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_6151_5.vcf.gz --id UKB-b:9571 --data /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/ukbiobank/raw-output/data.batch_6151_5.txt.gz --cohort_cases 9113 --cohort_controls 451227 --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": "2019-09-13T01:57:30.479110",
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"bcftools_viewCommand.1": "view -h /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/ukb-b-9571/ukb-b-9571.vcf.gz; Date=Sun May 10 06:12:28 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-9571/UKB-b-9571_data.vcf.gz \
--ref-ld-chr ../reference/eur_w_ld_chr/ \
--out /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-9571/ldsc.txt \
--w-ld-chr ../reference/eur_w_ld_chr/
Beginning analysis at Thu Oct 17 14:42:48 2019
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-9571/UKB-b-9571_data.vcf.gz ...
Read summary statistics for 5815209 SNPs.
Dropped 2495 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, 1201062 SNPs remain.
After merging with regression SNP LD, 1201062 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.0067 (0.0013)
Lambda GC: 1.0634
Mean Chi^2: 1.0786
Intercept: 1.0143 (0.0077)
Ratio: 0.1815 (0.0981)
Analysis finished at Thu Oct 17 14:43:51 2019
Total time elapsed: 1.0m:2.63sQC metrics
Metrics
Metrics
{
"af_correlation": 0.9218,
"inflation_factor": 1.0475,
"mean_EFFECT": -1.5137e-07,
"n": "-Inf",
"n_snps": 9851866,
"n_clumped_hits": 7,
"n_p_sig": 307,
"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": 52044,
"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": 1201062,
"ldsc_nsnp_merge_regression_ld": 1201062,
"ldsc_observed_scale_h2_beta": 0.0067,
"ldsc_observed_scale_h2_se": 0.0013,
"ldsc_intercept_beta": 1.0143,
"ldsc_intercept_se": 0.0077,
"ldsc_lambda_gc": 1.0634,
"ldsc_mean_chisq": 1.0786,
"ldsc_ratio": 0.1819
}
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 | 5812730 | 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 | 5815209 | 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 | 8.669761e+00 | 5.762427e+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 | 7.860192e+07 | 5.654112e+07 | 828.0000000 | 3.199830e+07 | 6.904876e+07 | 1.145251e+08 | 2.492385e+08 | ▇▆▅▂▁ |
| numeric | EFFECT | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | -2.000000e-07 | 4.489000e-04 | -0.0039666 | -2.709000e-04 | -4.000000e-07 | 2.720000e-04 | 3.420600e-03 | ▁▁▇▁▁ |
| numeric | SE | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 4.159000e-04 | 1.302000e-04 | 0.0002799 | 3.082000e-04 | 3.660000e-04 | 4.929000e-04 | 1.436500e-03 | ▇▂▁▁▁ |
| numeric | PVAL | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 4.899569e-01 | 2.923243e-01 | 0.0000000 | 2.300001e-01 | 4.899999e-01 | 7.400005e-01 | 1.000000e+00 | ▇▇▇▇▇ |
