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_23100.vcf.gz --id UKB-b:19393 --data /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/ukbiobank/raw-output/data.batch_23100.txt.gz --cohort_controls 454137 --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": "2019-09-13T04:02:45.453663",
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"bcftools_viewCommand": "view -h /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/ukb-b-19393/ukb-b-19393.vcf.gz; Date=Sun May 10 01:16:19 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-19393/UKB-b-19393_data.vcf.gz \
--ref-ld-chr ../reference/eur_w_ld_chr/ \
--out /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-19393/ldsc.txt \
--w-ld-chr ../reference/eur_w_ld_chr/
Beginning analysis at Thu Oct 17 14:41:17 2019
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-19393/UKB-b-19393_data.vcf.gz ...
Read summary statistics for 9851866 SNPs.
Dropped 14738 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, 1289166 SNPs remain.
After merging with regression SNP LD, 1289166 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.2215 (0.0064)
Lambda GC: 2.4061
Mean Chi^2: 3.2073
Intercept: 1.1965 (0.0174)
Ratio: 0.089 (0.0079)
Analysis finished at Thu Oct 17 14:43:10 2019
Total time elapsed: 1.0m:52.63sQC metrics
Metrics
Metrics
{
"af_correlation": 0.9499,
"inflation_factor": 1.92,
"mean_EFFECT": 0,
"n": "-Inf",
"n_snps": 9851866,
"n_clumped_hits": 435,
"n_p_sig": 60292,
"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": 184849,
"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": 1289166,
"ldsc_nsnp_merge_regression_ld": 1289166,
"ldsc_observed_scale_h2_beta": 0.2215,
"ldsc_observed_scale_h2_se": 0.0064,
"ldsc_intercept_beta": 1.1965,
"ldsc_intercept_se": 0.0174,
"ldsc_lambda_gc": 2.4061,
"ldsc_mean_chisq": 3.2073,
"ldsc_ratio": 0.089
}
Flags
| name | value |
|---|---|
| af_correlation | FALSE |
| inflation_factor | TRUE |
| 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 | 9837196 | 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 | 9851866 | 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 | 8.622825e+00 | 5.748290e+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 | 7.886027e+07 | 5.628334e+07 | 828.0000000 | 3.259061e+07 | 6.948835e+07 | 1.145912e+08 | 2.492385e+08 | ▇▆▅▂▁ |
| numeric | EFFECT | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 3.110000e-05 | 1.062190e-02 | -0.2666920 | -4.068000e-03 | 4.000000e-06 | 4.077900e-03 | 1.772590e-01 | ▁▁▇▇▁ |
| numeric | SE | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 6.732500e-03 | 6.372200e-03 | 0.0018812 | 2.306400e-03 | 3.867600e-03 | 8.923300e-03 | 9.893990e-02 | ▇▁▁▁▁ |
| numeric | PVAL | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 3.986164e-01 | 3.113579e-01 | 0.0000000 | 1.000000e-01 | 3.500000e-01 | 6.700003e-01 | 1.000000e+00 | ▇▅▃▃▃ |
