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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 /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ieu-a-import/processed/ieu-a-1019/ieu-a-1019.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/ieu-a-import/processed/ieu-a-1019/ldsc.txt \
--w-ld-chr /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/reference/eur_w_ld_chr/
Beginning analysis at Tue Feb 4 21:10:01 2020
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ieu-a-import/processed/ieu-a-1019/ieu-a-1019.vcf.gz ...
Read summary statistics for 722473 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, 668247 SNPs remain.
After merging with regression SNP LD, 668247 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.0759 (0.3235)
Lambda GC: 0.9979
Mean Chi^2: 0.9916
Intercept: 0.9896 (0.0063)
Ratio: NA (mean chi^2 < 1)
Analysis finished at Tue Feb 4 21:10:15 2020
Total time elapsed: 14.56s
{
"af_correlation": 0.922,
"inflation_factor": 0.9991,
"mean_EFFECT": -0.0012,
"n": 1374,
"n_snps": 722473,
"n_clumped_hits": 1,
"n_p_sig": 1,
"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": 5000,
"n_est": 1363.545,
"ratio_se_n": 0.9962,
"mean_diff": 0.0013,
"ratio_diff": 2.0382,
"sd_y_est1": 2.1354,
"sd_y_est2": 2.1273,
"r2_sum1": 0.0981,
"r2_sum2": 0.0215,
"r2_sum3": 0.0217,
"r2_sum4": 0.0219,
"ldsc_nsnp_merge_refpanel_ld": 668247,
"ldsc_nsnp_merge_regression_ld": 668247,
"ldsc_observed_scale_h2_beta": 0.0759,
"ldsc_observed_scale_h2_se": 0.3235,
"ldsc_intercept_beta": 0.9896,
"ldsc_intercept_se": 0.0063,
"ldsc_lambda_gc": 0.9979,
"ldsc_mean_chisq": 0.9916,
"ldsc_ratio": 1.2381
}
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 | 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×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 | 25 | 0 | 722473 | 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 | 24 | 0.9999668 | NA | NA | NA | NA | NA | 9.182708e+00 | 6.235181e+00 | 1.0000e+00 | 4.000000e+00 | 8.000000e+00 | 1.300000e+01 | 2.400000e+01 | ▇▆▃▃▂ |
numeric | POS | 0 | 1.0000000 | NA | NA | NA | NA | NA | 7.872254e+07 | 5.641375e+07 | 1.4380e+03 | 3.161567e+07 | 7.005013e+07 | 1.156412e+08 | 2.491982e+08 | ▇▆▅▂▁ |
numeric | EFFECT | 0 | 1.0000000 | NA | NA | NA | NA | NA | -1.245300e-03 | 1.333402e-01 | -2.6818e+00 | -7.267820e-02 | 0.000000e+00 | 7.232070e-02 | 1.431290e+00 | ▁▁▁▇▁ |
numeric | SE | 0 | 1.0000000 | NA | NA | NA | NA | NA | 1.199889e-01 | 5.619980e-02 | 7.6200e-02 | 8.501000e-02 | 9.752000e-02 | 1.304000e-01 | 1.123000e+00 | ▇▁▁▁▁ |
numeric | PVAL | 0 | 1.0000000 | NA | NA | NA | NA | NA | 5.002108e-01 | 2.880157e-01 | 0.0000e+00 | 2.509002e-01 | 5.002004e-01 | 7.492004e-01 | 1.000000e+00 | ▇▇▇▇▇ |
