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_1460.vcf.gz --id UKB-b:3444 --data /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/ukbiobank/raw-output/data.batch_41246_1460.txt.gz --cohort_cases 1558 --cohort_controls 442497 --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": "2019-09-13T13:18:08.255570",
"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-3444/mac_discard.txt -Oz /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-3444/UKB-b-3444_raw.vcf.gz; Date=Thu Oct 17 12:41:37 2019",
"bcftools_viewCommand.1": "view -h /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/ukb-b-3444/ukb-b-3444.vcf.gz; Date=Sat May 9 19:52:55 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-3444/UKB-b-3444_data.vcf.gz \
--ref-ld-chr ../reference/eur_w_ld_chr/ \
--out /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-3444/ldsc.txt \
--w-ld-chr ../reference/eur_w_ld_chr/
Beginning analysis at Thu Oct 17 14:43:41 2019
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-3444/UKB-b-3444_data.vcf.gz ...
Read summary statistics for 2596562 SNPs.
Dropped 305 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, 655093 SNPs remain.
After merging with regression SNP LD, 655093 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: -0.0009 (0.0013)
Lambda GC: 1.0223
Mean Chi^2: 1.0181
Intercept: 1.0273 (0.0103)
Ratio: 1.5109 (0.5696)
Analysis finished at Thu Oct 17 14:44:08 2019
Total time elapsed: 26.98s{
"af_correlation": 0.7795,
"inflation_factor": 1,
"mean_EFFECT": -2.6011e-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": 20579,
"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": 655093,
"ldsc_nsnp_merge_regression_ld": 655093,
"ldsc_observed_scale_h2_beta": "NA",
"ldsc_observed_scale_h2_se": "NA",
"ldsc_intercept_beta": 1.0273,
"ldsc_intercept_se": 0.0103,
"ldsc_lambda_gc": 1.0223,
"ldsc_mean_chisq": 1.0181,
"ldsc_ratio": 1.5083
}
| 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 | 2596260 | 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 | 2596562 | 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 | 8.663194e+00 | 5.768918e+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 | 7.853810e+07 | 5.661712e+07 | 5687.0000000 | 3.172572e+07 | 6.891138e+07 | 1.147085e+08 | 2.491917e+08 | ▇▆▅▂▁ |
| numeric | EFFECT | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | -3.000000e-07 | 1.353000e-04 | -0.0006411 | -9.090000e-05 | -2.000000e-07 | 9.100000e-05 | 6.908000e-04 | ▁▂▇▂▁ |
| numeric | SE | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 1.340000e-04 | 7.800000e-06 | 0.0001211 | 1.274000e-04 | 1.318000e-04 | 1.395000e-04 | 2.626000e-04 | ▇▁▁▁▁ |
