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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-61/ieu-a-61.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-61/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 11:16:38 2020
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ieu-a-import/processed/ieu-a-61/ieu-a-61.vcf.gz ...
Read summary statistics for 2532663 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, 1173396 SNPs remain.
After merging with regression SNP LD, 1173396 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.1323 (0.0061)
Lambda GC: 1.0353
Mean Chi^2: 1.1409
Intercept: 0.7611 (0.0066)
Ratio < 0 (usually indicates GC correction).
Analysis finished at Wed Feb 5 11:17:08 2020
Total time elapsed: 30.28s
{
"af_correlation": 0.9179,
"inflation_factor": 1.0475,
"mean_EFFECT": 0.0001,
"n": 232101,
"n_snps": 2532663,
"n_clumped_hits": 42,
"n_p_sig": 947,
"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": 44998,
"n_miss_AF_reference": 22355,
"n_est": 226402.0554,
"ratio_se_n": 0.9876,
"mean_diff": -0,
"ratio_diff": 6.7026,
"sd_y_est1": 1.4941,
"sd_y_est2": 1.4756,
"r2_sum1": 0.0144,
"r2_sum2": 0.0065,
"r2_sum3": 0.0066,
"r2_sum4": 0.0107,
"ldsc_nsnp_merge_refpanel_ld": 1173396,
"ldsc_nsnp_merge_regression_ld": 1173396,
"ldsc_observed_scale_h2_beta": 0.1323,
"ldsc_observed_scale_h2_se": 0.0061,
"ldsc_intercept_beta": 0.7611,
"ldsc_intercept_se": 0.0066,
"ldsc_lambda_gc": 1.0353,
"ldsc_mean_chisq": 1.1409,
"ldsc_ratio": -1.6955
}
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 | 2532663 | 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 | 8.595275e+00 | 5.662851e+00 | 1.0000 | 4.000000e+00 | 8.000000e+00 | 1.200000e+01 | 2.30000e+01 | ▇▅▅▂▂ |
numeric | POS | 0 | 1.0000000 | NA | NA | NA | NA | NA | 7.880942e+07 | 5.566636e+07 | 11523.0000 | 3.266337e+07 | 7.020579e+07 | 1.142403e+08 | 2.49219e+08 | ▇▆▅▂▁ |
numeric | EFFECT | 0 | 1.0000000 | NA | NA | NA | NA | NA | 5.790000e-05 | 9.300300e-03 | -0.2300 | -4.200000e-03 | 0.000000e+00 | 4.200000e-03 | 2.50000e-01 | ▁▁▇▁▁ |
numeric | SE | 0 | 1.0000000 | NA | NA | NA | NA | NA | 7.468300e-03 | 6.385000e-03 | 0.0033 | 4.600000e-03 | 5.400000e-03 | 7.600000e-03 | 1.40000e-01 | ▇▁▁▁▁ |
numeric | PVAL | 0 | 1.0000000 | NA | NA | NA | NA | NA | 4.930485e-01 | 2.929950e-01 | 0.0000 | 2.399999e-01 | 4.899999e-01 | 7.499995e-01 | 1.00000e+00 | ▇▇▇▇▇ |
numeric | PVAL_ztest | 0 | 1.0000000 | NA | NA | NA | NA | NA | 4.929952e-01 | 2.929508e-01 | 0.0000 | 2.372779e-01 | 4.932271e-01 | 7.470129e-01 | 1.00000e+00 | ▇▇▇▇▇ |
numeric | AF | 44998 | 0.9822329 | NA | NA | NA | NA | NA | 3.551792e-01 | 2.764967e-01 | 0.0083 | 1.167000e-01 | 2.917000e-01 | 5.583000e-01 | 9.91700e-01 | ▇▅▃▂▂ |
