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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-1007/ieu-a-1007.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-1007/ldsc.txt \
--w-ld-chr /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/reference/eur_w_ld_chr/
Beginning analysis at Wed Feb 5 08:24:05 2020
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ieu-a-import/processed/ieu-a-1007/ieu-a-1007.vcf.gz ...
Read summary statistics for 6412174 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, 1223918 SNPs remain.
After merging with regression SNP LD, 1223918 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.0905 (0.0069)
Lambda GC: 1.2365
Mean Chi^2: 1.3137
Intercept: 0.9902 (0.0101)
Ratio < 0 (usually indicates GC correction).
Analysis finished at Wed Feb 5 08:25:13 2020
Total time elapsed: 1.0m:8.11s
{
"af_correlation": 0.9262,
"inflation_factor": 1.222,
"mean_EFFECT": 0,
"n": 170911,
"n_snps": 6412174,
"n_clumped_hits": 10,
"n_p_sig": 2188,
"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": 39877,
"n_est": 229818.8392,
"ratio_se_n": 1.1596,
"mean_diff": -7.7331e-07,
"ratio_diff": 1.1251,
"sd_y_est1": 0.9075,
"sd_y_est2": 1.0523,
"r2_sum1": 0.0023,
"r2_sum2": 0.0028,
"r2_sum3": 0.0021,
"r2_sum4": 0.0022,
"ldsc_nsnp_merge_refpanel_ld": 1223918,
"ldsc_nsnp_merge_regression_ld": 1223918,
"ldsc_observed_scale_h2_beta": 0.0905,
"ldsc_observed_scale_h2_se": 0.0069,
"ldsc_intercept_beta": 0.9902,
"ldsc_intercept_se": 0.0101,
"ldsc_lambda_gc": 1.2365,
"ldsc_mean_chisq": 1.3137,
"ldsc_ratio": -0.0312
}
name | value |
---|---|
af_correlation | FALSE |
inflation_factor | TRUE |
n | FALSE |
is_snpid_non_unique | FALSE |
mean_EFFECT_nonfinite | FALSE |
mean_EFFECT_05 | FALSE |
mean_EFFECT_01 | FALSE |
mean_chisq | TRUE |
n_p_sig | TRUE |
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
(\(2 \times N \times MAF\)) 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 | 0 | 1.000000 | 3 | 57 | 0 | 6412174 | 0 | NA | NA | NA | NA | NA | NA | NA | NA |
character | REF | 0 | 1.000000 | 1 | 1 | 0 | 4 | 0 | NA | NA | NA | NA | NA | NA | NA | NA |
character | ALT | 0 | 1.000000 | 1 | 1 | 0 | 4 | 0 | NA | NA | NA | NA | NA | NA | NA | NA |
numeric | CHROM | 0 | 1.000000 | NA | NA | NA | NA | NA | 8.697242e+00 | 5.777413e+00 | 1.00000e+00 | 4.000000e+00 | 8.000000e+00 | 1.300000e+01 | 2.300000e+01 | ▇▅▅▂▂ |
numeric | POS | 0 | 1.000000 | NA | NA | NA | NA | NA | 7.860856e+07 | 5.661204e+07 | 8.28000e+02 | 3.198241e+07 | 6.909664e+07 | 1.146070e+08 | 2.492205e+08 | ▇▆▅▂▁ |
numeric | EFFECT | 0 | 1.000000 | NA | NA | NA | NA | NA | 2.940000e-05 | 6.514800e-03 | -6.30000e-02 | -4.000000e-03 | 0.000000e+00 | 4.000000e-03 | 8.500000e-02 | ▁▃▇▁▁ |
numeric | SE | 0 | 1.000000 | NA | NA | NA | NA | NA | 5.480600e-03 | 2.431700e-03 | 3.00000e-03 | 4.000000e-03 | 4.000000e-03 | 6.000000e-03 | 2.100000e-02 | ▇▂▁▁▁ |
