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_1309.vcf.gz --id UKB-b:3881 --data /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/ukbiobank/raw-output/data.batch_1309.txt.gz --cohort_controls 446462 --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-3881/UKB-b-3881_data.vcf.gz \
--ref-ld-chr ../reference/eur_w_ld_chr/ \
--out /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-3881/ldsc.txt \
--w-ld-chr ../reference/eur_w_ld_chr/
Beginning analysis at Thu Oct 17 14:43:48 2019
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-3881/UKB-b-3881_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: 0.0591 (0.0025)
Lambda GC: 1.4214
Mean Chi^2: 1.5614
Intercept: 1.0299 (0.0083)
Ratio: 0.0532 (0.0148)
Analysis finished at Thu Oct 17 14:45:33 2019
Total time elapsed: 1.0m:44.63sQC metrics
Metrics
Metrics
{
"af_correlation": 0.9499,
"inflation_factor": 1.2544,
"mean_EFFECT": -5.2803e-06,
"n": "-Inf",
"n_snps": 9851866,
"n_clumped_hits": 55,
"n_p_sig": 4432,
"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": 0.0591,
"ldsc_observed_scale_h2_se": 0.0025,
"ldsc_intercept_beta": 1.0299,
"ldsc_intercept_se": 0.0083,
"ldsc_lambda_gc": 1.4214,
"ldsc_mean_chisq": 1.5614,
"ldsc_ratio": 0.0533
}
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 | -5.300000e-06 | 6.026500e-03 | -0.1013810 | -2.003700e-03 | -8.000000e-07 | 1.999900e-03 | 9.021130e-02 | ▁▁▇▁▁ |
| numeric | SE | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 4.212700e-03 | 3.988000e-03 | 0.0011787 | 1.443000e-03 | 2.419700e-03 | 5.583400e-03 | 6.201520e-02 | ▇▁▁▁▁ |
| numeric | PVAL | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 4.599412e-01 | 2.999475e-01 | 0.0000000 | 1.900002e-01 | 4.500005e-01 | 7.199992e-01 | 1.000000e+00 | ▇▆▆▆▆ |
| numeric | PVAL_ztest | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 4.599427e-01 | 2.999224e-01 | 0.0000000 | 1.903376e-01 | 4.455330e-01 | 7.202005e-01 | 9.999997e-01 | ▇▆▆▆▆ |
| numeric | AF | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 2.035079e-01 | 2.568624e-01 | 0.0009720 | 1.316800e-02 | 7.790800e-02 | 3.164460e-01 | 9.990140e-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 | 0.0010957 | 0.0021684 | 0.6100002 | 0.6133587 | 0.623811 | 0.7821490 | NA |
| 1 | 54676 | rs2462492 | C | T | 0.0022008 | 0.0021484 | 0.3100002 | 0.3056577 | 0.400356 | NA | NA |
| 1 | 86028 | rs114608975 | T | C | -0.0047127 | 0.0034323 | 0.1700000 | 0.1697383 | 0.103585 | 0.0277556 | NA |
| 1 | 91536 | rs6702460 | G | T | 0.0008249 | 0.0021142 | 0.6999999 | 0.6964083 | 0.456840 | 0.4207270 | NA |
| 1 | 234313 | rs8179466 | C | T | 0.0069083 | 0.0041682 | 0.0969996 | 0.0974395 | 0.074522 | NA | NA |
| 1 | 534192 | rs6680723 | C | T | -0.0027881 | 0.0024160 | 0.2500000 | 0.2485072 | 0.240918 | NA | NA |
| 1 | 546697 | rs12025928 | A | G | -0.0031874 | 0.0030148 | 0.2900000 | 0.2903861 | 0.913509 | NA | NA |
| 1 | 693731 | rs12238997 | A | G | -0.0007329 | 0.0020243 | 0.7199992 | 0.7173061 | 0.116393 | 0.1417730 | NA |
| 1 | 705882 | rs72631875 | G | A | 0.0026569 | 0.0029666 | 0.3700002 | 0.3704603 | 0.067284 | 0.0315495 | NA |
| 1 | 706368 | rs55727773 | A | G | -0.0003267 | 0.0015000 | 0.8300000 | 0.8275851 | 0.515645 | 0.2751600 | NA |
| CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 22 | 51219704 | rs147475742 | G | A | 0.0040680 | 0.0031500 | 0.2000000 | 0.1965575 | 0.041935 | 0.0473243 | NA |
| 22 | 51219766 | rs182321900 | C | T | 0.0046038 | 0.0146920 | 0.7499995 | 0.7540136 | 0.001932 | NA | NA |
| 22 | 51220146 | rs868950473 | C | T | 0.0067118 | 0.0145488 | 0.6400000 | 0.6445627 | 0.001981 | NA | NA |
| 22 | 51221190 | rs369304721 | G | A | 0.0029613 | 0.0031437 | 0.3500000 | 0.3461955 | 0.049737 | NA | NA |
| 22 | 51221731 | rs115055839 | T | C | 0.0030789 | 0.0023510 | 0.1900002 | 0.1903368 | 0.073254 | 0.0625000 | NA |
| 22 | 51222100 | rs114553188 | G | T | 0.0018637 | 0.0027689 | 0.5000000 | 0.5009006 | 0.054446 | 0.0880591 | NA |
| 22 | 51223637 | rs375798137 | G | A | 0.0020383 | 0.0027823 | 0.4600002 | 0.4638009 | 0.054077 | 0.0788738 | NA |
| 22 | 51229805 | rs9616985 | T | C | 0.0030167 | 0.0023594 | 0.2000000 | 0.2010563 | 0.073094 | 0.0730831 | NA |
| 22 | 51232488 | rs376461333 | A | G | 0.0006884 | 0.0055645 | 0.9000000 | 0.9015425 | 0.020019 | NA | NA |
| 22 | 51237063 | rs3896457 | T | C | 0.0003261 | 0.0014432 | 0.8200001 | 0.8212580 | 0.298055 | 0.2050720 | NA |
bcf preview
1 49298 rs10399793 T C . PASS AF=0.623811 ES:SE:LP:AF:ID 0.00109568:0.00216844:0.21467:0.623811:rs10399793
1 54676 rs2462492 C T . PASS AF=0.400356 ES:SE:LP:AF:ID 0.0022008:0.00214843:0.508638:0.400356:rs2462492
1 86028 rs114608975 T C . PASS AF=0.103585 ES:SE:LP:AF:ID -0.00471273:0.00343232:0.769551:0.103585:rs114608975
1 91536 rs6702460 G T . PASS AF=0.45684 ES:SE:LP:AF:ID 0.000824893:0.00211417:0.154902:0.45684:rs6702460
1 234313 rs8179466 C T . PASS AF=0.074522 ES:SE:LP:AF:ID 0.00690829:0.00416816:1.01323:0.074522:rs8179466
1 534192 rs6680723 C T . PASS AF=0.240918 ES:SE:LP:AF:ID -0.00278808:0.00241605:0.60206:0.240918:rs6680723
1 546697 rs12025928 A G . PASS AF=0.913509 ES:SE:LP:AF:ID -0.00318742:0.00301475:0.537602:0.913509:rs12025928
1 693731 rs12238997 A G . PASS AF=0.116393 ES:SE:LP:AF:ID -0.000732921:0.0020243:0.142668:0.116393:rs12238997
1 705882 rs72631875 G A . PASS AF=0.067284 ES:SE:LP:AF:ID 0.00265693:0.00296661:0.431798:0.067284:rs72631875
1 706368 rs12029736 A G . PASS AF=0.515645 ES:SE:LP:AF:ID -0.000326704:0.00150002:0.0809219:0.515645:rs12029736
1 714596 rs149887893 T C . PASS AF=0.033044 ES:SE:LP:AF:ID -0.00157516:0.00377892:0.167491:0.033044:rs149887893
1 715265 rs12184267 C T . PASS AF=0.036663 ES:SE:LP:AF:ID -0.00170461:0.00343274:0.207608:0.036663:rs12184267
1 715367 rs12184277 A G . PASS AF=0.036783 ES:SE:LP:AF:ID -0.00130555:0.00341949:0.154902:0.036783:rs12184277
1 717485 rs12184279 C A . PASS AF=0.036478 ES:SE:LP:AF:ID -0.00165699:0.00344438:0.200659:0.036478:rs12184279
1 717587 rs144155419 G A . PASS AF=0.016383 ES:SE:LP:AF:ID 0.00763684:0.00531019:0.823909:0.016383:rs144155419
1 720381 rs116801199 G T . PASS AF=0.03702 ES:SE:LP:AF:ID -0.00133751:0.00340599:0.161151:0.03702:rs116801199
1 721290 rs12565286 G C . PASS AF=0.037115 ES:SE:LP:AF:ID -0.00131942:0.00339443:0.154902:0.037115:rs12565286
1 722670 rs116030099 T C . PASS AF=0.101186 ES:SE:LP:AF:ID 0.00342624:0.0024746:0.769551:0.101186:rs116030099
1 723891 rs2977670 G C . PASS AF=0.959055 ES:SE:LP:AF:ID 0.00061317:0.00327419:0.0705811:0.959055:rs2977670
1 724849 rs12126395 C A . PASS AF=0.031445 ES:SE:LP:AF:ID -0.00644627:0.00594562:0.552842:0.031445:rs12126395
