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:645,TotalVariants=9851866,VariantsNotRead=0,HarmonisedVariants=9851866,VariantsNotHarmonised=0,SwitchedAlleles=9851866,TotalControls=83410,StudyType=Continuous>",
"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_5134.vcf.gz --id UKB-b:645 --data /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/ukbiobank/raw-output/data.batch_5134.txt.gz --cohort_controls 83410 --ref /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/ukbiobank/human_g1k_v37.fasta --json /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/ukbiobank/ukb_gwas.json; 1.1.1",
"file_date": "2019-09-12T23:15:40.365957",
"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-645/mac_discard.txt -Oz /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-645/UKB-b-645_raw.vcf.gz; Date=Thu Oct 17 12:17:55 2019",
"bcftools_viewCommand.1": "view -h /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/ukb-b-645/ukb-b-645.vcf.gz; Date=Sun May 10 08:14:54 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-645/UKB-b-645_data.vcf.gz \
--ref-ld-chr ../reference/eur_w_ld_chr/ \
--out /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-645/ldsc.txt \
--w-ld-chr ../reference/eur_w_ld_chr/
Beginning analysis at Thu Oct 17 14:40:18 2019
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-645/UKB-b-645_data.vcf.gz ...
Read summary statistics for 8878036 SNPs.
Dropped 8206 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, 1286800 SNPs remain.
After merging with regression SNP LD, 1286800 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.3848 (0.0217)
Lambda GC: 1.3912
Mean Chi^2: 1.7078
Intercept: 1.0957 (0.013)
Ratio: 0.1352 (0.0184)
Analysis finished at Thu Oct 17 14:41:55 2019
Total time elapsed: 1.0m:37.59sQC metrics
Metrics
Metrics
{
"af_correlation": 0.9474,
"inflation_factor": 1.3107,
"mean_EFFECT": 0.0001,
"n": "-Inf",
"n_snps": 9851866,
"n_clumped_hits": 188,
"n_p_sig": 15994,
"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": 88966,
"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": 1286800,
"ldsc_nsnp_merge_regression_ld": 1286800,
"ldsc_observed_scale_h2_beta": 0.3848,
"ldsc_observed_scale_h2_se": 0.0217,
"ldsc_intercept_beta": 1.0957,
"ldsc_intercept_se": 0.013,
"ldsc_lambda_gc": 1.3912,
"ldsc_mean_chisq": 1.7078,
"ldsc_ratio": 0.1352
}
Flags
| name | value |
|---|---|
| af_correlation | FALSE |
| inflation_factor | TRUE |
| n | TRUE |
| is_snpid_non_unique | FALSE |
| mean_EFFECT_nonfinite | FALSE |
| mean_EFFECT_05 | FALSE |
| mean_EFFECT_01 | FALSE |
| mean_chisq | TRUE |
| n_p_sig | TRUE |
| 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 | 8869869 | 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 | 8878036 | 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 | 8.646674e+00 | 5.759678e+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 | 7.877942e+07 | 5.634531e+07 | 828.0000000 | 3.241435e+07 | 6.933640e+07 | 1.145509e+08 | 2.492385e+08 | ▇▆▅▂▁ |
