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"gwas_harmonisation_command": "--json /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ukb-a-import/processed/ukb-a-165/ukb-a-165_data.json --ref /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/QC/genomes/b37/human_g1k_v37.fasta; 1.1.1",
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"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/ukb-a-import/processed/ukb-a-165/ukb-a-165.vcf.gz -O z /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ukb-a-import/processed/ukb-a-165/ukb-a-165_data.vcf.gz; Date=Sun Feb 16 01:08:46 2020",
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"bcftools_viewCommand": "view -h /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/ukb-a-165/ukb-a-165.vcf.gz; Date=Sat May 9 16:27:49 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/ukb-a-import/processed/ukb-a-165/ukb-a-165.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/ukb-a-import/processed/ukb-a-165/ldsc.txt \
--w-ld-chr /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/reference/eur_w_ld_chr/
Beginning analysis at Sun Feb 16 01:52:45 2020
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ukb-a-import/processed/ukb-a-165/ukb-a-165.vcf.gz ...
Read summary statistics for 10877936 SNPs.
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, 1281483 SNPs remain.
After merging with regression SNP LD, 1281483 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.0033 (0.0014)
Lambda GC: 1.0389
Mean Chi^2: 1.0343
Intercept: 1.0128 (0.0066)
Ratio: 0.372 (0.1908)
Analysis finished at Sun Feb 16 01:54:32 2020
Total time elapsed: 1.0m:47.07s
{
"af_correlation": 0.9533,
"inflation_factor": 1.0269,
"mean_EFFECT": 1.6406e-06,
"n": 337159,
"n_snps": 10877936,
"n_clumped_hits": 3,
"n_p_sig": 59,
"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": 356865,
"n_est": 335660.7024,
"ratio_se_n": 0.9978,
"mean_diff": 0,
"ratio_diff": 221.9426,
"sd_y_est1": 0.057,
"sd_y_est2": 0.0569,
"r2_sum1": 1.0353e-06,
"r2_sum2": 0.0003,
"r2_sum3": 0.0003,
"r2_sum4": 0.0003,
"ldsc_nsnp_merge_refpanel_ld": 1281483,
"ldsc_nsnp_merge_regression_ld": 1281483,
"ldsc_observed_scale_h2_beta": 0.0033,
"ldsc_observed_scale_h2_se": 0.0014,
"ldsc_intercept_beta": 1.0128,
"ldsc_intercept_se": 0.0066,
"ldsc_lambda_gc": 1.0389,
"ldsc_mean_chisq": 1.0343,
"ldsc_ratio": 0.3732
}
name | value |
---|---|
name | value |
af_correlation | FALSE |
inflation_factor | FALSE |
n | FALSE |
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 | 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 | numeric.mean | numeric.sd | numeric.p0 | numeric.p25 | numeric.p50 | numeric.p75 | numeric.p100 | numeric.hist |
character | ID | 0 | 1.0000000 | 3 | 58 | 0 | 10877936 | 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 | 8.598638e+00 | 5.745666e+00 | 1.00000e+00 | 4.000000e+00 | 8.000000e+00 | 1.300000e+01 | 2.200000e+01 | ▇▅▃▂▂ |
numeric | POS | 0 | 1.0000000 | NA | NA | NA | NA | NA | 7.911383e+07 | 5.624931e+07 | 8.28000e+02 | 3.287294e+07 | 6.988889e+07 | 1.148258e+08 | 2.492251e+08 | ▇▆▅▂▁ |
numeric | EFFECT | 0 | 1.0000000 | NA | NA | NA | NA | NA | 1.600000e-06 | 8.264000e-04 | -8.49080e-03 | -2.342000e-04 | -6.800000e-06 | 2.131000e-04 | 1.312350e-02 | ▁▇▃▁▁ |
