manhattan_plot
qq_plot
af_plot
pz_plot
beta_std_plot
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"gwas_harmonisation_command": "--json /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/folkersen/processed/PROT-b-40/PROT-b-40_data.json --ref /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/QC/genomes/b37/human_g1k_v37.fasta; 1.1.1",
"file_date": "2019-10-28T01:57:32.843927",
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"bcftools_annotateCommand": "annotate -a /mnt/storage/home/gh13047/mr-eve/vcf-reference-datasets/dbsnp/dbsnp.v153.b37.vcf.gz -c ID -o /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/folkersen/processed/PROT-b-40/PROT-b-40.vcf.gz -O z /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/folkersen/processed/PROT-b-40/PROT-b-40_data.vcf.gz; Date=Mon Oct 28 02:42:03 2019",
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"bcftools_viewCommand": "view -h /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/prot-b-40/prot-b-40.vcf.gz; Date=Sat May 9 22:24:01 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/dev/folkersen-pqtl-gwas-import/processed/PROT-b-40/PROT-b-40.vcf.gz \
--ref-ld-chr /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/reference/eur_w_ld_chr/ \
--out /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/folkersen-pqtl-gwas-import/processed/PROT-b-40/ldsc.txt \
--w-ld-chr /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/reference/eur_w_ld_chr/
Beginning analysis at Mon Oct 28 22:10:18 2019
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/folkersen-pqtl-gwas-import/processed/PROT-b-40/PROT-b-40.vcf.gz ...
Read summary statistics for 5135036 SNPs.
Dropped 1 SNPs with duplicated rs numbers.
Reading reference panel LD Score from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/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 /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/reference/eur_w_ld_chr/[1-22] ...
Read regression weight LD Scores for 1290028 SNPs.
After merging with reference panel LD, 759193 SNPs remain.
After merging with regression SNP LD, 759193 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: -0.1722 (0.1597)
Lambda GC: 0.9707
Mean Chi^2: 0.9738
Intercept: 0.9871 (0.0093)
Ratio: NA (mean chi^2 < 1)
Analysis finished at Mon Oct 28 22:11:07 2019
Total time elapsed: 49.32s{
"af_correlation": 0.9563,
"inflation_factor": 0.9327,
"mean_EFFECT": 0.001,
"n": "-Inf",
"n_snps": 5135036,
"n_clumped_hits": 8,
"n_p_sig": 1357,
"n_mono": 545,
"n_ns": 317497,
"n_mac": 0,
"is_snpid_unique": false,
"n_miss_EFFECT": 0,
"n_miss_SE": 0,
"n_miss_PVAL": 0,
"n_miss_AF": 0,
"n_miss_AF_reference": 377170,
"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": 759193,
"ldsc_nsnp_merge_regression_ld": 759193,
"ldsc_observed_scale_h2_beta": "NA",
"ldsc_observed_scale_h2_se": "NA",
"ldsc_intercept_beta": 0.9871,
"ldsc_intercept_se": 0.0093,
"ldsc_lambda_gc": 0.9707,
"ldsc_mean_chisq": 0.9738,
"ldsc_ratio": 0.4924
}
| name | value |
|---|---|
| name | value |
| af_correlation | FALSE |
