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:18578,TotalVariants=9851866,VariantsNotRead=0,HarmonisedVariants=9851866,VariantsNotHarmonised=0,SwitchedAlleles=9851866,TotalControls=459771,TotalCases=3162,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_1078.vcf.gz --id UKB-b:18578 --data /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/ukbiobank/raw-output/data.batch_20002_1078.txt.gz --cohort_cases 3162 --cohort_controls 459771 --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": "2019-09-13T07:59:31.550725",
"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-18578/mac_discard.txt -Oz /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-18578/UKB-b-18578_raw.vcf.gz; Date=Thu Oct 17 12:36:36 2019",
"bcftools_viewCommand.1": "view -h /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/ukb-b-18578/ukb-b-18578.vcf.gz; Date=Sat May 9 16:03:14 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-18578/UKB-b-18578_data.vcf.gz \
--ref-ld-chr ../reference/eur_w_ld_chr/ \
--out /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-18578/ldsc.txt \
--w-ld-chr ../reference/eur_w_ld_chr/
Beginning analysis at Thu Oct 17 14:40:19 2019
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-18578/UKB-b-18578_data.vcf.gz ...
Read summary statistics for 4122395 SNPs.
Dropped 808 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, 975269 SNPs remain.
After merging with regression SNP LD, 975269 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.002 (0.001)
Lambda GC: 1.0186
Mean Chi^2: 1.0155
Intercept: 0.9951 (0.0083)
Ratio < 0 (usually indicates GC correction).
Analysis finished at Thu Oct 17 14:41:10 2019
Total time elapsed: 51.27sQC metrics
Metrics
Metrics
{
"af_correlation": 0.8801,
"inflation_factor": 1,
"mean_EFFECT": 8.0603e-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": 33713,
"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": 975269,
"ldsc_nsnp_merge_regression_ld": 975269,
"ldsc_observed_scale_h2_beta": 0.002,
"ldsc_observed_scale_h2_se": 0.001,
"ldsc_intercept_beta": 0.9951,
"ldsc_intercept_se": 0.0083,
"ldsc_lambda_gc": 1.0186,
"ldsc_mean_chisq": 1.0155,
"ldsc_ratio": -0.3161
}
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 | 1.000000 | 3 | 58 | 0 | 4121592 | 0 | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| character | REF | 0 | 1.000000 | 1 | 1 | 0 | 4 | 0 | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| character | ALT | 0 | 1.000000 | 1 | 1 | 0 | 4 | 0 | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| logical | N | 4122395 | 0.000000 | NA | NA | NA | NA | NA | NaN | : | NA | NA | NA | NA | NA | NA | NA | NA |
| numeric | CHROM | 0 | 1.000000 | NA | NA | NA | NA | NA | NA | NA | 8.656609e+00 | 5.766384e+00 | 1.0000000 | 4.000000e+00 | 8.000000e+00 | 1.300000e+01 | 2.200000e+01 | ▇▅▃▂▂ |
| numeric | POS | 0 | 1.000000 | NA | NA | NA | NA | NA | NA | NA | 7.858184e+07 | 5.674267e+07 | 828.0000000 | 3.165277e+07 | 6.893115e+07 | 1.146880e+08 | 2.492385e+08 | ▇▆▅▂▁ |
