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_41249_2011.vcf.gz --id UKB-b:2425 --data /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/ukbiobank/raw-output/data.batch_41249_2011.txt.gz --cohort_cases 3356 --cohort_controls 459043 --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": "2019-09-13T13:25:14.728121",
"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-2425/mac_discard.txt -Oz /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-2425/UKB-b-2425_raw.vcf.gz; Date=Thu Oct 17 12:40:13 2019",
"bcftools_viewCommand.1": "view -h /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/ukb-b-2425/ukb-b-2425.vcf.gz; Date=Sun May 10 04:05:46 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-2425/UKB-b-2425_data.vcf.gz \
--ref-ld-chr ../reference/eur_w_ld_chr/ \
--out /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-2425/ldsc.txt \
--w-ld-chr ../reference/eur_w_ld_chr/
Beginning analysis at Thu Oct 17 14:42:46 2019
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-2425/UKB-b-2425_data.vcf.gz ...
Read summary statistics for 4232462 SNPs.
Dropped 865 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, 994959 SNPs remain.
After merging with regression SNP LD, 994959 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.0021 (0.0014)
Lambda GC: 1.206
Mean Chi^2: 1.1998
Intercept: 1.1794 (0.0095)
Ratio: 0.8978 (0.0477)
Analysis finished at Thu Oct 17 14:43:41 2019
Total time elapsed: 54.67s{
"af_correlation": 0.8841,
"inflation_factor": 1.1999,
"mean_EFFECT": 1.4537e-06,
"n": "-Inf",
"n_snps": 9851866,
"n_clumped_hits": 2,
"n_p_sig": 2,
"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": 34795,
"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": 994959,
"ldsc_nsnp_merge_regression_ld": 994959,
"ldsc_observed_scale_h2_beta": 0.0021,
"ldsc_observed_scale_h2_se": 0.0014,
"ldsc_intercept_beta": 1.1794,
"ldsc_intercept_se": 0.0095,
"ldsc_lambda_gc": 1.206,
"ldsc_mean_chisq": 1.1998,
"ldsc_ratio": 0.8979
}
| 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 | 1.000000 | 3 | 58 | 0 | 4231602 | 0 | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| character | REF | 0 | 1.000000 | 1 | 1 | 0 | 4 | 0 | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| character | ALT | 0 | 1.000000 | 1 | 1 | 0 | 4 | 0 | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| logical | N | 4232462 | 0.000000 | NA | NA | NA | NA | NA | NaN | : | NA | NA | NA | NA | NA | NA | NA | NA |
| numeric | CHROM | 0 | 1.000000 | NA | NA | NA | NA | NA | NA | NA | 8.655209e+00 | 5.765387e+00 | 1.0000000 | 4.000000e+00 | 8.000000e+00 | 1.300000e+01 | 2.200000e+01 | ▇▅▃▂▂ |
| numeric | POS | 0 | 1.000000 | NA | NA | NA | NA | NA | NA | NA | 7.859560e+07 | 5.673439e+07 | 828.0000000 | 3.167476e+07 | 6.897254e+07 | 1.146799e+08 | 2.492385e+08 | ▇▆▅▂▁ |
| numeric | EFFECT | 0 | 1.000000 | NA | NA | NA | NA | NA | NA | NA | 1.500000e-06 | 2.316000e-04 | -0.0014516 | -1.519000e-04 | 1.700000e-06 | 1.534000e-04 | 1.680900e-03 | ▁▂▇▁▁ |
