Summary
Summary {data-width=650}
Manhattan plot
manhattan_plot
QQ plot
qq_plot
AF plot
af_plot
P-Z plot
pz_plot
beta_std plot
beta_std_plot
Metadata
{
"fileformat": "VCFv4.2",
"FILTER": "<ID=PASS,Description=\"All filters passed\">",
"INFO": "<ID=AF,Number=A,Type=Float,Description=\"Allele Frequency\">",
"FORMAT": "<ID=ES,Number=A,Type=Float,Description=\"Effect size estimate relative to the alternative allele\">",
"FORMAT.1": "<ID=SE,Number=A,Type=Float,Description=\"Standard error of effect size estimate\">",
"FORMAT.2": "<ID=LP,Number=A,Type=Float,Description=\"-log10 p-value for effect estimate\">",
"FORMAT.3": "<ID=AF,Number=A,Type=Float,Description=\"Alternate allele frequency in the association study\">",
"FORMAT.4": "<ID=SS,Number=A,Type=Float,Description=\"Sample size used to estimate genetic effect\">",
"FORMAT.5": "<ID=EZ,Number=A,Type=Float,Description=\"Z-score provided if it was used to derive the EFFECT and SE fields\">",
"FORMAT.6": "<ID=SI,Number=A,Type=Float,Description=\"Accuracy score of summary data imputation\">",
"FORMAT.7": "<ID=NC,Number=A,Type=Float,Description=\"Number of cases used to estimate genetic effect\">",
"FORMAT.8": "<ID=ID,Number=1,Type=String,Description=\"Study variant identifier\">",
"META": "<ID=TotalVariants,Number=1,Type=Integer,Description=\"Total number of variants in input\">",
"META.1": "<ID=VariantsNotRead,Number=1,Type=Integer,Description=\"Number of variants that could not be read\">",
"META.2": "<ID=HarmonisedVariants,Number=1,Type=Integer,Description=\"Total number of harmonised variants\">",
"META.3": "<ID=VariantsNotHarmonised,Number=1,Type=Integer,Description=\"Total number of variants that could not be harmonised\">",
"META.4": "<ID=SwitchedAlleles,Number=1,Type=Integer,Description=\"Total number of variants strand switched\">",
"META.5": "<ID=TotalControls,Number=1,Type=Integer,Description=\"Total number of controls in the association study\">",
"META.6": "<ID=TotalCases,Number=1,Type=Integer,Description=\"Total number of cases in the association study\">",
"META.7": "<ID=StudyType,Number=1,Type=String,Description=\"Type of GWAS study [Continuous or CaseControl]\">",
"SAMPLE": "<ID=UKB-b:15892,TotalVariants=9851866,VariantsNotRead=0,HarmonisedVariants=9851866,VariantsNotHarmonised=0,SwitchedAlleles=9851866,TotalControls=151546,StudyType=Continuous>",
"contig": "<ID=1,length=249250621,assembly=GRCh37>",
"contig.1": "<ID=2,length=243199373,assembly=GRCh37>",
"contig.2": "<ID=3,length=198022430,assembly=GRCh37>",
"contig.3": "<ID=4,length=191154276,assembly=GRCh37>",
"contig.4": "<ID=5,length=180915260,assembly=GRCh37>",
"contig.5": "<ID=6,length=171115067,assembly=GRCh37>",
"contig.6": "<ID=7,length=159138663,assembly=GRCh37>",
"contig.7": "<ID=8,length=146364022,assembly=GRCh37>",
"contig.8": "<ID=9,length=141213431,assembly=GRCh37>",
"contig.9": "<ID=10,length=135534747,assembly=GRCh37>",
"contig.10": "<ID=11,length=135006516,assembly=GRCh37>",
"contig.11": "<ID=12,length=133851895,assembly=GRCh37>",
"contig.12": "<ID=13,length=115169878,assembly=GRCh37>",
"contig.13": "<ID=14,length=107349540,assembly=GRCh37>",
"contig.14": "<ID=15,length=102531392,assembly=GRCh37>",
"contig.15": "<ID=16,length=90354753,assembly=GRCh37>",
"contig.16": "<ID=17,length=81195210,assembly=GRCh37>",
"contig.17": "<ID=18,length=78077248,assembly=GRCh37>",
"contig.18": "<ID=19,length=59128983,assembly=GRCh37>",
"contig.19": "<ID=20,length=63025520,assembly=GRCh37>",