| numeric | EFFECT | 0 | 1.000000 | NA | NA | NA | NA | NA | NA | NA | 8.000000e-07 | 2.061000e-04 | -0.0011710 | -1.346000e-04 | 5.000000e-07 | 1.367000e-04 | 1.222700e-03 | ▁▂▇▁▁ |
| numeric | SE | 0 | 1.000000 | NA | NA | NA | NA | NA | NA | NA | 2.025000e-04 | 2.960000e-05 | 0.0001652 | 1.768000e-04 | 1.927000e-04 | 2.227000e-04 | 6.042000e-04 | ▇▁▁▁▁ |
| numeric | PVAL | 0 | 1.000000 | NA | NA | NA | NA | NA | NA | NA | 4.976678e-01 | 2.894296e-01 | 0.0000012 | 2.500000e-01 | 5.000000e-01 | 7.499995e-01 | 1.000000e+00 | ▇▇▇▇▇ |
| numeric | PVAL_ztest | 0 | 1.000000 | NA | NA | NA | NA | NA | NA | NA | 4.976676e-01 | 2.894022e-01 | 0.0000012 | 2.468326e-01 | 4.962220e-01 | 7.485488e-01 | 9.999999e-01 | ▇▇▇▇▇ |
| numeric | AF | 0 | 1.000000 | NA | NA | NA | NA | NA | NA | NA | 3.891010e-01 | 2.165957e-01 | 0.1106900 | 2.005400e-01 | 3.391910e-01 | 5.485040e-01 | 8.893100e-01 | ▇▅▃▂▂ |
| numeric | AF_reference | 33713 | 0.991822 | NA | NA | NA | NA | NA | NA | NA | 3.786775e-01 | 2.195019e-01 | 0.0000000 | 1.980830e-01 | 3.362620e-01 | 5.365420e-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 | -0.0001876 | 0.0003040 | 0.5400003 | 0.5371259 | 0.623763 | 0.782149 | NA |
| 1 | 54676 | rs2462492 | C | T | 0.0000034 | 0.0003012 | 0.9900000 | 0.9909666 | 0.400401 | NA | NA |
| 1 | 91536 | rs6702460 | G | T | -0.0001331 | 0.0002965 | 0.6499995 | 0.6534382 | 0.456851 | 0.420727 | NA |
| 1 | 534192 | rs6680723 | C | T | -0.0005016 | 0.0003387 | 0.1400000 | 0.1386405 | 0.240960 | NA | NA |
| 1 | 693731 | rs12238997 | A | G | 0.0000528 | 0.0002839 | 0.8499999 | 0.8524243 | 0.116325 | 0.141773 | NA |
| 1 | 706368 | rs55727773 | A | G | -0.0001665 | 0.0002103 | 0.4299995 | 0.4283944 | 0.515650 | 0.275160 | NA |
| 1 | 729679 | rs4951859 | C | G | -0.0001110 | 0.0002460 | 0.6499995 | 0.6518225 | 0.843212 | 0.639976 | NA |
| 1 | 731718 | rs142557973 | T | C | 0.0000767 | 0.0002693 | 0.7800007 | 0.7757750 | 0.122307 | 0.154353 | NA |
| 1 | 734349 | rs141242758 | T | C | 0.0000749 | 0.0002694 | 0.7800007 | 0.7808965 | 0.121549 | 0.152556 | NA |
| 1 | 736289 | rs79010578 | T | A | 0.0000694 | 0.0002655 | 0.7899998 | 0.7937765 | 0.132330 | 0.139577 | NA |
| CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 22 | 51198027 | rs34939255 | A | G | 0.0000083 | 0.0002097 | 0.9699999 | 0.9685546 | 0.254557 | 0.0984425 | NA |
| 22 | 51208537 | rs72619593 | G | A | 0.0000837 | 0.0002803 | 0.7700005 | 0.7651127 | 0.120739 | 0.1142170 | NA |
| 22 | 51210289 | rs112565862 | C | T | -0.0000747 | 0.0002792 | 0.7899998 | 0.7889110 | 0.129955 | 0.1018370 | NA |
| 22 | 51211106 | rs9628250 | T | C | 0.0000714 | 0.0002079 | 0.7300002 | 0.7313191 | 0.271547 | 0.1671330 | NA |
| 22 | 51211392 | rs3888396 | T | C | -0.0000922 | 0.0002767 | 0.7400005 | 0.7388504 | 0.132635 | 0.1641370 | NA |
| 22 | 51212875 | rs2238837 | A | C | 0.0001436 | 0.0001976 | 0.4700002 | 0.4673873 | 0.331455 | 0.3724040 | NA |
