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:10260,TotalVariants=9851866,VariantsNotRead=0,HarmonisedVariants=9851866,VariantsNotHarmonised=0,SwitchedAlleles=9851866,TotalControls=60647,TotalCases=4302,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_20088_349.vcf.gz --id UKB-b:10260 --data /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/ukbiobank/raw-output/data.batch_20088_349.txt.gz --cohort_cases 4302 --cohort_controls 60647 --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": "2019-09-13T11:42:01.346863",
"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-10260/mac_discard.txt -Oz /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-10260/UKB-b-10260_raw.vcf.gz; Date=Thu Oct 17 12:23:42 2019",
"bcftools_viewCommand.1": "view -h /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/ukb-b-10260/ukb-b-10260.vcf.gz; Date=Sun May 10 08:23:40 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-10260/UKB-b-10260_data.vcf.gz \
--ref-ld-chr ../reference/eur_w_ld_chr/ \
--out /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-10260/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-10260/UKB-b-10260_data.vcf.gz ...
Read summary statistics for 4660750 SNPs.
Dropped 1142 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, 1066294 SNPs remain.
After merging with regression SNP LD, 1066294 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.0056 (0.0081)
Lambda GC: 1.0216
Mean Chi^2: 1.0195
Intercept: 1.0116 (0.0082)
Ratio: 0.5971 (0.4212)
Analysis finished at Thu Oct 17 14:41:16 2019
Total time elapsed: 57.17sQC metrics
Metrics
Metrics
{
"af_correlation": 0.8979,
"inflation_factor": 1.0475,
"mean_EFFECT": 5.2685e-06,
"n": "-Inf",
"n_snps": 9851866,
"n_clumped_hits": 0,
"n_p_sig": 0,
"n_mono": 0,
"n_ns": 0,
"n_mac": 0,
"is_snpid_unique": true,
"n_miss_EFFECT": 0,
"n_miss_SE": 0,
"n_miss_PVAL": 0,
"n_miss_AF": 0,
"n_miss_AF_reference": 39081,
"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": 1066294,
"ldsc_nsnp_merge_regression_ld": 1066294,
"ldsc_observed_scale_h2_beta": 0.0056,
"ldsc_observed_scale_h2_se": 0.0081,
"ldsc_intercept_beta": 1.0116,
"ldsc_intercept_se": 0.0082,
"ldsc_lambda_gc": 1.0216,
"ldsc_mean_chisq": 1.0195,
"ldsc_ratio": 0.5949
}
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 | 4659617 | 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 | 4660750 | 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 | 8.664320e+00 | 5.767105e+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 | 7.856877e+07 | 5.670124e+07 | 828.0000000 | 3.179269e+07 | 6.889136e+07 | 1.146826e+08 | 2.492385e+08 | ▇▆▅▂▁ |
| numeric | EFFECT | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 5.300000e-06 | 1.767700e-03 | -0.0124811 | -1.137700e-03 | -8.200000e-06 | 1.148100e-03 | 1.112460e-02 | ▁▁▇▂▁ |