| numeric | PVAL_ztest | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 4.899561e-01 | 2.922997e-01 | 0.0000000 | 2.339171e-01 | 4.861955e-01 | 7.438787e-01 | 1.000000e+00 | ▇▇▇▇▇ |
| numeric | AF | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 3.188263e-01 | 2.512736e-01 | 0.0384070 | 1.052040e-01 | 2.398030e-01 | 4.849610e-01 | 9.615930e-01 | ▇▃▂▂▁ |
| numeric | AF_reference | 52044 | 0.9910504 | NA | NA | NA | NA | NA | NA | NA | 3.148541e-01 | 2.448562e-01 | 0.0000000 | 1.136180e-01 | 2.464060e-01 | 4.750400e-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 | -0.0000550 | 0.0005151 | 0.9100000 | 0.9149956 | 0.623788 | 0.7821490 | NA |
| 1 | 54676 | rs2462492 | C | T | -0.0002771 | 0.0005103 | 0.5900000 | 0.5870908 | 0.400410 | NA | NA |
| 1 | 86028 | rs114608975 | T | C | 0.0005308 | 0.0008159 | 0.5199996 | 0.5153521 | 0.103546 | 0.0277556 | NA |
| 1 | 91536 | rs6702460 | G | T | 0.0000237 | 0.0005024 | 0.9599999 | 0.9623534 | 0.456857 | 0.4207270 | NA |
| 1 | 234313 | rs8179466 | C | T | -0.0006579 | 0.0009907 | 0.5099998 | 0.5066187 | 0.074507 | NA | NA |
| 1 | 534192 | rs6680723 | C | T | 0.0005050 | 0.0005740 | 0.3800004 | 0.3789633 | 0.240959 | NA | NA |
| 1 | 546697 | rs12025928 | A | G | -0.0005374 | 0.0007161 | 0.4500005 | 0.4529522 | 0.913490 | NA | NA |
| 1 | 693731 | rs12238997 | A | G | 0.0002115 | 0.0004810 | 0.6600001 | 0.6601001 | 0.116342 | 0.1417730 | NA |
| 1 | 705882 | rs72631875 | G | A | 0.0003920 | 0.0007049 | 0.5800000 | 0.5781006 | 0.067264 | 0.0315495 | NA |
| 1 | 706368 | rs55727773 | A | G | 0.0002062 | 0.0003563 | 0.5600000 | 0.5628141 | 0.515584 | 0.2751600 | NA |
| CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 22 | 51218377 | rs2519461 | G | C | -0.0007503 | 0.0005568 | 0.1800002 | 0.1777918 | 0.073623 | 0.0826677 | NA |
| 22 | 51219006 | rs28729663 | G | A | -0.0003304 | 0.0004298 | 0.4400003 | 0.4421488 | 0.137943 | 0.2052720 | NA |
| 22 | 51219387 | rs9616832 | T | C | -0.0007344 | 0.0005579 | 0.1900002 | 0.1880501 | 0.073746 | 0.0654952 | NA |
| 22 | 51219704 | rs147475742 | G | A | -0.0004050 | 0.0007476 | 0.5900000 | 0.5879690 | 0.041965 | 0.0473243 | NA |
| 22 | 51221190 | rs369304721 | G | A | -0.0003279 | 0.0007465 | 0.6600001 | 0.6604667 | 0.049731 | NA | NA |
| 22 | 51221731 | rs115055839 | T | C | -0.0007324 | 0.0005583 | 0.1900002 | 0.1895671 | 0.073236 | 0.0625000 | NA |
| 22 | 51222100 | rs114553188 | G | T | -0.0003315 | 0.0006573 | 0.6100002 | 0.6140243 | 0.054450 | 0.0880591 | NA |
| 22 | 51223637 | rs375798137 | G | A | -0.0003315 | 0.0006605 | 0.6200004 | 0.6157698 | 0.054079 | 0.0788738 | NA |
| 22 | 51229805 | rs9616985 | T | C | -0.0007240 | 0.0005603 | 0.2000000 | 0.1963084 | 0.073070 | 0.0730831 | NA |
| 22 | 51237063 | rs3896457 | T | C | 0.0004620 | 0.0003427 | 0.1800002 | 0.1775749 | 0.298005 | 0.2050720 | NA |
