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_5256.vcf.gz --id UKB-b:11480 --data /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/ukbiobank/raw-output/data.batch_5256.txt.gz --cohort_controls 97653 --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": "2019-09-12T23:16:57.488005",
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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-11480/UKB-b-11480_data.vcf.gz \
--ref-ld-chr ../reference/eur_w_ld_chr/ \
--out /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-11480/ldsc.txt \
--w-ld-chr ../reference/eur_w_ld_chr/
Beginning analysis at Thu Oct 17 14:40:19 2019
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-11480/UKB-b-11480_data.vcf.gz ...
Read summary statistics for 9007739 SNPs.
Dropped 8738 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, 1287226 SNPs remain.
After merging with regression SNP LD, 1287226 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.2037 (0.0126)
Lambda GC: 1.2438
Mean Chi^2: 1.4168
Intercept: 1.0397 (0.0101)
Ratio: 0.0953 (0.0241)
Analysis finished at Thu Oct 17 14:42:00 2019
Total time elapsed: 1.0m:41.34sQC metrics
Metrics
Metrics
{
"af_correlation": 0.9479,
"inflation_factor": 1.1999,
"mean_EFFECT": -0,
"n": "-Inf",
"n_snps": 9851866,
"n_clumped_hits": 109,
"n_p_sig": 6238,
"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": 93467,
"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": 1287226,
"ldsc_nsnp_merge_regression_ld": 1287226,
"ldsc_observed_scale_h2_beta": 0.2037,
"ldsc_observed_scale_h2_se": 0.0126,
"ldsc_intercept_beta": 1.0397,
"ldsc_intercept_se": 0.0101,
"ldsc_lambda_gc": 1.2438,
"ldsc_mean_chisq": 1.4168,
"ldsc_ratio": 0.0952
}
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 | 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 |
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 | 8999041 | 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 | 9007739 | 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 | 8.643121e+00 | 5.758235e+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 | 7.878827e+07 | 5.634077e+07 | 828.0000000 | 3.243030e+07 | 6.934949e+07 | 1.145443e+08 | 2.492385e+08 | ▇▆▅▂▁ |
| numeric | EFFECT | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | -4.210000e-05 | 1.528980e-02 | -0.3208980 | -6.253300e-03 | 6.700000e-06 | 6.193500e-03 | 2.107380e-01 | ▁▁▆▇▁ |
| numeric | SE | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 1.174890e-02 | 8.608800e-03 | 0.0042675 | 5.090300e-03 | 7.794600e-03 | 1.611610e-02 | 9.942580e-02 | ▇▁▁▁▁ |
| numeric | PVAL | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 4.723647e-01 | 2.976585e-01 | 0.0000000 | 2.099999e-01 | 4.600002e-01 | 7.300002e-01 | 1.000000e+00 | ▇▇▇▆▆ |
