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_4124.vcf.gz --id UKB-b:4657 --data /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/ukbiobank/raw-output/data.batch_4124.txt.gz --cohort_controls 146093 --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": "2019-09-13T13:26:05.128047",
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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-4657/UKB-b-4657_data.vcf.gz \
--ref-ld-chr ../reference/eur_w_ld_chr/ \
--out /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-4657/ldsc.txt \
--w-ld-chr ../reference/eur_w_ld_chr/
Beginning analysis at Thu Oct 17 14:44:33 2019
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-4657/UKB-b-4657_data.vcf.gz ...
Read summary statistics for 9301200 SNPs.
Dropped 10283 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, 1287944 SNPs remain.
After merging with regression SNP LD, 1287944 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.2913 (0.0263)
Lambda GC: 1.4259
Mean Chi^2: 1.9782
Intercept: 1.0995 (0.0136)
Ratio: 0.1017 (0.0139)
Analysis finished at Thu Oct 17 14:46:10 2019
Total time elapsed: 1.0m:36.87sQC metrics
Metrics
Metrics
{
"af_correlation": 0.9487,
"inflation_factor": 1.3107,
"mean_EFFECT": 0,
"n": "-Inf",
"n_snps": 9851866,
"n_clumped_hits": 229,
"n_p_sig": 27524,
"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": 111582,
"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": 1287944,
"ldsc_nsnp_merge_regression_ld": 1287944,
"ldsc_observed_scale_h2_beta": 0.2913,
"ldsc_observed_scale_h2_se": 0.0263,
"ldsc_intercept_beta": 1.0995,
"ldsc_intercept_se": 0.0136,
"ldsc_lambda_gc": 1.4259,
"ldsc_mean_chisq": 1.9782,
"ldsc_ratio": 0.1017
}
Flags
| name | value |
|---|---|
| af_correlation | FALSE |
| inflation_factor | TRUE |
| 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 | 9290969 | 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 | 9301200 | 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 | 8.635434e+00 | 5.754189e+00 | 1.000000 | 4.000000e+00 | 8.000000e+00 | 1.300000e+01 | 2.200000e+01 | ▇▅▃▂▂ |
| numeric | POS | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 7.880925e+07 | 5.630804e+07 | 828.000000 | 3.250005e+07 | 6.939113e+07 | 1.145405e+08 | 2.492385e+08 | ▇▆▅▂▁ |
| numeric | EFFECT | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 3.700000e-05 | 1.373320e-02 | -0.210546 | -5.340100e-03 | 4.800000e-06 | 5.344600e-03 | 3.736510e-01 | ▁▇▁▁▁ |
| numeric | SE | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 9.868900e-03 | 7.777400e-03 | 0.003308 | 3.988700e-03 | 6.297400e-03 | 1.353030e-02 | 8.288400e-02 | ▇▁▁▁▁ |
| numeric | PVAL | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 4.549630e-01 | 3.022685e-01 | 0.000000 | 1.800002e-01 | 4.400003e-01 | 7.199992e-01 | 1.000000e+00 | ▇▆▆▅▆ |
