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_5257.vcf.gz --id UKB-b:15178 --data /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/ukbiobank/raw-output/data.batch_5257.txt.gz --cohort_controls 97653 --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": "2019-09-12T23:16:49.330928",
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}
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-15178/UKB-b-15178_data.vcf.gz \
--ref-ld-chr ../reference/eur_w_ld_chr/ \
--out /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-15178/ldsc.txt \
--w-ld-chr ../reference/eur_w_ld_chr/
Beginning analysis at Thu Oct 17 14:44:03 2019
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-15178/UKB-b-15178_data.vcf.gz ...
Read summary statistics for 9007739 SNPs.
Dropped 8738 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, 1287226 SNPs remain.
After merging with regression SNP LD, 1287226 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.2597 (0.016)
Lambda GC: 1.3021
Mean Chi^2: 1.55
Intercept: 1.0642 (0.011)
Ratio: 0.1167 (0.0199)
Analysis finished at Thu Oct 17 14:45:41 2019
Total time elapsed: 1.0m:38.12sQC metrics
Metrics
Metrics
{
"af_correlation": 0.9479,
"inflation_factor": 1.1999,
"mean_EFFECT": -0.0001,
"n": "-Inf",
"n_snps": 9851866,
"n_clumped_hits": 145,
"n_p_sig": 11319,
"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": 93467,
"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": 1287226,
"ldsc_nsnp_merge_regression_ld": 1287226,
"ldsc_observed_scale_h2_beta": 0.2597,
"ldsc_observed_scale_h2_se": 0.016,
"ldsc_intercept_beta": 1.0642,
"ldsc_intercept_se": 0.011,
"ldsc_lambda_gc": 1.3021,
"ldsc_mean_chisq": 1.55,
"ldsc_ratio": 0.1167
}
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 | TRUE |
| n_p_sig | TRUE |
| 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 | 8999041 | 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 | 9007739 | 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 | 8.643121e+00 | 5.758235e+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 | 7.878827e+07 | 5.634077e+07 | 828.0000000 | 3.243030e+07 | 6.934949e+07 | 1.145443e+08 | 2.492385e+08 | ▇▆▅▂▁ |
| numeric | EFFECT | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | -8.390000e-05 | 1.536520e-02 | -0.3481700 | -6.368300e-03 | -3.590000e-05 | 6.253800e-03 | 2.436660e-01 | ▁▁▇▂▁ |
| numeric | SE | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 1.166680e-02 | 8.548500e-03 | 0.0042346 | 5.054800e-03 | 7.739800e-03 | 1.600320e-02 | 9.872110e-02 | ▇▁▁▁▁ |
| numeric | PVAL | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 4.663770e-01 | 2.985223e-01 | 0.0000000 | 2.000000e-01 | 4.600002e-01 | 7.300002e-01 | 1.000000e+00 | ▇▆▆▆▆ |
