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"Gwas2VCF_command": "--data /data/cromwell-executions/qc/d62384bd-1073-416b-8c01-a663b3167a9e/call-vcf/inputs/-261044354/upload.txt.gz --id ieu-b-4873 --json /data/cromwell-executions/qc/d62384bd-1073-416b-8c01-a663b3167a9e/call-vcf/inputs/-261044354/ieu-b-4873_data.json --ref /data/cromwell-executions/qc/d62384bd-1073-416b-8c01-a663b3167a9e/call-vcf/inputs/1899004205/human_g1k_v37.fasta --dbsnp /data/cromwell-executions/qc/d62384bd-1073-416b-8c01-a663b3167a9e/call-vcf/inputs/-307190728/dbsnp.v153.b37.vcf.gz --out /data/igd/ieu-b-4873/ieu-b-4873.vcf.gz --alias alias.txt; 1.3.0",
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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/d62384bd-1073-416b-8c01-a663b3167a9e/call-ldsc/inputs/-261044354/ieu-b-4873.vcf.gz \
--ref-ld-chr /data/ref/eur_w_ld_chr/ \
--out /data/igd/ieu-b-4873/ldsc.txt \
--w-ld-chr /data/ref/eur_w_ld_chr/
Beginning analysis at Mon Jan 10 04:41:02 2022
Reading summary statistics from /data/cromwell-executions/qc/d62384bd-1073-416b-8c01-a663b3167a9e/call-ldsc/inputs/-261044354/ieu-b-4873.vcf.gz ...
Read summary statistics for 0 SNPs.
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.
Traceback (most recent call last):
File "./ldsc/ldsc.py", line 647, in <module>
sumstats.estimate_h2(args, log)
File "/ldsc/ldscore/sumstats.py", line 330, in estimate_h2
args, log, args.h2)
File "/ldsc/ldscore/sumstats.py", line 252, in _read_ld_sumstats
sumstats = _merge_and_log(ref_ld, sumstats, 'reference panel LD', log)
File "/ldsc/ldscore/sumstats.py", line 238, in _merge_and_log
raise ValueError(msg.format(N=len(sumstats), F=noun))
ValueError: After merging with reference panel LD, 0 SNPs remain.
Analysis finished at Mon Jan 10 04:42:24 2022
Total time elapsed: 1.0m:21.93s
{
"af_correlation": 0.9502,
"inflation_factor": 1,
"mean_EFFECT": -0.0002,
"n": "-Inf",
"n_snps": 12321875,
"n_clumped_hits": 2,
"n_p_sig": 379,
"n_mono": 0,
"n_ns": 1293897,
"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": 1423040,
"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": 0,
"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 | 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 | NA |
n_p_sig | FALSE |
miss_EFFECT | FALSE |
miss_SE | FALSE |
miss_PVAL | FALSE |
ldsc_ratio | NA |
ldsc_intercept_beta | NA |
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 | 675 | 0.9999452 | 3 | 58 | 0 | 12276232 | 0 | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
character | REF | 0 | 1.0000000 | 1 | 88 | 0 | 17566 | 0 | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
character | ALT | 0 | 1.0000000 | 1 | 662 | 0 | 71704 | 0 | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
logical | N | 12321875 | 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 | 8.757492e+00 | 5.885387e+00 | 1.0000000 | 4.000000e+00 | 8.000000e+00 | 1.300000e+01 | 2.300000e+01 | ▇▅▅▂▂ |
