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:13480,TotalVariants=9851866,VariantsNotRead=0,HarmonisedVariants=9851866,VariantsNotHarmonised=0,SwitchedAlleles=9851866,TotalControls=461196,TotalCases=1737,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_20003_1199.vcf.gz --id UKB-b:13480 --data /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/ukbiobank/raw-output/data.batch_20003_1199.txt.gz --cohort_cases 1737 --cohort_controls 461196 --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": "2019-09-13T01:10:58.369873",
"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-13480/mac_discard.txt -Oz /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-13480/UKB-b-13480_raw.vcf.gz; Date=Thu Oct 17 12:29:00 2019",
"bcftools_viewCommand.1": "view -h /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/ukb-b-13480/ukb-b-13480.vcf.gz; Date=Thu May 7 10:09:59 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-13480/UKB-b-13480_data.vcf.gz \
--ref-ld-chr ../reference/eur_w_ld_chr/ \
--out /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-13480/ldsc.txt \
--w-ld-chr ../reference/eur_w_ld_chr/
Beginning analysis at Thu Oct 17 14:42:46 2019
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-13480/UKB-b-13480_data.vcf.gz ...
Read summary statistics for 2863320 SNPs.
Dropped 362 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, 716373 SNPs remain.
After merging with regression SNP LD, 716373 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.0014 (0.0012)
Lambda GC: 1.0469
Mean Chi^2: 1.0314
Intercept: 1.0161 (0.0095)
Ratio: 0.5115 (0.3032)
Analysis finished at Thu Oct 17 14:43:26 2019
Total time elapsed: 40.38sQC metrics
Metrics
Metrics
{
"af_correlation": 0.8054,
"inflation_factor": 1.0475,
"mean_EFFECT": -1.2947e-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": 22763,
"n_est": "NA",
"ratio_se_n": "NA",
"mean_diff": "NaN",
"ratio_diff": "NaN",
"sd_y_est1": "NA",
"sd_y_est2": "NA",
"r2_sum1": 0,
"r2_sum2": 0,
"r2_sum3": 0,
"r2_sum4": 0,
"ldsc_nsnp_merge_refpanel_ld": 716373,
"ldsc_nsnp_merge_regression_ld": 716373,
"ldsc_observed_scale_h2_beta": 0.0014,
"ldsc_observed_scale_h2_se": 0.0012,
"ldsc_intercept_beta": 1.0161,
"ldsc_intercept_se": 0.0095,
"ldsc_lambda_gc": 1.0469,
"ldsc_mean_chisq": 1.0314,
"ldsc_ratio": 0.5127
}
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 | 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 | 3 | 58 | 0 | 2862961 | 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 | 2863320 | 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 | 8.658598e+00 | 5.770620e+00 | 1.0000000 | 4.000000e+00 | 8.000000e+00 | 1.300000e+01 | 2.200000e+01 | <U+2587><U+2585><U+2583><U+2582><U+2582> |
| numeric | POS | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 7.856859e+07 | 5.666570e+07 | 828.0000000 | 3.168889e+07 | 6.899041e+07 | 1.147466e+08 | 2.492013e+08 | <U+2587><U+2586><U+2585><U+2582><U+2581> |
