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_K219.vcf.gz --id UKB-b:19886 --data /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/ukbiobank/raw-output/data.batch_41204_K219.txt.gz --cohort_cases 4360 --cohort_controls 458650 --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": "2019-09-12T22:44:04.768194",
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"bcftools_viewCommand.1": "view -h /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/ukb-b-19886/ukb-b-19886.vcf.gz; Date=Sun May 10 03:50:33 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-19886/UKB-b-19886_data.vcf.gz \
--ref-ld-chr ../reference/eur_w_ld_chr/ \
--out /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-19886/ldsc.txt \
--w-ld-chr ../reference/eur_w_ld_chr/
Beginning analysis at Thu Oct 17 14:41:55 2019
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-19886/UKB-b-19886_data.vcf.gz ...
Read summary statistics for 4683522 SNPs.
Dropped 1155 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, 1069735 SNPs remain.
After merging with regression SNP LD, 1069735 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.0028 (0.0011)
Lambda GC: 1.0439
Mean Chi^2: 1.0479
Intercept: 1.0196 (0.0083)
Ratio: 0.4084 (0.1735)
Analysis finished at Thu Oct 17 14:42:49 2019
Total time elapsed: 53.92sQC metrics
Metrics
Metrics
{
"af_correlation": 0.8984,
"inflation_factor": 1.0475,
"mean_EFFECT": 5.7723e-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": 39287,
"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": 1069735,
"ldsc_nsnp_merge_regression_ld": 1069735,
"ldsc_observed_scale_h2_beta": 0.0028,
"ldsc_observed_scale_h2_se": 0.0011,
"ldsc_intercept_beta": 1.0196,
"ldsc_intercept_se": 0.0083,
"ldsc_lambda_gc": 1.0439,
"ldsc_mean_chisq": 1.0479,
"ldsc_ratio": 0.4092
}
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 | 4682376 | 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 | 4683522 | 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 | 8.665683e+00 | 5.766725e+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 | 7.855207e+07 | 5.668308e+07 | 828.0000000 | 3.180441e+07 | 6.886619e+07 | 1.146354e+08 | 2.492385e+08 | ▇▆▅▂▁ |
| numeric | EFFECT | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 6.000000e-07 | 2.608000e-04 | -0.0016536 | -1.673000e-04 | 1.100000e-06 | 1.694000e-04 | 1.620100e-03 | ▁▁▇▁▁ |
| numeric | SE | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 2.504000e-04 | 4.830000e-05 | 0.0001937 | 2.091000e-04 | 2.336000e-04 | 2.821000e-04 | 7.085000e-04 | ▇▂▁▁▁ |
| numeric | PVAL | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 4.923698e-01 | 2.909319e-01 | 0.0000005 | 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 | 4.923697e-01 | 2.909054e-01 | 0.0000005 | 2.380123e-01 | 4.901784e-01 | 7.436289e-01 | 9.999998e-01 | ▇▇▇▇▇ |
