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:14560,TotalVariants=9851866,VariantsNotRead=0,HarmonisedVariants=9851866,VariantsNotHarmonised=0,SwitchedAlleles=9851866,TotalControls=460138,TotalCases=1233,StudyType=CaseControl>",
"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_41251_5000.vcf.gz --id UKB-b:14560 --data /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/ukbiobank/raw-output/data.batch_41251_5000.txt.gz --cohort_cases 1233 --cohort_controls 460138 --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": "2019-09-12T23:03:04.572581",
"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-14560/mac_discard.txt -Oz /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-14560/UKB-b-14560_raw.vcf.gz; Date=Thu Oct 17 12:30:50 2019",
"bcftools_viewCommand.1": "view -h /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/ukb-b-14560/ukb-b-14560.vcf.gz; Date=Sat May 9 20:03:46 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-14560/UKB-b-14560_data.vcf.gz \
--ref-ld-chr ../reference/eur_w_ld_chr/ \
--out /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-14560/ldsc.txt \
--w-ld-chr ../reference/eur_w_ld_chr/
Beginning analysis at Thu Oct 17 14:43:45 2019
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-14560/UKB-b-14560_data.vcf.gz ...
Read summary statistics for 1970990 SNPs.
Dropped 190 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, 505365 SNPs remain.
After merging with regression SNP LD, 505365 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: -0.0027 (0.0014)
Lambda GC: 1.1182
Mean Chi^2: 1.1141
Intercept: 1.1439 (0.0118)
Ratio: 1.2615 (0.1031)
Analysis finished at Thu Oct 17 14:44:14 2019
Total time elapsed: 29.14sQC metrics
Metrics
Metrics
{
"af_correlation": 0.6906,
"inflation_factor": 1.0966,
"mean_EFFECT": -1.3045e-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": 15643,
"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": 505365,
"ldsc_nsnp_merge_regression_ld": 505365,
"ldsc_observed_scale_h2_beta": "NA",
"ldsc_observed_scale_h2_se": "NA",
"ldsc_intercept_beta": 1.1439,
"ldsc_intercept_se": 0.0118,
"ldsc_lambda_gc": 1.1182,
"ldsc_mean_chisq": 1.1141,
"ldsc_ratio": 1.2612
}
Flags
| name | value |
|---|---|
| af_correlation | TRUE |
| 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 |
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 | 4 | 58 | 0 | 1970802 | 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 | 1970990 | 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 | 8.650320e+00 | 5.762987e+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 | 7.873947e+07 | 5.665058e+07 | 5687.0000000 | 3.185531e+07 | 6.927257e+07 | 1.148747e+08 | 2.491722e+08 | ▇▆▅▂▁ |
| numeric | EFFECT | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | -1.000000e-07 | 1.176000e-04 | -0.0005729 | -7.940000e-05 | -5.000000e-07 | 7.910000e-05 | 5.793000e-04 | ▁▂▇▂▁ |
