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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-1103/ieu-a-1103.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-1103/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 19:03:55 2020
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ieu-a-import/processed/ieu-a-1103/ieu-a-1103.vcf.gz ...
Read summary statistics for 2194720 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, 1069753 SNPs remain.
After merging with regression SNP LD, 1069753 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.0766 (0.04)
Lambda GC: 1.0253
Mean Chi^2: 1.0228
Intercept: 1.0045 (0.0069)
Ratio: 0.1984 (0.3034)
Analysis finished at Tue Feb 4 19:04:23 2020
Total time elapsed: 27.76s
{
"af_correlation": 0.9014,
"inflation_factor": 1,
"mean_EFFECT": 0,
"n": 11529,
"n_snps": 2194720,
"n_clumped_hits": 1,
"n_p_sig": 3,
"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": 668,
"n_miss_AF_reference": 18448,
"n_est": 10971.0565,
"ratio_se_n": 0.9755,
"mean_diff": 0.0001,
"ratio_diff": 6.8247,
"sd_y_est1": 0.2793,
"sd_y_est2": 0.2724,
"r2_sum1": 0.0002,
"r2_sum2": 0.0029,
"r2_sum3": 0.0031,
"r2_sum4": 0.0026,
"ldsc_nsnp_merge_refpanel_ld": 1069753,
"ldsc_nsnp_merge_regression_ld": 1069753,
"ldsc_observed_scale_h2_beta": 0.0766,
"ldsc_observed_scale_h2_se": 0.04,
"ldsc_intercept_beta": 1.0045,
"ldsc_intercept_se": 0.0069,
"ldsc_lambda_gc": 1.0253,
"ldsc_mean_chisq": 1.0228,
"ldsc_ratio": 0.1974
}
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
(\(2 \times N \times MAF\)) 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 | 1.0000000 | 3 | 42 | 0 | 2194720 | 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 | 8.601764e+00 | 5.664268e+00 | 1.0000e+00 | 4.000000e+00 | 8.000000e+00 | 1.200000e+01 | 2.300000e+01 | ▇▅▅▂▂ |
numeric | POS | 0 | 1.0000000 | NA | NA | NA | NA | NA | 7.872516e+07 | 5.573563e+07 | 1.1523e+04 | 3.243693e+07 | 7.008059e+07 | 1.143594e+08 | 2.492107e+08 | ▇▆▅▂▁ |
numeric | EFFECT | 0 | 1.0000000 | NA | NA | NA | NA | NA | 3.000000e-05 | 5.047500e-03 | -7.6000e-02 | -3.100000e-03 | 0.000000e+00 | 3.100000e-03 | 6.500000e-02 | ▁▁▇▁▁ |
numeric | SE | 0 | 1.0000000 | NA | NA | NA | NA | NA | 4.789800e-03 | 1.461100e-03 | 3.5000e-03 | 3.800000e-03 | 4.300000e-03 | 5.400000e-03 | 5.700000e-02 | ▇▁▁▁▁ |
numeric | PVAL | 0 | 1.0000000 | NA | NA | NA | NA | NA | 4.974853e-01 | 2.892685e-01 | 0.0000e+00 | 2.500000e-01 | 5.000000e-01 | 7.499995e-01 | 1.000000e+00 | ▇▇▇▇▇ |
numeric | PVAL_ztest | 0 | 1.0000000 | NA | NA | NA | NA | NA | 4.965064e-01 | 2.895362e-01 | 0.0000e+00 | 2.449144e-01 | 4.953539e-01 | 7.456925e-01 | 1.000000e+00 | ▇▇▇▇▇ |