numeric | PVAL_ztest | 0 | 1.0000000 | NA | NA | NA | NA | NA | 5.002111e-01 | 2.880187e-01 | 0.0000e+00 | 2.508665e-01 | 5.002401e-01 | 7.492259e-01 | 1.000000e+00 | ▇▇▇▇▇ |
numeric | AF | 0 | 1.0000000 | NA | NA | NA | NA | NA | 3.638353e-01 | 2.672112e-01 | 8.7340e-03 | 1.332000e-01 | 3.046000e-01 | 5.591000e-01 | 9.915560e-01 | ▇▅▃▃▂ |
numeric | AF_reference | 5000 | 0.9930793 | NA | NA | NA | NA | NA | 3.676907e-01 | 2.508123e-01 | 7.9870e-04 | 1.561500e-01 | 3.095050e-01 | 5.497200e-01 | 9.994700e-01 | ▇▇▅▃▂ |
numeric | N | 0 | 1.0000000 | NA | NA | NA | NA | NA | 1.367842e+03 | 1.664977e+01 | 4.6400e+02 | 1.367000e+03 | 1.373000e+03 | 1.374000e+03 | 1.374000e+03 | ▁▁▁▁▇ |
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 | 721290 | rs12565286 | G | C | -0.3143000 | 0.19980 | 0.1156999 | 0.1157019 | 0.05033 | 0.0371406 | 1371 |
1 | 752566 | rs3094315 | G | A | 0.0177567 | 0.10100 | 0.8603000 | 0.8604441 | 0.81360 | 0.7182510 | 1368 |
1 | 761732 | rs2286139 | C | T | -0.0953102 | 0.11370 | 0.4043002 | 0.4018845 | 0.85380 | 0.6257990 | 1351 |
1 | 777122 | rs2980319 | A | T | -0.0723207 | 0.11600 | 0.5309003 | 0.5329860 | 0.86230 | 0.7472040 | 1373 |
1 | 785989 | rs2980300 | T | C | -0.0198026 | 0.11070 | 0.8604000 | 0.8580278 | 0.83980 | 0.6269970 | 1373 |
1 | 798959 | rs11240777 | G | A | 0.1570040 | 0.09259 | 0.0906192 | 0.0899445 | 0.23030 | 0.4099440 | 1374 |
1 | 888659 | rs3748597 | T | C | 0.0155198 | 0.17160 | 0.9280001 | 0.9279362 | 0.94169 | 0.9227240 | 1372 |
1 | 918573 | rs2341354 | A | G | -0.1544360 | 0.08341 | 0.0641594 | 0.0640935 | 0.57470 | 0.5491210 | 1346 |
1 | 926431 | rs4970403 | A | T | -0.0468836 | 0.20010 | 0.8152999 | 0.8147514 | 0.95670 | 0.8927720 | 1374 |
1 | 947034 | rs2465126 | G | A | -0.0049875 | 0.18960 | 0.9794000 | 0.9790136 | 0.95070 | 0.8256790 | 1359 |
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 |
NA | 11719 | rs2853495 | G | A | -0.1052610 | 0.1144 | 0.3592998 | 0.3575134 | 0.50870 | NA | 1374 |
NA | 11812 | rs3088053 | A | G | -0.1423700 | 0.2116 | 0.5010003 | 0.5010579 | 0.08333 | NA | 1368 |
NA | 11914 | rs2853496 | G | A | -0.0068232 | 0.2945 | 0.9814000 | 0.9815156 | 0.03956 | NA | 1365 |
NA | 12007 | rs2853497 | G | A | -0.5461070 | 0.5120 | 0.2861001 | 0.2861456 | 0.01602 | NA | 1373 |
NA | 12308 | rs2853498 | A | G | -0.1638140 | 0.1419 | 0.2482001 | 0.2483228 | 0.21410 | NA | 1373 |
NA | 12612 | rs28359172 | A | G | 0.0953102 | 0.1950 | 0.6242995 | 0.6250044 | 0.09243 | NA | 1374 |
NA | 13617 | rs2853503 | T | C | 0.0188218 | 0.2058 | 0.9271000 | 0.9271297 | 0.08382 | NA | 1372 |
NA | 13708 | rs28359178 | G | A | 0.1371500 | 0.1754 | 0.4338005 | 0.4342575 | 0.11650 | NA | 1373 |
NA | 14470 | rs3135030 | T | C | 0.1406310 | 0.3833 | 0.7129006 | 0.7136971 | 0.02187 | NA | 1372 |
