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_41202_H269.vcf.gz --id UKB-b:12397 --data /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/ukbiobank/raw-output/data.batch_41202_H269.txt.gz --cohort_cases 8890 --cohort_controls 454120 --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": "2019-09-13T10:25:54.081729",
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"bcftools_viewCommand.1": "view -h /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/ukb-b-12397/ukb-b-12397.vcf.gz; Date=Sat May 9 23:10:56 2020"
}
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-12397/UKB-b-12397_data.vcf.gz \
--ref-ld-chr ../reference/eur_w_ld_chr/ \
--out /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-12397/ldsc.txt \
--w-ld-chr ../reference/eur_w_ld_chr/
Beginning analysis at Thu Oct 17 14:41:53 2019
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-12397/UKB-b-12397_data.vcf.gz ...
Read summary statistics for 5779002 SNPs.
Dropped 2445 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, 1198184 SNPs remain.
After merging with regression SNP LD, 1198184 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.009 (0.0012)
Lambda GC: 1.0752
Mean Chi^2: 1.085
Intercept: 1.0008 (0.0074)
Ratio: 0.0089 (0.0866)
Analysis finished at Thu Oct 17 14:42:59 2019
Total time elapsed: 1.0m:5.83sQC metrics
Metrics
Metrics
{
"af_correlation": 0.9213,
"inflation_factor": 1.0966,
"mean_EFFECT": 1.9816e-06,
"n": "-Inf",
"n_snps": 9851866,
"n_clumped_hits": 9,
"n_p_sig": 148,
"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": 51634,
"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": 1198184,
"ldsc_nsnp_merge_regression_ld": 1198184,
"ldsc_observed_scale_h2_beta": 0.009,
"ldsc_observed_scale_h2_se": 0.0012,
"ldsc_intercept_beta": 1.0008,
"ldsc_intercept_se": 0.0074,
"ldsc_lambda_gc": 1.0752,
"ldsc_mean_chisq": 1.085,
"ldsc_ratio": 0.0094
}
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 | 5776573 | 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 | 5779002 | 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 | 8.670440e+00 | 5.762442e+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 | 7.859624e+07 | 5.654633e+07 | 828.0000000 | 3.199372e+07 | 6.903365e+07 | 1.145199e+08 | 2.492385e+08 | ▇▆▅▂▁ |
| numeric | EFFECT | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 2.000000e-06 | 4.404000e-04 | -0.0041402 | -2.649000e-04 | 8.000000e-07 | 2.683000e-04 | 4.189700e-03 | ▁▁▇▁▁ |
| numeric | SE | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 4.069000e-04 | 1.256000e-04 | 0.0002752 | 3.028000e-04 | 3.588000e-04 | 4.814000e-04 | 1.319700e-03 | ▇▂▁▁▁ |
| numeric | PVAL | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 4.883936e-01 | 2.917741e-01 | 0.0000000 | 2.300001e-01 | 4.799997e-01 | 7.400005e-01 | 1.000000e+00 | ▇▇▇▇▇ |