| numeric | PVAL | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 4.975985e-01 | 2.897675e-01 | 0.0000048 | 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 | 4.975998e-01 | 2.897425e-01 | 0.0000048 | 2.468406e-01 | 4.964758e-01 | 7.481253e-01 | 9.999991e-01 | ▇▇▇▇▇ |
| numeric | AF | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 4.497418e-01 | 1.563404e-01 | 0.2246470 | 3.122300e-01 | 4.258890e-01 | 5.746140e-01 | 7.753530e-01 | ▇▆▅▃▃ |
| numeric | AF_reference | 20579 | 0.9920745 | NA | NA | NA | NA | NA | NA | NA | 4.317495e-01 | 1.794828e-01 | 0.0001997 | 2.897360e-01 | 4.147360e-01 | 5.632990e-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 | 0.0000752 | 0.0002228 | 0.7400005 | 0.7358406 | 0.623754 | 0.7821490 | NA |
| 1 | 54676 | rs2462492 | C | T | 0.0002108 | 0.0002207 | 0.3400001 | 0.3394788 | 0.400423 | NA | NA |
| 1 | 91536 | rs6702460 | G | T | -0.0001525 | 0.0002173 | 0.4799997 | 0.4828884 | 0.456858 | 0.4207270 | NA |
| 1 | 534192 | rs6680723 | C | T | 0.0004813 | 0.0002483 | 0.0530005 | 0.0525468 | 0.240915 | NA | NA |
| 1 | 706368 | rs55727773 | A | G | -0.0000216 | 0.0001541 | 0.8900000 | 0.8885924 | 0.515717 | 0.2751600 | NA |
| 1 | 763394 | rs369924889 | G | A | -0.0003310 | 0.0001807 | 0.0669993 | 0.0669325 | 0.706659 | 0.6176120 | NA |
| 1 | 768253 | rs2977608 | A | C | 0.0000544 | 0.0001475 | 0.7099994 | 0.7122601 | 0.761332 | 0.4894170 | NA |
| 1 | 776546 | rs12124819 | A | G | 0.0002822 | 0.0001648 | 0.0870001 | 0.0868057 | 0.265297 | 0.0756789 | NA |
| 1 | 808631 | rs11240779 | G | A | 0.0002280 | 0.0001498 | 0.1299999 | 0.1279534 | 0.772641 | 0.4534740 | NA |
| 1 | 808928 | rs11240780 | C | T | 0.0002177 | 0.0001500 | 0.1499999 | 0.1467629 | 0.772871 | 0.4522760 | 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 | -1.50e-06 | 0.0001451 | 0.9900000 | 0.9917045 | 0.713706 | 0.6369810 | NA |
| 22 | 51181919 | rs9616825 | G | C | 4.00e-06 | 0.0001443 | 0.9800000 | 0.9779598 | 0.695493 | 0.6194090 | NA |
| 22 | 51182485 | rs6009961 | A | G | -3.10e-06 | 0.0001455 | 0.9800000 | 0.9827657 | 0.715541 | 0.6383790 | NA |
| 22 | 51186143 | rs2879914 | T | C | 9.15e-05 | 0.0001349 | 0.5000000 | 0.4978427 | 0.382029 | 0.2733630 | NA |
| 22 | 51186228 | rs3865766 | C | T | -1.00e-05 | 0.0001315 | 0.9400001 | 0.9392958 | 0.451296 | 0.4532750 | NA |
| 22 | 51197266 | rs61290853 | A | G | -6.95e-05 | 0.0001358 | 0.6100002 | 0.6087984 | 0.386528 | 0.4229230 | NA |
| 22 | 51198027 | rs34939255 | A | G | 1.80e-06 | 0.0001537 | 0.9900000 | 0.9906171 | 0.254378 | 0.0984425 | NA |
| 22 | 51211106 | rs9628250 | T | C | 5.88e-05 | 0.0001524 | 0.6999999 | 0.6997885 | 0.271369 | 0.1671330 | NA |
| 22 | 51212875 | rs2238837 | A | C | 1.44e-05 | 0.0001448 | 0.9199999 | 0.9209470 | 0.331620 | 0.3724040 | NA |
| 22 | 51237063 | rs3896457 | T | C | 5.26e-05 | 0.0001482 | 0.7199992 | 0.7225550 | 0.298162 | 0.2050720 | NA |