| 22 | 51213613 | rs34726907 | C | T | -0.0003669 | 0.0002603 | 0.1600000 | 0.1585717 | 0.127816 | 0.1727240 | NA |
| 22 | 51216564 | rs9616970 | T | C | -0.0003955 | 0.0002592 | 0.1299999 | 0.1269585 | 0.128330 | 0.1563500 | NA |
| 22 | 51219006 | rs28729663 | G | A | -0.0003715 | 0.0002537 | 0.1400000 | 0.1430630 | 0.137953 | 0.2052720 | NA |
| 22 | 51237063 | rs3896457 | T | C | -0.0000256 | 0.0002022 | 0.9000000 | 0.8993414 | 0.297971 | 0.2050720 | NA |
bcf preview
1 49298 rs10399793 T C . PASS AF=0.623763 ES:SE:LP:AF:ID -0.00018762:0.000304003:0.267606:0.623763:rs10399793
1 54676 rs2462492 C T . PASS AF=0.400401 ES:SE:LP:AF:ID 3.40983e-06:0.000301171:0.00436481:0.400401:rs2462492
1 91536 rs6702460 G T . PASS AF=0.456851 ES:SE:LP:AF:ID -0.000133146:0.000296545:0.187087:0.456851:rs6702460
1 534192 rs6680723 C T . PASS AF=0.24096 ES:SE:LP:AF:ID -0.000501613:0.000338728:0.853872:0.24096:rs6680723
1 693731 rs12238997 A G . PASS AF=0.116325 ES:SE:LP:AF:ID 5.28074e-05:0.000283871:0.0705811:0.116325:rs12238997
1 706368 rs12029736 A G . PASS AF=0.51565 ES:SE:LP:AF:ID -0.000166528:0.000210278:0.366532:0.51565:rs12029736
1 729679 rs4951859 C G . PASS AF=0.843212 ES:SE:LP:AF:ID -0.000111008:0.000246011:0.187087:0.843212:rs4951859
1 731718 rs58276399 T C . PASS AF=0.122307 ES:SE:LP:AF:ID 7.66988e-05:0.00026928:0.107905:0.122307:rs58276399
1 734349 rs141242758 T C . PASS AF=0.121549 ES:SE:LP:AF:ID 7.49319e-05:0.000269393:0.107905:0.121549:rs141242758
1 736289 rs79010578 T A . PASS AF=0.13233 ES:SE:LP:AF:ID 6.94077e-05:0.000265513:0.102373:0.13233:rs79010578
1 752566 rs3094315 G A . PASS AF=0.838951 ES:SE:LP:AF:ID -1.2623e-06:0.000238244:-0:0.838951:rs3094315
1 752721 rs3131972 A G . PASS AF=0.83858 ES:SE:LP:AF:ID 3.91964e-06:0.000237987:0.00436481:0.83858:rs3131972
1 753405 rs3115860 C A . PASS AF=0.869781 ES:SE:LP:AF:ID 2.75074e-05:0.00025537:0.0409586:0.869781:rs3115860
1 753541 rs2073813 G A . PASS AF=0.129871 ES:SE:LP:AF:ID -3.56229e-05:0.000255893:0.05061:0.129871:rs2073813
1 754182 rs3131969 A G . PASS AF=0.869123 ES:SE:LP:AF:ID 2.80868e-05:0.00025487:0.0409586:0.869123:rs3131969
1 754192 rs3131968 A G . PASS AF=0.869221 ES:SE:LP:AF:ID 2.26343e-05:0.000254971:0.0315171:0.869221:rs3131968
1 754334 rs3131967 T C . PASS AF=0.869126 ES:SE:LP:AF:ID 3.29936e-05:0.000254865:0.0457575:0.869126:rs3131967
1 754503 rs3115859 G A . PASS AF=0.838033 ES:SE:LP:AF:ID 2.00125e-05:0.000237327:0.0315171:0.838033:rs3115859
1 754964 rs3131966 C T . PASS AF=0.838664 ES:SE:LP:AF:ID 2.74857e-05:0.000237994:0.0409586:0.838664:rs3131966
1 755775 rs3131965 A G . PASS AF=0.839777 ES:SE:LP:AF:ID 3.51258e-05:0.000241213:0.0555173:0.839777:rs3131965
1 755890 rs3115858 A T . PASS AF=0.869405 ES:SE:LP:AF:ID 3.83508e-05:0.00025457:0.0555173:0.869405:rs3115858
1 756604 rs3131962 A G . PASS AF=0.868952 ES:SE:LP:AF:ID 4.39257e-05:0.00025393:0.0655015:0.868952:rs3131962
1 757640 rs3115853 G A . PASS AF=0.867905 ES:SE:LP:AF:ID 3.64582e-06:0.000253443:0.00436481:0.867905:rs3115853
