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_41210_Y588.vcf.gz --id UKB-b:13683 --data /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/ukbiobank/raw-output/data.batch_41210_Y588.txt.gz --cohort_cases 1096 --cohort_controls 461914 --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": "2019-09-12T17:35:42.218088",
"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-13683/mac_discard.txt -Oz /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-13683/UKB-b-13683_raw.vcf.gz; Date=Thu Oct 17 12:29:23 2019",
"bcftools_viewCommand.1": "view -h /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/ukb-b-13683/ukb-b-13683.vcf.gz; Date=Sat May 9 19:00:08 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-13683/UKB-b-13683_data.vcf.gz \
--ref-ld-chr ../reference/eur_w_ld_chr/ \
--out /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-13683/ldsc.txt \
--w-ld-chr ../reference/eur_w_ld_chr/
Beginning analysis at Thu Oct 17 14:42:51 2019
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-13683/UKB-b-13683_data.vcf.gz ...
Read summary statistics for 1622488 SNPs.
Dropped 148 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, 418922 SNPs remain.
After merging with regression SNP LD, 418922 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.0003 (0.0014)
Lambda GC: 0.9939
Mean Chi^2: 0.9996
Intercept: 0.9962 (0.0117)
Ratio: NA (mean chi^2 < 1)
Analysis finished at Thu Oct 17 14:43:18 2019
Total time elapsed: 26.89s{
"af_correlation": 0.6209,
"inflation_factor": 1,
"mean_EFFECT": 3.3335e-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": 12901,
"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": 418922,
"ldsc_nsnp_merge_regression_ld": 418922,
"ldsc_observed_scale_h2_beta": 0.0003,
"ldsc_observed_scale_h2_se": 0.0014,
"ldsc_intercept_beta": 0.9962,
"ldsc_intercept_se": 0.0117,
"ldsc_lambda_gc": 0.9939,
"ldsc_mean_chisq": 0.9996,
"ldsc_ratio": 9.5
}
| name | value |
|---|---|
| name | value |
| af_correlation | TRUE |
| 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 | 1622342 | 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 | 1622488 | 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 | 8.663016e+00 | 5.766969e+00 | 1.00000e+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 | 7.855601e+07 | 5.655231e+07 | 1.23330e+04 | 3.174853e+07 | 6.910822e+07 | 1.144674e+08 | 2.491722e+08 | ▇▆▅▂▁ |
| numeric | EFFECT | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 3.000000e-07 | 1.036000e-04 | -5.02500e-04 | -6.930000e-05 | 1.100000e-06 | 6.980000e-05 | 4.898000e-04 | ▁▂▇▂▁ |
| numeric | SE | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 1.039000e-04 | 3.000000e-06 | 9.75000e-05 | 1.018000e-04 | 1.032000e-04 | 1.055000e-04 | 1.979000e-04 | ▇▁▁▁▁ |