| numeric | EFFECT | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | -1.000000e-07 | 1.400000e-04 | -0.0008531 | -9.470000e-05 | -2.000000e-07 | 9.420000e-05 | 8.077000e-04 | <U+2581><U+2581><U+2587><U+2582><U+2581> |
| numeric | SE | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 1.376000e-04 | 9.600000e-06 | 0.0001226 | 1.293000e-04 | 1.348000e-04 | 1.444000e-04 | 2.846000e-04 | <U+2587><U+2581><U+2581><U+2581><U+2581> |
| numeric | PVAL | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 4.949063e-01 | 2.902655e-01 | 0.0000001 | 2.399999e-01 | 4.899999e-01 | 7.499995e-01 | 1.000000e+00 | <U+2587><U+2587><U+2587><U+2587><U+2587> |
| numeric | PVAL_ztest | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 4.949046e-01 | 2.902379e-01 | 0.0000001 | 2.428674e-01 | 4.912148e-01 | 7.470484e-01 | 9.999996e-01 | <U+2587><U+2587><U+2587><U+2587><U+2587> |
| numeric | AF | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 4.401244e-01 | 1.689699e-01 | 0.2014970 | 2.917060e-01 | 4.115655e-01 | 5.734350e-01 | 7.985030e-01 | <U+2587><U+2586><U+2585><U+2583><U+2583> |
| numeric | AF_reference | 22763 | 0.9920501 | NA | NA | NA | NA | NA | NA | NA | 4.233951e-01 | 1.874770e-01 | 0.0001997 | 2.733630e-01 | 4.025560e-01 | 5.611020e-01 | 1.000000e+00 | <U+2582><U+2587><U+2586><U+2583><U+2581> |
Head and tail
| CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 | 49298 | rs200943160 | T | C | 0.0004883 | 0.0002256 | 0.0299999 | 0.0304534 | 0.623763 | 0.7821490 | NA |
| 1 | 54676 | rs2462492 | C | T | -0.0001175 | 0.0002235 | 0.5999997 | 0.5991917 | 0.400401 | NA | NA |
| 1 | 91536 | rs6702460 | G | T | -0.0000760 | 0.0002201 | 0.7300002 | 0.7300161 | 0.456851 | 0.4207270 | NA |
| 1 | 534192 | rs6680723 | C | T | -0.0002591 | 0.0002514 | 0.2999998 | 0.3026291 | 0.240960 | NA | NA |
| 1 | 706368 | rs55727773 | A | G | 0.0000233 | 0.0001561 | 0.8800001 | 0.8814378 | 0.515650 | 0.2751600 | NA |
| 1 | 763394 | rs369924889 | G | A | -0.0001760 | 0.0001830 | 0.3400001 | 0.3360526 | 0.706753 | 0.6176120 | NA |
| 1 | 768253 | rs2977608 | A | C | 0.0000968 | 0.0001493 | 0.5199996 | 0.5167545 | 0.761304 | 0.4894170 | NA |
| 1 | 776546 | rs12124819 | A | G | -0.0000156 | 0.0001668 | 0.9299999 | 0.9254845 | 0.265390 | 0.0756789 | NA |
| 1 | 798400 | rs10900604 | A | G | -0.0000750 | 0.0001593 | 0.6400000 | 0.6376693 | 0.206580 | 0.4105430 | NA |
| 1 | 798959 | rs11240777 | G | A | -0.0000665 | 0.0001594 | 0.6800001 | 0.6766041 | 0.206409 | 0.4099440 | NA |
| CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 22 | 51180501 | rs5770999 | T | C | -0.0002593 | 0.0001469 | 0.0769999 | 0.0774825 | 0.713658 | 0.6369810 | NA |
| 22 | 51181919 | rs9616825 | G | C | -0.0002501 | 0.0001461 | 0.0870001 | 0.0870118 | 0.695471 | 0.6194090 | NA |
| 22 | 51182485 | rs6009961 | A | G | -0.0002817 | 0.0001473 | 0.0560003 | 0.0559065 | 0.715505 | 0.6383790 | NA |
| 22 | 51186143 | rs2879914 | T | C | -0.0000025 | 0.0001366 | 0.9900000 | 0.9852837 | 0.381826 | 0.2733630 | NA |
| 22 | 51186228 | rs3865766 | C | T | -0.0000372 | 0.0001332 | 0.7800007 | 0.7798748 | 0.451063 | 0.4532750 | NA |