1 49298 rs10399793 T C . PASS AF=0.623754 ES:SE:LP:AF:ID 7.51619e-05:0.00022279:0.130768:0.623754:rs10399793
1 54676 rs2462492 C T . PASS AF=0.400423 ES:SE:LP:AF:ID 0.000210847:0.000220737:0.468521:0.400423:rs2462492
1 91536 rs6702460 G T . PASS AF=0.456858 ES:SE:LP:AF:ID -0.000152471:0.000217299:0.318759:0.456858:rs6702460
1 534192 rs6680723 C T . PASS AF=0.240915 ES:SE:LP:AF:ID 0.000481301:0.000248269:1.27572:0.240915:rs6680723
1 706368 rs12029736 A G . PASS AF=0.515717 ES:SE:LP:AF:ID -2.15918e-05:0.000154133:0.05061:0.515717:rs12029736
1 763394 rs3115847 G A . PASS AF=0.706659 ES:SE:LP:AF:ID -0.000331047:0.00018069:1.17393:0.706659:rs3115847
1 768253 rs2977608 A C . PASS AF=0.761332 ES:SE:LP:AF:ID 5.44168e-05:0.000147542:0.148742:0.761332:rs2977608
1 776546 rs12124819 A G . PASS AF=0.265297 ES:SE:LP:AF:ID 0.000282171:0.000164772:1.06048:0.265297:rs12124819
1 808631 rs11240779 G A . PASS AF=0.772641 ES:SE:LP:AF:ID 0.000228:0.000149781:0.886057:0.772641:rs11240779
1 808928 rs11240780 C T . PASS AF=0.772871 ES:SE:LP:AF:ID 0.000217707:0.000150033:0.823909:0.772871:rs11240780
1 814495 rs74461805 C A . PASS AF=0.340404 ES:SE:LP:AF:ID 4.66232e-05:0.000211369:0.0809219:0.340404:rs74461805
1 830181 rs28444699 A G . PASS AF=0.69724 ES:SE:LP:AF:ID 4.32461e-06:0.00014137:0.00877392:0.69724:rs28444699
1 831489 rs4970385 C T . PASS AF=0.705407 ES:SE:LP:AF:ID 1.67793e-05:0.000138809:0.0457575:0.705407:rs4970385
1 831909 rs9697642 C T . PASS AF=0.705451 ES:SE:LP:AF:ID 1.73647e-05:0.000138804:0.0457575:0.705451:rs9697642
1 832066 rs9697380 G C . PASS AF=0.705637 ES:SE:LP:AF:ID 1.49314e-05:0.000138809:0.0409586:0.705637:rs9697380
1 832318 rs4500250 C A . PASS AF=0.705664 ES:SE:LP:AF:ID 1.4247e-05:0.000138824:0.0362122:0.705664:rs4500250
1 832398 rs4553118 T C . PASS AF=0.73011 ES:SE:LP:AF:ID -2.05246e-05:0.000142614:0.05061:0.73011:rs4553118
1 832918 rs28765502 T C . PASS AF=0.294369 ES:SE:LP:AF:ID -1.57369e-05:0.000138817:0.0409586:0.294369:rs28765502
1 833223 rs13303211 C T . PASS AF=0.236694 ES:SE:LP:AF:ID -6.72943e-06:0.000147829:0.0177288:0.236694:rs13303211
1 833302 rs28752186 C T . PASS AF=0.236683 ES:SE:LP:AF:ID -6.62139e-06:0.000147828:0.0177288:0.236683:rs28752186
1 833641 rs28594623 T C . PASS AF=0.239752 ES:SE:LP:AF:ID -3.54725e-05:0.000147353:0.091515:0.239752:rs28594623
1 833824 rs28484835 T C . PASS AF=0.236686 ES:SE:LP:AF:ID -8.96771e-06:0.000147827:0.0222764:0.236686:rs28484835
1 834832 rs4411087 G C . PASS AF=0.237171 ES:SE:LP:AF:ID -8.01367e-06:0.000147715:0.0177288:0.237171:rs4411087
1 835499 rs4422948 A G . PASS AF=0.24115 ES:SE:LP:AF:ID 7.08536e-05:0.000146677:0.200659:0.24115:rs4422948
1 836896 rs28705752 T C . PASS AF=0.269506 ES:SE:LP:AF:ID 1.83282e-05:0.000141532:0.0457575:0.269506:rs28705752