| inflation_factor | FALSE |
| n | TRUE |
| is_snpid_non_unique | TRUE |
| mean_EFFECT_nonfinite | FALSE |
| mean_EFFECT_05 | FALSE |
| mean_EFFECT_01 | FALSE |
| mean_chisq | FALSE |
| 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 |
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 | 3 | 58 | 0 | 5135032 | 0 | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| character | REF | 0 | 1.0000000 | 1 | 3 | 0 | 80 | 0 | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| character | ALT | 0 | 1.0000000 | 1 | 3 | 0 | 80 | 0 | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| logical | N | 5135036 | 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 | 8.356760e+00 | 5.629048e+00 | 1.0000 | 3.000000e+00 | 7.000000e+00 | 1.200000e+01 | 2.200000e+01 | ▇▅▃▂▂ |
| numeric | POS | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 7.977423e+07 | 5.495317e+07 | 29422.0000 | 3.532730e+07 | 7.050636e+07 | 1.143548e+08 | 2.492183e+08 | ▇▇▅▂▁ |
| numeric | EFFECT | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 9.602000e-04 | 2.801010e-01 | -25.2631 | -3.790000e-02 | -1.400000e-03 | 3.430000e-02 | 5.324260e+01 | ▁▇▁▁▁ |
| numeric | SE | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 1.307205e-01 | 2.354823e-01 | 0.0233 | 3.380000e-02 | 4.740000e-02 | 1.080000e-01 | 3.317800e+00 | ▇▁▁▁▁ |
| numeric | PVAL | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 5.105293e-01 | 2.855052e-01 | 0.0000 | 2.676998e-01 | 5.148005e-01 | 7.569009e-01 | 1.000000e+00 | ▇▇▇▇▇ |
| numeric | PVAL_ztest | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 5.103722e-01 | 2.856005e-01 | 0.0000 | 2.674412e-01 | 5.146620e-01 | 7.568202e-01 | 1.000000e+00 | ▇▇▇▇▇ |
| numeric | AF | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 2.781589e-01 | 2.817943e-01 | 0.0000 | 3.560000e-02 | 1.762000e-01 | 4.617000e-01 | 1.000000e+00 | ▇▃▂▂▁ |
| numeric | AF_reference | 377170 | 0.9265497 | NA | NA | NA | NA | NA | NA | NA | 2.522964e-01 | 2.538675e-01 | 0.0000 | 3.654150e-02 | 1.659350e-01 | 4.039540e-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 | 780785 | rs2977612 | T | A | -0.0138 | 0.0464 | 0.7669005 | 0.7661506 | 0.8252 | 0.669329 | NA |
| 1 | 782981 | rs6594026 | C | T | 0.0136 | 0.0458 | 0.7666992 | 0.7665098 | 0.1534 | 0.297923 | NA |
| 1 | 783318 | rs6686696 | A | G | 0.0213 | 0.0717 | 0.7669994 | 0.7664122 | 0.0799 | 0.183107 | NA |
| 1 | 785050 | rs2905062 | G | A | -0.0101 | 0.0340 | 0.7669005 | 0.7664216 | 0.8365 | 0.626997 | NA |
| 1 | 785989 | rs2980300 | T | C | -0.0112 | 0.0377 | 0.7669005 | 0.7664037 | 0.8083 | 0.626997 | NA |
| 1 | 787121 | rs12077234 | T | A | 0.0177 | 0.0596 | 0.7667998 | 0.7664819 | 0.1319 | NA | NA |
| 1 | 787399 | rs2905055 | G | T | -0.0137 | 0.0461 | 0.7664997 | 0.7663291 | 0.8001 | 0.646366 | NA |
| 1 | 787685 | rs2905054 | G | T | -0.0131 | 0.0441 | 0.7674993 | 0.7664267 | 0.7668 | 0.622204 | NA |
| 1 | 787844 | rs2905053 | C | T | -0.0142 | 0.0480 | 0.7667998 | 0.7673574 | 0.8114 | 0.651757 | NA |
