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:8080,TotalVariants=9851866,VariantsNotRead=0,HarmonisedVariants=9851866,VariantsNotHarmonised=0,SwitchedAlleles=9851866,TotalControls=231069,TotalCases=18641,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_6153_4.vcf.gz --id UKB-b:8080 --data /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/ukbiobank/raw-output/data.batch_6153_4.txt.gz --cohort_cases 18641 --cohort_controls 231069 --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": "2019-09-13T01:54:33.151957",
"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-8080/mac_discard.txt -Oz /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-8080/UKB-b-8080_raw.vcf.gz; Date=Thu Oct 17 12:20:21 2019",
"bcftools_viewCommand.1": "view -h /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/ukb-b-8080/ukb-b-8080.vcf.gz; Date=Sat May 9 17:01:34 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-8080/UKB-b-8080_data.vcf.gz \
--ref-ld-chr ../reference/eur_w_ld_chr/ \
--out /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-8080/ldsc.txt \
--w-ld-chr ../reference/eur_w_ld_chr/
Beginning analysis at Thu Oct 17 14:41:09 2019
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-8080/UKB-b-8080_data.vcf.gz ...
Read summary statistics for 6832387 SNPs.
Dropped 4041 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, 1257793 SNPs remain.
After merging with regression SNP LD, 1257793 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.0155 (0.0021)
Lambda GC: 1.0848
Mean Chi^2: 1.0875
Intercept: 1.0112 (0.0065)
Ratio: 0.1283 (0.0746)
Analysis finished at Thu Oct 17 14:42:29 2019
Total time elapsed: 1.0m:20.36sQC metrics
Metrics
Metrics
{
"af_correlation": 0.9342,
"inflation_factor": 1.0966,
"mean_EFFECT": 1.7932e-06,
"n": "-Inf",
"n_snps": 9851866,
"n_clumped_hits": 1,
"n_p_sig": 103,
"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": 62785,
"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": 1257793,
"ldsc_nsnp_merge_regression_ld": 1257793,
"ldsc_observed_scale_h2_beta": 0.0155,
"ldsc_observed_scale_h2_se": 0.0021,
"ldsc_intercept_beta": 1.0112,
"ldsc_intercept_se": 0.0065,
"ldsc_lambda_gc": 1.0848,
"ldsc_mean_chisq": 1.0875,
"ldsc_ratio": 0.128
}
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 | 1.0000000 | 3 | 58 | 0 | 6828368 | 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 | 6832387 | 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 | 8.664370e+00 | 5.764803e+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 | 7.861422e+07 | 5.646741e+07 | 828.0000000 | 3.210410e+07 | 6.905472e+07 | 1.145104e+08 | 2.492385e+08 | ▇▆▅▂▁ |
| numeric | EFFECT | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 1.800000e-06 | 1.410100e-03 | -0.0158576 | -7.771000e-04 | -9.000000e-07 | 7.746000e-04 | 1.249080e-02 | ▁▁▇▂▁ |
| numeric | SE | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 1.256200e-03 | 5.570000e-04 | 0.0007167 | 8.073000e-04 | 1.025100e-03 | 1.565000e-03 | 6.266000e-03 | ▇▂▁▁▁ |
| numeric | PVAL | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 4.883752e-01 | 2.919294e-01 | 0.0000000 | 2.300001e-01 | 4.799997e-01 | 7.400005e-01 | 1.000000e+00 | ▇▇▇▇▇ |
| numeric | PVAL_ztest | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 4.883740e-01 | 2.919028e-01 | 0.0000000 | 2.326799e-01 | 4.837867e-01 | 7.412624e-01 | 9.999993e-01 | ▇▇▇▇▇ |