| numeric | SE | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 1.116000e-04 | 4.100000e-06 | 0.0001035 | 1.083000e-04 | 1.105000e-04 | 1.142000e-04 | 2.123000e-04 | ▇▁▁▁▁ |
| numeric | PVAL | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 4.829108e-01 | 2.929079e-01 | 0.0000003 | 2.200002e-01 | 4.799997e-01 | 7.400005e-01 | 1.000000e+00 | ▇▇▇▇▆ |
| numeric | PVAL_ztest | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 4.829096e-01 | 2.928823e-01 | 0.0000003 | 2.247293e-01 | 4.768942e-01 | 7.370652e-01 | 9.999999e-01 | ▇▇▇▇▇ |
| numeric | AF | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 4.700266e-01 | 1.236000e-01 | 0.2838610 | 3.614650e-01 | 4.551555e-01 | 5.713200e-01 | 7.161390e-01 | ▇▆▆▅▅ |
| numeric | AF_reference | 15643 | 0.9920634 | NA | NA | NA | NA | NA | NA | NA | 4.496145e-01 | 1.595149e-01 | 0.0001997 | 3.268770e-01 | 4.404950e-01 | 5.652960e-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 | 0.0000829 | 0.0001905 | 0.6600001 | 0.6632376 | 0.623771 | 0.782149 | NA |
| 1 | 54676 | rs2462492 | C | T | 0.0000520 | 0.0001887 | 0.7800007 | 0.7828698 | 0.400405 | NA | NA |
| 1 | 91536 | rs6702460 | G | T | 0.0001029 | 0.0001858 | 0.5800000 | 0.5796559 | 0.456838 | 0.420727 | NA |
| 1 | 706368 | rs55727773 | A | G | 0.0000932 | 0.0001317 | 0.4799997 | 0.4792844 | 0.515617 | 0.275160 | NA |
| 1 | 763394 | rs369924889 | G | A | -0.0000817 | 0.0001544 | 0.5999997 | 0.5970265 | 0.706741 | 0.617612 | NA |
| 1 | 814495 | rs74461805 | C | A | 0.0001800 | 0.0001806 | 0.3200000 | 0.3189986 | 0.340379 | NA | NA |
| 1 | 830181 | rs28444699 | A | G | 0.0001193 | 0.0001208 | 0.3200000 | 0.3234564 | 0.697201 | 0.691294 | NA |
| 1 | 831489 | rs4970385 | C | T | 0.0001061 | 0.0001187 | 0.3700002 | 0.3712243 | 0.705361 | 0.649161 | NA |
| 1 | 831909 | rs9697642 | C | T | 0.0001051 | 0.0001187 | 0.3800004 | 0.3758881 | 0.705406 | 0.648562 | NA |
| 1 | 832066 | rs9697380 | G | C | 0.0001086 | 0.0001187 | 0.3599996 | 0.3598646 | 0.705592 | 0.664337 | NA |
| CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 22 | 51165664 | rs8137951 | G | A | 0.0002908 | 0.0001168 | 0.0129999 | 0.0127923 | 0.301509 | 0.406350 | NA |
| 22 | 51174048 | rs9628245 | G | C | -0.0000050 | 0.0001224 | 0.9699999 | 0.9673046 | 0.380101 | 0.433107 | NA |
| 22 | 51180501 | rs5770999 | T | C | 0.0000797 | 0.0001240 | 0.5199996 | 0.5206023 | 0.713644 | 0.636981 | NA |
| 22 | 51181919 | rs9616825 | G | C | 0.0000863 | 0.0001234 | 0.4799997 | 0.4845162 | 0.695464 | 0.619409 | NA |
| 22 | 51182485 | rs6009961 | A | G | 0.0000744 | 0.0001244 | 0.5500004 | 0.5497546 | 0.715487 | 0.638379 | NA |
| 22 | 51186143 | rs2879914 | T | C | 0.0001744 | 0.0001154 | 0.1299999 | 0.1305953 | 0.381782 | 0.273363 | NA |
| 22 | 51186228 | rs3865766 | C | T | 0.0001977 | 0.0001124 | 0.0790005 | 0.0786477 | 0.451014 | 0.453275 | NA |
