Summary
Summary {data-width=650}
Manhattan plot
manhattan_plot
QQ plot
qq_plot
AF plot
af_plot
P-Z plot
pz_plot
beta_std plot
beta_std_plot
Metadata
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"gwas_harmonisation_command": "--out /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/ukbiobank/vcf_09_19b/bgzip_vcf/data.batch_3476.vcf.gz --id UKB-b:1572 --data /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/ukbiobank/raw-output/data.batch_3476.txt.gz --cohort_controls 33404 --ref /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/ukbiobank/human_g1k_v37.fasta --json /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/ukbiobank/ukb_gwas.json; 1.1.1",
"file_date": "2019-09-13T03:44:17.712871",
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}
LDSC
*********************************************************************
* 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/public/UKB-b-1572/UKB-b-1572_data.vcf.gz \
--ref-ld-chr ../reference/eur_w_ld_chr/ \
--out /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-1572/ldsc.txt \
--w-ld-chr ../reference/eur_w_ld_chr/
Beginning analysis at Thu Oct 17 14:44:18 2019
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-1572/UKB-b-1572_data.vcf.gz ...
Read summary statistics for 7668545 SNPs.
Dropped 5482 SNPs with duplicated rs numbers.
Reading reference panel LD Score from ../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 ../reference/eur_w_ld_chr/[1-22] ...
Read regression weight LD Scores for 1290028 SNPs.
After merging with reference panel LD, 1278925 SNPs remain.
After merging with regression SNP LD, 1278925 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.0874 (0.0146)
Lambda GC: 1.0473
Mean Chi^2: 1.0609
Intercept: 1.0034 (0.0056)
Ratio: 0.0563 (0.0923)
Analysis finished at Thu Oct 17 14:45:44 2019
Total time elapsed: 1.0m:26.37sQC metrics
Metrics
Metrics
{
"af_correlation": 0.9411,
"inflation_factor": 1.0475,
"mean_EFFECT": 4.9093e-06,
"n": "-Inf",
"n_snps": 9851866,
"n_clumped_hits": 3,
"n_p_sig": 365,
"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": 71329,
"n_est": "NA",
"ratio_se_n": "NA",
"mean_diff": "NaN",
"ratio_diff": "NaN",
"sd_y_est1": "NaN",
"sd_y_est2": "NA",
"r2_sum1": 0,
"r2_sum2": 0,
"r2_sum3": 0,
"r2_sum4": 0,
"ldsc_nsnp_merge_refpanel_ld": 1278925,
"ldsc_nsnp_merge_regression_ld": 1278925,
"ldsc_observed_scale_h2_beta": 0.0874,
"ldsc_observed_scale_h2_se": 0.0146,
"ldsc_intercept_beta": 1.0034,
"ldsc_intercept_se": 0.0056,
"ldsc_lambda_gc": 1.0473,
"ldsc_mean_chisq": 1.0609,
"ldsc_ratio": 0.0558
}
Flags
| 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 | FALSE |
| ldsc_intercept_beta | FALSE |
| n_clumped_hits | FALSE |
| r2_sum1 | FALSE |
| r2_sum2 | FALSE |
| r2_sum3 | FALSE |
| r2_sum4 | FALSE |
Definitions
General metrics
af_correlation: Correlation coefficient betweenAFandAF_reference.inflation_factor(lambda): Genomic inflation factor.mean_EFFECT: Mean ofEFFECTsize.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 below5e-8.n_mono: Number of monomorphic (MAF == 1orMAF == 0) SNPs.n_ns: Number of SNPs with nonsense values:- alleles other than
A, C, G or T. - P-values
< 0or> 1. - negative or infinite standard errors (
<= 0or= Infinity). - infinite beta estimates or allele frequencies
< 0or> 1.
