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_5097.vcf.gz --id UKB-b:13538 --data /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/ukbiobank/raw-output/data.batch_5097.txt.gz --cohort_controls 83410 --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": "2019-09-12T23:09:49.961706",
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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-13538/UKB-b-13538_data.vcf.gz \
--ref-ld-chr ../reference/eur_w_ld_chr/ \
--out /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-13538/ldsc.txt \
--w-ld-chr ../reference/eur_w_ld_chr/
Beginning analysis at Thu Oct 17 14:42:50 2019
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-13538/UKB-b-13538_data.vcf.gz ...
Read summary statistics for 8878036 SNPs.
Dropped 8206 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, 1286800 SNPs remain.
After merging with regression SNP LD, 1286800 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.3902 (0.0221)
Lambda GC: 1.4105
Mean Chi^2: 1.7201
Intercept: 1.0939 (0.0129)
Ratio: 0.1304 (0.0179)
Analysis finished at Thu Oct 17 14:44:28 2019
Total time elapsed: 1.0m:38.58sQC metrics
Metrics
Metrics
{
"af_correlation": 0.9474,
"inflation_factor": 1.3107,
"mean_EFFECT": 0,
"n": "-Inf",
"n_snps": 9851866,
"n_clumped_hits": 199,
"n_p_sig": 16217,
"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": 88966,
"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": 1286800,
"ldsc_nsnp_merge_regression_ld": 1286800,
"ldsc_observed_scale_h2_beta": 0.3902,
"ldsc_observed_scale_h2_se": 0.0221,
"ldsc_intercept_beta": 1.0939,
"ldsc_intercept_se": 0.0129,
"ldsc_lambda_gc": 1.4105,
"ldsc_mean_chisq": 1.7201,
"ldsc_ratio": 0.1304
}
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 | 8869869 | 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 | 8878036 | 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 | 8.646674e+00 | 5.759678e+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 | 7.877942e+07 | 5.634531e+07 | 828.0000000 | 3.241435e+07 | 6.933640e+07 | 1.145509e+08 | 2.492385e+08 | ▇▆▅▂▁ |
| numeric | EFFECT | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 4.020000e-05 | 1.584530e-02 | -0.2286190 | -6.703200e-03 | -5.800000e-06 | 6.758800e-03 | 3.892310e-01 | ▁▇▁▁▁ |
| numeric | SE | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 1.179220e-02 | 8.416900e-03 | 0.0044109 | 5.250200e-03 | 7.933100e-03 | 1.611640e-02 | 1.009570e-01 | ▇▁▁▁▁ |
| numeric | PVAL | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 4.562715e-01 | 3.014260e-01 | 0.0000000 | 1.800002e-01 | 4.400003e-01 | 7.199992e-01 | 1.000000e+00 | ▇▆▆▅▆ |