| numeric | SE | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 1.717100e-03 | 3.276000e-04 | 0.0013327 | 1.436600e-03 | 1.603400e-03 | 1.932800e-03 | 4.897800e-03 | ▇▂▁▁▁ |
| numeric | PVAL | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 4.962345e-01 | 2.896613e-01 | 0.0000025 | 2.399999e-01 | 4.899999e-01 | 7.499995e-01 | 1.000000e+00 | ▇▇▇▇▇ |
| numeric | PVAL_ztest | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 4.962333e-01 | 2.896370e-01 | 0.0000025 | 2.439275e-01 | 4.946228e-01 | 7.473669e-01 | 9.999996e-01 | ▇▇▇▇▇ |
| numeric | AF | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 3.661954e-01 | 2.309869e-01 | 0.0813580 | 1.664070e-01 | 3.065240e-01 | 5.307820e-01 | 9.186420e-01 | ▇▅▃▂▂ |
| numeric | AF_reference | 39081 | 0.9916149 | NA | NA | NA | NA | NA | NA | NA | 3.582068e-01 | 2.297053e-01 | 0.0000000 | 1.687300e-01 | 3.071090e-01 | 5.197680e-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 | -0.0000537 | 0.0024561 | 0.9800000 | 0.9825692 | 0.623812 | 0.7821490 | NA |
| 1 | 54676 | rs2462492 | C | T | 0.0023826 | 0.0024489 | 0.3300000 | 0.3305997 | 0.399144 | NA | NA |
| 1 | 86028 | rs114608975 | T | C | -0.0003319 | 0.0038983 | 0.9299999 | 0.9321548 | 0.103536 | 0.0277556 | NA |
| 1 | 91536 | rs6702460 | G | T | 0.0046622 | 0.0024087 | 0.0530005 | 0.0529197 | 0.455916 | 0.4207270 | NA |
| 1 | 534192 | rs6680723 | C | T | 0.0015277 | 0.0027434 | 0.5800000 | 0.5776202 | 0.242057 | NA | NA |
| 1 | 546697 | rs12025928 | A | G | 0.0028886 | 0.0034039 | 0.4000000 | 0.3961028 | 0.912862 | NA | NA |
| 1 | 693731 | rs12238997 | A | G | -0.0012984 | 0.0022875 | 0.5700002 | 0.5702907 | 0.117313 | 0.1417730 | NA |
| 1 | 706368 | rs55727773 | A | G | 0.0030339 | 0.0016980 | 0.0739997 | 0.0739667 | 0.513304 | 0.2751600 | NA |
| 1 | 722670 | rs116030099 | T | C | -0.0023924 | 0.0027708 | 0.3900004 | 0.3879080 | 0.102736 | 0.0413339 | NA |
| 1 | 729679 | rs4951859 | C | G | 0.0027082 | 0.0019783 | 0.1700000 | 0.1710175 | 0.841441 | 0.6399760 | NA |
| CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 22 | 51198027 | rs34939255 | A | G | 0.0013843 | 0.0016925 | 0.4100001 | 0.4134319 | 0.254586 | 0.0984425 | NA |
| 22 | 51208537 | rs72619593 | G | A | -0.0032911 | 0.0022617 | 0.1499999 | 0.1456359 | 0.120936 | 0.1142170 | NA |
| 22 | 51210289 | rs112565862 | C | T | -0.0010561 | 0.0022557 | 0.6400000 | 0.6396585 | 0.129762 | 0.1018370 | NA |
| 22 | 51211106 | rs9628250 | T | C | 0.0016834 | 0.0016789 | 0.3200000 | 0.3160180 | 0.271468 | 0.1671330 | NA |
| 22 | 51211392 | rs3888396 | T | C | -0.0006824 | 0.0022356 | 0.7600007 | 0.7601883 | 0.132383 | 0.1641370 | NA |
| 22 | 51212875 | rs2238837 | A | C | -0.0026704 | 0.0015959 | 0.0940005 | 0.0942826 | 0.331351 | 0.3724040 | NA |
| 22 | 51213613 | rs34726907 | C | T | -0.0000930 | 0.0021179 | 0.9599999 | 0.9649833 | 0.126422 | 0.1727240 | NA |