- alleles other than
n_mac: Number of cases whereMAC(\(2 \times N \times MAF\)) is less than6.is_snpid_unique:trueif the combination ofIDREFALTis unique and therefore no duplication in snpid.n_miss_<*>: Number ofNAobservations 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 expectratio_se_nto 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.- \(\widehat{\beta_j^{std}} = \sqrt{\frac{{z}_j^2 / ({z}_j^2 + n -2)}{2 \times {MAF}_j \times (1 - {MAF}_j)}} \times sign({z}_j)\),
- \({z}_j = \frac{\beta_j}{{se}_j}\),
- and \(\beta_j\) is the reported effect size.
ratio_diff: \(\texttt{ratio_diff} = |\frac{\texttt{mean_diff}}{\texttt{mean_diff2}}|\), absolute ratio between the mean ofdiffand the mean ofdiff2(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.- \(\texttt{mean_diff2} = \sum_{j} \frac{\widehat{\beta_j^{std}} - \beta^{\prime}_j}{\texttt{n_snps}}\)
- \(\beta^{\prime}_j = \frac{\beta_j}{\widehat{\texttt{sd2}}_{y}}\)
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.- \(\widehat{\texttt{sd1}}_{y} = \frac{\sqrt{n} \times median({se}_j)}{C}\),
- \(C = median(\frac{1}{\sqrt{2 \times {MAF}_j \times (1 - {MAF}_j)}})\),
- and \({se}_j\) is the reported standard error.
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.- \(\widehat{\texttt{sd2}}_{y} = median(\widehat{sd_j})\),
- \(\widehat{sd_j} = \frac{\beta_j}{\widehat{\beta_j^{std}}}\),
r2 metrics
Sum of variance explained, calculated from the clumped top hits sample.
r2_sum<*>:r2statistics under various assumptions1: \(r^2 = \sum_j{\frac{2 \times \beta_j^2 \times {MAF}_j \times (1 - {MAF}_j)}{\texttt{var1}}}\), \(\texttt{var1} = 1\).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: NOTis_snpid_unique.mean_EFFECT_nonfinite:mean(EFFECT)isNA,NaN, orInf.mean_EFFECT_05:abs(mean(EFFECT))> 0.5.mean_EFFECT_01:abs(mean(EFFECT))> 0.1.mean_chisq:ldsc_mean_chisq> 1.3 orldsc_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<*>> 0.5
Plots
- Manhattan plot
- Red line: \(-log_{10}^{5 \times 10^{-8}}\)
- Blue line: \(-log_{10}^{5 \times 10^{-5}}\)
- QQ plot
- AF plot
- P-Z plot
- beta_std plot: Scatter plot between \(\widehat{\beta_j^{std}}\) and \(\beta_j\)
Diagnostics
Details
Summary stats
| skim_type | skim_variable | n_missing | complete_rate | character.min | character.max | character.empty | character.n_unique | character.whitespace | logical.mean | logical.count | numeric.mean | numeric.sd | numeric.p0 | numeric.p25 | numeric.p50 | numeric.p75 | numeric.p100 | numeric.hist |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| character | ID | 0 | 1.0000000 | 3 | 58 | 0 | 7663088 | 0 | NA | NA | 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 | NA | NA |
| character | ALT | 0 | 1.0000000 | 1 | 1 | 0 | 4 | 0 | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| logical | N | 7668545 | 0.0000000 | NA | NA | NA | NA | NA | NaN | : | NA | NA | NA | NA | NA | NA | NA | NA |
| numeric | CHROM | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 8.662080e+00 | 5.764540e+00 | 1.0000000 | 4.000000e+00 | 8.000000e+00 | 1.300000e+01 | 2.200000e+01 | ▇▅▅▂▂ |
