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-81/PROT-b-81_data.json --ref /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/QC/genomes/b37/human_g1k_v37.fasta; 1.1.1",
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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-81/PROT-b-81.vcf.gz -O z /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/folkersen/processed/PROT-b-81/PROT-b-81_data.vcf.gz; Date=Mon Oct 28 02:15:36 2019",
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"bcftools_viewCommand": "view -h /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/prot-b-81/prot-b-81.vcf.gz; Date=Sat May 9 18:40:17 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-81/PROT-b-81.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-81/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 22:10:17 2019
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/folkersen-pqtl-gwas-import/processed/PROT-b-81/PROT-b-81.vcf.gz ...
Read summary statistics for 4217519 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, 625178 SNPs remain.
After merging with regression SNP LD, 625178 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.1745 (0.1801)
Lambda GC: 1.003
Mean Chi^2: 1.0078
Intercept: 0.9941 (0.0109)
Ratio < 0 (usually indicates GC correction).
Analysis finished at Mon Oct 28 22:11:00 2019
Total time elapsed: 42.56s{
"af_correlation": 0.956,
"inflation_factor": 1.0103,
"mean_EFFECT": 0.0041,
"n": "-Inf",
"n_snps": 4217519,
"n_clumped_hits": 0,
"n_p_sig": 9,
"n_mono": 417,
"n_ns": 261122,
"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": 311294,
"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": 625178,
"ldsc_nsnp_merge_regression_ld": 625178,
"ldsc_observed_scale_h2_beta": 0.1745,
"ldsc_observed_scale_h2_se": 0.1801,
"ldsc_intercept_beta": 0.9941,
"ldsc_intercept_se": 0.0109,
"ldsc_lambda_gc": 1.003,
"ldsc_mean_chisq": 1.0078,
"ldsc_ratio": -0.7564
}
| 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 | FALSE |
| 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 | 4217516 | 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 | 4217519 | 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 | 9.844030e+00 | 5.113267e+00 | 1.0000 | 5.000000e+00 | 9.000000e+00 | 1.300000e+01 | 2.200000e+01 | ▇▇▇▅▃ |
| numeric | POS | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 7.057353e+07 | 4.563585e+07 | 34918.0000 | 3.236389e+07 | 6.477455e+07 | 1.035942e+08 | 1.977961e+08 | ▇▇▆▃▁ |
| numeric | EFFECT | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 4.058700e-03 | 2.794070e-01 | -15.2037 | -3.650000e-02 | 4.000000e-04 | 3.770000e-02 | 8.204900e+00 | ▁▁▁▇▁ |