NA | 15218 | rs2853506 | A | G | 0.1856490 | 0.2822 | 0.5104004 | 0.5106260 | 0.04079 | NA | 1373 |
1 721290 rs12565286 G C . PASS AF=0.05033 ES:SE:LP:AF:SS:ID -0.3143:0.1998:0.936667:0.05033:1371:rs12565286
1 752566 rs3094315 G A . PASS AF=0.8136 ES:SE:LP:AF:SS:ID 0.0177567:0.101:0.0653501:0.8136:1368:rs3094315
1 761732 rs2286139 C T . PASS AF=0.8538 ES:SE:LP:AF:SS:ID -0.0953102:0.1137:0.393296:0.8538:1351:rs2286139
1 777122 rs2980319 A T . PASS AF=0.8623 ES:SE:LP:AF:SS:ID -0.0723207:0.116:0.274987:0.8623:1373:rs2980319
1 785989 rs2980300 T C . PASS AF=0.8398 ES:SE:LP:AF:SS:ID -0.0198026:0.1107:0.0652996:0.8398:1373:rs2980300
1 798959 rs11240777 G A . PASS AF=0.2303 ES:SE:LP:AF:SS:ID 0.157004:0.09259:1.04278:0.2303:1374:rs11240777
1 888659 rs3748597 T C . PASS AF=0.94169 ES:SE:LP:AF:SS:ID 0.0155198:0.1716:0.032452:0.94169:1372:rs3748597
1 918573 rs2341354 A G . PASS AF=0.5747 ES:SE:LP:AF:SS:ID -0.154436:0.08341:1.19274:0.5747:1346:rs2341354
1 926431 rs4970403 A T . PASS AF=0.9567 ES:SE:LP:AF:SS:ID -0.0468836:0.2001:0.0886826:0.9567:1374:rs4970403
1 947034 rs2465126 G A . PASS AF=0.9507 ES:SE:LP:AF:SS:ID -0.00498754:0.1896:0.0090399:0.9507:1359:rs2465126
1 949608 rs1921 G A . PASS AF=0.3999 ES:SE:LP:AF:SS:ID 0.0962189:0.08437:0.593119:0.3999:1364:rs1921
1 990417 rs2465136 T C . PASS AF=0.2991 ES:SE:LP:AF:SS:ID -0.058795:0.08856:0.295163:0.2991:1371:rs2465136
1 1018704 rs9442372 A G . PASS AF=0.5512 ES:SE:LP:AF:SS:ID 0.086975:0.08275:0.532688:0.5512:1358:rs9442372
1 1039098 rs11260595 C A . PASS AF=0.02725 ES:SE:LP:AF:SS:ID -0.390675:0.2726:0.819014:0.02725:1358:rs11260595
1 1041700 rs6604968 A G . PASS AF=0.1348 ES:SE:LP:AF:SS:ID -0.138113:0.12:0.602234:0.1348:1372:rs6604968
1 1048955 rs4970405 A G . PASS AF=0.09767 ES:SE:LP:AF:SS:ID -0.10948:0.1379:0.369369:0.09767:1372:rs4970405
1 1097335 rs9442385 T G . PASS AF=0.93252 ES:SE:LP:AF:SS:ID 0.0381173:0.1651:0.0875122:0.93252:1356:rs9442385
1 1129672 rs11260554 G T . PASS AF=0.1107 ES:SE:LP:AF:SS:ID -0.106472:0.1296:0.385841:0.1107:1368:rs11260554
1 1130727 rs10907175 A C . PASS AF=0.09789 ES:SE:LP:AF:SS:ID 0.0944007:0.1376:0.307858:0.09789:1374:rs10907175
1 1156131 rs2887286 T C . PASS AF=0.1696 ES:SE:LP:AF:SS:ID 0.14583:0.1053:0.780154:0.1696:1374:rs2887286
1 1158277 rs3813199 G A . PASS AF=0.103 ES:SE:LP:AF:SS:ID 0.00498754:0.1343:0.0120211:0.103:1374:rs3813199
1 1158631 rs6603781 A G . PASS AF=0.8927 ES:SE:LP:AF:SS:ID -0.00299551:0.13:0.008641:0.8927:1351:rs6603781
1 1165310 rs11260562 G A . PASS AF=0.04492 ES:SE:LP:AF:SS:ID -0.113617:0.1975:0.247721:0.04492:1369:rs11260562
1 1195690 rs11260568 G C . PASS AF=0.01202 ES:SE:LP:AF:SS:ID -1.05757:0.4889:1.51499:0.01202:1373:rs11260568
1 1198618 rs12563338 T A . PASS AF=0.03621 ES:SE:LP:AF:SS:ID 0.34359:0.2059:1.02091:0.03621:1367:rs12563338
