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_3084.vcf.gz --id UKB-b:11364 --data /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/ukbiobank/raw-output/data.batch_3084.txt.gz --cohort_controls 40613 --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": "2019-09-12T19:38:49.837771",
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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-11364/UKB-b-11364_data.vcf.gz \
--ref-ld-chr ../reference/eur_w_ld_chr/ \
--out /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-11364/ldsc.txt \
--w-ld-chr ../reference/eur_w_ld_chr/
Beginning analysis at Thu Oct 17 14:40:18 2019
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-11364/UKB-b-11364_data.vcf.gz ...
Read summary statistics for 7939558 SNPs.
Dropped 6016 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, 1281557 SNPs remain.
After merging with regression SNP LD, 1281557 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.3011 (0.0304)
Lambda GC: 1.1676
Mean Chi^2: 1.2663
Intercept: 1.0206 (0.0087)
Ratio: 0.0775 (0.0328)
Analysis finished at Thu Oct 17 14:41:50 2019
Total time elapsed: 1.0m:31.82sQC metrics
Metrics
Metrics
{
"af_correlation": 0.9425,
"inflation_factor": 1.1474,
"mean_EFFECT": 3.814e-06,
"n": "-Inf",
"n_snps": 9851866,
"n_clumped_hits": 56,
"n_p_sig": 4102,
"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": 74070,
"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": 1281557,
"ldsc_nsnp_merge_regression_ld": 1281557,
"ldsc_observed_scale_h2_beta": 0.3011,
"ldsc_observed_scale_h2_se": 0.0304,
"ldsc_intercept_beta": 1.0206,
"ldsc_intercept_se": 0.0087,
"ldsc_lambda_gc": 1.1676,
"ldsc_mean_chisq": 1.2663,
"ldsc_ratio": 0.0774
}
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 | 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 | 7933569 | 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 | 7939558 | 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 | 8.660405e+00 | 5.763588e+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 | 7.870876e+07 | 5.642285e+07 | 828.0000000 | 3.225644e+07 | 6.918309e+07 | 1.145575e+08 | 2.492385e+08 | ▇▆▅▂▁ |
| numeric | EFFECT | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 3.800000e-06 | 1.729030e-02 | -0.2182920 | -8.236100e-03 | 5.600000e-06 | 8.193100e-03 | 2.236540e-01 | ▁▁▇▁▁ |
| numeric | SE | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 1.415850e-02 | 8.411200e-03 | 0.0065021 | 7.536400e-03 | 1.044350e-02 | 1.858040e-02 | 7.876590e-02 | ▇▂▁▁▁ |
| numeric | PVAL | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 4.777720e-01 | 2.952804e-01 | 0.0000000 | 2.200002e-01 | 4.700002e-01 | 7.300002e-01 | 1.000000e+00 | ▇▇▇▆▇ |
