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_41204_Z888.vcf.gz --id UKB-b:4601 --data /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/ukbiobank/raw-output/data.batch_41204_Z888.txt.gz --cohort_cases 2694 --cohort_controls 460316 --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": "2019-09-13T09:07:15.503020",
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"bcftools_viewCommand.1": "view -h /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/ukb-b-4601/ukb-b-4601.vcf.gz; Date=Sun May 10 06:06:50 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-4601/UKB-b-4601_data.vcf.gz \
--ref-ld-chr ../reference/eur_w_ld_chr/ \
--out /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-4601/ldsc.txt \
--w-ld-chr ../reference/eur_w_ld_chr/
Beginning analysis at Thu Oct 17 14:44:30 2019
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-4601/UKB-b-4601_data.vcf.gz ...
Read summary statistics for 3811120 SNPs.
Dropped 667 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, 916920 SNPs remain.
After merging with regression SNP LD, 916920 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.0019 (0.0012)
Lambda GC: 1.0535
Mean Chi^2: 1.0447
Intercept: 1.0255 (0.0086)
Ratio: 0.5714 (0.1926)
Analysis finished at Thu Oct 17 14:45:21 2019
Total time elapsed: 51.22sQC metrics
Metrics
Metrics
{
"af_correlation": 0.8672,
"inflation_factor": 1.0475,
"mean_EFFECT": 3.7222e-07,
"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": 30915,
"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": 916920,
"ldsc_nsnp_merge_regression_ld": 916920,
"ldsc_observed_scale_h2_beta": 0.0019,
"ldsc_observed_scale_h2_se": 0.0012,
"ldsc_intercept_beta": 1.0255,
"ldsc_intercept_se": 0.0086,
"ldsc_lambda_gc": 1.0535,
"ldsc_mean_chisq": 1.0447,
"ldsc_ratio": 0.5705
}
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 | 3810456 | 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 | 3811120 | 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 | 8.661506e+00 | 5.769070e+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 | 7.856622e+07 | 5.676737e+07 | 828.0000000 | 3.161002e+07 | 6.889777e+07 | 1.147183e+08 | 2.492385e+08 | ▇▆▅▂▁ |
| numeric | EFFECT | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 4.000000e-07 | 1.874000e-04 | -0.0010122 | -1.239000e-04 | 4.000000e-07 | 1.243000e-04 | 1.053300e-03 | ▁▂▇▁▁ |
| numeric | SE | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 1.822000e-04 | 2.260000e-05 | 0.0001525 | 1.626000e-04 | 1.749000e-04 | 1.978000e-04 | 5.577000e-04 | ▇▁▁▁▁ |
| numeric | PVAL | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 4.929034e-01 | 2.900363e-01 | 0.0000006 | 2.399999e-01 | 4.899999e-01 | 7.400005e-01 | 1.000000e+00 | ▇▇▇▇▇ |
