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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/ukb-d-import/processed/ukb-d-20499/ukb-d-20499.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-d-import/processed/ukb-d-20499/ldsc.txt \
--w-ld-chr /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/reference/eur_w_ld_chr/
Beginning analysis at Mon Nov 25 17:19:05 2019
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ukb-d-import/processed/ukb-d-20499/ukb-d-20499.vcf.gz ...
Read summary statistics for 13571560 SNPs.
Dropped 12696 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, 1283502 SNPs remain.
After merging with regression SNP LD, 1283502 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.0646 (0.0053)
Lambda GC: 1.1414
Mean Chi^2: 1.1599
Intercept: 1.0087 (0.0075)
Ratio: 0.0543 (0.0471)
Analysis finished at Mon Nov 25 17:21:42 2019
Total time elapsed: 2.0m:36.7s
{
"af_correlation": 0.9521,
"inflation_factor": 1.0923,
"mean_EFFECT": 0,
"n": 117677,
"n_snps": 13571560,
"n_clumped_hits": 3,
"n_p_sig": 125,
"n_mono": 0,
"n_ns": 1251353,
"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": 564587,
"n_est": 118105.9668,
"ratio_se_n": 1.0018,
"mean_diff": 0,
"ratio_diff": 21.6747,
"sd_y_est1": 0.4798,
"sd_y_est2": 0.4807,
"r2_sum1": 0.0002,
"r2_sum2": 0.0009,
"r2_sum3": 0.0009,
"r2_sum4": 0.0009,
"ldsc_nsnp_merge_refpanel_ld": 1283502,
"ldsc_nsnp_merge_regression_ld": 1283502,
"ldsc_observed_scale_h2_beta": 0.0646,
"ldsc_observed_scale_h2_se": 0.0053,
"ldsc_intercept_beta": 1.0087,
"ldsc_intercept_se": 0.0075,
"ldsc_lambda_gc": 1.1414,
"ldsc_mean_chisq": 1.1599,
"ldsc_ratio": 0.0544
}
name | value |
---|---|
name | value |
af_correlation | FALSE |
inflation_factor | FALSE |
n | FALSE |
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 | 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 | 94 | 0 | 13559528 | 0 | NA | NA | NA | NA | NA | NA | NA | NA |
character | REF | 0 | 1.0000000 | 1 | 100 | 0 | 57053 | 0 | NA | NA | NA | NA | NA | NA | NA | NA |
character | ALT | 0 | 1.0000000 | 1 | 342 | 0 | 33331 | 0 | NA | NA | NA | NA | NA | NA | NA | NA |
numeric | CHROM | 0 | 1.0000000 | NA | NA | NA | NA | NA | 9.051455e+00 | 6.185087e+00 | 1.00000e+00 | 4.000000e+00 | 8.000000e+00 | 1.300000e+01 | 2.300000e+01 | ▇▅▅▂▂ |
numeric | POS | 0 | 1.0000000 | NA | NA | NA | NA | NA | 7.902505e+07 | 5.591561e+07 | 3.02000e+02 | 3.292850e+07 | 7.013920e+07 | 1.148580e+08 | 2.492309e+08 | ▇▆▅▂▁ |
numeric | EFFECT | 0 | 1.0000000 | NA | NA | NA | NA | NA | 2.160000e-05 | 1.160330e-02 | -1.34366e-01 | -3.203200e-03 | 2.140000e-05 | 3.233100e-03 | 1.518720e-01 | ▁▁▇▁▁ |
numeric | SE | 0 | 1.0000000 | NA | NA | NA | NA | NA | 8.286800e-03 | 7.987900e-03 | 1.63780e-03 | 2.365100e-03 | 4.352600e-03 | 1.189810e-02 | 3.995540e-02 | ▇▂▁▁▁ |
numeric | PVAL | 0 | 1.0000000 | NA | NA | NA | NA | NA | 4.856737e-01 | 2.927586e-01 | 0.00000e+00 | 2.285362e-01 | 4.808515e-01 | 7.391899e-01 | 1.000000e+00 | ▇▇▇▇▇ |