| numeric | PVAL_ztest | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 4.777724e-01 | 2.952544e-01 | 0.0000000 | 2.166891e-01 | 4.701343e-01 | 7.339825e-01 | 1.000000e+00 | ▇▇▆▆▆ |
| numeric | AF | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 2.471889e-01 | 2.607850e-01 | 0.0086180 | 3.650920e-02 | 1.388410e-01 | 3.914740e-01 | 9.913820e-01 | ▇▂▂▁▁ |
| numeric | AF_reference | 74070 | 0.9906708 | NA | NA | NA | NA | NA | NA | NA | 2.463905e-01 | 2.526037e-01 | 0.0000000 | 3.873800e-02 | 1.541530e-01 | 3.865810e-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 | -0.0031724 | 0.0119528 | 0.7899998 | 0.7906912 | 0.623882 | 0.7821490 | NA |
| 1 | 54676 | rs2462492 | C | T | -0.0176850 | 0.0118726 | 0.1400000 | 0.1363389 | 0.401861 | NA | NA |
| 1 | 86028 | rs114608975 | T | C | 0.0201013 | 0.0187956 | 0.2800000 | 0.2848587 | 0.103927 | 0.0277556 | NA |
| 1 | 91536 | rs6702460 | G | T | -0.0190114 | 0.0115938 | 0.1000000 | 0.1010488 | 0.458825 | 0.4207270 | NA |
| 1 | 234313 | rs8179466 | C | T | -0.0250425 | 0.0231783 | 0.2800000 | 0.2799513 | 0.073683 | NA | NA |
| 1 | 534192 | rs6680723 | C | T | -0.0038930 | 0.0132345 | 0.7700005 | 0.7686374 | 0.242155 | NA | NA |
| 1 | 546697 | rs12025928 | A | G | 0.0101449 | 0.0168887 | 0.5500004 | 0.5480454 | 0.915728 | NA | NA |
| 1 | 693731 | rs12238997 | A | G | 0.0099978 | 0.0113554 | 0.3800004 | 0.3786166 | 0.112708 | 0.1417730 | NA |
| 1 | 705882 | rs72631875 | G | A | 0.0125713 | 0.0167420 | 0.4500005 | 0.4527225 | 0.064258 | 0.0315495 | NA |
| 1 | 706368 | rs55727773 | A | G | -0.0065711 | 0.0083040 | 0.4299995 | 0.4287594 | 0.513756 | 0.2751600 | NA |
| CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 22 | 51219006 | rs28729663 | G | A | 0.0075894 | 0.0099786 | 0.4500005 | 0.4469148 | 0.139274 | 0.2052720 | NA |
| 22 | 51219387 | rs9616832 | T | C | -0.0057970 | 0.0128467 | 0.6499995 | 0.6518163 | 0.076170 | 0.0654952 | NA |
| 22 | 51219704 | rs147475742 | G | A | 0.0015667 | 0.0173984 | 0.9299999 | 0.9282500 | 0.042286 | 0.0473243 | NA |
| 22 | 51221190 | rs369304721 | G | A | 0.0081481 | 0.0172925 | 0.6400000 | 0.6375039 | 0.051070 | NA | NA |
| 22 | 51221731 | rs115055839 | T | C | -0.0039914 | 0.0128472 | 0.7600007 | 0.7560426 | 0.075698 | 0.0625000 | NA |
| 22 | 51222100 | rs114553188 | G | T | 0.0236095 | 0.0154276 | 0.1299999 | 0.1259322 | 0.053592 | 0.0880591 | NA |
| 22 | 51223637 | rs375798137 | G | A | 0.0240190 | 0.0154997 | 0.1199999 | 0.1212273 | 0.053223 | 0.0788738 | NA |
| 22 | 51229805 | rs9616985 | T | C | -0.0032220 | 0.0128943 | 0.8000000 | 0.8026818 | 0.075449 | 0.0730831 | NA |
| 22 | 51232488 | rs376461333 | A | G | 0.0638825 | 0.0307287 | 0.0379997 | 0.0376247 | 0.019783 | NA | NA |