| numeric | PVAL_ztest | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 4.723649e-01 | 2.976332e-01 | 0.0000000 | 2.075978e-01 | 4.633039e-01 | 7.307749e-01 | 1.000000e+00 | ▇▆▆▆▆ |
| numeric | AF | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 2.202167e-01 | 2.585375e-01 | 0.0035850 | 2.051700e-02 | 1.015160e-01 | 3.472660e-01 | 9.964150e-01 | ▇▂▁▁▁ |
| numeric | AF_reference | 93467 | 0.9896237 | NA | NA | NA | NA | NA | NA | NA | 2.205272e-01 | 2.504438e-01 | 0.0000000 | 1.777160e-02 | 1.190100e-01 | 3.456470e-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 | 0.0199897 | 0.0078770 | 0.0109999 | 0.0111578 | 0.623639 | 0.7821490 | NA |
| 1 | 54676 | rs2462492 | C | T | -0.0043994 | 0.0078268 | 0.5700002 | 0.5740542 | 0.398765 | NA | NA |
| 1 | 86028 | rs114608975 | T | C | 0.0143714 | 0.0124137 | 0.2500000 | 0.2469845 | 0.104042 | 0.0277556 | NA |
| 1 | 91536 | rs6702460 | G | T | 0.0095646 | 0.0076922 | 0.2099999 | 0.2137135 | 0.455650 | 0.4207270 | NA |
| 1 | 234313 | rs8179466 | C | T | -0.0045211 | 0.0150603 | 0.7600007 | 0.7640237 | 0.074856 | NA | NA |
| 1 | 534192 | rs6680723 | C | T | -0.0083735 | 0.0088088 | 0.3400001 | 0.3418176 | 0.240319 | NA | NA |
| 1 | 546697 | rs12025928 | A | G | 0.0014092 | 0.0109058 | 0.9000000 | 0.8971892 | 0.912775 | NA | NA |
| 1 | 693731 | rs12238997 | A | G | 0.0069826 | 0.0073221 | 0.3400001 | 0.3402699 | 0.117798 | 0.1417730 | NA |
| 1 | 705882 | rs72631875 | G | A | -0.0153805 | 0.0107122 | 0.1499999 | 0.1510613 | 0.067670 | 0.0315495 | NA |
| 1 | 706368 | rs55727773 | A | G | -0.0028411 | 0.0054317 | 0.5999997 | 0.6009253 | 0.514152 | 0.2751600 | NA |
| CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 22 | 51219006 | rs28729663 | G | A | -0.0069335 | 0.0065833 | 0.2900000 | 0.2922487 | 0.137058 | 0.2052720 | NA |
| 22 | 51219387 | rs9616832 | T | C | -0.0141805 | 0.0085787 | 0.0980009 | 0.0983342 | 0.072551 | 0.0654952 | NA |
| 22 | 51219704 | rs147475742 | G | A | -0.0164809 | 0.0114225 | 0.1499999 | 0.1490641 | 0.041724 | 0.0473243 | NA |
| 22 | 51221190 | rs369304721 | G | A | -0.0213832 | 0.0114765 | 0.0619998 | 0.0624319 | 0.049105 | NA | NA |
| 22 | 51221731 | rs115055839 | T | C | -0.0138334 | 0.0085806 | 0.1100001 | 0.1069246 | 0.072094 | 0.0625000 | NA |
| 22 | 51222100 | rs114553188 | G | T | 0.0031047 | 0.0100423 | 0.7600007 | 0.7571989 | 0.054410 | 0.0880591 | NA |
| 22 | 51223637 | rs375798137 | G | A | 0.0028459 | 0.0100966 | 0.7800007 | 0.7780423 | 0.054005 | 0.0788738 | NA |
| 22 | 51229805 | rs9616985 | T | C | -0.0145999 | 0.0086112 | 0.0899995 | 0.0899907 | 0.071952 | 0.0730831 | NA |
| 22 | 51232488 | rs376461333 | A | G | -0.0119200 | 0.0202850 | 0.5600000 | 0.5567831 | 0.020047 | NA | NA |