numeric | POS | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 7.871202e+07 | 5.622121e+07 | 302.0000000 | 3.252510e+07 | 6.928045e+07 | 1.144492e+08 | 2.492405e+08 | ▇▆▅▂▁ |
numeric | EFFECT | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | -1.720000e-04 | 5.013960e-02 | -0.8641880 | -1.489120e-02 | -2.500000e-05 | 1.472380e-02 | 1.406890e+00 | ▁▇▁▁▁ |
numeric | SE | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 3.606720e-02 | 3.491660e-02 | 0.0076617 | 1.259430e-02 | 2.023210e-02 | 4.668000e-02 | 6.902350e-01 | ▇▁▁▁▁ |
numeric | PVAL | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 4.981701e-01 | 2.887263e-01 | 0.0000000 | 2.500000e-01 | 5.000000e-01 | 7.499995e-01 | 1.000000e+00 | ▇▇▇▇▇ |
numeric | PVAL_ztest | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 4.981694e-01 | 2.886995e-01 | 0.0000000 | 2.477413e-01 | 4.970369e-01 | 7.481186e-01 | 1.000000e+00 | ▇▇▇▇▇ |
numeric | AF | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 2.594005e-01 | 3.020533e-01 | 0.0003990 | 1.658200e-02 | 1.144970e-01 | 4.378615e-01 | 9.995770e-01 | ▇▂▁▁▁ |
numeric | AF_reference | 1423040 | 0.8845111 | NA | NA | NA | NA | NA | NA | NA | 2.132160e-01 | 2.513550e-01 | 0.0000000 | 1.218050e-02 | 1.056310e-01 | 3.376600e-01 | 1.000000e+00 | ▇▂▁▁▁ |
CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
---|---|---|---|---|---|---|---|---|---|---|---|
1 | 10177 | rs1264289758 | AC | A | 0.0220743 | 0.0161324 | 0.1700000 | 0.1712117 | 0.599124 | NA | NA |
1 | 10352 | rs1557426776 | TA | T | -0.0119876 | 0.0166593 | 0.4700002 | 0.4717873 | 0.607470 | NA | NA |
1 | 11008 | rs575272151 | C | G | 0.0209790 | 0.0272783 | 0.4400003 | 0.4418501 | 0.088641 | 0.0880591 | NA |
1 | 11012 | rs544419019 | C | G | 0.0209790 | 0.0272783 | 0.4400003 | 0.4418501 | 0.088641 | 0.0880591 | NA |
1 | 13110 | rs540538026 | G | A | -0.0244399 | 0.0373231 | 0.5099998 | 0.5125839 | 0.058376 | 0.0267572 | NA |
1 | 13116 | rs62635286 | T | G | -0.0064877 | 0.0217763 | 0.7700005 | 0.7657623 | 0.188494 | 0.0970447 | NA |
1 | 13118 | rs200579949 | A | G | -0.0064877 | 0.0217763 | 0.7700005 | 0.7657623 | 0.188494 | 0.0970447 | NA |
1 | 13273 | rs531730856 | G | C | 0.0040488 | 0.0255008 | 0.8700001 | 0.8738474 | 0.135583 | 0.0950479 | NA |
1 | 14464 | rs546169444 | A | T | 0.0298589 | 0.0233551 | 0.2000000 | 0.2010822 | 0.156562 | 0.0958466 | NA |
1 | 14599 | rs531646671 | T | A | -0.0117903 | 0.0212842 | 0.5800000 | 0.5796157 | 0.189594 | 0.1475640 | NA |
CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
---|---|---|---|---|---|---|---|---|---|---|---|
23 | 154901936 | rs697727 | A | G | 0.0149131 | 0.0088662 | 0.0929994 | 0.0925663 | 0.751551 | 0.643179 | NA |
23 | 154901964 | rs697726 | G | A | -0.0029061 | 0.0093487 | 0.7600007 | 0.7559079 | 0.349022 | 0.117616 | NA |
23 | 154902105 | rs696316 | G | T | 0.0149135 | 0.0088662 | 0.0929994 | 0.0925568 | 0.751550 | 0.636026 | NA |
23 | 154902889 | rs697725 | A | T | 0.0149005 | 0.0088613 | 0.0929994 | 0.0926620 | 0.751010 | 0.584106 | NA |