| numeric | PVAL_ztest | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 4.663776e-01 | 2.984958e-01 | 0.0000000 | 1.994505e-01 | 4.559188e-01 | 7.250026e-01 | 1.000000e+00 | ▇▆▆▆▆ |
| numeric | AF | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 2.202167e-01 | 2.585375e-01 | 0.0035850 | 2.051700e-02 | 1.015160e-01 | 3.472660e-01 | 9.964150e-01 | ▇▂▁▁▁ |
| numeric | AF_reference | 93467 | 0.9896237 | NA | NA | NA | NA | NA | NA | NA | 2.205272e-01 | 2.504438e-01 | 0.0000000 | 1.777160e-02 | 1.190100e-01 | 3.456470e-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 | 0.0059294 | 0.0078171 | 0.4500005 | 0.4481423 | 0.623639 | 0.7821490 | NA |
| 1 | 54676 | rs2462492 | C | T | 0.0051754 | 0.0077672 | 0.5099998 | 0.5052119 | 0.398765 | NA | NA |
| 1 | 86028 | rs114608975 | T | C | 0.0125149 | 0.0123192 | 0.3100002 | 0.3096838 | 0.104042 | 0.0277556 | NA |
| 1 | 91536 | rs6702460 | G | T | 0.0116151 | 0.0076336 | 0.1299999 | 0.1281174 | 0.455650 | 0.4207270 | NA |
| 1 | 234313 | rs8179466 | C | T | -0.0135812 | 0.0149456 | 0.3599996 | 0.3635038 | 0.074856 | NA | NA |
| 1 | 534192 | rs6680723 | C | T | -0.0028841 | 0.0087417 | 0.7400005 | 0.7414548 | 0.240319 | NA | NA |
| 1 | 546697 | rs12025928 | A | G | 0.0023776 | 0.0108227 | 0.8300000 | 0.8261118 | 0.912775 | NA | NA |
| 1 | 693731 | rs12238997 | A | G | 0.0072650 | 0.0072664 | 0.3200000 | 0.3174024 | 0.117798 | 0.1417730 | NA |
| 1 | 705882 | rs72631875 | G | A | -0.0138167 | 0.0106307 | 0.1900002 | 0.1937045 | 0.067670 | 0.0315495 | NA |
| 1 | 706368 | rs55727773 | A | G | -0.0020050 | 0.0053903 | 0.7099994 | 0.7099207 | 0.514152 | 0.2751600 | NA |
| CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 22 | 51219006 | rs28729663 | G | A | -0.0021817 | 0.0065423 | 0.7400005 | 0.7387769 | 0.137058 | 0.2052720 | NA |
| 22 | 51219387 | rs9616832 | T | C | -0.0089297 | 0.0085253 | 0.2900000 | 0.2948961 | 0.072551 | 0.0654952 | NA |
| 22 | 51219704 | rs147475742 | G | A | -0.0195332 | 0.0113513 | 0.0850002 | 0.0852890 | 0.041724 | 0.0473243 | NA |
| 22 | 51221190 | rs369304721 | G | A | -0.0162083 | 0.0114050 | 0.1600000 | 0.1552710 | 0.049105 | NA | NA |
| 22 | 51221731 | rs115055839 | T | C | -0.0086214 | 0.0085271 | 0.3100002 | 0.3119872 | 0.072094 | 0.0625000 | NA |
| 22 | 51222100 | rs114553188 | G | T | 0.0075951 | 0.0099798 | 0.4500005 | 0.4466259 | 0.054410 | 0.0880591 | NA |
| 22 | 51223637 | rs375798137 | G | A | 0.0077039 | 0.0100337 | 0.4400003 | 0.4426022 | 0.054005 | 0.0788738 | NA |
| 22 | 51229805 | rs9616985 | T | C | -0.0088067 | 0.0085576 | 0.2999998 | 0.3034286 | 0.071952 | 0.0730831 | NA |
| 22 | 51232488 | rs376461333 | A | G | -0.0091818 | 0.0201586 | 0.6499995 | 0.6487636 | 0.020047 | NA | NA |