| numeric | PVAL_ztest | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 3.986174e-01 | 3.113356e-01 | 0.0000000 | 1.040862e-01 | 3.549456e-01 | 6.656173e-01 | 1.000000e+00 | ▇▅▃▃▃ |
| numeric | AF | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 2.035077e-01 | 2.568615e-01 | 0.0009840 | 1.316900e-02 | 7.791400e-02 | 3.164560e-01 | 9.990080e-01 | ▇▂▁▁▁ |
| numeric | AF_reference | 184849 | 0.9812372 | NA | NA | NA | NA | NA | NA | NA | 2.068392e-01 | 2.482924e-01 | 0.0000000 | 1.198080e-02 | 9.984030e-02 | 3.202880e-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 | -0.0006177 | 0.0034576 | 0.8600001 | 0.8582182 | 0.623731 | 0.7821490 | NA |
| 1 | 54676 | rs2462492 | C | T | 0.0023714 | 0.0034260 | 0.4899999 | 0.4888351 | 0.400368 | NA | NA |
| 1 | 86028 | rs114608975 | T | C | 0.0085170 | 0.0054771 | 0.1199999 | 0.1199415 | 0.103558 | 0.0277556 | NA |
| 1 | 91536 | rs6702460 | G | T | 0.0009831 | 0.0033726 | 0.7700005 | 0.7706763 | 0.456856 | 0.4207270 | NA |
| 1 | 234313 | rs8179466 | C | T | -0.0119041 | 0.0066530 | 0.0739997 | 0.0735684 | 0.074493 | NA | NA |
| 1 | 534192 | rs6680723 | C | T | 0.0003764 | 0.0038531 | 0.9199999 | 0.9221870 | 0.240923 | NA | NA |
| 1 | 546697 | rs12025928 | A | G | 0.0018584 | 0.0048066 | 0.6999999 | 0.6990248 | 0.913456 | NA | NA |
| 1 | 693731 | rs12238997 | A | G | -0.0008829 | 0.0032307 | 0.7800007 | 0.7846234 | 0.116217 | 0.1417730 | NA |
| 1 | 705882 | rs72631875 | G | A | -0.0003958 | 0.0047310 | 0.9299999 | 0.9333227 | 0.067321 | 0.0315495 | NA |
| 1 | 706368 | rs55727773 | A | G | 0.0003143 | 0.0023923 | 0.9000000 | 0.8954701 | 0.515796 | 0.2751600 | NA |
| CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 22 | 51219704 | rs147475742 | G | A | 0.0023202 | 0.0050484 | 0.6499995 | 0.6458126 | 0.041955 | 0.0473243 | NA |
| 22 | 51219766 | rs182321900 | C | T | -0.0146690 | 0.0234940 | 0.5300002 | 0.5323832 | 0.001942 | NA | NA |
| 22 | 51220146 | rs868950473 | C | T | -0.0188825 | 0.0232701 | 0.4199997 | 0.4171079 | 0.001991 | NA | NA |
| 22 | 51221190 | rs369304721 | G | A | 0.0044976 | 0.0050388 | 0.3700002 | 0.3720677 | 0.049758 | NA | NA |
| 22 | 51221731 | rs115055839 | T | C | 0.0053078 | 0.0037692 | 0.1600000 | 0.1590748 | 0.073269 | 0.0625000 | NA |
| 22 | 51222100 | rs114553188 | G | T | -0.0006226 | 0.0044379 | 0.8900000 | 0.8884228 | 0.054483 | 0.0880591 | NA |
| 22 | 51223637 | rs375798137 | G | A | -0.0005482 | 0.0044593 | 0.9000000 | 0.9021628 | 0.054114 | 0.0788738 | NA |
| 22 | 51229805 | rs9616985 | T | C | 0.0051436 | 0.0037829 | 0.1700000 | 0.1739244 | 0.073103 | 0.0730831 | NA |
| 22 | 51232488 | rs376461333 | A | G | 0.0039398 | 0.0089105 | 0.6600001 | 0.6583760 | 0.020055 | NA | NA |