| numeric | PVAL_ztest | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 4.549628e-01 | 3.022454e-01 | 0.000000 | 1.816706e-01 | 4.393922e-01 | 7.173439e-01 | 9.999998e-01 | ▇▆▆▅▅ |
| numeric | AF | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 2.138961e-01 | 2.578310e-01 | 0.002396 | 1.755200e-02 | 9.267900e-02 | 3.358770e-01 | 9.976040e-01 | ▇▂▁▁▁ |
| numeric | AF_reference | 111582 | 0.9880035 | NA | NA | NA | NA | NA | NA | NA | 2.148898e-01 | 2.496236e-01 | 0.000000 | 1.497600e-02 | 1.110220e-01 | 3.356630e-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 | -0.0026366 | 0.0061067 | 0.6700003 | 0.6659186 | 0.623858 | 0.7821490 | NA |
| 1 | 54676 | rs2462492 | C | T | -0.0020253 | 0.0060620 | 0.7400005 | 0.7383108 | 0.399276 | NA | NA |
| 1 | 86028 | rs114608975 | T | C | -0.0027884 | 0.0096607 | 0.7700005 | 0.7728587 | 0.103773 | 0.0277556 | NA |
| 1 | 91536 | rs6702460 | G | T | 0.0014361 | 0.0059727 | 0.8100000 | 0.8099906 | 0.456124 | 0.4207270 | NA |
| 1 | 234313 | rs8179466 | C | T | 0.0025807 | 0.0118034 | 0.8300000 | 0.8269295 | 0.074427 | NA | NA |
| 1 | 534192 | rs6680723 | C | T | 0.0092881 | 0.0068225 | 0.1700000 | 0.1733873 | 0.241230 | NA | NA |
| 1 | 546697 | rs12025928 | A | G | 0.0224181 | 0.0084672 | 0.0080999 | 0.0081054 | 0.912996 | NA | NA |
| 1 | 693731 | rs12238997 | A | G | 0.0014337 | 0.0056961 | 0.8000000 | 0.8012758 | 0.116812 | 0.1417730 | NA |
| 1 | 705882 | rs72631875 | G | A | -0.0103102 | 0.0083143 | 0.2099999 | 0.2149568 | 0.067755 | 0.0315495 | NA |
| 1 | 706368 | rs55727773 | A | G | -0.0058583 | 0.0042141 | 0.1600000 | 0.1644802 | 0.515065 | 0.2751600 | NA |
| CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 22 | 51219006 | rs28729663 | G | A | -0.0010594 | 0.0051236 | 0.8400000 | 0.8361881 | 0.137285 | 0.2052720 | NA |
| 22 | 51219387 | rs9616832 | T | C | -0.0027613 | 0.0066581 | 0.6800001 | 0.6783414 | 0.072957 | 0.0654952 | NA |
| 22 | 51219704 | rs147475742 | G | A | -0.0096852 | 0.0088868 | 0.2800000 | 0.2757873 | 0.041772 | 0.0473243 | NA |
| 22 | 51221190 | rs369304721 | G | A | -0.0107862 | 0.0089083 | 0.2300001 | 0.2259723 | 0.049254 | NA | NA |
| 22 | 51221731 | rs115055839 | T | C | -0.0023757 | 0.0066631 | 0.7199992 | 0.7214312 | 0.072437 | 0.0625000 | NA |
| 22 | 51222100 | rs114553188 | G | T | -0.0044160 | 0.0078148 | 0.5700002 | 0.5720139 | 0.054393 | 0.0880591 | NA |
| 22 | 51223637 | rs375798137 | G | A | -0.0042319 | 0.0078554 | 0.5900000 | 0.5900792 | 0.053999 | 0.0788738 | NA |
| 22 | 51229805 | rs9616985 | T | C | -0.0024712 | 0.0066873 | 0.7099994 | 0.7117279 | 0.072305 | 0.0730831 | NA |
| 22 | 51232488 | rs376461333 | A | G | 0.0023808 | 0.0156636 | 0.8800001 | 0.8791878 | 0.020180 | NA | NA |
