ |
numeric | SE | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 6.183280e-02 | 5.850000e-02 | 0.0123000 | 1.600000e-02 | 3.390000e-02 | 9.450000e-02 | 7.747000e-01 | ▇▁▁▁▁ |
numeric | PVAL | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 4.974678e-01 | 2.895548e-01 | 0.0000002 | 2.454709e-01 | 5.011872e-01 | 7.413102e-01 | 1.000000e+00 | ▇▇▇▇▇ |
numeric | PVAL_ztest | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 4.974155e-01 | 2.894975e-01 | 0.0000002 | 2.464191e-01 | 4.964668e-01 | 7.479923e-01 | 1.000000e+00 | ▇▇▇▇▇ |
numeric | AF | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 1.704462e-01 | 2.461625e-01 | 0.0010000 | 5.052400e-03 | 3.933600e-02 | 2.479800e-01 | 9.990000e-01 | ▇▁▁▁▁ |
numeric | AF_reference | 433877 | 0.9630251 | NA | NA | NA | NA | NA | NA | NA | 1.762844e-01 | 2.405031e-01 | 0.0000000 | 3.394600e-03 | 5.890580e-02 | 2.647760e-01 | 1.000000e+00 | ▇▂▁▁▁ |
CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
---|---|---|---|---|---|---|---|---|---|---|---|
CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
1 | 54676 | rs2462492 | C | T | 0.0001 | 0.0222 | 1.0000000 | 0.9964059 | 0.3996650 | NA | NA |
1 | 55326 | rs3107975 | T | C | 0.0096 | 0.1127 | 0.9332541 | 0.9321168 | 0.0089751 | 0.0459265 | NA |
1 | 57033 | rs2691311 | T | C | 0.0774 | 0.2601 | 0.7585776 | 0.7660254 | 0.0018298 | NA | NA |
1 | 86028 | rs114608975 | T | C | -0.0360 | 0.0357 | 0.3090303 | 0.3132609 | 0.1044800 | 0.0277556 | NA |
1 | 91536 | rs6702460 | G | T | 0.0134 | 0.0217 | 0.5370318 | 0.5368974 | 0.4542200 | 0.4207270 | NA |
1 | 234313 | rs8179466 | C | T | -0.0125 | 0.0433 | 0.7762471 | 0.7728235 | 0.0749740 | NA | NA |
1 | 526736 | rs28863004 | C | G | -0.0305 | 0.1542 | 0.8511380 | 0.8432054 | 0.0058798 | 0.1317890 | NA |
1 | 533198 | rs78497331 | C | T | -0.2406 | 0.3822 | 0.5248075 | 0.5290130 | 0.0010150 | 0.0814696 | NA |
1 | 534192 | rs6680723 | C | T | 0.0035 | 0.0252 | 0.8912509 | 0.8895380 | 0.2387500 | NA | NA |
1 | 534583 | rs6683466 | C | G | -0.0514 | 0.1301 | 0.6918310 | 0.6927833 | 0.0068656 | NA | NA |
CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
---|---|---|---|---|---|---|---|---|---|---|---|
CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
22 | 51221731 | rs115055839 | T | C | -0.0008 | 0.0236 | 0.9772370 | 0.9729582 | 0.0764300 | 0.0625000 | NA |
22 | 51222100 | rs114553188 | G | T | 0.0342 | 0.0285 | 0.2290868 | 0.2301393 | 0.0538360 | 0.0880591 | NA |
22 | 51226692 | rs150189434 | G | A | 0.0745 | 0.1485 | 0.6165950 | 0.6158902 | 0.0020807 | 0.0155751 | NA |
22 | 51227766 | rs186062720 | T | C | -0.0119 | 0.1708 | 0.9549930 | 0.9444546 | 0.0021656 | 0.0005990 | NA |
22 | 51229805 | rs9616985 | T | C | -0.0009 | 0.0237 | 0.9772370 | 0.9697079 | 0.0763670 | 0.0730831 | NA |
