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_20088_336.vcf.gz --id UKB-b:17348 --data /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/ukbiobank/raw-output/data.batch_20088_336.txt.gz --cohort_cases 2621 --cohort_controls 62328 --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": "2019-09-13T13:39:25.191005",
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"bcftools_viewCommand.1": "view -h /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/ukb-b-17348/ukb-b-17348.vcf.gz; Date=Sun May 10 14:30:59 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-17348/UKB-b-17348_data.vcf.gz \
--ref-ld-chr ../reference/eur_w_ld_chr/ \
--out /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-17348/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-17348/UKB-b-17348_data.vcf.gz ...
Read summary statistics for 3757053 SNPs.
Dropped 653 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, 906503 SNPs remain.
After merging with regression SNP LD, 906503 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.0008 (0.0081)
Lambda GC: 1.0267
Mean Chi^2: 1.028
Intercept: 1.0268 (0.0088)
Ratio: 0.9578 (0.3135)
Analysis finished at Thu Oct 17 14:41:06 2019
Total time elapsed: 47.74sQC metrics
Metrics
Metrics
{
"af_correlation": 0.8649,
"inflation_factor": 1.0475,
"mean_EFFECT": -4.9989e-06,
"n": "-Inf",
"n_snps": 9851866,
"n_clumped_hits": 0,
"n_p_sig": 0,
"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": 30407,
"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": 906503,
"ldsc_nsnp_merge_regression_ld": 906503,
"ldsc_observed_scale_h2_beta": 0.0008,
"ldsc_observed_scale_h2_se": 0.0081,
"ldsc_intercept_beta": 1.0268,
"ldsc_intercept_se": 0.0088,
"ldsc_lambda_gc": 1.0267,
"ldsc_mean_chisq": 1.028,
"ldsc_ratio": 0.9571
}
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 | TRUE |
| 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 | 3756403 | 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 | 3757053 | 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 | 8.662675e+00 | 5.769610e+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 | 7.855499e+07 | 5.675072e+07 | 828.0000000 | 3.159982e+07 | 6.890056e+07 | 1.147146e+08 | 2.492385e+08 | ▇▆▅▂▁ |
| numeric | EFFECT | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | -5.000000e-06 | 1.279000e-03 | -0.0073190 | -8.578000e-04 | -1.080000e-05 | 8.383000e-04 | 7.741900e-03 | ▁▂▇▁▁ |
| numeric | SE | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 1.252300e-03 | 1.507000e-04 | 0.0010533 | 1.121300e-03 | 1.203800e-03 | 1.356800e-03 | 3.871400e-03 | ▇▁▁▁▁ |
| numeric | PVAL | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 4.952032e-01 | 2.898139e-01 | 0.0000006 | 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 | 4.952012e-01 | 2.897881e-01 | 0.0000006 | 2.433215e-01 | 4.932750e-01 | 7.452842e-01 | 1.000000e+00 | ▇▇▇▇▇ |