numeric | AF | 668 | 0.9996956 | NA | NA | NA | NA | NA | 3.805996e-01 | 2.568901e-01 | 4.0000e-03 | 1.590000e-01 | 3.240000e-01 | 5.740000e-01 | 9.960000e-01 | ▇▆▅▃▂ |
numeric | AF_reference | 18448 | 0.9915944 | NA | NA | NA | NA | NA | 3.804243e-01 | 2.429695e-01 | 1.9970e-04 | 1.769170e-01 | 3.288740e-01 | 5.593050e-01 | 1.000000e+00 | ▇▇▅▃▂ |
numeric | N | 0 | 1.0000000 | NA | NA | NA | NA | NA | 1.138784e+04 | 4.594501e+02 | 3.9830e+03 | 1.147700e+04 | 1.152000e+04 | 1.152200e+04 | 1.152900e+04 | ▁▁▁▁▇ |
CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
---|---|---|---|---|---|---|---|---|---|---|---|
1 | 723819 | rs11804171 | T | A | 0.0110 | 0.0130 | 0.4199997 | 0.3974669 | 0.034 | 0.1345850 | 7442 |
1 | 723891 | rs2977670 | G | C | -0.0110 | 0.0140 | 0.4400003 | 0.4320349 | 0.934 | 0.7799520 | 7183 |
1 | 750235 | rs12138618 | G | A | -0.0064 | 0.0190 | 0.7300002 | 0.7362359 | 0.062 | NA | 7550 |
1 | 752566 | rs3094315 | G | A | 0.0016 | 0.0065 | 0.8100000 | 0.8055631 | 0.835 | 0.7182510 | 8547 |
1 | 754192 | rs3131968 | A | G | 0.0037 | 0.0076 | 0.6300007 | 0.6263702 | 0.885 | 0.6785140 | 8288 |
1 | 768448 | rs12562034 | G | A | -0.0050 | 0.0110 | 0.6499995 | 0.6494363 | 0.102 | 0.1918930 | 7701 |
1 | 775659 | rs2905035 | A | G | 0.0034 | 0.0076 | 0.6600001 | 0.6546091 | 0.885 | 0.7450080 | 8447 |
1 | 776546 | rs12124819 | A | G | 0.0098 | 0.0093 | 0.2900000 | 0.2919912 | 0.288 | 0.0756789 | 7780 |
1 | 777122 | rs2980319 | A | T | 0.0069 | 0.0063 | 0.2700001 | 0.2734123 | 0.866 | 0.7472040 | 10834 |
1 | 779322 | rs4040617 | A | G | -0.0037 | 0.0076 | 0.6200004 | 0.6263702 | 0.133 | 0.2264380 | 7924 |
CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
---|---|---|---|---|---|---|---|---|---|---|---|
22 | 51212875 | rs2238837 | A | C | -0.0010 | 0.0045 | 0.8300000 | 0.8241409 | 0.385 | 0.3724040 | 10973 |
22 | 51216564 | rs9616970 | T | C | 0.0097 | 0.0072 | 0.1800002 | 0.1779087 | 0.146 | 0.1563500 | 10548 |
22 | 51217134 | rs117417021 | A | G | -0.0012 | 0.0056 | 0.8400000 | 0.8303243 | 0.415 | 0.2671730 | 8261 |
22 | 51222100 | rs114553188 | G | T | 0.0130 | 0.0110 | 0.2399999 | 0.2372779 | 0.062 | 0.0880591 | 7899 |
22 | 51223637 | rs375798137 | G | A | 0.0120 | 0.0110 | 0.2800000 | 0.2753129 | 0.062 | 0.0788738 | 7684 |
22 | 51229805 | rs9616985 | T | C | -0.0015 | 0.0120 | 0.9000000 | 0.9005236 | 0.092 | 0.0730831 | 6948 |
23 | 35921591 | rs2204667 | C | G | -0.0092 | 0.0051 | 0.0749998 | 0.0712436 | 0.162 | NA | 11136 |
23 | 51666786 | rs14115 | A | G | -0.0160 | 0.0076 | 0.0350002 | 0.0352684 | 0.027 | NA | 11528 |
