manhattan_plot
qq_plot
af_plot
pz_plot
beta_std_plot
{
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"gwas_harmonisation_command": "--json /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ubm-a-import/processed/ubm-a-430/ubm-a-430_data.json --ref /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/QC/genomes/b37/human_g1k_v37.fasta; 1.1.1",
"file_date": "2020-02-08T08:30:57.289401",
"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-430/ubm-a-430.vcf.gz -O z /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ubm-a-import/processed/ubm-a-430/ubm-a-430_data.vcf.gz; Date=Sat Feb 8 09:05:29 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-430/ubm-a-430.vcf.gz; Date=Sat May 9 14:02:26 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-430/ubm-a-430.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-430/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 09:43:14 2020
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ubm-a-import/processed/ubm-a-430/ubm-a-430.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: 0.1619 (0.0541)
Lambda GC: 1.0233
Mean Chi^2: 1.0264
Intercept: 1.0011 (0.0058)
Ratio: 0.0425 (0.2211)
Analysis finished at Sat Feb 8 09:44:45 2020
Total time elapsed: 1.0m:31.22s
{
"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": 0.1619,
"ldsc_observed_scale_h2_se": 0.0541,
"ldsc_intercept_beta": 1.0011,
"ldsc_intercept_se": 0.0058,
"ldsc_lambda_gc": 1.0233,
"ldsc_mean_chisq": 1.0264,
"ldsc_ratio": 0.0417
}
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
(\(2 \times N \times MAF\)) 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 | 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 | -1.369000e-04 | 9.576820e-02 | -1.8595000 | -2.490000e-02 | 0.000000e+00 | 2.480000e-02 | 1.506300e+00 | ▁▁▇▁▁ |
numeric | SE | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 6.943040e-02 | 6.582960e-02 | 0.0138000 | 1.790000e-02 | 3.800000e-02 | 1.060000e-01 | 9.912000e-01 | ▇▁▁▁▁ |
numeric | PVAL | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 4.976093e-01 | 2.893443e-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 | 4.975554e-01 | 2.892875e-01 | 0.0000002 | 2.466451e-01 | 4.966071e-01 | 7.482331e-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 |
---|---|---|---|---|---|---|---|---|---|---|---|
1 | 54676 | rs2462492 | C | T | -0.0198 | 0.0249 | 0.4265805 | 0.4265084 | 0.3996650 | NA | NA |
1 | 55326 | rs3107975 | T | C | -0.2951 | 0.1255 | 0.0186209 | 0.0187032 | 0.0089751 | 0.0459265 | NA |
1 | 57033 | rs2691311 | T | C | 0.2078 | 0.2970 | 0.4786301 | 0.4841376 | 0.0018298 | NA | NA |
1 | 86028 | rs114608975 | T | C | 0.0643 | 0.0395 | 0.1047131 | 0.1035571 | 0.1044800 | 0.0277556 | NA |
1 | 91536 | rs6702460 | G | T | -0.0327 | 0.0242 | 0.1778279 | 0.1766187 | 0.4542200 | 0.4207270 | NA |
1 | 234313 | rs8179466 | C | T | -0.0299 | 0.0486 | 0.5370318 | 0.5384053 | 0.0749740 | NA | NA |
1 | 526736 | rs28863004 | C | G | 0.2625 | 0.1720 | 0.1258931 | 0.1269693 | 0.0058798 | 0.1317890 | NA |
1 | 533198 | rs78497331 | C | T | 0.0192 | 0.4211 | 0.9549930 | 0.9636332 | 0.0010150 | 0.0814696 | NA |