| numeric | PVAL | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 5.017334e-01 | 2.886511e-01 | 1.00000e-06 | 2.500000e-01 | 5.000000e-01 | 7.499995e-01 | 1.000000e+00 | ▇▇▇▇▇ |
| numeric | PVAL_ztest | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 5.017327e-01 | 2.886212e-01 | 1.00000e-06 | 2.523924e-01 | 5.029578e-01 | 7.517445e-01 | 9.999999e-01 | ▇▇▇▇▇ |
| numeric | AF | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 4.792384e-01 | 1.036362e-01 | 3.19344e-01 | 3.883380e-01 | 4.689590e-01 | 5.648570e-01 | 6.806560e-01 | ▇▇▆▅▅ |
| numeric | AF_reference | 12901 | 0.9920486 | NA | NA | NA | NA | NA | NA | NA | 4.579815e-01 | 1.488878e-01 | 1.99700e-04 | 3.458470e-01 | 4.512780e-01 | 5.646960e-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 | 0.0001107 | 0.0001794 | 0.5400003 | 0.5370787 | 0.623765 | 0.782149 | NA |
| 1 | 54676 | rs2462492 | C | T | 0.0002016 | 0.0001777 | 0.2599998 | 0.2565760 | 0.400401 | NA | NA |
| 1 | 91536 | rs6702460 | G | T | 0.0003619 | 0.0001749 | 0.0389996 | 0.0385678 | 0.456846 | 0.420727 | NA |
| 1 | 706368 | rs55727773 | A | G | 0.0001444 | 0.0001241 | 0.2399999 | 0.2444535 | 0.515645 | 0.275160 | NA |
| 1 | 814495 | rs74461805 | C | A | -0.0001479 | 0.0001701 | 0.3800004 | 0.3846117 | 0.340396 | NA | NA |
| 1 | 840753 | rs4970382 | T | C | -0.0000105 | 0.0001031 | 0.9199999 | 0.9189835 | 0.400124 | 0.468850 | NA |
| 1 | 843405 | rs11516185 | A | G | 0.0000158 | 0.0001280 | 0.9000000 | 0.9019263 | 0.362606 | 0.375399 | NA |
| 1 | 850218 | rs6664536 | T | A | 0.0000387 | 0.0001028 | 0.7099994 | 0.7064602 | 0.590331 | 0.345248 | NA |
| 1 | 850371 | rs6679046 | G | T | 0.0000526 | 0.0001034 | 0.6100002 | 0.6106653 | 0.603723 | 0.508786 | NA |
| 1 | 850780 | rs6657440 | C | T | 0.0000553 | 0.0001033 | 0.5900000 | 0.5923512 | 0.603942 | 0.560304 | 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 | 51158499 | rs8136930 | T | G | 0.0001186 | 0.0001014 | 0.2399999 | 0.2422565 | 0.461636 | 0.544728 | NA |
| 22 | 51161019 | rs5770994 | C | T | -0.0001606 | 0.0001011 | 0.1100001 | 0.1120912 | 0.482204 | 0.425719 | NA |
| 22 | 51163039 | rs715584 | G | T | 0.0001681 | 0.0001027 | 0.1000000 | 0.1015189 | 0.426975 | 0.473642 | NA |
| 22 | 51164109 | rs5770995 | G | C | 0.0001309 | 0.0001020 | 0.2000000 | 0.1995049 | 0.452705 | 0.510982 | NA |
| 22 | 51164115 | rs5770996 | C | T | 0.0001227 | 0.0001020 | 0.2300001 | 0.2290794 | 0.456917 | 0.514776 | NA |
| 22 | 51174048 | rs9628245 | G | C | -0.0000153 | 0.0001152 | 0.8900000 | 0.8946724 | 0.380135 | 0.433107 | NA |
| 22 | 51186143 | rs2879914 | T | C | 0.0001717 | 0.0001086 | 0.1100001 | 0.1139158 | 0.381825 | 0.273363 | NA |
| 22 | 51186228 | rs3865766 | C | T | 0.0001045 | 0.0001059 | 0.3200000 | 0.3237026 | 0.451061 | 0.453275 | NA |
| 22 | 51197266 | rs61290853 | A | G | 0.0001637 | 0.0001093 | 0.1299999 | 0.1341057 | 0.386333 | 0.422923 | NA |