23 | 70163799 | rs1626496 | A | C | 0.0026 | 0.0068 | 0.6999999 | 0.7021996 | 0.069 | NA | 11521 |
23 | 118495837 | rs12882977 | G | A | -0.0056 | 0.0040 | 0.1600000 | 0.1615133 | 0.508 | 0.2307280 | 9234 |
1 723819 rs11804171 T A . PASS AF=0.034 ES:SE:LP:AF:SS:ID 0.011:0.013:0.376751:0.034:7442:rs11804171
1 723891 rs2977670 G C . PASS AF=0.934 ES:SE:LP:AF:SS:ID -0.011:0.014:0.356547:0.934:7183:rs2977670
1 750235 rs12138618 G A . PASS AF=0.062 ES:SE:LP:AF:SS:ID -0.0064:0.019:0.136677:0.062:7550:rs12138618
1 752566 rs3094315 G A . PASS AF=0.835 ES:SE:LP:AF:SS:ID 0.0016:0.0065:0.091515:0.835:8547:rs3094315
1 754192 rs3131968 A G . PASS AF=0.885 ES:SE:LP:AF:SS:ID 0.0037:0.0076:0.200659:0.885:8288:rs3131968
1 768448 rs12562034 G A . PASS AF=0.102 ES:SE:LP:AF:SS:ID -0.005:0.011:0.187087:0.102:7701:rs12562034
1 775659 rs2905035 A G . PASS AF=0.885 ES:SE:LP:AF:SS:ID 0.0034:0.0076:0.180456:0.885:8447:rs2905035
1 776546 rs12124819 A G . PASS AF=0.288 ES:SE:LP:AF:SS:ID 0.0098:0.0093:0.537602:0.288:7780:rs12124819
1 777122 rs2980319 A T . PASS AF=0.866 ES:SE:LP:AF:SS:ID 0.0069:0.0063:0.568636:0.866:10834:rs2980319
1 779322 rs4040617 A G . PASS AF=0.133 ES:SE:LP:AF:SS:ID -0.0037:0.0076:0.207608:0.133:7924:rs4040617
1 780785 rs2977612 T A . PASS AF=0.877 ES:SE:LP:AF:SS:ID 0.0031:0.0076:0.161151:0.877:8447:rs2977612
1 785050 rs2905062 G A . PASS AF=0.868 ES:SE:LP:AF:SS:ID 0.0051:0.0076:0.29243:0.868:8547:rs2905062
1 785989 rs2980300 T C . PASS AF=0.868 ES:SE:LP:AF:SS:ID 0.0093:0.006:0.920819:0.868:10834:rs2980300
1 798026 rs4951864 C T . PASS AF=0.9 ES:SE:LP:AF:SS:ID 0.0051:0.012:0.180456:0.9:8122:rs4951864
1 798801 rs12132517 G A . PASS AF=0.108 ES:SE:LP:AF:SS:ID -0.0069:0.012:0.259637:0.108:8022:rs12132517
1 798959 rs11240777 G A . PASS AF=0.219 ES:SE:LP:AF:SS:ID -0.009:0.0057:0.920819:0.219:10790:rs11240777
1 846864 rs950122 G C . PASS AF=0.138 ES:SE:LP:AF:SS:ID 0.0059:0.013:0.180456:0.138:7098:rs950122
1 882033 rs2272756 G A . PASS AF=0.23 ES:SE:LP:AF:SS:ID -0.0074:0.011:0.30103:0.23:7875:rs2272756
1 962210 rs3128126 A G . PASS AF=0.415 ES:SE:LP:AF:SS:ID -0.0072:0.0073:0.481486:0.415:8191:rs3128126
1 990380 rs3121561 C T . PASS AF=0.254 ES:SE:LP:AF:SS:ID -0.0002:0.0057:0.0132283:0.254:10864:rs3121561
1 998501 rs3813193 G C . PASS AF=0.146 ES:SE:LP:AF:SS:ID -0.0059:0.0079:0.337242:0.146:8984:rs3813193
1 1003629 rs4075116 C T . PASS AF=0.734 ES:SE:LP:AF:SS:ID 0.0038:0.0048:0.376751:0.734:11315:rs4075116
1 1005806 rs3934834 C T . PASS AF=0.124 ES:SE:LP:AF:SS:ID -0.0081:0.0067:0.638272:0.124:11276:rs3934834
1 1017170 rs3766193 C G . PASS AF=0.587 ES:SE:LP:AF:SS:ID 0.0087:0.0042:1.42022:0.587:11271:rs3766193