| numeric | AF | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 3.651812e-01 | 2.315165e-01 | 0.0802760 | 1.648830e-01 | 3.051510e-01 | 5.299890e-01 | 9.197240e-01 | ▇▅▃▂▂ |
| numeric | AF_reference | 39287 | 0.9916117 | NA | NA | NA | NA | NA | NA | NA | 3.572487e-01 | 2.301304e-01 | 0.0000000 | 1.675320e-01 | 3.057110e-01 | 5.189700e-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 | -0.0008472 | 0.0003565 | 0.0170000 | 0.0174742 | 0.623765 | 0.7821490 | NA |
| 1 | 54676 | rs2462492 | C | T | 0.0005556 | 0.0003532 | 0.1199999 | 0.1156716 | 0.400401 | NA | NA |
| 1 | 86028 | rs114608975 | T | C | -0.0004348 | 0.0005647 | 0.4400003 | 0.4413024 | 0.103556 | 0.0277556 | NA |
| 1 | 91536 | rs6702460 | G | T | -0.0006108 | 0.0003477 | 0.0790005 | 0.0790064 | 0.456846 | 0.4207270 | NA |
| 1 | 534192 | rs6680723 | C | T | -0.0003479 | 0.0003972 | 0.3800004 | 0.3811694 | 0.240959 | NA | NA |
| 1 | 546697 | rs12025928 | A | G | -0.0005022 | 0.0004956 | 0.3100002 | 0.3108975 | 0.913475 | NA | NA |
| 1 | 693731 | rs12238997 | A | G | 0.0001045 | 0.0003329 | 0.7499995 | 0.7536868 | 0.116329 | 0.1417730 | NA |
| 1 | 706368 | rs55727773 | A | G | 0.0000557 | 0.0002466 | 0.8200001 | 0.8214175 | 0.515645 | 0.2751600 | NA |
| 1 | 722670 | rs116030099 | T | C | -0.0001825 | 0.0004069 | 0.6499995 | 0.6537546 | 0.101200 | 0.0413339 | NA |
| 1 | 729679 | rs4951859 | C | G | -0.0001282 | 0.0002885 | 0.6600001 | 0.6566375 | 0.843204 | 0.6399760 | NA |
| CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 22 | 51198027 | rs34939255 | A | G | 0.0001533 | 0.0002459 | 0.5300002 | 0.5329978 | 0.254562 | 0.0984425 | NA |
| 22 | 51208537 | rs72619593 | G | A | 0.0001811 | 0.0003287 | 0.5800000 | 0.5816609 | 0.120735 | 0.1142170 | NA |
| 22 | 51210289 | rs112565862 | C | T | -0.0000333 | 0.0003274 | 0.9199999 | 0.9190996 | 0.129958 | 0.1018370 | NA |
| 22 | 51211106 | rs9628250 | T | C | 0.0001058 | 0.0002438 | 0.6600001 | 0.6642912 | 0.271547 | 0.1671330 | NA |
| 22 | 51211392 | rs3888396 | T | C | -0.0000961 | 0.0003244 | 0.7700005 | 0.7671022 | 0.132638 | 0.1641370 | NA |
| 22 | 51212875 | rs2238837 | A | C | 0.0001946 | 0.0002317 | 0.4000000 | 0.4009961 | 0.331457 | 0.3724040 | NA |
| 22 | 51213613 | rs34726907 | C | T | 0.0001874 | 0.0003052 | 0.5400003 | 0.5391518 | 0.127814 | 0.1727240 | NA |
| 22 | 51216564 | rs9616970 | T | C | 0.0002101 | 0.0003039 | 0.4899999 | 0.4893926 | 0.128328 | 0.1563500 | NA |
| 22 | 51219006 | rs28729663 | G | A | 0.0002107 | 0.0002975 | 0.4799997 | 0.4786310 | 0.137950 | 0.2052720 | NA |
| 22 | 51237063 | rs3896457 | T | C | 0.0001001 | 0.0002372 | 0.6700003 | 0.6728597 | 0.297974 | 0.2050720 | NA |