"contig.20": "<ID=21,length=48129895,assembly=GRCh37>",
"contig.21": "<ID=22,length=51304566,assembly=GRCh37>",
"contig.22": "<ID=X,length=155270560,assembly=GRCh37>",
"contig.23": "<ID=Y,length=59373566,assembly=GRCh37>",
"contig.24": "<ID=MT,length=16569,assembly=GRCh37>",
"contig.25": "<ID=GL000207.1,length=4262,assembly=GRCh37>",
"contig.26": "<ID=GL000226.1,length=15008,assembly=GRCh37>",
"contig.27": "<ID=GL000229.1,length=19913,assembly=GRCh37>",
"contig.28": "<ID=GL000231.1,length=27386,assembly=GRCh37>",
"contig.29": "<ID=GL000210.1,length=27682,assembly=GRCh37>",
"contig.30": "<ID=GL000239.1,length=33824,assembly=GRCh37>",
"contig.31": "<ID=GL000235.1,length=34474,assembly=GRCh37>",
"contig.32": "<ID=GL000201.1,length=36148,assembly=GRCh37>",
"contig.33": "<ID=GL000247.1,length=36422,assembly=GRCh37>",
"contig.34": "<ID=GL000245.1,length=36651,assembly=GRCh37>",
"contig.35": "<ID=GL000197.1,length=37175,assembly=GRCh37>",
"contig.36": "<ID=GL000203.1,length=37498,assembly=GRCh37>",
"contig.37": "<ID=GL000246.1,length=38154,assembly=GRCh37>",
"contig.38": "<ID=GL000249.1,length=38502,assembly=GRCh37>",
"contig.39": "<ID=GL000196.1,length=38914,assembly=GRCh37>",
"contig.40": "<ID=GL000248.1,length=39786,assembly=GRCh37>",
"contig.41": "<ID=GL000244.1,length=39929,assembly=GRCh37>",
"contig.42": "<ID=GL000238.1,length=39939,assembly=GRCh37>",
"contig.43": "<ID=GL000202.1,length=40103,assembly=GRCh37>",
"contig.44": "<ID=GL000234.1,length=40531,assembly=GRCh37>",
"contig.45": "<ID=GL000232.1,length=40652,assembly=GRCh37>",
"contig.46": "<ID=GL000206.1,length=41001,assembly=GRCh37>",
"contig.47": "<ID=GL000240.1,length=41933,assembly=GRCh37>",
"contig.48": "<ID=GL000236.1,length=41934,assembly=GRCh37>",
"contig.49": "<ID=GL000241.1,length=42152,assembly=GRCh37>",
"contig.50": "<ID=GL000243.1,length=43341,assembly=GRCh37>",
"contig.51": "<ID=GL000242.1,length=43523,assembly=GRCh37>",
"contig.52": "<ID=GL000230.1,length=43691,assembly=GRCh37>",
"contig.53": "<ID=GL000237.1,length=45867,assembly=GRCh37>",
"contig.54": "<ID=GL000233.1,length=45941,assembly=GRCh37>",
"contig.55": "<ID=GL000204.1,length=81310,assembly=GRCh37>",
"contig.56": "<ID=GL000198.1,length=90085,assembly=GRCh37>",
"contig.57": "<ID=GL000208.1,length=92689,assembly=GRCh37>",
"contig.58": "<ID=GL000191.1,length=106433,assembly=GRCh37>",
"contig.59": "<ID=GL000227.1,length=128374,assembly=GRCh37>",
"contig.60": "<ID=GL000228.1,length=129120,assembly=GRCh37>",
"contig.61": "<ID=GL000214.1,length=137718,assembly=GRCh37>",
"contig.62": "<ID=GL000221.1,length=155397,assembly=GRCh37>",
"contig.63": "<ID=GL000209.1,length=159169,assembly=GRCh37>",
"contig.64": "<ID=GL000218.1,length=161147,assembly=GRCh37>",
"contig.65": "<ID=GL000220.1,length=161802,assembly=GRCh37>",
"contig.66": "<ID=GL000213.1,length=164239,assembly=GRCh37>",
"contig.67": "<ID=GL000211.1,length=166566,assembly=GRCh37>",
"contig.68": "<ID=GL000199.1,length=169874,assembly=GRCh37>",
"contig.69": "<ID=GL000217.1,length=172149,assembly=GRCh37>",
"contig.70": "<ID=GL000216.1,length=172294,assembly=GRCh37>",
"contig.71": "<ID=GL000215.1,length=172545,assembly=GRCh37>",
"contig.72": "<ID=GL000205.1,length=174588,assembly=GRCh37>",
"contig.73": "<ID=GL000219.1,length=179198,assembly=GRCh37>",
"contig.74": "<ID=GL000224.1,length=179693,assembly=GRCh37>",
"contig.75": "<ID=GL000223.1,length=180455,assembly=GRCh37>",