1 1017197 rs3766192 C T . PASS AF=0.571 ES:SE:LP:AF:SS:ID 0.0079:0.004:1.31876:0.571:11271:rs3766192
1 1017587 rs3766191 C T . PASS AF=0.124 ES:SE:LP:AF:SS:ID -0.0073:0.0069:0.537602:0.124:11271:rs3766191
1 1018562 rs9442371 C T . PASS AF=0.608 ES:SE:LP:AF:SS:ID 0.0074:0.0039:1.20761:0.608:11271:rs9442371
1 1018704 rs9442372 A G . PASS AF=0.588 ES:SE:LP:AF:SS:ID 0.0067:0.0039:1.08092:0.588:11271:rs9442372
1 1021346 rs10907177 A G . PASS AF=0.137 ES:SE:LP:AF:SS:ID -0.0059:0.0068:0.420216:0.137:11271:rs10907177
1 1021415 rs3737728 A G . PASS AF=0.735 ES:SE:LP:AF:SS:ID 0.0083:0.0047:1.13077:0.735:11322:rs3737728
1 1021583 rs10907178 A C . PASS AF=0.112 ES:SE:LP:AF:SS:ID -0.0081:0.0078:0.522879:0.112:8620:rs10907178
1 1021695 rs9442398 A G . PASS AF=0.726 ES:SE:LP:AF:SS:ID 0.0086:0.0048:1.13077:0.726:11315:rs9442398
1 1022037 rs6701114 C T . PASS AF=0.585 ES:SE:LP:AF:SS:ID 0.0097:0.0043:1.58503:0.585:11271:rs6701114
1 1025301 rs9442400 T C . PASS AF=0.952 ES:SE:LP:AF:SS:ID 0.013:0.02:0.30103:0.952:7730:rs9442400
1 1026707 rs4074137 C A . PASS AF=0.623 ES:SE:LP:AF:SS:ID 0.0068:0.0053:0.69897:0.623:8620:rs4074137
1 1030565 rs6687776 C T . PASS AF=0.133 ES:SE:LP:AF:SS:ID -0.0018:0.0061:0.119186:0.133:11278:rs6687776
1 1030633 rs6678318 G A . PASS AF=0.134 ES:SE:LP:AF:SS:ID -0.0017:0.0061:0.107905:0.134:11012:rs6678318
1 1031540 rs9651273 A G . PASS AF=0.717 ES:SE:LP:AF:SS:ID 0.0087:0.0049:1.14267:0.717:10913:rs9651273
1 1036959 rs11579015 T C . PASS AF=0.046 ES:SE:LP:AF:SS:ID -0.002:0.0068:0.113509:0.046:11271:rs11579015
1 1040026 rs6671356 T C . PASS AF=0.115 ES:SE:LP:AF:SS:ID -0.0041:0.0063:0.283997:0.115:11271:rs6671356
1 1046164 rs6666280 C T . PASS AF=0.062 ES:SE:LP:AF:SS:ID -0.0038:0.0064:0.251812:0.062:11270:rs6666280
1 1048955 rs4970405 A G . PASS AF=0.088 ES:SE:LP:AF:SS:ID -0.0049:0.0063:0.356547:0.088:11277:rs4970405
1 1049950 rs12726255 A G . PASS AF=0.115 ES:SE:LP:AF:SS:ID -0.004:0.0062:0.283997:0.115:11277:rs12726255
1 1053452 rs4970409 G A . PASS AF=0.093 ES:SE:LP:AF:SS:ID -0.0041:0.0069:0.259637:0.093:11171:rs4970409
1 1060174 rs7548798 C T . PASS AF=0.314 ES:SE:LP:AF:SS:ID -0.012:0.0065:1.20066:0.314:7738:rs7548798
1 1060608 rs17160824 G A . PASS AF=0.097 ES:SE:LP:AF:SS:ID -0.003:0.0069:0.180456:0.097:11271:rs17160824
1 1061115 rs17160826 T C . PASS AF=0.051 ES:SE:LP:AF:SS:ID -0.0009:0.0071:0.0457575:0.051:11271:rs17160826
1 1061152 rs12748370 T C . PASS AF=0.055 ES:SE:LP:AF:SS:ID 0.0002:0.0072:0.0132283:0.055:11171:rs12748370
1 1061166 rs11807848 T C . PASS AF=0.389 ES:SE:LP:AF:SS:ID -0.0059:0.0049:0.638272:0.389:10907:rs11807848
1 1062638 rs9442373 C A . PASS AF=0.575 ES:SE:LP:AF:SS:ID 0.0038:0.0048:0.366532:0.575:10907:rs9442373