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:12181,TotalVariants=9851866,VariantsNotRead=0,HarmonisedVariants=9851866,VariantsNotHarmonised=0,SwitchedAlleles=9851866,TotalControls=368549,TotalCases=93308,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_6159_1.vcf.gz --id UKB-b:12181 --data /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/ukbiobank/raw-output/data.batch_6159_1.txt.gz --cohort_cases 93308 --cohort_controls 368549 --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": "2019-09-13T01:56:13.597753",
"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-12181/mac_discard.txt -Oz /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-12181/UKB-b-12181_raw.vcf.gz; Date=Thu Oct 17 12:26:44 2019",
"bcftools_viewCommand.1": "view -h /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/ukb-b-12181/ukb-b-12181.vcf.gz; Date=Sun May 10 01:16:17 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-12181/UKB-b-12181_data.vcf.gz \
--ref-ld-chr ../reference/eur_w_ld_chr/ \
--out /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-12181/ldsc.txt \
--w-ld-chr ../reference/eur_w_ld_chr/
Beginning analysis at Thu Oct 17 14:41:26 2019
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-12181/UKB-b-12181_data.vcf.gz ...
Read summary statistics for 8963117 SNPs.
Dropped 8564 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, 1286998 SNPs remain.
After merging with regression SNP LD, 1286998 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.0414 (0.0022)
Lambda GC: 1.3019
Mean Chi^2: 1.4044
Intercept: 1.0293 (0.0085)
Ratio: 0.0725 (0.021)
Analysis finished at Thu Oct 17 14:43:09 2019
Total time elapsed: 1.0m:43.65sQC metrics
Metrics
Metrics
{
"af_correlation": 0.9475,
"inflation_factor": 1.1999,
"mean_EFFECT": 0,
"n": "-Inf",
"n_snps": 9851866,
"n_clumped_hits": 48,
"n_p_sig": 6082,
"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": 91987,
"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": 1286998,
"ldsc_nsnp_merge_regression_ld": 1286998,
"ldsc_observed_scale_h2_beta": 0.0414,
"ldsc_observed_scale_h2_se": 0.0022,
"ldsc_intercept_beta": 1.0293,
"ldsc_intercept_se": 0.0085,
"ldsc_lambda_gc": 1.3019,
"ldsc_mean_chisq": 1.4044,
"ldsc_ratio": 0.0725
}
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 | 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 | 8954592 | 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 | 8963117 | 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 | 8.644577e+00 | 5.758418e+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 | 7.879157e+07 | 5.633850e+07 | 828.0000000 | 3.243212e+07 | 6.935802e+07 | 1.145510e+08 | 2.492385e+08 | ▇▆▅▂▁ |
| numeric | EFFECT | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 2.630000e-05 | 2.839600e-03 | -0.0546560 | -1.172700e-03 | 1.100000e-05 | 1.202500e-03 | 2.972020e-02 | ▁▁▁▇▁ |