bcf preview
1 49298 rs10399793 T C . PASS AF=0.623765 ES:SE:LP:AF:ID -0.000847242:0.000356497:1.76955:0.623765:rs10399793
1 54676 rs2462492 C T . PASS AF=0.400401 ES:SE:LP:AF:ID 0.000555621:0.000353178:0.920819:0.400401:rs2462492
1 86028 rs114608975 T C . PASS AF=0.103556 ES:SE:LP:AF:ID -0.000434785:0.000564659:0.356547:0.103556:rs114608975
1 91536 rs6702460 G T . PASS AF=0.456846 ES:SE:LP:AF:ID -0.000610809:0.000347746:1.10237:0.456846:rs6702460
1 534192 rs6680723 C T . PASS AF=0.240959 ES:SE:LP:AF:ID -0.000347862:0.000397219:0.420216:0.240959:rs6680723
1 546697 rs12025928 A G . PASS AF=0.913475 ES:SE:LP:AF:ID -0.000502162:0.000495551:0.508638:0.913475:rs12025928
1 693731 rs12238997 A G . PASS AF=0.116329 ES:SE:LP:AF:ID 0.000104452:0.000332881:0.124939:0.116329:rs12238997
1 706368 rs12029736 A G . PASS AF=0.515645 ES:SE:LP:AF:ID 5.56597e-05:0.000246585:0.0861861:0.515645:rs12029736
1 722670 rs116030099 T C . PASS AF=0.1012 ES:SE:LP:AF:ID -0.000182494:0.000406851:0.187087:0.1012:rs116030099
1 729679 rs4951859 C G . PASS AF=0.843204 ES:SE:LP:AF:ID -0.000128249:0.000288485:0.180456:0.843204:rs4951859
1 731718 rs58276399 T C . PASS AF=0.122312 ES:SE:LP:AF:ID 2.99942e-06:0.000315771:0.00436481:0.122312:rs58276399
1 734349 rs141242758 T C . PASS AF=0.121554 ES:SE:LP:AF:ID 1.2089e-05:0.000315904:0.0132283:0.121554:rs141242758
1 736289 rs79010578 T A . PASS AF=0.132335 ES:SE:LP:AF:ID 0.000107935:0.000311355:0.136677:0.132335:rs79010578
1 752566 rs3094315 G A . PASS AF=0.838945 ES:SE:LP:AF:ID -5.60212e-05:0.000279378:0.0757207:0.838945:rs3094315
1 752721 rs3131972 A G . PASS AF=0.838573 ES:SE:LP:AF:ID -5.29009e-05:0.000279077:0.0705811:0.838573:rs3131972
1 753405 rs3115860 C A . PASS AF=0.869776 ES:SE:LP:AF:ID 0.000123672:0.00029946:0.167491:0.869776:rs3115860
1 753541 rs2073813 G A . PASS AF=0.129876 ES:SE:LP:AF:ID -0.000108:0.000300073:0.142668:0.129876:rs2073813
1 754182 rs3131969 A G . PASS AF=0.869117 ES:SE:LP:AF:ID 0.000105917:0.000298873:0.142668:0.869117:rs3131969
1 754192 rs3131968 A G . PASS AF=0.869215 ES:SE:LP:AF:ID 9.76335e-05:0.000298992:0.130768:0.869215:rs3131968
1 754334 rs3131967 T C . PASS AF=0.869121 ES:SE:LP:AF:ID 0.000114276:0.000298868:0.154902:0.869121:rs3131967
1 754503 rs3115859 G A . PASS AF=0.838026 ES:SE:LP:AF:ID -4.03827e-05:0.000278303:0.0555173:0.838026:rs3115859
1 754964 rs3131966 C T . PASS AF=0.838657 ES:SE:LP:AF:ID -4.4316e-05:0.000279085:0.0604807:0.838657:rs3131966
1 755775 rs3131965 A G . PASS AF=0.83977 ES:SE:LP:AF:ID -3.35081e-05:0.000282859:0.0409586:0.83977:rs3131965
1 755890 rs3115858 A T . PASS AF=0.8694 ES:SE:LP:AF:ID 0.000126936:0.000298522:0.173925:0.8694:rs3115858
1 756604 rs3131962 A G . PASS AF=0.868947 ES:SE:LP:AF:ID 0.000103431:0.000297771:0.136677:0.868947:rs3131962