numeric | PVAL_ztest | 0 | 1.0000000 | NA | NA | NA | NA | NA | 4.856724e-01 | 2.927594e-01 | 0.00000e+00 | 2.285332e-01 | 4.808493e-01 | 7.391896e-01 | 9.999997e-01 | ▇▇▇▇▇ |
numeric | AF | 0 | 1.0000000 | NA | NA | NA | NA | NA | 1.909976e-01 | 2.544492e-01 | 1.00000e-03 | 7.483500e-03 | 6.026490e-02 | 2.956750e-01 | 9.990000e-01 | ▇▂▁▁▁ |
numeric | AF_reference | 564587 | 0.9583993 | NA | NA | NA | NA | NA | 1.964726e-01 | 2.471288e-01 | 0.00000e+00 | 5.790700e-03 | 8.446490e-02 | 3.083070e-01 | 1.000000e+00 | ▇▂▁▁▁ |
numeric | N | 0 | 1.0000000 | NA | NA | NA | NA | NA | 1.176770e+05 | 0.000000e+00 | 1.17677e+05 | 1.176770e+05 | 1.176770e+05 | 1.176770e+05 | 1.176770e+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 | 692794 | rs530212009 | CA | C | 0.0000202 | 0.0034436 | 0.9953110 | 0.9953110 | 0.1117450 | 0.1894970 | 117677 |
1 | 693731 | rs12238997 | A | G | 0.0013553 | 0.0032611 | 0.6777086 | 0.6777070 | 0.1167660 | 0.1417730 | 117677 |
1 | 707522 | rs371890604 | G | C | 0.0016619 | 0.0036594 | 0.6497361 | 0.6497356 | 0.0983539 | 0.1293930 | 117677 |
1 | 717587 | rs144155419 | G | A | -0.0023337 | 0.0087678 | 0.7901090 | 0.7901079 | 0.0157666 | 0.0045926 | 117677 |
1 | 723329 | rs189787166 | A | T | 0.0123955 | 0.0255888 | 0.6280960 | 0.6280941 | 0.0017740 | 0.0003994 | 117677 |
1 | 730087 | rs148120343 | T | C | 0.0019985 | 0.0045391 | 0.6597281 | 0.6597266 | 0.0569111 | 0.0127796 | 117677 |
1 | 731718 | rs142557973 | T | C | 0.0014232 | 0.0030943 | 0.6455635 | 0.6455643 | 0.1226810 | 0.1543530 | 117677 |
1 | 732032 | rs61770163 | A | C | -0.0002948 | 0.0032980 | 0.9287730 | 0.9287726 | 0.1222610 | 0.1555510 | 117677 |
1 | 734349 | rs141242758 | T | C | 0.0015311 | 0.0030959 | 0.6209162 | 0.6209138 | 0.1219370 | 0.1525560 | 117677 |
1 | 740284 | rs61770167 | C | T | -0.0087562 | 0.0141217 | 0.5352233 | 0.5352221 | 0.0058700 | 0.0023962 | 117677 |
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 |
23 | 154923311 | rs141127553 | C | T | -0.0060709 | 0.0036382 | 0.0951897 | 0.0951864 | 0.0555143 | 0.0309934 | 117677 |
23 | 154923374 | rs111332691 | T | A | -0.0013389 | 0.0039665 | 0.7357072 | 0.7357078 | 0.0447709 | 0.0116556 | 117677 |
23 | 154925045 | rs509981 | C | T | 0.0028093 | 0.0019102 | 0.1413781 | 0.1413753 | 0.2446450 | 0.3634440 | 117677 |
23 | 154925895 | rs538470 | C | T | 0.0028084 | 0.0019534 | 0.1505178 | 0.1505157 | 0.2410730 | 0.3634440 | 117677 |
23 | 154927581 | rs644138 | G | A | 0.0011008 | 0.0017973 | 0.5402453 | 0.5402447 | 0.3005210 | 0.4635760 | 117677 |
23 | 154929412 | rs557132 | C | T | 0.0027506 | 0.0019107 | 0.1499909 | 0.1499887 | 0.2445190 | 0.3568210 | 117677 |
23 | 154929637 | rs35185538 | CT | C | 0.0035937 | 0.0019959 | 0.0717794 | 0.0717759 | 0.2287620 | 0.3011920 | 117677 |
23 | 154929952 | rs4012982 | CAA | C | 0.0028750 | 0.0020108 | 0.1527981 | 0.1527963 | 0.2386030 | 0.3165560 | 117677 |
23 | 154930230 | rs781880 | A | G | 0.0027156 | 0.0019102 | 0.1551290 | 0.1551271 | 0.2449430 | 0.3618540 | 117677 |
23 | 154930487 | rs781879 | T | A | 0.0094786 | 0.0064925 | 0.1443128 | 0.1443104 | 0.0196688 | 0.1263580 | 117677 |