| 1 | 790758 | 1_790758_GTA_G | G | GTA | -0.0151 | 0.0510 | 0.7667998 | 0.7671702 | 0.7799 | NA | 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 | 51163039 | rs715584 | G | T | -0.0143 | 0.0301 | 0.6343997 | 0.6347278 | 0.4131 | 0.4736420 | NA |
| 22 | 51163138 | rs715586 | C | T | 0.0313 | 0.0361 | 0.3859002 | 0.3859223 | 0.1273 | 0.0902556 | NA |
| 22 | 51163910 | rs192700691 | C | T | 0.0012 | 0.1073 | 0.9912000 | 0.9910770 | 0.0304 | 0.0295527 | NA |
| 22 | 51164109 | rs5770995 | G | C | -0.0159 | 0.0283 | 0.5741006 | 0.5742268 | 0.4411 | 0.5109820 | NA |
| 22 | 51164115 | rs5770996 | C | T | -0.0155 | 0.0284 | 0.5861004 | 0.5852209 | 0.4446 | 0.5147760 | NA |
| 22 | 51164287 | rs6009957 | T | C | -0.0344 | 0.0273 | 0.2085000 | 0.2076429 | 0.3052 | 0.4155350 | NA |
| 22 | 51165664 | rs8137951 | G | A | -0.0325 | 0.0266 | 0.2221002 | 0.2217816 | 0.2954 | 0.4063500 | NA |
| 22 | 51171693 | rs756638 | G | A | 0.0160 | 0.0387 | 0.6786002 | 0.6792867 | 0.3046 | 0.3049120 | NA |
| 22 | 51175626 | rs3810648 | A | G | 0.0027 | 0.0603 | 0.9644999 | 0.9642858 | 0.0735 | 0.1084270 | NA |
| 22 | 51178090 | rs2285395 | G | A | 0.0190 | 0.0572 | 0.7406005 | 0.7397625 | 0.0481 | 0.0666933 | NA |
1 780785 rs2977612 T A . PASS AF=0.8252 ES:SE:LP:AF:ID -0.0138:0.0464:0.115261:0.8252:rs2977612
1 782981 rs6594026 C T . PASS AF=0.1534 ES:SE:LP:AF:ID 0.0136:0.0458:0.115375:0.1534:rs6594026
1 783318 rs6686696 A G . PASS AF=0.0799 ES:SE:LP:AF:ID 0.0213:0.0717:0.115205:0.0799:rs6686696
1 785050 rs2905062 G A . PASS AF=0.8365 ES:SE:LP:AF:ID -0.0101:0.034:0.115261:0.8365:rs2905062
1 785989 rs2980300 T C . PASS AF=0.8083 ES:SE:LP:AF:ID -0.0112:0.0377:0.115261:0.8083:rs2980300
1 787121 rs12077234 T A . PASS AF=0.1319 ES:SE:LP:AF:ID 0.0177:0.0596:0.115318:0.1319:rs12077234
1 787399 rs2905055 G T . PASS AF=0.8001 ES:SE:LP:AF:ID -0.0137:0.0461:0.115488:0.8001:rs2905055
1 787685 rs2905054 G T . PASS AF=0.7668 ES:SE:LP:AF:ID -0.0131:0.0441:0.114922:0.7668:rs2905054
1 787844 rs2905053 C T . PASS AF=0.8114 ES:SE:LP:AF:ID -0.0142:0.048:0.115318:0.8114:rs2905053
1 790758 1_790758_GTA_G G GTA . PASS AF=0.7799 ES:SE:LP:AF:ID -0.0151:0.051:0.115318:0.7799:1_790758_GTA_G
1 1108637 rs4970421 G A . PASS AF=0.0713 ES:SE:LP:AF:ID 0.1333:0.0757:1.10563:0.0713:rs4970421
1 1112982 rs6671609 C T . PASS AF=0.1436 ES:SE:LP:AF:ID 0.1012:0.06:1.03631:0.1436:rs6671609
1 1115994 rs13376597 G A . PASS AF=0.1429 ES:SE:LP:AF:ID 0.0968:0.0581:1.01882:0.1429:rs13376597
1 1116231 rs13374146 T C . PASS AF=0.0678 ES:SE:LP:AF:ID 0.1068:0.0612:1.09028:0.0678:rs13374146
1 1117398 rs12097586 A G . PASS AF=0.4246 ES:SE:LP:AF:ID 0.0016:0.0437:0.0130492:0.4246:rs12097586
1 1117486 rs13376670 A G . PASS AF=0.1481 ES:SE:LP:AF:ID 0.0956:0.0571:1.02743:0.1481:rs13376670
1 1118275 rs61733845 C T . PASS AF=0.05 ES:SE:LP:AF:ID 0.1074:0.0576:1.20628:0.05:rs61733845
1 1118578 rs111290899 G A . PASS AF=0.0504 ES:SE:LP:AF:ID 0.1064:0.0588:1.15027:0.0504:rs111290899
1 1119657 rs4560982 G C . PASS AF=0.4012 ES:SE:LP:AF:ID -0.0222:0.0392:0.242604:0.4012:rs4560982