| 22 | 51237063 | rs3896457 | T | C | 0.0010144 | 0.0052042 | 0.8499999 | 0.8454644 | 0.298272 | 0.2050720 | NA |
bcf preview
1 49298 rs10399793 T C . PASS AF=0.623639 ES:SE:LP:AF:ID 0.00592937:0.00781707:0.346787:0.623639:rs10399793
1 54676 rs2462492 C T . PASS AF=0.398765 ES:SE:LP:AF:ID 0.00517541:0.00776725:0.29243:0.398765:rs2462492
1 86028 rs114608975 T C . PASS AF=0.104042 ES:SE:LP:AF:ID 0.0125149:0.0123192:0.508638:0.104042:rs114608975
1 91536 rs6702460 G T . PASS AF=0.45565 ES:SE:LP:AF:ID 0.0116151:0.00763364:0.886057:0.45565:rs6702460
1 234313 rs8179466 C T . PASS AF=0.074856 ES:SE:LP:AF:ID -0.0135812:0.0149456:0.443698:0.074856:rs8179466
1 534192 rs6680723 C T . PASS AF=0.240319 ES:SE:LP:AF:ID -0.00288413:0.00874171:0.130768:0.240319:rs6680723
1 546697 rs12025928 A G . PASS AF=0.912775 ES:SE:LP:AF:ID 0.00237765:0.0108227:0.0809219:0.912775:rs12025928
1 693731 rs12238997 A G . PASS AF=0.117798 ES:SE:LP:AF:ID 0.00726497:0.00726635:0.49485:0.117798:rs12238997
1 705882 rs72631875 G A . PASS AF=0.06767 ES:SE:LP:AF:ID -0.0138167:0.0106307:0.721246:0.06767:rs72631875
1 706368 rs12029736 A G . PASS AF=0.514152 ES:SE:LP:AF:ID -0.00200499:0.0053903:0.148742:0.514152:rs12029736
1 714596 rs149887893 T C . PASS AF=0.033619 ES:SE:LP:AF:ID 0.041719:0.0134522:2.72125:0.033619:rs149887893
1 715265 rs12184267 C T . PASS AF=0.037258 ES:SE:LP:AF:ID 0.0372682:0.012238:2.63827:0.037258:rs12184267
1 715367 rs12184277 A G . PASS AF=0.03734 ES:SE:LP:AF:ID 0.0382512:0.0121976:2.76955:0.03734:rs12184277
1 717485 rs12184279 C A . PASS AF=0.037031 ES:SE:LP:AF:ID 0.0380867:0.0122831:2.72125:0.037031:rs12184279
1 717587 rs144155419 G A . PASS AF=0.016817 ES:SE:LP:AF:ID -0.018796:0.018868:0.49485:0.016817:rs144155419
1 720381 rs116801199 G T . PASS AF=0.037595 ES:SE:LP:AF:ID 0.0387194:0.0121458:2.85387:0.037595:rs116801199
1 721290 rs12565286 G C . PASS AF=0.037684 ES:SE:LP:AF:ID 0.03805:0.0121077:2.76955:0.037684:rs12565286
1 722670 rs116030099 T C . PASS AF=0.101333 ES:SE:LP:AF:ID -0.00359155:0.00891204:0.161151:0.101333:rs116030099
1 723891 rs2977670 G C . PASS AF=0.958113 ES:SE:LP:AF:ID -0.0322225:0.0116493:2.24413:0.958113:rs2977670
1 724849 rs12126395 C A . PASS AF=0.031747 ES:SE:LP:AF:ID 0.00565278:0.0213514:0.102373:0.031747:rs12126395
1 725060 rs865924913 A T . PASS AF=0.052584 ES:SE:LP:AF:ID -0.00415171:0.0171926:0.091515:0.052584:rs865924913
1 726794 rs28454925 C G . PASS AF=0.037155 ES:SE:LP:AF:ID 0.0370753:0.0121916:2.61979:0.037155:rs28454925
1 729632 rs116720794 C T . PASS AF=0.03747 ES:SE:LP:AF:ID 0.0361687:0.0120881:2.55284:0.03747:rs116720794
1 729679 rs4951859 C G . PASS AF=0.841023 ES:SE:LP:AF:ID -0.0129606:0.00629559:1.39794:0.841023:rs4951859