1 692794 rs530212009 CA C . PASS AF=0.111745 ES:SE:LP:AF:SS:ID 2.02376e-05:0.0034436:0.0020412:0.111745:117677:1_692794_CA_C
1 693731 rs12238997 A G . PASS AF=0.116766 ES:SE:LP:AF:SS:ID 0.00135529:0.00326109:0.168957:0.116766:117677:rs12238997
1 707522 rs371890604 G C . PASS AF=0.0983539 ES:SE:LP:AF:SS:ID 0.00166186:0.00365944:0.187263:0.0983539:117677:rs371890604
1 717587 rs144155419 G A . PASS AF=0.0157666 ES:SE:LP:AF:SS:ID -0.00233374:0.00876784:0.102313:0.0157666:117677:rs144155419
1 723329 rs189787166 A T . PASS AF=0.001774 ES:SE:LP:AF:SS:ID 0.0123955:0.0255888:0.201974:0.001774:117677:rs189787166
1 730087 rs148120343 T C . PASS AF=0.0569111 ES:SE:LP:AF:SS:ID 0.00199851:0.00453907:0.180635:0.0569111:117677:rs148120343
1 731718 rs58276399 T C . PASS AF=0.122681 ES:SE:LP:AF:SS:ID 0.00142318:0.00309432:0.190061:0.122681:117677:rs58276399
1 732032 rs61770163 A C . PASS AF=0.122261 ES:SE:LP:AF:SS:ID -0.000294809:0.00329804:0.0320904:0.122261:117677:rs61770163
1 734349 rs141242758 T C . PASS AF=0.121937 ES:SE:LP:AF:SS:ID 0.0015311:0.00309591:0.206967:0.121937:117677:rs141242758
1 740284 rs61770167 C T . PASS AF=0.00587004 ES:SE:LP:AF:SS:ID -0.00875622:0.0141217:0.271465:0.00587004:117677:rs61770167
1 742813 rs112573343 C T . PASS AF=0.00182795 ES:SE:LP:AF:SS:ID 0.0557856:0.0271567:1.3984:0.00182795:117677:rs112573343
1 749963 rs529266287 T TAA . PASS AF=0.868987 ES:SE:LP:AF:SS:ID -0.0013473:0.00305068:0.181279:0.868987:117677:rs529266287
1 750230 rs190826124 G C . PASS AF=0.00158321 ES:SE:LP:AF:SS:ID -0.000309087:0.0271426:0.00396404:0.00158321:117677:rs190826124
1 751343 rs28544273 T A . PASS AF=0.123708 ES:SE:LP:AF:SS:ID 0.00125706:0.00302267:0.169091:0.123708:117677:rs28544273
1 751488 rs200141114 G GA . PASS AF=0.14333 ES:SE:LP:AF:SS:ID 0.00263526:0.00298961:0.422435:0.14333:117677:rs200141114
1 751756 rs28527770 T C . PASS AF=0.12383 ES:SE:LP:AF:SS:ID 0.00122887:0.00301847:0.164993:0.12383:117677:rs28527770
1 753405 rs3115860 C A . PASS AF=0.869768 ES:SE:LP:AF:SS:ID -0.00199321:0.00293954:0.303007:0.869768:117677:rs3115860
1 753425 rs3131970 T C . PASS AF=0.874545 ES:SE:LP:AF:SS:ID -0.00176203:0.00298899:0.255299:0.874545:117677:rs3131970
1 753541 rs2073813 G A . PASS AF=0.129695 ES:SE:LP:AF:SS:ID 0.00167173:0.00294775:0.243644:0.129695:117677:rs2073813
1 754105 rs12184325 C T . PASS AF=0.0365322 ES:SE:LP:AF:SS:ID 0.0110507:0.00535315:1.40906:0.0365322:117677:rs12184325
1 754182 rs3131969 A G . PASS AF=0.869361 ES:SE:LP:AF:SS:ID -0.00204039:0.00293674:0.312298:0.869361:117677:rs3131969
1 754192 rs3131968 A G . PASS AF=0.869428 ES:SE:LP:AF:SS:ID -0.00198331:0.0029378:0.301365:0.869428:117677:rs3131968
1 754334 rs3131967 T C . PASS AF=0.86936 ES:SE:LP:AF:SS:ID -0.00201863:0.00293666:0.308177:0.86936:117677:rs3131967
1 754433 rs150578204 G A . PASS AF=0.00510457 ES:SE:LP:AF:SS:ID 0.000351179:0.0150447:0.00816412:0.00510457:117677:rs150578204
1 754458 rs142682604 G T . PASS AF=0.00507359 ES:SE:LP:AF:SS:ID -0.000162546:0.0150781:0.00375152:0.00507359:117677:rs142682604