numeric | SE | 0 | 1.0000000 | NA | NA | NA | NA | NA | 5.981000e-04 | 5.665000e-04 | 1.37200e-04 | 1.695000e-04 | 3.255000e-04 | 8.698000e-04 | 3.117700e-03 | ▇▂▁▁▁ |
numeric | PVAL | 0 | 1.0000000 | NA | NA | NA | NA | NA | 4.965865e-01 | 2.889459e-01 | 0.00000e+00 | 2.463139e-01 | 4.942970e-01 | 7.472381e-01 | 1.000000e+00 | ▇▇▇▇▇ |
numeric | PVAL_ztest | 0 | 1.0000000 | NA | NA | NA | NA | NA | 4.965860e-01 | 2.889462e-01 | 0.00000e+00 | 2.463131e-01 | 4.942965e-01 | 7.472372e-01 | 9.999999e-01 | ▇▇▇▇▇ |
numeric | AF | 0 | 1.0000000 | NA | NA | NA | NA | NA | 1.820865e-01 | 2.503832e-01 | 1.00090e-03 | 6.878700e-03 | 5.191440e-02 | 2.739880e-01 | 9.989990e-01 | ▇▂▁▁▁ |
numeric | AF_reference | 356865 | 0.9671937 | NA | NA | NA | NA | NA | 1.877709e-01 | 2.439191e-01 | 0.00000e+00 | 5.191700e-03 | 7.468050e-02 | 2.873400e-01 | 1.000000e+00 | ▇▂▁▁▁ |
numeric | N | 0 | 1.0000000 | NA | NA | NA | NA | NA | 3.371590e+05 | 0.000000e+00 | 3.37159e+05 | 3.371590e+05 | 3.371590e+05 | 3.371590e+05 | 3.371590e+05 | ▁▁▇▁▁ |
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 | 693731 | rs12238997 | A | G | 0.0001804 | 0.0002290 | 0.4309501 | 0.4309489 | 0.1169260 | 0.1417730 | 337159 |
1 | 717587 | rs144155419 | G | A | 0.0001690 | 0.0006152 | 0.7835018 | 0.7835024 | 0.0143862 | 0.0045926 | 337159 |
1 | 730087 | rs148120343 | T | C | -0.0001046 | 0.0003192 | 0.7431646 | 0.7431647 | 0.0554733 | 0.0127796 | 337159 |
1 | 731718 | rs142557973 | T | C | 0.0000858 | 0.0002173 | 0.6931049 | 0.6931046 | 0.1216580 | 0.1543530 | 337159 |
1 | 734349 | rs141242758 | T | C | 0.0000878 | 0.0002174 | 0.6863079 | 0.6863073 | 0.1215130 | 0.1525560 | 337159 |
1 | 740284 | rs61770167 | C | T | -0.0008736 | 0.0009897 | 0.3774157 | 0.3774155 | 0.0058556 | 0.0023962 | 337159 |
1 | 742813 | rs112573343 | C | T | 0.0014075 | 0.0018677 | 0.4510888 | 0.4510874 | 0.0015525 | 0.1030350 | 337159 |
1 | 753405 | rs3115860 | C | A | -0.0000579 | 0.0002066 | 0.7791875 | 0.7791863 | 0.8706760 | 0.7517970 | 337159 |
1 | 753541 | rs2073813 | G | A | 0.0000341 | 0.0002071 | 0.8693501 | 0.8693495 | 0.1288330 | 0.3019170 | 337159 |
1 | 754182 | rs3131969 | A | G | -0.0000498 | 0.0002063 | 0.8094380 | 0.8094374 | 0.8703180 | 0.6785140 | 337159 |
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 | 51219387 | rs9616832 | T | C | 0.0000778 | 0.0002660 | 0.7698888 | 0.7698890 | 0.0729806 | 0.0654952 | 337159 |
22 | 51219704 | rs147475742 | G | A | 0.0000474 | 0.0003566 | 0.8942491 | 0.8942494 | 0.0418225 | 0.0473243 | 337159 |
22 | 51219766 | rs182321900 | C | T | -0.0009292 | 0.0018335 | 0.6123180 | 0.6123185 | 0.0014546 | NA | 337159 |
22 | 51220088 | rs566371895 | G | A | 0.0024038 | 0.0011992 | 0.0450267 | 0.0450260 | 0.0039843 | 0.0003994 | 337159 |
22 | 51220146 | rs868950473 | C | T | -0.0010137 | 0.0018060 | 0.5746098 | 0.5746104 | 0.0015139 | NA | 337159 |
22 | 51221731 | rs115055839 | T | C | 0.0000897 | 0.0002662 | 0.7360223 | 0.7360228 | 0.0728101 | 0.0625000 | 337159 |
22 | 51223637 | rs375798137 | G | A | -0.0000976 | 0.0003136 | 0.7557428 | 0.7557430 | 0.0540289 | 0.0788738 | 337159 |