| 22 | 51237063 | rs3896457 | T | C | -0.0008731 | 0.0052369 | 0.8700001 | 0.8675892 | 0.298272 | 0.2050720 | NA |
bcf preview
1 49298 rs10399793 T C . PASS AF=0.623639 ES:SE:LP:AF:ID 0.0199897:0.00787704:1.95861:0.623639:rs10399793
1 54676 rs2462492 C T . PASS AF=0.398765 ES:SE:LP:AF:ID -0.0043994:0.00782685:0.244125:0.398765:rs2462492
1 86028 rs114608975 T C . PASS AF=0.104042 ES:SE:LP:AF:ID 0.0143714:0.0124137:0.60206:0.104042:rs114608975
1 91536 rs6702460 G T . PASS AF=0.45565 ES:SE:LP:AF:ID 0.00956464:0.00769221:0.677781:0.45565:rs6702460
1 234313 rs8179466 C T . PASS AF=0.074856 ES:SE:LP:AF:ID -0.00452112:0.0150603:0.119186:0.074856:rs8179466
1 534192 rs6680723 C T . PASS AF=0.240319 ES:SE:LP:AF:ID -0.00837346:0.00880879:0.468521:0.240319:rs6680723
1 546697 rs12025928 A G . PASS AF=0.912775 ES:SE:LP:AF:ID 0.00140917:0.0109058:0.0457575:0.912775:rs12025928
1 693731 rs12238997 A G . PASS AF=0.117798 ES:SE:LP:AF:ID 0.00698259:0.0073221:0.468521:0.117798:rs12238997
1 705882 rs72631875 G A . PASS AF=0.06767 ES:SE:LP:AF:ID -0.0153805:0.0107122:0.823909:0.06767:rs72631875
1 706368 rs12029736 A G . PASS AF=0.514152 ES:SE:LP:AF:ID -0.00284114:0.00543166:0.221849:0.514152:rs12029736
1 714596 rs149887893 T C . PASS AF=0.033619 ES:SE:LP:AF:ID 0.0290498:0.0135554:1.49485:0.033619:rs149887893
1 715265 rs12184267 C T . PASS AF=0.037258 ES:SE:LP:AF:ID 0.0240946:0.0123319:1.29243:0.037258:rs12184267
1 715367 rs12184277 A G . PASS AF=0.03734 ES:SE:LP:AF:ID 0.025259:0.0122912:1.39794:0.03734:rs12184277
1 717485 rs12184279 C A . PASS AF=0.037031 ES:SE:LP:AF:ID 0.0255489:0.0123774:1.40894:0.037031:rs12184279
1 717587 rs144155419 G A . PASS AF=0.016817 ES:SE:LP:AF:ID -0.0169741:0.0190128:0.431798:0.016817:rs144155419
1 720381 rs116801199 G T . PASS AF=0.037595 ES:SE:LP:AF:ID 0.0256259:0.012239:1.4437:0.037595:rs116801199
1 721290 rs12565286 G C . PASS AF=0.037684 ES:SE:LP:AF:ID 0.0253581:0.0122006:1.42022:0.037684:rs12565286
1 722670 rs116030099 T C . PASS AF=0.101333 ES:SE:LP:AF:ID -0.0157545:0.00898042:1.10237:0.101333:rs116030099
1 723891 rs2977670 G C . PASS AF=0.958113 ES:SE:LP:AF:ID -0.0198078:0.0117387:1.03621:0.958113:rs2977670
1 724849 rs12126395 C A . PASS AF=0.031747 ES:SE:LP:AF:ID 0.0366039:0.0215152:1.05061:0.031747:rs12126395
1 725060 rs865924913 A T . PASS AF=0.052584 ES:SE:LP:AF:ID -0.00637722:0.0173245:0.148742:0.052584:rs865924913
1 726794 rs28454925 C G . PASS AF=0.037155 ES:SE:LP:AF:ID 0.0231085:0.0122851:1.22185:0.037155:rs28454925
1 729632 rs116720794 C T . PASS AF=0.03747 ES:SE:LP:AF:ID 0.0229402:0.0121808:1.22185:0.03747:rs116720794
1 729679 rs4951859 C G . PASS AF=0.841023 ES:SE:LP:AF:ID -0.0107208:0.00634389:1.04096:0.841023:rs4951859