| numeric | AF | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 4.043924e-01 | 2.047482e-01 | 0.1335370 | 2.254870e-01 | 3.609900e-01 | 5.581690e-01 | 8.664630e-01 | ▇▅▃▃▂ |
| numeric | AF_reference | 30407 | 0.9919067 | NA | NA | NA | NA | NA | NA | NA | 3.921523e-01 | 2.113106e-01 | 0.0000000 | 2.188500e-01 | 3.558310e-01 | 5.457270e-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 | 0.0012193 | 0.0019412 | 0.5300002 | 0.5299368 | 0.623812 | 0.782149 | NA |
| 1 | 54676 | rs2462492 | C | T | 0.0005668 | 0.0019355 | 0.7700005 | 0.7696537 | 0.399144 | NA | NA |
| 1 | 91536 | rs6702460 | G | T | 0.0035483 | 0.0019037 | 0.0619998 | 0.0623402 | 0.455916 | 0.420727 | NA |
| 1 | 534192 | rs6680723 | C | T | -0.0000367 | 0.0021683 | 0.9900000 | 0.9864775 | 0.242057 | NA | NA |
| 1 | 706368 | rs55727773 | A | G | 0.0004235 | 0.0013420 | 0.7499995 | 0.7523186 | 0.513304 | 0.275160 | NA |
| 1 | 729679 | rs4951859 | C | G | -0.0002421 | 0.0015636 | 0.8800001 | 0.8769334 | 0.841441 | 0.639976 | NA |
| 1 | 736289 | rs79010578 | T | A | 0.0005180 | 0.0016864 | 0.7600007 | 0.7586980 | 0.134139 | 0.139577 | NA |
| 1 | 752566 | rs3094315 | G | A | -0.0001888 | 0.0015125 | 0.9000000 | 0.9006432 | 0.837029 | 0.718251 | NA |
| 1 | 752721 | rs3131972 | A | G | 0.0000427 | 0.0015114 | 0.9800000 | 0.9774686 | 0.836733 | 0.653355 | NA |
| 1 | 754503 | rs3115859 | G | A | -0.0001765 | 0.0015070 | 0.9100000 | 0.9067744 | 0.836159 | 0.663938 | NA |
| CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 22 | 51186143 | rs2879914 | T | C | -0.0028255 | 0.0011751 | 0.0160000 | 0.0161988 | 0.380077 | 0.2733630 | NA |
| 22 | 51186228 | rs3865766 | C | T | -0.0015237 | 0.0011446 | 0.1800002 | 0.1831428 | 0.449547 | 0.4532750 | NA |
| 22 | 51192586 | rs5771006 | G | A | -0.0033843 | 0.0015431 | 0.0280001 | 0.0282944 | 0.167396 | 0.0848642 | NA |
| 22 | 51193227 | rs34608236 | T | G | 0.0006388 | 0.0015737 | 0.6800001 | 0.6847889 | 0.168560 | 0.0692891 | NA |
| 22 | 51197266 | rs61290853 | A | G | -0.0018291 | 0.0011796 | 0.1199999 | 0.1209875 | 0.386693 | 0.4229230 | NA |
| 22 | 51198027 | rs34939255 | A | G | 0.0016861 | 0.0013378 | 0.2099999 | 0.2075353 | 0.254586 | 0.0984425 | NA |
| 22 | 51211106 | rs9628250 | T | C | 0.0028638 | 0.0013270 | 0.0309999 | 0.0309221 | 0.271468 | 0.1671330 | NA |
| 22 | 51212875 | rs2238837 | A | C | -0.0036382 | 0.0012614 | 0.0039000 | 0.0039248 | 0.331351 | 0.3724040 | NA |
| 22 | 51219006 | rs28729663 | G | A | 0.0023170 | 0.0016324 | 0.1600000 | 0.1557829 | 0.136315 | 0.2052720 | NA |
| 22 | 51237063 | rs3896457 | T | C | -0.0031718 | 0.0012887 | 0.0140001 | 0.0138469 | 0.298393 | 0.2050720 | NA |