| numeric | PVAL_ztest | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 4.883948e-01 | 2.917483e-01 | 0.0000000 | 2.326200e-01 | 4.847437e-01 | 7.409430e-01 | 9.999997e-01 | ▇▇▇▇▇ |
| numeric | AF | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 3.202443e-01 | 2.508373e-01 | 0.0393710 | 1.067970e-01 | 2.417890e-01 | 4.864700e-01 | 9.606290e-01 | ▇▃▂▂▁ |
| numeric | AF_reference | 51634 | 0.9910652 | NA | NA | NA | NA | NA | NA | NA | 3.161764e-01 | 2.445328e-01 | 0.0000000 | 1.150160e-01 | 2.482030e-01 | 4.764380e-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 | -0.0002170 | 0.0005065 | 0.6700003 | 0.6683581 | 0.623765 | 0.7821490 | NA |
| 1 | 54676 | rs2462492 | C | T | 0.0005392 | 0.0005018 | 0.2800000 | 0.2825852 | 0.400401 | NA | NA |
| 1 | 86028 | rs114608975 | T | C | -0.0000739 | 0.0008022 | 0.9299999 | 0.9265750 | 0.103556 | 0.0277556 | NA |
| 1 | 91536 | rs6702460 | G | T | 0.0002144 | 0.0004941 | 0.6600001 | 0.6642526 | 0.456846 | 0.4207270 | NA |
| 1 | 234313 | rs8179466 | C | T | -0.0020978 | 0.0009742 | 0.0309999 | 0.0312909 | 0.074506 | NA | NA |
| 1 | 534192 | rs6680723 | C | T | 0.0003703 | 0.0005644 | 0.5099998 | 0.5117704 | 0.240959 | NA | NA |
| 1 | 546697 | rs12025928 | A | G | 0.0001693 | 0.0007041 | 0.8100000 | 0.8099404 | 0.913475 | NA | NA |
| 1 | 693731 | rs12238997 | A | G | -0.0000664 | 0.0004729 | 0.8900000 | 0.8882767 | 0.116329 | 0.1417730 | NA |
| 1 | 705882 | rs72631875 | G | A | 0.0006190 | 0.0006930 | 0.3700002 | 0.3717589 | 0.067288 | 0.0315495 | NA |
| 1 | 706368 | rs55727773 | A | G | 0.0002890 | 0.0003503 | 0.4100001 | 0.4094048 | 0.515645 | 0.2751600 | NA |
| CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 22 | 51218377 | rs2519461 | G | C | 0.0003038 | 0.0005475 | 0.5800000 | 0.5790138 | 0.073622 | 0.0826677 | NA |
| 22 | 51219006 | rs28729663 | G | A | 0.0010420 | 0.0004226 | 0.0140001 | 0.0136819 | 0.137950 | 0.2052720 | NA |
| 22 | 51219387 | rs9616832 | T | C | 0.0003348 | 0.0005486 | 0.5400003 | 0.5416448 | 0.073744 | 0.0654952 | NA |
| 22 | 51219704 | rs147475742 | G | A | 0.0006368 | 0.0007351 | 0.3900004 | 0.3863539 | 0.041954 | 0.0473243 | NA |
| 22 | 51221190 | rs369304721 | G | A | 0.0008548 | 0.0007339 | 0.2399999 | 0.2441591 | 0.049731 | NA | NA |
| 22 | 51221731 | rs115055839 | T | C | 0.0003315 | 0.0005489 | 0.5500004 | 0.5459577 | 0.073235 | 0.0625000 | NA |
| 22 | 51222100 | rs114553188 | G | T | 0.0015114 | 0.0006463 | 0.0189998 | 0.0193502 | 0.054460 | 0.0880591 | NA |
| 22 | 51223637 | rs375798137 | G | A | 0.0014882 | 0.0006494 | 0.0219999 | 0.0219232 | 0.054089 | 0.0788738 | NA |
| 22 | 51229805 | rs9616985 | T | C | 0.0003655 | 0.0005509 | 0.5099998 | 0.5070632 | 0.073071 | 0.0730831 | NA |
