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_2375.vcf.gz --id UKB-b:5945 --data /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/ukbiobank/raw-output/data.batch_2375.txt.gz --cohort_controls 204568 --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",
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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-5945/UKB-b-5945_data.vcf.gz \
--ref-ld-chr ../reference/eur_w_ld_chr/ \
--out /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-5945/ldsc.txt \
--w-ld-chr ../reference/eur_w_ld_chr/
Beginning analysis at Thu Oct 17 14:45:40 2019
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-5945/UKB-b-5945_data.vcf.gz ...
Read summary statistics for 9513261 SNPs.
Dropped 11742 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, 1288386 SNPs remain.
After merging with regression SNP LD, 1288386 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.1246 (0.0063)
Lambda GC: 1.3576
Mean Chi^2: 1.5477
Intercept: 1.0588 (0.01)
Ratio: 0.1074 (0.0183)
Analysis finished at Thu Oct 17 14:47:07 2019
Total time elapsed: 1.0m:27.1sQC metrics
Metrics
Metrics
{
"af_correlation": 0.9491,
"inflation_factor": 1.2544,
"mean_EFFECT": -0,
"n": "-Inf",
"n_snps": 9851866,
"n_clumped_hits": 122,
"n_p_sig": 10314,
"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": 135280,
"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": 1288386,
"ldsc_nsnp_merge_regression_ld": 1288386,
"ldsc_observed_scale_h2_beta": 0.1246,
"ldsc_observed_scale_h2_se": 0.0063,
"ldsc_intercept_beta": 1.0588,
"ldsc_intercept_se": 0.01,
"ldsc_lambda_gc": 1.3576,
"ldsc_mean_chisq": 1.5477,
"ldsc_ratio": 0.1074
}
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 | 9501580 | 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 | 9513261 | 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 | 8.628755e+00 | 5.751657e+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 | 7.883279e+07 | 5.630710e+07 | 828.0000000 | 3.253762e+07 | 6.941734e+07 | 1.145660e+08 | 2.492385e+08 | ▇▆▅▂▁ |
| numeric | EFFECT | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | -1.100000e-05 | 5.733400e-03 | -0.0733641 | -2.122500e-03 | -1.040000e-05 | 2.093000e-03 | 9.681040e-02 | ▁▁▇▁▁ |
| numeric | SE | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 4.170700e-03 | 3.510100e-03 | 0.0013130 | 1.589700e-03 | 2.568000e-03 | 5.669700e-03 | 4.434240e-02 | ▇▁▁▁▁ |
| numeric | PVAL | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 4.637697e-01 | 2.994225e-01 | 0.0000000 | 2.000000e-01 | 4.500005e-01 | 7.199992e-01 | 1.000000e+00 | ▇▆▆▆▆ |
| numeric | PVAL_ztest | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 4.637707e-01 | 2.993970e-01 | 0.0000000 | 1.951181e-01 | 4.514932e-01 | 7.237638e-01 | 9.999997e-01 | ▇▆▆▆▆ |