| numeric | SE | 0 | 1.000000 | NA | NA | NA | NA | NA | NA | NA | 2.093000e-04 | 3.240000e-05 | 0.0001692 | 1.813000e-04 | 1.984000e-04 | 2.312000e-04 | 6.185000e-04 | ▇▁▁▁▁ |
| numeric | PVAL | 0 | 1.000000 | NA | NA | NA | NA | NA | NA | NA | 4.708635e-01 | 2.953827e-01 | 0.0000000 | 2.099999e-01 | 4.600002e-01 | 7.300002e-01 | 1.000000e+00 | ▇▆▆▆▆ |
| numeric | PVAL_ztest | 0 | 1.000000 | NA | NA | NA | NA | NA | NA | NA | 4.708626e-01 | 2.953580e-01 | 0.0000000 | 2.086377e-01 | 4.582449e-01 | 7.260982e-01 | 9.999999e-01 | ▇▇▆▆▆ |
| numeric | AF | 0 | 1.000000 | NA | NA | NA | NA | NA | NA | NA | 3.842950e-01 | 2.197513e-01 | 0.1042910 | 1.932360e-01 | 3.321510e-01 | 5.450430e-01 | 8.957090e-01 | ▇▅▃▂▂ |
| numeric | AF_reference | 34795 | 0.991779 | NA | NA | NA | NA | NA | NA | NA | 3.744319e-01 | 2.216709e-01 | 0.0000000 | 1.918930e-01 | 3.302720e-01 | 5.331470e-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 | -0.0004767 | 0.0003111 | 0.1299999 | 0.1254593 | 0.623761 | 0.782149 | NA |
| 1 | 54676 | rs2462492 | C | T | -0.0003883 | 0.0003083 | 0.2099999 | 0.2078046 | 0.400407 | NA | NA |
| 1 | 91536 | rs6702460 | G | T | -0.0004772 | 0.0003035 | 0.1199999 | 0.1158867 | 0.456863 | 0.420727 | NA |
| 1 | 534192 | rs6680723 | C | T | -0.0002968 | 0.0003467 | 0.3900004 | 0.3919603 | 0.240956 | NA | NA |
| 1 | 693731 | rs12238997 | A | G | -0.0000756 | 0.0002905 | 0.7899998 | 0.7946681 | 0.116333 | 0.141773 | NA |
| 1 | 706368 | rs55727773 | A | G | -0.0000178 | 0.0002152 | 0.9299999 | 0.9340268 | 0.515654 | 0.275160 | NA |
| 1 | 729679 | rs4951859 | C | G | -0.0000474 | 0.0002518 | 0.8499999 | 0.8508209 | 0.843210 | 0.639976 | NA |
| 1 | 731718 | rs142557973 | T | C | 0.0000296 | 0.0002756 | 0.9100000 | 0.9145051 | 0.122316 | 0.154353 | NA |
| 1 | 734349 | rs141242758 | T | C | 0.0000106 | 0.0002757 | 0.9699999 | 0.9694274 | 0.121560 | 0.152556 | NA |
| 1 | 736289 | rs79010578 | T | A | 0.0001433 | 0.0002717 | 0.5999997 | 0.5979326 | 0.132333 | 0.139577 | 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 | 51198027 | rs34939255 | A | G | -0.0001297 | 0.0002148 | 0.5500004 | 0.5459242 | 0.254560 | 0.0984425 | NA |
| 22 | 51208537 | rs72619593 | G | A | 0.0005042 | 0.0002871 | 0.0790005 | 0.0789878 | 0.120741 | 0.1142170 | NA |
| 22 | 51210289 | rs112565862 | C | T | -0.0005494 | 0.0002859 | 0.0549997 | 0.0546379 | 0.129957 | 0.1018370 | NA |
| 22 | 51211106 | rs9628250 | T | C | -0.0000160 | 0.0002129 | 0.9400001 | 0.9399321 | 0.271540 | 0.1671330 | NA |
| 22 | 51211392 | rs3888396 | T | C | -0.0004995 | 0.0002833 | 0.0779992 | 0.0779378 | 0.132637 | 0.1641370 | NA |
| 22 | 51212875 | rs2238837 | A | C | 0.0002598 | 0.0002023 | 0.2000000 | 0.1990632 | 0.331477 | 0.3724040 | NA |
| 22 | 51213613 | rs34726907 | C | T | 0.0000683 | 0.0002665 | 0.8000000 | 0.7976538 | 0.127819 | 0.1727240 | NA |