| numeric | AF | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 2.814449e-01 | 2.590833e-01 | 0.0187760 | 6.500150e-02 | 1.873780e-01 | 4.401630e-01 | 9.812240e-01 | ▇▃▂▁▁ |
| numeric | AF_reference | 62785 | 0.9908107 | NA | NA | NA | NA | NA | NA | NA | 2.794870e-01 | 2.512021e-01 | 0.0000000 | 7.348240e-02 | 1.986820e-01 | 4.325080e-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 | 0.0000356 | 0.0013215 | 0.9800000 | 0.9784820 | 0.623403 | 0.7821490 | NA |
| 1 | 54676 | rs2462492 | C | T | -0.0002162 | 0.0013064 | 0.8700001 | 0.8685700 | 0.400976 | NA | NA |
| 1 | 86028 | rs114608975 | T | C | -0.0021563 | 0.0020967 | 0.2999998 | 0.3037520 | 0.103437 | 0.0277556 | NA |
| 1 | 91536 | rs6702460 | G | T | 0.0026809 | 0.0012872 | 0.0369999 | 0.0372699 | 0.457088 | 0.4207270 | NA |
| 1 | 234313 | rs8179466 | C | T | -0.0031199 | 0.0025421 | 0.2200002 | 0.2197160 | 0.074451 | NA | NA |
| 1 | 534192 | rs6680723 | C | T | 0.0009062 | 0.0014713 | 0.5400003 | 0.5379480 | 0.241186 | NA | NA |
| 1 | 546697 | rs12025928 | A | G | 0.0050035 | 0.0018356 | 0.0064000 | 0.0064141 | 0.913577 | NA | NA |
| 1 | 693731 | rs12238997 | A | G | 0.0003114 | 0.0012311 | 0.8000000 | 0.8003413 | 0.116703 | 0.1417730 | NA |
| 1 | 705882 | rs72631875 | G | A | -0.0025712 | 0.0018077 | 0.1499999 | 0.1549286 | 0.067069 | 0.0315495 | NA |
| 1 | 706368 | rs55727773 | A | G | -0.0016415 | 0.0009130 | 0.0719996 | 0.0721739 | 0.515134 | 0.2751600 | NA |
| CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 22 | 51219006 | rs28729663 | G | A | 0.0016030 | 0.0011035 | 0.1499999 | 0.1463430 | 0.137913 | 0.2052720 | NA |
| 22 | 51219387 | rs9616832 | T | C | 0.0023336 | 0.0014320 | 0.1000000 | 0.1031745 | 0.073612 | 0.0654952 | NA |
| 22 | 51219704 | rs147475742 | G | A | 0.0040233 | 0.0019190 | 0.0359998 | 0.0360281 | 0.041843 | 0.0473243 | NA |
| 22 | 51221190 | rs369304721 | G | A | 0.0020921 | 0.0019174 | 0.2800000 | 0.2752282 | 0.049574 | NA | NA |
| 22 | 51221731 | rs115055839 | T | C | 0.0023405 | 0.0014325 | 0.1000000 | 0.1022904 | 0.073145 | 0.0625000 | NA |
| 22 | 51222100 | rs114553188 | G | T | 0.0005904 | 0.0016833 | 0.7300002 | 0.7257618 | 0.054643 | 0.0880591 | NA |
| 22 | 51223637 | rs375798137 | G | A | 0.0005391 | 0.0016913 | 0.7499995 | 0.7498958 | 0.054278 | 0.0788738 | NA |
| 22 | 51229805 | rs9616985 | T | C | 0.0022605 | 0.0014376 | 0.1199999 | 0.1158674 | 0.073012 | 0.0730831 | NA |
| 22 | 51232488 | rs376461333 | A | G | 0.0001727 | 0.0033826 | 0.9599999 | 0.9592709 | 0.020061 | NA | NA |
| 22 | 51237063 | rs3896457 | T | C | 0.0004482 | 0.0008781 | 0.6100002 | 0.6097571 | 0.297860 | 0.2050720 | NA |
bcf preview
1 49298 rs10399793 T C . PASS AF=0.623403 ES:SE:LP:AF:ID 3.56426e-05:0.00132146:0.00877392:0.623403:rs10399793
1 54676 rs2462492 C T . PASS AF=0.400976 ES:SE:LP:AF:ID -0.000216185:0.00130645:0.0604807:0.400976:rs2462492
1 86028 rs114608975 T C . PASS AF=0.103437 ES:SE:LP:AF:ID -0.00215631:0.00209672:0.522879:0.103437:rs114608975
1 91536 rs6702460 G T . PASS AF=0.457088 ES:SE:LP:AF:ID 0.00268089:0.00128716:1.4318:0.457088:rs6702460
1 234313 rs8179466 C T . PASS AF=0.074451 ES:SE:LP:AF:ID -0.00311989:0.00254211:0.657577:0.074451:rs8179466
1 534192 rs6680723 C T . PASS AF=0.241186 ES:SE:LP:AF:ID 0.000906177:0.00147126:0.267606:0.241186:rs6680723
