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:5948,TotalVariants=9851866,VariantsNotRead=0,HarmonisedVariants=9851866,VariantsNotHarmonised=0,SwitchedAlleles=9851866,TotalControls=461026,TotalCases=1984,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_41202_R35.vcf.gz --id UKB-b:5948 --data /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/ukbiobank/raw-output/data.batch_41202_R35.txt.gz --cohort_cases 1984 --cohort_controls 461026 --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": "2019-09-12T18:44:09.453086",
"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-5948/mac_discard.txt -Oz /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-5948/UKB-b-5948_raw.vcf.gz; Date=Thu Oct 17 12:45:33 2019",
"bcftools_viewCommand.1": "view -h /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/ukb-b-5948/ukb-b-5948.vcf.gz; Date=Sun May 10 10:40:44 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-5948/UKB-b-5948_data.vcf.gz \
--ref-ld-chr ../reference/eur_w_ld_chr/ \
--out /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-5948/ldsc.txt \
--w-ld-chr ../reference/eur_w_ld_chr/
Beginning analysis at Thu Oct 17 14:45:40 2019
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-5948/UKB-b-5948_data.vcf.gz ...
Read summary statistics for 3170937 SNPs.
Dropped 439 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, 784946 SNPs remain.
After merging with regression SNP LD, 784946 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.0035 (0.0012)
Lambda GC: 1.0233
Mean Chi^2: 1.0315
Intercept: 0.9942 (0.0097)
Ratio < 0 (usually indicates GC correction).
Analysis finished at Thu Oct 17 14:46:21 2019
Total time elapsed: 40.73sQC metrics
Metrics
Metrics
{
"af_correlation": 0.83,
"inflation_factor": 1.0475,
"mean_EFFECT": 1.052e-06,
"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": 25346,
"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": 784946,
"ldsc_nsnp_merge_regression_ld": 784946,
"ldsc_observed_scale_h2_beta": 0.0035,
"ldsc_observed_scale_h2_se": 0.0012,
"ldsc_intercept_beta": 0.9942,
"ldsc_intercept_se": 0.0097,
"ldsc_lambda_gc": 1.0233,
"ldsc_mean_chisq": 1.0315,
"ldsc_ratio": -0.1841
}
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 | FALSE |
| n_p_sig | FALSE |
| 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 | 3170501 | 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 | 3170937 | 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 | 8.662840e+00 | 5.772715e+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 | 7.854404e+07 | 5.670640e+07 | 828.0000000 | 3.160183e+07 | 6.892612e+07 | 1.147902e+08 | 2.492013e+08 | ▇▆▅▂▁ |
| numeric | EFFECT | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 1.100000e-06 | 1.529000e-04 | -0.0007814 | -1.008000e-04 | 5.000000e-07 | 1.028000e-04 | 8.552000e-04 | ▁▂▇▁▁ |