| numeric | SE | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 2.182200e-03 | 1.585400e-03 | 0.0008013 | 9.538000e-04 | 1.454600e-03 | 2.990400e-03 | 1.858590e-02 | ▇▁▁▁▁ |
| numeric | PVAL | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 4.666342e-01 | 2.981376e-01 | 0.0000000 | 2.000000e-01 | 4.600002e-01 | 7.199992e-01 | 1.000000e+00 | ▇▆▆▆▆ |
| numeric | PVAL_ztest | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 4.666358e-01 | 2.981129e-01 | 0.0000000 | 1.998625e-01 | 4.557138e-01 | 7.247861e-01 | 1.000000e+00 | ▇▆▆▆▆ |
| numeric | AF | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 2.211532e-01 | 2.586511e-01 | 0.0037520 | 2.097900e-02 | 1.028340e-01 | 3.490160e-01 | 9.962480e-01 | ▇▂▁▁▁ |
| numeric | AF_reference | 91987 | 0.9897372 | NA | NA | NA | NA | NA | NA | NA | 2.213572e-01 | 2.505608e-01 | 0.0000000 | 1.837060e-02 | 1.202080e-01 | 3.472440e-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 | -0.0000297 | 0.0014741 | 0.9800000 | 0.9839052 | 0.623794 | 0.7821490 | NA |
| 1 | 54676 | rs2462492 | C | T | 0.0019969 | 0.0014603 | 0.1700000 | 0.1714698 | 0.400412 | NA | NA |
| 1 | 86028 | rs114608975 | T | C | -0.0054230 | 0.0023349 | 0.0200000 | 0.0202024 | 0.103543 | 0.0277556 | NA |
| 1 | 91536 | rs6702460 | G | T | 0.0002918 | 0.0014379 | 0.8400000 | 0.8391963 | 0.456865 | 0.4207270 | NA |
| 1 | 234313 | rs8179466 | C | T | 0.0006577 | 0.0028348 | 0.8200001 | 0.8165221 | 0.074516 | NA | NA |
| 1 | 534192 | rs6680723 | C | T | 0.0018663 | 0.0016425 | 0.2599998 | 0.2558503 | 0.240948 | NA | NA |
| 1 | 546697 | rs12025928 | A | G | 0.0030639 | 0.0020487 | 0.1299999 | 0.1347765 | 0.913458 | NA | NA |
| 1 | 693731 | rs12238997 | A | G | 0.0031428 | 0.0013764 | 0.0219999 | 0.0224146 | 0.116328 | 0.1417730 | NA |
| 1 | 705882 | rs72631875 | G | A | -0.0009191 | 0.0020170 | 0.6499995 | 0.6486131 | 0.067284 | 0.0315495 | NA |
| 1 | 706368 | rs55727773 | A | G | -0.0019880 | 0.0010196 | 0.0510000 | 0.0512017 | 0.515613 | 0.2751600 | NA |
| CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 22 | 51219006 | rs28729663 | G | A | 0.0010631 | 0.0012307 | 0.3900004 | 0.3876907 | 0.137952 | 0.2052720 | NA |
| 22 | 51219387 | rs9616832 | T | C | 0.0029885 | 0.0015974 | 0.0610000 | 0.0613712 | 0.073740 | 0.0654952 | NA |
| 22 | 51219704 | rs147475742 | G | A | 0.0019386 | 0.0021404 | 0.3700002 | 0.3650770 | 0.041958 | 0.0473243 | NA |
| 22 | 51221190 | rs369304721 | G | A | 0.0039880 | 0.0021370 | 0.0619998 | 0.0620209 | 0.049729 | NA | NA |
| 22 | 51221731 | rs115055839 | T | C | 0.0028545 | 0.0015984 | 0.0739997 | 0.0741311 | 0.073230 | 0.0625000 | NA |
| 22 | 51222100 | rs114553188 | G | T | -0.0011254 | 0.0018817 | 0.5500004 | 0.5497778 | 0.054472 | 0.0880591 | NA |
| 22 | 51223637 | rs375798137 | G | A | -0.0011559 | 0.0018908 | 0.5400003 | 0.5409673 | 0.054101 | 0.0788738 | NA |