| numeric | PVAL_ztest | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 4.562726e-01 | 3.014012e-01 | 0.0000000 | 1.846005e-01 | 4.413819e-01 | 7.176110e-01 | 9.999999e-01 | ▇▆▆▆▅ |
| numeric | AF | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 2.231463e-01 | 2.588611e-01 | 0.0041970 | 2.201400e-02 | 1.057010e-01 | 3.522500e-01 | 9.958030e-01 | ▇▂▁▁▁ |
| numeric | AF_reference | 88966 | 0.9899791 | NA | NA | NA | NA | NA | NA | NA | 2.232303e-01 | 2.508099e-01 | 0.0000000 | 1.936900e-02 | 1.228040e-01 | 3.502400e-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 | 0.0148167 | 0.0081405 | 0.0690001 | 0.0687408 | 0.623505 | 0.7821490 | NA |
| 1 | 54676 | rs2462492 | C | T | -0.0121230 | 0.0080821 | 0.1299999 | 0.1336192 | 0.399158 | NA | NA |
| 1 | 86028 | rs114608975 | T | C | -0.0028337 | 0.0128242 | 0.8300000 | 0.8251215 | 0.103979 | 0.0277556 | NA |
| 1 | 91536 | rs6702460 | G | T | 0.0042357 | 0.0079443 | 0.5900000 | 0.5939101 | 0.455954 | 0.4207270 | NA |
| 1 | 234313 | rs8179466 | C | T | 0.0167057 | 0.0156364 | 0.2900000 | 0.2853467 | 0.074560 | NA | NA |
| 1 | 534192 | rs6680723 | C | T | 0.0008271 | 0.0090993 | 0.9299999 | 0.9275764 | 0.240218 | NA | NA |
| 1 | 546697 | rs12025928 | A | G | -0.0266722 | 0.0112765 | 0.0179999 | 0.0180159 | 0.912844 | NA | NA |
| 1 | 693731 | rs12238997 | A | G | 0.0070367 | 0.0075714 | 0.3500000 | 0.3526941 | 0.117537 | 0.1417730 | NA |
| 1 | 705882 | rs72631875 | G | A | -0.0016221 | 0.0111004 | 0.8800001 | 0.8838196 | 0.067410 | 0.0315495 | NA |
| 1 | 706368 | rs55727773 | A | G | -0.0023815 | 0.0056143 | 0.6700003 | 0.6714280 | 0.515046 | 0.2751600 | NA |
| CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 22 | 51219006 | rs28729663 | G | A | -0.0075257 | 0.0068217 | 0.2700001 | 0.2699423 | 0.137482 | 0.2052720 | NA |
| 22 | 51219387 | rs9616832 | T | C | 0.0029441 | 0.0088833 | 0.7400005 | 0.7403273 | 0.072750 | 0.0654952 | NA |
| 22 | 51219704 | rs147475742 | G | A | 0.0101558 | 0.0118300 | 0.3900004 | 0.3906283 | 0.041805 | 0.0473243 | NA |
| 22 | 51221190 | rs369304721 | G | A | 0.0103366 | 0.0119067 | 0.3900004 | 0.3853215 | 0.049124 | NA | NA |
| 22 | 51221731 | rs115055839 | T | C | 0.0028082 | 0.0088846 | 0.7499995 | 0.7519496 | 0.072308 | 0.0625000 | NA |
| 22 | 51222100 | rs114553188 | G | T | -0.0213518 | 0.0104092 | 0.0400000 | 0.0402433 | 0.054502 | 0.0880591 | NA |
| 22 | 51223637 | rs375798137 | G | A | -0.0215684 | 0.0104616 | 0.0389996 | 0.0392389 | 0.054135 | 0.0788738 | NA |
| 22 | 51229805 | rs9616985 | T | C | 0.0020005 | 0.0089178 | 0.8200001 | 0.8225012 | 0.072184 | 0.0730831 | NA |
| 22 | 51232488 | rs376461333 | A | G | -0.0475746 | 0.0210681 | 0.0239999 | 0.0239373 | 0.020055 | NA | NA |
| 22 | 51237063 | rs3896457 | T | C | -0.0037865 | 0.0054371 | 0.4899999 | 0.4861708 | 0.297913 | 0.2050720 | NA |