| numeric | SE | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 1.318065e-01 | 2.360986e-01 | 0.0233 | 3.390000e-02 | 4.740000e-02 | 1.090000e-01 | 3.319800e+00 | ▇▁▁▁▁ |
| numeric | PVAL | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 4.987661e-01 | 2.885233e-01 | 0.0000 | 2.498999e-01 | 4.978001e-01 | 7.481006e-01 | 1.000000e+00 | ▇▇▇▇▇ |
| numeric | PVAL_ztest | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 4.985788e-01 | 2.886386e-01 | 0.0000 | 2.494989e-01 | 4.976503e-01 | 7.480081e-01 | 1.000000e+00 | ▇▇▇▇▇ |
| numeric | AF | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 2.803965e-01 | 2.812576e-01 | 0.0000 | 3.810000e-02 | 1.804000e-01 | 4.641000e-01 | 1.000000e+00 | ▇▃▂▂▁ |
| numeric | AF_reference | 311294 | 0.9261903 | NA | NA | NA | NA | NA | NA | NA | 2.547631e-01 | 2.537602e-01 | 0.0000 | 3.913740e-02 | 1.693290e-01 | 4.075480e-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 | 104917910 | rs113234741 | G | A | 0.4183 | 0.5733 | 0.4666003 | 0.4656131 | 0.0156 | NA | NA |
| 2 | 18642530 | rs111710788 | G | C | 0.0825 | 0.0815 | 0.3117001 | 0.3114090 | 0.9708 | NA | NA |
| 2 | 161008726 | rs77875881 | C | T | 0.0807 | 0.0506 | 0.1109001 | 0.1107432 | 0.1037 | 0.0095847 | NA |
| 3 | 60363 | rs141398405 | A | G | 0.0526 | 0.0716 | 0.4626004 | 0.4625607 | 0.0556 | 0.0257588 | NA |
| 3 | 60596 | rs13067307 | C | A | -0.0082 | 0.0268 | 0.7589008 | 0.7596274 | 0.4852 | 0.5591050 | NA |
| 3 | 60648 | rs138886950 | A | G | -0.1274 | 0.0961 | 0.1852000 | 0.1849383 | 0.0470 | 0.0325479 | NA |
| 3 | 61044 | rs9755941 | T | C | 0.0090 | 0.0256 | 0.7243993 | 0.7251664 | 0.5048 | 0.5976440 | NA |
| 3 | 61113 | rs9756992 | A | T | 0.0019 | 0.0246 | 0.9387000 | 0.9384360 | 0.4468 | 0.5710860 | NA |
| 3 | 61466 | rs13081384 | G | C | 0.0310 | 0.0290 | 0.2846997 | 0.2850852 | 0.2629 | 0.1725240 | NA |
| 3 | 61495 | rs13060385 | A | G | 0.0027 | 0.0273 | 0.9213001 | 0.9212168 | 0.4530 | 0.4826280 | 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 | 0.0573 | 0.0301 | 0.0569600 | 0.0569552 | 0.4131 | 0.4736420 | NA |
| 22 | 51163138 | rs715586 | C | T | 0.0607 | 0.0361 | 0.0931001 | 0.0926774 | 0.1273 | 0.0902556 | NA |
| 22 | 51163910 | rs192700691 | C | T | 0.1128 | 0.1074 | 0.2933999 | 0.2935897 | 0.0304 | 0.0295527 | NA |
| 22 | 51164109 | rs5770995 | G | C | 0.0422 | 0.0283 | 0.1360000 | 0.1359179 | 0.4411 | 0.5109820 | NA |
| 22 | 51164115 | rs5770996 | C | T | 0.0426 | 0.0284 | 0.1340001 | 0.1336144 | 0.4446 | 0.5147760 | NA |
| 22 | 51164287 | rs6009957 | T | C | 0.0148 | 0.0274 | 0.5882000 | 0.5890964 | 0.3052 | 0.4155350 | NA |