| 22 | 51229805 | rs9616985 | T | C | 0.0028264 | 0.0016042 | 0.0779992 | 0.0780889 | 0.073065 | 0.0730831 | NA |
| 22 | 51232488 | rs376461333 | A | G | 0.0006957 | 0.0037793 | 0.8499999 | 0.8539478 | 0.020044 | NA | NA |
| 22 | 51237063 | rs3896457 | T | C | 0.0002679 | 0.0009812 | 0.7800007 | 0.7847981 | 0.297957 | 0.2050720 | NA |
bcf preview
1 49298 rs10399793 T C . PASS AF=0.623794 ES:SE:LP:AF:ID -2.97373e-05:0.0014741:0.00877392:0.623794:rs10399793
1 54676 rs2462492 C T . PASS AF=0.400412 ES:SE:LP:AF:ID 0.0019969:0.00146026:0.769551:0.400412:rs2462492
1 86028 rs114608975 T C . PASS AF=0.103543 ES:SE:LP:AF:ID -0.00542301:0.00233492:1.69897:0.103543:rs114608975
1 91536 rs6702460 G T . PASS AF=0.456865 ES:SE:LP:AF:ID 0.000291783:0.00143791:0.0757207:0.456865:rs6702460
1 234313 rs8179466 C T . PASS AF=0.074516 ES:SE:LP:AF:ID 0.000657734:0.00283481:0.0861861:0.074516:rs8179466
1 534192 rs6680723 C T . PASS AF=0.240948 ES:SE:LP:AF:ID 0.00186632:0.00164252:0.585027:0.240948:rs6680723
1 546697 rs12025928 A G . PASS AF=0.913458 ES:SE:LP:AF:ID 0.00306386:0.00204868:0.886057:0.913458:rs12025928
1 693731 rs12238997 A G . PASS AF=0.116328 ES:SE:LP:AF:ID 0.00314278:0.00137644:1.65758:0.116328:rs12238997
1 705882 rs72631875 G A . PASS AF=0.067284 ES:SE:LP:AF:ID -0.000919108:0.00201696:0.187087:0.067284:rs72631875
1 706368 rs12029736 A G . PASS AF=0.515613 ES:SE:LP:AF:ID -0.00198804:0.00101962:1.29243:0.515613:rs12029736
1 714596 rs149887893 T C . PASS AF=0.033001 ES:SE:LP:AF:ID -0.00224143:0.00257052:0.420216:0.033001:rs149887893
1 715265 rs12184267 C T . PASS AF=0.036618 ES:SE:LP:AF:ID -0.00215806:0.00233488:0.443698:0.036618:rs12184267
1 715367 rs12184277 A G . PASS AF=0.036735 ES:SE:LP:AF:ID -0.00233441:0.00232605:0.49485:0.036735:rs12184277
1 717485 rs12184279 C A . PASS AF=0.036435 ES:SE:LP:AF:ID -0.00194925:0.00234278:0.387216:0.036435:rs12184279
1 717587 rs144155419 G A . PASS AF=0.016406 ES:SE:LP:AF:ID -0.00252147:0.00360749:0.318759:0.016406:rs144155419
1 720381 rs116801199 G T . PASS AF=0.036974 ES:SE:LP:AF:ID -0.00201939:0.00231685:0.420216:0.036974:rs116801199
1 721290 rs12565286 G C . PASS AF=0.03707 ES:SE:LP:AF:ID -0.0020766:0.00230891:0.431798:0.03707:rs12565286
1 722670 rs116030099 T C . PASS AF=0.101218 ES:SE:LP:AF:ID -0.00043467:0.00168211:0.09691:0.101218:rs116030099
1 723891 rs2977670 G C . PASS AF=0.9591 ES:SE:LP:AF:ID 0.00255537:0.00222695:0.60206:0.9591:rs2977670
1 724849 rs12126395 C A . PASS AF=0.031445 ES:SE:LP:AF:ID -0.00469943:0.00404337:0.60206:0.031445:rs12126395
1 725060 rs865924913 A T . PASS AF=0.05326 ES:SE:LP:AF:ID 0.000590676:0.00321545:0.0705811:0.05326:rs865924913
1 726794 rs28454925 C G . PASS AF=0.03659 ES:SE:LP:AF:ID -0.00210615:0.00232382:0.443698:0.03659:rs28454925
1 729632 rs116720794 C T . PASS AF=0.036907 ES:SE:LP:AF:ID -0.00259804:0.00230264:0.585027:0.036907:rs116720794