| numeric | SE | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 1.497000e-04 | 1.270000e-05 | 0.0001310 | 1.386000e-04 | 1.458000e-04 | 1.587000e-04 | 3.239000e-04 | ▇▁▁▁▁ |
| numeric | PVAL | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 4.948793e-01 | 2.906488e-01 | 0.0000004 | 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 | 4.948806e-01 | 2.906221e-01 | 0.0000004 | 2.413933e-01 | 4.935392e-01 | 7.470486e-01 | 1.000000e+00 | ▇▇▇▇▇ |
| numeric | AF | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 4.283370e-01 | 1.824349e-01 | 0.1764120 | 2.682130e-01 | 3.949090e-01 | 5.699670e-01 | 8.235880e-01 | ▇▆▅▃▃ |
| numeric | AF_reference | 25346 | 0.9920068 | NA | NA | NA | NA | NA | NA | NA | 4.131306e-01 | 1.962616e-01 | 0.0000000 | 2.545930e-01 | 3.871810e-01 | 5.571090e-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 | -0.0000738 | 0.0002410 | 0.7600007 | 0.7594928 | 0.623765 | 0.7821490 | NA |
| 1 | 54676 | rs2462492 | C | T | -0.0003632 | 0.0002388 | 0.1299999 | 0.1282986 | 0.400401 | NA | NA |
| 1 | 91536 | rs6702460 | G | T | -0.0007130 | 0.0002351 | 0.0024000 | 0.0024281 | 0.456846 | 0.4207270 | NA |
| 1 | 534192 | rs6680723 | C | T | -0.0003149 | 0.0002686 | 0.2399999 | 0.2410052 | 0.240959 | NA | NA |
| 1 | 706368 | rs55727773 | A | G | -0.0000794 | 0.0001667 | 0.6300007 | 0.6337895 | 0.515645 | 0.2751600 | NA |
| 1 | 763394 | rs369924889 | G | A | -0.0000360 | 0.0001955 | 0.8499999 | 0.8540366 | 0.706753 | 0.6176120 | NA |
| 1 | 768253 | rs2977608 | A | C | -0.0003043 | 0.0001595 | 0.0560003 | 0.0564528 | 0.761297 | 0.4894170 | NA |
| 1 | 776546 | rs12124819 | A | G | -0.0001491 | 0.0001782 | 0.4000000 | 0.4027875 | 0.265385 | 0.0756789 | NA |
| 1 | 798400 | rs10900604 | A | G | 0.0003004 | 0.0001702 | 0.0779992 | 0.0775973 | 0.206591 | 0.4105430 | NA |
| 1 | 798959 | rs11240777 | G | A | 0.0003025 | 0.0001703 | 0.0759994 | 0.0756254 | 0.206420 | 0.4099440 | NA |
| CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 22 | 51180501 | rs5770999 | T | C | 0.0003466 | 0.0001569 | 0.0269998 | 0.0271944 | 0.713656 | 0.6369810 | NA |
| 22 | 51181919 | rs9616825 | G | C | 0.0003359 | 0.0001561 | 0.0309999 | 0.0314480 | 0.695470 | 0.6194090 | NA |
| 22 | 51182485 | rs6009961 | A | G | 0.0003604 | 0.0001574 | 0.0219999 | 0.0220398 | 0.715502 | 0.6383790 | NA |
| 22 | 51186143 | rs2879914 | T | C | 0.0001723 | 0.0001460 | 0.2399999 | 0.2377743 | 0.381825 | 0.2733630 | NA |
| 22 | 51186228 | rs3865766 | C | T | 0.0002674 | 0.0001423 | 0.0599998 | 0.0601252 | 0.451061 | 0.4532750 | NA |
| 22 | 51197266 | rs61290853 | A | G | 0.0002639 | 0.0001469 | 0.0719996 | 0.0724303 | 0.386333 | 0.4229230 | NA |
| 22 | 51198027 | rs34939255 | A | G | 0.0000919 | 0.0001663 | 0.5800000 | 0.5805148 | 0.254562 | 0.0984425 | NA |
| 22 | 51211106 | rs9628250 | T | C | 0.0000244 | 0.0001649 | 0.8800001 | 0.8821491 | 0.271547 | 0.1671330 | NA |
