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_E785.vcf.gz --id UKB-b:17462 --data /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/ukbiobank/raw-output/data.batch_41204_E785.txt.gz --cohort_cases 3439 --cohort_controls 459571 --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": "2019-09-13T11:21:24.171782",
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"bcftools_viewCommand.1": "view -h /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/ukb-b-17462/ukb-b-17462.vcf.gz; Date=Sun May 10 02:25:41 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-17462/UKB-b-17462_data.vcf.gz \
--ref-ld-chr ../reference/eur_w_ld_chr/ \
--out /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-17462/ldsc.txt \
--w-ld-chr ../reference/eur_w_ld_chr/
Beginning analysis at Thu Oct 17 14:40:19 2019
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-17462/UKB-b-17462_data.vcf.gz ...
Read summary statistics for 4276082 SNPs.
Dropped 897 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, 1002490 SNPs remain.
After merging with regression SNP LD, 1002490 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.0041 (0.0012)
Lambda GC: 1.0544
Mean Chi^2: 1.0643
Intercept: 1.0236 (0.0085)
Ratio: 0.3665 (0.1319)
Analysis finished at Thu Oct 17 14:41:12 2019
Total time elapsed: 53.76sQC metrics
Metrics
Metrics
{
"af_correlation": 0.8857,
"inflation_factor": 1.0475,
"mean_EFFECT": 6.3981e-07,
"n": "-Inf",
"n_snps": 9851866,
"n_clumped_hits": 2,
"n_p_sig": 7,
"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": 35251,
"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": 1002490,
"ldsc_nsnp_merge_regression_ld": 1002490,
"ldsc_observed_scale_h2_beta": 0.0041,
"ldsc_observed_scale_h2_se": 0.0012,
"ldsc_intercept_beta": 1.0236,
"ldsc_intercept_se": 0.0085,
"ldsc_lambda_gc": 1.0544,
"ldsc_mean_chisq": 1.0643,
"ldsc_ratio": 0.367
}
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 | 4275190 | 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 | 4276082 | 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 | 8.654921e+00 | 5.765738e+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 | 7.859000e+07 | 5.672427e+07 | 828.0000000 | 3.169487e+07 | 6.896091e+07 | 1.146855e+08 | 2.492385e+08 | ▇▆▅▂▁ |
| numeric | EFFECT | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 6.000000e-07 | 2.236000e-04 | -0.0013301 | -1.451000e-04 | 7.000000e-07 | 1.457000e-04 | 1.532200e-03 | ▁▂▇▁▁ |
| numeric | SE | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 2.138000e-04 | 3.380000e-05 | 0.0001721 | 1.846000e-04 | 2.025000e-04 | 2.366000e-04 | 6.294000e-04 | ▇▁▁▁▁ |
| numeric | PVAL | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 4.907661e-01 | 2.915061e-01 | 0.0000000 | 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 | 4.907669e-01 | 2.914805e-01 | 0.0000000 | 2.354641e-01 | 4.888758e-01 | 7.431997e-01 | 1.000000e+00 | ▇▇▇▇▇ |