| 22 | 51216564 | rs9616970 | T | C | 0.0000634 | 0.0002654 | 0.8100000 | 0.8110808 | 0.128334 | 0.1563500 | NA |
| 22 | 51219006 | rs28729663 | G | A | 0.0000231 | 0.0002598 | 0.9299999 | 0.9290309 | 0.137954 | 0.2052720 | NA |
| 22 | 51237063 | rs3896457 | T | C | 0.0002278 | 0.0002071 | 0.2700001 | 0.2714394 | 0.297981 | 0.2050720 | NA |
1 49298 rs10399793 T C . PASS AF=0.623761 ES:SE:LP:AF:ID -0.000476743:0.000311138:0.886057:0.623761:rs10399793
1 54676 rs2462492 C T . PASS AF=0.400407 ES:SE:LP:AF:ID -0.000388282:0.000308252:0.677781:0.400407:rs2462492
1 91536 rs6702460 G T . PASS AF=0.456863 ES:SE:LP:AF:ID -0.000477206:0.000303513:0.920819:0.456863:rs6702460
1 534192 rs6680723 C T . PASS AF=0.240956 ES:SE:LP:AF:ID -0.000296785:0.000346684:0.408935:0.240956:rs6680723
1 693731 rs12238997 A G . PASS AF=0.116333 ES:SE:LP:AF:ID -7.56115e-05:0.00029053:0.102373:0.116333:rs12238997
1 706368 rs12029736 A G . PASS AF=0.515654 ES:SE:LP:AF:ID -1.78149e-05:0.000215209:0.0315171:0.515654:rs12029736
1 729679 rs4951859 C G . PASS AF=0.84321 ES:SE:LP:AF:ID -4.73531e-05:0.000251783:0.0705811:0.84321:rs4951859
1 731718 rs58276399 T C . PASS AF=0.122316 ES:SE:LP:AF:ID 2.95873e-05:0.000275595:0.0409586:0.122316:rs58276399
1 734349 rs141242758 T C . PASS AF=0.12156 ES:SE:LP:AF:ID 1.0567e-05:0.00027571:0.0132283:0.12156:rs141242758
1 736289 rs79010578 T A . PASS AF=0.132333 ES:SE:LP:AF:ID 0.000143307:0.000271736:0.221849:0.132333:rs79010578
1 752566 rs3094315 G A . PASS AF=0.83895 ES:SE:LP:AF:ID -6.45711e-05:0.000243834:0.102373:0.83895:rs3094315
1 752721 rs3131972 A G . PASS AF=0.838579 ES:SE:LP:AF:ID -6.35055e-05:0.000243571:0.102373:0.838579:rs3131972
1 753405 rs3115860 C A . PASS AF=0.869772 ES:SE:LP:AF:ID -0.000102299:0.000261359:0.154902:0.869772:rs3115860
1 753541 rs2073813 G A . PASS AF=0.129881 ES:SE:LP:AF:ID 7.52715e-05:0.000261893:0.113509:0.129881:rs2073813
1 754182 rs3131969 A G . PASS AF=0.869113 ES:SE:LP:AF:ID -8.52192e-05:0.000260846:0.130768:0.869113:rs3131969
1 754192 rs3131968 A G . PASS AF=0.869212 ES:SE:LP:AF:ID -8.38807e-05:0.00026095:0.124939:0.869212:rs3131968
1 754334 rs3131967 T C . PASS AF=0.869117 ES:SE:LP:AF:ID -8.54559e-05:0.000260841:0.130768:0.869117:rs3131967
1 754503 rs3115859 G A . PASS AF=0.838031 ES:SE:LP:AF:ID -6.36428e-05:0.000242895:0.102373:0.838031:rs3115859
1 754964 rs3131966 C T . PASS AF=0.838662 ES:SE:LP:AF:ID -5.95816e-05:0.000243578:0.091515:0.838662:rs3131966
1 755775 rs3131965 A G . PASS AF=0.839774 ES:SE:LP:AF:ID -6.96243e-05:0.000246871:0.107905:0.839774:rs3131965
1 755890 rs3115858 A T . PASS AF=0.869397 ES:SE:LP:AF:ID -0.000106785:0.00026054:0.167491:0.869397:rs3115858
1 756604 rs3131962 A G . PASS AF=0.868943 ES:SE:LP:AF:ID -0.000117557:0.000259884:0.187087:0.868943:rs3131962
1 757640 rs3115853 G A . PASS AF=0.867896 ES:SE:LP:AF:ID -9.94258e-05:0.000259386:0.154902:0.867896:rs3115853