| 22 | 51197266 | rs61290853 | A | G | -0.0000914 | 0.0001375 | 0.5099998 | 0.5060977 | 0.386333 | 0.4229230 | NA |
| 22 | 51198027 | rs34939255 | A | G | -0.0002631 | 0.0001556 | 0.0909997 | 0.0908911 | 0.254557 | 0.0984425 | NA |
| 22 | 51211106 | rs9628250 | T | C | -0.0002419 | 0.0001543 | 0.1199999 | 0.1169528 | 0.271547 | 0.1671330 | NA |
| 22 | 51212875 | rs2238837 | A | C | -0.0000363 | 0.0001466 | 0.8000000 | 0.8044263 | 0.331455 | 0.3724040 | NA |
| 22 | 51237063 | rs3896457 | T | C | -0.0002031 | 0.0001501 | 0.1800002 | 0.1759347 | 0.297971 | 0.2050720 | NA |
bcf preview
1 49298 rs10399793 T C . PASS AF=0.623763 ES:SE:LP:AF:ID 0.000488287:0.000225626:1.52288:0.623763:rs10399793
1 54676 rs2462492 C T . PASS AF=0.400401 ES:SE:LP:AF:ID -0.000117476:0.000223524:0.221849:0.400401:rs2462492
1 91536 rs6702460 G T . PASS AF=0.456851 ES:SE:LP:AF:ID -7.59543e-05:0.000220091:0.136677:0.456851:rs6702460
1 534192 rs6680723 C T . PASS AF=0.24096 ES:SE:LP:AF:ID -0.000259144:0.000251398:0.522879:0.24096:rs6680723
1 706368 rs12029736 A G . PASS AF=0.51565 ES:SE:LP:AF:ID 2.32766e-05:0.000156065:0.0555173:0.51565:rs12029736
1 763394 rs3115847 G A . PASS AF=0.706753 ES:SE:LP:AF:ID -0.000176017:0.000182971:0.468521:0.706753:rs3115847
1 768253 rs2977608 A C . PASS AF=0.761304 ES:SE:LP:AF:ID 9.68236e-05:0.000149337:0.283997:0.761304:rs2977608
1 776546 rs12124819 A G . PASS AF=0.26539 ES:SE:LP:AF:ID -1.56015e-05:0.000166812:0.0315171:0.26539:rs12124819
1 798400 rs10900604 A G . PASS AF=0.20658 ES:SE:LP:AF:ID -7.5031e-05:0.000159315:0.19382:0.20658:rs10900604
1 798959 rs11240777 G A . PASS AF=0.206409 ES:SE:LP:AF:ID -6.64789e-05:0.000159383:0.167491:0.206409:rs11240777
1 808631 rs11240779 G A . PASS AF=0.772626 ES:SE:LP:AF:ID 0.000133677:0.000151616:0.420216:0.772626:rs11240779
1 808928 rs11240780 C T . PASS AF=0.772854 ES:SE:LP:AF:ID 0.000135695:0.000151871:0.431798:0.772854:rs11240780
1 814495 rs74461805 C A . PASS AF=0.340397 ES:SE:LP:AF:ID -2.39815e-05:0.000213995:0.0409586:0.340397:rs74461805
1 830181 rs28444699 A G . PASS AF=0.697259 ES:SE:LP:AF:ID -0.000171779:0.000143169:0.638272:0.697259:rs28444699
1 831489 rs4970385 C T . PASS AF=0.705403 ES:SE:LP:AF:ID -0.000147779:0.000140579:0.537602:0.705403:rs4970385
1 831909 rs9697642 C T . PASS AF=0.705448 ES:SE:LP:AF:ID -0.000148786:0.000140574:0.537602:0.705448:rs9697642
1 832066 rs9697380 G C . PASS AF=0.705634 ES:SE:LP:AF:ID -0.000151447:0.000140581:0.552842:0.705634:rs9697380
1 832318 rs4500250 C A . PASS AF=0.705662 ES:SE:LP:AF:ID -0.00015025:0.000140596:0.537602:0.705662:rs4500250
1 832398 rs4553118 T C . PASS AF=0.730134 ES:SE:LP:AF:ID -0.000184008:0.000144427:0.69897:0.730134:rs4553118
1 832918 rs28765502 T C . PASS AF=0.294371 ES:SE:LP:AF:ID 0.000149098:0.000140589:0.537602:0.294371:rs28765502
1 833223 rs13303211 C T . PASS AF=0.236696 ES:SE:LP:AF:ID 0.000147097:0.00014968:0.481486:0.236696:rs13303211
1 833302 rs28752186 C T . PASS AF=0.236684 ES:SE:LP:AF:ID 0.000147189:0.000149681:0.481486:0.236684:rs28752186