| 22 | 51212875 | rs2238837 | A | C | 0.0001989 | 0.0001566 | 0.2000000 | 0.2041150 | 0.331457 | 0.3724040 | NA |
| 22 | 51237063 | rs3896457 | T | C | 0.0001517 | 0.0001604 | 0.3400001 | 0.3441834 | 0.297974 | 0.2050720 | NA |
bcf preview
1 49298 rs10399793 T C . PASS AF=0.623765 ES:SE:LP:AF:ID -7.37967e-05:0.00024105:0.119186:0.623765:rs10399793
1 54676 rs2462492 C T . PASS AF=0.400401 ES:SE:LP:AF:ID -0.000363187:0.000238806:0.886057:0.400401:rs2462492
1 91536 rs6702460 G T . PASS AF=0.456846 ES:SE:LP:AF:ID -0.000712961:0.000235133:2.61979:0.456846:rs6702460
1 534192 rs6680723 C T . PASS AF=0.240959 ES:SE:LP:AF:ID -0.00031491:0.000268585:0.619789:0.240959:rs6680723
1 706368 rs12029736 A G . PASS AF=0.515645 ES:SE:LP:AF:ID -7.94311e-05:0.000166732:0.200659:0.515645:rs12029736
1 763394 rs3115847 G A . PASS AF=0.706753 ES:SE:LP:AF:ID -3.5962e-05:0.000195477:0.0705811:0.706753:rs3115847
1 768253 rs2977608 A C . PASS AF=0.761297 ES:SE:LP:AF:ID -0.000304334:0.000159544:1.25181:0.761297:rs2977608
1 776546 rs12124819 A G . PASS AF=0.265385 ES:SE:LP:AF:ID -0.000149105:0.000178216:0.39794:0.265385:rs12124819
1 798400 rs10900604 A G . PASS AF=0.206591 ES:SE:LP:AF:ID 0.000300369:0.0001702:1.10791:0.206591:rs10900604
1 798959 rs11240777 G A . PASS AF=0.20642 ES:SE:LP:AF:ID 0.000302516:0.000170273:1.11919:0.20642:rs11240777
1 808631 rs11240779 G A . PASS AF=0.772619 ES:SE:LP:AF:ID -0.000299933:0.000161977:1.19382:0.772619:rs11240779
1 808928 rs11240780 C T . PASS AF=0.772847 ES:SE:LP:AF:ID -0.000295368:0.00016225:1.16115:0.772847:rs11240780
1 814495 rs74461805 C A . PASS AF=0.340396 ES:SE:LP:AF:ID 1.86981e-05:0.000228618:0.0315171:0.340396:rs74461805
1 830181 rs28444699 A G . PASS AF=0.697255 ES:SE:LP:AF:ID 0.000280207:0.000152957:1.17393:0.697255:rs28444699
1 831489 rs4970385 C T . PASS AF=0.705397 ES:SE:LP:AF:ID 0.000153865:0.000150189:0.508638:0.705397:rs4970385
1 831909 rs9697642 C T . PASS AF=0.705442 ES:SE:LP:AF:ID 0.000158483:0.000150184:0.537602:0.705442:rs9697642
1 832066 rs9697380 G C . PASS AF=0.705627 ES:SE:LP:AF:ID 0.00015605:0.000150191:0.522879:0.705627:rs9697380
1 832318 rs4500250 C A . PASS AF=0.705655 ES:SE:LP:AF:ID 0.000155278:0.000150207:0.522879:0.705655:rs4500250
1 832398 rs4553118 T C . PASS AF=0.730129 ES:SE:LP:AF:ID 0.000245901:0.0001543:0.958607:0.730129:rs4553118
1 832918 rs28765502 T C . PASS AF=0.294377 ES:SE:LP:AF:ID -0.000156861:0.0001502:0.522879:0.294377:rs28765502
1 833223 rs13303211 C T . PASS AF=0.236703 ES:SE:LP:AF:ID -4.3112e-05:0.000159911:0.102373:0.236703:rs13303211
1 833302 rs28752186 C T . PASS AF=0.236691 ES:SE:LP:AF:ID -4.28108e-05:0.000159913:0.102373:0.236691:rs28752186
1 833641 rs28594623 T C . PASS AF=0.23975 ES:SE:LP:AF:ID -2.89472e-05:0.0001594:0.0655015:0.23975:rs28594623
1 833824 rs28484835 T C . PASS AF=0.236693 ES:SE:LP:AF:ID -4.2811e-05:0.000159911:0.102373:0.236693:rs28484835