| 22 | 51237063 | rs3896457 | T | C | 0.0026227 | 0.0023148 | 0.2599998 | 0.2572047 | 0.297916 | 0.2050720 | NA |
bcf preview
1 49298 rs10399793 T C . PASS AF=0.623731 ES:SE:LP:AF:ID -0.000617677:0.00345761:0.0655015:0.623731:rs10399793
1 54676 rs2462492 C T . PASS AF=0.400368 ES:SE:LP:AF:ID 0.00237135:0.003426:0.309804:0.400368:rs2462492
1 86028 rs114608975 T C . PASS AF=0.103558 ES:SE:LP:AF:ID 0.00851695:0.00547707:0.920819:0.103558:rs114608975
1 91536 rs6702460 G T . PASS AF=0.456856 ES:SE:LP:AF:ID 0.000983089:0.00337263:0.113509:0.456856:rs6702460
1 234313 rs8179466 C T . PASS AF=0.074493 ES:SE:LP:AF:ID -0.0119041:0.00665298:1.13077:0.074493:rs8179466
1 534192 rs6680723 C T . PASS AF=0.240923 ES:SE:LP:AF:ID 0.000376369:0.00385311:0.0362122:0.240923:rs6680723
1 546697 rs12025928 A G . PASS AF=0.913456 ES:SE:LP:AF:ID 0.00185843:0.00480665:0.154902:0.913456:rs12025928
1 693731 rs12238997 A G . PASS AF=0.116217 ES:SE:LP:AF:ID -0.000882939:0.00323067:0.107905:0.116217:rs12238997
1 705882 rs72631875 G A . PASS AF=0.067321 ES:SE:LP:AF:ID -0.000395819:0.00473099:0.0315171:0.067321:rs72631875
1 706368 rs12029736 A G . PASS AF=0.515796 ES:SE:LP:AF:ID 0.000314313:0.00239229:0.0457575:0.515796:rs12029736
1 714596 rs149887893 T C . PASS AF=0.032985 ES:SE:LP:AF:ID -0.00181867:0.00603149:0.119186:0.032985:rs149887893
1 715265 rs12184267 C T . PASS AF=0.036595 ES:SE:LP:AF:ID -0.00256628:0.00547933:0.19382:0.036595:rs12184267
1 715367 rs12184277 A G . PASS AF=0.036714 ES:SE:LP:AF:ID -0.00251248:0.00545813:0.187087:0.036714:rs12184277
1 717485 rs12184279 C A . PASS AF=0.036411 ES:SE:LP:AF:ID -0.00387288:0.0054978:0.318759:0.036411:rs12184279
1 717587 rs144155419 G A . PASS AF=0.016388 ES:SE:LP:AF:ID -0.00271783:0.00846764:0.124939:0.016388:rs144155419
1 720381 rs116801199 G T . PASS AF=0.036951 ES:SE:LP:AF:ID -0.00328536:0.00543685:0.259637:0.036951:rs116801199
1 721290 rs12565286 G C . PASS AF=0.037049 ES:SE:LP:AF:ID -0.00346873:0.0054181:0.283997:0.037049:rs12565286
1 722670 rs116030099 T C . PASS AF=0.101236 ES:SE:LP:AF:ID 0.00273137:0.00394609:0.309804:0.101236:rs116030099
1 723891 rs2977670 G C . PASS AF=0.959101 ES:SE:LP:AF:ID 0.00469317:0.00522431:0.431798:0.959101:rs2977670
1 724849 rs12126395 C A . PASS AF=0.031458 ES:SE:LP:AF:ID 0.0131142:0.00947829:0.769551:0.031458:rs12126395
1 725060 rs865924913 A T . PASS AF=0.053256 ES:SE:LP:AF:ID -0.000315246:0.0075388:0.0132283:0.053256:rs865924913
1 726794 rs28454925 C G . PASS AF=0.03657 ES:SE:LP:AF:ID -0.00421394:0.00545285:0.356547:0.03657:rs28454925
1 729632 rs116720794 C T . PASS AF=0.036891 ES:SE:LP:AF:ID -0.0053628:0.00540299:0.49485:0.036891:rs116720794
1 729679 rs4951859 C G . PASS AF=0.843327 ES:SE:LP:AF:ID 0.00266565:0.00279919:0.468521:0.843327:rs4951859