22 | 51230673 | rs555680442 | G | C | -0.0724 | 0.1465 | 0.6165950 | 0.6211664 | 0.0027488 | 0.0017971 | NA |
22 | 51231424 | rs539541647 | A | G | 0.1806 | 0.2076 | 0.3801894 | 0.3843320 | 0.0011219 | 0.0011981 | NA |
22 | 51232488 | rs376461333 | A | G | 0.0132 | 0.0580 | 0.8128311 | 0.8199679 | 0.0194930 | NA | NA |
22 | 51237063 | rs3896457 | T | C | -0.0063 | 0.0149 | 0.6760830 | 0.6724275 | 0.2945100 | 0.2050720 | NA |
22 | 51239586 | rs535432390 | T | G | 0.0073 | 0.1438 | 0.9549930 | 0.9595128 | 0.0025620 | 0.0001997 | NA |
1 54676 rs2462492 C T . PASS AF=0.399665 ES:SE:LP:AF:ID 0.0001:0.0222:-0:0.399665:rs2462492
1 55326 rs3107975 T C . PASS AF=0.0089751 ES:SE:LP:AF:ID 0.0096:0.1127:0.0300001:0.0089751:rs3107975
1 57033 rs2691311 T C . PASS AF=0.0018298 ES:SE:LP:AF:ID 0.0774:0.2601:0.12:0.0018298:rs74447903
1 86028 rs114608975 T C . PASS AF=0.10448 ES:SE:LP:AF:ID -0.036:0.0357:0.509999:0.10448:rs114608975
1 91536 rs6702460 G T . PASS AF=0.45422 ES:SE:LP:AF:ID 0.0134:0.0217:0.27:0.45422:rs6702460
1 234313 rs8179466 C T . PASS AF=0.074974 ES:SE:LP:AF:ID -0.0125:0.0433:0.11:0.074974:rs8179466
1 526736 rs28863004 C G . PASS AF=0.0058798 ES:SE:LP:AF:ID -0.0305:0.1542:0.07:0.0058798:rs28863004
1 533198 rs78497331 C T . PASS AF=0.001015 ES:SE:LP:AF:ID -0.2406:0.3822:0.28:0.001015:rs78497331
1 534192 rs6680723 C T . PASS AF=0.23875 ES:SE:LP:AF:ID 0.0035:0.0252:0.05:0.23875:rs6680723
1 534583 rs6683466 C G . PASS AF=0.0068656 ES:SE:LP:AF:ID -0.0514:0.1301:0.16:0.0068656:rs6683466
1 544584 rs576404767 C T . PASS AF=0.0016212 ES:SE:LP:AF:ID -0.0048:0.2196:0.0100001:0.0016212:rs576404767
1 546697 rs12025928 A G . PASS AF=0.91442 ES:SE:LP:AF:ID -0.0055:0.0314:0.0599998:0.91442:rs12025928
1 564862 rs1988726 T C . PASS AF=0.0012083 ES:SE:LP:AF:ID -0.1745:0.3105:0.24:0.0012083:rs1988726
1 565111 rs573042692 T C . PASS AF=0.0015048 ES:SE:LP:AF:ID 0.007:0.2715:0.0100001:0.0015048:rs573042692
1 565130 rs371431021 G A . PASS AF=0.0043852 ES:SE:LP:AF:ID 0.2974:0.1664:1.13:0.0043852:rs371431021
1 565196 rs538567606 T C . PASS AF=0.0021264 ES:SE:LP:AF:ID -0.2644:0.238:0.570001:0.0021264:rs538567606
1 565469 rs554127336 C T . PASS AF=0.0016408 ES:SE:LP:AF:ID 0.0067:0.252:0.0100001:0.0016408:rs554127336
1 565490 rs7349153 T C . PASS AF=0.001359 ES:SE:LP:AF:ID -0.1469:0.294:0.21:0.001359:rs7349153
1 566024 rs6421779 G A . PASS AF=0.0012223 ES:SE:LP:AF:ID 0.1168:0.2954:0.16:0.0012223:rs6421779
1 566792 rs9283152 T C . PASS AF=0.002176 ES:SE:LP:AF:ID -0.3555:0.244:0.84:0.002176:rs9283152
1 566933 rs113120793 A G . PASS AF=0.0012255 ES:SE:LP:AF:ID -0.1658:0.3103:0.23:0.0012255:rs113120793
1 566960 rs2185540 T C . PASS AF=0.0013642 ES:SE:LP:AF:ID -0.1135:0.2964:0.15:0.0013642:rs2185540
