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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-1065/ieu-a-1065.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-1065/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 10:47:10 2020
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ieu-a-import/processed/ieu-a-1065/ieu-a-1065.vcf.gz ...
Read summary statistics for 2399807 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, 1141285 SNPs remain.
After merging with regression SNP LD, 1141285 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: -0.1138 (0.1723)
Lambda GC: 0.9817
Mean Chi^2: 0.9858
Intercept: 0.9918 (0.0065)
Ratio: NA (mean chi^2 < 1)
Analysis finished at Tue Feb 4 10:47:42 2020
Total time elapsed: 31.36s
{
"af_correlation": 0.9207,
"inflation_factor": 0.9824,
"mean_EFFECT": -0.0001,
"n": 2645,
"n_snps": 2399807,
"n_clumped_hits": 0,
"n_p_sig": 0,
"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": 20188,
"n_est": 2561.2608,
"ratio_se_n": 0.984,
"mean_diff": 0,
"ratio_diff": 1.0045,
"sd_y_est1": 1.0179,
"sd_y_est2": 1.0016,
"r2_sum1": 0,
"r2_sum2": 0,
"r2_sum3": 0,
"r2_sum4": 0,
"ldsc_nsnp_merge_refpanel_ld": 1141285,
"ldsc_nsnp_merge_regression_ld": 1141285,
"ldsc_observed_scale_h2_beta": "NA",
"ldsc_observed_scale_h2_se": "NA",
"ldsc_intercept_beta": 0.9918,
"ldsc_intercept_se": 0.0065,
"ldsc_lambda_gc": 0.9817,
"ldsc_mean_chisq": 0.9858,
"ldsc_ratio": 0.5775
}
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
(\(2 \times N \times MAF\)) 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 | 2399807 | 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 | 8.595156e+00 | 5.661989e+00 | 1.0000e+00 | 4.000000e+00 | 8.000000e+00 | 1.200000e+01 | 2.30000e+01 | ▇▅▅▂▂ |
numeric | POS | 0 | 1.0000000 | NA | NA | NA | NA | NA | 7.877922e+07 | 5.567137e+07 | 1.1523e+04 | 3.263012e+07 | 7.015307e+07 | 1.142824e+08 | 2.49219e+08 | ▇▆▅▂▁ |
numeric | EFFECT | 0 | 1.0000000 | NA | NA | NA | NA | NA | -1.375000e-04 | 4.802350e-02 | -3.3870e+00 | -2.490000e-02 | -1.000000e-04 | 2.450000e-02 | 2.16500e+00 | ▁▁▁▇▁ |
numeric | SE | 0 | 1.0000000 | NA | NA | NA | NA | NA | 4.194210e-02 | 2.408480e-02 | 2.6300e-02 | 2.890000e-02 | 3.380000e-02 | 4.530000e-02 | 9.88100e-01 | ▇▁▁▁▁ |
numeric | PVAL | 0 | 1.0000000 | NA | NA | NA | NA | NA | 5.029465e-01 | 2.885811e-01 | 7.0000e-07 | 2.534002e-01 | 5.037998e-01 | 7.536002e-01 | 1.00000e+00 | ▇▇▇▇▇ |
numeric | PVAL_ztest | 0 | 1.0000000 | NA | NA | NA | NA | NA | 5.029467e-01 | 2.885821e-01 | 7.0000e-07 | 2.533333e-01 | 5.036794e-01 | 7.536208e-01 | 1.00000e+00 | ▇▇▇▇▇ |