22 | 51226692 | rs150189434 | G | A | -0.0009792 | 0.0018752 | 0.6015296 | 0.6015289 | 0.0013983 | 0.0155751 | 337159 |
22 | 51229805 | rs9616985 | T | C | 0.0000985 | 0.0002672 | 0.7125527 | 0.7125514 | 0.0727671 | 0.0730831 | 337159 |
22 | 51237063 | rs3896457 | T | C | -0.0000668 | 0.0001626 | 0.6813747 | 0.6813740 | 0.2968410 | 0.2050720 | 337159 |
1 693731 rs12238997 A G . PASS AF=0.116926 ES:SE:LP:AF:SS:ID 0.000180384:0.000229039:0.365573:0.116926:337159:rs12238997
1 717587 rs144155419 G A . PASS AF=0.0143862 ES:SE:LP:AF:SS:ID 0.000169037:0.000615222:0.10596:0.0143862:337159:rs144155419
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1 731718 rs58276399 T C . PASS AF=0.121658 ES:SE:LP:AF:SS:ID 8.57529e-05:0.000217291:0.159201:0.121658:337159:rs58276399
1 734349 rs141242758 T C . PASS AF=0.121513 ES:SE:LP:AF:SS:ID 8.78077e-05:0.000217415:0.163481:0.121513:337159:rs141242758
1 740284 rs61770167 C T . PASS AF=0.00585559 ES:SE:LP:AF:SS:ID -0.000873576:0.000989699:0.42318:0.00585559:337159:rs61770167
1 742813 rs112573343 C T . PASS AF=0.0015525 ES:SE:LP:AF:SS:ID 0.00140749:0.00186768:0.345738:0.0015525:337159:rs112573343
1 753405 rs3115860 C A . PASS AF=0.870676 ES:SE:LP:AF:SS:ID -5.79169e-05:0.000206566:0.108358:0.870676:337159:rs3115860
1 753541 rs2073813 G A . PASS AF=0.128833 ES:SE:LP:AF:SS:ID 3.4062e-05:0.000207083:0.0608053:0.128833:337159:rs2073813
1 754182 rs3131969 A G . PASS AF=0.870318 ES:SE:LP:AF:SS:ID -4.97612e-05:0.000206348:0.0918164:0.870318:337159:rs3131969
1 754192 rs3131968 A G . PASS AF=0.870409 ES:SE:LP:AF:SS:ID -5.32824e-05:0.000206446:0.0989047:0.870409:337159:rs3131968
1 754334 rs3131967 T C . PASS AF=0.870037 ES:SE:LP:AF:SS:ID -4.95559e-05:0.00020634:0.0914072:0.870037:337159:rs3131967
1 754433 rs150578204 G A . PASS AF=0.00465304 ES:SE:LP:AF:SS:ID 0.000259169:0.00105278:0.0939102:0.00465304:337159:rs150578204
1 754458 rs142682604 G T . PASS AF=0.00464711 ES:SE:LP:AF:SS:ID 0.000262242:0.00105564:0.0948466:0.00464711:337159:rs142682604
1 755435 rs184270342 T G . PASS AF=0.00590897 ES:SE:LP:AF:SS:ID 0.000313914:0.00102801:0.119133:0.00590897:337159:rs184270342
1 755890 rs3115858 A T . PASS AF=0.870329 ES:SE:LP:AF:SS:ID -7.09308e-05:0.000205982:0.136332:0.870329:337159:rs3115858
1 756604 rs3131962 A G . PASS AF=0.87002 ES:SE:LP:AF:SS:ID -7.37604e-05:0.000205488:0.14289:0.87002:337159:rs3131962
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1 757734 rs4951929 C T . PASS AF=0.870219 ES:SE:LP:AF:SS:ID -7.80442e-05:0.000205658:0.152225:0.870219:337159:rs4951929
1 757936 rs4951862 C A . PASS AF=0.870219 ES:SE:LP:AF:SS:ID -7.82771e-05:0.000205672:0.152732:0.870219:337159:rs4951862
1 758144 rs3131956 A G . PASS AF=0.870222 ES:SE:LP:AF:SS:ID -7.82119e-05:0.000205679:0.15258:0.870222:337159:rs3131956
1 758626 rs3131954 C T . PASS AF=0.870396 ES:SE:LP:AF:SS:ID -6.01941e-05:0.000206207:0.113309:0.870396:337159:rs3131954
1 761732 rs2286139 C T . PASS AF=0.867743 ES:SE:LP:AF:SS:ID -7.43894e-05:0.000205223:0.144485:0.867743:337159:rs2286139
1 766007 rs61768174 A C . PASS AF=0.106958 ES:SE:LP:AF:SS:ID 7.63421e-05:0.000228508:0.13176:0.106958:337159:rs61768174