"contig.76": "<ID=GL000195.1,length=182896,assembly=GRCh37>",
"contig.77": "<ID=GL000212.1,length=186858,assembly=GRCh37>",
"contig.78": "<ID=GL000222.1,length=186861,assembly=GRCh37>",
"contig.79": "<ID=GL000200.1,length=187035,assembly=GRCh37>",
"contig.80": "<ID=GL000193.1,length=189789,assembly=GRCh37>",
"contig.81": "<ID=GL000194.1,length=191469,assembly=GRCh37>",
"contig.82": "<ID=GL000225.1,length=211173,assembly=GRCh37>",
"contig.83": "<ID=GL000192.1,length=547496,assembly=GRCh37>",
"gwas_harmonisation_command": "--out /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/ukbiobank/vcf_09_19b/bgzip_vcf/data.batch_4194.vcf.gz --id UKB-b:15892 --data /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/ukbiobank/raw-output/data.batch_4194.txt.gz --cohort_controls 151546 --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": "2019-09-12T23:04:29.042850",
"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-15892/mac_discard.txt -Oz /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-15892/UKB-b-15892_raw.vcf.gz; Date=Thu Oct 17 12:32:36 2019",
"bcftools_viewCommand.1": "view -h /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/ukb-b-15892/ukb-b-15892.vcf.gz; Date=Sat May 9 14:05:06 2020"
}
LDSC
*********************************************************************
* 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-15892/UKB-b-15892_data.vcf.gz \
--ref-ld-chr ../reference/eur_w_ld_chr/ \
--out /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-15892/ldsc.txt \
--w-ld-chr ../reference/eur_w_ld_chr/
Beginning analysis at Thu Oct 17 14:44:33 2019
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-15892/UKB-b-15892_data.vcf.gz ...
Read summary statistics for 9326797 SNPs.
Dropped 10427 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, 1288004 SNPs remain.
After merging with regression SNP LD, 1288004 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.1321 (0.0088)
Lambda GC: 1.2742
Mean Chi^2: 1.4297
Intercept: 1.0356 (0.0097)
Ratio: 0.0829 (0.0226)
Analysis finished at Thu Oct 17 14:46:12 2019
Total time elapsed: 1.0m:38.76sQC metrics
Metrics
Metrics
{
"af_correlation": 0.9488,
"inflation_factor": 1.1999,
"mean_EFFECT": -0.0001,
"n": "-Inf",
"n_snps": 9851866,
"n_clumped_hits": 80,
"n_p_sig": 8767,
"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": 113693,
"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": 1288004,
"ldsc_nsnp_merge_regression_ld": 1288004,
"ldsc_observed_scale_h2_beta": 0.1321,
"ldsc_observed_scale_h2_se": 0.0088,
"ldsc_intercept_beta": 1.0356,
"ldsc_intercept_se": 0.0097,
"ldsc_lambda_gc": 1.2742,
"ldsc_mean_chisq": 1.4297,
"ldsc_ratio": 0.0828
}
Flags
| 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 | TRUE |
| 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 |
Definitions
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(\(2 \times N \times MAF\)) 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, \(\widehat{n}\).ratio_se_n: \(\texttt{ratio_se_n} = \frac{\sqrt{\widehat{n}}}{\sqrt{n}}\). 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: \(\texttt{mean_diff} = \sum_{j} \frac{\widehat{\beta_j^{std}} - \beta_j}{\texttt{n_snps}}\), 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.- \(\widehat{\beta_j^{std}} = \sqrt{\frac{{z}_j^2 / ({z}_j^2 + n -2)}{2 \times {MAF}_j \times (1 - {MAF}_j)}} \times sign({z}_j)\),
- \({z}_j = \frac{\beta_j}{{se}_j}\),
- and \(\beta_j\) is the reported effect size.