numeric | AF_reference | 22355 | 0.9911733 | NA | NA | NA | NA | NA | 3.599256e-01 | 2.573037e-01 | 0.0000 | 1.433710e-01 | 2.969250e-01 | 5.453270e-01 | 1.00000e+00 | ▇▆▃▃▂ |
numeric | N | 0 | 1.0000000 | NA | NA | NA | NA | NA | 1.485824e+05 | 2.290490e+04 | 50003.0000 | 1.435790e+05 | 1.537770e+05 | 1.539240e+05 | 2.32101e+05 | ▁▁▇▁▁ |
CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
---|---|---|---|---|---|---|---|---|---|---|---|
1 | 721290 | rs12565286 | G | C | 0.0021 | 0.0160 | 0.9000000 | 0.8955775 | 0.06780 | 0.0371406 | 75902 |
1 | 723819 | rs11804171 | T | A | 0.0140 | 0.0200 | 0.4899999 | 0.4839273 | 0.03704 | 0.1345850 | 57209 |
1 | 752566 | rs3094315 | G | A | -0.0012 | 0.0077 | 0.8800001 | 0.8761559 | 0.84480 | 0.7182510 | 83973 |
1 | 754192 | rs3131968 | A | G | -0.0069 | 0.0100 | 0.5099998 | 0.4901942 | 0.87500 | 0.6785140 | 61521 |
1 | 768448 | rs12562034 | G | A | -0.0060 | 0.0130 | 0.6400000 | 0.6444123 | 0.09167 | 0.1918930 | 57610 |
1 | 775659 | rs2905035 | A | G | -0.0012 | 0.0083 | 0.8900000 | 0.8850438 | 0.87500 | 0.7450080 | 95427 |
1 | 777122 | rs2980319 | A | T | -0.0013 | 0.0083 | 0.8800001 | 0.8755392 | 0.87500 | 0.7472040 | 95429 |
1 | 779322 | rs4040617 | A | G | 0.0039 | 0.0090 | 0.6600001 | 0.6647726 | 0.12500 | 0.2264380 | 83587 |
1 | 780785 | rs2977612 | T | A | -0.0050 | 0.0090 | 0.5800000 | 0.5785147 | 0.86610 | 0.6693290 | 83687 |
1 | 785050 | rs2905062 | G | A | -0.0046 | 0.0066 | 0.4899999 | 0.4858218 | NA | 0.6269970 | 131640 |
CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
---|---|---|---|---|---|---|---|---|---|---|---|
22 | 51217134 | rs117417021 | A | G | 0.0091 | 0.0077 | 0.2399999 | 0.2372779 | 0.441700 | 0.2671730 | 90723 |
22 | 51222100 | rs114553188 | G | T | -0.0150 | 0.0130 | 0.2200002 | 0.2485632 | 0.066700 | 0.0880591 | 119050 |
22 | 51223637 | rs375798137 | G | A | -0.0150 | 0.0130 | 0.2200002 | 0.2485632 | 0.066700 | 0.0788738 | 119048 |
22 | 51229805 | rs9616985 | T | C | 0.0140 | 0.0150 | 0.3500000 | 0.3506479 | 0.091700 | 0.0730831 | 85329 |
23 | 35921591 | rs2204667 | C | G | 0.0010 | 0.0059 | 0.8700001 | 0.8654100 | 0.166700 | NA | 153879 |
23 | 51666786 | rs14115 | A | G | 0.0140 | 0.0097 | 0.1499999 | 0.1489363 | 0.025000 | NA | 141866 |
23 | 70163799 | rs1626496 | A | C | -0.0026 | 0.0085 | 0.7600007 | 0.7596942 | 0.075000 | NA | 153769 |
23 | 74963352 | rs1053838 | T | G | -0.0420 | 0.0640 | 0.5199996 | 0.5116633 | 0.991379 | NA | 54959 |
23 | 91415872 | rs6562597 | G | A | -0.0110 | 0.0170 | 0.4899999 | 0.5175939 | 0.008300 | 0.0021192 | 135297 |
