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"Gwas2VCF_command": "--data /data/cromwell-executions/qc/4609c784-4e85-45c3-b6f5-4e15aa03c9e5/call-vcf/inputs/562856351/upload.txt.gz --id ieu-b-89 --json /data/cromwell-executions/qc/4609c784-4e85-45c3-b6f5-4e15aa03c9e5/call-vcf/inputs/562856351/ieu-b-89_data.json --ref /data/cromwell-executions/qc/4609c784-4e85-45c3-b6f5-4e15aa03c9e5/call-vcf/inputs/1899004205/human_g1k_v37.fasta --dbsnp /data/cromwell-executions/qc/4609c784-4e85-45c3-b6f5-4e15aa03c9e5/call-vcf/inputs/-307190728/dbsnp.v153.b37.vcf.gz --out /data/igd/ieu-b-89/ieu-b-89.vcf.gz --alias alias.txt --cohort_cases 2497 --cohort_controls 2928; 1.3.0",
"file_date": "2020-12-17T01:26:31.690703",
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}
*********************************************************************
* 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 /data/cromwell-executions/qc/4609c784-4e85-45c3-b6f5-4e15aa03c9e5/call-ldsc/inputs/562856351/ieu-b-89.vcf.gz \
--ref-ld-chr /data/ref/eur_w_ld_chr/ \
--out /data/igd/ieu-b-89/ldsc.txt \
--w-ld-chr /data/ref/eur_w_ld_chr/
Beginning analysis at Thu Dec 17 01:38:37 2020
Reading summary statistics from /data/cromwell-executions/qc/4609c784-4e85-45c3-b6f5-4e15aa03c9e5/call-ldsc/inputs/562856351/ieu-b-89.vcf.gz ...
Read summary statistics for 7295664 SNPs.
Dropped 20623 SNPs with duplicated rs numbers.
Reading reference panel LD Score from /data/ref/eur_w_ld_chr/[1-22] ... (ldscore_fromlist)
Read reference panel LD Scores for 1290028 SNPs.
Removing partitioned LD Scores with zero variance.
Reading regression weight LD Score from /data/ref/eur_w_ld_chr/[1-22] ... (ldscore_fromlist)
Read regression weight LD Scores for 1290028 SNPs.
After merging with reference panel LD, 1100557 SNPs remain.
After merging with regression SNP LD, 1100557 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.1405 (0.0847)
Lambda GC: 1.0536
Mean Chi^2: 1.058
Intercept: 1.043 (0.0067)
Ratio: 0.7404 (0.1148)
Analysis finished at Thu Dec 17 01:40:01 2020
Total time elapsed: 1.0m:24.34s
{
"af_correlation": 0.9365,
"inflation_factor": 1.0685,
"mean_EFFECT": 0,
"n": 5425,
"n_snps": 7296579,
"n_clumped_hits": 1,
"n_p_sig": 14,
"n_mono": 3717,
"n_ns": 0,
"n_mac": 3243,
"is_snpid_unique": false,
"n_miss_EFFECT": 0,
"n_miss_SE": 0,
"n_miss_PVAL": 0,
"n_miss_AF": 0,
"n_miss_AF_reference": 64438,
"n_est": 5227.0686,
"ratio_se_n": 0.9816,
"mean_diff": "NaN",
"ratio_diff": "NaN",
"sd_y_est1": 2.2284,
"sd_y_est2": 2.1874,
"r2_sum1": 0.0435,
"r2_sum2": 0.0088,
"r2_sum3": 0.0091,
"r2_sum4": 0.0061,
"ldsc_nsnp_merge_refpanel_ld": 1100557,