1 1119858 rs1320565 C T . PASS AF=0.1126 ES:SE:LP:AF:ID -0.0099:0.0603:0.0604308:0.1126:rs1320565
1 1120431 rs1320571 G A . PASS AF=0.0525 ES:SE:LP:AF:ID -0.0347:0.0551:0.276626:0.0525:rs1320571
1 1121014 rs3813204 G A . PASS AF=0.1364 ES:SE:LP:AF:ID -0.0421:0.0571:0.336865:0.1364:rs3813204
1 1121341 rs4297230 C T . PASS AF=0.1422 ES:SE:LP:AF:ID -0.046:0.0557:0.388808:0.1422:rs4297230
1 1121358 rs80057011 A C . PASS AF=0.0928 ES:SE:LP:AF:ID 0.007:0.0656:0.0385789:0.0928:rs80057011
1 1121480 rs12063663 T C . PASS AF=0.0923 ES:SE:LP:AF:ID 0.013:0.0654:0.0744301:0.0923:rs12063663
1 1121625 rs4081334 C G . PASS AF=0.1418 ES:SE:LP:AF:ID -0.0466:0.0552:0.399354:0.1418:rs4081334
1 1121657 rs11260548 T C . PASS AF=0.2302 ES:SE:LP:AF:ID -0.0173:0.0371:0.193142:0.2302:rs11260548
1 1121715 rs4081333 C T . PASS AF=0.0882 ES:SE:LP:AF:ID 0.0135:0.0644:0.0791465:0.0882:rs4081333
1 1121794 rs11260549 G A . PASS AF=0.1326 ES:SE:LP:AF:ID -0.0436:0.055:0.368962:0.1326:rs11260549
1 1121835 rs57346441 C CTG . PASS AF=0.2304 ES:SE:LP:AF:ID -0.0175:0.0363:0.200177:0.2304:1_1121835_C_CTG
1 1122024 rs4314833 T C . PASS AF=0.1279 ES:SE:LP:AF:ID -0.0405:0.0561:0.327717:0.1279:rs4314833
1 1122196 rs4634847 A G . PASS AF=0.1342 ES:SE:LP:AF:ID -0.0449:0.0547:0.384681:0.1342:rs4634847
1 1122283 rs12064046 T G . PASS AF=0.0862 ES:SE:LP:AF:ID 0.0129:0.0639:0.076031:0.0862:rs12064046
1 1122319 rs7415847 C T . PASS AF=0.1199 ES:SE:LP:AF:ID -0.0423:0.0599:0.31894:0.1199:rs7415847
1 1122468 rs7545694 T C . PASS AF=0.2031 ES:SE:LP:AF:ID -0.0181:0.04:0.186753:0.2031:rs7545694
1 1122516 rs11260551 G A . PASS AF=0.1274 ES:SE:LP:AF:ID -0.0382:0.0559:0.306537:0.1274:rs11260551
1 1122539 rs12063897 A G . PASS AF=0.0866 ES:SE:LP:AF:ID 0.0134:0.0631:0.0800855:0.0866:rs12063897
1 1122915 rs28595293 A G . PASS AF=0.2718 ES:SE:LP:AF:ID -0.0272:0.032:0.403953:0.2718:rs28595293
1 1122916 rs28460227 A G . PASS AF=0.0856 ES:SE:LP:AF:ID 0.014:0.0632:0.0836513:0.0856:rs28460227
1 1122937 rs28648687 G A . PASS AF=0.0856 ES:SE:LP:AF:ID 0.014:0.0632:0.0837567:0.0856:rs28648687
1 1123106 rs12401472 G A . PASS AF=0.128 ES:SE:LP:AF:ID -0.0381:0.0554:0.308388:0.128:rs12401472
1 1123434 rs12066716 T A . PASS AF=0.1323 ES:SE:LP:AF:ID -0.0299:0.0537:0.238298:0.1323:rs12066716
1 1124257 rs10907172 A G . PASS AF=0.1273 ES:SE:LP:AF:ID -0.0379:0.0552:0.307947:0.1273:rs10907172
1 1124399 rs10907173 C G . PASS AF=0.1324 ES:SE:LP:AF:ID -0.0415:0.054:0.354479:0.1324:rs10907173
1 1124663 rs6684820 G A . PASS AF=0.2737 ES:SE:LP:AF:ID -0.0265:0.0313:0.400444:0.2737:rs6684820
1 1124819 rs6694487 C T . PASS AF=0.0867 ES:SE:LP:AF:ID 0.0121:0.0625:0.0721679:0.0867:rs6694487
1 1124891 rs61768485 G A . PASS AF=0.1266 ES:SE:LP:AF:ID -0.0379:0.055:0.308565:0.1266:rs61768485
1 1125110 rs12124436 T C . PASS AF=0.1248 ES:SE:LP:AF:ID -0.0371:0.0548:0.302335:0.1248:rs12124436
1 1125220 rs12065129 C T . PASS AF=0.0864 ES:SE:LP:AF:ID 0.0116:0.0619:0.0699174:0.0864:rs12065129
1 1125348 rs12029885 T C . PASS AF=0.1261 ES:SE:LP:AF:ID -0.0421:0.0552:0.35047:0.1261:rs12029885