| numeric | AF | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 3.824625e-01 | 2.209996e-01 | 0.1017740 | 1.903840e-01 | 3.295660e-01 | 5.437820e-01 | 8.982260e-01 | ▇▅▃▂▂ |
| numeric | AF_reference | 35251 | 0.9917562 | NA | NA | NA | NA | NA | NA | NA | 3.727845e-01 | 2.225631e-01 | 0.0000000 | 1.894970e-01 | 3.278750e-01 | 5.319490e-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 | 0.0002672 | 0.0003167 | 0.4000000 | 0.3988324 | 0.623765 | 0.7821490 | NA |
| 1 | 54676 | rs2462492 | C | T | -0.0001649 | 0.0003138 | 0.5999997 | 0.5993159 | 0.400401 | NA | NA |
| 1 | 86028 | rs114608975 | T | C | -0.0001582 | 0.0005017 | 0.7499995 | 0.7524704 | 0.103556 | 0.0277556 | NA |
| 1 | 91536 | rs6702460 | G | T | 0.0001888 | 0.0003089 | 0.5400003 | 0.5411101 | 0.456846 | 0.4207270 | NA |
| 1 | 534192 | rs6680723 | C | T | 0.0004967 | 0.0003529 | 0.1600000 | 0.1593028 | 0.240959 | NA | NA |
| 1 | 693731 | rs12238997 | A | G | 0.0000567 | 0.0002957 | 0.8499999 | 0.8479826 | 0.116329 | 0.1417730 | NA |
| 1 | 706368 | rs55727773 | A | G | -0.0001351 | 0.0002191 | 0.5400003 | 0.5374836 | 0.515645 | 0.2751600 | NA |
| 1 | 729679 | rs4951859 | C | G | 0.0000827 | 0.0002563 | 0.7499995 | 0.7470163 | 0.843204 | 0.6399760 | NA |
| 1 | 731718 | rs142557973 | T | C | 0.0000018 | 0.0002805 | 0.9900000 | 0.9949659 | 0.122312 | 0.1543530 | NA |
| 1 | 734349 | rs141242758 | T | C | -0.0000030 | 0.0002807 | 0.9900000 | 0.9915269 | 0.121554 | 0.1525560 | NA |
| CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 22 | 51198027 | rs34939255 | A | G | -0.0006615 | 0.0002185 | 0.0025000 | 0.0024638 | 0.254562 | 0.0984425 | NA |
| 22 | 51208537 | rs72619593 | G | A | 0.0006311 | 0.0002920 | 0.0309999 | 0.0306997 | 0.120735 | 0.1142170 | NA |
| 22 | 51210289 | rs112565862 | C | T | -0.0001859 | 0.0002909 | 0.5199996 | 0.5226501 | 0.129958 | 0.1018370 | NA |
| 22 | 51211106 | rs9628250 | T | C | -0.0006654 | 0.0002166 | 0.0021000 | 0.0021264 | 0.271547 | 0.1671330 | NA |
| 22 | 51211392 | rs3888396 | T | C | -0.0002327 | 0.0002882 | 0.4199997 | 0.4194205 | 0.132638 | 0.1641370 | NA |
| 22 | 51212875 | rs2238837 | A | C | 0.0008938 | 0.0002058 | 0.0000140 | 0.0000141 | 0.331457 | 0.3724040 | NA |
| 22 | 51213613 | rs34726907 | C | T | 0.0002899 | 0.0002712 | 0.2800000 | 0.2849966 | 0.127814 | 0.1727240 | NA |
| 22 | 51216564 | rs9616970 | T | C | 0.0003326 | 0.0002700 | 0.2200002 | 0.2180382 | 0.128328 | 0.1563500 | NA |
| 22 | 51219006 | rs28729663 | G | A | 0.0003572 | 0.0002643 | 0.1800002 | 0.1765264 | 0.137950 | 0.2052720 | NA |
| 22 | 51237063 | rs3896457 | T | C | 0.0007194 | 0.0002107 | 0.0006400 | 0.0006395 | 0.297974 | 0.2050720 | NA |