numeric | AF | 0 | 1.0000000 | NA | NA | NA | NA | NA | 3.633291e-01 | 2.711903e-01 | 1.0060e-02 | 1.285000e-01 | 2.999000e-01 | 5.624500e-01 | 9.89940e-01 | ▇▅▃▃▂ |
numeric | AF_reference | 20188 | 0.9915877 | NA | NA | NA | NA | NA | 3.650602e-01 | 2.532621e-01 | 1.9970e-04 | 1.523560e-01 | 3.051120e-01 | 5.485220e-01 | 1.00000e+00 | ▇▆▅▃▂ |
numeric | N | 0 | 1.0000000 | NA | NA | NA | NA | NA | 2.645000e+03 | 0.000000e+00 | 2.6450e+03 | 2.645000e+03 | 2.645000e+03 | 2.645000e+03 | 2.64500e+03 | ▁▁▇▁▁ |
CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
---|---|---|---|---|---|---|---|---|---|---|---|
1 | 721290 | rs12565286 | G | C | -0.2304 | 0.1170 | 0.0490004 | 0.0489266 | 0.03048 | 0.0371406 | 2645 |
1 | 723819 | rs11804171 | T | A | -0.2363 | 0.1162 | 0.0419199 | 0.0419957 | 0.03048 | 0.1345850 | 2645 |
1 | 723891 | rs2977670 | G | C | 0.2304 | 0.1146 | 0.0443905 | 0.0443813 | 0.96924 | 0.7799520 | 2645 |
1 | 750235 | rs12138618 | G | A | -0.1229 | 0.0819 | 0.1333000 | 0.1334563 | 0.08166 | NA | 2645 |
1 | 752566 | rs3094315 | G | A | -0.0897 | 0.0547 | 0.1012999 | 0.1010356 | 0.79180 | 0.7182510 | 2645 |
1 | 754192 | rs3131968 | A | G | -0.1293 | 0.0575 | 0.0243899 | 0.0245319 | 0.81280 | 0.6785140 | 2645 |
1 | 768448 | rs12562034 | G | A | -0.0243 | 0.0629 | 0.6989997 | 0.6992541 | 0.11050 | 0.1918930 | 2645 |
1 | 775659 | rs2905035 | A | G | -0.1388 | 0.0578 | 0.0164502 | 0.0163332 | 0.81280 | 0.7450080 | 2645 |
1 | 777122 | rs2980319 | A | T | -0.1315 | 0.0579 | 0.0232001 | 0.0231375 | 0.81280 | 0.7472040 | 2645 |
1 | 779322 | rs4040617 | A | G | 0.1315 | 0.0579 | 0.0232001 | 0.0231375 | 0.18720 | 0.2264380 | 2645 |
CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
---|---|---|---|---|---|---|---|---|---|---|---|
22 | 51212875 | rs2238837 | A | C | 0.0086 | 0.0420 | 0.8372000 | 0.8377582 | 0.40970 | 0.3724040 | 2645 |
22 | 51216564 | rs9616970 | T | C | 0.0187 | 0.0462 | 0.6856998 | 0.6856525 | 0.13400 | 0.1563500 | 2645 |
22 | 51217134 | rs117417021 | A | G | 0.0086 | 0.0418 | 0.8363000 | 0.8369927 | 0.48450 | 0.2671730 | 2645 |
22 | 51222100 | rs114553188 | G | T | 0.0187 | 0.0644 | 0.7718999 | 0.7715311 | 0.07936 | 0.0880591 | 2645 |
22 | 51223637 | rs375798137 | G | A | 0.0187 | 0.0644 | 0.7718999 | 0.7715311 | 0.07936 | 0.0788738 | 2645 |
22 | 51229805 | rs9616985 | T | C | 0.0051 | 0.0607 | 0.9331000 | 0.9330407 | 0.05405 | 0.0730831 | 2645 |
23 | 35921591 | rs2204667 | C | G | 0.0206 | 0.0362 | 0.5699005 | 0.5693149 | 0.15410 | NA | 2645 |
23 | 51666786 | rs14115 | A | G | 0.0044 | 0.0687 | 0.9488001 | 0.9489331 | 0.06200 | NA | 2645 |
23 | 70163799 | rs1626496 | A | C | -0.0671 | 0.0530 | 0.2057998 | 0.2054996 | 0.03939 | NA | 2645 |