bcf preview
1 49298 rs10399793 T C . PASS AF=0.623812 ES:SE:LP:AF:ID 0.00121926:0.00194118:0.275724:0.623812:rs10399793
1 54676 rs2462492 C T . PASS AF=0.399144 ES:SE:LP:AF:ID 0.00056678:0.00193554:0.113509:0.399144:rs2462492
1 91536 rs6702460 G T . PASS AF=0.455916 ES:SE:LP:AF:ID 0.00354832:0.00190374:1.20761:0.455916:rs6702460
1 534192 rs6680723 C T . PASS AF=0.242057 ES:SE:LP:AF:ID -3.67492e-05:0.00216826:0.00436481:0.242057:rs6680723
1 706368 rs12029736 A G . PASS AF=0.513304 ES:SE:LP:AF:ID 0.00042351:0.00134199:0.124939:0.513304:rs12029736
1 729679 rs4951859 C G . PASS AF=0.841441 ES:SE:LP:AF:ID -0.000242128:0.00156355:0.0555173:0.841441:rs4951859
1 736289 rs79010578 T A . PASS AF=0.134139 ES:SE:LP:AF:ID 0.000518047:0.0016864:0.119186:0.134139:rs79010578
1 752566 rs3094315 G A . PASS AF=0.837029 ES:SE:LP:AF:ID -0.000188839:0.00151254:0.0457575:0.837029:rs3094315
1 752721 rs3131972 A G . PASS AF=0.836733 ES:SE:LP:AF:ID 4.26869e-05:0.00151143:0.00877392:0.836733:rs3131972
1 754503 rs3115859 G A . PASS AF=0.836159 ES:SE:LP:AF:ID -0.000176483:0.00150701:0.0409586:0.836159:rs3115859
1 754964 rs3131966 C T . PASS AF=0.836793 ES:SE:LP:AF:ID -0.00014187:0.00151114:0.0315171:0.836793:rs3131966
1 755775 rs3131965 A G . PASS AF=0.838109 ES:SE:LP:AF:ID -0.000922517:0.00153241:0.259637:0.838109:rs3131965
1 760912 rs1048488 C T . PASS AF=0.836369 ES:SE:LP:AF:ID -0.000328143:0.00150325:0.0809219:0.836369:rs1048488
1 761147 rs3115850 T C . PASS AF=0.836495 ES:SE:LP:AF:ID -0.000268117:0.00150428:0.0655015:0.836495:rs3115850
1 761732 rs2286139 C T . PASS AF=0.860851 ES:SE:LP:AF:ID 0.00043678:0.00161116:0.102373:0.860851:rs2286139
1 763394 rs3115847 G A . PASS AF=0.705804 ES:SE:LP:AF:ID 0.000724467:0.00157221:0.19382:0.705804:rs3115847
1 768253 rs2977608 A C . PASS AF=0.758252 ES:SE:LP:AF:ID 0.000428619:0.00127429:0.130768:0.758252:rs2977608
1 776546 rs12124819 A G . PASS AF=0.263729 ES:SE:LP:AF:ID -0.00196323:0.0014399:0.769551:0.263729:rs12124819
1 787399 rs2905055 G T . PASS AF=0.859749 ES:SE:LP:AF:ID 6.41856e-05:0.00161924:0.0132283:0.859749:rs2905055
1 787685 rs2905054 G T . PASS AF=0.860334 ES:SE:LP:AF:ID -1.14368e-05:0.00162015:0.00436481:0.860334:rs2905054
1 795988 rs59380221 C T . PASS AF=0.144405 ES:SE:LP:AF:ID -0.000906813:0.0016748:0.229148:0.144405:rs59380221
1 798400 rs10900604 A G . PASS AF=0.209824 ES:SE:LP:AF:ID -0.000498881:0.00135855:0.148742:0.209824:rs10900604
1 798959 rs11240777 G A . PASS AF=0.209642 ES:SE:LP:AF:ID -0.000515831:0.00135927:0.154902:0.209642:rs11240777
1 808631 rs11240779 G A . PASS AF=0.76828 ES:SE:LP:AF:ID -0.000221854:0.00129187:0.0655015:0.76828:rs11240779