"ldsc_nsnp_merge_regression_ld": 1100557,
"ldsc_observed_scale_h2_beta": 0.1405,
"ldsc_observed_scale_h2_se": 0.0847,
"ldsc_intercept_beta": 1.043,
"ldsc_intercept_se": 0.0067,
"ldsc_lambda_gc": 1.0536,
"ldsc_mean_chisq": 1.058,
"ldsc_ratio": 0.7414
}
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 | FALSE |
n_p_sig | FALSE |
miss_EFFECT | FALSE |
miss_SE | FALSE |
miss_PVAL | FALSE |
ldsc_ratio | TRUE |
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 | numeric.mean | numeric.sd | numeric.p0 | numeric.p25 | numeric.p50 | numeric.p75 | numeric.p100 | numeric.hist |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
character | ID | 899 | 0.9998768 | 3 | 58 | 0 | 7295597 | 0 | 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 |
character | ALT | 0 | 1.0000000 | 1 | 1 | 0 | 4 | 0 | NA | NA | NA | NA | NA | NA | NA | NA |
numeric | CHROM | 0 | 1.0000000 | NA | NA | NA | NA | NA | 8.648624e+00 | 5.753575e+00 | 1.000 | 4.000000e+00 | 8.000000e+00 | 1.300000e+01 | 2.200000e+01 | ▇▅▅▂▂ |
numeric | POS | 0 | 1.0000000 | NA | NA | NA | NA | NA | 7.875014e+07 | 5.640781e+07 | 828.000 | 3.227700e+07 | 6.931142e+07 | 1.146199e+08 | 2.492164e+08 | ▇▆▅▂▁ |
numeric | EFFECT | 0 | 1.0000000 | NA | NA | NA | NA | NA | 1.840000e-05 | 2.706886e-01 | -6.908 | -4.800000e-02 | 0.000000e+00 | 4.700000e-02 | 3.111250e+02 | ▇▁▁▁▁ |
numeric | SE | 0 | 1.0000000 | NA | NA | NA | NA | NA | 8.665050e-02 | 3.993046e-01 | 0.040 | 4.600000e-02 | 6.300000e-02 | 1.070000e-01 | 6.465710e+02 | ▇▁▁▁▁ |
numeric | PVAL | 0 | 1.0000000 | NA | NA | NA | NA | NA | 4.899499e-01 | 2.915677e-01 | 0.000 | 2.347048e-01 | 4.856764e-01 | 7.430294e-01 | 1.000000e+00 | ▇▇▇▇▇ |
numeric | PVAL_ztest | 0 | 1.0000000 | NA | NA | NA | NA | NA | 4.900118e-01 | 2.916149e-01 | 0.000 | 2.346268e-01 | 4.858218e-01 | 7.434616e-01 | 1.000000e+00 | ▇▇▇▇▇ |
numeric | AF | 0 | 1.0000000 | NA | NA | NA | NA | NA | 2.603091e-01 | 2.624417e-01 | 0.000 | 4.600000e-02 | 1.560000e-01 | 4.100000e-01 | 1.000000e+00 | ▇▂▂▁▁ |
numeric | AF_reference | 64438 | 0.9911687 | NA | NA | NA | NA | NA | 2.596061e-01 | 2.523799e-01 | 0.000 | 5.491210e-02 | 1.695290e-01 | 4.027560e-01 | 1.000000e+00 | ▇▃▂▁▁ |
numeric | N | 0 | 1.0000000 | NA | NA | NA | NA | NA | 5.424791e+03 | 3.896377e+00 | 5049.000 | 5.425000e+03 | 5.425000e+03 | 5.425000e+03 | 5.425000e+03 | ▁▁▁▁▇ |
CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
---|---|---|---|---|---|---|---|---|---|---|---|
1 | 693731 | rs12238997 | A | G | -0.046 | 0.111 | 0.6777601 | 0.6785706 | 0.118 | 0.141773 | 5425 |
1 | 729679 | rs4951859 | C | G | 0.046 | 0.100 | 0.6425294 | 0.6455162 | 0.830 | 0.639976 | 5425 |