| numeric | AF | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 2.095620e-01 | 2.572957e-01 | 0.0017110 | 1.567000e-02 | 8.655100e-02 | 3.279490e-01 | 9.982890e-01 | ▇▂▁▁▁ |
| numeric | AF_reference | 135280 | 0.9857798 | NA | NA | NA | NA | NA | NA | NA | 2.112921e-01 | 2.490170e-01 | 0.0000000 | 1.337860e-02 | 1.062300e-01 | 3.292730e-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 | 0.0024545 | 0.0024114 | 0.3100002 | 0.3087440 | 0.624119 | 0.7821490 | NA |
| 1 | 54676 | rs2462492 | C | T | -0.0015986 | 0.0023952 | 0.5000000 | 0.5045033 | 0.399864 | NA | NA |
| 1 | 86028 | rs114608975 | T | C | 0.0020401 | 0.0038110 | 0.5900000 | 0.5924230 | 0.103755 | 0.0277556 | NA |
| 1 | 91536 | rs6702460 | G | T | -0.0004449 | 0.0023566 | 0.8499999 | 0.8502617 | 0.456596 | 0.4207270 | NA |
| 1 | 234313 | rs8179466 | C | T | 0.0028348 | 0.0046351 | 0.5400003 | 0.5408054 | 0.074603 | NA | NA |
| 1 | 534192 | rs6680723 | C | T | -0.0014750 | 0.0026899 | 0.5800000 | 0.5834675 | 0.240730 | NA | NA |
| 1 | 546697 | rs12025928 | A | G | 0.0015912 | 0.0033568 | 0.6400000 | 0.6354919 | 0.913383 | NA | NA |
| 1 | 693731 | rs12238997 | A | G | 0.0021004 | 0.0022574 | 0.3500000 | 0.3521314 | 0.115977 | 0.1417730 | NA |
| 1 | 705882 | rs72631875 | G | A | -0.0002668 | 0.0033032 | 0.9400001 | 0.9356162 | 0.067494 | 0.0315495 | NA |
| 1 | 706368 | rs55727773 | A | G | -0.0002425 | 0.0016713 | 0.8800001 | 0.8846120 | 0.516421 | 0.2751600 | NA |
| CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 22 | 51219704 | rs147475742 | G | A | -0.0019938 | 0.0035084 | 0.5700002 | 0.5698290 | 0.042027 | 0.0473243 | NA |
| 22 | 51219766 | rs182321900 | C | T | -0.0087992 | 0.0161165 | 0.5900000 | 0.5850838 | 0.001984 | NA | NA |
| 22 | 51220146 | rs868950473 | C | T | -0.0069044 | 0.0159809 | 0.6700003 | 0.6657123 | 0.002037 | NA | NA |
| 22 | 51221190 | rs369304721 | G | A | -0.0064726 | 0.0034981 | 0.0640000 | 0.0642641 | 0.049868 | NA | NA |
| 22 | 51221731 | rs115055839 | T | C | -0.0049509 | 0.0026198 | 0.0589997 | 0.0587905 | 0.073274 | 0.0625000 | NA |
| 22 | 51222100 | rs114553188 | G | T | 0.0011637 | 0.0030874 | 0.7099994 | 0.7062397 | 0.054346 | 0.0880591 | NA |
| 22 | 51223637 | rs375798137 | G | A | 0.0009259 | 0.0031026 | 0.7700005 | 0.7653833 | 0.053966 | 0.0788738 | NA |
| 22 | 51229805 | rs9616985 | T | C | -0.0049443 | 0.0026296 | 0.0599998 | 0.0600782 | 0.073067 | 0.0730831 | NA |
| 22 | 51232488 | rs376461333 | A | G | 0.0025091 | 0.0061958 | 0.6899999 | 0.6854968 | 0.020053 | NA | NA |
| 22 | 51237063 | rs3896457 | T | C | -0.0006897 | 0.0016099 | 0.6700003 | 0.6683563 | 0.298140 | 0.2050720 | NA |
bcf preview