| 22 | 51237063 | rs3896457 | T | C | 0.0013770 | 0.0040713 | 0.7400005 | 0.7352027 | 0.297610 | 0.2050720 | NA |
bcf preview
1 49298 rs10399793 T C . PASS AF=0.623858 ES:SE:LP:AF:ID -0.00263661:0.00610671:0.173925:0.623858:rs10399793
1 54676 rs2462492 C T . PASS AF=0.399276 ES:SE:LP:AF:ID -0.00202526:0.006062:0.130768:0.399276:rs2462492
1 86028 rs114608975 T C . PASS AF=0.103773 ES:SE:LP:AF:ID -0.00278843:0.00966066:0.113509:0.103773:rs114608975
1 91536 rs6702460 G T . PASS AF=0.456124 ES:SE:LP:AF:ID 0.00143607:0.00597272:0.091515:0.456124:rs6702460
1 234313 rs8179466 C T . PASS AF=0.074427 ES:SE:LP:AF:ID 0.00258071:0.0118034:0.0809219:0.074427:rs8179466
1 534192 rs6680723 C T . PASS AF=0.24123 ES:SE:LP:AF:ID 0.00928811:0.00682247:0.769551:0.24123:rs6680723
1 546697 rs12025928 A G . PASS AF=0.912996 ES:SE:LP:AF:ID 0.0224181:0.00846718:2.09152:0.912996:rs12025928
1 693731 rs12238997 A G . PASS AF=0.116812 ES:SE:LP:AF:ID 0.00143368:0.00569607:0.09691:0.116812:rs12238997
1 705882 rs72631875 G A . PASS AF=0.067755 ES:SE:LP:AF:ID -0.0103102:0.00831434:0.677781:0.067755:rs72631875
1 706368 rs12029736 A G . PASS AF=0.515065 ES:SE:LP:AF:ID -0.00585833:0.00421414:0.79588:0.515065:rs12029736
1 714596 rs149887893 T C . PASS AF=0.033485 ES:SE:LP:AF:ID -0.00763317:0.0105431:0.327902:0.033485:rs149887893
1 715265 rs12184267 C T . PASS AF=0.03719 ES:SE:LP:AF:ID -0.00866241:0.00957223:0.431798:0.03719:rs12184267
1 715367 rs12184277 A G . PASS AF=0.037317 ES:SE:LP:AF:ID -0.00935929:0.00953454:0.481486:0.037317:rs12184277
1 717485 rs12184279 C A . PASS AF=0.03697 ES:SE:LP:AF:ID -0.00993932:0.00960752:0.522879:0.03697:rs12184279
1 717587 rs144155419 G A . PASS AF=0.016363 ES:SE:LP:AF:ID 0.00261362:0.0149861:0.0655015:0.016363:rs144155419
1 720381 rs116801199 G T . PASS AF=0.037549 ES:SE:LP:AF:ID -0.00900865:0.00949741:0.468521:0.037549:rs116801199
1 721290 rs12565286 G C . PASS AF=0.03764 ES:SE:LP:AF:ID -0.00881523:0.00946754:0.455932:0.03764:rs12565286
1 722670 rs116030099 T C . PASS AF=0.101693 ES:SE:LP:AF:ID 0.0145135:0.00693665:1.4437:0.101693:rs116030099
1 723891 rs2977670 G C . PASS AF=0.958412 ES:SE:LP:AF:ID 0.00708858:0.00913399:0.356547:0.958412:rs2977670
1 724849 rs12126395 C A . PASS AF=0.031744 ES:SE:LP:AF:ID -0.0155195:0.0166596:0.455932:0.031744:rs12126395
1 725060 rs865924913 A T . PASS AF=0.052663 ES:SE:LP:AF:ID -0.0164534:0.0134706:0.657577:0.052663:rs865924913
1 726794 rs28454925 C G . PASS AF=0.037126 ES:SE:LP:AF:ID -0.00806206:0.00953207:0.39794:0.037126:rs28454925
1 729632 rs116720794 C T . PASS AF=0.037438 ES:SE:LP:AF:ID -0.0092461:0.00944882:0.481486:0.037438:rs116720794
1 729679 rs4951859 C G . PASS AF=0.84216 ES:SE:LP:AF:ID 0.00140243:0.00492921:0.107905:0.84216:rs4951859
1 730087 rs148120343 T C . PASS AF=0.056067 ES:SE:LP:AF:ID -0.00201555:0.00800338:0.09691:0.056067:rs148120343
