manhattan_plot
qq_plot
af_plot
pz_plot
beta_std_plot
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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_41246_1800.vcf.gz --id UKB-b:8114 --data /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/ukbiobank/raw-output/data.batch_41246_1800.txt.gz --cohort_cases 1703 --cohort_controls 442389 --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": "2019-09-13T13:20:05.243834",
"bcftools_viewVersion": "1.9-74-g6af271c+htslib-1.9-64-g226b4a8",
"bcftools_viewCommand": "view -T ^/mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-8114/mac_discard.txt -Oz /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-8114/UKB-b-8114_raw.vcf.gz; Date=Thu Oct 17 12:20:23 2019",
"bcftools_viewCommand.1": "view -h /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/ukb-b-8114/ukb-b-8114.vcf.gz; Date=Sat May 9 16:54:15 2020"
}
*********************************************************************
* 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-8114/UKB-b-8114_data.vcf.gz \
--ref-ld-chr ../reference/eur_w_ld_chr/ \
--out /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-8114/ldsc.txt \
--w-ld-chr ../reference/eur_w_ld_chr/
Beginning analysis at Thu Oct 17 14:41:11 2019
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-8114/UKB-b-8114_data.vcf.gz ...
Read summary statistics for 2815307 SNPs.
Dropped 349 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, 705473 SNPs remain.
After merging with regression SNP LD, 705473 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.001 (0.0013)
Lambda GC: 1.0227
Mean Chi^2: 1.027
Intercept: 1.0174 (0.0102)
Ratio: 0.6431 (0.3765)
Analysis finished at Thu Oct 17 14:41:50 2019
Total time elapsed: 39.16s{
"af_correlation": 0.8012,
"inflation_factor": 1.0475,
"mean_EFFECT": -1.9422e-07,
"n": "-Inf",
"n_snps": 9851866,
"n_clumped_hits": 0,
"n_p_sig": 0,
"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": 22359,
"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": 705473,
"ldsc_nsnp_merge_regression_ld": 705473,
"ldsc_observed_scale_h2_beta": 0.001,
"ldsc_observed_scale_h2_se": 0.0013,
"ldsc_intercept_beta": 1.0174,
"ldsc_intercept_se": 0.0102,
"ldsc_lambda_gc": 1.0227,
"ldsc_mean_chisq": 1.027,
"ldsc_ratio": 0.6444
}
| name | value |
|---|---|
| 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 | FALSE |
| n_p_sig | FALSE |
| miss_EFFECT | FALSE |
| miss_SE | FALSE |
| miss_PVAL | FALSE |
| ldsc_ratio | TRUE |
| ldsc_intercept_beta | FALSE |
| n_clumped_hits | FALSE |
| r2_sum1 | FALSE |
| r2_sum2 | FALSE |
| r2_sum3 | FALSE |
| r2_sum4 | FALSE |
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×N×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, ˆn.ratio_se_n: ratio_se_n=√ˆn√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: mean_diff=∑j^βstdj−βjn_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.- ^βstdj=√z2j/(z2j+n−2)2×MAFj×(1−MAFj)×sign(zj),
- zj=βjsej,
- and βj is the reported effect size.
ratio_diff: ratio_diff=|mean_diffmean_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.- mean_diff2=∑j^βstdj−β′jn_snps
- β′j=βj^sd2y
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.- ^sd1y=√n×median(sej)C,
- C=median(1√2×MAFj×(1−MAFj)),
- and sej 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.- ^sd2y=median(^sdj),
- ^sdj=βj^βstdj,
r2 metrics
Sum of variance explained, calculated from the clumped top hits sample.
r2_sum<*>:r2statistics under various assumptions1: r2=∑j2×β2j×MAFj×(1−MAFj)var1, var1=1.2: r2=∑j2×β2j×MAFj×(1−MAFj)var2, var2=^sd1y2,3: r2=∑j2×β2j×MAFj×(1−MAFj)var3, var3=^sd2y2,4: r2=∑jFjFj+n−2, F=β2jse2j.