1 49298 rs10399793 T C . PASS AF=0.624119 ES:SE:LP:AF:ID 0.00245447:0.0024114:0.508638:0.624119:rs10399793
1 54676 rs2462492 C T . PASS AF=0.399864 ES:SE:LP:AF:ID -0.00159862:0.00239522:0.30103:0.399864:rs2462492
1 86028 rs114608975 T C . PASS AF=0.103755 ES:SE:LP:AF:ID 0.00204013:0.00381099:0.229148:0.103755:rs114608975
1 91536 rs6702460 G T . PASS AF=0.456596 ES:SE:LP:AF:ID -0.000444899:0.00235665:0.0705811:0.456596:rs6702460
1 234313 rs8179466 C T . PASS AF=0.074603 ES:SE:LP:AF:ID 0.0028348:0.00463509:0.267606:0.074603:rs8179466
1 534192 rs6680723 C T . PASS AF=0.24073 ES:SE:LP:AF:ID -0.00147495:0.00268991:0.236572:0.24073:rs6680723
1 546697 rs12025928 A G . PASS AF=0.913383 ES:SE:LP:AF:ID 0.00159118:0.00335684:0.19382:0.913383:rs12025928
1 693731 rs12238997 A G . PASS AF=0.115977 ES:SE:LP:AF:ID 0.00210039:0.00225736:0.455932:0.115977:rs12238997
1 705882 rs72631875 G A . PASS AF=0.067494 ES:SE:LP:AF:ID -0.000266837:0.00330322:0.0268721:0.067494:rs72631875
1 706368 rs12029736 A G . PASS AF=0.516421 ES:SE:LP:AF:ID -0.000242542:0.00167126:0.0555173:0.516421:rs12029736
1 714596 rs149887893 T C . PASS AF=0.033108 ES:SE:LP:AF:ID -0.001161:0.0042051:0.107905:0.033108:rs149887893
1 715265 rs12184267 C T . PASS AF=0.036774 ES:SE:LP:AF:ID -0.000767286:0.00381583:0.0757207:0.036774:rs12184267
1 715367 rs12184277 A G . PASS AF=0.036896 ES:SE:LP:AF:ID -0.000828496:0.0038008:0.0809219:0.036896:rs12184277
1 717485 rs12184279 C A . PASS AF=0.036611 ES:SE:LP:AF:ID -0.000428432:0.00382698:0.0409586:0.036611:rs12184279
1 717587 rs144155419 G A . PASS AF=0.016509 ES:SE:LP:AF:ID -0.00506707:0.00589289:0.408935:0.016509:rs144155419
1 720381 rs116801199 G T . PASS AF=0.037161 ES:SE:LP:AF:ID -0.000781391:0.00378433:0.0757207:0.037161:rs116801199
1 721290 rs12565286 G C . PASS AF=0.037258 ES:SE:LP:AF:ID -0.00102059:0.00377122:0.102373:0.037258:rs12565286
1 722670 rs116030099 T C . PASS AF=0.101414 ES:SE:LP:AF:ID -0.00214714:0.00275382:0.356547:0.101414:rs116030099
1 723891 rs2977670 G C . PASS AF=0.958921 ES:SE:LP:AF:ID 0.00254537:0.00363897:0.318759:0.958921:rs2977670
1 724849 rs12126395 C A . PASS AF=0.031448 ES:SE:LP:AF:ID -0.00101607:0.00664655:0.0555173:0.031448:rs12126395
1 725060 rs865924913 A T . PASS AF=0.053107 ES:SE:LP:AF:ID -0.00320195:0.00528239:0.267606:0.053107:rs865924913
1 726794 rs28454925 C G . PASS AF=0.036754 ES:SE:LP:AF:ID -0.00131389:0.003798:0.136677:0.036754:rs28454925
1 729632 rs116720794 C T . PASS AF=0.037048 ES:SE:LP:AF:ID -0.000857346:0.00376349:0.0861861:0.037048:rs116720794
1 729679 rs4951859 C G . PASS AF=0.843397 ES:SE:LP:AF:ID -0.00135783:0.00195405:0.309804:0.843397:rs4951859
1 730087 rs148120343 T C . PASS AF=0.055789 ES:SE:LP:AF:ID 0.0031169:0.00316614:0.49485:0.055789:rs148120343