1 | 534192 | rs6680723 | C | T | 0.0222 | 0.0281 | 0.4265805 | 0.4295070 | 0.2387500 | NA | NA |
1 | 534583 | rs6683466 | C | G | 0.0257 | 0.1432 | 0.8511380 | 0.8575692 | 0.0068656 | NA | NA |
CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
---|---|---|---|---|---|---|---|---|---|---|---|
22 | 51221731 | rs115055839 | T | C | 0.0115 | 0.0264 | 0.6606934 | 0.6631226 | 0.0764300 | 0.0625000 | NA |
22 | 51222100 | rs114553188 | G | T | 0.0146 | 0.0318 | 0.6456542 | 0.6461484 | 0.0538360 | 0.0880591 | NA |
22 | 51226692 | rs150189434 | G | A | -0.1827 | 0.1656 | 0.2691529 | 0.2699139 | 0.0020807 | 0.0155751 | NA |
22 | 51227766 | rs186062720 | T | C | -0.1226 | 0.1835 | 0.5011872 | 0.5040571 | 0.0021656 | 0.0005990 | NA |
22 | 51229805 | rs9616985 | T | C | 0.0124 | 0.0265 | 0.6456542 | 0.6398386 | 0.0763670 | 0.0730831 | NA |
22 | 51230673 | rs555680442 | G | C | 0.0139 | 0.1644 | 0.9332541 | 0.9326192 | 0.0027488 | 0.0017971 | NA |
22 | 51231424 | rs539541647 | A | G | 0.4942 | 0.2362 | 0.0363078 | 0.0364122 | 0.0011219 | 0.0011981 | NA |
22 | 51232488 | rs376461333 | A | G | 0.0225 | 0.0653 | 0.7244360 | 0.7304225 | 0.0194930 | NA | NA |
22 | 51237063 | rs3896457 | T | C | 0.0041 | 0.0168 | 0.8128311 | 0.8071939 | 0.2945100 | 0.2050720 | NA |
22 | 51239586 | rs535432390 | T | G | 0.1665 | 0.1595 | 0.2951209 | 0.2965376 | 0.0025620 | 0.0001997 | NA |
1 54676 rs2462492 C T . PASS AF=0.399665 ES:SE:LP:AF:ID -0.0198:0.0249:0.369999:0.399665:rs2462492
1 55326 rs3107975 T C . PASS AF=0.0089751 ES:SE:LP:AF:ID -0.2951:0.1255:1.73:0.0089751:rs3107975
1 57033 rs2691311 T C . PASS AF=0.0018298 ES:SE:LP:AF:ID 0.2078:0.297:0.32:0.0018298:rs74447903
1 86028 rs114608975 T C . PASS AF=0.10448 ES:SE:LP:AF:ID 0.0643:0.0395:0.979999:0.10448:rs114608975
1 91536 rs6702460 G T . PASS AF=0.45422 ES:SE:LP:AF:ID -0.0327:0.0242:0.75:0.45422:rs6702460
1 234313 rs8179466 C T . PASS AF=0.074974 ES:SE:LP:AF:ID -0.0299:0.0486:0.27:0.074974:rs8179466
1 526736 rs28863004 C G . PASS AF=0.0058798 ES:SE:LP:AF:ID 0.2625:0.172:0.899998:0.0058798:rs28863004
1 533198 rs78497331 C T . PASS AF=0.001015 ES:SE:LP:AF:ID 0.0192:0.4211:0.0199998:0.001015:rs78497331
1 534192 rs6680723 C T . PASS AF=0.23875 ES:SE:LP:AF:ID 0.0222:0.0281:0.369999:0.23875:rs6680723
1 534583 rs6683466 C G . PASS AF=0.0068656 ES:SE:LP:AF:ID 0.0257:0.1432:0.07:0.0068656:rs6683466
1 544584 rs576404767 C T . PASS AF=0.0016212 ES:SE:LP:AF:ID 0.4522:0.2457:1.18:0.0016212:rs576404767
1 546697 rs12025928 A G . PASS AF=0.91442 ES:SE:LP:AF:ID -0.073:0.0351:1.43:0.91442:rs12025928
1 564862 rs1988726 T C . PASS AF=0.0012083 ES:SE:LP:AF:ID -0.3718:0.3347:0.570001:0.0012083:rs1988726
1 565111 rs573042692 T C . PASS AF=0.0015048 ES:SE:LP:AF:ID -0.4053:0.3111:0.72:0.0015048:rs573042692
1 565130 rs371431021 G A . PASS AF=0.0043852 ES:SE:LP:AF:ID -0.1656:0.1852:0.43:0.0043852:rs371431021
1 565196 rs538567606 T C . PASS AF=0.0021264 ES:SE:LP:AF:ID 0.0426:0.2642:0.0599998:0.0021264:rs538567606
1 565469 rs554127336 C T . PASS AF=0.0016408 ES:SE:LP:AF:ID -0.2094:0.282:0.34:0.0016408:rs554127336
1 565490 rs7349153 T C . PASS AF=0.001359 ES:SE:LP:AF:ID -0.3667:0.3115:0.620001:0.001359:rs7349153