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 χ2 statistics.ldsc_ratio: ldsc_intercept_beta−1ldsc_mean_chisq−1, the proportion of the inflation in the mean χ2 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 h2 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: −log5×10−810
- Blue line: −log5×10−510
- QQ plot
- AF plot
- P-Z plot
- beta_std plot: Scatter plot between ^βstdj and βj
| 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 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 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 | 4 | 58 | 0 | 2814961 | 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 | 2815307 | 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 | 8.659450e+00 | 5.770780e+00 | 1.0000e+00 | 4.000000e+00 | 8.000000e+00 | 1.300000e+01 | 2.200000e+01 | ▇▅▃▂▂ |
| numeric | POS | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 7.857176e+07 | 5.666377e+07 | 5.6870e+03 | 3.169883e+07 | 6.898126e+07 | 1.147533e+08 | 2.492013e+08 | ▇▆▅▂▁ |
| numeric | EFFECT | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | -2.000000e-07 | 1.442000e-04 | -8.4630e-04 | -9.680000e-05 | -1.000000e-07 | 9.600000e-05 | 9.065000e-04 | ▁▂▇▁▁ |
| numeric | SE | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 1.417000e-04 | 9.600000e-06 | 1.2660e-04 | 1.334000e-04 | 1.389000e-04 | 1.484000e-04 | 2.887000e-04 | ▇▁▁▁▁ |
| numeric | PVAL | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 4.957478e-01 | 2.898055e-01 | 7.0000e-07 | 2.399999e-01 | 4.899999e-01 | 7.499995e-01 | 1.000000e+00 | ▇▇▇▇▇ |
| numeric | PVAL_ztest | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 4.957436e-01 | 2.897780e-01 | 7.0000e-07 | 2.438228e-01 | 4.946793e-01 | 7.463167e-01 | 9.999997e-01 | ▇▇▇▇▇ |
| numeric | AF | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 4.419185e-01 | 1.667675e-01 | 2.0552e-01 | 2.954255e-01 | 4.141040e-01 | 5.737925e-01 | 7.944800e-01 | ▇▆▅▃▃ |
| numeric | AF_reference | 22359 | 0.9920581 | NA | NA | NA | NA | NA | NA | NA | 4.249089e-01 | 1.861179e-01 | 1.9970e-04 | 2.763580e-01 | 4.047520e-01 | 5.615020e-01 | 1.000000e+00 | ▂▇▆▃▁ |
| CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
|---|---|---|---|---|---|---|---|---|---|---|---|
| CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
| 1 | 49298 | rs200943160 | T | C | 0.0004539 | 0.0002329 | 0.0510000 | 0.0513077 | 0.623760 | 0.7821490 | NA |
| 1 | 54676 | rs2462492 | C | T | 0.0000516 | 0.0002307 | 0.8200001 | 0.8229268 | 0.400420 | NA | NA |
| 1 | 91536 | rs6702460 | G | T | 0.0000721 | 0.0002271 | 0.7499995 | 0.7508413 | 0.456864 | 0.4207270 | NA |
| 1 | 534192 | rs6680723 | C | T | 0.0001411 | 0.0002595 | 0.5900000 | 0.5867029 | 0.240912 | NA | NA |
| 1 | 706368 | rs55727773 | A | G | -0.0000666 | 0.0001611 | 0.6800001 | 0.6792521 | 0.515726 | 0.2751600 | NA |
| 1 | 763394 | rs369924889 | G | A | -0.0002234 | 0.0001889 | 0.2399999 | 0.2368565 | 0.706660 | 0.6176120 | NA |
| 1 | 768253 | rs2977608 | A | C | -0.0001169 | 0.0001542 | 0.4500005 | 0.4482648 | 0.761327 | 0.4894170 | NA |
| 1 | 776546 | rs12124819 | A | G | -0.0000463 | 0.0001722 | 0.7899998 | 0.7878813 | 0.265287 | 0.0756789 | NA |
| 1 | 798400 | rs10900604 | A | G | 0.0001667 | 0.0001645 | 0.3100002 | 0.3108060 | 0.206586 | 0.4105430 | NA |
| 1 | 798959 | rs11240777 | G | A | 0.0001664 | 0.0001646 | 0.3100002 | 0.3118659 | 0.206415 | 0.4099440 | NA |
| CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
|---|---|---|---|---|---|---|---|---|---|---|---|
| CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
| 22 | 51180501 | rs5770999 | T | C | -0.0000931 | 0.0001516 | 0.5400003 | 0.5393293 | 0.713710 | 0.6369810 | NA |
| 22 | 51181919 | rs9616825 | G | C | -0.0000710 | 0.0001509 | 0.6400000 | 0.6376817 | 0.695495 | 0.6194090 | NA |
| 22 | 51182485 | rs6009961 | A | G | -0.0000873 | 0.0001521 | 0.5700002 | 0.5660677 | 0.715544 | 0.6383790 | NA |
| 22 | 51186143 | rs2879914 | T | C | -0.0001178 | 0.0001410 | 0.4000000 | 0.4034998 | 0.382020 | 0.2733630 | NA |
| 22 | 51186228 | rs3865766 | C | T | -0.0000537 | 0.0001375 | 0.6999999 | 0.6958173 | 0.451290 | 0.4532750 | NA |
| 22 | 51197266 | rs61290853 | A | G | 0.0000115 | 0.0001419 | 0.9400001 | 0.9353407 | 0.386519 | 0.4229230 | NA |
| 22 | 51198027 | rs34939255 | A | G | -0.0000722 | 0.0001607 | 0.6499995 | 0.6530529 | 0.254389 | 0.0984425 | NA |
| 22 | 51211106 | rs9628250 | T | C | -0.0001442 | 0.0001593 | 0.3700002 | 0.3655049 | 0.271378 | 0.1671330 | NA |
| 22 | 51212875 | rs2238837 | A | C | -0.0000385 | 0.0001513 | 0.8000000 | 0.7991463 | 0.331618 | 0.3724040 | NA |
| 22 | 51237063 | rs3896457 | T | C | -0.0000673 | 0.0001549 | 0.6600001 | 0.6642019 | 0.298151 | 0.2050720 | NA |
1 49298 rs10399793 T C . PASS AF=0.62376 ES:SE:LP:AF:ID 0.000453865:0.000232883:1.29243:0.62376:rs10399793
1 54676 rs2462492 C T . PASS AF=0.40042 ES:SE:LP:AF:ID 5.16335e-05:0.000230731:0.0861861:0.40042:rs2462492
1 91536 rs6702460 G T . PASS AF=0.456864 ES:SE:LP:AF:ID 7.21235e-05:0.000227139:0.124939:0.456864:rs6702460
1 534192 rs6680723 C T . PASS AF=0.240912 ES:SE:LP:AF:ID 0.000141083:0.000259525:0.229148:0.240912:rs6680723
1 706368 rs12029736 A G . PASS AF=0.515726 ES:SE:LP:AF:ID -6.66164e-05:0.00016111:0.167491:0.515726:rs12029736
1 763394 rs3115847 G A . PASS AF=0.70666 ES:SE:LP:AF:ID -0.000223413:0.000188872:0.619789:0.70666:rs3115847
1 768253 rs2977608 A C . PASS AF=0.761327 ES:SE:LP:AF:ID -0.000116949:0.000154223:0.346787:0.761327:rs2977608
1 776546 rs12124819 A G . PASS AF=0.265287 ES:SE:LP:AF:ID -4.63415e-05:0.000172233:0.102373:0.265287:rs12124819
1 798400 rs10900604 A G . PASS AF=0.206586 ES:SE:LP:AF:ID 0.000166722:0.000164496:0.508638:0.206586:rs10900604
1 798959 rs11240777 G A . PASS AF=0.206415 ES:SE:LP:AF:ID 0.000166429:0.000164567:0.508638:0.206415:rs11240777
1 808631 rs11240779 G A . PASS AF=0.772638 ES:SE:LP:AF:ID -0.000159528:0.000156562:0.508638:0.772638:rs11240779
1 808928 rs11240780 C T . PASS AF=0.772871 ES:SE:LP:AF:ID -0.000141322:0.000156826:0.431798:0.772871:rs11240780
1 814495 rs74461805 C A . PASS AF=0.340414 ES:SE:LP:AF:ID -0.00018153:0.00022094:0.387216:0.340414:rs74461805
1 830181 rs28444699 A G . PASS AF=0.697247 ES:SE:LP:AF:ID 0.000122528:0.000147769:0.387216:0.697247:rs28444699
1 831489 rs4970385 C T . PASS AF=0.705408 ES:SE:LP:AF:ID 8.74831e-05:0.000145091:0.259637:0.705408:rs4970385
1 831909 rs9697642 C T . PASS AF=0.705451 ES:SE:LP:AF:ID 8.80766e-05:0.000145086:0.267606:0.705451:rs9697642
1 832066 rs9697380 G C . PASS AF=0.705638 ES:SE:LP:AF:ID 8.97584e-05:0.000145091:0.267606:0.705638:rs9697380
1 832318 rs4500250 C A . PASS AF=0.705665 ES:SE:LP:AF:ID 8.92268e-05:0.000145107:0.267606:0.705665:rs4500250
1 832398 rs4553118 T C . PASS AF=0.730108 ES:SE:LP:AF:ID 8.56388e-05:0.000149067:0.244125:0.730108:rs4553118