| numeric | POS | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 7.867515e+07 | 5.644109e+07 | 828.0000000 | 3.219784e+07 | 6.912058e+07 | 1.145663e+08 | 2.492385e+08 | ▇▆▅▂▁ |
| numeric | EFFECT | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 4.900000e-06 | 1.600020e-02 | -0.1470600 | -7.807500e-03 | 1.110000e-05 | 7.823100e-03 | 1.603950e-01 | ▁▁▇▁▁ |
| numeric | SE | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 1.381560e-02 | 7.699100e-03 | 0.0066932 | 7.726000e-03 | 1.046770e-02 | 1.791910e-02 | 8.249310e-02 | ▇▂▁▁▁ |
| numeric | PVAL | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 4.935229e-01 | 2.908503e-01 | 0.0000000 | 2.399999e-01 | 4.899999e-01 | 7.499995e-01 | 1.000000e+00 | ▇▇▇▇▇ |
| numeric | PVAL_ztest | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 4.935238e-01 | 2.908242e-01 | 0.0000000 | 2.395634e-01 | 4.921778e-01 | 7.454784e-01 | 1.000000e+00 | ▇▇▇▇▇ |
| numeric | AF | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 2.550398e-01 | 2.608230e-01 | 0.0104780 | 4.229100e-02 | 1.501220e-01 | 4.030200e-01 | 9.895220e-01 | ▇▂▂▁▁ |
| numeric | AF_reference | 71329 | 0.9906985 | NA | NA | NA | NA | NA | NA | NA | 2.540621e-01 | 2.526870e-01 | 0.0000000 | 4.632590e-02 | 1.643370e-01 | 3.975640e-01 | 1.000000e+00 | ▇▃▂▁▁ |
Head and tail
| CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 | 49298 | rs200943160 | T | C | 0.0116427 | 0.0123831 | 0.3500000 | 0.3471105 | 0.622084 | 0.7821490 | NA |
| 1 | 54676 | rs2462492 | C | T | 0.0032682 | 0.0122622 | 0.7899998 | 0.7898307 | 0.399547 | NA | NA |
| 1 | 86028 | rs114608975 | T | C | -0.0410413 | 0.0196913 | 0.0369999 | 0.0371388 | 0.103497 | 0.0277556 | NA |
| 1 | 91536 | rs6702460 | G | T | 0.0143843 | 0.0121204 | 0.2399999 | 0.2353127 | 0.455921 | 0.4207270 | NA |
| 1 | 234313 | rs8179466 | C | T | 0.0088237 | 0.0239966 | 0.7099994 | 0.7130926 | 0.073938 | NA | NA |
| 1 | 534192 | rs6680723 | C | T | -0.0181302 | 0.0136688 | 0.1800002 | 0.1847096 | 0.243799 | NA | NA |
| 1 | 546697 | rs12025928 | A | G | -0.0121326 | 0.0174848 | 0.4899999 | 0.4877486 | 0.914848 | NA | NA |
| 1 | 693731 | rs12238997 | A | G | 0.0007118 | 0.0115329 | 0.9500000 | 0.9507868 | 0.116399 | 0.1417730 | NA |
| 1 | 705882 | rs72631875 | G | A | 0.0015272 | 0.0171240 | 0.9299999 | 0.9289346 | 0.066321 | 0.0315495 | NA |
| 1 | 706368 | rs55727773 | A | G | -0.0055569 | 0.0085718 | 0.5199996 | 0.5168089 | 0.512890 | 0.2751600 | NA |
| CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 22 | 51219006 | rs28729663 | G | A | 0.0086327 | 0.0104385 | 0.4100001 | 0.4082327 | 0.135596 | 0.2052720 | NA |
| 22 | 51219387 | rs9616832 | T | C | 0.0235557 | 0.0135437 | 0.0819993 | 0.0819931 | 0.071977 | 0.0654952 | NA |
| 22 | 51219704 | rs147475742 | G | A | 0.0279439 | 0.0181587 | 0.1199999 | 0.1238357 | 0.040905 | 0.0473243 | NA |
| 22 | 51221190 | rs369304721 | G | A | 0.0260980 | 0.0181576 | 0.1499999 | 0.1506315 | 0.048348 | NA | NA |