bcf preview
1 49298 rs10399793 T C . PASS AF=0.623765 ES:SE:LP:AF:ID 0.000267221:0.000316722:0.39794:0.623765:rs10399793
1 54676 rs2462492 C T . PASS AF=0.400401 ES:SE:LP:AF:ID -0.000164852:0.000313774:0.221849:0.400401:rs2462492
1 86028 rs114608975 T C . PASS AF=0.103556 ES:SE:LP:AF:ID -0.000158215:0.000501659:0.124939:0.103556:rs114608975
1 91536 rs6702460 G T . PASS AF=0.456846 ES:SE:LP:AF:ID 0.000188809:0.000308948:0.267606:0.456846:rs6702460
1 534192 rs6680723 C T . PASS AF=0.240959 ES:SE:LP:AF:ID 0.00049668:0.000352901:0.79588:0.240959:rs6680723
1 693731 rs12238997 A G . PASS AF=0.116329 ES:SE:LP:AF:ID 5.66917e-05:0.000295742:0.0705811:0.116329:rs12238997
1 706368 rs12029736 A G . PASS AF=0.515645 ES:SE:LP:AF:ID -0.000135086:0.000219074:0.267606:0.515645:rs12029736
1 729679 rs4951859 C G . PASS AF=0.843204 ES:SE:LP:AF:ID 8.26756e-05:0.000256298:0.124939:0.843204:rs4951859
1 731718 rs58276399 T C . PASS AF=0.122312 ES:SE:LP:AF:ID 1.77004e-06:0.00028054:0.00436481:0.122312:rs58276399
1 734349 rs141242758 T C . PASS AF=0.121554 ES:SE:LP:AF:ID -2.9805e-06:0.000280658:0.00436481:0.121554:rs141242758
1 736289 rs79010578 T A . PASS AF=0.132335 ES:SE:LP:AF:ID -8.37182e-05:0.000276617:0.119186:0.132335:rs79010578
1 752566 rs3094315 G A . PASS AF=0.838945 ES:SE:LP:AF:ID -3.01213e-05:0.000248208:0.0457575:0.838945:rs3094315
1 752721 rs3131972 A G . PASS AF=0.838573 ES:SE:LP:AF:ID -2.95852e-05:0.000247941:0.0409586:0.838573:rs3131972
1 753405 rs3115860 C A . PASS AF=0.869776 ES:SE:LP:AF:ID -0.000103364:0.000266049:0.154902:0.869776:rs3115860
1 753541 rs2073813 G A . PASS AF=0.129876 ES:SE:LP:AF:ID 0.000123139:0.000266594:0.19382:0.129876:rs2073813
1 754182 rs3131969 A G . PASS AF=0.869117 ES:SE:LP:AF:ID -0.000102495:0.000265528:0.154902:0.869117:rs3131969
1 754192 rs3131968 A G . PASS AF=0.869215 ES:SE:LP:AF:ID -0.000110498:0.000265633:0.167491:0.869215:rs3131968
1 754334 rs3131967 T C . PASS AF=0.869121 ES:SE:LP:AF:ID -9.42845e-05:0.000265523:0.142668:0.869121:rs3131967
1 754503 rs3115859 G A . PASS AF=0.838026 ES:SE:LP:AF:ID -2.33819e-05:0.000247253:0.0362122:0.838026:rs3115859
1 754964 rs3131966 C T . PASS AF=0.838657 ES:SE:LP:AF:ID -2.11485e-05:0.000247947:0.0315171:0.838657:rs3131966
1 755775 rs3131965 A G . PASS AF=0.83977 ES:SE:LP:AF:ID -1.67601e-05:0.000251301:0.0222764:0.83977:rs3131965
1 755890 rs3115858 A T . PASS AF=0.8694 ES:SE:LP:AF:ID -9.1226e-05:0.000265216:0.136677:0.8694:rs3115858
1 756604 rs3131962 A G . PASS AF=0.868947 ES:SE:LP:AF:ID -9.52627e-05:0.000264548:0.142668:0.868947:rs3131962
1 757640 rs3115853 G A . PASS AF=0.867898 ES:SE:LP:AF:ID -7.88407e-05:0.000264041:0.113509:0.867898:rs3115853
1 757734 rs4951929 C T . PASS AF=0.86909 ES:SE:LP:AF:ID -9.48148e-05:0.000264765:0.142668:0.86909:rs4951929