1 757640 rs3115853 G A . PASS AF=0.867898 ES:SE:LP:AF:ID 6.57261e-05:0.0002972:0.0861861:0.867898:rs3115853
1 757734 rs4951929 C T . PASS AF=0.86909 ES:SE:LP:AF:ID 0.00010658:0.000298014:0.142668:0.86909:rs4951929
1 757936 rs4951862 C A . PASS AF=0.869098 ES:SE:LP:AF:ID 0.000106566:0.000298037:0.142668:0.869098:rs4951862
1 758144 rs3131956 A G . PASS AF=0.869106 ES:SE:LP:AF:ID 0.000106589:0.000298044:0.142668:0.869106:rs3131956
1 758626 rs3131954 C T . PASS AF=0.869584 ES:SE:LP:AF:ID 0.000126435:0.000298862:0.173925:0.869584:rs3131954
1 760912 rs1048488 C T . PASS AF=0.838306 ES:SE:LP:AF:ID -3.99208e-05:0.000277775:0.05061:0.838306:rs1048488
1 761147 rs3115850 T C . PASS AF=0.838427 ES:SE:LP:AF:ID -4.43089e-05:0.000277971:0.0604807:0.838427:rs3115850
1 761732 rs2286139 C T . PASS AF=0.862254 ES:SE:LP:AF:ID 2.37076e-05:0.000296966:0.0268721:0.862254:rs2286139
1 763394 rs3115847 G A . PASS AF=0.706753 ES:SE:LP:AF:ID 0.000125016:0.000289098:0.173925:0.706753:rs3115847
1 766007 rs61768174 A C . PASS AF=0.105145 ES:SE:LP:AF:ID 3.48544e-05:0.000333035:0.0362122:0.105145:rs61768174
1 768253 rs2977608 A C . PASS AF=0.761297 ES:SE:LP:AF:ID 0.000168597:0.000235954:0.327902:0.761297:rs2977608
1 768448 rs12562034 G A . PASS AF=0.10649 ES:SE:LP:AF:ID -0.000201833:0.000325218:0.275724:0.10649:rs12562034
1 769223 rs60320384 C G . PASS AF=0.129581 ES:SE:LP:AF:ID -8.76414e-05:0.000299894:0.113509:0.129581:rs60320384
1 771823 rs2977605 T C . PASS AF=0.868906 ES:SE:LP:AF:ID 0.000104085:0.000298292:0.136677:0.868906:rs2977605
1 771967 rs59066358 G A . PASS AF=0.129682 ES:SE:LP:AF:ID -9.23633e-05:0.0002997:0.119186:0.129682:rs59066358
1 772755 rs2905039 A C . PASS AF=0.868916 ES:SE:LP:AF:ID 0.000131189:0.000298298:0.180456:0.868916:rs2905039
1 776546 rs12124819 A G . PASS AF=0.265385 ES:SE:LP:AF:ID 0.000577864:0.00026357:1.55284:0.265385:rs12124819
1 777122 rs2980319 A T . PASS AF=0.870039 ES:SE:LP:AF:ID 9.00824e-05:0.000298906:0.119186:0.870039:rs2980319
1 777232 rs112618790 C T . PASS AF=0.095141 ES:SE:LP:AF:ID -0.000219099:0.000346427:0.275724:0.095141:rs112618790
1 778745 rs1055606 A G . PASS AF=0.12858 ES:SE:LP:AF:ID -7.15991e-05:0.000300086:0.091515:0.12858:rs1055606
1 779322 rs4040617 A G . PASS AF=0.128877 ES:SE:LP:AF:ID -6.53748e-05:0.000299577:0.0809219:0.128877:rs4040617
1 780785 rs2977612 T A . PASS AF=0.86878 ES:SE:LP:AF:ID 6.85281e-05:0.000298109:0.0861861:0.86878:rs2977612
1 781845 rs61768199 A G . PASS AF=0.101873 ES:SE:LP:AF:ID 6.07001e-06:0.000337786:0.00436481:0.101873:rs61768199
1 782981 rs6594026 C T . PASS AF=0.129518 ES:SE:LP:AF:ID -8.8454e-05:0.000299481:0.113509:0.129518:rs6594026
1 785050 rs2905062 G A . PASS AF=0.868533 ES:SE:LP:AF:ID 4.33432e-05:0.000298039:0.0555173:0.868533:rs2905062