ratio_diff: \(\texttt{ratio_diff} = |\frac{\texttt{mean_diff}}{\texttt{mean_diff2}}|\), 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.- \(\texttt{mean_diff2} = \sum_{j} \frac{\widehat{\beta_j^{std}} - \beta^{\prime}_j}{\texttt{n_snps}}\)
- \(\beta^{\prime}_j = \frac{\beta_j}{\widehat{\texttt{sd2}}_{y}}\)
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.- \(\widehat{\texttt{sd1}}_{y} = \frac{\sqrt{n} \times median({se}_j)}{C}\),
- \(C = median(\frac{1}{\sqrt{2 \times {MAF}_j \times (1 - {MAF}_j)}})\),
- and \({se}_j\) 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.- \(\widehat{\texttt{sd2}}_{y} = median(\widehat{sd_j})\),
- \(\widehat{sd_j} = \frac{\beta_j}{\widehat{\beta_j^{std}}}\),
r2 metrics
Sum of variance explained, calculated from the clumped top hits sample.
r2_sum<*>:r2statistics under various assumptions1: \(r^2 = \sum_j{\frac{2 \times \beta_j^2 \times {MAF}_j \times (1 - {MAF}_j)}{\texttt{var1}}}\), \(\texttt{var1} = 1\).2: \(r^2 = \sum_j{\frac{2 \times \beta_j^2 \times {MAF}_j \times (1 - {MAF}_j)}{\texttt{var2}}}\), \(\texttt{var2} = {\widehat{\texttt{sd1}}_{y}}^2\),3: \(r^2 = \sum_j{\frac{2 \times \beta_j^2 \times {MAF}_j \times (1 - {MAF}_j)}{\texttt{var3}}}\), \(\texttt{var3} = {\widehat{\texttt{sd2}}_{y}}^2\),4: \(r^2 = \sum_j{\frac{F_j}{F_j + n - 2}}\), \(F = \frac{\beta_j^2}{{se}_j^2}\).
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 \(\chi^2\) statistics.ldsc_ratio: \(\frac{\texttt{ldsc_intercept_beta} - 1}{\texttt{ldsc_mean_chisq} - 1}\), the proportion of the inflation in the mean \(\chi^2\) 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 \(h^2\) 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: \(-log_{10}^{5 \times 10^{-8}}\)
- Blue line: \(-log_{10}^{5 \times 10^{-5}}\)
- QQ plot
- AF plot
- P-Z plot
- beta_std plot: Scatter plot between \(\widehat{\beta_j^{std}}\) and \(\beta_j\)
Diagnostics
Details
Summary stats
| 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 | 9316422 | 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 | 9326797 | 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 | 8.634468e+00 | 5.753952e+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 | 7.881299e+07 | 5.630869e+07 | 828.0000000 | 3.250525e+07 | 6.939252e+07 | 1.145427e+08 | 2.492385e+08 | ▇▆▅▂▁ |
| numeric | EFFECT | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | -5.090000e-05 | 1.389570e-02 | -0.1922070 | -5.324200e-03 | -4.000000e-05 | 5.219400e-03 | 2.893080e-01 | ▁▇▇▁▁ |
| numeric | SE | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 1.037350e-02 | 8.233000e-03 | 0.0034603 | 4.165300e-03 | 6.593200e-03 | 1.421580e-02 | 1.203020e-01 | ▇▁▁▁▁ |
| numeric | PVAL | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 4.702819e-01 | 2.972076e-01 | 0.0000000 | 2.099999e-01 | 4.600002e-01 | 7.300002e-01 | 1.000000e+00 | ▇▆▆▆▆ |