| 22 | 51197266 | rs61290853 | A | G | 0.0001822 | 0.0001161 | 0.1199999 | 0.1165480 | 0.386292 | 0.422923 | NA |
| 22 | 51212875 | rs2238837 | A | C | 0.0002336 | 0.0001238 | 0.0589997 | 0.0591156 | 0.331411 | 0.372404 | NA |
| 22 | 51237063 | rs3896457 | T | C | 0.0002088 | 0.0001267 | 0.0990011 | 0.0994536 | 0.297936 | 0.205072 | NA |
bcf preview
1 49298 rs10399793 T C . PASS AF=0.623771 ES:SE:LP:AF:ID 8.29362e-05:0.000190462:0.180456:0.623771:rs10399793
1 54676 rs2462492 C T . PASS AF=0.400405 ES:SE:LP:AF:ID 5.19939e-05:0.00018867:0.107905:0.400405:rs2462492
1 91536 rs6702460 G T . PASS AF=0.456838 ES:SE:LP:AF:ID 0.000102899:0.000185776:0.236572:0.456838:rs6702460
1 706368 rs12029736 A G . PASS AF=0.515617 ES:SE:LP:AF:ID 9.31908e-05:0.000131727:0.318759:0.515617:rs12029736
1 763394 rs3115847 G A . PASS AF=0.706741 ES:SE:LP:AF:ID -8.16506e-05:0.000154442:0.221849:0.706741:rs3115847
1 814495 rs74461805 C A . PASS AF=0.340379 ES:SE:LP:AF:ID 0.000180009:0.000180638:0.49485:0.340379:rs74461805
1 830181 rs28444699 A G . PASS AF=0.697201 ES:SE:LP:AF:ID 0.000119315:0.00012084:0.49485:0.697201:rs28444699
1 831489 rs4970385 C T . PASS AF=0.705361 ES:SE:LP:AF:ID 0.000106101:0.000118657:0.431798:0.705361:rs4970385
1 831909 rs9697642 C T . PASS AF=0.705406 ES:SE:LP:AF:ID 0.000105067:0.000118653:0.420216:0.705406:rs9697642
1 832066 rs9697380 G C . PASS AF=0.705592 ES:SE:LP:AF:ID 0.000108646:0.000118658:0.443698:0.705592:rs9697380
1 832318 rs4500250 C A . PASS AF=0.70562 ES:SE:LP:AF:ID 0.000108526:0.000118671:0.443698:0.70562:rs4500250
1 832918 rs28765502 T C . PASS AF=0.294413 ES:SE:LP:AF:ID -0.000103619:0.000118666:0.420216:0.294413:rs28765502
1 840753 rs4970382 T C . PASS AF=0.400159 ES:SE:LP:AF:ID -0.000132317:0.00010945:0.638272:0.400159:rs4970382
1 843405 rs11516185 A G . PASS AF=0.36258 ES:SE:LP:AF:ID -0.000231503:0.00013587:1.05552:0.36258:rs11516185
1 850218 rs6664536 T A . PASS AF=0.590303 ES:SE:LP:AF:ID -1.13289e-05:0.000109138:0.0362122:0.590303:rs6664536
1 850371 rs6679046 G T . PASS AF=0.603695 ES:SE:LP:AF:ID 3.77305e-06:0.00010975:0.0132283:0.603695:rs6679046
1 850780 rs6657440 C T . PASS AF=0.603918 ES:SE:LP:AF:ID -1.40022e-07:0.000109734:-0:0.603918:rs6657440
1 852037 rs4970463 G A . PASS AF=0.589658 ES:SE:LP:AF:ID -1.57406e-05:0.000109316:0.05061:0.589658:rs4970463
1 852063 rs28436996 G A . PASS AF=0.589637 ES:SE:LP:AF:ID -1.52753e-05:0.000109267:0.05061:0.589637:rs28436996
1 852875 rs13303369 C T . PASS AF=0.607644 ES:SE:LP:AF:ID 3.46483e-06:0.00010998:0.0132283:0.607644:rs13303369
1 853954 rs1806509 C A . PASS AF=0.607804 ES:SE:LP:AF:ID 2.79436e-06:0.000109995:0.00877392:0.607804:rs1806509
1 854777 rs13303019 A G . PASS AF=0.61029 ES:SE:LP:AF:ID -7.79127e-06:0.000110101:0.0268721:0.61029:rs13303019
1 854978 rs13303057 A C . PASS AF=0.603256 ES:SE:LP:AF:ID 2.14487e-06:0.000109776:0.00877392:0.603256:rs13303057
1 855075 rs6673914 C G . PASS AF=0.610311 ES:SE:LP:AF:ID -7.51382e-06:0.000110103:0.0222764:0.610311:rs6673914