| numeric | PVAL_ztest | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 4.929010e-01 | 2.900104e-01 | 0.0000006 | 2.399794e-01 | 4.909182e-01 | 7.432401e-01 | 9.999995e-01 | ▇▇▇▇▇ |
| numeric | AF | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 4.020584e-01 | 2.065836e-01 | 0.1299190 | 2.216970e-01 | 3.576130e-01 | 5.567010e-01 | 8.700810e-01 | ▇▅▃▃▂ |
| numeric | AF_reference | 30915 | 0.9918882 | NA | NA | NA | NA | NA | NA | NA | 3.901114e-01 | 2.125667e-01 | 0.0000000 | 2.156550e-01 | 3.530350e-01 | 5.443290e-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 | -0.0001351 | 0.0002806 | 0.6300007 | 0.6302836 | 0.623765 | 0.782149 | NA |
| 1 | 54676 | rs2462492 | C | T | 0.0000762 | 0.0002780 | 0.7800007 | 0.7838970 | 0.400401 | NA | NA |
| 1 | 91536 | rs6702460 | G | T | 0.0000754 | 0.0002737 | 0.7800007 | 0.7830500 | 0.456846 | 0.420727 | NA |
| 1 | 534192 | rs6680723 | C | T | 0.0002519 | 0.0003127 | 0.4199997 | 0.4205415 | 0.240959 | NA | NA |
| 1 | 706368 | rs55727773 | A | G | 0.0000967 | 0.0001941 | 0.6200004 | 0.6184905 | 0.515645 | 0.275160 | NA |
| 1 | 729679 | rs4951859 | C | G | 0.0001327 | 0.0002271 | 0.5600000 | 0.5590506 | 0.843204 | 0.639976 | NA |
| 1 | 736289 | rs79010578 | T | A | -0.0001812 | 0.0002451 | 0.4600002 | 0.4597539 | 0.132335 | 0.139577 | NA |
| 1 | 752566 | rs3094315 | G | A | 0.0001763 | 0.0002199 | 0.4199997 | 0.4228667 | 0.838945 | 0.718251 | NA |
| 1 | 752721 | rs3131972 | A | G | 0.0001553 | 0.0002197 | 0.4799997 | 0.4796958 | 0.838573 | 0.653355 | NA |
| 1 | 753405 | rs3115860 | C | A | 0.0002540 | 0.0002357 | 0.2800000 | 0.2812081 | 0.869776 | 0.751797 | NA |
| CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 22 | 51192586 | rs5771006 | G | A | 0.0001820 | 0.0002231 | 0.4100001 | 0.4147804 | 0.167627 | 0.0848642 | NA |
| 22 | 51193227 | rs34608236 | T | G | -0.0002783 | 0.0002281 | 0.2200002 | 0.2224096 | 0.168490 | 0.0692891 | NA |
| 22 | 51197266 | rs61290853 | A | G | 0.0000621 | 0.0001710 | 0.7199992 | 0.7164504 | 0.386333 | 0.4229230 | NA |
| 22 | 51198027 | rs34939255 | A | G | -0.0003653 | 0.0001936 | 0.0589997 | 0.0591407 | 0.254562 | 0.0984425 | NA |
| 22 | 51210289 | rs112565862 | C | T | -0.0000330 | 0.0002577 | 0.9000000 | 0.8980612 | 0.129958 | 0.1018370 | NA |
| 22 | 51211106 | rs9628250 | T | C | -0.0003500 | 0.0001919 | 0.0680002 | 0.0681701 | 0.271547 | 0.1671330 | NA |
| 22 | 51211392 | rs3888396 | T | C | -0.0000149 | 0.0002554 | 0.9500000 | 0.9535604 | 0.132638 | 0.1641370 | NA |
| 22 | 51212875 | rs2238837 | A | C | 0.0005281 | 0.0001824 | 0.0038000 | 0.0037799 | 0.331457 | 0.3724040 | NA |
| 22 | 51219006 | rs28729663 | G | A | -0.0000757 | 0.0002342 | 0.7499995 | 0.7465492 | 0.137950 | 0.2052720 | NA |