bcf preview
1 49298 rs10399793 T C . PASS AF=0.623788 ES:SE:LP:AF:ID -5.49789e-05:0.000515075:0.0409586:0.623788:rs10399793
1 54676 rs2462492 C T . PASS AF=0.40041 ES:SE:LP:AF:ID -0.000277105:0.000510269:0.229148:0.40041:rs2462492
1 86028 rs114608975 T C . PASS AF=0.103546 ES:SE:LP:AF:ID 0.000530753:0.000815882:0.283997:0.103546:rs114608975
1 91536 rs6702460 G T . PASS AF=0.456857 ES:SE:LP:AF:ID 2.37137e-05:0.000502403:0.0177288:0.456857:rs6702460
1 234313 rs8179466 C T . PASS AF=0.074507 ES:SE:LP:AF:ID -0.000657937:0.000990702:0.29243:0.074507:rs8179466
1 534192 rs6680723 C T . PASS AF=0.240959 ES:SE:LP:AF:ID 0.000504979:0.000573965:0.420216:0.240959:rs6680723
1 546697 rs12025928 A G . PASS AF=0.91349 ES:SE:LP:AF:ID -0.000537425:0.000716087:0.346787:0.91349:rs12025928
1 693731 rs12238997 A G . PASS AF=0.116342 ES:SE:LP:AF:ID 0.000211512:0.000480955:0.180456:0.116342:rs12238997
1 705882 rs72631875 G A . PASS AF=0.067264 ES:SE:LP:AF:ID 0.000392032:0.000704889:0.236572:0.067264:rs72631875
1 706368 rs12029736 A G . PASS AF=0.515584 ES:SE:LP:AF:ID 0.000206161:0.000356269:0.251812:0.515584:rs12029736
1 722670 rs116030099 T C . PASS AF=0.101206 ES:SE:LP:AF:ID 7.62339e-05:0.00058782:0.0457575:0.101206:rs116030099
1 723891 rs2977670 G C . PASS AF=0.959072 ES:SE:LP:AF:ID -0.00022882:0.000777965:0.113509:0.959072:rs2977670
1 725060 rs865924913 A T . PASS AF=0.05326 ES:SE:LP:AF:ID 0.000497282:0.00112347:0.180456:0.05326:rs865924913
1 729679 rs4951859 C G . PASS AF=0.843178 ES:SE:LP:AF:ID -0.0001576:0.000416825:0.148742:0.843178:rs4951859
1 730087 rs148120343 T C . PASS AF=0.055936 ES:SE:LP:AF:ID -0.000729968:0.000674795:0.552842:0.055936:rs148120343
1 731718 rs58276399 T C . PASS AF=0.122324 ES:SE:LP:AF:ID 0.000129856:0.00045624:0.107905:0.122324:rs58276399
1 734349 rs141242758 T C . PASS AF=0.121567 ES:SE:LP:AF:ID 0.0001242:0.000456423:0.102373:0.121567:rs141242758
1 736289 rs79010578 T A . PASS AF=0.132371 ES:SE:LP:AF:ID 8.87411e-05:0.000449852:0.0757207:0.132371:rs79010578
1 752566 rs3094315 G A . PASS AF=0.838923 ES:SE:LP:AF:ID -3.41004e-05:0.000403669:0.0315171:0.838923:rs3094315
1 752721 rs3131972 A G . PASS AF=0.838551 ES:SE:LP:AF:ID -2.86412e-05:0.000403234:0.0268721:0.838551:rs3131972
1 753405 rs3115860 C A . PASS AF=0.869773 ES:SE:LP:AF:ID -2.06645e-05:0.000432687:0.0177288:0.869773:rs3115860
1 753541 rs2073813 G A . PASS AF=0.129876 ES:SE:LP:AF:ID 1.24096e-05:0.00043357:0.00877392:0.129876:rs2073813
1 754182 rs3131969 A G . PASS AF=0.869115 ES:SE:LP:AF:ID -3.0799e-06:0.000431842:0.00436481:0.869115:rs3131969
1 754192 rs3131968 A G . PASS AF=0.869212 ES:SE:LP:AF:ID 1.05331e-05:0.000432013:0.00877392:0.869212:rs3131968
1 754334 rs3131967 T C . PASS AF=0.869117 ES:SE:LP:AF:ID -3.86742e-06:0.000431833:0.00436481:0.869117:rs3131967