| 22 | 51237063 | rs3896457 | T | C | -0.0003199 | 0.0003369 | 0.3400001 | 0.3424736 | 0.297974 | 0.2050720 | NA |
bcf preview
1 49298 rs10399793 T C . PASS AF=0.623765 ES:SE:LP:AF:ID -0.000216985:0.000506498:0.173925:0.623765:rs10399793
1 54676 rs2462492 C T . PASS AF=0.400401 ES:SE:LP:AF:ID 0.000539182:0.000501784:0.552842:0.400401:rs2462492
1 86028 rs114608975 T C . PASS AF=0.103556 ES:SE:LP:AF:ID -7.39311e-05:0.000802248:0.0315171:0.103556:rs114608975
1 91536 rs6702460 G T . PASS AF=0.456846 ES:SE:LP:AF:ID 0.000214449:0.000494066:0.180456:0.456846:rs6702460
1 234313 rs8179466 C T . PASS AF=0.074506 ES:SE:LP:AF:ID -0.00209776:0.000974183:1.50864:0.074506:rs8179466
1 534192 rs6680723 C T . PASS AF=0.240959 ES:SE:LP:AF:ID 0.000370264:0.000564355:0.29243:0.240959:rs6680723
1 546697 rs12025928 A G . PASS AF=0.913475 ES:SE:LP:AF:ID 0.000169329:0.000704062:0.091515:0.913475:rs12025928
1 693731 rs12238997 A G . PASS AF=0.116329 ES:SE:LP:AF:ID -6.64419e-05:0.000472946:0.05061:0.116329:rs12238997
1 705882 rs72631875 G A . PASS AF=0.067288 ES:SE:LP:AF:ID 0.00061902:0.000693049:0.431798:0.067288:rs72631875
1 706368 rs12029736 A G . PASS AF=0.515645 ES:SE:LP:AF:ID 0.00028901:0.00035034:0.387216:0.515645:rs12029736
1 722670 rs116030099 T C . PASS AF=0.1012 ES:SE:LP:AF:ID -0.00061312:0.00057804:0.537602:0.1012:rs116030099
1 723891 rs2977670 G C . PASS AF=0.959091 ES:SE:LP:AF:ID 0.000609659:0.00076512:0.366532:0.959091:rs2977670
1 725060 rs865924913 A T . PASS AF=0.053255 ES:SE:LP:AF:ID 0.000949241:0.00110498:0.408935:0.053255:rs865924913
1 729679 rs4951859 C G . PASS AF=0.843204 ES:SE:LP:AF:ID 0.00010673:0.000409869:0.102373:0.843204:rs4951859
1 730087 rs148120343 T C . PASS AF=0.055912 ES:SE:LP:AF:ID -0.000511128:0.000663645:0.356547:0.055912:rs148120343
1 731718 rs58276399 T C . PASS AF=0.122312 ES:SE:LP:AF:ID 0.00013271:0.000448637:0.113509:0.122312:rs58276399
1 734349 rs141242758 T C . PASS AF=0.121554 ES:SE:LP:AF:ID 0.000129521:0.000448825:0.113509:0.121554:rs141242758
1 736289 rs79010578 T A . PASS AF=0.132335 ES:SE:LP:AF:ID -0.000358915:0.000442363:0.376751:0.132335:rs79010578
1 752566 rs3094315 G A . PASS AF=0.838945 ES:SE:LP:AF:ID 0.000196672:0.000396931:0.207608:0.838945:rs3094315
1 752721 rs3131972 A G . PASS AF=0.838573 ES:SE:LP:AF:ID 0.000176888:0.000396504:0.180456:0.838573:rs3131972
1 753405 rs3115860 C A . PASS AF=0.869776 ES:SE:LP:AF:ID -9.49314e-06:0.000425463:0.00877392:0.869776:rs3115860
1 753541 rs2073813 G A . PASS AF=0.129876 ES:SE:LP:AF:ID 5.57293e-05:0.000426333:0.0457575:0.129876:rs2073813
1 754182 rs3131969 A G . PASS AF=0.869117 ES:SE:LP:AF:ID -4.1377e-05:0.000424629:0.0362122:0.869117:rs3131969
1 754192 rs3131968 A G . PASS AF=0.869215 ES:SE:LP:AF:ID -4.70208e-05:0.000424797:0.0409586:0.869215:rs3131968
1 754334 rs3131967 T C . PASS AF=0.869121 ES:SE:LP:AF:ID -4.26753e-05:0.000424621:0.0362122:0.869121:rs3131967