1 730087 rs148120343 T C . PASS AF=0.056091 ES:SE:LP:AF:ID -0.00106403:0.0102505:0.0362122:0.056091:rs148120343
1 731718 rs58276399 T C . PASS AF=0.123639 ES:SE:LP:AF:ID 0.00743675:0.00690062:0.552842:0.123639:rs58276399
1 732989 rs369030935 C T . PASS AF=0.025832 ES:SE:LP:AF:ID -0.0140469:0.0169575:0.387216:0.025832:rs369030935
1 734349 rs141242758 T C . PASS AF=0.122835 ES:SE:LP:AF:ID 0.00746551:0.0069042:0.552842:0.122835:rs141242758
1 736289 rs79010578 T A . PASS AF=0.1335 ES:SE:LP:AF:ID 0.0185836:0.00680774:2.20066:0.1335:rs79010578
1 736689 rs181876450 T C . PASS AF=0.011218 ES:SE:LP:AF:ID -0.010521:0.0246622:0.173925:0.011218:rs181876450
1 740284 rs61770167 C T . PASS AF=0.006027 ES:SE:LP:AF:ID 0.074082:0.0309702:1.76955:0.006027:rs61770167
1 752478 rs146277091 G A . PASS AF=0.037422 ES:SE:LP:AF:ID 0.0376362:0.0119579:2.79588:0.037422:rs146277091
1 752566 rs3094315 G A . PASS AF=0.836824 ES:SE:LP:AF:ID -0.0112194:0.00609038:1.18709:0.836824:rs3094315
1 752721 rs3131972 A G . PASS AF=0.83637 ES:SE:LP:AF:ID -0.0108339:0.00608303:1.12494:0.83637:rs3131972
1 753405 rs3115860 C A . PASS AF=0.86807 ES:SE:LP:AF:ID -0.00551529:0.00652584:0.39794:0.86807:rs3115860
1 753541 rs2073813 G A . PASS AF=0.131612 ES:SE:LP:AF:ID 0.00621947:0.00653958:0.468521:0.131612:rs2073813
1 754063 rs12184312 G T . PASS AF=0.037855 ES:SE:LP:AF:ID 0.0360185:0.0117704:2.65758:0.037855:rs12184312
1 754105 rs12184325 C T . PASS AF=0.038104 ES:SE:LP:AF:ID 0.0366666:0.011697:2.76955:0.038104:rs12184325
1 754182 rs3131969 A G . PASS AF=0.867362 ES:SE:LP:AF:ID -0.0053332:0.0065124:0.387216:0.867362:rs3131969
1 754192 rs3131968 A G . PASS AF=0.86747 ES:SE:LP:AF:ID -0.00525772:0.00651559:0.376751:0.86747:rs3131968
1 754211 rs12184313 G A . PASS AF=0.038052 ES:SE:LP:AF:ID 0.0358461:0.0117447:2.63827:0.038052:rs12184313
1 754334 rs3131967 T C . PASS AF=0.86736 ES:SE:LP:AF:ID -0.00524634:0.00651201:0.376751:0.86736:rs3131967
1 754433 rs150578204 G A . PASS AF=0.005081 ES:SE:LP:AF:ID -0.0252292:0.0337875:0.337242:0.005081:rs150578204
1 754458 rs142682604 G T . PASS AF=0.005048 ES:SE:LP:AF:ID -0.0265851:0.0338793:0.366532:0.005048:rs142682604
1 754503 rs3115859 G A . PASS AF=0.835916 ES:SE:LP:AF:ID -0.010985:0.00607035:1.1549:0.835916:rs3115859
1 754629 rs10454459 A G . PASS AF=0.038072 ES:SE:LP:AF:ID 0.0360092:0.0117601:2.65758:0.038072:rs10454459
1 754964 rs3131966 C T . PASS AF=0.836522 ES:SE:LP:AF:ID -0.0104346:0.00608673:1.0655:0.836522:rs3131966
1 755240 rs181660517 T G . PASS AF=0.013098 ES:SE:LP:AF:ID 0.0355452:0.0219084:1:0.013098:rs181660517
1 755435 rs184270342 T G . PASS AF=0.005542 ES:SE:LP:AF:ID 0.0510965:0.0328686:0.920819:0.005542:rs184270342
1 755775 rs3131965 A G . PASS AF=0.837811 ES:SE:LP:AF:ID -0.0106935:0.00617042:1.08092:0.837811:rs3131965