1 833927 rs28593608 T C . PASS AF=0.212421 ES:SE:LP:AF:ID -0.000148074:0.000166206:0.431798:0.212421:rs28593608
1 834198 rs28385272 T C . PASS AF=0.212316 ES:SE:LP:AF:ID -0.000145233:0.000166235:0.420216:0.212316:rs28385272
1 834832 rs4411087 G C . PASS AF=0.237178 ES:SE:LP:AF:ID -4.34672e-05:0.000159789:0.102373:0.237178:rs4411087
1 834928 rs4422949 A G . PASS AF=0.212962 ES:SE:LP:AF:ID -0.000144589:0.000165999:0.420216:0.212962:rs4422949
1 834999 rs28570054 G A . PASS AF=0.212924 ES:SE:LP:AF:ID -0.000141611:0.000166033:0.408935:0.212924:rs28570054
1 835499 rs4422948 A G . PASS AF=0.241162 ES:SE:LP:AF:ID -1.56457e-05:0.000158674:0.0362122:0.241162:rs4422948
1 836529 rs28731045 C G . PASS AF=0.213543 ES:SE:LP:AF:ID -0.000139669:0.000165788:0.39794:0.213543:rs28731045
1 836896 rs28705752 T C . PASS AF=0.269511 ES:SE:LP:AF:ID -1.42632e-05:0.000153108:0.0315171:0.269511:rs28705752
1 836924 rs72890788 G A . PASS AF=0.213513 ES:SE:LP:AF:ID -0.000147732:0.000165808:0.431798:0.213513:rs72890788
1 838387 rs4970384 T C . PASS AF=0.214587 ES:SE:LP:AF:ID -0.000133626:0.000165489:0.376751:0.214587:rs4970384
1 838555 rs4970383 C A . PASS AF=0.246204 ES:SE:LP:AF:ID -0.000103287:0.000157582:0.29243:0.246204:rs4970383
1 839103 rs28562941 A G . PASS AF=0.270019 ES:SE:LP:AF:ID -2.09263e-05:0.000153216:0.05061:0.270019:rs28562941
1 840753 rs4970382 T C . PASS AF=0.400124 ES:SE:LP:AF:ID -6.84176e-05:0.000138537:0.207608:0.400124:rs4970382
1 841085 rs1574243 C G . PASS AF=0.237102 ES:SE:LP:AF:ID -8.84292e-05:0.000160916:0.236572:0.237102:rs1574243
1 842013 rs7419119 T G . PASS AF=0.215391 ES:SE:LP:AF:ID -9.58815e-05:0.0001656:0.251812:0.215391:rs7419119
1 842362 rs28540380 C T . PASS AF=0.235323 ES:SE:LP:AF:ID -5.87321e-05:0.000163326:0.142668:0.235323:rs28540380
1 843405 rs11516185 A G . PASS AF=0.362606 ES:SE:LP:AF:ID 0.000192392:0.000171974:0.585027:0.362606:rs11516185
1 844300 rs61769713 C G . PASS AF=0.818811 ES:SE:LP:AF:ID 2.66487e-05:0.000176746:0.0555173:0.818811:rs61769713
1 845283 rs7366404 G T . PASS AF=0.814497 ES:SE:LP:AF:ID 6.46511e-05:0.000175189:0.148742:0.814497:rs7366404
1 845635 rs117086422 C T . PASS AF=0.205429 ES:SE:LP:AF:ID -5.24808e-05:0.000168416:0.119186:0.205429:rs117086422
1 845938 rs57760052 G A . PASS AF=0.210864 ES:SE:LP:AF:ID -3.65805e-05:0.000166796:0.0809219:0.210864:rs57760052
1 846078 rs28612348 C T . PASS AF=0.196785 ES:SE:LP:AF:ID -8.38897e-05:0.000170997:0.207608:0.196785:rs28612348
1 846338 rs4970334 A G . PASS AF=0.813828 ES:SE:LP:AF:ID 7.88052e-05:0.00017504:0.187087:0.813828:rs4970334
1 846398 rs58781670 G A . PASS AF=0.204447 ES:SE:LP:AF:ID -9.16633e-05:0.000168991:0.229148:0.204447:rs58781670
1 846489 rs4970333 T C . PASS AF=0.81392 ES:SE:LP:AF:ID 7.71087e-05:0.000175161:0.180456:0.81392:rs4970333
1 846808 rs4475691 C T . PASS AF=0.198378 ES:SE:LP:AF:ID -8.90863e-05:0.000170511:0.221849:0.198378:rs4475691