1 754503 rs3115859 G A . PASS AF=0.838026 ES:SE:LP:AF:ID 0.000208065:0.000395403:0.221849:0.838026:rs3115859
1 754964 rs3131966 C T . PASS AF=0.838657 ES:SE:LP:AF:ID 0.000180385:0.000396515:0.187087:0.838657:rs3131966
1 755775 rs3131965 A G . PASS AF=0.83977 ES:SE:LP:AF:ID 0.000210775:0.000401877:0.221849:0.83977:rs3131965
1 755890 rs3115858 A T . PASS AF=0.8694 ES:SE:LP:AF:ID -2.17913e-05:0.00042413:0.0177288:0.8694:rs3115858
1 756604 rs3131962 A G . PASS AF=0.868947 ES:SE:LP:AF:ID -5.91533e-05:0.000423063:0.05061:0.868947:rs3131962
1 757640 rs3115853 G A . PASS AF=0.867898 ES:SE:LP:AF:ID -9.29371e-06:0.000422251:0.00877392:0.867898:rs3115853
1 757734 rs4951929 C T . PASS AF=0.86909 ES:SE:LP:AF:ID -3.31259e-05:0.000423409:0.0268721:0.86909:rs4951929
1 757936 rs4951862 C A . PASS AF=0.869098 ES:SE:LP:AF:ID -3.30712e-05:0.000423441:0.0268721:0.869098:rs4951862
1 758144 rs3131956 A G . PASS AF=0.869106 ES:SE:LP:AF:ID -3.44962e-05:0.000423451:0.0268721:0.869106:rs3131956
1 758626 rs3131954 C T . PASS AF=0.869584 ES:SE:LP:AF:ID -2.09296e-05:0.000424614:0.0177288:0.869584:rs3131954
1 760912 rs1048488 C T . PASS AF=0.838306 ES:SE:LP:AF:ID 0.000237926:0.000394653:0.259637:0.838306:rs1048488
1 761147 rs3115850 T C . PASS AF=0.838427 ES:SE:LP:AF:ID 0.000237274:0.000394932:0.259637:0.838427:rs3115850
1 761732 rs2286139 C T . PASS AF=0.862254 ES:SE:LP:AF:ID -5.46995e-05:0.00042192:0.0457575:0.862254:rs2286139
1 763394 rs3115847 G A . PASS AF=0.706753 ES:SE:LP:AF:ID -0.000212663:0.000410741:0.221849:0.706753:rs3115847
1 766007 rs61768174 A C . PASS AF=0.105145 ES:SE:LP:AF:ID -0.000112908:0.000473165:0.091515:0.105145:rs61768174
1 768253 rs2977608 A C . PASS AF=0.761297 ES:SE:LP:AF:ID 0.000121649:0.000335236:0.142668:0.761297:rs2977608
1 768448 rs12562034 G A . PASS AF=0.10649 ES:SE:LP:AF:ID -0.000340019:0.000462059:0.337242:0.10649:rs12562034
1 769223 rs60320384 C G . PASS AF=0.129581 ES:SE:LP:AF:ID 8.15379e-05:0.000426079:0.0705811:0.129581:rs60320384
1 771823 rs2977605 T C . PASS AF=0.868906 ES:SE:LP:AF:ID -4.96905e-05:0.000423803:0.0409586:0.868906:rs2977605
1 771967 rs59066358 G A . PASS AF=0.129682 ES:SE:LP:AF:ID 5.51679e-05:0.000425804:0.0457575:0.129682:rs59066358
1 772755 rs2905039 A C . PASS AF=0.868916 ES:SE:LP:AF:ID -6.17749e-05:0.000423811:0.0555173:0.868916:rs2905039
1 776546 rs12124819 A G . PASS AF=0.265385 ES:SE:LP:AF:ID 0.000216277:0.000374471:0.251812:0.265385:rs12124819
1 777122 rs2980319 A T . PASS AF=0.870039 ES:SE:LP:AF:ID -6.34265e-05:0.000424676:0.0555173:0.870039:rs2980319
1 777232 rs112618790 C T . PASS AF=0.095141 ES:SE:LP:AF:ID -0.000140397:0.000492192:0.107905:0.095141:rs112618790
1 778745 rs1055606 A G . PASS AF=0.12858 ES:SE:LP:AF:ID 8.25164e-05:0.000426353:0.0705811:0.12858:rs1055606