1 757734 rs4951929 C T . PASS AF=0.869095 ES:SE:LP:AF:ID 4.43835e-05:0.000254137:0.0655015:0.869095:rs4951929
1 757936 rs4951862 C A . PASS AF=0.869104 ES:SE:LP:AF:ID 4.43257e-05:0.000254157:0.0655015:0.869104:rs4951862
1 758144 rs3131956 A G . PASS AF=0.869112 ES:SE:LP:AF:ID 4.41706e-05:0.000254163:0.0655015:0.869112:rs3131956
1 758626 rs3131954 C T . PASS AF=0.869589 ES:SE:LP:AF:ID 4.11019e-05:0.00025486:0.0604807:0.869589:rs3131954
1 760912 rs1048488 C T . PASS AF=0.838313 ES:SE:LP:AF:ID 3.79287e-06:0.000236876:0.00436481:0.838313:rs1048488
1 761147 rs3115850 T C . PASS AF=0.838434 ES:SE:LP:AF:ID 6.72373e-06:0.000237044:0.00877392:0.838434:rs3115850
1 761732 rs2286139 C T . PASS AF=0.862261 ES:SE:LP:AF:ID -2.76434e-05:0.000253244:0.0409586:0.862261:rs2286139
1 763394 rs3115847 G A . PASS AF=0.706753 ES:SE:LP:AF:ID -0.000281735:0.000246531:0.60206:0.706753:rs3115847
1 768253 rs2977608 A C . PASS AF=0.761304 ES:SE:LP:AF:ID 6.16664e-05:0.000201213:0.119186:0.761304:rs2977608
1 769223 rs60320384 C G . PASS AF=0.129576 ES:SE:LP:AF:ID -2.34699e-05:0.00025574:0.0315171:0.129576:rs60320384
1 771823 rs2977605 T C . PASS AF=0.868911 ES:SE:LP:AF:ID 1.9394e-05:0.000254374:0.0268721:0.868911:rs2977605
1 771967 rs59066358 G A . PASS AF=0.129677 ES:SE:LP:AF:ID -1.61319e-05:0.000255575:0.0222764:0.129677:rs59066358
1 772755 rs2905039 A C . PASS AF=0.868921 ES:SE:LP:AF:ID 1.85377e-05:0.000254379:0.0268721:0.868921:rs2905039
1 776546 rs12124819 A G . PASS AF=0.26539 ES:SE:LP:AF:ID -0.000139104:0.000224758:0.267606:0.26539:rs12124819
1 777122 rs2980319 A T . PASS AF=0.870044 ES:SE:LP:AF:ID 2.33917e-05:0.000254898:0.0315171:0.870044:rs2980319
1 778745 rs1055606 A G . PASS AF=0.128576 ES:SE:LP:AF:ID -5.14063e-06:0.000255904:0.00877392:0.128576:rs1055606
1 779322 rs4040617 A G . PASS AF=0.128873 ES:SE:LP:AF:ID -9.00758e-06:0.00025547:0.0132283:0.128873:rs4040617
1 780785 rs2977612 T A . PASS AF=0.868786 ES:SE:LP:AF:ID -2.11446e-07:0.000254218:-0:0.868786:rs2977612
1 782981 rs6594026 C T . PASS AF=0.129513 ES:SE:LP:AF:ID -1.55086e-05:0.000255388:0.0222764:0.129513:rs6594026
1 785050 rs2905062 G A . PASS AF=0.868539 ES:SE:LP:AF:ID -2.94542e-05:0.000254159:0.0409586:0.868539:rs2905062
1 785989 rs2980300 T C . PASS AF=0.86848 ES:SE:LP:AF:ID -3.37007e-05:0.000254317:0.05061:0.86848:rs2980300
1 787399 rs2905055 G T . PASS AF=0.86078 ES:SE:LP:AF:ID -2.42735e-05:0.000254143:0.0362122:0.86078:rs2905055
1 787606 rs3863622 G T . PASS AF=0.128461 ES:SE:LP:AF:ID -3.27309e-05:0.000256764:0.0457575:0.128461:rs3863622
1 787685 rs2905054 G T . PASS AF=0.861493 ES:SE:LP:AF:ID 4.06693e-06:0.000254311:0.00436481:0.861493:rs2905054
1 787844 rs2905053 C T . PASS AF=0.869229 ES:SE:LP:AF:ID -1.5181e-05:0.000255247:0.0222764:0.869229:rs2905053
1 791191 rs111818025 G A . PASS AF=0.127879 ES:SE:LP:AF:ID -3.80754e-05:0.000258409:0.0555173:0.127879:rs111818025
1 795988 rs59380221 C T . PASS AF=0.143051 ES:SE:LP:AF:ID -0.000133368:0.000263602:0.21467:0.143051:rs59380221