1 768253 rs2977608 A C . PASS AF=0.763932 ES:SE:LP:AF:SS:ID -0.000217684:0.000162839:0.741631:0.763932:337159:rs2977608
1 768448 rs12562034 G A . PASS AF=0.105257 ES:SE:LP:AF:SS:ID 0.000326113:0.000224795:0.833097:0.105257:337159:rs12562034
1 768819 rs12562811 C T . PASS AF=0.00692766 ES:SE:LP:AF:SS:ID -0.000936606:0.000835129:0.581579:0.00692766:337159:rs12562811
1 769223 rs60320384 C G . PASS AF=0.128651 ES:SE:LP:AF:SS:ID 5.62329e-05:0.000206775:0.104766:0.128651:337159:rs60320384
1 769224 rs141644775 G A . PASS AF=0.00143239 ES:SE:LP:AF:SS:ID -0.00189017:0.00194288:0.480675:0.00143239:337159:rs141644775
1 770181 rs146076599 A G . PASS AF=0.00907328 ES:SE:LP:AF:SS:ID 0.000947565:0.000792393:0.634952:0.00907328:337159:rs146076599
1 770377 rs112563271 A T . PASS AF=0.00692321 ES:SE:LP:AF:SS:ID -0.000922554:0.000838759:0.56643:0.00692321:337159:rs112563271
1 771823 rs2977605 T C . PASS AF=0.869934 ES:SE:LP:AF:SS:ID -5.97109e-05:0.000205858:0.112512:0.869934:337159:rs2977605
1 771967 rs59066358 G A . PASS AF=0.128709 ES:SE:LP:AF:SS:ID 4.57962e-05:0.000206681:0.0837351:0.128709:337159:rs59066358
1 772755 rs2905039 A C . PASS AF=0.870112 ES:SE:LP:AF:SS:ID -6.06036e-05:0.000205867:0.114375:0.870112:337159:rs2905039
1 774736 rs28830877 A C . PASS AF=0.998797 ES:SE:LP:AF:SS:ID -0.00232851:0.00213865:0.558693:0.998797:337159:rs28830877
1 776556 rs151160018 C T . PASS AF=0.00851871 ES:SE:LP:AF:SS:ID 1.43051e-05:0.000772564:0.00646369:0.00851871:337159:rs151160018
1 777122 rs2980319 A T . PASS AF=0.871122 ES:SE:LP:AF:SS:ID -6.90544e-05:0.000206217:0.132103:0.871122:337159:rs2980319
1 777232 rs112618790 C T . PASS AF=0.0961319 ES:SE:LP:AF:SS:ID 0.000417323:0.000238087:1.0989:0.0961319:337159:rs112618790
1 778745 rs1055606 A G . PASS AF=0.127871 ES:SE:LP:AF:SS:ID 6.48212e-05:0.000206895:0.1226:0.127871:337159:rs1055606
1 779322 rs4040617 A G . PASS AF=0.127984 ES:SE:LP:AF:SS:ID 6.76012e-05:0.000206615:0.128702:0.127984:337159:rs4040617
1 780785 rs2977612 T A . PASS AF=0.870455 ES:SE:LP:AF:SS:ID -7.2039e-05:0.000205879:0.138819:0.870455:337159:rs2977612
1 781367 rs149821290 A C . PASS AF=0.00989772 ES:SE:LP:AF:SS:ID 0.000535696:0.000732733:0.332806:0.00989772:337159:rs149821290
1 781845 rs61768199 A G . PASS AF=0.1044 ES:SE:LP:AF:SS:ID 5.34649e-05:0.000231515:0.087584:0.1044:337159:rs61768199
1 782721 rs185280546 G A . PASS AF=0.0143713 ES:SE:LP:AF:SS:ID 0.000264882:0.000626646:0.172297:0.0143713:337159:rs185280546
1 782981 rs6594026 C T . PASS AF=0.128338 ES:SE:LP:AF:SS:ID 6.12864e-05:0.000206728:0.115273:0.128338:337159:rs6594026
1 783193 rs145767270 G C . PASS AF=0.0143639 ES:SE:LP:AF:SS:ID 0.000285693:0.000629304:0.187192:0.0143639:337159:rs145767270
1 783194 rs138555831 G T . PASS AF=0.0143713 ES:SE:LP:AF:SS:ID 0.00028849:0.000629228:0.18936:0.0143713:337159:rs138555831
1 783711 rs184266993 G A . PASS AF=0.00541372 ES:SE:LP:AF:SS:ID 0.000809697:0.00100603:0.375809:0.00541372:337159:rs184266993
1 785050 rs2905062 G A . PASS AF=0.87014 ES:SE:LP:AF:SS:ID -8.28066e-05:0.00020591:0.16268:0.87014:337159:rs2905062
1 785989 rs2980300 T C . PASS AF=0.87009 ES:SE:LP:AF:SS:ID -8.32898e-05:0.000206041:0.163652:0.87009:337159:rs2980300