1 729679 rs4951859 C G . PASS AF=0.843217 ES:SE:LP:AF:ID -0.00087456:0.00119289:0.337242:0.843217:rs4951859
1 730087 rs148120343 T C . PASS AF=0.055923 ES:SE:LP:AF:ID 0.00392283:0.00193123:1.37675:0.055923:rs148120343
1 731718 rs58276399 T C . PASS AF=0.122311 ES:SE:LP:AF:ID 0.0023401:0.00130568:1.13668:0.122311:rs58276399
1 732989 rs369030935 C T . PASS AF=0.025715 ES:SE:LP:AF:ID 0.00272042:0.00321141:0.39794:0.025715:rs369030935
1 734349 rs141242758 T C . PASS AF=0.121553 ES:SE:LP:AF:ID 0.00235191:0.00130624:1.14267:0.121553:rs141242758
1 736289 rs79010578 T A . PASS AF=0.132335 ES:SE:LP:AF:ID 0.00131008:0.0012874:0.508638:0.132335:rs79010578
1 736689 rs181876450 T C . PASS AF=0.011123 ES:SE:LP:AF:ID -0.00704528:0.00468352:0.886057:0.011123:rs181876450
1 740284 rs61770167 C T . PASS AF=0.005697 ES:SE:LP:AF:ID 0.00523723:0.00604436:0.408935:0.005697:rs61770167
1 752478 rs146277091 G A . PASS AF=0.03682 ES:SE:LP:AF:ID -0.00221149:0.00227941:0.481486:0.03682:rs146277091
1 752566 rs3094315 G A . PASS AF=0.838951 ES:SE:LP:AF:ID -0.00153436:0.0011552:0.744727:0.838951:rs3094315
1 752721 rs3131972 A G . PASS AF=0.838581 ES:SE:LP:AF:ID -0.00149083:0.00115397:0.69897:0.838581:rs3131972
1 753405 rs3115860 C A . PASS AF=0.869775 ES:SE:LP:AF:ID -0.00250061:0.00123827:1.36653:0.869775:rs3115860
1 753541 rs2073813 G A . PASS AF=0.129877 ES:SE:LP:AF:ID 0.00250928:0.00124078:1.36653:0.129877:rs2073813
1 754063 rs12184312 G T . PASS AF=0.037331 ES:SE:LP:AF:ID -0.00173518:0.00224076:0.356547:0.037331:rs12184312
1 754105 rs12184325 C T . PASS AF=0.037575 ES:SE:LP:AF:ID -0.0016939:0.00222659:0.346787:0.037575:rs12184325
1 754182 rs3131969 A G . PASS AF=0.869118 ES:SE:LP:AF:ID -0.00239374:0.00123584:1.27572:0.869118:rs3131969
1 754192 rs3131968 A G . PASS AF=0.869216 ES:SE:LP:AF:ID -0.0024339:0.00123634:1.3098:0.869216:rs3131968
1 754211 rs12184313 G A . PASS AF=0.037532 ES:SE:LP:AF:ID -0.00179303:0.00223626:0.376751:0.037532:rs12184313
1 754334 rs3131967 T C . PASS AF=0.869121 ES:SE:LP:AF:ID -0.00241149:0.00123582:1.29243:0.869121:rs3131967
1 754433 rs150578204 G A . PASS AF=0.005126 ES:SE:LP:AF:ID -0.00358745:0.00634303:0.244125:0.005126:rs150578204
1 754458 rs142682604 G T . PASS AF=0.005091 ES:SE:LP:AF:ID -0.00328489:0.00635967:0.21467:0.005091:rs142682604
1 754503 rs3115859 G A . PASS AF=0.838034 ES:SE:LP:AF:ID -0.00146665:0.00115076:0.69897:0.838034:rs3115859
1 754629 rs10454459 A G . PASS AF=0.037544 ES:SE:LP:AF:ID -0.002031:0.00223943:0.443698:0.037544:rs10454459
1 754964 rs3131966 C T . PASS AF=0.838665 ES:SE:LP:AF:ID -0.00145133:0.001154:0.677781:0.838665:rs3131966
1 755240 rs181660517 T G . PASS AF=0.013776 ES:SE:LP:AF:ID -0.0019682:0.0040276:0.200659:0.013776:rs181660517
1 755435 rs184270342 T G . PASS AF=0.00555 ES:SE:LP:AF:ID -0.00793329:0.00621355:0.69897:0.00555:rs184270342
1 755775 rs3131965 A G . PASS AF=0.839775 ES:SE:LP:AF:ID -0.00193574:0.00116959:1.00877:0.839775:rs3131965