| 22 | 51165664 | rs8137951 | G | A | 0.0154 | 0.0266 | 0.5627001 | 0.5626247 | 0.2954 | 0.4063500 | NA |
| 22 | 51171693 | rs756638 | G | A | 0.0084 | 0.0387 | 0.8275000 | 0.8281661 | 0.3046 | 0.3049120 | NA |
| 22 | 51175626 | rs3810648 | A | G | 0.0887 | 0.0604 | 0.1418999 | 0.1419568 | 0.0735 | 0.1084270 | NA |
| 22 | 51178090 | rs2285395 | G | A | 0.0840 | 0.0573 | 0.1424000 | 0.1426568 | 0.0481 | 0.0666933 | NA |
1 104917910 rs113234741 G A . PASS AF=0.0156 ES:SE:LP:AF:ID 0.4183:0.5733:0.331055:0.0156:rs113234741
2 18642530 rs111710788 G C . PASS AF=0.9708 ES:SE:LP:AF:ID 0.0825:0.0815:0.506263:0.9708:rs111710788
2 161008726 rs77875881 C T . PASS AF=0.1037 ES:SE:LP:AF:ID 0.0807:0.0506:0.955068:0.1037:rs77875881
3 60363 rs141398405 A G . PASS AF=0.0556 ES:SE:LP:AF:ID 0.0526:0.0716:0.334794:0.0556:rs141398405
3 60596 rs13067307 C A . PASS AF=0.4852 ES:SE:LP:AF:ID -0.0082:0.0268:0.119815:0.4852:rs13067307
3 60648 rs138886950 A G . PASS AF=0.047 ES:SE:LP:AF:ID -0.1274:0.0961:0.732359:0.047:rs138886950
3 61044 rs9755941 T C . PASS AF=0.5048 ES:SE:LP:AF:ID 0.009:0.0256:0.140022:0.5048:rs9755941
3 61113 rs9756992 A T . PASS AF=0.4468 ES:SE:LP:AF:ID 0.0019:0.0246:0.0274732:0.4468:rs9756992
3 61466 rs13081384 G C . PASS AF=0.2629 ES:SE:LP:AF:ID 0.031:0.029:0.545613:0.2629:rs13081384
3 61495 rs13060385 A G . PASS AF=0.453 ES:SE:LP:AF:ID 0.0027:0.0273:0.0355989:0.453:rs13060385
3 61662 rs73009205 T C . PASS AF=0.0581 ES:SE:LP:AF:ID 0.0505:0.0682:0.337714:0.0581:rs73009205
3 61762 rs62240674 T A . PASS AF=0.3163 ES:SE:LP:AF:ID 0.0154:0.026:0.257118:0.3163:rs62240674
3 62226 rs9799162 C T . PASS AF=0.3198 ES:SE:LP:AF:ID 0.0172:0.0261:0.29243:0.3198:rs9799162
3 62309 rs9681823 T G . PASS AF=0.2467 ES:SE:LP:AF:ID 0.0171:0.0339:0.212115:0.2467:rs9681823
3 62337 rs180933565 G A . PASS AF=0.002 ES:SE:LP:AF:ID -0.6497:0.4567:0.809949:0.002:rs180933565
3 62425 rs73009208 A C . PASS AF=0.0582 ES:SE:LP:AF:ID 0.0501:0.0679:0.336582:0.0582:rs73009208
3 62437 rs9682412 A T . PASS AF=0.7703 ES:SE:LP:AF:ID 0.0292:0.0317:0.446845:0.7703:rs9682412
3 62614 rs9799274 G C . PASS AF=0.316 ES:SE:LP:AF:ID 0.0153:0.0259:0.256725:0.316:rs9799274
3 62746 rs13073823 C G . PASS AF=0.1151 ES:SE:LP:AF:ID -0.0391:0.0405:0.474566:0.1151:rs13073823
3 62759 rs34815673 A C . PASS AF=0.1151 ES:SE:LP:AF:ID -0.0391:0.0405:0.474696:0.1151:rs34815673
3 62886 rs58497705 A T . PASS AF=0.3197 ES:SE:LP:AF:ID 0.0169:0.0261:0.287687:0.3197:rs58497705
3 62971 rs9682645 C A . PASS AF=0.3262 ES:SE:LP:AF:ID 0.0194:0.0276:0.315873:0.3262:rs9682645
3 62981 rs59670147 C T . PASS AF=0.3197 ES:SE:LP:AF:ID 0.0168:0.0261:0.284916:0.3197:rs59670147