1 566024 rs6421779 G A . PASS AF=0.0012223 ES:SE:LP:AF:ID -0.3798:0.3143:0.64:0.0012223:rs6421779
1 566792 rs9283152 T C . PASS AF=0.002176 ES:SE:LP:AF:ID -0.1295:0.2618:0.21:0.002176:rs9283152
1 566933 rs113120793 A G . PASS AF=0.0012255 ES:SE:LP:AF:ID -0.3502:0.3345:0.53:0.0012255:rs113120793
1 566960 rs2185540 T C . PASS AF=0.0013642 ES:SE:LP:AF:ID -0.4061:0.3169:0.700001:0.0013642:rs2185540
1 567006 rs565235853 G T . PASS AF=0.002852 ES:SE:LP:AF:ID 0.1942:0.1582:0.66:0.002852:rs565235853
1 567092 rs9326622 T C . PASS AF=0.0013225 ES:SE:LP:AF:ID -0.4077:0.3174:0.700001:0.0013225:rs9326622
1 567119 rs9283153 A C . PASS AF=0.0014721 ES:SE:LP:AF:ID -0.2422:0.3062:0.369999:0.0014721:rs9283153
1 567867 rs2000096 A G . PASS AF=0.0028155 ES:SE:LP:AF:ID -0.1072:0.233:0.19:0.0028155:rs2000096
1 568072 rs2853820 A G . PASS AF=0.0014994 ES:SE:LP:AF:ID -0.3357:0.2916:0.599999:0.0014994:rs2853820
1 568463 rs2153587 A G . PASS AF=0.0011247 ES:SE:LP:AF:ID -0.3462:0.3356:0.52:0.0011247:rs2153587
1 568800 rs375217967 G A . PASS AF=0.016753 ES:SE:LP:AF:ID -0.0394:0.097:0.16:0.016753:rs375217967
1 569004 rs9285835 T C . PASS AF=0.015599 ES:SE:LP:AF:ID -0.0413:0.0901:0.19:0.015599:rs9285835
1 569543 rs538153094 G A . PASS AF=0.0015978 ES:SE:LP:AF:ID 0.6448:0.3303:1.29:0.0015978:rs538153094
1 569604 rs9645429 G A . PASS AF=0.001787 ES:SE:LP:AF:ID -0.4628:0.2743:1.04:0.001787:rs9645429
1 601550 rs2491328 G A . PASS AF=0.0035313 ES:SE:LP:AF:ID -0.077:0.2027:0.15:0.0035313:rs78266750
1 693731 rs12238997 A G . PASS AF=0.12069 ES:SE:LP:AF:ID -0.0105:0.0231:0.19:0.12069:rs12238997
1 705882 rs72631875 G A . PASS AF=0.064537 ES:SE:LP:AF:ID 0.0468:0.0351:0.74:0.064537:rs72631875
1 705942 rs544671234 A T . PASS AF=0.0034158 ES:SE:LP:AF:ID 0.0933:0.1559:0.26:0.0034158:rs544671234
1 713092 rs4565649 G A . PASS AF=0.0019147 ES:SE:LP:AF:ID -0.1728:0.1876:0.45:0.0019147:rs4565649
1 714277 rs138660747 C A . PASS AF=0.0072919 ES:SE:LP:AF:ID 0.0525:0.1163:0.19:0.0072919:rs138660747
1 714596 rs149887893 T C . PASS AF=0.028642 ES:SE:LP:AF:ID 0.0139:0.0468:0.12:0.028642:rs149887893
1 715205 rs141090730 C G . PASS AF=0.0018524 ES:SE:LP:AF:ID -0.1805:0.1937:0.45:0.0018524:rs141090730
1 715265 rs12184267 C T . PASS AF=0.03198 ES:SE:LP:AF:ID 0.0162:0.0424:0.15:0.03198:rs12184267
1 715367 rs12184277 A G . PASS AF=0.032112 ES:SE:LP:AF:ID 0.0087:0.0422:0.0799999:0.032112:rs12184277
1 717474 rs141784362 C T . PASS AF=0.0016827 ES:SE:LP:AF:ID -0.1251:0.2052:0.27:0.0016827:rs141784362
1 717485 rs12184279 C A . PASS AF=0.031853 ES:SE:LP:AF:ID 0.0095:0.0425:0.0799999:0.031853:rs12184279
1 717587 rs144155419 G A . PASS AF=0.01666 ES:SE:LP:AF:ID -0.0422:0.0613:0.31:0.01666:rs144155419
1 718336 rs188996809 T C . PASS AF=0.0018748 ES:SE:LP:AF:ID -0.4153:0.2648:0.929999:0.0018748:rs188996809
1 720381 rs116801199 G T . PASS AF=0.032321 ES:SE:LP:AF:ID 0.0162:0.042:0.16:0.032321:rs116801199
1 720583 rs551231909 G A . PASS AF=0.001407 ES:SE:LP:AF:ID -0.1918:0.2375:0.38:0.001407:rs551231909
1 720984 rs564367954 T G . PASS AF=0.0016131 ES:SE:LP:AF:ID 0.1525:0.2339:0.29:0.0016131:rs564367954
1 721290 rs12565286 G C . PASS AF=0.032465 ES:SE:LP:AF:ID 0.0109:0.0418:0.1:0.032465:rs12565286