| numeric | EFFECT | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 5.470000e-05 | 1.573850e-02 | -0.2299110 | -6.622400e-03 | 1.620000e-05 | 6.700800e-03 | 3.975250e-01 | ▁▇▁▁▁ |
| numeric | SE | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 1.174510e-02 | 8.383400e-03 | 0.0043937 | 5.229300e-03 | 7.901400e-03 | 1.605200e-02 | 1.005480e-01 | ▇▁▁▁▁ |
| numeric | PVAL | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 4.579865e-01 | 3.014661e-01 | 0.0000000 | 1.900002e-01 | 4.400003e-01 | 7.199992e-01 | 1.000000e+00 | ▇▆▆▅▆ |
| numeric | PVAL_ztest | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 4.579883e-01 | 3.014392e-01 | 0.0000000 | 1.861001e-01 | 4.444686e-01 | 7.194076e-01 | 9.999999e-01 | ▇▆▆▆▆ |
| numeric | AF | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 2.231463e-01 | 2.588611e-01 | 0.0041970 | 2.201400e-02 | 1.057010e-01 | 3.522500e-01 | 9.958030e-01 | ▇▂▁▁▁ |
| numeric | AF_reference | 88966 | 0.9899791 | NA | NA | NA | NA | NA | NA | NA | 2.232303e-01 | 2.508099e-01 | 0.0000000 | 1.936900e-02 | 1.228040e-01 | 3.502400e-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 | 0.0145245 | 0.0081058 | 0.0729995 | 0.0731528 | 0.623505 | 0.7821490 | NA |
| 1 | 54676 | rs2462492 | C | T | -0.0086351 | 0.0080476 | 0.2800000 | 0.2832702 | 0.399158 | NA | NA |
| 1 | 86028 | rs114608975 | T | C | -0.0183060 | 0.0127694 | 0.1499999 | 0.1516912 | 0.103979 | 0.0277556 | NA |
| 1 | 91536 | rs6702460 | G | T | 0.0102084 | 0.0079104 | 0.2000000 | 0.1968758 | 0.455954 | 0.4207270 | NA |
| 1 | 234313 | rs8179466 | C | T | 0.0156375 | 0.0155696 | 0.3200000 | 0.3152046 | 0.074560 | NA | NA |
| 1 | 534192 | rs6680723 | C | T | 0.0020839 | 0.0090605 | 0.8200001 | 0.8180933 | 0.240218 | NA | NA |
| 1 | 546697 | rs12025928 | A | G | -0.0189082 | 0.0112284 | 0.0920005 | 0.0921890 | 0.912844 | NA | NA |
| 1 | 693731 | rs12238997 | A | G | 0.0088642 | 0.0075391 | 0.2399999 | 0.2396869 | 0.117537 | 0.1417730 | NA |
| 1 | 705882 | rs72631875 | G | A | -0.0064774 | 0.0110530 | 0.5600000 | 0.5578565 | 0.067410 | 0.0315495 | NA |
| 1 | 706368 | rs55727773 | A | G | -0.0038713 | 0.0055903 | 0.4899999 | 0.4886230 | 0.515046 | 0.2751600 | NA |
| CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 22 | 51219006 | rs28729663 | G | A | -0.0043300 | 0.0067939 | 0.5199996 | 0.5239042 | 0.137482 | 0.2052720 | NA |
| 22 | 51219387 | rs9616832 | T | C | 0.0038802 | 0.0088470 | 0.6600001 | 0.6609607 | 0.072750 | 0.0654952 | NA |
| 22 | 51219704 | rs147475742 | G | A | 0.0108285 | 0.0117817 | 0.3599996 | 0.3580460 | 0.041805 | 0.0473243 | NA |
| 22 | 51221190 | rs369304721 | G | A | 0.0101355 | 0.0118581 | 0.3900004 | 0.3926994 | 0.049124 | NA | NA |
| 22 | 51221731 | rs115055839 | T | C | 0.0038977 | 0.0088483 | 0.6600001 | 0.6595734 | 0.072308 | 0.0625000 | NA |
| 22 | 51222100 | rs114553188 | G | T | -0.0146343 | 0.0103667 | 0.1600000 | 0.1580488 | 0.054502 | 0.0880591 | NA |