1 754503 rs3115859 G A . PASS AF=0.838004 ES:SE:LP:AF:ID -3.22057e-05:0.00040212:0.0268721:0.838004:rs3115859
1 754964 rs3131966 C T . PASS AF=0.838637 ES:SE:LP:AF:ID -3.4642e-05:0.000403254:0.0315171:0.838637:rs3131966
1 755775 rs3131965 A G . PASS AF=0.839752 ES:SE:LP:AF:ID 1.82558e-05:0.000408698:0.0177288:0.839752:rs3131965
1 755890 rs3115858 A T . PASS AF=0.869397 ES:SE:LP:AF:ID 1.9251e-05:0.000431332:0.0177288:0.869397:rs3115858
1 756604 rs3131962 A G . PASS AF=0.868944 ES:SE:LP:AF:ID 2.65241e-05:0.000430246:0.0222764:0.868944:rs3131962
1 757640 rs3115853 G A . PASS AF=0.867895 ES:SE:LP:AF:ID 1.90612e-05:0.000429422:0.0177288:0.867895:rs3115853
1 757734 rs4951929 C T . PASS AF=0.869087 ES:SE:LP:AF:ID 2.92738e-05:0.000430598:0.0222764:0.869087:rs4951929
1 757936 rs4951862 C A . PASS AF=0.869095 ES:SE:LP:AF:ID 2.84467e-05:0.000430631:0.0222764:0.869095:rs4951862
1 758144 rs3131956 A G . PASS AF=0.869103 ES:SE:LP:AF:ID 2.92097e-05:0.000430641:0.0222764:0.869103:rs3131956
1 758626 rs3131954 C T . PASS AF=0.869581 ES:SE:LP:AF:ID 1.24203e-05:0.000431823:0.00877392:0.869581:rs3131954
1 760912 rs1048488 C T . PASS AF=0.838285 ES:SE:LP:AF:ID -3.24556e-05:0.000401355:0.0268721:0.838285:rs1048488
1 761147 rs3115850 T C . PASS AF=0.838406 ES:SE:LP:AF:ID -2.87278e-05:0.000401637:0.0268721:0.838406:rs3115850
1 761732 rs2286139 C T . PASS AF=0.862249 ES:SE:LP:AF:ID -0.000101752:0.000429094:0.091515:0.862249:rs2286139
1 763394 rs3115847 G A . PASS AF=0.706771 ES:SE:LP:AF:ID 0.000205581:0.000417714:0.207608:0.706771:rs3115847
1 766007 rs61768174 A C . PASS AF=0.105159 ES:SE:LP:AF:ID -9.74937e-05:0.000481182:0.0757207:0.105159:rs61768174
1 768253 rs2977608 A C . PASS AF=0.761255 ES:SE:LP:AF:ID 5.20512e-05:0.000340927:0.0555173:0.761255:rs2977608
1 768448 rs12562034 G A . PASS AF=0.106528 ES:SE:LP:AF:ID -1.97499e-05:0.000469884:0.0132283:0.106528:rs12562034
1 769223 rs60320384 C G . PASS AF=0.129582 ES:SE:LP:AF:ID -8.24525e-06:0.000433309:0.00877392:0.129582:rs60320384
1 771823 rs2977605 T C . PASS AF=0.868903 ES:SE:LP:AF:ID 2.89452e-05:0.000430996:0.0222764:0.868903:rs2977605
1 771967 rs59066358 G A . PASS AF=0.129683 ES:SE:LP:AF:ID -5.20992e-06:0.000433027:0.00436481:0.129683:rs59066358
1 772755 rs2905039 A C . PASS AF=0.868913 ES:SE:LP:AF:ID 4.42732e-05:0.000431004:0.0362122:0.868913:rs2905039
1 776546 rs12124819 A G . PASS AF=0.265374 ES:SE:LP:AF:ID -0.000358028:0.000380852:0.455932:0.265374:rs12124819
1 777122 rs2980319 A T . PASS AF=0.870033 ES:SE:LP:AF:ID 7.89361e-05:0.000431883:0.0705811:0.870033:rs2980319
1 777232 rs112618790 C T . PASS AF=0.095179 ES:SE:LP:AF:ID -0.000202978:0.00050051:0.161151:0.095179:rs112618790
1 778745 rs1055606 A G . PASS AF=0.128585 ES:SE:LP:AF:ID -5.34137e-05:0.000433585:0.0457575:0.128585:rs1055606