1 832918 rs28765502 T C . PASS AF=0.294368 ES:SE:LP:AF:ID -8.97627e-05:0.0001451:0.267606:0.294368:rs28765502
1 833223 rs13303211 C T . PASS AF=0.236697 ES:SE:LP:AF:ID -0.000162086:0.00015452:0.537602:0.236697:rs13303211
1 833302 rs28752186 C T . PASS AF=0.236687 ES:SE:LP:AF:ID -0.000161814:0.000154519:0.522879:0.236687:rs28752186
1 833641 rs28594623 T C . PASS AF=0.239756 ES:SE:LP:AF:ID -0.000160562:0.000154023:0.522879:0.239756:rs28594623
1 833824 rs28484835 T C . PASS AF=0.236689 ES:SE:LP:AF:ID -0.000159373:0.000154517:0.522879:0.236689:rs28484835
1 833927 rs28593608 T C . PASS AF=0.212449 ES:SE:LP:AF:ID -0.00016932:0.000160607:0.537602:0.212449:rs28593608
1 834198 rs28385272 T C . PASS AF=0.212344 ES:SE:LP:AF:ID -0.000166768:0.000160636:0.522879:0.212344:rs28385272
1 834832 rs4411087 G C . PASS AF=0.237174 ES:SE:LP:AF:ID -0.000156072:0.0001544:0.508638:0.237174:rs4411087
1 834928 rs4422949 A G . PASS AF=0.212988 ES:SE:LP:AF:ID -0.000160588:0.000160407:0.49485:0.212988:rs4422949
1 834999 rs28570054 G A . PASS AF=0.212949 ES:SE:LP:AF:ID -0.000164596:0.000160439:0.522879:0.212949:rs28570054
1 835499 rs4422948 A G . PASS AF=0.241151 ES:SE:LP:AF:ID -0.000103476:0.000153317:0.30103:0.241151:rs4422948
1 836529 rs28731045 C G . PASS AF=0.213569 ES:SE:LP:AF:ID -0.000150962:0.000160205:0.455932:0.213569:rs28731045
1 836896 rs28705752 T C . PASS AF=0.269507 ES:SE:LP:AF:ID -0.000106799:0.000147937:0.327902:0.269507:rs28705752
1 836924 rs72890788 G A . PASS AF=0.213537 ES:SE:LP:AF:ID -0.000150993:0.000160225:0.455932:0.213537:rs72890788
1 838387 rs4970384 T C . PASS AF=0.214603 ES:SE:LP:AF:ID -0.000135047:0.000159925:0.39794:0.214603:rs4970384
1 838555 rs4970383 C A . PASS AF=0.246242 ES:SE:LP:AF:ID -9.07909e-05:0.000152267:0.259637:0.246242:rs4970383
1 839103 rs28562941 A G . PASS AF=0.27001 ES:SE:LP:AF:ID -0.000101733:0.000148037:0.309804:0.27001:rs28562941
1 840753 rs4970382 T C . PASS AF=0.400267 ES:SE:LP:AF:ID -2.28715e-05:0.000133852:0.0655015:0.400267:rs4970382
1 841085 rs1574243 C G . PASS AF=0.237176 ES:SE:LP:AF:ID -0.000145323:0.000155462:0.455932:0.237176:rs1574243
1 842013 rs7419119 T G . PASS AF=0.215412 ES:SE:LP:AF:ID -0.0001855:0.000160025:0.60206:0.215412:rs7419119
1 842362 rs28540380 C T . PASS AF=0.235349 ES:SE:LP:AF:ID -7.71186e-05:0.000157843:0.200659:0.235349:rs28540380
1 843405 rs11516185 A G . PASS AF=0.362626 ES:SE:LP:AF:ID 6.98499e-05:0.000166159:0.173925:0.362626:rs11516185
1 845938 rs57760052 G A . PASS AF=0.210822 ES:SE:LP:AF:ID -7.44803e-05:0.000161215:0.19382:0.210822:rs57760052
1 847491 rs28407778 G A . PASS AF=0.214151 ES:SE:LP:AF:ID -0.000100097:0.000160148:0.275724:0.214151:rs28407778
1 848090 rs4246505 G A . PASS AF=0.212474 ES:SE:LP:AF:ID -8.02104e-05:0.000160566:0.207608:0.212474:rs4246505
1 848445 rs4626817 G A . PASS AF=0.209255 ES:SE:LP:AF:ID -0.000107041:0.000162151:0.29243:0.209255:rs4626817
1 848456 rs11507767 A G . PASS AF=0.209204 ES:SE:LP:AF:ID -0.00010931:0.000162181:0.30103:0.209204:rs11507767
1 848738 rs3829741 C T . PASS AF=0.212299 ES:SE:LP:AF:ID -7.93386e-05:0.000160711:0.207608:0.212299:rs3829741
1 850062 rs28723578 A T . PASS AF=0.214366 ES:SE:LP:AF:ID -9.01451e-05:0.000159996:0.244125:0.214366:rs28723578
1 850123 rs28622257 C T . PASS AF=0.212743 ES:SE:LP:AF:ID -6.87763e-05:0.0001604:0.173925:0.212743:rs28622257
1 850218 rs6664536 T A . PASS AF=0.590354 ES:SE:LP:AF:ID -2.55451e-05:0.000133478:0.0705811:0.590354:rs6664536