numeric | PVAL | 0 | 1.000000 | NA | NA | NA | NA | NA | 4.669281e-01 | 2.977737e-01 | 0.00000e+00 | 2.004001e-01 | 4.559004e-01 | 7.245994e-01 | 1.000000e+00 | ▇▆▆▆▆ |
numeric | PVAL_ztest | 0 | 1.000000 | NA | NA | NA | NA | NA | 4.701350e-01 | 3.020695e-01 | 0.00000e+00 | 2.112995e-01 | 4.532547e-01 | 7.388827e-01 | 1.000000e+00 | ▇▆▆▆▇ |
numeric | AF | 0 | 1.000000 | NA | NA | NA | NA | NA | 3.052619e-01 | 2.541503e-01 | 1.11900e-02 | 9.142000e-02 | 2.220000e-01 | 4.701000e-01 | 9.888100e-01 | ▇▃▂▂▁ |
numeric | AF_reference | 39877 | 0.993781 | NA | NA | NA | NA | NA | 3.043005e-01 | 2.479503e-01 | 1.99700e-04 | 1.002400e-01 | 2.322280e-01 | 4.644570e-01 | 1.000000e+00 | ▇▅▂▂▁ |
numeric | N | 0 | 1.000000 | NA | NA | NA | NA | NA | 1.709110e+05 | 0.000000e+00 | 1.70911e+05 | 1.709110e+05 | 1.709110e+05 | 1.709110e+05 | 1.709110e+05 | ▁▁▇▁▁ |
CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
---|---|---|---|---|---|---|---|---|---|---|---|
1 | 662622 | rs61769339 | G | A | 0.005 | 0.007 | 0.4862001 | 0.4750505 | 0.09515 | 0.1475640 | 170911 |
1 | 704637 | rs142559957 | G | A | -0.004 | 0.010 | 0.7120000 | 0.6891565 | 0.04851 | 0.0473243 | 170911 |
1 | 705882 | rs72631875 | G | A | -0.004 | 0.008 | 0.5761002 | 0.6170751 | 0.08209 | 0.0315495 | 170911 |
1 | 714019 | rs114983708 | A | G | -0.009 | 0.010 | 0.3730001 | 0.3681203 | 0.04664 | 0.1383790 | 170911 |
1 | 714427 | rs12028261 | G | A | 0.009 | 0.018 | 0.6211007 | 0.6170751 | 0.98507 | 0.7727640 | 170911 |
1 | 715367 | rs12184277 | A | G | -0.006 | 0.010 | 0.5605005 | 0.5485062 | 0.04664 | 0.0281550 | 170911 |
1 | 719914 | rs187772768 | C | G | -0.006 | 0.010 | 0.5350003 | 0.5485062 | 0.04851 | 0.0277556 | 170911 |
1 | 720381 | rs116801199 | G | T | -0.007 | 0.011 | 0.5018998 | 0.5245394 | 0.04291 | 0.0359425 | 170911 |
1 | 721290 | rs12565286 | G | C | -0.006 | 0.010 | 0.5619996 | 0.5485062 | 0.04664 | 0.0371406 | 170911 |
1 | 721757 | rs189147642 | T | A | -0.007 | 0.010 | 0.5143006 | 0.4839273 | 0.04851 | 0.0281550 | 170911 |
CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
---|---|---|---|---|---|---|---|---|---|---|---|
22 | 51219387 | rs9616832 | T | C | 0.005 | 0.008 | 0.5184000 | 0.5319711 | 0.07463 | 0.0654952 | 170911 |
22 | 51219704 | rs147475742 | G | A | 0.007 | 0.010 | 0.4763005 | 0.4839273 | 0.04851 | 0.0473243 | 170911 |
22 | 51221731 | rs115055839 | T | C | 0.006 | 0.008 | 0.4431003 | 0.4532547 | 0.07836 | 0.0625000 | 170911 |
22 | 51222052 | rs2879915 | G | A | 0.003 | 0.005 | 0.5064004 | 0.5485062 | 0.21640 | 0.2194490 | 170911 |
22 | 51224600 | rs187908482 | G | A | 0.000 | 0.007 | 0.9458000 | 1.0000000 | 0.09515 | 0.0387380 | 170911 |
22 | 51227891 | rs6010091 | G | A | 0.004 | 0.004 | 0.2817001 | 0.3173105 | 0.34700 | 0.4039540 | 170911 |