| 22 | 51237063 | rs3896457 | T | C | 0.0003408 | 0.0001867 | 0.0680002 | 0.0678956 | 0.297974 | 0.2050720 | NA |
bcf preview
1 49298 rs10399793 T C . PASS AF=0.623765 ES:SE:LP:AF:ID -0.000135075:0.00028063:0.200659:0.623765:rs10399793
1 54676 rs2462492 C T . PASS AF=0.400401 ES:SE:LP:AF:ID 7.62448e-05:0.000278018:0.107905:0.400401:rs2462492
1 91536 rs6702460 G T . PASS AF=0.456846 ES:SE:LP:AF:ID 7.53739e-05:0.000273742:0.107905:0.456846:rs6702460
1 534192 rs6680723 C T . PASS AF=0.240959 ES:SE:LP:AF:ID 0.000251863:0.000312686:0.376751:0.240959:rs6680723
1 706368 rs12029736 A G . PASS AF=0.515645 ES:SE:LP:AF:ID 9.66645e-05:0.000194109:0.207608:0.515645:rs12029736
1 729679 rs4951859 C G . PASS AF=0.843204 ES:SE:LP:AF:ID 0.000132679:0.000227092:0.251812:0.843204:rs4951859
1 736289 rs79010578 T A . PASS AF=0.132335 ES:SE:LP:AF:ID -0.000181187:0.000245095:0.337242:0.132335:rs79010578
1 752566 rs3094315 G A . PASS AF=0.838945 ES:SE:LP:AF:ID 0.000176259:0.000219923:0.376751:0.838945:rs3094315
1 752721 rs3131972 A G . PASS AF=0.838573 ES:SE:LP:AF:ID 0.000155273:0.000219687:0.318759:0.838573:rs3131972
1 753405 rs3115860 C A . PASS AF=0.869776 ES:SE:LP:AF:ID 0.000254027:0.000235732:0.552842:0.869776:rs3115860
1 754182 rs3131969 A G . PASS AF=0.869117 ES:SE:LP:AF:ID 0.000226761:0.00023527:0.468521:0.869117:rs3131969
1 754192 rs3131968 A G . PASS AF=0.869215 ES:SE:LP:AF:ID 0.000222426:0.000235363:0.468521:0.869215:rs3131968
1 754334 rs3131967 T C . PASS AF=0.869121 ES:SE:LP:AF:ID 0.000225916:0.000235265:0.468521:0.869121:rs3131967
1 754503 rs3115859 G A . PASS AF=0.838026 ES:SE:LP:AF:ID 0.000142029:0.000219077:0.283997:0.838026:rs3115859
1 754964 rs3131966 C T . PASS AF=0.838657 ES:SE:LP:AF:ID 0.000133003:0.000219693:0.267606:0.838657:rs3131966
1 755775 rs3131965 A G . PASS AF=0.83977 ES:SE:LP:AF:ID 0.000237298:0.000222664:0.537602:0.83977:rs3131965
1 755890 rs3115858 A T . PASS AF=0.8694 ES:SE:LP:AF:ID 0.000256969:0.000234993:0.568636:0.8694:rs3115858
1 756604 rs3131962 A G . PASS AF=0.868947 ES:SE:LP:AF:ID 0.000256467:0.000234402:0.568636:0.868947:rs3131962
1 757640 rs3115853 G A . PASS AF=0.867898 ES:SE:LP:AF:ID 0.000220313:0.000233952:0.455932:0.867898:rs3115853
1 757734 rs4951929 C T . PASS AF=0.86909 ES:SE:LP:AF:ID 0.000253764:0.000234594:0.552842:0.86909:rs4951929
1 757936 rs4951862 C A . PASS AF=0.869098 ES:SE:LP:AF:ID 0.000253753:0.000234612:0.552842:0.869098:rs4951862
1 758144 rs3131956 A G . PASS AF=0.869106 ES:SE:LP:AF:ID 0.000254152:0.000234617:0.552842:0.869106:rs3131956
1 758626 rs3131954 C T . PASS AF=0.869584 ES:SE:LP:AF:ID 0.000250766:0.000235261:0.537602:0.869584:rs3131954
1 760912 rs1048488 C T . PASS AF=0.838306 ES:SE:LP:AF:ID 0.000183901:0.000218661:0.39794:0.838306:rs1048488
1 761147 rs3115850 T C . PASS AF=0.838427 ES:SE:LP:AF:ID 0.000185133:0.000218816:0.39794:0.838427:rs3115850