| 22 | 51216564 | rs9616970 | T | C | 0.0001746 | 0.0021096 | 0.9299999 | 0.9340464 | 0.126887 | 0.1563500 | NA |
| 22 | 51219006 | rs28729663 | G | A | -0.0000728 | 0.0020653 | 0.9699999 | 0.9718820 | 0.136315 | 0.2052720 | NA |
| 22 | 51237063 | rs3896457 | T | C | -0.0017458 | 0.0016304 | 0.2800000 | 0.2842718 | 0.298393 | 0.2050720 | NA |
bcf preview
1 49298 rs10399793 T C . PASS AF=0.623812 ES:SE:LP:AF:ID -5.36603e-05:0.00245608:0.00877392:0.623812:rs10399793
1 54676 rs2462492 C T . PASS AF=0.399144 ES:SE:LP:AF:ID 0.00238259:0.00244894:0.481486:0.399144:rs2462492
1 86028 rs114608975 T C . PASS AF=0.103536 ES:SE:LP:AF:ID -0.00033188:0.00389832:0.0315171:0.103536:rs114608975
1 91536 rs6702460 G T . PASS AF=0.455916 ES:SE:LP:AF:ID 0.00466222:0.0024087:1.27572:0.455916:rs6702460
1 534192 rs6680723 C T . PASS AF=0.242057 ES:SE:LP:AF:ID 0.00152769:0.00274338:0.236572:0.242057:rs6680723
1 546697 rs12025928 A G . PASS AF=0.912862 ES:SE:LP:AF:ID 0.00288859:0.00340394:0.39794:0.912862:rs12025928
1 693731 rs12238997 A G . PASS AF=0.117313 ES:SE:LP:AF:ID -0.00129845:0.00228752:0.244125:0.117313:rs12238997
1 706368 rs12029736 A G . PASS AF=0.513304 ES:SE:LP:AF:ID 0.00303393:0.00169795:1.13077:0.513304:rs12029736
1 722670 rs116030099 T C . PASS AF=0.102736 ES:SE:LP:AF:ID -0.0023924:0.00277085:0.408935:0.102736:rs116030099
1 729679 rs4951859 C G . PASS AF=0.841441 ES:SE:LP:AF:ID 0.00270815:0.00197828:0.769551:0.841441:rs4951859
1 731718 rs58276399 T C . PASS AF=0.123078 ES:SE:LP:AF:ID -0.00198641:0.00217288:0.443698:0.123078:rs58276399
1 734349 rs141242758 T C . PASS AF=0.12233 ES:SE:LP:AF:ID -0.0019798:0.00217358:0.443698:0.12233:rs141242758
1 736289 rs79010578 T A . PASS AF=0.134139 ES:SE:LP:AF:ID -0.00173004:0.00213372:0.376751:0.134139:rs79010578
1 752566 rs3094315 G A . PASS AF=0.837029 ES:SE:LP:AF:ID 0.00244366:0.00191374:0.69897:0.837029:rs3094315
1 752721 rs3131972 A G . PASS AF=0.836733 ES:SE:LP:AF:ID 0.00264249:0.00191234:0.769551:0.836733:rs3131972
1 753405 rs3115860 C A . PASS AF=0.868562 ES:SE:LP:AF:ID 0.00193812:0.00205491:0.455932:0.868562:rs3115860
1 753541 rs2073813 G A . PASS AF=0.131004 ES:SE:LP:AF:ID -0.00183295:0.00206019:0.431798:0.131004:rs2073813
1 754182 rs3131969 A G . PASS AF=0.867976 ES:SE:LP:AF:ID 0.00199118:0.0020516:0.481486:0.867976:rs3131969
1 754192 rs3131968 A G . PASS AF=0.86805 ES:SE:LP:AF:ID 0.00201989:0.00205244:0.481486:0.86805:rs3131968
1 754334 rs3131967 T C . PASS AF=0.867987 ES:SE:LP:AF:ID 0.00204276:0.00205155:0.49485:0.867987:rs3131967
1 754503 rs3115859 G A . PASS AF=0.836159 ES:SE:LP:AF:ID 0.0024779:0.00190674:0.721246:0.836159:rs3115859
1 754964 rs3131966 C T . PASS AF=0.836793 ES:SE:LP:AF:ID 0.00236274:0.00191197:0.657577:0.836793:rs3131966
1 755775 rs3131965 A G . PASS AF=0.838109 ES:SE:LP:AF:ID 0.00253087:0.00193888:0.721246:0.838109:rs3131965