22 | 51229805 | rs9616985 | T | C | 0.002 | 0.008 | 0.8245999 | 0.8025873 | 0.07836 | 0.0730831 | 170911 |
22 | 51229855 | rs144549712 | G | A | -0.006 | 0.006 | 0.2791997 | 0.3173105 | 0.13250 | 0.1160140 | 170911 |
22 | 51237063 | rs3896457 | T | C | 0.005 | 0.005 | 0.2703000 | 0.3173105 | 0.23320 | 0.2050720 | 170911 |
23 | 100784211 | rs188350543 | C | A | -0.005 | 0.004 | 0.2263002 | 0.2112995 | 0.72200 | 0.6498010 | 170911 |
1 662622 rs61769339 G A . PASS AF=0.09515 ES:SE:LP:AF:SS:ID 0.005:0.007:0.313185:0.09515:170911:rs61769339
1 704637 rs142559957 G A . PASS AF=0.04851 ES:SE:LP:AF:SS:ID -0.004:0.01:0.14752:0.04851:170911:rs142559957
1 705882 rs72631875 G A . PASS AF=0.08209 ES:SE:LP:AF:SS:ID -0.004:0.008:0.239502:0.08209:170911:rs72631875
1 714019 rs114983708 A G . PASS AF=0.04664 ES:SE:LP:AF:SS:ID -0.009:0.01:0.428291:0.04664:170911:rs114983708
1 714427 rs12028261 G A . PASS AF=0.98507 ES:SE:LP:AF:SS:ID 0.009:0.018:0.206838:0.98507:170911:rs12028261
1 715367 rs12184277 A G . PASS AF=0.04664 ES:SE:LP:AF:SS:ID -0.006:0.01:0.251424:0.04664:170911:rs12184277
1 719914 rs187772768 C G . PASS AF=0.04851 ES:SE:LP:AF:SS:ID -0.006:0.01:0.271646:0.04851:170911:rs187772768
1 720381 rs116801199 G T . PASS AF=0.04291 ES:SE:LP:AF:SS:ID -0.007:0.011:0.299383:0.04291:170911:rs116801199
1 721290 rs12565286 G C . PASS AF=0.04664 ES:SE:LP:AF:SS:ID -0.006:0.01:0.250264:0.04664:170911:rs12565286
1 721757 rs189147642 T A . PASS AF=0.04851 ES:SE:LP:AF:SS:ID -0.007:0.01:0.288783:0.04851:170911:rs189147642
1 722670 rs116030099 T C . PASS AF=0.1082 ES:SE:LP:AF:SS:ID 0.005:0.007:0.313096:0.1082:170911:rs116030099
1 723307 rs28659788 C G . PASS AF=0.04104 ES:SE:LP:AF:SS:ID -0.007:0.011:0.299383:0.04104:170911:rs28659788
1 723742 rs28375378 T C . PASS AF=0.03918 ES:SE:LP:AF:SS:ID -0.008:0.011:0.339324:0.03918:170911:rs28375378
1 723819 rs11804171 T A . PASS AF=0.04851 ES:SE:LP:AF:SS:ID -0.005:0.01:0.19071:0.04851:170911:rs11804171
1 723891 rs2977670 G C . PASS AF=0.9459 ES:SE:LP:AF:SS:ID 0.005:0.009:0.221559:0.9459:170911:rs2977670
1 726794 rs28454925 C G . PASS AF=0.04851 ES:SE:LP:AF:SS:ID -0.007:0.01:0.334888:0.04851:170911:rs28454925
1 727841 rs116587930 G A . PASS AF=0.06157 ES:SE:LP:AF:SS:ID 0.009:0.009:0.4642:0.06157:170911:rs116587930
1 729679 rs4951859 C G . PASS AF=0.8489 ES:SE:LP:AF:SS:ID 0.001:0.006:0.0614302:0.8489:170911:rs4951859
1 730087 rs148120343 T C . PASS AF=0.06157 ES:SE:LP:AF:SS:ID 0.008:0.009:0.438779:0.06157:170911:rs148120343
1 732809 rs12131618 T C . PASS AF=0.05224 ES:SE:LP:AF:SS:ID -0.007:0.01:0.327995:0.05224:170911:rs12131618
1 734349 rs141242758 T C . PASS AF=0.1045 ES:SE:LP:AF:SS:ID 0.002:0.007:0.105075:0.1045:170911:rs141242758
1 735985 rs12405651 G A . PASS AF=0.03358 ES:SE:LP:AF:SS:ID -0.005:0.012:0.157953:0.03358:170911:rs12405651
1 736289 rs79010578 T A . PASS AF=0.1269 ES:SE:LP:AF:SS:ID -0.003:0.006:0.223662:0.1269:170911:rs79010578
