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:13532,TotalVariants=9851866,VariantsNotRead=0,HarmonisedVariants=9851866,VariantsNotHarmonised=0,SwitchedAlleles=9851866,TotalControls=461723,TotalCases=1210,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_20002_1224.vcf.gz --id UKB-b:13532 --data /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/ukbiobank/raw-output/data.batch_20002_1224.txt.gz --cohort_cases 1210 --cohort_controls 461723 --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": "2019-09-13T08:07:00.890246",
"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-13532/mac_discard.txt -Oz /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-13532/UKB-b-13532_raw.vcf.gz; Date=Thu Oct 17 12:29:03 2019",
"bcftools_viewCommand.1": "view -h /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/ukb-b-13532/ukb-b-13532.vcf.gz; Date=Sun May 10 14:50:38 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-13532/UKB-b-13532_data.vcf.gz \
--ref-ld-chr ../reference/eur_w_ld_chr/ \
--out /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-13532/ldsc.txt \
--w-ld-chr ../reference/eur_w_ld_chr/
Beginning analysis at Thu Oct 17 14:42:48 2019
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-13532/UKB-b-13532_data.vcf.gz ...
Read summary statistics for 1917359 SNPs.
Dropped 185 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, 492261 SNPs remain.
After merging with regression SNP LD, 492261 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: -0.0006 (0.0013)
Lambda GC: 1.0181
Mean Chi^2: 1.0111
Intercept: 1.018 (0.012)
Ratio: 1.6172 (1.075)
Analysis finished at Thu Oct 17 14:43:18 2019
Total time elapsed: 29.7sQC metrics
Metrics
Metrics
{
"af_correlation": 0.6812,
"inflation_factor": 1.0475,
"mean_EFFECT": 1.8766e-08,
"n": "-Inf",
"n_snps": 9851866,
"n_clumped_hits": 1,
"n_p_sig": 3,
"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": 15186,
"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": 492261,
"ldsc_nsnp_merge_regression_ld": 492261,
"ldsc_observed_scale_h2_beta": "NA",
"ldsc_observed_scale_h2_se": "NA",
"ldsc_intercept_beta": 1.018,
"ldsc_intercept_se": 0.012,
"ldsc_lambda_gc": 1.0181,
"ldsc_mean_chisq": 1.0111,
"ldsc_ratio": 1.6216
}
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 | 1917176 | 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 | 1917359 | 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 | 8.650116e+00 | 5.763230e+00 | 1.00000e+00 | 4.000000e+00 | 8.000000e+00 | 1.300000e+01 | 2.200000e+01 | ▇▅▅▂▂ |
| numeric | POS | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 7.872705e+07 | 5.663091e+07 | 1.23330e+04 | 3.187346e+07 | 6.928559e+07 | 1.148672e+08 | 2.491722e+08 | ▇▆▅▂▁ |
| numeric | EFFECT | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 0.000000e+00 | 1.112000e-04 | -5.24200e-04 | -7.520000e-05 | -1.000000e-07 | 7.530000e-05 | 6.904000e-04 | ▁▅▇▁▁ |