1 757734 rs4951929 C T . PASS AF=0.869087 ES:SE:LP:AF:ID -0.000115194:0.000260097:0.180456:0.869087:rs4951929
1 757936 rs4951862 C A . PASS AF=0.869095 ES:SE:LP:AF:ID -0.000115535:0.000260117:0.180456:0.869095:rs4951862
1 758144 rs3131956 A G . PASS AF=0.869103 ES:SE:LP:AF:ID -0.000105812:0.000260123:0.167491:0.869103:rs3131956
1 758626 rs3131954 C T . PASS AF=0.869581 ES:SE:LP:AF:ID -0.00011141:0.000260838:0.173925:0.869581:rs3131954
1 760912 rs1048488 C T . PASS AF=0.838311 ES:SE:LP:AF:ID -6.91251e-05:0.000242435:0.107905:0.838311:rs1048488
1 761147 rs3115850 T C . PASS AF=0.838432 ES:SE:LP:AF:ID -7.02757e-05:0.000242606:0.113509:0.838432:rs3115850
1 761732 rs2286139 C T . PASS AF=0.862253 ES:SE:LP:AF:ID -0.000112037:0.000259181:0.173925:0.862253:rs2286139
1 763394 rs3115847 G A . PASS AF=0.706732 ES:SE:LP:AF:ID -1.96851e-05:0.000252318:0.0268721:0.706732:rs3115847
1 766007 rs61768174 A C . PASS AF=0.10515 ES:SE:LP:AF:ID 0.000313833:0.000290652:0.552842:0.10515:rs61768174
1 768253 rs2977608 A C . PASS AF=0.761319 ES:SE:LP:AF:ID -3.73602e-05:0.000205939:0.0655015:0.761319:rs2977608
1 768448 rs12562034 G A . PASS AF=0.106464 ES:SE:LP:AF:ID -5.06789e-05:0.00028387:0.0655015:0.106464:rs12562034
1 769223 rs60320384 C G . PASS AF=0.129586 ES:SE:LP:AF:ID 6.76322e-05:0.000261737:0.09691:0.129586:rs60320384
1 771823 rs2977605 T C . PASS AF=0.868902 ES:SE:LP:AF:ID -0.000120314:0.000260339:0.19382:0.868902:rs2977605
1 771967 rs59066358 G A . PASS AF=0.129685 ES:SE:LP:AF:ID 8.46487e-05:0.000261569:0.124939:0.129685:rs59066358
1 772755 rs2905039 A C . PASS AF=0.868911 ES:SE:LP:AF:ID -0.000121024:0.000260344:0.19382:0.868911:rs2905039
1 776546 rs12124819 A G . PASS AF=0.26539 ES:SE:LP:AF:ID -0.000277716:0.000230032:0.638272:0.26539:rs12124819
1 777122 rs2980319 A T . PASS AF=0.870036 ES:SE:LP:AF:ID -8.11547e-05:0.000260876:0.119186:0.870036:rs2980319
1 778745 rs1055606 A G . PASS AF=0.128584 ES:SE:LP:AF:ID 3.63089e-05:0.000261906:0.05061:0.128584:rs1055606
1 779322 rs4040617 A G . PASS AF=0.128881 ES:SE:LP:AF:ID 4.58454e-05:0.000261461:0.0655015:0.128881:rs4040617
1 780785 rs2977612 T A . PASS AF=0.868776 ES:SE:LP:AF:ID -7.08082e-05:0.000260179:0.102373:0.868776:rs2977612
1 782981 rs6594026 C T . PASS AF=0.129522 ES:SE:LP:AF:ID 5.3253e-05:0.000261376:0.0757207:0.129522:rs6594026
1 785050 rs2905062 G A . PASS AF=0.86853 ES:SE:LP:AF:ID -6.61153e-05:0.000260118:0.09691:0.86853:rs2905062
1 785989 rs2980300 T C . PASS AF=0.868471 ES:SE:LP:AF:ID -6.31225e-05:0.00026028:0.091515:0.868471:rs2980300
1 787399 rs2905055 G T . PASS AF=0.860774 ES:SE:LP:AF:ID -6.89556e-05:0.000260104:0.102373:0.860774:rs2905055
1 787606 rs3863622 G T . PASS AF=0.12847 ES:SE:LP:AF:ID 4.92709e-05:0.000262786:0.0705811:0.12847:rs3863622
1 787685 rs2905054 G T . PASS AF=0.861488 ES:SE:LP:AF:ID -4.03581e-05:0.000260274:0.0555173:0.861488:rs2905054
1 787844 rs2905053 C T . PASS AF=0.869222 ES:SE:LP:AF:ID -6.77409e-05:0.000261233:0.09691:0.869222:rs2905053