1 731718 rs58276399 T C . PASS AF=0.121928 ES:SE:LP:AF:ID 0.00167373:0.00214209:0.366532:0.121928:rs58276399
1 732989 rs369030935 C T . PASS AF=0.025888 ES:SE:LP:AF:ID 0.000550704:0.00524227:0.0362122:0.025888:rs369030935
1 734349 rs141242758 T C . PASS AF=0.12119 ES:SE:LP:AF:ID 0.00161504:0.00214292:0.346787:0.12119:rs141242758
1 736289 rs79010578 T A . PASS AF=0.132058 ES:SE:LP:AF:ID 0.00248102:0.00211069:0.619789:0.132058:rs79010578
1 736689 rs181876450 T C . PASS AF=0.011179 ES:SE:LP:AF:ID -0.00318699:0.00764469:0.167491:0.011179:rs181876450
1 740284 rs61770167 C T . PASS AF=0.005643 ES:SE:LP:AF:ID 0.0028438:0.00997921:0.107905:0.005643:rs61770167
1 742813 rs112573343 C T . PASS AF=0.002272 ES:SE:LP:AF:ID -0.0320546:0.0166444:1.26761:0.002272:rs112573343
1 752478 rs146277091 G A . PASS AF=0.036962 ES:SE:LP:AF:ID -0.00189003:0.00372548:0.21467:0.036962:rs146277091
1 752566 rs3094315 G A . PASS AF=0.839183 ES:SE:LP:AF:ID -0.00229039:0.00189323:0.638272:0.839183:rs3094315
1 752721 rs3131972 A G . PASS AF=0.838826 ES:SE:LP:AF:ID -0.00226178:0.00189109:0.638272:0.838826:rs3131972
1 753405 rs3115860 C A . PASS AF=0.870158 ES:SE:LP:AF:ID -0.00234596:0.00203123:0.60206:0.870158:rs3115860
1 753541 rs2073813 G A . PASS AF=0.129476 ES:SE:LP:AF:ID 0.00260113:0.00203498:0.69897:0.129476:rs2073813
1 754063 rs12184312 G T . PASS AF=0.037521 ES:SE:LP:AF:ID -0.00216516:0.00366035:0.259637:0.037521:rs12184312
1 754105 rs12184325 C T . PASS AF=0.037741 ES:SE:LP:AF:ID -0.00206503:0.00363881:0.244125:0.037741:rs12184325
1 754182 rs3131969 A G . PASS AF=0.869519 ES:SE:LP:AF:ID -0.00232967:0.00202703:0.60206:0.869519:rs3131969
1 754192 rs3131968 A G . PASS AF=0.869646 ES:SE:LP:AF:ID -0.00246894:0.0020279:0.657577:0.869646:rs3131968
1 754211 rs12184313 G A . PASS AF=0.037713 ES:SE:LP:AF:ID -0.00220664:0.00365392:0.259637:0.037713:rs12184313
1 754334 rs3131967 T C . PASS AF=0.869524 ES:SE:LP:AF:ID -0.00231749:0.00202702:0.60206:0.869524:rs3131967
1 754433 rs150578204 G A . PASS AF=0.005183 ES:SE:LP:AF:ID 0.0104597:0.0103119:0.508638:0.005183:rs150578204
1 754458 rs142682604 G T . PASS AF=0.005146 ES:SE:LP:AF:ID 0.0116588:0.0103423:0.585027:0.005146:rs142682604
1 754503 rs3115859 G A . PASS AF=0.838274 ES:SE:LP:AF:ID -0.00213249:0.0018858:0.585027:0.838274:rs3115859
1 754629 rs10454459 A G . PASS AF=0.037726 ES:SE:LP:AF:ID -0.00231664:0.00365863:0.275724:0.037726:rs10454459
1 754964 rs3131966 C T . PASS AF=0.838894 ES:SE:LP:AF:ID -0.00214705:0.00189102:0.585027:0.838894:rs3131966
1 755240 rs181660517 T G . PASS AF=0.013677 ES:SE:LP:AF:ID -0.0041974:0.00662871:0.275724:0.013677:rs181660517
1 755435 rs184270342 T G . PASS AF=0.005508 ES:SE:LP:AF:ID -0.0156063:0.0102068:0.886057:0.005508:rs184270342