| 22 | 51223637 | rs375798137 | G | A | -0.0146747 | 0.0104189 | 0.1600000 | 0.1589922 | 0.054135 | 0.0788738 | NA |
| 22 | 51229805 | rs9616985 | T | C | 0.0033411 | 0.0088814 | 0.7099994 | 0.7067720 | 0.072184 | 0.0730831 | NA |
| 22 | 51232488 | rs376461333 | A | G | -0.0323146 | 0.0209821 | 0.1199999 | 0.1235352 | 0.020055 | NA | NA |
| 22 | 51237063 | rs3896457 | T | C | -0.0059847 | 0.0054149 | 0.2700001 | 0.2690619 | 0.297913 | 0.2050720 | NA |
bcf preview
1 49298 rs10399793 T C . PASS AF=0.623505 ES:SE:LP:AF:ID 0.0145245:0.00810575:1.13668:0.623505:rs10399793
1 54676 rs2462492 C T . PASS AF=0.399158 ES:SE:LP:AF:ID -0.00863508:0.00804759:0.552842:0.399158:rs2462492
1 86028 rs114608975 T C . PASS AF=0.103979 ES:SE:LP:AF:ID -0.018306:0.0127694:0.823909:0.103979:rs114608975
1 91536 rs6702460 G T . PASS AF=0.455954 ES:SE:LP:AF:ID 0.0102084:0.0079104:0.69897:0.455954:rs6702460
1 234313 rs8179466 C T . PASS AF=0.07456 ES:SE:LP:AF:ID 0.0156375:0.0155696:0.49485:0.07456:rs8179466
1 534192 rs6680723 C T . PASS AF=0.240218 ES:SE:LP:AF:ID 0.00208389:0.00906047:0.0861861:0.240218:rs6680723
1 546697 rs12025928 A G . PASS AF=0.912844 ES:SE:LP:AF:ID -0.0189082:0.0112284:1.03621:0.912844:rs12025928
1 693731 rs12238997 A G . PASS AF=0.117537 ES:SE:LP:AF:ID 0.00886421:0.00753907:0.619789:0.117537:rs12238997
1 705882 rs72631875 G A . PASS AF=0.06741 ES:SE:LP:AF:ID -0.00647737:0.011053:0.251812:0.06741:rs72631875
1 706368 rs12029736 A G . PASS AF=0.515046 ES:SE:LP:AF:ID -0.0038713:0.00559032:0.309804:0.515046:rs12029736
1 714596 rs149887893 T C . PASS AF=0.033464 ES:SE:LP:AF:ID 0.014459:0.0139765:0.522879:0.033464:rs149887893
1 715265 rs12184267 C T . PASS AF=0.037138 ES:SE:LP:AF:ID 0.0177592:0.0127042:0.79588:0.037138:rs12184267
1 715367 rs12184277 A G . PASS AF=0.037222 ES:SE:LP:AF:ID 0.0167545:0.0126626:0.721246:0.037222:rs12184277
1 717485 rs12184279 C A . PASS AF=0.036892 ES:SE:LP:AF:ID 0.0196607:0.0127556:0.920819:0.036892:rs12184279
1 717587 rs144155419 G A . PASS AF=0.016769 ES:SE:LP:AF:ID -0.0111321:0.0195976:0.244125:0.016769:rs144155419
1 720381 rs116801199 G T . PASS AF=0.037477 ES:SE:LP:AF:ID 0.0181586:0.0126106:0.823909:0.037477:rs116801199
1 721290 rs12565286 G C . PASS AF=0.037563 ES:SE:LP:AF:ID 0.0176211:0.0125707:0.79588:0.037563:rs12565286
1 722670 rs116030099 T C . PASS AF=0.100858 ES:SE:LP:AF:ID -0.00380318:0.00926888:0.167491:0.100858:rs116030099
1 723891 rs2977670 G C . PASS AF=0.958184 ES:SE:LP:AF:ID -0.012005:0.0120865:0.49485:0.958184:rs2977670
1 724849 rs12126395 C A . PASS AF=0.03191 ES:SE:LP:AF:ID -0.0282946:0.0219827:0.69897:0.03191:rs12126395
1 725060 rs865924913 A T . PASS AF=0.052678 ES:SE:LP:AF:ID 0.00533616:0.0177782:0.119186:0.052678:rs865924913
1 726794 rs28454925 C G . PASS AF=0.037038 ES:SE:LP:AF:ID 0.0192937:0.0126564:0.886057:0.037038:rs28454925
1 729632 rs116720794 C T . PASS AF=0.037361 ES:SE:LP:AF:ID 0.0208981:0.012548:1.01773:0.037361:rs116720794