| 22 | 51221731 | rs115055839 | T | C | 0.0228834 | 0.0135512 | 0.0909997 | 0.0912842 | 0.071560 | 0.0625000 | NA |
| 22 | 51222100 | rs114553188 | G | T | -0.0142150 | 0.0159446 | 0.3700002 | 0.3726479 | 0.053891 | 0.0880591 | NA |
| 22 | 51223637 | rs375798137 | G | A | -0.0141043 | 0.0160153 | 0.3800004 | 0.3784929 | 0.053513 | 0.0788738 | NA |
| 22 | 51229805 | rs9616985 | T | C | 0.0225924 | 0.0135845 | 0.0959997 | 0.0962922 | 0.071460 | 0.0730831 | NA |
| 22 | 51232488 | rs376461333 | A | G | -0.0462991 | 0.0325603 | 0.1600000 | 0.1550409 | 0.019329 | NA | NA |
| 22 | 51237063 | rs3896457 | T | C | 0.0000854 | 0.0082299 | 0.9900000 | 0.9917243 | 0.297355 | 0.2050720 | NA |
bcf preview
1 49298 rs10399793 T C . PASS AF=0.622084 ES:SE:LP:AF:ID 0.0116427:0.0123831:0.455932:0.622084:rs10399793
1 54676 rs2462492 C T . PASS AF=0.399547 ES:SE:LP:AF:ID 0.00326825:0.0122622:0.102373:0.399547:rs2462492
1 86028 rs114608975 T C . PASS AF=0.103497 ES:SE:LP:AF:ID -0.0410413:0.0196913:1.4318:0.103497:rs114608975
1 91536 rs6702460 G T . PASS AF=0.455921 ES:SE:LP:AF:ID 0.0143843:0.0121204:0.619789:0.455921:rs6702460
1 234313 rs8179466 C T . PASS AF=0.073938 ES:SE:LP:AF:ID 0.00882369:0.0239966:0.148742:0.073938:rs8179466
1 534192 rs6680723 C T . PASS AF=0.243799 ES:SE:LP:AF:ID -0.0181302:0.0136688:0.744727:0.243799:rs6680723
1 546697 rs12025928 A G . PASS AF=0.914848 ES:SE:LP:AF:ID -0.0121326:0.0174848:0.309804:0.914848:rs12025928
1 693731 rs12238997 A G . PASS AF=0.116399 ES:SE:LP:AF:ID 0.000711796:0.0115329:0.0222764:0.116399:rs12238997
1 705882 rs72631875 G A . PASS AF=0.066321 ES:SE:LP:AF:ID 0.00152721:0.017124:0.0315171:0.066321:rs72631875
1 706368 rs12029736 A G . PASS AF=0.51289 ES:SE:LP:AF:ID -0.00555686:0.0085718:0.283997:0.51289:rs12029736
1 714596 rs149887893 T C . PASS AF=0.033183 ES:SE:LP:AF:ID 0.0177429:0.0215454:0.387216:0.033183:rs149887893
1 715265 rs12184267 C T . PASS AF=0.036827 ES:SE:LP:AF:ID 0.0202258:0.0195502:0.522879:0.036827:rs12184267
1 715367 rs12184277 A G . PASS AF=0.036896 ES:SE:LP:AF:ID 0.0199021:0.0194937:0.508638:0.036896:rs12184277
1 717485 rs12184279 C A . PASS AF=0.03663 ES:SE:LP:AF:ID 0.0176934:0.0196155:0.431798:0.03663:rs12184279
1 717587 rs144155419 G A . PASS AF=0.016741 ES:SE:LP:AF:ID -0.012378:0.0298851:0.167491:0.016741:rs144155419
1 720381 rs116801199 G T . PASS AF=0.037181 ES:SE:LP:AF:ID 0.0197399:0.0193999:0.508638:0.037181:rs116801199
1 721290 rs12565286 G C . PASS AF=0.037303 ES:SE:LP:AF:ID 0.0188943:0.0193164:0.481486:0.037303:rs12565286
1 722670 rs116030099 T C . PASS AF=0.099764 ES:SE:LP:AF:ID -0.00805732:0.0142274:0.244125:0.099764:rs116030099
1 723891 rs2977670 G C . PASS AF=0.958679 ES:SE:LP:AF:ID -0.0208185:0.0185505:0.585027:0.958679:rs2977670
1 724849 rs12126395 C A . PASS AF=0.030977 ES:SE:LP:AF:ID 0.0540293:0.0345495:0.920819:0.030977:rs12126395
1 725060 rs865924913 A T . PASS AF=0.053446 ES:SE:LP:AF:ID -0.0327462:0.0270328:0.638272:0.053446:rs865924913
1 726794 rs28454925 C G . PASS AF=0.036905 ES:SE:LP:AF:ID 0.0195342:0.0194333:0.508638:0.036905:rs28454925