1 808928 rs11240780 C T . PASS AF=0.768417 ES:SE:LP:AF:ID -0.000214278:0.00129352:0.0604807:0.768417:rs11240780
1 814495 rs74461805 C A . PASS AF=0.340108 ES:SE:LP:AF:ID -0.000142764:0.00183772:0.0268721:0.340108:rs74461805
1 824398 rs7538305 A C . PASS AF=0.14012 ES:SE:LP:AF:ID -0.00125912:0.00162201:0.356547:0.14012:rs7538305
1 830181 rs28444699 A G . PASS AF=0.696612 ES:SE:LP:AF:ID 0.00195309:0.00122948:0.958607:0.696612:rs28444699
1 831489 rs4970385 C T . PASS AF=0.705031 ES:SE:LP:AF:ID 0.00277418:0.00120721:1.65758:0.705031:rs4970385
1 831909 rs9697642 C T . PASS AF=0.705083 ES:SE:LP:AF:ID 0.00280219:0.00120721:1.69897:0.705083:rs9697642
1 832066 rs9697380 G C . PASS AF=0.705261 ES:SE:LP:AF:ID 0.00277501:0.00120715:1.65758:0.705261:rs9697380
1 832318 rs4500250 C A . PASS AF=0.705286 ES:SE:LP:AF:ID 0.00277162:0.00120732:1.65758:0.705286:rs4500250
1 832398 rs4553118 T C . PASS AF=0.730154 ES:SE:LP:AF:ID 0.00255424:0.00124062:1.39794:0.730154:rs4553118
1 832918 rs28765502 T C . PASS AF=0.294729 ES:SE:LP:AF:ID -0.00277173:0.00120728:1.65758:0.294729:rs28765502
1 833223 rs13303211 C T . PASS AF=0.237157 ES:SE:LP:AF:ID -0.00242248:0.00128529:1.22915:0.237157:rs13303211
1 833302 rs28752186 C T . PASS AF=0.237168 ES:SE:LP:AF:ID -0.00242495:0.00128531:1.22915:0.237168:rs28752186
1 833641 rs28594623 T C . PASS AF=0.240204 ES:SE:LP:AF:ID -0.00248809:0.0012815:1.284:0.240204:rs28594623
1 833824 rs28484835 T C . PASS AF=0.23716 ES:SE:LP:AF:ID -0.00242282:0.00128537:1.22915:0.23716:rs28484835
1 833927 rs28593608 T C . PASS AF=0.212467 ES:SE:LP:AF:ID -0.00220189:0.00133613:1.00436:0.212467:rs28593608
1 834198 rs28385272 T C . PASS AF=0.21236 ES:SE:LP:AF:ID -0.00217225:0.00133647:1:0.21236:rs28385272
1 834832 rs4411087 G C . PASS AF=0.237633 ES:SE:LP:AF:ID -0.00243977:0.00128441:1.24413:0.237633:rs4411087
1 834928 rs4422949 A G . PASS AF=0.213048 ES:SE:LP:AF:ID -0.00216778:0.00133414:1:0.213048:rs4422949
1 834999 rs28570054 G A . PASS AF=0.213007 ES:SE:LP:AF:ID -0.00220462:0.00133439:1.00436:0.213007:rs28570054
1 835499 rs4422948 A G . PASS AF=0.241744 ES:SE:LP:AF:ID -0.00280851:0.0012748:1.55284:0.241744:rs4422948
1 836529 rs28731045 C G . PASS AF=0.213504 ES:SE:LP:AF:ID -0.00221788:0.00133279:1.01773:0.213504:rs28731045
1 836896 rs28705752 T C . PASS AF=0.269687 ES:SE:LP:AF:ID -0.00125066:0.0012318:0.508638:0.269687:rs28705752
1 836924 rs72890788 G A . PASS AF=0.213501 ES:SE:LP:AF:ID -0.00223554:0.00133296:1.02687:0.213501:rs72890788
1 838387 rs4970384 T C . PASS AF=0.214599 ES:SE:LP:AF:ID -0.00222484:0.00133039:1.02687:0.214599:rs4970384
1 838555 rs4970383 C A . PASS AF=0.245985 ES:SE:LP:AF:ID -0.000910035:0.00126814:0.327902:0.245985:rs4970383
1 839103 rs28562941 A G . PASS AF=0.270067 ES:SE:LP:AF:ID -0.00119673:0.00123281:0.481486:0.270067:rs28562941