23 | 118495837 | rs12882977 | G | A | -0.0007 | 0.0043 | 0.8700001 | 0.8706832 | 0.516700 | 0.2307280 | 153927 |
1 721290 rs12565286 G C . PASS AF=0.0678 ES:SE:LP:AF:SS:ID 0.0021:0.016:0.0457575:0.0678:75902:rs12565286
1 723819 rs11804171 T A . PASS AF=0.03704 ES:SE:LP:AF:SS:ID 0.014:0.02:0.309804:0.03704:57209:rs11804171
1 752566 rs3094315 G A . PASS AF=0.8448 ES:SE:LP:AF:SS:ID -0.0012:0.0077:0.0555173:0.8448:83973:rs3094315
1 754192 rs3131968 A G . PASS AF=0.875 ES:SE:LP:AF:SS:ID -0.0069:0.01:0.29243:0.875:61521:rs3131968
1 768448 rs12562034 G A . PASS AF=0.09167 ES:SE:LP:AF:SS:ID -0.006:0.013:0.19382:0.09167:57610:rs12562034
1 775659 rs2905035 A G . PASS AF=0.875 ES:SE:LP:AF:SS:ID -0.0012:0.0083:0.05061:0.875:95427:rs2905035
1 777122 rs2980319 A T . PASS AF=0.875 ES:SE:LP:AF:SS:ID -0.0013:0.0083:0.0555173:0.875:95429:rs2980319
1 779322 rs4040617 A G . PASS AF=0.125 ES:SE:LP:AF:SS:ID 0.0039:0.009:0.180456:0.125:83587:rs4040617
1 780785 rs2977612 T A . PASS AF=0.8661 ES:SE:LP:AF:SS:ID -0.005:0.009:0.236572:0.8661:83687:rs2977612
1 785050 rs2905062 G A . PASS . ES:SE:LP:SS:ID -0.0046:0.0066:0.309804:131640:rs2905062
1 785989 rs2980300 T C . PASS AF=0.8729 ES:SE:LP:AF:SS:ID -0.005:0.009:0.236572:0.8729:83587:rs2980300
1 798026 rs4951864 C T . PASS AF=0.9 ES:SE:LP:AF:SS:ID 0.0029:0.015:0.0705811:0.9:50146:rs4951864
1 798801 rs12132517 G A . PASS AF=0.1083 ES:SE:LP:AF:SS:ID -0.0067:0.015:0.180456:0.1083:50067:rs12132517
1 798959 rs11240777 G A . PASS AF=0.1667 ES:SE:LP:AF:SS:ID 0.002:0.009:0.0861861:0.1667:76647:rs11240777
1 962210 rs3128126 A G . PASS AF=0.425 ES:SE:LP:AF:SS:ID -0.0048:0.0093:0.21467:0.425:60944:rs3128126
1 990380 rs3121561 C T . PASS AF=0.2667 ES:SE:LP:AF:SS:ID -0.003:0.0076:0.161151:0.2667:109323:rs3121561
1 998501 rs3813193 G C . PASS AF=0.15 ES:SE:LP:AF:SS:ID 0.0026:0.0077:0.130768:0.15:101681:rs3813193
1 1003629 rs4075116 C T . PASS AF=0.7373 ES:SE:LP:AF:SS:ID 0.0045:0.0055:0.387216:0.7373:148028:rs4075116
1 1005806 rs3934834 C T . PASS AF=0.1167 ES:SE:LP:AF:SS:ID 0.0042:0.0071:0.259637:0.1167:113607:rs3934834
1 1017170 rs3766193 C G . PASS AF=0.5667 ES:SE:LP:AF:SS:ID 0.0035:0.0052:0.30103:0.5667:149534:rs3766193
1 1017197 rs3766192 C T . PASS AF=0.5763 ES:SE:LP:AF:SS:ID 0.0042:0.0048:0.420216:0.5763:150197:rs3766192
1 1017587 rs3766191 C T . PASS AF=0.09649 ES:SE:LP:AF:SS:ID 0.0039:0.0073:0.229148:0.09649:113439:rs3766191
1 1018562 rs9442371 C T . PASS AF=0.5917 ES:SE:LP:AF:SS:ID 0.0033:0.0048:0.309804:0.5917:150278:rs9442371
1 1018704 rs9442372 A G . PASS AF=0.6017 ES:SE:LP:AF:SS:ID 0.0033:0.0048:0.309804:0.6017:150260:rs9442372
1 1021346 rs10907177 A G . PASS AF=0.1271 ES:SE:LP:AF:SS:ID 0.0047:0.0074:0.275724:0.1271:113395:rs10907177