1 755890 rs3115858 A T . PASS AF=0.868228 ES:SE:LP:AF:ID 0.00189589:0.00204891:0.455932:0.868228:rs3115858
1 756604 rs3131962 A G . PASS AF=0.867742 ES:SE:LP:AF:ID 0.00196859:0.00204348:0.468521:0.867742:rs3131962
1 757640 rs3115853 G A . PASS AF=0.866644 ES:SE:LP:AF:ID 0.00241024:0.00203974:0.619789:0.866644:rs3115853
1 757734 rs4951929 C T . PASS AF=0.867911 ES:SE:LP:AF:ID 0.00192857:0.00204556:0.455932:0.867911:rs4951929
1 757936 rs4951862 C A . PASS AF=0.867923 ES:SE:LP:AF:ID 0.00192972:0.0020457:0.455932:0.867923:rs4951862
1 758144 rs3131956 A G . PASS AF=0.867932 ES:SE:LP:AF:ID 0.00195014:0.00204577:0.468521:0.867932:rs3131956
1 758626 rs3131954 C T . PASS AF=0.868398 ES:SE:LP:AF:ID 0.00181432:0.00205115:0.420216:0.868398:rs3131954
1 760912 rs1048488 C T . PASS AF=0.836369 ES:SE:LP:AF:ID 0.00201394:0.00190199:0.537602:0.836369:rs1048488
1 761147 rs3115850 T C . PASS AF=0.836495 ES:SE:LP:AF:ID 0.00204091:0.00190329:0.552842:0.836495:rs3115850
1 761732 rs2286139 C T . PASS AF=0.860851 ES:SE:LP:AF:ID 0.00255833:0.00203852:0.677781:0.860851:rs2286139
1 763394 rs3115847 G A . PASS AF=0.705804 ES:SE:LP:AF:ID 0.0025392:0.00198924:0.69897:0.705804:rs3115847
1 766007 rs61768174 A C . PASS AF=0.106094 ES:SE:LP:AF:ID -0.0011006:0.002289:0.200659:0.106094:rs61768174
1 768253 rs2977608 A C . PASS AF=0.758252 ES:SE:LP:AF:ID 0.00197229:0.00161229:0.657577:0.758252:rs2977608
1 768448 rs12562034 G A . PASS AF=0.108262 ES:SE:LP:AF:ID -0.00115141:0.0022191:0.221849:0.108262:rs12562034
1 769223 rs60320384 C G . PASS AF=0.13066 ES:SE:LP:AF:ID -0.00168503:0.0020594:0.387216:0.13066:rs60320384
1 771823 rs2977605 T C . PASS AF=0.867852 ES:SE:LP:AF:ID 0.00194583:0.00204815:0.468521:0.867852:rs2977605
1 771967 rs59066358 G A . PASS AF=0.130756 ES:SE:LP:AF:ID -0.00162112:0.00205802:0.366532:0.130756:rs59066358
1 772755 rs2905039 A C . PASS AF=0.867878 ES:SE:LP:AF:ID 0.00192943:0.00204827:0.455932:0.867878:rs2905039
1 776546 rs12124819 A G . PASS AF=0.263729 ES:SE:LP:AF:ID 0.0010583:0.00182183:0.251812:0.263729:rs12124819
1 777122 rs2980319 A T . PASS AF=0.869067 ES:SE:LP:AF:ID 0.00199091:0.00205366:0.481486:0.869067:rs2980319
1 777232 rs112618790 C T . PASS AF=0.096639 ES:SE:LP:AF:ID -0.000565829:0.0023655:0.091515:0.096639:rs112618790
1 778745 rs1055606 A G . PASS AF=0.129594 ES:SE:LP:AF:ID -0.00167137:0.00206149:0.376751:0.129594:rs1055606
1 779322 rs4040617 A G . PASS AF=0.129863 ES:SE:LP:AF:ID -0.00174711:0.00205798:0.39794:0.129863:rs4040617
1 780785 rs2977612 T A . PASS AF=0.867843 ES:SE:LP:AF:ID 0.00205885:0.00204856:0.508638:0.867843:rs2977612
1 781845 rs61768199 A G . PASS AF=0.102807 ES:SE:LP:AF:ID -0.00119152:0.0023233:0.21467:0.102807:rs61768199
1 782981 rs6594026 C T . PASS AF=0.130424 ES:SE:LP:AF:ID -0.00187999:0.00205838:0.443698:0.130424:rs6594026
1 785050 rs2905062 G A . PASS AF=0.867493 ES:SE:LP:AF:ID 0.00208552:0.00204795:0.508638:0.867493:rs2905062