1 856099 rs28534711 T G . PASS AF=0.389962 ES:SE:LP:AF:ID 5.4019e-06:0.000110125:0.0177288:0.389962:rs28534711
1 856108 rs28742275 A G . PASS AF=0.389946 ES:SE:LP:AF:ID 5.60011e-06:0.00011013:0.0177288:0.389946:rs28742275
1 856476 rs4040605 A G . PASS AF=0.350363 ES:SE:LP:AF:ID -5.0051e-05:0.000113137:0.180456:0.350363:rs4040605
1 866893 rs2880024 T C . PASS AF=0.610543 ES:SE:LP:AF:ID 8.49777e-05:0.000110721:0.356547:0.610543:rs2880024
1 868418 rs28546443 C T . PASS AF=0.297855 ES:SE:LP:AF:ID -0.000138098:0.000121651:0.585027:0.297855:rs28546443
1 870645 rs28576697 T C . PASS AF=0.291272 ES:SE:LP:AF:ID -4.43384e-05:0.000120686:0.148742:0.291272:rs28576697
1 873558 rs1110052 G T . PASS AF=0.715254 ES:SE:LP:AF:ID 1.86806e-05:0.000118987:0.0555173:0.715254:rs1110052
1 875770 rs4970379 A G . PASS AF=0.600047 ES:SE:LP:AF:ID 0.000149062:0.000111643:0.744727:0.600047:rs4970379
1 881627 rs2272757 G A . PASS AF=0.652386 ES:SE:LP:AF:ID 5.73948e-05:0.000112779:0.21467:0.652386:rs2272757
1 891059 rs13303065 C T . PASS AF=0.652424 ES:SE:LP:AF:ID 5.09469e-05:0.000112762:0.187087:0.652424:rs13303065
1 891945 rs13303106 A G . PASS AF=0.652486 ES:SE:LP:AF:ID 5.78194e-05:0.000112893:0.21467:0.652486:rs13303106
1 903245 rs28690976 A G . PASS AF=0.566894 ES:SE:LP:AF:ID 0.000132588:0.000112116:0.619789:0.566894:rs28690976
1 909073 rs3892467 C T . PASS AF=0.386671 ES:SE:LP:AF:ID 0.000266494:0.000111822:1.76955:0.386671:rs3892467
1 909238 rs3829740 G C . PASS AF=0.571392 ES:SE:LP:AF:ID 0.000248909:0.000108287:1.65758:0.571392:rs3829740
1 910394 rs28477686 C T . PASS AF=0.324412 ES:SE:LP:AF:ID -0.000155207:0.000117396:0.721246:0.324412:rs28477686
1 912049 rs7367995 T C . PASS AF=0.585269 ES:SE:LP:AF:ID 0.000149569:0.000109397:0.769551:0.585269:rs7367995
1 913889 rs2340596 G A . PASS AF=0.599237 ES:SE:LP:AF:ID 0.000113049:0.000109576:0.522879:0.599237:rs2340596
1 914333 rs13302979 C G . PASS AF=0.602538 ES:SE:LP:AF:ID 0.000103693:0.000109906:0.455932:0.602538:rs13302979
1 914852 rs13303368 G C . PASS AF=0.600098 ES:SE:LP:AF:ID 0.000111602:0.000109696:0.508638:0.600098:rs13303368
1 914940 rs13303033 T C . PASS AF=0.584318 ES:SE:LP:AF:ID 0.000149804:0.000109083:0.769551:0.584318:rs13303033
1 916834 rs6694632 G A . PASS AF=0.589134 ES:SE:LP:AF:ID 0.000147885:0.000109249:0.744727:0.589134:rs6694632
1 918384 rs13303118 G T . PASS AF=0.584231 ES:SE:LP:AF:ID 0.00013679:0.000109031:0.677781:0.584231:rs13303118
1 918573 rs2341354 A G . PASS AF=0.589359 ES:SE:LP:AF:ID 0.000136042:0.000109165:0.677781:0.589359:rs2341354
1 919501 rs4970414 G T . PASS AF=0.583961 ES:SE:LP:AF:ID 0.000103637:0.000112898:0.443698:0.583961:rs4970414
1 921716 rs13303278 C A . PASS AF=0.567937 ES:SE:LP:AF:ID 0.000140197:0.000108937:0.69897:0.567937:rs13303278
1 924528 rs34712273 C A . PASS AF=0.57854 ES:SE:LP:AF:ID 0.000121676:0.000109249:0.568636:0.57854:rs34712273