1 838555 rs4970383 C A . PASS AF=0.24624 ES:SE:LP:AF:ID 7.34112e-05:0.000145674:0.21467:0.24624:rs4970383
1 839103 rs28562941 A G . PASS AF=0.270009 ES:SE:LP:AF:ID 7.33394e-06:0.000141629:0.0177288:0.270009:rs28562941
1 840753 rs4970382 T C . PASS AF=0.40027 ES:SE:LP:AF:ID -1.79294e-05:0.000128054:0.05061:0.40027:rs4970382
1 841085 rs1574243 C G . PASS AF=0.237175 ES:SE:LP:AF:ID 4.95712e-05:0.000148731:0.130768:0.237175:rs1574243
1 842362 rs28540380 C T . PASS AF=0.235344 ES:SE:LP:AF:ID 0.000103806:0.000151007:0.309804:0.235344:rs28540380
1 843405 rs11516185 A G . PASS AF=0.362626 ES:SE:LP:AF:ID -4.03076e-05:0.000158964:0.09691:0.362626:rs11516185
1 850218 rs6664536 T A . PASS AF=0.590345 ES:SE:LP:AF:ID 1.68219e-05:0.000127693:0.0457575:0.590345:rs6664536
1 850371 rs6679046 G T . PASS AF=0.60371 ES:SE:LP:AF:ID 5.21895e-05:0.000128415:0.167491:0.60371:rs6679046
1 850780 rs6657440 C T . PASS AF=0.603932 ES:SE:LP:AF:ID 5.62255e-05:0.000128397:0.180456:0.603932:rs6657440
1 852037 rs4970463 G A . PASS AF=0.589707 ES:SE:LP:AF:ID 1.57921e-05:0.0001279:0.0457575:0.589707:rs4970463
1 852063 rs28436996 G A . PASS AF=0.589692 ES:SE:LP:AF:ID 1.25593e-05:0.000127844:0.0362122:0.589692:rs28436996
1 852875 rs13303369 C T . PASS AF=0.607682 ES:SE:LP:AF:ID 3.16494e-05:0.000128689:0.091515:0.607682:rs13303369
1 853954 rs1806509 C A . PASS AF=0.607841 ES:SE:LP:AF:ID 2.9747e-05:0.000128706:0.0861861:0.607841:rs1806509
1 854777 rs13303019 A G . PASS AF=0.610325 ES:SE:LP:AF:ID 4.4961e-05:0.000128833:0.136677:0.610325:rs13303019
1 854978 rs13303057 A C . PASS AF=0.603278 ES:SE:LP:AF:ID 4.77209e-05:0.000128446:0.148742:0.603278:rs13303057
1 855075 rs6673914 C G . PASS AF=0.610343 ES:SE:LP:AF:ID 4.70893e-05:0.000128836:0.148742:0.610343:rs6673914
1 856099 rs28534711 T G . PASS AF=0.389931 ES:SE:LP:AF:ID -4.26314e-05:0.000128861:0.130768:0.389931:rs28534711
1 856108 rs28742275 A G . PASS AF=0.389915 ES:SE:LP:AF:ID -4.28256e-05:0.000128868:0.130768:0.389915:rs28742275
1 856476 rs4040605 A G . PASS AF=0.35033 ES:SE:LP:AF:ID -1.12092e-05:0.000132367:0.0315171:0.35033:rs4040605
1 858801 rs7418179 A G . PASS AF=0.765924 ES:SE:LP:AF:ID -0.000152891:0.000148627:0.522879:0.765924:rs7418179
1 860416 rs61464428 G A . PASS AF=0.766738 ES:SE:LP:AF:ID -0.000131964:0.000148702:0.431798:0.766738:rs61464428
1 860688 rs60837925 G A . PASS AF=0.766195 ES:SE:LP:AF:ID -0.00013626:0.000148599:0.443698:0.766195:rs60837925
1 861630 rs2879816 G A . PASS AF=0.766348 ES:SE:LP:AF:ID -0.000143212:0.000148635:0.468521:0.766348:rs2879816
1 862866 rs3892970 C T . PASS AF=0.763216 ES:SE:LP:AF:ID -0.000129667:0.000148499:0.420216:0.763216:rs3892970
1 864938 rs2340587 G A . PASS AF=0.760106 ES:SE:LP:AF:ID -9.95515e-05:0.000147399:0.30103:0.760106:rs2340587