23 | 154903118 | rs479770 | G | A | 0.0149076 | 0.0088665 | 0.0929994 | 0.0926969 | 0.751556 | 0.643444 | NA |
23 | 154903224 | rs480725 | A | T | 0.0149065 | 0.0088665 | 0.0929994 | 0.0927217 | 0.751557 | 0.643444 | NA |
23 | 154903937 | rs674707 | G | A | 0.0148980 | 0.0088666 | 0.0929994 | 0.0929128 | 0.751561 | 0.643444 | NA |
23 | 154909055 | rs473529 | C | G | -0.0189218 | 0.0083449 | 0.0230001 | 0.0233614 | 0.305233 | 0.463046 | NA |
23 | 154918266 | rs642043 | C | T | -0.0172474 | 0.0083719 | 0.0389996 | 0.0393839 | 0.303013 | 0.478675 | NA |
23 | 154927581 | rs644138 | G | A | -0.0173425 | 0.0083742 | 0.0379997 | 0.0383629 | 0.302869 | 0.463576 | NA |
1 10177 rs1264289758 AC A . PASS AF=0.599124 ES:SE:LP:AF:ID 0.0220743:0.0161324:0.769551:0.599124:rs1264289758
1 10352 rs1557426776 TA T . PASS AF=0.60747 ES:SE:LP:AF:ID -0.0119876:0.0166593:0.327902:0.60747:rs1557426776
1 11008 rs575272151 C G . PASS AF=0.088641 ES:SE:LP:AF:ID 0.020979:0.0272783:0.356547:0.088641:rs575272151
1 11012 rs544419019 C G . PASS AF=0.088641 ES:SE:LP:AF:ID 0.020979:0.0272783:0.356547:0.088641:rs544419019
1 13110 rs540538026 G A . PASS AF=0.058376 ES:SE:LP:AF:ID -0.0244399:0.0373231:0.29243:0.058376:rs540538026
1 13116 rs62635286 T G . PASS AF=0.188494 ES:SE:LP:AF:ID -0.00648765:0.0217763:0.113509:0.188494:rs62635286
1 13118 rs62028691 A G . PASS AF=0.188494 ES:SE:LP:AF:ID -0.00648765:0.0217763:0.113509:0.188494:rs62028691
1 13273 rs531730856 G C . PASS AF=0.135583 ES:SE:LP:AF:ID 0.00404885:0.0255008:0.0604807:0.135583:rs531730856
1 14464 rs546169444 A T . PASS AF=0.156562 ES:SE:LP:AF:ID 0.0298589:0.0233551:0.69897:0.156562:rs546169444
1 14599 rs707680 T A . PASS AF=0.189594 ES:SE:LP:AF:ID -0.0117903:0.0212842:0.236572:0.189594:rs707680
1 14604 rs1418508701 A G . PASS AF=0.189594 ES:SE:LP:AF:ID -0.0117903:0.0212842:0.236572:0.189594:rs1418508701
1 14930 rs6682385 A G . PASS AF=0.472035 ES:SE:LP:AF:ID 0.00838339:0.0164667:0.21467:0.472035:rs6682385
1 14933 rs199856693 G A . PASS AF=0.045447 ES:SE:LP:AF:ID 0.00423866:0.0403509:0.0362122:0.045447:rs199856693
1 15211 rs3982632 T G . PASS AF=0.73762 ES:SE:LP:AF:ID 0.00683911:0.0188084:0.142668:0.73762:rs3982632
1 15820 rs1316988498 G T . PASS AF=0.273544 ES:SE:LP:AF:ID 0.00727474:0.019447:0.148742:0.273544:rs1316988498
1 15903 rs557514207 GC G . PASS AF=0.580619 ES:SE:LP:AF:ID -0.0132391:0.0160215:0.387216:0.580619:rs557514207
1 28590 rs1344649620 T TTGG . PASS AF=0.956322 ES:SE:LP:AF:ID 0.0273224:0.0454731:0.259637:0.956322:rs1344649620
1 30923 rs1165072081 G T . PASS AF=0.909708 ES:SE:LP:AF:ID 0.0156875:0.0302718:0.221849:0.909708:rs1165072081
1 47159 rs540662756 T C . PASS AF=0.062914 ES:SE:LP:AF:ID -0.051514:0.0342106:0.886057:0.062914:rs540662756
1 49298 rs10399793 T C . PASS AF=0.625075 ES:SE:LP:AF:ID -0.00888518:0.0191257:0.19382:0.625075:rs10399793
1 49554 rs539322794 A G . PASS AF=0.091892 ES:SE:LP:AF:ID -0.0357178:0.0296648:0.638272:0.091892:rs539322794
1 51479 rs116400033 T A . PASS AF=0.214666 ES:SE:LP:AF:ID -0.00919113:0.0205287:0.187087:0.214666:rs116400033