1 729679 rs4951859 C G . PASS AF=0.841197 ES:SE:LP:AF:ID -0.00958405:0.00652596:0.853872:0.841197:rs4951859
1 730087 rs148120343 T C . PASS AF=0.055916 ES:SE:LP:AF:ID -0.00402565:0.0106478:0.148742:0.055916:rs148120343
1 731718 rs58276399 T C . PASS AF=0.12353 ES:SE:LP:AF:ID 0.00906218:0.00715507:0.677781:0.12353:rs58276399
1 732989 rs369030935 C T . PASS AF=0.025888 ES:SE:LP:AF:ID 0.000923229:0.0175839:0.0177288:0.025888:rs369030935
1 734349 rs141242758 T C . PASS AF=0.122691 ES:SE:LP:AF:ID 0.00847141:0.00715943:0.619789:0.122691:rs141242758
1 736289 rs79010578 T A . PASS AF=0.133313 ES:SE:LP:AF:ID 0.0138049:0.00705831:1.30103:0.133313:rs79010578
1 736689 rs181876450 T C . PASS AF=0.01125 ES:SE:LP:AF:ID -0.00108599:0.0255264:0.0132283:0.01125:rs181876450
1 740284 rs61770167 C T . PASS AF=0.006038 ES:SE:LP:AF:ID 0.0450112:0.032087:0.79588:0.006038:rs61770167
1 752478 rs146277091 G A . PASS AF=0.037341 ES:SE:LP:AF:ID 0.0194605:0.0124056:0.920819:0.037341:rs146277091
1 752566 rs3094315 G A . PASS AF=0.837078 ES:SE:LP:AF:ID -0.00817969:0.00631716:0.69897:0.837078:rs3094315
1 752721 rs3131972 A G . PASS AF=0.836668 ES:SE:LP:AF:ID -0.00806276:0.00631057:0.69897:0.836668:rs3131972
1 753405 rs3115860 C A . PASS AF=0.868267 ES:SE:LP:AF:ID -0.00502912:0.00677453:0.337242:0.868267:rs3115860
1 753541 rs2073813 G A . PASS AF=0.131381 ES:SE:LP:AF:ID 0.00605502:0.00678847:0.431798:0.131381:rs2073813
1 754063 rs12184312 G T . PASS AF=0.037784 ES:SE:LP:AF:ID 0.0191967:0.0122114:0.920819:0.037784:rs12184312
1 754105 rs12184325 C T . PASS AF=0.038035 ES:SE:LP:AF:ID 0.0191124:0.0121358:0.920819:0.038035:rs12184325
1 754182 rs3131969 A G . PASS AF=0.867594 ES:SE:LP:AF:ID -0.0047344:0.00676186:0.318759:0.867594:rs3131969
1 754192 rs3131968 A G . PASS AF=0.867673 ES:SE:LP:AF:ID -0.00476503:0.00676432:0.318759:0.867673:rs3131968
1 754211 rs12184313 G A . PASS AF=0.037976 ES:SE:LP:AF:ID 0.0197982:0.0121864:1:0.037976:rs12184313
1 754334 rs3131967 T C . PASS AF=0.867592 ES:SE:LP:AF:ID -0.00482899:0.00676143:0.318759:0.867592:rs3131967
1 754433 rs150578204 G A . PASS AF=0.00506 ES:SE:LP:AF:ID -0.00486658:0.0351052:0.05061:0.00506:rs150578204
1 754458 rs142682604 G T . PASS AF=0.005027 ES:SE:LP:AF:ID -0.00519208:0.0352069:0.0555173:0.005027:rs142682604
1 754503 rs3115859 G A . PASS AF=0.836191 ES:SE:LP:AF:ID -0.00827803:0.00629625:0.721246:0.836191:rs3115859
1 754629 rs10454459 A G . PASS AF=0.037994 ES:SE:LP:AF:ID 0.0202034:0.0122023:1.00877:0.037994:rs10454459
1 754964 rs3131966 C T . PASS AF=0.836792 ES:SE:LP:AF:ID -0.00839004:0.00631346:0.744727:0.836792:rs3131966
1 755240 rs181660517 T G . PASS AF=0.013255 ES:SE:LP:AF:ID 0.0226987:0.0225739:0.508638:0.013255:rs181660517
1 755435 rs184270342 T G . PASS AF=0.005432 ES:SE:LP:AF:ID -0.0246414:0.0344895:0.327902:0.005432:rs184270342
1 755775 rs3131965 A G . PASS AF=0.838 ES:SE:LP:AF:ID -0.00886377:0.00639788:0.769551:0.838:rs3131965