1 567006 rs565235853 G T . PASS AF=0.002852 ES:SE:LP:AF:ID 0.1361:0.1434:0.47:0.002852:rs565235853
1 567092 rs9326622 T C . PASS AF=0.0013225 ES:SE:LP:AF:ID -0.1205:0.2969:0.16:0.0013225:rs9326622
1 567119 rs9283153 A C . PASS AF=0.0014721 ES:SE:LP:AF:ID -0.142:0.2858:0.21:0.0014721:rs9283153
1 567867 rs2000096 A G . PASS AF=0.0028155 ES:SE:LP:AF:ID -0.2139:0.2146:0.5:0.0028155:rs2000096
1 568072 rs2853820 A G . PASS AF=0.0014994 ES:SE:LP:AF:ID -0.1337:0.2716:0.21:0.0014994:rs2853820
1 568463 rs2153587 A G . PASS AF=0.0011247 ES:SE:LP:AF:ID -0.1557:0.3153:0.21:0.0011247:rs2153587
1 568800 rs375217967 G A . PASS AF=0.016753 ES:SE:LP:AF:ID -0.1404:0.0865:0.979999:0.016753:rs375217967
1 569004 rs9285835 T C . PASS AF=0.015599 ES:SE:LP:AF:ID 0.0279:0.0814:0.14:0.015599:rs9285835
1 569543 rs538153094 G A . PASS AF=0.0015978 ES:SE:LP:AF:ID 0.1869:0.2971:0.28:0.0015978:rs538153094
1 569604 rs9645429 G A . PASS AF=0.001787 ES:SE:LP:AF:ID -0.2672:0.2442:0.56:0.001787:rs9645429
1 601550 rs2491328 G A . PASS AF=0.0035313 ES:SE:LP:AF:ID -0.0415:0.1825:0.0899997:0.0035313:rs78266750
1 693731 rs12238997 A G . PASS AF=0.12069 ES:SE:LP:AF:ID -0.0061:0.0207:0.11:0.12069:rs12238997
1 705882 rs72631875 G A . PASS AF=0.064537 ES:SE:LP:AF:ID 0.0137:0.0314:0.18:0.064537:rs72631875
1 705942 rs544671234 A T . PASS AF=0.0034158 ES:SE:LP:AF:ID 0.0331:0.1382:0.0899997:0.0034158:rs544671234
1 713092 rs4565649 G A . PASS AF=0.0019147 ES:SE:LP:AF:ID 0.1084:0.1748:0.27:0.0019147:rs4565649
1 714277 rs138660747 C A . PASS AF=0.0072919 ES:SE:LP:AF:ID -0.1173:0.1013:0.61:0.0072919:rs138660747
1 714596 rs149887893 T C . PASS AF=0.028642 ES:SE:LP:AF:ID 0.0205:0.0418:0.2:0.028642:rs149887893
1 715205 rs141090730 C G . PASS AF=0.0018524 ES:SE:LP:AF:ID 0.1178:0.1802:0.29:0.0018524:rs141090730
1 715265 rs12184267 C T . PASS AF=0.03198 ES:SE:LP:AF:ID 0.0262:0.0378:0.31:0.03198:rs12184267
1 715367 rs12184277 A G . PASS AF=0.032112 ES:SE:LP:AF:ID 0.0198:0.0377:0.22:0.032112:rs12184277
1 717474 rs141784362 C T . PASS AF=0.0016827 ES:SE:LP:AF:ID 0.0209:0.1908:0.0399999:0.0016827:rs141784362
1 717485 rs12184279 C A . PASS AF=0.031853 ES:SE:LP:AF:ID 0.0228:0.038:0.26:0.031853:rs12184279
1 717587 rs144155419 G A . PASS AF=0.01666 ES:SE:LP:AF:ID 0.0465:0.0543:0.41:0.01666:rs144155419
1 718336 rs188996809 T C . PASS AF=0.0018748 ES:SE:LP:AF:ID -0.1187:0.2136:0.24:0.0018748:rs188996809
1 720381 rs116801199 G T . PASS AF=0.032321 ES:SE:LP:AF:ID 0.0247:0.0375:0.29:0.032321:rs116801199
1 720583 rs551231909 G A . PASS AF=0.001407 ES:SE:LP:AF:ID -0.1602:0.2195:0.33:0.001407:rs551231909
1 720984 rs564367954 T G . PASS AF=0.0016131 ES:SE:LP:AF:ID 0.2381:0.1982:0.64:0.0016131:rs564367954
1 721290 rs12565286 G C . PASS AF=0.032465 ES:SE:LP:AF:ID 0.0205:0.0373:0.23:0.032465:rs12565286