1 833641 rs28594623 T C . PASS AF=0.239743 ES:SE:LP:AF:ID 0.000158328:0.000149201:0.537602:0.239743:rs28594623
1 833824 rs28484835 T C . PASS AF=0.236686 ES:SE:LP:AF:ID 0.000141091:0.00014968:0.455932:0.236686:rs28484835
1 833927 rs28593608 T C . PASS AF=0.212416 ES:SE:LP:AF:ID 0.000182763:0.000155572:0.619789:0.212416:rs28593608
1 834198 rs28385272 T C . PASS AF=0.212311 ES:SE:LP:AF:ID 0.000178787:0.000155599:0.60206:0.212311:rs28385272
1 834832 rs4411087 G C . PASS AF=0.237171 ES:SE:LP:AF:ID 0.000139851:0.000149565:0.455932:0.237171:rs4411087
1 834928 rs4422949 A G . PASS AF=0.212956 ES:SE:LP:AF:ID 0.000172525:0.000155378:0.568636:0.212956:rs4422949
1 834999 rs28570054 G A . PASS AF=0.212918 ES:SE:LP:AF:ID 0.000174629:0.00015541:0.585027:0.212918:rs28570054
1 835499 rs4422948 A G . PASS AF=0.241155 ES:SE:LP:AF:ID 8.82002e-05:0.000148521:0.259637:0.241155:rs4422948
1 836529 rs28731045 C G . PASS AF=0.213538 ES:SE:LP:AF:ID 0.000175939:0.000155181:0.585027:0.213538:rs28731045
1 836896 rs28705752 T C . PASS AF=0.269503 ES:SE:LP:AF:ID 9.31366e-06:0.000143312:0.0222764:0.269503:rs28705752
1 836924 rs72890788 G A . PASS AF=0.213508 ES:SE:LP:AF:ID 0.000176138:0.000155199:0.585027:0.213508:rs72890788
1 838387 rs4970384 T C . PASS AF=0.214583 ES:SE:LP:AF:ID 0.000190801:0.0001549:0.657577:0.214583:rs4970384
1 838555 rs4970383 C A . PASS AF=0.246197 ES:SE:LP:AF:ID 4.31219e-05:0.0001475:0.113509:0.246197:rs4970383
1 839103 rs28562941 A G . PASS AF=0.27001 ES:SE:LP:AF:ID 1.07775e-05:0.000143413:0.0268721:0.27001:rs28562941
1 840753 rs4970382 T C . PASS AF=0.400106 ES:SE:LP:AF:ID 2.23111e-06:0.000129673:0.00436481:0.400106:rs4970382
1 841085 rs1574243 C G . PASS AF=0.237094 ES:SE:LP:AF:ID 0.000113436:0.000150621:0.346787:0.237094:rs1574243
1 842013 rs7419119 T G . PASS AF=0.215384 ES:SE:LP:AF:ID 0.000152914:0.000155004:0.49485:0.215384:rs7419119
1 842362 rs28540380 C T . PASS AF=0.235321 ES:SE:LP:AF:ID 0.000135793:0.000152874:0.431798:0.235321:rs28540380
1 843405 rs11516185 A G . PASS AF=0.362599 ES:SE:LP:AF:ID 9.6436e-05:0.000160975:0.259637:0.362599:rs11516185
1 845635 rs117086422 C T . PASS AF=0.20543 ES:SE:LP:AF:ID 0.00010309:0.00015764:0.29243:0.20543:rs117086422
1 845938 rs57760052 G A . PASS AF=0.210865 ES:SE:LP:AF:ID 8.89048e-05:0.000156123:0.244125:0.210865:rs57760052
1 846398 rs58781670 G A . PASS AF=0.204448 ES:SE:LP:AF:ID 7.78346e-05:0.000158179:0.207608:0.204448:rs58781670
1 847228 rs3905286 C T . PASS AF=0.203588 ES:SE:LP:AF:ID 0.000143229:0.000158318:0.431798:0.203588:rs3905286
1 847491 rs28407778 G A . PASS AF=0.2142 ES:SE:LP:AF:ID 0.000133276:0.000155081:0.408935:0.2142:rs28407778
1 848090 rs4246505 G A . PASS AF=0.212516 ES:SE:LP:AF:ID 0.00014061:0.000155489:0.431798:0.212516:rs4246505
1 848445 rs4626817 G A . PASS AF=0.209298 ES:SE:LP:AF:ID 0.000152739:0.000157021:0.481486:0.209298:rs4626817
1 848456 rs11507767 A G . PASS AF=0.209247 ES:SE:LP:AF:ID 0.000153232:0.00015705:0.481486:0.209247:rs11507767
1 848738 rs3829741 C T . PASS AF=0.21234 ES:SE:LP:AF:ID 0.000138928:0.000155629:0.431798:0.21234:rs3829741