| numeric | PVAL_ztest | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 4.702828e-01 | 2.971826e-01 | 0.0000000 | 2.057199e-01 | 4.601817e-01 | 7.276115e-01 | 9.999999e-01 | ▇▆▆▆▆ |
| numeric | AF | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 2.133665e-01 | 2.577661e-01 | 0.0023100 | 1.731300e-02 | 9.192900e-02 | 3.349410e-01 | 9.976900e-01 | ▇▂▁▁▁ |
| numeric | AF_reference | 113693 | 0.9878101 | NA | NA | NA | NA | NA | NA | NA | 2.144387e-01 | 2.495472e-01 | 0.0000000 | 1.477640e-02 | 1.104230e-01 | 3.348640e-01 | 1.000000e+00 | ▇▂▁▁▁ |
Head and tail
| CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 | 49298 | rs200943160 | T | C | -0.0070452 | 0.0063761 | 0.2700001 | 0.2691818 | 0.623778 | 0.7821490 | NA |
| 1 | 54676 | rs2462492 | C | T | 0.0012161 | 0.0063327 | 0.8499999 | 0.8477126 | 0.399250 | NA | NA |
| 1 | 86028 | rs114608975 | T | C | 0.0060964 | 0.0100914 | 0.5500004 | 0.5457623 | 0.103813 | 0.0277556 | NA |
| 1 | 91536 | rs6702460 | G | T | -0.0036762 | 0.0062399 | 0.5600000 | 0.5557646 | 0.456274 | 0.4207270 | NA |
| 1 | 234313 | rs8179466 | C | T | 0.0016225 | 0.0123209 | 0.9000000 | 0.8952307 | 0.074486 | NA | NA |
| 1 | 534192 | rs6680723 | C | T | 0.0043218 | 0.0071326 | 0.5400003 | 0.5445669 | 0.241089 | NA | NA |
| 1 | 546697 | rs12025928 | A | G | -0.0019978 | 0.0088488 | 0.8200001 | 0.8213770 | 0.913064 | NA | NA |
| 1 | 693731 | rs12238997 | A | G | 0.0000546 | 0.0059469 | 0.9900000 | 0.9926793 | 0.116894 | 0.1417730 | NA |
| 1 | 705882 | rs72631875 | G | A | 0.0046031 | 0.0086994 | 0.5999997 | 0.5967159 | 0.067604 | 0.0315495 | NA |
| 1 | 706368 | rs55727773 | A | G | 0.0116581 | 0.0044026 | 0.0080999 | 0.0080973 | 0.515024 | 0.2751600 | NA |
| CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 22 | 51219006 | rs28729663 | G | A | -0.0013246 | 0.0053390 | 0.8000000 | 0.8040521 | 0.137083 | 0.2052720 | NA |
| 22 | 51219387 | rs9616832 | T | C | -0.0008526 | 0.0069446 | 0.9000000 | 0.9022825 | 0.072732 | 0.0654952 | NA |
| 22 | 51219704 | rs147475742 | G | A | 0.0091493 | 0.0092713 | 0.3200000 | 0.3237190 | 0.041665 | 0.0473243 | NA |
| 22 | 51221190 | rs369304721 | G | A | 0.0008828 | 0.0092919 | 0.9199999 | 0.9243119 | 0.049110 | NA | NA |
| 22 | 51221731 | rs115055839 | T | C | -0.0009061 | 0.0069502 | 0.9000000 | 0.8962771 | 0.072205 | 0.0625000 | NA |
| 22 | 51222100 | rs114553188 | G | T | -0.0060231 | 0.0081343 | 0.4600002 | 0.4590240 | 0.054454 | 0.0880591 | NA |
| 22 | 51223637 | rs375798137 | G | A | -0.0067584 | 0.0081762 | 0.4100001 | 0.4084680 | 0.054064 | 0.0788738 | NA |
| 22 | 51229805 | rs9616985 | T | C | -0.0000416 | 0.0069758 | 1.0000000 | 0.9952475 | 0.072060 | 0.0730831 | NA |
| 22 | 51232488 | rs376461333 | A | G | -0.0006238 | 0.0163383 | 0.9699999 | 0.9695446 | 0.020170 | NA | NA |