1 1021415 rs3737728 A G . PASS AF=0.7167 ES:SE:LP:AF:SS:ID 0.0058:0.0052:0.585027:0.7167:150869:rs3737728
1 1021583 rs10907178 A C . PASS . ES:SE:LP:SS:ID 0.0045:0.0074:0.267606:111190:rs10907178
1 1021695 rs9442398 A G . PASS AF=0.725 ES:SE:LP:AF:SS:ID 0.0056:0.0053:0.537602:0.725:150618:rs9442398
1 1022037 rs6701114 C T . PASS AF=0.5667 ES:SE:LP:AF:SS:ID 0.0031:0.0053:0.251812:0.5667:138137:rs6701114
1 1026707 rs4074137 C A . PASS AF=0.6 ES:SE:LP:AF:SS:ID -0.002:0.0058:0.136677:0.6:111416:rs4074137
1 1030565 rs6687776 C T . PASS AF=0.08333 ES:SE:LP:AF:SS:ID 0.0063:0.0068:0.455932:0.08333:114783:rs6687776
1 1030633 rs6678318 G A . PASS AF=0.08621 ES:SE:LP:AF:SS:ID 0.004:0.0076:0.221849:0.08621:100316:rs6678318
1 1031540 rs9651273 A G . PASS AF=0.6583 ES:SE:LP:AF:SS:ID -0.0001:0.0059:0.00436481:0.6583:111353:rs9651273
1 1036959 rs11579015 T C . PASS AF=0.05 ES:SE:LP:AF:SS:ID 0.0064:0.0081:0.366532:0.05:132784:rs11579015
1 1040026 rs6671356 T C . PASS AF=0.075 ES:SE:LP:AF:SS:ID 0.0057:0.0073:0.366532:0.075:122872:rs6671356
1 1046164 rs6666280 C T . PASS AF=0.06667 ES:SE:LP:AF:SS:ID 0.0071:0.0076:0.455932:0.06667:129134:rs6666280
1 1048955 rs4970405 A G . PASS AF=0.05172 ES:SE:LP:AF:SS:ID 0.006:0.0081:0.337242:0.05172:132694:rs4970405
1 1049950 rs12726255 A G . PASS AF=0.06667 ES:SE:LP:AF:SS:ID 0.0063:0.0075:0.39794:0.06667:129130:rs12726255
1 1053452 rs4970409 G A . PASS AF=0.05 ES:SE:LP:AF:SS:ID 0.0064:0.0085:0.346787:0.05:130536:rs4970409
1 1060174 rs7548798 C T . PASS AF=0.3981 ES:SE:LP:AF:SS:ID -0.0009:0.0073:0.0457575:0.3981:84660:rs7548798
1 1060235 rs7540009 G A . PASS AF=0.01667 ES:SE:LP:AF:SS:ID -0.0001:0.016:0.00436481:0.01667:104928:rs7540009
1 1060608 rs17160824 G A . PASS AF=0.05833 ES:SE:LP:AF:SS:ID 0.0059:0.0085:0.309804:0.05833:132644:rs17160824
1 1061115 rs17160826 T C . PASS AF=0.05455 ES:SE:LP:AF:SS:ID 0.0071:0.0085:0.39794:0.05455:132658:rs17160826
1 1061152 rs12748370 T C . PASS . ES:SE:LP:SS:ID 0.0073:0.0086:0.39794:130454:rs12748370
1 1061166 rs11807848 T C . PASS AF=0.4123 ES:SE:LP:AF:SS:ID 0.0019:0.0059:0.124939:0.4123:109740:rs11807848
1 1062015 rs9659914 C T . PASS AF=0.01667 ES:SE:LP:AF:SS:ID 0.0056:0.017:0.124939:0.01667:93183:rs9659914
1 1062638 rs9442373 C A . PASS AF=0.5517 ES:SE:LP:AF:SS:ID 0.0005:0.0058:0.0315171:0.5517:108942:rs9442373
1 1064535 rs6682475 G C . PASS AF=0.7542 ES:SE:LP:AF:SS:ID -0.012:0.0086:0.744727:0.7542:84942:rs6682475
1 1064979 rs2298217 C T . PASS AF=0.08333 ES:SE:LP:AF:SS:ID 0.0051:0.0076:0.30103:0.08333:103039:rs2298217
1 1066403 rs10907182 T C . PASS AF=0.675 ES:SE:LP:AF:SS:ID -0.0003:0.0061:0.0177288:0.675:106305:rs10907182