| 22 | 51212875 | rs2238837 | A | C | 0.0002040 | 0.0001165 | 0.0800000 | 0.0800081 | 0.331457 | 0.372404 | NA |
1 49298 rs10399793 T C . PASS AF=0.623765 ES:SE:LP:AF:ID 0.000110702:0.000179351:0.267606:0.623765:rs10399793
1 54676 rs2462492 C T . PASS AF=0.400401 ES:SE:LP:AF:ID 0.000201584:0.000177682:0.585027:0.400401:rs2462492
1 91536 rs6702460 G T . PASS AF=0.456846 ES:SE:LP:AF:ID 0.000361929:0.000174949:1.40894:0.456846:rs6702460
1 706368 rs12029736 A G . PASS AF=0.515645 ES:SE:LP:AF:ID 0.000144391:0.000124055:0.619789:0.515645:rs12029736
1 814495 rs74461805 C A . PASS AF=0.340396 ES:SE:LP:AF:ID -0.000147891:0.000170101:0.420216:0.340396:rs74461805
1 840753 rs4970382 T C . PASS AF=0.400124 ES:SE:LP:AF:ID -1.04844e-05:0.000103077:0.0362122:0.400124:rs4970382
1 843405 rs11516185 A G . PASS AF=0.362606 ES:SE:LP:AF:ID 1.57678e-05:0.000127956:0.0457575:0.362606:rs11516185
1 850218 rs6664536 T A . PASS AF=0.590331 ES:SE:LP:AF:ID 3.87073e-05:0.000102777:0.148742:0.590331:rs6664536
1 850371 rs6679046 G T . PASS AF=0.603723 ES:SE:LP:AF:ID 5.26195e-05:0.000103353:0.21467:0.603723:rs6679046
1 850780 rs6657440 C T . PASS AF=0.603942 ES:SE:LP:AF:ID 5.5331e-05:0.000103339:0.229148:0.603942:rs6657440
1 852037 rs4970463 G A . PASS AF=0.589686 ES:SE:LP:AF:ID 4.59008e-05:0.000102944:0.180456:0.589686:rs4970463
1 852063 rs28436996 G A . PASS AF=0.589665 ES:SE:LP:AF:ID 4.71442e-05:0.000102897:0.187087:0.589665:rs28436996
1 852875 rs13303369 C T . PASS AF=0.607671 ES:SE:LP:AF:ID 4.07345e-05:0.00010357:0.161151:0.607671:rs13303369
1 853954 rs1806509 C A . PASS AF=0.607829 ES:SE:LP:AF:ID 3.8949e-05:0.000103584:0.148742:0.607829:rs1806509
1 854777 rs13303019 A G . PASS AF=0.610316 ES:SE:LP:AF:ID 2.4094e-05:0.000103686:0.0861861:0.610316:rs13303019
1 854978 rs13303057 A C . PASS AF=0.603283 ES:SE:LP:AF:ID 5.69287e-05:0.000103379:0.236572:0.603283:rs13303057
1 855075 rs6673914 C G . PASS AF=0.610337 ES:SE:LP:AF:ID 1.93282e-05:0.000103688:0.0705811:0.610337:rs6673914
1 856099 rs28534711 T G . PASS AF=0.389936 ES:SE:LP:AF:ID -2.53144e-05:0.000103707:0.091515:0.389936:rs28534711
1 856108 rs28742275 A G . PASS AF=0.38992 ES:SE:LP:AF:ID -2.51809e-05:0.000103713:0.091515:0.38992:rs28742275
1 856476 rs4040605 A G . PASS AF=0.350356 ES:SE:LP:AF:ID 1.00668e-05:0.000106542:0.0362122:0.350356:rs4040605
1 866893 rs2880024 T C . PASS AF=0.610552 ES:SE:LP:AF:ID -4.02821e-05:0.000104269:0.154902:0.610552:rs2880024
1 875770 rs4970379 A G . PASS AF=0.600085 ES:SE:LP:AF:ID 4.83476e-05:0.000105136:0.187087:0.600085:rs4970379
1 881627 rs2272757 G A . PASS AF=0.652393 ES:SE:LP:AF:ID 1.24772e-06:0.000106206:0.00436481:0.652393:rs2272757
1 891059 rs13303065 C T . PASS AF=0.652432 ES:SE:LP:AF:ID -8.81305e-06:0.000106189:0.0315171:0.652432:rs13303065