3 63411 rs13072188 A C . PASS AF=0.4445 ES:SE:LP:AF:ID 0.0017:0.0241:0.0246601:0.4445:rs13072188
3 63989 3_63989_C_CAT CAT C . PASS AF=0.641 ES:SE:LP:AF:ID -0.0123:0.031:0.159518:0.641:3_63989_C_CAT
3 64165 rs9311287 C A . PASS AF=0.1836 ES:SE:LP:AF:ID -0.0433:0.0365:0.62764:0.1836:rs9311287
3 64189 rs113405791 C T . PASS AF=0.0583 ES:SE:LP:AF:ID 0.0499:0.0673:0.338471:0.0583:rs113405791
3 64221 rs9311316 C T . PASS AF=0.7677 ES:SE:LP:AF:ID 0.0282:0.0317:0.427709:0.7677:rs9311316
3 64492 rs34166985 T A . PASS AF=0.2673 ES:SE:LP:AF:ID 0.0295:0.0281:0.533281:0.2673:rs34166985
3 64940 rs142582846 G A . PASS AF=0.0453 ES:SE:LP:AF:ID -0.1324:0.0982:0.750068:0.0453:rs142582846
3 65592 rs150394040 T C . PASS AF=0.0442 ES:SE:LP:AF:ID -0.1345:0.098:0.769551:0.0442:rs150394040
3 65982 rs73009220 G A . PASS AF=0.2977 ES:SE:LP:AF:ID 0.0391:0.0293:0.740884:0.2977:rs73009220
3 66083 rs9713920 T C . PASS AF=0.1463 ES:SE:LP:AF:ID -0.0635:0.0398:0.95546:0.1463:rs9713920
3 66164 rs35007339 C G . PASS AF=0.6275 ES:SE:LP:AF:ID 0.0536:0.0281:1.24911:0.6275:rs35007339
3 66342 rs28716985 T G . PASS AF=0.3315 ES:SE:LP:AF:ID 0.0164:0.0267:0.268653:0.3315:rs28716985
3 66519 3_66519_G_GA GA G . PASS AF=0.9529 ES:SE:LP:AF:ID 0.1246:0.0935:0.738499:0.9529:3_66519_G_GA
3 66866 rs9683305 C T . PASS AF=0.3009 ES:SE:LP:AF:ID 0.0361:0.029:0.671824:0.3009:rs9683305
3 66894 rs9681213 G A . PASS AF=0.3018 ES:SE:LP:AF:ID 0.0361:0.0289:0.674484:0.3018:rs9681213
3 67116 rs9681345 G A . PASS AF=0.3018 ES:SE:LP:AF:ID 0.0361:0.0289:0.674484:0.3018:rs9681345
3 67176 rs150705890 C T . PASS AF=0.0096 ES:SE:LP:AF:ID 0.0046:0.1337:0.0120657:0.0096:rs150705890
3 67279 rs67010098 G A . PASS AF=0.2406 ES:SE:LP:AF:ID 0.0485:0.0297:0.9897:0.2406:rs67010098
3 67801 rs9681389 G C . PASS AF=0.4932 ES:SE:LP:AF:ID -0.0088:0.0266:0.130358:0.4932:rs9681389
3 67818 rs62240679 T G . PASS AF=0.3244 ES:SE:LP:AF:ID 0.0156:0.0265:0.254613:0.3244:rs62240679
3 68079 rs12631621 G C . PASS AF=0.1186 ES:SE:LP:AF:ID -0.0347:0.04:0.413863:0.1186:rs12631621
3 68204 rs67723366 G C . PASS AF=0.1225 ES:SE:LP:AF:ID -0.03:0.0389:0.356942:0.1225:rs67723366
3 68426 rs71306185 C T . PASS AF=0.1071 ES:SE:LP:AF:ID -0.043:0.0428:0.501689:0.1071:rs71306185
3 68528 rs113565524 C G . PASS AF=0.0231 ES:SE:LP:AF:ID -0.033:0.1075:0.119701:0.0231:rs113565524
3 69244 rs13089679 T C . PASS AF=0.2871 ES:SE:LP:AF:ID 0.0279:0.0263:0.538802:0.2871:rs13089679
3 69456 rs112317660 G T . PASS AF=0.0237 ES:SE:LP:AF:ID -0.0302:0.1074:0.108686:0.0237:rs112317660
3 70895 rs9682794 T C . PASS AF=0.3279 ES:SE:LP:AF:ID 0.0177:0.0268:0.293709:0.3279:rs9682794