1 730087 rs148120343 T C . PASS AF=0.055859 ES:SE:LP:AF:ID -0.00557903:0.00453293:0.657577:0.055859:rs148120343
1 731718 rs58276399 T C . PASS AF=0.122192 ES:SE:LP:AF:ID -0.00178785:0.00306458:0.251812:0.122192:rs58276399
1 732989 rs369030935 C T . PASS AF=0.02573 ES:SE:LP:AF:ID -0.00927666:0.00753023:0.657577:0.02573:rs369030935
1 734349 rs141242758 T C . PASS AF=0.121433 ES:SE:LP:AF:ID -0.00147055:0.00306588:0.200659:0.121433:rs141242758
1 736289 rs79010578 T A . PASS AF=0.132218 ES:SE:LP:AF:ID -0.00294691:0.00302118:0.481486:0.132218:rs79010578
1 736689 rs181876450 T C . PASS AF=0.011127 ES:SE:LP:AF:ID 0.00499087:0.0109886:0.187087:0.011127:rs181876450
1 740284 rs61770167 C T . PASS AF=0.005695 ES:SE:LP:AF:ID 0.0189954:0.0141778:0.744727:0.005695:rs61770167
1 742813 rs112573343 C T . PASS AF=0.002287 ES:SE:LP:AF:ID 0.00269443:0.023739:0.0409586:0.002287:rs112573343
1 746189 rs139221807 A G . PASS AF=0.001038 ES:SE:LP:AF:ID 0.00312949:0.0388034:0.0268721:0.001038:rs139221807
1 752478 rs146277091 G A . PASS AF=0.036803 ES:SE:LP:AF:ID -0.00425618:0.00534851:0.366532:0.036803:rs146277091
1 752566 rs3094315 G A . PASS AF=0.839054 ES:SE:LP:AF:ID 0.00272379:0.0027107:0.508638:0.839054:rs3094315
1 752721 rs3131972 A G . PASS AF=0.838683 ES:SE:LP:AF:ID 0.00318428:0.00270773:0.619789:0.838683:rs3131972
1 753405 rs3115860 C A . PASS AF=0.869871 ES:SE:LP:AF:ID 0.00194738:0.00290584:0.30103:0.869871:rs3115860
1 753541 rs2073813 G A . PASS AF=0.129767 ES:SE:LP:AF:ID -0.00272376:0.00291192:0.455932:0.129767:rs2073813
1 754063 rs12184312 G T . PASS AF=0.037315 ES:SE:LP:AF:ID -0.00551435:0.00525783:0.537602:0.037315:rs12184312
1 754105 rs12184325 C T . PASS AF=0.037561 ES:SE:LP:AF:ID -0.00529859:0.00522448:0.508638:0.037561:rs12184325
1 754182 rs3131969 A G . PASS AF=0.869216 ES:SE:LP:AF:ID 0.0023445:0.00290012:0.376751:0.869216:rs3131969
1 754192 rs3131968 A G . PASS AF=0.869313 ES:SE:LP:AF:ID 0.00230636:0.00290128:0.366532:0.869313:rs3131968
1 754211 rs12184313 G A . PASS AF=0.037513 ES:SE:LP:AF:ID -0.0055699:0.00524742:0.537602:0.037513:rs12184313
1 754334 rs3131967 T C . PASS AF=0.86922 ES:SE:LP:AF:ID 0.00235222:0.00290007:0.376751:0.86922:rs3131967
1 754433 rs150578204 G A . PASS AF=0.00513 ES:SE:LP:AF:ID -0.0115412:0.0148702:0.356547:0.00513:rs150578204
1 754458 rs142682604 G T . PASS AF=0.005096 ES:SE:LP:AF:ID -0.0117458:0.0149087:0.366532:0.005096:rs142682604
1 754503 rs3115859 G A . PASS AF=0.838139 ES:SE:LP:AF:ID 0.00327391:0.00270026:0.638272:0.838139:rs3115859
1 754629 rs10454459 A G . PASS AF=0.037526 ES:SE:LP:AF:ID -0.00598546:0.00525486:0.60206:0.037526:rs10454459
1 754964 rs3131966 C T . PASS AF=0.838771 ES:SE:LP:AF:ID 0.00321116:0.00270788:0.619789:0.838771:rs3131966
1 755240 rs181660517 T G . PASS AF=0.013777 ES:SE:LP:AF:ID 0.0116043:0.00944664:0.657577:0.013777:rs181660517