1 | 731718 | rs142557973 | T | C | -0.043 | 0.100 | 0.6688443 | 0.6671956 | 0.126 | 0.154353 | 5425 |
1 | 734349 | rs141242758 | T | C | -0.047 | 0.100 | 0.6399691 | 0.6383550 | 0.125 | 0.152556 | 5425 |
1 | 752566 | rs3094315 | G | A | 0.040 | 0.057 | 0.4785001 | 0.4828323 | 0.823 | 0.718251 | 5424 |
1 | 752721 | rs3131972 | A | G | 0.044 | 0.057 | 0.4431003 | 0.4401560 | 0.822 | 0.653355 | 5423 |
1 | 753405 | rs3115860 | C | A | 0.077 | 0.088 | 0.3858211 | 0.3815739 | 0.859 | 0.751797 | 5425 |
1 | 753541 | rs2073813 | G | A | -0.063 | 0.088 | 0.4715948 | 0.4740475 | 0.142 | 0.301917 | 5425 |
1 | 754182 | rs3131969 | A | G | 0.075 | 0.087 | 0.3872362 | 0.3886496 | 0.856 | 0.678514 | 5425 |
1 | 754192 | rs3131968 | A | G | 0.075 | 0.087 | 0.3878136 | 0.3886496 | 0.856 | 0.678514 | 5425 |
CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
---|---|---|---|---|---|---|---|---|---|---|---|
22 | 51218224 | rs9616975 | C | A | -0.015 | 0.124 | 0.9022054 | 0.9037166 | 0.074 | 0.0619010 | 5425 |
22 | 51218377 | rs2519461 | G | C | -0.017 | 0.124 | 0.8895028 | 0.8909543 | 0.074 | 0.0826677 | 5425 |
22 | 51219006 | rs28729663 | G | A | -0.062 | 0.091 | 0.4962780 | 0.4956699 | 0.144 | 0.2052720 | 5425 |
22 | 51219387 | rs9616832 | T | C | -0.015 | 0.125 | 0.9051495 | 0.9044831 | 0.074 | 0.0654952 | 5425 |
22 | 51219704 | rs147475742 | G | A | 0.031 | 0.184 | 0.8622986 | 0.8662070 | 0.040 | 0.0473243 | 5425 |
22 | 51221731 | rs115055839 | T | C | -0.015 | 0.125 | 0.9020842 | 0.9044831 | 0.074 | 0.0625000 | 5425 |
22 | 51222100 | rs114553188 | G | T | -0.007 | 0.140 | 0.9595299 | 0.9601224 | 0.057 | 0.0880591 | 5425 |
22 | 51223637 | rs375798137 | G | A | -0.009 | 0.141 | 0.9483274 | 0.9491058 | 0.057 | 0.0788738 | 5425 |
22 | 51229805 | rs9616985 | T | C | -0.012 | 0.127 | 0.9227259 | 0.9247214 | 0.074 | 0.0730831 | 5425 |
22 | 51237063 | rs3896457 | T | C | -0.016 | 0.075 | 0.8281408 | 0.8310670 | 0.287 | 0.2050720 | 5425 |
1 693731 rs12238997 A G . PASS AF=0.118 ES:SE:LP:AF:SS:SI:NC:ID -0.046:0.111:0.168924:0.118:5425:0.324:2497:rs12238997
1 729679 rs4951859 C G . PASS AF=0.83 ES:SE:LP:AF:SS:SI:NC:ID 0.046:0.1:0.192107:0.83:5425:0.361:2497:rs4951859
1 731718 rs58276399 T C . PASS AF=0.126 ES:SE:LP:AF:SS:SI:NC:ID -0.043:0.1:0.174675:0.126:5425:0.378:2497:rs58276399
1 734349 rs141242758 T C . PASS AF=0.125 ES:SE:LP:AF:SS:SI:NC:ID -0.047:0.1:0.193841:0.125:5425:0.379:2497:rs141242758
1 752566 rs3094315 G A . PASS AF=0.823 ES:SE:LP:AF:SS:SI:NC:ID 0.04:0.057:0.320118:0.823:5424:1:2497:rs3094315