1 725060 rs865924913 A T . PASS AF=0.053233 ES:SE:LP:AF:ID 0.00595408:0.00473031:0.677781:0.053233:rs865924913
1 726794 rs28454925 C G . PASS AF=0.036636 ES:SE:LP:AF:ID -0.00136385:0.00341637:0.161151:0.036636:rs28454925
1 729632 rs116720794 C T . PASS AF=0.036953 ES:SE:LP:AF:ID -0.00101416:0.00338514:0.119186:0.036953:rs116720794
1 729679 rs4951859 C G . PASS AF=0.84312 ES:SE:LP:AF:ID 0.000361409:0.00175429:0.0757207:0.84312:rs4951859
1 730087 rs148120343 T C . PASS AF=0.055981 ES:SE:LP:AF:ID -0.00338159:0.00283946:0.638272:0.055981:rs148120343
1 731718 rs58276399 T C . PASS AF=0.122366 ES:SE:LP:AF:ID -0.000688469:0.00192034:0.142668:0.122366:rs58276399
1 732989 rs369030935 C T . PASS AF=0.025723 ES:SE:LP:AF:ID -0.00244225:0.00472238:0.21467:0.025723:rs369030935
1 734349 rs141242758 T C . PASS AF=0.121606 ES:SE:LP:AF:ID -0.000550238:0.00192118:0.113509:0.121606:rs141242758
1 736289 rs79010578 T A . PASS AF=0.132441 ES:SE:LP:AF:ID -0.00147448:0.00189306:0.356547:0.132441:rs79010578
1 736689 rs181876450 T C . PASS AF=0.011138 ES:SE:LP:AF:ID -0.00553674:0.0068824:0.376751:0.011138:rs181876450
1 740284 rs61770167 C T . PASS AF=0.005696 ES:SE:LP:AF:ID 0.00695633:0.008892:0.366532:0.005696:rs61770167
1 742813 rs112573343 C T . PASS AF=0.002264 ES:SE:LP:AF:ID 0.0174458:0.0149599:0.619789:0.002264:rs112573343
1 746189 rs139221807 A G . PASS AF=0.001027 ES:SE:LP:AF:ID -0.0198264:0.0245082:0.376751:0.001027:rs139221807
1 752478 rs146277091 G A . PASS AF=0.036868 ES:SE:LP:AF:ID -0.000614893:0.00335113:0.0705811:0.036868:rs146277091
1 752566 rs3094315 G A . PASS AF=0.838837 ES:SE:LP:AF:ID -0.000220077:0.00169907:0.0457575:0.838837:rs3094315
1 752721 rs3131972 A G . PASS AF=0.838462 ES:SE:LP:AF:ID -0.000426663:0.00169721:0.09691:0.838462:rs3131972
1 753405 rs3115860 C A . PASS AF=0.869701 ES:SE:LP:AF:ID -0.000264014:0.00182134:0.0555173:0.869701:rs3115860
1 753541 rs2073813 G A . PASS AF=0.129953 ES:SE:LP:AF:ID 0.00039216:0.001825:0.0809219:0.129953:rs2073813
1 754063 rs12184312 G T . PASS AF=0.037373 ES:SE:LP:AF:ID -0.000486501:0.00329447:0.0555173:0.037373:rs12184312
1 754105 rs12184325 C T . PASS AF=0.037616 ES:SE:LP:AF:ID -0.000258511:0.00327373:0.0268721:0.037616:rs12184325
1 754182 rs3131969 A G . PASS AF=0.869042 ES:SE:LP:AF:ID -0.000554308:0.00181775:0.119186:0.869042:rs3131969
1 754192 rs3131968 A G . PASS AF=0.869142 ES:SE:LP:AF:ID -0.000555204:0.00181849:0.119186:0.869142:rs3131968
1 754211 rs12184313 G A . PASS AF=0.037573 ES:SE:LP:AF:ID -0.000491392:0.00328793:0.0555173:0.037573:rs12184313
1 754334 rs3131967 T C . PASS AF=0.869043 ES:SE:LP:AF:ID -0.000519209:0.00181771:0.107905:0.869043:rs3131967
1 754433 rs150578204 G A . PASS AF=0.005131 ES:SE:LP:AF:ID 0.00417193:0.00932094:0.187087:0.005131:rs150578204
1 754458 rs142682604 G T . PASS AF=0.005097 ES:SE:LP:AF:ID 0.00391556:0.00934541:0.167491:0.005097:rs142682604
1 754503 rs3115859 G A . PASS AF=0.837917 ES:SE:LP:AF:ID -0.000382094:0.00169253:0.0861861:0.837917:rs3115859
1 754629 rs10454459 A G . PASS AF=0.037586 ES:SE:LP:AF:ID -0.000629519:0.00329253:0.0705811:0.037586:rs10454459
1 754964 rs3131966 C T . PASS AF=0.838548 ES:SE:LP:AF:ID -0.000425458:0.00169729:0.09691:0.838548:rs3131966
1 755240 rs181660517 T G . PASS AF=0.013787 ES:SE:LP:AF:ID -0.00924644:0.00592145:0.920819:0.013787:rs181660517