1 731718 rs58276399 T C . PASS AF=0.122764 ES:SE:LP:AF:ID 0.00155961:0.00540531:0.113509:0.122764:rs58276399
1 732989 rs369030935 C T . PASS AF=0.02571 ES:SE:LP:AF:ID -0.00673831:0.0132965:0.21467:0.02571:rs369030935
1 734349 rs141242758 T C . PASS AF=0.121982 ES:SE:LP:AF:ID 0.00126568:0.00540804:0.091515:0.121982:rs141242758
1 736289 rs79010578 T A . PASS AF=0.133207 ES:SE:LP:AF:ID -0.00262009:0.00531927:0.207608:0.133207:rs79010578
1 736689 rs181876450 T C . PASS AF=0.011256 ES:SE:LP:AF:ID -0.00111291:0.0192545:0.0222764:0.011256:rs181876450
1 740284 rs61770167 C T . PASS AF=0.005816 ES:SE:LP:AF:ID 0.0286595:0.0246885:0.60206:0.005816:rs61770167
1 752478 rs146277091 G A . PASS AF=0.037381 ES:SE:LP:AF:ID -0.0081151:0.00935236:0.408935:0.037381:rs146277091
1 752566 rs3094315 G A . PASS AF=0.837818 ES:SE:LP:AF:ID -0.000585971:0.00477132:0.0457575:0.837818:rs3094315
1 752721 rs3131972 A G . PASS AF=0.837429 ES:SE:LP:AF:ID -0.000907062:0.00476559:0.0705811:0.837429:rs3131972
1 753405 rs3115860 C A . PASS AF=0.869073 ES:SE:LP:AF:ID -0.00432285:0.00511625:0.39794:0.869073:rs3115860
1 753541 rs2073813 G A . PASS AF=0.130628 ES:SE:LP:AF:ID 0.00489488:0.00512618:0.468521:0.130628:rs2073813
1 754063 rs12184312 G T . PASS AF=0.037875 ES:SE:LP:AF:ID -0.00656355:0.0091989:0.318759:0.037875:rs12184312
1 754105 rs12184325 C T . PASS AF=0.038133 ES:SE:LP:AF:ID -0.00589912:0.00913982:0.283997:0.038133:rs12184325
1 754182 rs3131969 A G . PASS AF=0.868403 ES:SE:LP:AF:ID -0.00470184:0.00510583:0.443698:0.868403:rs3131969
1 754192 rs3131968 A G . PASS AF=0.868505 ES:SE:LP:AF:ID -0.00484834:0.00510781:0.468521:0.868505:rs3131968
1 754211 rs12184313 G A . PASS AF=0.038057 ES:SE:LP:AF:ID -0.00643357:0.00918052:0.318759:0.038057:rs12184313
1 754334 rs3131967 T C . PASS AF=0.868395 ES:SE:LP:AF:ID -0.00457509:0.00510548:0.431798:0.868395:rs3131967
1 754433 rs150578204 G A . PASS AF=0.005177 ES:SE:LP:AF:ID 0.0380821:0.0261476:0.823909:0.005177:rs150578204
1 754458 rs142682604 G T . PASS AF=0.005148 ES:SE:LP:AF:ID 0.0378704:0.0262031:0.823909:0.005148:rs142682604
1 754503 rs3115859 G A . PASS AF=0.836925 ES:SE:LP:AF:ID -0.00113588:0.00475362:0.091515:0.836925:rs3115859
1 754629 rs10454459 A G . PASS AF=0.038066 ES:SE:LP:AF:ID -0.0061266:0.00919326:0.29243:0.038066:rs10454459
1 754964 rs3131966 C T . PASS AF=0.837563 ES:SE:LP:AF:ID -0.00105934:0.00476697:0.0861861:0.837563:rs3131966
1 755240 rs181660517 T G . PASS AF=0.013271 ES:SE:LP:AF:ID 0.0136873:0.0170318:0.376751:0.013271:rs181660517
1 755435 rs184270342 T G . PASS AF=0.00547 ES:SE:LP:AF:ID 0.000317006:0.0258546:0.00436481:0.00547:rs184270342
1 755775 rs3131965 A G . PASS AF=0.838798 ES:SE:LP:AF:ID -0.00125444:0.00483261:0.09691:0.838798:rs3131965