| 22 | 51237063 | rs3896457 | T | C | -0.0133910 | 0.0079499 | 0.0920005 | 0.0921002 | 0.300040 | 0.2050720 | NA |
bcf preview
1 49298 rs10399793 T C . PASS AF=0.623882 ES:SE:LP:AF:ID -0.00317243:0.0119528:0.102373:0.623882:rs10399793
1 54676 rs2462492 C T . PASS AF=0.401861 ES:SE:LP:AF:ID -0.017685:0.0118726:0.853872:0.401861:rs2462492
1 86028 rs114608975 T C . PASS AF=0.103927 ES:SE:LP:AF:ID 0.0201013:0.0187956:0.552842:0.103927:rs114608975
1 91536 rs6702460 G T . PASS AF=0.458825 ES:SE:LP:AF:ID -0.0190114:0.0115938:1:0.458825:rs6702460
1 234313 rs8179466 C T . PASS AF=0.073683 ES:SE:LP:AF:ID -0.0250425:0.0231783:0.552842:0.073683:rs8179466
1 534192 rs6680723 C T . PASS AF=0.242155 ES:SE:LP:AF:ID -0.00389303:0.0132345:0.113509:0.242155:rs6680723
1 546697 rs12025928 A G . PASS AF=0.915728 ES:SE:LP:AF:ID 0.0101449:0.0168887:0.259637:0.915728:rs12025928
1 693731 rs12238997 A G . PASS AF=0.112708 ES:SE:LP:AF:ID 0.00999784:0.0113554:0.420216:0.112708:rs12238997
1 705882 rs72631875 G A . PASS AF=0.064258 ES:SE:LP:AF:ID 0.0125713:0.016742:0.346787:0.064258:rs72631875
1 706368 rs12029736 A G . PASS AF=0.513756 ES:SE:LP:AF:ID -0.00657106:0.00830396:0.366532:0.513756:rs12029736
1 714596 rs149887893 T C . PASS AF=0.031782 ES:SE:LP:AF:ID -0.0308645:0.021278:0.823909:0.031782:rs149887893
1 715265 rs12184267 C T . PASS AF=0.035201 ES:SE:LP:AF:ID -0.0285393:0.0193439:0.853872:0.035201:rs12184267
1 715367 rs12184277 A G . PASS AF=0.035252 ES:SE:LP:AF:ID -0.0292948:0.0192845:0.886057:0.035252:rs12184277
1 717485 rs12184279 C A . PASS AF=0.035033 ES:SE:LP:AF:ID -0.0271303:0.0194042:0.79588:0.035033:rs12184279
1 717587 rs144155419 G A . PASS AF=0.016372 ES:SE:LP:AF:ID -0.0289325:0.0294112:0.481486:0.016372:rs144155419
1 720381 rs116801199 G T . PASS AF=0.035597 ES:SE:LP:AF:ID -0.0273161:0.0191808:0.823909:0.035597:rs116801199
1 721290 rs12565286 G C . PASS AF=0.035636 ES:SE:LP:AF:ID -0.0257601:0.0191294:0.744727:0.035636:rs12565286
1 722670 rs116030099 T C . PASS AF=0.1009 ES:SE:LP:AF:ID 0.00613198:0.0136899:0.187087:0.1009:rs116030099
1 723891 rs2977670 G C . PASS AF=0.96074 ES:SE:LP:AF:ID 0.0225774:0.0184575:0.657577:0.96074:rs2977670
1 724849 rs12126395 C A . PASS AF=0.031119 ES:SE:LP:AF:ID -0.0586818:0.0328751:1.13077:0.031119:rs12126395
1 725060 rs865924913 A T . PASS AF=0.05433 ES:SE:LP:AF:ID 0.0240415:0.025906:0.455932:0.05433:rs865924913
1 726794 rs28454925 C G . PASS AF=0.035163 ES:SE:LP:AF:ID -0.0281304:0.0192582:0.853872:0.035163:rs28454925
1 729632 rs116720794 C T . PASS AF=0.035499 ES:SE:LP:AF:ID -0.0290044:0.019066:0.886057:0.035499:rs116720794
1 729679 rs4951859 C G . PASS AF=0.848068 ES:SE:LP:AF:ID -0.00533188:0.0098215:0.229148:0.848068:rs4951859
1 730087 rs148120343 T C . PASS AF=0.054239 ES:SE:LP:AF:ID 0.0260636:0.0159163:1:0.054239:rs148120343