1 54490 rs141149254 G A . PASS AF=0.1553 ES:SE:LP:AF:ID 0.0106676:0.0230879:0.19382:0.1553:rs141149254
1 54676 rs2462492 C T . PASS AF=0.399922 ES:SE:LP:AF:ID 0.0126544:0.0191013:0.29243:0.399922:rs2462492
1 54712 rs573184866 TTTTC T . PASS AF=0.416481 ES:SE:LP:AF:ID -0.0157499:0.0151309:0.522879:0.416481:rs573184866
1 54716 rs1166278911 C T . PASS AF=0.416415 ES:SE:LP:AF:ID -0.00715662:0.0174243:0.167491:0.416415:rs1166278911
1 55545 rs28396308 C T . PASS AF=0.251591 ES:SE:LP:AF:ID -0.0168659:0.0196613:0.408935:0.251591:rs28396308
1 58814 rs114420996 G A . PASS AF=0.089376 ES:SE:LP:AF:ID -0.0134124:0.0298543:0.187087:0.089376:rs114420996
1 59040 rs62637815 T C . PASS AF=0.087947 ES:SE:LP:AF:ID -0.0276404:0.0299868:0.443698:0.087947:rs62637815
1 60351 rs62637817 A G . PASS AF=0.080378 ES:SE:LP:AF:ID -0.011597:0.0310823:0.148742:0.080378:rs62637817
1 62777 rs3844233 A T . PASS AF=0.435691 ES:SE:LP:AF:ID 0.030378:0.0165702:1.17393:0.435691:rs3844233
1 63268 rs28664618 T C . PASS AF=0.381047 ES:SE:LP:AF:ID -0.00953503:0.0177395:0.229148:0.381047:rs28664618
1 63671 rs80011619 G A . PASS AF=0.1582 ES:SE:LP:AF:ID -0.0370863:0.0226712:1:0.1582:rs80011619
1 63735 rs61158452 C CCTA . PASS AF=0.683089 ES:SE:LP:AF:ID 0.0101242:0.017622:0.244125:0.683089:rs61158452
1 64931 rs62639104 G A . PASS AF=0.079109 ES:SE:LP:AF:ID -0.011521:0.0313529:0.148742:0.079109:rs62639104
1 68082 rs367789441 T C . PASS AF=0.069252 ES:SE:LP:AF:ID 0.00660449:0.0324265:0.0757207:0.069252:rs367789441
1 69428 rs140739101 T G . PASS AF=0.032733 ES:SE:LP:AF:ID 0.0746865:0.0484812:0.920819:0.032733:rs140739101
1 69761 rs200505207 A T . PASS AF=0.0725 ES:SE:LP:AF:ID 0.00312128:0.0318761:0.0362122:0.0725:rs200505207
1 69897 rs200676709 T C . PASS AF=0.752094 ES:SE:LP:AF:ID 0.000731217:0.020041:0.0132283:0.752094:rs200676709
1 74790 rs13328700 C G . PASS AF=0.034051 ES:SE:LP:AF:ID -0.00123945:0.0455369:0.00877392:0.034051:rs13328700
1 74792 rs1335672253 G A . PASS AF=0.034051 ES:SE:LP:AF:ID -0.00123945:0.0455369:0.00877392:0.034051:rs1335672253
1 76838 rs563953605 T G . PASS AF=0.07639 ES:SE:LP:AF:ID -0.0268995:0.0321041:0.39794:0.07639:rs563953605
1 76854 rs367666799 A G . PASS AF=0.077895 ES:SE:LP:AF:ID -0.0434171:0.0306621:0.79588:0.077895:rs367666799
1 77866 rs563593912 C T . PASS AF=0.076183 ES:SE:LP:AF:ID -0.0274566:0.0321029:0.408935:0.076183:rs563593912
1 77874 rs62641297 G A . PASS AF=0.076183 ES:SE:LP:AF:ID -0.0274566:0.0321029:0.408935:0.076183:rs62641297
1 81260 rs571136476 C T . PASS AF=0.041643 ES:SE:LP:AF:ID 0.0252632:0.0443006:0.244125:0.041643:rs571136476
1 81587 rs536406113 C T . PASS AF=0.059673 ES:SE:LP:AF:ID 0.0170846:0.0346286:0.207608:0.059673:rs536406113
1 82163 rs139113303 G A . PASS AF=0.075685 ES:SE:LP:AF:ID -0.0479908:0.0311216:0.920819:0.075685:rs139113303
1 82609 rs149189449 C G . PASS AF=0.075701 ES:SE:LP:AF:ID -0.047506:0.0311186:0.886057:0.075701:rs149189449
1 83514 rs201754587 C T . PASS AF=0.354828 ES:SE:LP:AF:ID 0.0269082:0.0179424:0.886057:0.354828:rs201754587