bcf preview
1 49298 rs10399793 T C . PASS AF=0.623505 ES:SE:LP:AF:ID 0.0148167:0.00814051:1.16115:0.623505:rs10399793
1 54676 rs2462492 C T . PASS AF=0.399158 ES:SE:LP:AF:ID -0.012123:0.0080821:0.886057:0.399158:rs2462492
1 86028 rs114608975 T C . PASS AF=0.103979 ES:SE:LP:AF:ID -0.00283367:0.0128242:0.0809219:0.103979:rs114608975
1 91536 rs6702460 G T . PASS AF=0.455954 ES:SE:LP:AF:ID 0.00423574:0.00794432:0.229148:0.455954:rs6702460
1 234313 rs8179466 C T . PASS AF=0.07456 ES:SE:LP:AF:ID 0.0167057:0.0156364:0.537602:0.07456:rs8179466
1 534192 rs6680723 C T . PASS AF=0.240218 ES:SE:LP:AF:ID 0.000827079:0.00909933:0.0315171:0.240218:rs6680723
1 546697 rs12025928 A G . PASS AF=0.912844 ES:SE:LP:AF:ID -0.0266722:0.0112765:1.74473:0.912844:rs12025928
1 693731 rs12238997 A G . PASS AF=0.117537 ES:SE:LP:AF:ID 0.00703668:0.0075714:0.455932:0.117537:rs12238997
1 705882 rs72631875 G A . PASS AF=0.06741 ES:SE:LP:AF:ID -0.00162209:0.0111004:0.0555173:0.06741:rs72631875
1 706368 rs12029736 A G . PASS AF=0.515046 ES:SE:LP:AF:ID -0.00238152:0.00561429:0.173925:0.515046:rs12029736
1 714596 rs149887893 T C . PASS AF=0.033464 ES:SE:LP:AF:ID 0.00595668:0.0140365:0.173925:0.033464:rs149887893
1 715265 rs12184267 C T . PASS AF=0.037138 ES:SE:LP:AF:ID 0.0103773:0.0127587:0.376751:0.037138:rs12184267
1 715367 rs12184277 A G . PASS AF=0.037222 ES:SE:LP:AF:ID 0.00974626:0.0127169:0.356547:0.037222:rs12184277
1 717485 rs12184279 C A . PASS AF=0.036892 ES:SE:LP:AF:ID 0.0121996:0.0128103:0.468521:0.036892:rs12184279
1 717587 rs144155419 G A . PASS AF=0.016769 ES:SE:LP:AF:ID -0.0140852:0.0196817:0.327902:0.016769:rs144155419
1 720381 rs116801199 G T . PASS AF=0.037477 ES:SE:LP:AF:ID 0.0114765:0.0126647:0.443698:0.037477:rs116801199
1 721290 rs12565286 G C . PASS AF=0.037563 ES:SE:LP:AF:ID 0.0105691:0.0126246:0.39794:0.037563:rs12565286
1 722670 rs116030099 T C . PASS AF=0.100858 ES:SE:LP:AF:ID -0.00557932:0.00930863:0.259637:0.100858:rs116030099
1 723891 rs2977670 G C . PASS AF=0.958184 ES:SE:LP:AF:ID -0.00609374:0.0121383:0.207608:0.958184:rs2977670
1 724849 rs12126395 C A . PASS AF=0.03191 ES:SE:LP:AF:ID -0.0261805:0.022077:0.619789:0.03191:rs12126395
1 725060 rs865924913 A T . PASS AF=0.052678 ES:SE:LP:AF:ID 0.010179:0.0178544:0.244125:0.052678:rs865924913
1 726794 rs28454925 C G . PASS AF=0.037038 ES:SE:LP:AF:ID 0.0117312:0.0127107:0.443698:0.037038:rs28454925
1 729632 rs116720794 C T . PASS AF=0.037361 ES:SE:LP:AF:ID 0.0126856:0.0126018:0.508638:0.037361:rs116720794
1 729679 rs4951859 C G . PASS AF=0.841197 ES:SE:LP:AF:ID -0.00582344:0.00655395:0.431798:0.841197:rs4951859
1 730087 rs148120343 T C . PASS AF=0.055916 ES:SE:LP:AF:ID -0.00433136:0.0106935:0.161151:0.055916:rs148120343