1 752721 rs3131972 A G . PASS AF=0.822 ES:SE:LP:AF:SS:SI:NC:ID 0.044:0.057:0.353498:0.822:5423:1:2496:rs3131972
1 753405 rs3115860 C A . PASS AF=0.859 ES:SE:LP:AF:SS:SI:NC:ID 0.077:0.088:0.413614:0.859:5425:0.473:2497:rs3115860
1 753541 rs1388595942 G A . PASS AF=0.142 ES:SE:LP:AF:SS:SI:NC:ID -0.063:0.088:0.326431:0.142:5425:0.481:2497:rs1388595942
1 754182 rs3131969 A G . PASS AF=0.856 ES:SE:LP:AF:SS:SI:NC:ID 0.075:0.087:0.412024:0.856:5425:0.493:2497:rs3131969
1 754192 rs3131968 A G . PASS AF=0.856 ES:SE:LP:AF:SS:SI:NC:ID 0.075:0.087:0.411377:0.856:5425:0.494:2497:rs3131968
1 754334 rs3131967 T C . PASS AF=0.856 ES:SE:LP:AF:SS:SI:NC:ID 0.074:0.087:0.405501:0.856:5425:0.494:2497:rs3131967
1 754503 rs3115859 G A . PASS AF=0.824 ES:SE:LP:AF:SS:SI:NC:ID 0.068:0.09:0.348394:0.824:5425:0.417:2497:rs3115859
1 754964 rs3131966 C T . PASS AF=0.825 ES:SE:LP:AF:SS:SI:NC:ID 0.07:0.09:0.363747:0.825:5425:0.42:2497:rs3131966
1 755775 rs3131965 A G . PASS AF=0.829 ES:SE:LP:AF:SS:SI:NC:ID 0.069:0.09:0.348493:0.829:5425:0.403:2497:rs3131965
1 755890 rs1280367067 A T . PASS AF=0.858 ES:SE:LP:AF:SS:SI:NC:ID 0.078:0.088:0.424623:0.858:5425:0.48:2497:rs1280367067
1 756604 rs3131962 A G . PASS AF=0.858 ES:SE:LP:AF:SS:SI:NC:ID 0.077:0.087:0.42425:0.858:5425:0.482:2497:rs3131962
1 757640 rs3115853 G A . PASS AF=0.854 ES:SE:LP:AF:SS:SI:NC:ID 0.072:0.086:0.396287:0.854:5425:0.525:2497:rs3115853
1 757734 rs1557551770 C T . PASS AF=0.858 ES:SE:LP:AF:SS:SI:NC:ID 0.077:0.087:0.423079:0.858:5425:0.484:2497:rs1557551770
1 757936 rs1360886751 C A . PASS AF=0.858 ES:SE:LP:AF:SS:SI:NC:ID 0.077:0.087:0.423494:0.858:5425:0.485:2497:rs1360886751
1 758144 rs3131956 A G . PASS AF=0.858 ES:SE:LP:AF:SS:SI:NC:ID 0.077:0.087:0.424241:0.858:5425:0.485:2497:rs3131956
1 758626 rs3131954 C T . PASS AF=0.859 ES:SE:LP:AF:SS:SI:NC:ID 0.078:0.087:0.427021:0.859:5425:0.484:2497:rs3131954
1 760912 rs1048488 C T . PASS AF=0.827 ES:SE:LP:AF:SS:SI:NC:ID 0.07:0.089:0.36485:0.827:5425:0.408:2497:rs1048488
1 761147 rs3115850 T C . PASS AF=0.827 ES:SE:LP:AF:SS:SI:NC:ID 0.072:0.089:0.378875:0.827:5425:0.409:2497:rs3115850
1 761732 rs2286139 C T . PASS AF=0.847 ES:SE:LP:AF:SS:SI:NC:ID 0.073:0.084:0.413208:0.847:5425:0.532:2497:rs2286139
1 766007 rs61768174 A C . PASS AF=0.108 ES:SE:LP:AF:SS:SI:NC:ID -0.088:0.095:0.453288:0.108:5425:0.458:2497:rs61768174
1 768253 rs2977608 A C . PASS AF=0.744 ES:SE:LP:AF:SS:SI:NC:ID -0.001:0.058:0.00716093:0.744:5425:0.651:2497:rs2977608
1 768448 rs12562034 G A . PASS AF=0.11 ES:SE:LP:AF:SS:SI:NC:ID 0.113:0.101:0.583958:0.11:5425:0.395:2497:rs12562034
1 768819 rs12562811 C T . PASS AF=0.011 ES:SE:LP:AF:SS:SI:NC:ID -0.064:0.362:0.0656183:0.011:5425:0.332:2497:rs12562811