1 757936 rs4951862 C A . PASS AF=0.869098 ES:SE:LP:AF:ID -9.5009e-05:0.000264785:0.142668:0.869098:rs4951862
1 758144 rs3131956 A G . PASS AF=0.869106 ES:SE:LP:AF:ID -9.53663e-05:0.000264791:0.142668:0.869106:rs3131956
1 758626 rs3131954 C T . PASS AF=0.869584 ES:SE:LP:AF:ID -8.03537e-05:0.000265518:0.119186:0.869584:rs3131954
1 760912 rs1048488 C T . PASS AF=0.838306 ES:SE:LP:AF:ID -4.71811e-05:0.000246784:0.0705811:0.838306:rs1048488
1 761147 rs3115850 T C . PASS AF=0.838427 ES:SE:LP:AF:ID -4.47909e-05:0.000246958:0.0655015:0.838427:rs3115850
1 761732 rs2286139 C T . PASS AF=0.862254 ES:SE:LP:AF:ID -7.02383e-05:0.000263834:0.102373:0.862254:rs2286139
1 763394 rs3115847 G A . PASS AF=0.706753 ES:SE:LP:AF:ID 6.77015e-05:0.000256843:0.102373:0.706753:rs3115847
1 766007 rs61768174 A C . PASS AF=0.105145 ES:SE:LP:AF:ID 0.000154947:0.000295878:0.221849:0.105145:rs61768174
1 768253 rs2977608 A C . PASS AF=0.761297 ES:SE:LP:AF:ID -0.000177655:0.000209629:0.39794:0.761297:rs2977608
1 768448 rs12562034 G A . PASS AF=0.10649 ES:SE:LP:AF:ID 0.000252646:0.000288934:0.420216:0.10649:rs12562034
1 769223 rs60320384 C G . PASS AF=0.129581 ES:SE:LP:AF:ID 0.000124331:0.000266435:0.19382:0.129581:rs60320384
1 771823 rs2977605 T C . PASS AF=0.868906 ES:SE:LP:AF:ID -9.03879e-05:0.000265011:0.136677:0.868906:rs2977605
1 771967 rs59066358 G A . PASS AF=0.129682 ES:SE:LP:AF:ID 0.000109959:0.000266263:0.167491:0.129682:rs59066358
1 772755 rs2905039 A C . PASS AF=0.868916 ES:SE:LP:AF:ID -7.2566e-05:0.000265016:0.107905:0.868916:rs2905039
1 776546 rs12124819 A G . PASS AF=0.265385 ES:SE:LP:AF:ID -0.000103403:0.000234163:0.180456:0.265385:rs12124819
1 777122 rs2980319 A T . PASS AF=0.870039 ES:SE:LP:AF:ID -0.000104153:0.000265557:0.161151:0.870039:rs2980319
1 778745 rs1055606 A G . PASS AF=0.12858 ES:SE:LP:AF:ID 0.00012674:0.000266606:0.200659:0.12858:rs1055606
1 779322 rs4040617 A G . PASS AF=0.128877 ES:SE:LP:AF:ID 0.00011525:0.000266153:0.180456:0.128877:rs4040617
1 780785 rs2977612 T A . PASS AF=0.86878 ES:SE:LP:AF:ID -0.000102128:0.000264848:0.154902:0.86878:rs2977612
1 781845 rs61768199 A G . PASS AF=0.101873 ES:SE:LP:AF:ID 9.17197e-05:0.000300099:0.119186:0.101873:rs61768199
1 782981 rs6594026 C T . PASS AF=0.129518 ES:SE:LP:AF:ID 0.00011134:0.000266068:0.167491:0.129518:rs6594026
1 785050 rs2905062 G A . PASS AF=0.868533 ES:SE:LP:AF:ID -8.405e-05:0.000264787:0.124939:0.868533:rs2905062
1 785989 rs2980300 T C . PASS AF=0.868474 ES:SE:LP:AF:ID -8.61428e-05:0.000264952:0.124939:0.868474:rs2980300
1 787399 rs2905055 G T . PASS AF=0.860776 ES:SE:LP:AF:ID -9.46905e-05:0.000264771:0.142668:0.860776:rs2905055
1 787606 rs3863622 G T . PASS AF=0.128466 ES:SE:LP:AF:ID 0.00011419:0.000267502:0.173925:0.128466:rs3863622