1 731718 rs58276399 T C . PASS AF=0.12353 ES:SE:LP:AF:ID 0.00639439:0.00718576:0.431798:0.12353:rs58276399
1 732989 rs369030935 C T . PASS AF=0.025888 ES:SE:LP:AF:ID 0.00642246:0.0176593:0.142668:0.025888:rs369030935
1 734349 rs141242758 T C . PASS AF=0.122691 ES:SE:LP:AF:ID 0.00579488:0.00719014:0.376751:0.122691:rs141242758
1 736289 rs79010578 T A . PASS AF=0.133313 ES:SE:LP:AF:ID 0.00921087:0.00708858:0.721246:0.133313:rs79010578
1 736689 rs181876450 T C . PASS AF=0.01125 ES:SE:LP:AF:ID 0.00423428:0.0256359:0.0604807:0.01125:rs181876450
1 740284 rs61770167 C T . PASS AF=0.006038 ES:SE:LP:AF:ID 0.0416576:0.0322246:0.69897:0.006038:rs61770167
1 752478 rs146277091 G A . PASS AF=0.037341 ES:SE:LP:AF:ID 0.0117192:0.0124588:0.455932:0.037341:rs146277091
1 752566 rs3094315 G A . PASS AF=0.837078 ES:SE:LP:AF:ID -0.00441023:0.00634425:0.309804:0.837078:rs3094315
1 752721 rs3131972 A G . PASS AF=0.836668 ES:SE:LP:AF:ID -0.00441297:0.00633763:0.309804:0.836668:rs3131972
1 753405 rs3115860 C A . PASS AF=0.868267 ES:SE:LP:AF:ID -0.00264048:0.00680358:0.154902:0.868267:rs3115860
1 753541 rs2073813 G A . PASS AF=0.131381 ES:SE:LP:AF:ID 0.00386412:0.00681758:0.244125:0.131381:rs2073813
1 754063 rs12184312 G T . PASS AF=0.037784 ES:SE:LP:AF:ID 0.0125921:0.0122637:0.522879:0.037784:rs12184312
1 754105 rs12184325 C T . PASS AF=0.038035 ES:SE:LP:AF:ID 0.0125189:0.0121879:0.522879:0.038035:rs12184325
1 754182 rs3131969 A G . PASS AF=0.867594 ES:SE:LP:AF:ID -0.0025101:0.00679086:0.148742:0.867594:rs3131969
1 754192 rs3131968 A G . PASS AF=0.867673 ES:SE:LP:AF:ID -0.00252255:0.00679334:0.148742:0.867673:rs3131968
1 754211 rs12184313 G A . PASS AF=0.037976 ES:SE:LP:AF:ID 0.0128239:0.0122387:0.537602:0.037976:rs12184313
1 754334 rs3131967 T C . PASS AF=0.867592 ES:SE:LP:AF:ID -0.00257057:0.00679043:0.148742:0.867592:rs3131967
1 754433 rs150578204 G A . PASS AF=0.00506 ES:SE:LP:AF:ID -0.00410277:0.0352558:0.0409586:0.00506:rs150578204
1 754458 rs142682604 G T . PASS AF=0.005027 ES:SE:LP:AF:ID -0.00538846:0.0353579:0.0555173:0.005027:rs142682604
1 754503 rs3115859 G A . PASS AF=0.836191 ES:SE:LP:AF:ID -0.00443955:0.00632325:0.318759:0.836191:rs3115859
1 754629 rs10454459 A G . PASS AF=0.037994 ES:SE:LP:AF:ID 0.0130361:0.0122547:0.537602:0.037994:rs10454459
1 754964 rs3131966 C T . PASS AF=0.836792 ES:SE:LP:AF:ID -0.00466025:0.00634054:0.337242:0.836792:rs3131966
1 755240 rs181660517 T G . PASS AF=0.013255 ES:SE:LP:AF:ID 0.00245941:0.0226707:0.0409586:0.013255:rs181660517
1 755435 rs184270342 T G . PASS AF=0.005432 ES:SE:LP:AF:ID -0.0230439:0.0346374:0.29243:0.005432:rs184270342
1 755775 rs3131965 A G . PASS AF=0.838 ES:SE:LP:AF:ID -0.00447881:0.00642532:0.309804:0.838:rs3131965