1 736736 rs10454457 A G . PASS AF=0.03918 ES:SE:LP:AF:SS:ID -0.007:0.011:0.284414:0.03918:170911:rs10454457
1 739528 rs3094317 G A . PASS AF=0.91791 ES:SE:LP:AF:SS:ID 0.005:0.008:0.267606:0.91791:170911:rs3094317
1 746727 rs144595511 G A . PASS AF=0.04478 ES:SE:LP:AF:SS:ID -0.007:0.01:0.30777:0.04478:170911:rs144595511
1 748141 rs2427893 G A . PASS AF=0.01679 ES:SE:LP:AF:SS:ID -0.007:0.017:0.183494:0.01679:170911:rs2427893
1 752478 rs146277091 G A . PASS AF=0.04104 ES:SE:LP:AF:SS:ID -0.004:0.011:0.140561:0.04104:170911:rs146277091
1 752566 rs3094315 G A . PASS AF=0.8451 ES:SE:LP:AF:SS:ID 0.002:0.005:0.137392:0.8451:170911:rs3094315
1 752617 rs149886465 C A . PASS AF=0.04478 ES:SE:LP:AF:SS:ID -0.005:0.01:0.204537:0.04478:170911:rs149886465
1 752721 rs3131972 A G . PASS AF=0.8414 ES:SE:LP:AF:SS:ID 0.002:0.005:0.188358:0.8414:170911:rs3131972
1 752894 rs3131971 T C . PASS AF=0.8228 ES:SE:LP:AF:SS:ID 0.001:0.005:0.0479344:0.8228:170911:rs3131971
1 753474 rs2073814 C G . PASS AF=0.8358 ES:SE:LP:AF:SS:ID 0:0.005:0.0180003:0.8358:170911:rs2073814
1 753541 rs2073813 G A . PASS AF=0.1213 ES:SE:LP:AF:SS:ID 0.001:0.007:0.045661:0.1213:170911:rs2073813
1 754063 rs12184312 G T . PASS AF=0.05037 ES:SE:LP:AF:SS:ID -0.005:0.01:0.189364:0.05037:170911:rs12184312
1 754105 rs12184325 C T . PASS AF=0.05037 ES:SE:LP:AF:SS:ID 0:0.01:0.0169152:0.05037:170911:rs12184325
1 754182 rs3131969 A G . PASS AF=0.8787 ES:SE:LP:AF:SS:ID -0.001:0.006:0.0397195:0.8787:170911:rs3131969
1 754192 rs3131968 A G . PASS AF=0.8787 ES:SE:LP:AF:SS:ID -0.001:0.006:0.0316105:0.8787:170911:rs3131968
1 754334 rs3131967 T C . PASS AF=0.8638 ES:SE:LP:AF:SS:ID -0.001:0.006:0.0387213:0.8638:170911:rs3131967
1 754503 rs3115859 G A . PASS AF=0.8414 ES:SE:LP:AF:SS:ID 0.001:0.005:0.0478374:0.8414:170911:rs3115859
1 754964 rs3131966 C T . PASS AF=0.8302 ES:SE:LP:AF:SS:ID 0:0.005:0.0198602:0.8302:170911:rs3131966
1 755890 rs3115858 A T . PASS AF=0.8713 ES:SE:LP:AF:SS:ID -0.001:0.006:0.0656026:0.8713:170911:rs3115858
1 756604 rs3131962 A G . PASS AF=0.8451 ES:SE:LP:AF:SS:ID -0.001:0.005:0.0344691:0.8451:170911:rs3131962
1 756912 rs6699990 A G . PASS AF=0.02612 ES:SE:LP:AF:SS:ID -0.009:0.014:0.286678:0.02612:170911:rs6699990
1 757640 rs3115853 G A . PASS AF=0.8787 ES:SE:LP:AF:SS:ID 0:0.006:0.0177288:0.8787:170911:rs3115853
1 757734 rs4951929 C T . PASS AF=0.8787 ES:SE:LP:AF:SS:ID -0.001:0.006:0.0457092:0.8787:170911:rs4951929
1 757936 rs4951862 C A . PASS AF=0.8769 ES:SE:LP:AF:SS:ID -0.001:0.006:0.0474982:0.8769:170911:rs4951862
1 758048 rs3131957 A G . PASS AF=0.1343 ES:SE:LP:AF:SS:ID -0.005:0.006:0.370794:0.1343:170911:rs3131957
1 758144 rs3131956 A G . PASS AF=0.8489 ES:SE:LP:AF:SS:ID 0:0.005:0.0283995:0.8489:170911:rs3131956
1 758626 rs3131954 C T . PASS AF=0.8731 ES:SE:LP:AF:SS:ID -0.001:0.006:0.0441199:0.8731:170911:rs3131954