1 761732 rs2286139 C T . PASS AF=0.862254 ES:SE:LP:AF:ID 0.000238974:0.000233769:0.508638:0.862254:rs2286139
1 763394 rs3115847 G A . PASS AF=0.706753 ES:SE:LP:AF:ID 0.000223395:0.000227575:0.481486:0.706753:rs3115847
1 768253 rs2977608 A C . PASS AF=0.761297 ES:SE:LP:AF:ID 0.000156824:0.000185741:0.39794:0.761297:rs2977608
1 771823 rs2977605 T C . PASS AF=0.868906 ES:SE:LP:AF:ID 0.000253689:0.000234812:0.552842:0.868906:rs2977605
1 772755 rs2905039 A C . PASS AF=0.868916 ES:SE:LP:AF:ID 0.000244:0.000234817:0.522879:0.868916:rs2905039
1 776546 rs12124819 A G . PASS AF=0.265385 ES:SE:LP:AF:ID -3.8696e-05:0.000207479:0.0705811:0.265385:rs12124819
1 777122 rs2980319 A T . PASS AF=0.870039 ES:SE:LP:AF:ID 0.000209576:0.000235296:0.431798:0.870039:rs2980319
1 780785 rs2977612 T A . PASS AF=0.86878 ES:SE:LP:AF:ID 0.000195895:0.000234668:0.39794:0.86878:rs2977612
1 785050 rs2905062 G A . PASS AF=0.868533 ES:SE:LP:AF:ID 0.000193069:0.000234613:0.387216:0.868533:rs2905062
1 785989 rs2980300 T C . PASS AF=0.868474 ES:SE:LP:AF:ID 0.000193958:0.000234759:0.387216:0.868474:rs2980300
1 787399 rs2905055 G T . PASS AF=0.860776 ES:SE:LP:AF:ID 0.000135392:0.000234599:0.251812:0.860776:rs2905055
1 787685 rs2905054 G T . PASS AF=0.861487 ES:SE:LP:AF:ID 0.000192402:0.000234752:0.387216:0.861487:rs2905054
1 787844 rs2905053 C T . PASS AF=0.869224 ES:SE:LP:AF:ID 0.000196957:0.000235618:0.39794:0.869224:rs2905053
1 795988 rs59380221 C T . PASS AF=0.143053 ES:SE:LP:AF:ID -8.29257e-05:0.00024333:0.136677:0.143053:rs59380221
1 798400 rs10900604 A G . PASS AF=0.206591 ES:SE:LP:AF:ID 5.30468e-06:0.000198147:0.00877392:0.206591:rs10900604
1 798959 rs11240777 G A . PASS AF=0.20642 ES:SE:LP:AF:ID 9.28036e-06:0.000198232:0.0177288:0.20642:rs11240777
1 808631 rs11240779 G A . PASS AF=0.772619 ES:SE:LP:AF:ID 3.87052e-05:0.000188574:0.0757207:0.772619:rs11240779
1 808928 rs11240780 C T . PASS AF=0.772847 ES:SE:LP:AF:ID 4.9613e-05:0.000188892:0.102373:0.772847:rs11240780
1 814495 rs74461805 C A . PASS AF=0.340396 ES:SE:LP:AF:ID -7.23319e-05:0.000266157:0.102373:0.340396:rs74461805
1 824398 rs7538305 A C . PASS AF=0.138699 ES:SE:LP:AF:ID -8.66576e-05:0.000235045:0.148742:0.138699:rs7538305
1 830181 rs28444699 A G . PASS AF=0.697255 ES:SE:LP:AF:ID 5.75718e-05:0.000178073:0.124939:0.697255:rs28444699
1 831489 rs4970385 C T . PASS AF=0.705397 ES:SE:LP:AF:ID 0.00011118:0.00017485:0.283997:0.705397:rs4970385
1 831909 rs9697642 C T . PASS AF=0.705442 ES:SE:LP:AF:ID 0.00010971:0.000174845:0.275724:0.705442:rs9697642
1 832066 rs9697380 G C . PASS AF=0.705627 ES:SE:LP:AF:ID 0.000107278:0.000174853:0.267606:0.705627:rs9697380
1 832318 rs4500250 C A . PASS AF=0.705655 ES:SE:LP:AF:ID 0.000108934:0.000174871:0.275724:0.705655:rs4500250