1 891945 rs13303106 A G . PASS AF=0.652494 ES:SE:LP:AF:ID 1.41157e-06:0.000106313:0.00436481:0.652494:rs13303106
1 903245 rs28690976 A G . PASS AF=0.566938 ES:SE:LP:AF:ID -2.65261e-05:0.000105592:0.09691:0.566938:rs28690976
1 909073 rs3892467 C T . PASS AF=0.386681 ES:SE:LP:AF:ID -0.000173762:0.000105305:1.00436:0.386681:rs3892467
1 909238 rs3829740 G C . PASS AF=0.571408 ES:SE:LP:AF:ID -0.000159457:0.000101985:0.920819:0.571408:rs3829740
1 910394 rs28477686 C T . PASS AF=0.324458 ES:SE:LP:AF:ID 0.00011421:0.00011054:0.522879:0.324458:rs28477686
1 912049 rs7367995 T C . PASS AF=0.585249 ES:SE:LP:AF:ID -0.00016084:0.000103019:0.920819:0.585249:rs7367995
1 913889 rs2340596 G A . PASS AF=0.59921 ES:SE:LP:AF:ID -0.000133537:0.000103186:0.69897:0.59921:rs2340596
1 914333 rs13302979 C G . PASS AF=0.602516 ES:SE:LP:AF:ID -0.000171002:0.000103499:1.00877:0.602516:rs13302979
1 914852 rs13303368 G C . PASS AF=0.600074 ES:SE:LP:AF:ID -0.000131383:0.0001033:0.69897:0.600074:rs13303368
1 914940 rs13303033 T C . PASS AF=0.584289 ES:SE:LP:AF:ID -0.000110843:0.000102721:0.552842:0.584289:rs13303033
1 916834 rs6694632 G A . PASS AF=0.589102 ES:SE:LP:AF:ID -0.000137583:0.000102878:0.744727:0.589102:rs6694632
1 918384 rs13303118 G T . PASS AF=0.584202 ES:SE:LP:AF:ID -0.000111097:0.000102673:0.552842:0.584202:rs13303118
1 918573 rs2341354 A G . PASS AF=0.589327 ES:SE:LP:AF:ID -0.000132894:0.000102799:0.69897:0.589327:rs2341354
1 919501 rs4970414 G T . PASS AF=0.583926 ES:SE:LP:AF:ID -3.25865e-06:0.000106311:0.00877392:0.583926:rs4970414
1 921716 rs13303278 C A . PASS AF=0.567888 ES:SE:LP:AF:ID -0.000123521:0.000102587:0.638272:0.567888:rs13303278
1 924528 rs34712273 C A . PASS AF=0.578491 ES:SE:LP:AF:ID -8.14079e-05:0.000102881:0.366532:0.578491:rs34712273
1 930533 rs3128110 C G . PASS AF=0.386082 ES:SE:LP:AF:ID 4.57559e-06:0.000104195:0.0177288:0.386082:rs3128110
1 930567 rs3121574 A G . PASS AF=0.386124 ES:SE:LP:AF:ID 4.22039e-06:0.000104197:0.0132283:0.386124:rs3121574
1 930751 rs3128111 C G . PASS AF=0.385079 ES:SE:LP:AF:ID 1.43342e-05:0.000104261:0.05061:0.385079:rs3128111
1 931166 rs2710880 A G . PASS AF=0.386765 ES:SE:LP:AF:ID -7.27164e-07:0.000104214:0.00436481:0.386765:rs2710880
1 931362 rs2799060 G A . PASS AF=0.385571 ES:SE:LP:AF:ID 8.59547e-06:0.000104265:0.0315171:0.385571:rs2799060
1 933790 rs9442392 G A . PASS AF=0.578604 ES:SE:LP:AF:ID -7.72585e-05:0.000102846:0.346787:0.578604:rs9442392
1 936111 rs1936360 C T . PASS AF=0.573545 ES:SE:LP:AF:ID -5.99733e-05:0.000102821:0.251812:0.573545:rs1936360
1 940005 rs2799056 A G . PASS AF=0.399264 ES:SE:LP:AF:ID -4.73682e-05:0.000103834:0.187087:0.399264:rs2799056
1 940096 rs4503294 C T . PASS AF=0.565308 ES:SE:LP:AF:ID -3.43835e-05:0.000102527:0.130768:0.565308:rs4503294
1 941284 rs3128116 C T . PASS AF=0.397398 ES:SE:LP:AF:ID -3.98544e-05:0.000103856:0.154902:0.397398:rs3128116