1 769223 rs60320384 C G . PASS AF=0.138 ES:SE:LP:AF:SS:SI:NC:ID -0.065:0.085:0.351351:0.138:5425:0.491:2497:rs60320384
1 770377 rs112563271 A T . PASS AF=0.013 ES:SE:LP:AF:SS:SI:NC:ID -0.198:0.2:0.495393:0.013:5422:1:2497:rs112563271
1 771823 rs2977605 T C . PASS AF=0.859 ES:SE:LP:AF:SS:SI:NC:ID 0.078:0.084:0.447516:0.859:5425:0.517:2497:rs2977605
1 771967 rs59066358 G A . PASS AF=0.139 ES:SE:LP:AF:SS:SI:NC:ID -0.069:0.085:0.381414:0.139:5425:0.5:2497:rs59066358
1 772755 rs2905039 A C . PASS AF=0.859 ES:SE:LP:AF:SS:SI:NC:ID 0.081:0.084:0.470533:0.859:5425:0.521:2497:rs2905039
1 777122 rs2980319 A T . PASS AF=0.861 ES:SE:LP:AF:SS:SI:NC:ID 0.069:0.084:0.386642:0.861:5425:0.528:2497:rs2980319
1 777232 rs112618790 C T . PASS AF=0.093 ES:SE:LP:AF:SS:SI:NC:ID 0.109:0.104:0.535725:0.093:5425:0.426:2497:rs112618790
1 778745 rs1055606 A G . PASS AF=0.136 ES:SE:LP:AF:SS:SI:NC:ID -0.059:0.084:0.311772:0.136:5425:0.513:2497:rs1055606
1 779322 rs4040617 A G . PASS AF=0.137 ES:SE:LP:AF:SS:SI:NC:ID -0.058:0.084:0.309371:0.137:5425:0.522:2497:rs4040617
1 780785 rs2977612 T A . PASS AF=0.857 ES:SE:LP:AF:SS:SI:NC:ID 0.07:0.081:0.403074:0.857:5425:0.563:2497:rs2977612
1 781845 rs1391043716 A G . PASS AF=0.103 ES:SE:LP:AF:SS:SI:NC:ID -0.089:0.094:0.458016:0.103:5425:0.485:2497:rs1391043716
1 782981 rs6594026 C T . PASS AF=0.14 ES:SE:LP:AF:SS:SI:NC:ID -0.061:0.082:0.336371:0.14:5425:0.552:2497:rs6594026
1 785050 rs2905062 G A . PASS AF=0.856 ES:SE:LP:AF:SS:SI:NC:ID 0.065:0.08:0.382034:0.856:5425:0.606:2497:rs2905062
1 785989 rs2980300 T C . PASS AF=0.856 ES:SE:LP:AF:SS:SI:NC:ID 0.066:0.08:0.384265:0.856:5425:0.609:2497:rs2980300
1 787399 rs2905055 G T . PASS AF=0.849 ES:SE:LP:AF:SS:SI:NC:ID 0.057:0.081:0.320147:0.849:5425:0.579:2497:rs2905055
1 787606 rs3863622 G T . PASS AF=0.136 ES:SE:LP:AF:SS:SI:NC:ID -0.058:0.082:0.31297:0.136:5425:0.544:2497:rs3863622
1 787685 rs2905054 G T . PASS AF=0.848 ES:SE:LP:AF:SS:SI:NC:ID 0.054:0.08:0.29783:0.848:5425:0.587:2497:rs2905054
1 787844 rs2905053 C T . PASS AF=0.858 ES:SE:LP:AF:SS:SI:NC:ID 0.061:0.08:0.353229:0.858:5425:0.605:2497:rs2905053
1 790465 rs61768207 G A . PASS AF=0.102 ES:SE:LP:AF:SS:SI:NC:ID -0.087:0.094:0.450257:0.102:5425:0.522:2497:rs61768207
1 791191 rs111818025 G A . PASS AF=0.135 ES:SE:LP:AF:SS:SI:NC:ID -0.053:0.082:0.288166:0.135:5425:0.549:2497:rs111818025
1 791853 rs6684487 G A . PASS AF=0.094 ES:SE:LP:AF:SS:SI:NC:ID 0.11:0.098:0.576124:0.094:5425:0.481:2497:rs6684487
1 794332 rs12127425 G A . PASS AF=0.08 ES:SE:LP:AF:SS:SI:NC:ID 0.072:0.099:0.333225:0.08:5425:0.552:2497:rs12127425