| 22 | 51237063 | rs3896457 | T | C | 0.0007242 | 0.0042390 | 0.8600001 | 0.8643463 | 0.297651 | 0.2050720 | NA |
bcf preview
1 49298 rs10399793 T C . PASS AF=0.623778 ES:SE:LP:AF:ID -0.00704523:0.00637607:0.568636:0.623778:rs10399793
1 54676 rs2462492 C T . PASS AF=0.39925 ES:SE:LP:AF:ID 0.00121611:0.00633266:0.0705811:0.39925:rs2462492
1 86028 rs114608975 T C . PASS AF=0.103813 ES:SE:LP:AF:ID 0.00609644:0.0100914:0.259637:0.103813:rs114608975
1 91536 rs6702460 G T . PASS AF=0.456274 ES:SE:LP:AF:ID -0.0036762:0.0062399:0.251812:0.456274:rs6702460
1 234313 rs8179466 C T . PASS AF=0.074486 ES:SE:LP:AF:ID 0.00162252:0.0123209:0.0457575:0.074486:rs8179466
1 534192 rs6680723 C T . PASS AF=0.241089 ES:SE:LP:AF:ID 0.00432182:0.00713264:0.267606:0.241089:rs6680723
1 546697 rs12025928 A G . PASS AF=0.913064 ES:SE:LP:AF:ID -0.00199784:0.00884884:0.0861861:0.913064:rs12025928
1 693731 rs12238997 A G . PASS AF=0.116894 ES:SE:LP:AF:ID 5.45644e-05:0.00594687:0.00436481:0.116894:rs12238997
1 705882 rs72631875 G A . PASS AF=0.067604 ES:SE:LP:AF:ID 0.00460309:0.00869937:0.221849:0.067604:rs72631875
1 706368 rs12029736 A G . PASS AF=0.515024 ES:SE:LP:AF:ID 0.0116581:0.00440263:2.09152:0.515024:rs12029736
1 714596 rs149887893 T C . PASS AF=0.033571 ES:SE:LP:AF:ID 0.00341877:0.0109991:0.119186:0.033571:rs149887893
1 715265 rs12184267 C T . PASS AF=0.037272 ES:SE:LP:AF:ID -0.00141915:0.00998979:0.05061:0.037272:rs12184267
1 715367 rs12184277 A G . PASS AF=0.037398 ES:SE:LP:AF:ID -0.00164551:0.00995086:0.0604807:0.037398:rs12184277
1 717485 rs12184279 C A . PASS AF=0.037056 ES:SE:LP:AF:ID -0.00139997:0.0100263:0.05061:0.037056:rs12184279
1 717587 rs144155419 G A . PASS AF=0.016376 ES:SE:LP:AF:ID -0.00707261:0.0156419:0.187087:0.016376:rs144155419
1 720381 rs116801199 G T . PASS AF=0.037638 ES:SE:LP:AF:ID -0.000655479:0.00991123:0.0222764:0.037638:rs116801199
1 721290 rs12565286 G C . PASS AF=0.037737 ES:SE:LP:AF:ID 0.000318592:0.00987887:0.0132283:0.037737:rs12565286
1 722670 rs116030099 T C . PASS AF=0.101553 ES:SE:LP:AF:ID -0.0124869:0.00725197:1.07058:0.101553:rs116030099
1 723891 rs2977670 G C . PASS AF=0.958296 ES:SE:LP:AF:ID 0.00513061:0.00952954:0.229148:0.958296:rs2977670
1 724849 rs12126395 C A . PASS AF=0.031684 ES:SE:LP:AF:ID -0.0289932:0.0174351:1.01773:0.031684:rs12126395
1 725060 rs865924913 A T . PASS AF=0.052652 ES:SE:LP:AF:ID 0.0117928:0.0140615:0.39794:0.052652:rs865924913
1 726794 rs28454925 C G . PASS AF=0.03721 ES:SE:LP:AF:ID 6.83795e-05:0.00994707:0.00436481:0.03721:rs28454925
1 729632 rs116720794 C T . PASS AF=0.037535 ES:SE:LP:AF:ID 0.000499509:0.00985887:0.0177288:0.037535:rs116720794
1 729679 rs4951859 C G . PASS AF=0.841985 ES:SE:LP:AF:ID 0.00236818:0.00514613:0.187087:0.841985:rs4951859