| numeric | SE | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 1.102000e-04 | 3.900000e-06 | 1.02400e-04 | 1.071000e-04 | 1.092000e-04 | 1.126000e-04 | 2.100000e-04 | ▇▁▁▁▁ |
| numeric | PVAL | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 4.965191e-01 | 2.895151e-01 | 0.00000e+00 | 2.399999e-01 | 4.899999e-01 | 7.499995e-01 | 1.000000e+00 | ▇▇▇▇▇ |
| numeric | PVAL_ztest | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 4.965162e-01 | 2.894830e-01 | 0.00000e+00 | 2.447173e-01 | 4.944069e-01 | 7.476937e-01 | 9.999997e-01 | ▇▇▇▇▇ |
| numeric | AF | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 4.716631e-01 | 1.206265e-01 | 2.89257e-01 | 3.656930e-01 | 4.574030e-01 | 5.706975e-01 | 7.107430e-01 | ▇▆▆▅▅ |
| numeric | AF_reference | 15186 | 0.9920797 | NA | NA | NA | NA | NA | NA | NA | 4.510498e-01 | 1.578899e-01 | 1.99700e-04 | 3.298720e-01 | 4.422920e-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 | 0.0001274 | 0.0001884 | 0.5000000 | 0.4989303 | 0.623763 | 0.782149 | NA |
| 1 | 54676 | rs2462492 | C | T | 0.0001625 | 0.0001866 | 0.3800004 | 0.3839143 | 0.400401 | NA | NA |
| 1 | 91536 | rs6702460 | G | T | 0.0001974 | 0.0001838 | 0.2800000 | 0.2826312 | 0.456851 | 0.420727 | NA |
| 1 | 706368 | rs55727773 | A | G | -0.0000002 | 0.0001303 | 1.0000000 | 0.9987641 | 0.515650 | 0.275160 | NA |
| 1 | 763394 | rs369924889 | G | A | 0.0000456 | 0.0001528 | 0.7700005 | 0.7652908 | 0.706753 | 0.617612 | NA |
| 1 | 814495 | rs74461805 | C | A | -0.0000250 | 0.0001787 | 0.8900000 | 0.8888756 | 0.340397 | NA | NA |
| 1 | 830181 | rs28444699 | A | G | -0.0000268 | 0.0001195 | 0.8200001 | 0.8223200 | 0.697259 | 0.691294 | NA |
| 1 | 831489 | rs4970385 | C | T | -0.0000919 | 0.0001174 | 0.4299995 | 0.4335817 | 0.705403 | 0.649161 | NA |
| 1 | 831909 | rs9697642 | C | T | -0.0000981 | 0.0001174 | 0.4000000 | 0.4032194 | 0.705448 | 0.648562 | NA |
| 1 | 832066 | rs9697380 | G | C | -0.0000976 | 0.0001174 | 0.4100001 | 0.4058552 | 0.705634 | 0.664337 | NA |
| CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 22 | 51164115 | rs5770996 | C | T | 0.0000884 | 0.0001071 | 0.4100001 | 0.4094421 | 0.456928 | 0.514776 | NA |
| 22 | 51164287 | rs6009957 | T | C | 0.0001662 | 0.0001152 | 0.1499999 | 0.1490583 | 0.306554 | 0.415535 | NA |
| 22 | 51165664 | rs8137951 | G | A | 0.0001668 | 0.0001155 | 0.1499999 | 0.1488039 | 0.301558 | 0.406350 | NA |
| 22 | 51174048 | rs9628245 | G | C | 0.0000128 | 0.0001210 | 0.9199999 | 0.9159829 | 0.380130 | 0.433107 | NA |
| 22 | 51181919 | rs9616825 | G | C | 0.0001022 | 0.0001220 | 0.4000000 | 0.4022450 | 0.695471 | 0.619409 | NA |
| 22 | 51186143 | rs2879914 | T | C | 0.0000148 | 0.0001141 | 0.9000000 | 0.8966502 | 0.381826 | 0.273363 | NA |
| 22 | 51186228 | rs3865766 | C | T | 0.0000298 | 0.0001112 | 0.7899998 | 0.7885310 | 0.451063 | 0.453275 | NA |