1 731718 rs58276399 T C . PASS AF=0.118715 ES:SE:LP:AF:ID 0.0126281:0.0107524:0.619789:0.118715:rs58276399
1 732989 rs369030935 C T . PASS AF=0.026176 ES:SE:LP:AF:ID -0.0321078:0.0258136:0.677781:0.026176:rs369030935
1 734349 rs141242758 T C . PASS AF=0.117985 ES:SE:LP:AF:ID 0.012545:0.0107618:0.619789:0.117985:rs141242758
1 736289 rs79010578 T A . PASS AF=0.127457 ES:SE:LP:AF:ID 0.00986795:0.0106317:0.455932:0.127457:rs79010578
1 736689 rs181876450 T C . PASS AF=0.011719 ES:SE:LP:AF:ID 0.00466385:0.0366187:0.0457575:0.011719:rs181876450
1 752478 rs146277091 G A . PASS AF=0.035231 ES:SE:LP:AF:ID -0.0271291:0.0189212:0.823909:0.035231:rs146277091
1 752566 rs3094315 G A . PASS AF=0.844081 ES:SE:LP:AF:ID -0.00382696:0.00952089:0.161151:0.844081:rs3094315
1 752721 rs3131972 A G . PASS AF=0.843762 ES:SE:LP:AF:ID -0.00444514:0.00951088:0.19382:0.843762:rs3131972
1 753405 rs3115860 C A . PASS AF=0.873824 ES:SE:LP:AF:ID -0.00933009:0.0102085:0.443698:0.873824:rs3115860
1 753541 rs2073813 G A . PASS AF=0.125756 ES:SE:LP:AF:ID 0.0110297:0.010237:0.552842:0.125756:rs2073813
1 754063 rs12184312 G T . PASS AF=0.035873 ES:SE:LP:AF:ID -0.0264521:0.0185596:0.823909:0.035873:rs12184312
1 754105 rs12184325 C T . PASS AF=0.036099 ES:SE:LP:AF:ID -0.0266375:0.0184442:0.823909:0.036099:rs12184325
1 754182 rs3131969 A G . PASS AF=0.873233 ES:SE:LP:AF:ID -0.0100456:0.0101899:0.49485:0.873233:rs3131969
1 754192 rs3131968 A G . PASS AF=0.873396 ES:SE:LP:AF:ID -0.00961164:0.0101962:0.455932:0.873396:rs3131968
1 754211 rs12184313 G A . PASS AF=0.036056 ES:SE:LP:AF:ID -0.0265665:0.0185295:0.823909:0.036056:rs12184313
1 754334 rs3131967 T C . PASS AF=0.87325 ES:SE:LP:AF:ID -0.0101501:0.0101894:0.49485:0.87325:rs3131967
1 754503 rs3115859 G A . PASS AF=0.843261 ES:SE:LP:AF:ID -0.00392802:0.00948834:0.167491:0.843261:rs3115859
1 754629 rs10454459 A G . PASS AF=0.036051 ES:SE:LP:AF:ID -0.025507:0.0185595:0.769551:0.036051:rs10454459
1 754964 rs3131966 C T . PASS AF=0.843845 ES:SE:LP:AF:ID -0.00394389:0.00951498:0.167491:0.843845:rs3131966
1 755240 rs181660517 T G . PASS AF=0.014003 ES:SE:LP:AF:ID -0.0455445:0.0326055:0.79588:0.014003:rs181660517
1 755775 rs3131965 A G . PASS AF=0.844672 ES:SE:LP:AF:ID -0.00542581:0.00964232:0.244125:0.844672:rs3131965
1 755890 rs3115858 A T . PASS AF=0.873462 ES:SE:LP:AF:ID -0.0091059:0.0101768:0.431798:0.873462:rs3115858
1 756604 rs3131962 A G . PASS AF=0.872965 ES:SE:LP:AF:ID -0.00916237:0.0101504:0.431798:0.872965:rs3131962
1 757640 rs3115853 G A . PASS AF=0.872051 ES:SE:LP:AF:ID -0.00930876:0.010133:0.443698:0.872051:rs3115853
1 757734 rs4951929 C T . PASS AF=0.873174 ES:SE:LP:AF:ID -0.00879913:0.0101607:0.408935:0.873174:rs4951929