1 1211292 rs6685064 C T . PASS AF=0.06477 ES:SE:LP:AF:SS:ID 0.260825:0.1562:1.02393:0.06477:1374:rs6685064
1 1217058 rs3753340 G A . PASS AF=0.02054 ES:SE:LP:AF:SS:ID -0.740868:0.3414:1.52259:0.02054:1363:rs3753340
1 1218086 rs6603788 C T . PASS AF=0.07465 ES:SE:LP:AF:SS:ID 0.0563803:0.1508:0.150212:0.07465:1373:rs6603788
1 1242215 rs4970431 A G . PASS AF=0.97785 ES:SE:LP:AF:SS:ID 0.0320068:0.2811:0.0412928:0.97785:1309:rs4970431
1 1297065 rs2765023 C T . PASS AF=0.1129 ES:SE:LP:AF:SS:ID 0.0227395:0.1291:0.0657036:0.1129:1373:rs2765023
1 1297422 rs2765021 C T . PASS AF=0.93061 ES:SE:LP:AF:SS:ID 0.0143018:0.1594:0.0322181:0.93061:1369:rs2765021
1 1311716 rs2649589 G A . PASS AF=0.92978 ES:SE:LP:AF:SS:ID 0.00110061:0.1624:0.00230788:0.92978:1360:rs2649589
1 1333436 rs1240743 C A . PASS AF=0.6267 ES:SE:LP:AF:SS:ID 0.164639:0.0857:1.26209:0.6267:1373:rs1240743
1 1365570 rs1695824 A C . PASS AF=0.2031 ES:SE:LP:AF:SS:ID -0.018979:0.1024:0.069051:0.2031:1374:rs1695824
1 1462766 rs9439462 C T . PASS AF=0.03367 ES:SE:LP:AF:SS:ID 0.107957:0.2153:0.209996:0.03367:1366:rs9439462
1 1467485 rs1987191 T C . PASS AF=0.01969 ES:SE:LP:AF:SS:ID -0.26958:0.3043:0.425274:0.01969:1371:rs1987191
1 1478153 rs3766180 T C . PASS AF=0.274 ES:SE:LP:AF:SS:ID 0.00697561:0.08979:0.0290491:0.274:1374:rs3766180
1 1500941 rs6603791 A G . PASS AF=0.3126 ES:SE:LP:AF:SS:ID 0.0544882:0.08595:0.281831:0.3126:1374:rs6603791
1 1506035 rs7540231 G A . PASS AF=0.8452 ES:SE:LP:AF:SS:ID -0.127513:0.1088:0.615288:0.8452:1373:rs7540231
1 1510801 rs7519837 C T . PASS AF=0.2999 ES:SE:LP:AF:SS:ID 0.0168571:0.0876:0.0697643:0.2999:1374:rs7519837
1 1647686 rs909823 A C . PASS AF=0.93421 ES:SE:LP:AF:SS:ID -0.150143:0.1623:0.450016:0.93421:1368:rs909823
1 1688192 rs2281173 A G . PASS AF=0.92031 ES:SE:LP:AF:SS:ID -0.220741:0.1494:0.855426:0.92031:1374:rs2281173
1 1692321 rs1107910 T C . PASS AF=0.4429 ES:SE:LP:AF:SS:ID -0.0565704:0.08192:0.309715:0.4429:1374:rs1107910
1 1721479 rs2272908 C T . PASS AF=0.516 ES:SE:LP:AF:SS:ID -0.0246926:0.08158:0.118729:0.516:1374:rs2272908
1 1722932 rs3737628 C T . PASS AF=0.5144 ES:SE:LP:AF:SS:ID -0.0478373:0.08306:0.24849:0.5144:1356:rs3737628
1 1746694 rs12742323 G T . PASS AF=0.1619 ES:SE:LP:AF:SS:ID -0.0968414:0.1108:0.418164:0.1619:1353:rs12742323
1 1759026 rs9786963 T C . PASS AF=0.94756 ES:SE:LP:AF:SS:ID -0.290428:0.1795:0.975104:0.94756:1373:rs9786963
1 1759054 rs10907187 G A . PASS AF=0.2616 ES:SE:LP:AF:SS:ID 0.0592119:0.08988:0.291919:0.2616:1374:rs10907187
1 1778090 rs12126768 T G . PASS AF=0.1653 ES:SE:LP:AF:SS:ID -0.117208:0.1104:0.540608:0.1653:1373:rs12126768
1 1783201 rs12402876 G A . PASS AF=0.2593 ES:SE:LP:AF:SS:ID 0.07139:0.09301:0.355069:0.2593:1313:rs12402876