1 730087 rs148120343 T C . PASS AF=0.056091 ES:SE:LP:AF:ID 0.00190045:0.0103291:0.0705811:0.056091:rs148120343
1 731718 rs58276399 T C . PASS AF=0.123639 ES:SE:LP:AF:ID 0.00777167:0.00695356:0.585027:0.123639:rs58276399
1 732989 rs369030935 C T . PASS AF=0.025832 ES:SE:LP:AF:ID -0.022593:0.0170876:0.721246:0.025832:rs369030935
1 734349 rs141242758 T C . PASS AF=0.122835 ES:SE:LP:AF:ID 0.00756989:0.00695717:0.552842:0.122835:rs141242758
1 736289 rs79010578 T A . PASS AF=0.1335 ES:SE:LP:AF:ID 0.0136795:0.00685997:1.33724:0.1335:rs79010578
1 736689 rs181876450 T C . PASS AF=0.011218 ES:SE:LP:AF:ID -0.0118358:0.0248514:0.200659:0.011218:rs181876450
1 740284 rs61770167 C T . PASS AF=0.006027 ES:SE:LP:AF:ID 0.0663487:0.0312078:1.46852:0.006027:rs61770167
1 752478 rs146277091 G A . PASS AF=0.037422 ES:SE:LP:AF:ID 0.0250672:0.0120497:1.4318:0.037422:rs146277091
1 752566 rs3094315 G A . PASS AF=0.836824 ES:SE:LP:AF:ID -0.00836872:0.00613711:0.769551:0.836824:rs3094315
1 752721 rs3131972 A G . PASS AF=0.83637 ES:SE:LP:AF:ID -0.00805907:0.0061297:0.721246:0.83637:rs3131972
1 753405 rs3115860 C A . PASS AF=0.86807 ES:SE:LP:AF:ID -0.00448973:0.00657591:0.309804:0.86807:rs3115860
1 753541 rs2073813 G A . PASS AF=0.131612 ES:SE:LP:AF:ID 0.00558792:0.00658976:0.39794:0.131612:rs2073813
1 754063 rs12184312 G T . PASS AF=0.037855 ES:SE:LP:AF:ID 0.0225851:0.0118608:1.24413:0.037855:rs12184312
1 754105 rs12184325 C T . PASS AF=0.038104 ES:SE:LP:AF:ID 0.0231238:0.0117867:1.30103:0.038104:rs12184325
1 754182 rs3131969 A G . PASS AF=0.867362 ES:SE:LP:AF:ID -0.00445745:0.00656237:0.30103:0.867362:rs3131969
1 754192 rs3131968 A G . PASS AF=0.86747 ES:SE:LP:AF:ID -0.00447338:0.00656558:0.30103:0.86747:rs3131968
1 754211 rs12184313 G A . PASS AF=0.038052 ES:SE:LP:AF:ID 0.0228779:0.0118349:1.27572:0.038052:rs12184313
1 754334 rs3131967 T C . PASS AF=0.86736 ES:SE:LP:AF:ID -0.0042416:0.00656198:0.283997:0.86736:rs3131967
1 754433 rs150578204 G A . PASS AF=0.005081 ES:SE:LP:AF:ID -0.0358805:0.0340467:0.537602:0.005081:rs150578204
1 754458 rs142682604 G T . PASS AF=0.005048 ES:SE:LP:AF:ID -0.0377883:0.0341393:0.568636:0.005048:rs142682604
1 754503 rs3115859 G A . PASS AF=0.835916 ES:SE:LP:AF:ID -0.00791794:0.00611693:0.69897:0.835916:rs3115859
1 754629 rs10454459 A G . PASS AF=0.038072 ES:SE:LP:AF:ID 0.023354:0.0118504:1.3098:0.038072:rs10454459
1 754964 rs3131966 C T . PASS AF=0.836522 ES:SE:LP:AF:ID -0.00753984:0.00613343:0.657577:0.836522:rs3131966
1 755240 rs181660517 T G . PASS AF=0.013098 ES:SE:LP:AF:ID 0.0351153:0.0220765:0.958607:0.013098:rs181660517
1 755435 rs184270342 T G . PASS AF=0.005542 ES:SE:LP:AF:ID 0.0404372:0.0331208:0.657577:0.005542:rs184270342
1 755775 rs3131965 A G . PASS AF=0.837811 ES:SE:LP:AF:ID -0.00775535:0.00621776:0.677781:0.837811:rs3131965