| 22 | 51197266 | rs61290853 | A | G | 0.0000037 | 0.0001148 | 0.9699999 | 0.9744701 | 0.386333 | 0.422923 | NA |
| 22 | 51212875 | rs2238837 | A | C | 0.0000574 | 0.0001224 | 0.6400000 | 0.6390131 | 0.331455 | 0.372404 | NA |
| 22 | 51237063 | rs3896457 | T | C | -0.0000030 | 0.0001253 | 0.9800000 | 0.9807077 | 0.297971 | 0.205072 | NA |
bcf preview
1 49298 rs10399793 T C . PASS AF=0.623763 ES:SE:LP:AF:ID 0.000127381:0.000188385:0.30103:0.623763:rs10399793
1 54676 rs2462492 C T . PASS AF=0.400401 ES:SE:LP:AF:ID 0.0001625:0.00018663:0.420216:0.400401:rs2462492
1 91536 rs6702460 G T . PASS AF=0.456851 ES:SE:LP:AF:ID 0.00019744:0.000183763:0.552842:0.456851:rs6702460
1 706368 rs12029736 A G . PASS AF=0.51565 ES:SE:LP:AF:ID -2.0184e-07:0.000130305:-0:0.51565:rs12029736
1 763394 rs3115847 G A . PASS AF=0.706753 ES:SE:LP:AF:ID 4.5608e-05:0.00015277:0.113509:0.706753:rs3115847
1 814495 rs74461805 C A . PASS AF=0.340397 ES:SE:LP:AF:ID -2.49656e-05:0.000178674:0.05061:0.340397:rs74461805
1 830181 rs28444699 A G . PASS AF=0.697259 ES:SE:LP:AF:ID -2.68437e-05:0.000119538:0.0861861:0.697259:rs28444699
1 831489 rs4970385 C T . PASS AF=0.705403 ES:SE:LP:AF:ID -9.19137e-05:0.000117375:0.366532:0.705403:rs4970385
1 831909 rs9697642 C T . PASS AF=0.705448 ES:SE:LP:AF:ID -9.81087e-05:0.000117371:0.39794:0.705448:rs9697642
1 832066 rs9697380 G C . PASS AF=0.705634 ES:SE:LP:AF:ID -9.75649e-05:0.000117377:0.387216:0.705634:rs9697380
1 832318 rs4500250 C A . PASS AF=0.705662 ES:SE:LP:AF:ID -9.46839e-05:0.000117389:0.376751:0.705662:rs4500250
1 832918 rs28765502 T C . PASS AF=0.294371 ES:SE:LP:AF:ID 9.53191e-05:0.000117384:0.376751:0.294371:rs28765502
1 840753 rs4970382 T C . PASS AF=0.400106 ES:SE:LP:AF:ID 6.00583e-05:0.000108269:0.236572:0.400106:rs4970382
1 843405 rs11516185 A G . PASS AF=0.362599 ES:SE:LP:AF:ID 0.000109593:0.000134404:0.387216:0.362599:rs11516185
1 850218 rs6664536 T A . PASS AF=0.590333 ES:SE:LP:AF:ID 9.36517e-05:0.000107952:0.408935:0.590333:rs6664536
1 850371 rs6679046 G T . PASS AF=0.603726 ES:SE:LP:AF:ID 0.00013633:0.000108558:0.677781:0.603726:rs6679046
1 850780 rs6657440 C T . PASS AF=0.603944 ES:SE:LP:AF:ID 0.000145476:0.000108542:0.744727:0.603944:rs6657440
1 852037 rs4970463 G A . PASS AF=0.589688 ES:SE:LP:AF:ID 9.30953e-05:0.000108127:0.408935:0.589688:rs4970463
1 852063 rs28436996 G A . PASS AF=0.589667 ES:SE:LP:AF:ID 9.3847e-05:0.000108079:0.408935:0.589667:rs28436996
1 852875 rs13303369 C T . PASS AF=0.607674 ES:SE:LP:AF:ID 0.000168988:0.000108785:0.920819:0.607674:rs13303369
1 853954 rs1806509 C A . PASS AF=0.607833 ES:SE:LP:AF:ID 0.000169814:0.0001088:0.920819:0.607833:rs1806509
1 854777 rs13303019 A G . PASS AF=0.610318 ES:SE:LP:AF:ID 0.000195606:0.000108907:1.14267:0.610318:rs13303019
1 854978 rs13303057 A C . PASS AF=0.603286 ES:SE:LP:AF:ID 0.000144997:0.000108584:0.744727:0.603286:rs13303057
1 855075 rs6673914 C G . PASS AF=0.610338 ES:SE:LP:AF:ID 0.000195466:0.000108909:1.13668:0.610338:rs6673914