1 730087 rs148120343 T C . PASS AF=0.05609 ES:SE:LP:AF:ID 0.00822649:0.00835719:0.49485:0.05609:rs148120343
1 731718 rs58276399 T C . PASS AF=0.122816 ES:SE:LP:AF:ID -0.000547101:0.00564446:0.0362122:0.122816:rs58276399
1 732989 rs369030935 C T . PASS AF=0.025783 ES:SE:LP:AF:ID 0.0103754:0.0138685:0.346787:0.025783:rs369030935
1 734349 rs141242758 T C . PASS AF=0.122036 ES:SE:LP:AF:ID -0.000708586:0.00564723:0.0457575:0.122036:rs141242758
1 736289 rs79010578 T A . PASS AF=0.133326 ES:SE:LP:AF:ID 0.000242994:0.00555441:0.0132283:0.133326:rs79010578
1 736689 rs181876450 T C . PASS AF=0.011239 ES:SE:LP:AF:ID -0.0167291:0.020136:0.387216:0.011239:rs181876450
1 740284 rs61770167 C T . PASS AF=0.005842 ES:SE:LP:AF:ID -0.0173789:0.025733:0.30103:0.005842:rs61770167
1 752478 rs146277091 G A . PASS AF=0.037484 ES:SE:LP:AF:ID -4.83979e-05:0.00975732:-0:0.037484:rs146277091
1 752566 rs3094315 G A . PASS AF=0.837749 ES:SE:LP:AF:ID 0.00132827:0.00498336:0.102373:0.837749:rs3094315
1 752721 rs3131972 A G . PASS AF=0.837362 ES:SE:LP:AF:ID 0.00199655:0.00497775:0.161151:0.837362:rs3131972
1 753405 rs3115860 C A . PASS AF=0.869087 ES:SE:LP:AF:ID 0.00122324:0.00534435:0.0861861:0.869087:rs3115860
1 753541 rs2073813 G A . PASS AF=0.13062 ES:SE:LP:AF:ID -0.00276382:0.00535487:0.21467:0.13062:rs2073813
1 754063 rs12184312 G T . PASS AF=0.037976 ES:SE:LP:AF:ID -0.000129368:0.00959663:0.00436481:0.037976:rs12184312
1 754105 rs12184325 C T . PASS AF=0.03823 ES:SE:LP:AF:ID -7.3722e-05:0.00953573:0.00436481:0.03823:rs12184325
1 754182 rs3131969 A G . PASS AF=0.868408 ES:SE:LP:AF:ID 0.00213223:0.00533358:0.161151:0.868408:rs3131969
1 754192 rs3131968 A G . PASS AF=0.868517 ES:SE:LP:AF:ID 0.00168904:0.005336:0.124939:0.868517:rs3131968
1 754211 rs12184313 G A . PASS AF=0.038161 ES:SE:LP:AF:ID -5.52992e-05:0.00957705:-0:0.038161:rs12184313
1 754334 rs3131967 T C . PASS AF=0.868405 ES:SE:LP:AF:ID 0.00212084:0.00533323:0.161151:0.868405:rs3131967
1 754433 rs150578204 G A . PASS AF=0.005106 ES:SE:LP:AF:ID -0.02687:0.0275361:0.481486:0.005106:rs150578204
1 754458 rs142682604 G T . PASS AF=0.005076 ES:SE:LP:AF:ID -0.0265089:0.0275972:0.468521:0.005076:rs142682604
1 754503 rs3115859 G A . PASS AF=0.836845 ES:SE:LP:AF:ID 0.00214195:0.00496477:0.173925:0.836845:rs3115859
1 754629 rs10454459 A G . PASS AF=0.038173 ES:SE:LP:AF:ID -0.00039101:0.00959012:0.0132283:0.038173:rs10454459
1 754964 rs3131966 C T . PASS AF=0.837479 ES:SE:LP:AF:ID 0.0023476:0.00497859:0.19382:0.837479:rs3131966
1 755240 rs181660517 T G . PASS AF=0.013263 ES:SE:LP:AF:ID 0.00716815:0.0178075:0.161151:0.013263:rs181660517
1 755435 rs184270342 T G . PASS AF=0.005456 ES:SE:LP:AF:ID -0.0234234:0.0270626:0.408935:0.005456:rs184270342
1 755775 rs3131965 A G . PASS AF=0.838709 ES:SE:LP:AF:ID 0.00115949:0.00504681:0.0861861:0.838709:rs3131965