23 | 118495837 | rs12882977 | G | A | -0.0021 | 0.0278 | 0.9392000 | 0.9397854 | 0.42180 | 0.2307280 | 2645 |
1 721290 rs12565286 G C . PASS AF=0.03048 ES:SE:LP:AF:SS:ID -0.2304:0.117:1.3098:0.03048:2645:rs12565286
1 723819 rs11804171 T A . PASS AF=0.03048 ES:SE:LP:AF:SS:ID -0.2363:0.1162:1.37758:0.03048:2645:rs11804171
1 723891 rs2977670 G C . PASS AF=0.96924 ES:SE:LP:AF:SS:ID 0.2304:0.1146:1.35271:0.96924:2645:rs2977670
1 750235 rs12138618 G A . PASS AF=0.08166 ES:SE:LP:AF:SS:ID -0.1229:0.0819:0.87517:0.08166:2645:rs12138618
1 752566 rs3094315 G A . PASS AF=0.7918 ES:SE:LP:AF:SS:ID -0.0897:0.0547:0.994391:0.7918:2645:rs3094315
1 754192 rs3131968 A G . PASS AF=0.8128 ES:SE:LP:AF:SS:ID -0.1293:0.0575:1.61279:0.8128:2645:rs3131968
1 768448 rs12562034 G A . PASS AF=0.1105 ES:SE:LP:AF:SS:ID -0.0243:0.0629:0.155523:0.1105:2645:rs12562034
1 775659 rs2905035 A G . PASS AF=0.8128 ES:SE:LP:AF:SS:ID -0.1388:0.0578:1.78383:0.8128:2645:rs2905035
1 777122 rs2980319 A T . PASS AF=0.8128 ES:SE:LP:AF:SS:ID -0.1315:0.0579:1.63451:0.8128:2645:rs2980319
1 779322 rs4040617 A G . PASS AF=0.1872 ES:SE:LP:AF:SS:ID 0.1315:0.0579:1.63451:0.1872:2645:rs4040617
1 780785 rs2977612 T A . PASS AF=0.8128 ES:SE:LP:AF:SS:ID -0.1315:0.0579:1.63451:0.8128:2645:rs2977612
1 785050 rs2905062 G A . PASS AF=0.8131 ES:SE:LP:AF:SS:ID -0.1315:0.0579:1.63451:0.8131:2645:rs2905062
1 798026 rs4951864 C T . PASS AF=0.8899 ES:SE:LP:AF:SS:ID 0.0195:0.0659:0.115091:0.8899:2645:rs4951864
1 798801 rs12132517 G A . PASS AF=0.1104 ES:SE:LP:AF:SS:ID -0.0279:0.0656:0.173472:0.1104:2645:rs12132517
1 798959 rs11240777 G A . PASS AF=0.2142 ES:SE:LP:AF:SS:ID 0.0626:0.0544:0.602755:0.2142:2645:rs11240777
1 962210 rs3128126 A G . PASS AF=0.4612 ES:SE:LP:AF:SS:ID 0.0055:0.0434:0.0465786:0.4612:2645:rs3128126
1 990380 rs3121561 C T . PASS AF=0.2895 ES:SE:LP:AF:SS:ID 0.0744:0.0482:0.911155:0.2895:2645:rs3121561
1 998501 rs3813193 G C . PASS AF=0.2294 ES:SE:LP:AF:SS:ID 0.0075:0.0396:0.0708877:0.2294:2645:rs3813193
1 1003629 rs4075116 C T . PASS AF=0.7401 ES:SE:LP:AF:SS:ID -0.0044:0.0313:0.0516849:0.7401:2645:rs4075116
1 1005806 rs3934834 C T . PASS AF=0.2293 ES:SE:LP:AF:SS:ID 0.0083:0.0397:0.0785737:0.2293:2645:rs3934834
1 1017170 rs3766193 C G . PASS AF=0.5155 ES:SE:LP:AF:SS:ID -0.0368:0.0388:0.46382:0.5155:2645:rs3766193
1 1017197 rs3766192 C T . PASS AF=0.5106 ES:SE:LP:AF:SS:ID -0.0382:0.0384:0.494714:0.5106:2645:rs3766192
1 1017587 rs3766191 C T . PASS AF=0.2174 ES:SE:LP:AF:SS:ID 0.0175:0.0418:0.170503:0.2174:2645:rs3766191
1 1018562 rs9442371 C T . PASS AF=0.5106 ES:SE:LP:AF:SS:ID -0.0162:0.0283:0.246723:0.5106:2645:rs9442371
1 1018704 rs9442372 A G . PASS AF=0.5104 ES:SE:LP:AF:SS:ID -0.0162:0.0283:0.246723:0.5104:2645:rs9442372