1 856099 rs28534711 T G . PASS AF=0.389935 ES:SE:LP:AF:ID -0.000194921:0.00010893:1.13077:0.389935:rs28534711
1 856108 rs28742275 A G . PASS AF=0.389918 ES:SE:LP:AF:ID -0.000194687:0.000108935:1.13077:0.389918:rs28742275
1 856476 rs4040605 A G . PASS AF=0.350351 ES:SE:LP:AF:ID -0.000149086:0.000111908:0.744727:0.350351:rs4040605
1 866893 rs2880024 T C . PASS AF=0.610554 ES:SE:LP:AF:ID 5.63746e-05:0.000109521:0.21467:0.610554:rs2880024
1 868418 rs28546443 C T . PASS AF=0.297865 ES:SE:LP:AF:ID 5.61942e-05:0.000120333:0.19382:0.297865:rs28546443
1 870645 rs28576697 T C . PASS AF=0.291287 ES:SE:LP:AF:ID -0.00017926:0.000119373:0.886057:0.291287:rs28576697
1 875770 rs4970379 A G . PASS AF=0.600084 ES:SE:LP:AF:ID 8.02442e-05:0.000110431:0.327902:0.600084:rs4970379
1 881627 rs2272757 G A . PASS AF=0.65239 ES:SE:LP:AF:ID 0.000101981:0.000111554:0.443698:0.65239:rs2272757
1 891059 rs13303065 C T . PASS AF=0.652428 ES:SE:LP:AF:ID 0.000116042:0.000111537:0.522879:0.652428:rs13303065
1 891945 rs13303106 A G . PASS AF=0.65249 ES:SE:LP:AF:ID 0.000110862:0.000111667:0.49485:0.65249:rs13303106
1 903245 rs28690976 A G . PASS AF=0.566937 ES:SE:LP:AF:ID 2.36321e-06:0.00011091:0.00877392:0.566937:rs28690976
1 909073 rs3892467 C T . PASS AF=0.386683 ES:SE:LP:AF:ID 4.1473e-05:0.000110608:0.148742:0.386683:rs3892467
1 909238 rs3829740 G C . PASS AF=0.571412 ES:SE:LP:AF:ID -5.0933e-05:0.00010712:0.200659:0.571412:rs3829740
1 910394 rs28477686 C T . PASS AF=0.324456 ES:SE:LP:AF:ID -7.94513e-05:0.000116107:0.309804:0.324456:rs28477686
1 912049 rs7367995 T C . PASS AF=0.58525 ES:SE:LP:AF:ID 1.16223e-05:0.000108207:0.0409586:0.58525:rs7367995
1 913889 rs2340596 G A . PASS AF=0.599213 ES:SE:LP:AF:ID 1.49534e-05:0.000108383:0.05061:0.599213:rs2340596
1 914333 rs13302979 C G . PASS AF=0.602521 ES:SE:LP:AF:ID 3.27023e-05:0.000108711:0.119186:0.602521:rs13302979
1 914852 rs13303368 G C . PASS AF=0.600078 ES:SE:LP:AF:ID 1.87833e-05:0.000108502:0.0655015:0.600078:rs13303368
1 914940 rs13303033 T C . PASS AF=0.584292 ES:SE:LP:AF:ID 2.3676e-05:0.000107894:0.0809219:0.584292:rs13303033
1 916834 rs6694632 G A . PASS AF=0.589106 ES:SE:LP:AF:ID 4.23651e-05:0.000108058:0.154902:0.589106:rs6694632
1 918384 rs13303118 G T . PASS AF=0.584205 ES:SE:LP:AF:ID 2.19346e-05:0.000107843:0.0757207:0.584205:rs13303118
1 918573 rs2341354 A G . PASS AF=0.589331 ES:SE:LP:AF:ID 4.53003e-05:0.000107975:0.173925:0.589331:rs2341354
1 919501 rs4970414 G T . PASS AF=0.583932 ES:SE:LP:AF:ID 5.88738e-06:0.000111666:0.0177288:0.583932:rs4970414
1 921716 rs13303278 C A . PASS AF=0.567888 ES:SE:LP:AF:ID -9.92835e-06:0.000107753:0.0315171:0.567888:rs13303278
1 924528 rs34712273 C A . PASS AF=0.578492 ES:SE:LP:AF:ID 1.73926e-05:0.000108063:0.0604807:0.578492:rs34712273
1 930533 rs3128110 C G . PASS AF=0.386078 ES:SE:LP:AF:ID -6.99351e-05:0.000109444:0.283997:0.386078:rs3128110