1 755435 rs184270342 T G . PASS AF=0.00568504 ES:SE:LP:AF:SS:ID -0.0102024:0.0144805:0.317778:0.00568504:117677:rs184270342
1 755890 rs3115858 A T . PASS AF=0.869435 ES:SE:LP:AF:SS:ID -0.00190538:0.00293127:0.287619:0.869435:117677:rs3115858
1 756434 rs61768170 G C . PASS AF=0.126972 ES:SE:LP:AF:SS:ID 0.00145991:0.00299216:0.203694:0.126972:117677:rs61768170
1 756604 rs3131962 A G . PASS AF=0.868955 ES:SE:LP:AF:SS:ID -0.00181817:0.00292355:0.272455:0.868955:117677:rs3131962
1 757640 rs3115853 G A . PASS AF=0.868354 ES:SE:LP:AF:SS:ID -0.00177195:0.00292244:0.264162:0.868354:117677:rs3115853
1 757734 rs4951929 C T . PASS AF=0.869145 ES:SE:LP:AF:SS:ID -0.00188502:0.00292646:0.284421:0.869145:117677:rs4951929
1 757936 rs4951862 C A . PASS AF=0.869152 ES:SE:LP:AF:SS:ID -0.00188589:0.00292667:0.284557:0.869152:117677:rs4951862
1 758144 rs3131956 A G . PASS AF=0.869154 ES:SE:LP:AF:SS:ID -0.00188309:0.00292668:0.284037:0.869154:117677:rs3131956
1 758626 rs3131954 C T . PASS AF=0.86959 ES:SE:LP:AF:SS:ID -0.00198928:0.00293419:0.30295:0.86959:117677:rs3131954
1 759293 rs10157329 T A . PASS AF=0.0995957 ES:SE:LP:AF:SS:ID 0.00200805:0.00341107:0.254868:0.0995957:117677:rs10157329
1 759600 rs545998451 AGT A . PASS AF=0.0065427 ES:SE:LP:AF:SS:ID -0.00642314:0.0131477:0.204001:0.0065427:117677:1_759600_AGT_A
1 759837 rs3115851 T A . PASS AF=0.873645 ES:SE:LP:AF:SS:ID -0.00173773:0.00297919:0.252045:0.873645:117677:rs3115851
1 761732 rs2286139 C T . PASS AF=0.862934 ES:SE:LP:AF:SS:ID -0.00210824:0.00292168:0.327394:0.862934:117677:rs2286139
1 761752 rs1057213 C T . PASS AF=0.868335 ES:SE:LP:AF:SS:ID -0.00170905:0.0029498:0.250006:0.868335:117677:rs1057213
1 762273 rs3115849 G A . PASS AF=0.865338 ES:SE:LP:AF:SS:ID -0.0015593:0.00295025:0.22393:0.865338:117677:rs3115849
1 762485 rs12095200 C A . PASS AF=0.0997639 ES:SE:LP:AF:SS:ID 0.000523238:0.00352522:0.0545285:0.0997639:117677:rs12095200
1 762589 rs3115848 G C . PASS AF=0.870631 ES:SE:LP:AF:SS:ID -0.0019318:0.00298506:0.286063:0.870631:117677:rs3115848
1 762592 rs3131950 C G . PASS AF=0.870631 ES:SE:LP:AF:SS:ID -0.00193168:0.00298506:0.28604:0.870631:117677:rs3131950
1 762601 rs3131949 T C . PASS AF=0.870629 ES:SE:LP:AF:SS:ID -0.00193775:0.00298506:0.287146:0.870629:117677:rs3131949
1 762632 rs3131948 T A . PASS AF=0.870952 ES:SE:LP:AF:SS:ID -0.00196289:0.00298633:0.291584:0.870952:117677:rs3131948
1 764191 rs7515915 T G . PASS AF=0.126564 ES:SE:LP:AF:SS:ID 0.00128775:0.00298892:0.176145:0.126564:117677:rs7515915
1 766007 rs61768174 A C . PASS AF=0.106341 ES:SE:LP:AF:SS:ID 0.00172608:0.00324821:0.225376:0.106341:117677:rs61768174
1 766105 rs2519015 T A . PASS AF=0.854374 ES:SE:LP:AF:SS:ID -0.00279351:0.00292085:0.469966:0.854374:117677:rs2519015
1 767393 rs538667473 A C . PASS AF=0.00169052 ES:SE:LP:AF:SS:ID 0.0100655:0.0256659:0.15806:0.00169052:117677:rs538667473
1 768116 rs376645387 A AGTTTT . PASS AF=0.839056 ES:SE:LP:AF:SS:ID -0.00388309:0.00289374:0.745614:0.839056:117677:rs376645387