1 729632 rs116720794 C T . PASS AF=0.037119 ES:SE:LP:AF:ID 0.0181197:0.0192867:0.455932:0.037119:rs116720794
1 729679 rs4951859 C G . PASS AF=0.842371 ES:SE:LP:AF:ID -0.0102397:0.00995143:0.522879:0.842371:rs4951859
1 730087 rs148120343 T C . PASS AF=0.057061 ES:SE:LP:AF:ID 0.0113883:0.0160876:0.318759:0.057061:rs148120343
1 731718 rs58276399 T C . PASS AF=0.123083 ES:SE:LP:AF:ID 0.00436259:0.0109037:0.161151:0.123083:rs58276399
1 732989 rs369030935 C T . PASS AF=0.025697 ES:SE:LP:AF:ID -0.000563181:0.0271961:0.00877392:0.025697:rs369030935
1 734349 rs141242758 T C . PASS AF=0.122269 ES:SE:LP:AF:ID 0.00413539:0.0109106:0.154902:0.122269:rs141242758
1 736289 rs79010578 T A . PASS AF=0.132492 ES:SE:LP:AF:ID 0.00832159:0.010787:0.356547:0.132492:rs79010578
1 736689 rs181876450 T C . PASS AF=0.011631 ES:SE:LP:AF:ID 0.0726807:0.0386461:1.22185:0.011631:rs181876450
1 752478 rs146277091 G A . PASS AF=0.037141 ES:SE:LP:AF:ID 0.0141348:0.0190669:0.337242:0.037141:rs146277091
1 752566 rs3094315 G A . PASS AF=0.838561 ES:SE:LP:AF:ID -0.00211439:0.00966518:0.0809219:0.838561:rs3094315
1 752721 rs3131972 A G . PASS AF=0.838153 ES:SE:LP:AF:ID -0.00241035:0.00965037:0.09691:0.838153:rs3131972
1 753405 rs3115860 C A . PASS AF=0.869311 ES:SE:LP:AF:ID 0.00107274:0.0103731:0.0362122:0.869311:rs3115860
1 753541 rs2073813 G A . PASS AF=0.1306 ES:SE:LP:AF:ID -0.00162419:0.0103819:0.0555173:0.1306:rs2073813
1 754063 rs12184312 G T . PASS AF=0.037589 ES:SE:LP:AF:ID 0.0155294:0.0187591:0.387216:0.037589:rs12184312
1 754105 rs12184325 C T . PASS AF=0.037857 ES:SE:LP:AF:ID 0.0163737:0.0186415:0.420216:0.037857:rs12184325
1 754182 rs3131969 A G . PASS AF=0.868684 ES:SE:LP:AF:ID 0.000439735:0.0103506:0.0132283:0.868684:rs3131969
1 754192 rs3131968 A G . PASS AF=0.868747 ES:SE:LP:AF:ID 0.00045674:0.0103528:0.0177288:0.868747:rs3131968
1 754211 rs12184313 G A . PASS AF=0.03781 ES:SE:LP:AF:ID 0.0157677:0.0187111:0.39794:0.03781:rs12184313
1 754334 rs3131967 T C . PASS AF=0.868698 ES:SE:LP:AF:ID 0.000588209:0.0103502:0.0222764:0.868698:rs3131967
1 754503 rs3115859 G A . PASS AF=0.837638 ES:SE:LP:AF:ID -0.00193785:0.00962847:0.0757207:0.837638:rs3115859
1 754629 rs10454459 A G . PASS AF=0.037833 ES:SE:LP:AF:ID 0.0171087:0.0187366:0.443698:0.037833:rs10454459
1 754964 rs3131966 C T . PASS AF=0.838296 ES:SE:LP:AF:ID -0.00234083:0.00965671:0.091515:0.838296:rs3131966
1 755240 rs181660517 T G . PASS AF=0.01385 ES:SE:LP:AF:ID 0.0205441:0.0338713:0.267606:0.01385:rs181660517
1 755775 rs3131965 A G . PASS AF=0.839463 ES:SE:LP:AF:ID -0.00233958:0.00978828:0.091515:0.839463:rs3131965
1 755890 rs3115858 A T . PASS AF=0.868932 ES:SE:LP:AF:ID 0.0008948:0.0103392:0.0315171:0.868932:rs3115858
1 756604 rs3131962 A G . PASS AF=0.868451 ES:SE:LP:AF:ID 7.7695e-05:0.0103143:0.00436481:0.868451:rs3131962
1 757640 rs3115853 G A . PASS AF=0.867382 ES:SE:LP:AF:ID 0.000152836:0.0102947:0.00436481:0.867382:rs3115853
1 757734 rs4951929 C T . PASS AF=0.868671 ES:SE:LP:AF:ID 0.000321766:0.0103246:0.00877392:0.868671:rs4951929