1 1021346 rs10907177 A G . PASS AF=0.2168 ES:SE:LP:AF:SS:ID 0.0153:0.0414:0.147764:0.2168:2645:rs10907177
1 1021415 rs3737728 A G . PASS AF=0.7174 ES:SE:LP:AF:SS:ID -0.0006:0.031:0.00621119:0.7174:2645:rs3737728
1 1021583 rs10907178 A C . PASS AF=0.2168 ES:SE:LP:AF:SS:ID 0.0153:0.0414:0.147764:0.2168:2645:rs10907178
1 1021695 rs9442398 A G . PASS AF=0.7424 ES:SE:LP:AF:SS:ID 0.0022:0.0311:0.025166:0.7424:2645:rs9442398
1 1022037 rs6701114 C T . PASS AF=0.4994 ES:SE:LP:AF:SS:ID -0.0139:0.028:0.208309:0.4994:2645:rs6701114
1 1025301 rs9442400 T C . PASS AF=0.98189 ES:SE:LP:AF:SS:ID -0.1194:0.1503:0.369572:0.98189:2645:rs9442400
1 1026707 rs4074137 C A . PASS AF=0.6052 ES:SE:LP:AF:SS:ID -0.0054:0.0283:0.0716554:0.6052:2645:rs4074137
1 1030565 rs6687776 C T . PASS AF=0.1886 ES:SE:LP:AF:SS:ID -0.0171:0.0379:0.185686:0.1886:2645:rs6687776
1 1030633 rs6678318 G A . PASS AF=0.1857 ES:SE:LP:AF:SS:ID -0.0171:0.0379:0.185686:0.1857:2645:rs6678318
1 1031540 rs9651273 A G . PASS AF=0.7296 ES:SE:LP:AF:SS:ID -0.0227:0.0315:0.326426:0.7296:2645:rs9651273
1 1036959 rs11579015 T C . PASS AF=0.0529 ES:SE:LP:AF:SS:ID -0.0363:0.0455:0.370692:0.0529:2645:rs11579015
1 1040026 rs6671356 T C . PASS AF=0.09919 ES:SE:LP:AF:SS:ID -0.0266:0.0406:0.290052:0.09919:2645:rs6671356
1 1046164 rs6666280 C T . PASS AF=0.09919 ES:SE:LP:AF:SS:ID -0.0274:0.0402:0.304869:0.09919:2645:rs6666280
1 1048955 rs4970405 A G . PASS AF=0.05322 ES:SE:LP:AF:SS:ID -0.028:0.0452:0.270673:0.05322:2645:rs4970405
1 1049950 rs12726255 A G . PASS AF=0.1112 ES:SE:LP:AF:SS:ID -0.0325:0.0401:0.378824:0.1112:2645:rs12726255
1 1053452 rs4970409 G A . PASS AF=0.06613 ES:SE:LP:AF:SS:ID -0.0312:0.0449:0.312739:0.06613:2645:rs4970409
1 1060174 rs7548798 C T . PASS AF=0.3258 ES:SE:LP:AF:SS:ID 0.0247:0.0298:0.39126:0.3258:2645:rs7548798
1 1060235 rs7540009 G A . PASS AF=0.04543 ES:SE:LP:AF:SS:ID -0.0311:0.0839:0.148008:0.04543:2645:rs7540009
1 1060608 rs17160824 G A . PASS AF=0.06642 ES:SE:LP:AF:SS:ID -0.0336:0.0448:0.343614:0.06642:2645:rs17160824
1 1061115 rs17160826 T C . PASS AF=0.06642 ES:SE:LP:AF:SS:ID -0.0369:0.0451:0.38384:0.06642:2645:rs17160826
1 1061152 rs12748370 T C . PASS AF=0.06642 ES:SE:LP:AF:SS:ID -0.038:0.0452:0.398483:0.06642:2645:rs12748370
1 1061166 rs11807848 T C . PASS AF=0.3921 ES:SE:LP:AF:SS:ID 0.0092:0.0284:0.127145:0.3921:2645:rs11807848
1 1062015 rs9659914 C T . PASS AF=0.04457 ES:SE:LP:AF:SS:ID -0.023:0.0856:0.103198:0.04457:2645:rs9659914
1 1062638 rs9442373 C A . PASS AF=0.5233 ES:SE:LP:AF:SS:ID 0.0082:0.0279:0.113735:0.5233:2645:rs9442373
1 1064535 rs6682475 G C . PASS AF=0.7884 ES:SE:LP:AF:SS:ID 0.0426:0.0349:0.653061:0.7884:2645:rs6682475