1 546697 rs12025928 A G . PASS AF=0.913577 ES:SE:LP:AF:ID 0.00500352:0.0018356:2.19382:0.913577:rs12025928
1 693731 rs12238997 A G . PASS AF=0.116703 ES:SE:LP:AF:ID 0.000311362:0.00123114:0.09691:0.116703:rs12238997
1 705882 rs72631875 G A . PASS AF=0.067069 ES:SE:LP:AF:ID -0.0025712:0.00180773:0.823909:0.067069:rs72631875
1 706368 rs12029736 A G . PASS AF=0.515134 ES:SE:LP:AF:ID -0.00164154:0.000912971:1.14267:0.515134:rs12029736
1 714596 rs149887893 T C . PASS AF=0.03287 ES:SE:LP:AF:ID -0.000207815:0.00230671:0.0315171:0.03287:rs149887893
1 715265 rs12184267 C T . PASS AF=0.03645 ES:SE:LP:AF:ID -0.000857001:0.00209671:0.167491:0.03645:rs12184267
1 715367 rs12184277 A G . PASS AF=0.036557 ES:SE:LP:AF:ID -0.000730408:0.00208923:0.136677:0.036557:rs12184277
1 717485 rs12184279 C A . PASS AF=0.036249 ES:SE:LP:AF:ID -0.000972922:0.00210464:0.19382:0.036249:rs12184279
1 720381 rs116801199 G T . PASS AF=0.036782 ES:SE:LP:AF:ID -0.000948229:0.00208141:0.187087:0.036782:rs116801199
1 721290 rs12565286 G C . PASS AF=0.036873 ES:SE:LP:AF:ID -0.000833489:0.00207448:0.161151:0.036873:rs12565286
1 722670 rs116030099 T C . PASS AF=0.101076 ES:SE:LP:AF:ID 0.00120727:0.00150727:0.376751:0.101076:rs116030099
1 723891 rs2977670 G C . PASS AF=0.959309 ES:SE:LP:AF:ID 0.00135:0.00200044:0.30103:0.959309:rs2977670
1 724849 rs12126395 C A . PASS AF=0.031432 ES:SE:LP:AF:ID -0.00647255:0.00360839:1.13668:0.031432:rs12126395
1 725060 rs865924913 A T . PASS AF=0.053418 ES:SE:LP:AF:ID 0.00363057:0.00287175:0.677781:0.053418:rs865924913
1 726794 rs28454925 C G . PASS AF=0.036416 ES:SE:LP:AF:ID -0.000557046:0.00208661:0.102373:0.036416:rs28454925
1 729632 rs116720794 C T . PASS AF=0.036745 ES:SE:LP:AF:ID -0.000536037:0.00206764:0.09691:0.036745:rs116720794
1 729679 rs4951859 C G . PASS AF=0.843032 ES:SE:LP:AF:ID -5.54841e-05:0.00106845:0.0177288:0.843032:rs4951859
1 730087 rs148120343 T C . PASS AF=0.056041 ES:SE:LP:AF:ID 0.00160858:0.00172863:0.455932:0.056041:rs148120343
1 731718 rs58276399 T C . PASS AF=0.122705 ES:SE:LP:AF:ID 0.000674967:0.00116768:0.251812:0.122705:rs58276399
1 732989 rs369030935 C T . PASS AF=0.025586 ES:SE:LP:AF:ID -0.00161595:0.00288287:0.236572:0.025586:rs369030935
1 734349 rs141242758 T C . PASS AF=0.121928 ES:SE:LP:AF:ID 0.000621748:0.00116821:0.229148:0.121928:rs141242758
1 736289 rs79010578 T A . PASS AF=0.132582 ES:SE:LP:AF:ID 0.000344872:0.00115223:0.119186:0.132582:rs79010578
1 752478 rs146277091 G A . PASS AF=0.036653 ES:SE:LP:AF:ID -0.000815593:0.00204703:0.161151:0.036653:rs146277091
1 752566 rs3094315 G A . PASS AF=0.838725 ES:SE:LP:AF:ID -3.44119e-05:0.0010342:0.0132283:0.838725:rs3094315
1 752721 rs3131972 A G . PASS AF=0.838352 ES:SE:LP:AF:ID 2.0663e-05:0.00103318:0.00877392:0.838352:rs3131972
1 753405 rs3115860 C A . PASS AF=0.869399 ES:SE:LP:AF:ID -0.000465713:0.00110757:0.173925:0.869399:rs3115860
1 753541 rs2073813 G A . PASS AF=0.130253 ES:SE:LP:AF:ID 0.000516396:0.00111003:0.19382:0.130253:rs2073813
1 754063 rs12184312 G T . PASS AF=0.037121 ES:SE:LP:AF:ID -0.00051705:0.00201321:0.09691:0.037121:rs12184312
1 754105 rs12184325 C T . PASS AF=0.037384 ES:SE:LP:AF:ID -0.000519406:0.00199977:0.09691:0.037384:rs12184325
1 754182 rs3131969 A G . PASS AF=0.868732 ES:SE:LP:AF:ID -0.000451762:0.00110553:0.167491:0.868732:rs3131969
1 754192 rs3131968 A G . PASS AF=0.868802 ES:SE:LP:AF:ID -0.000465627:0.00110592:0.173925:0.868802:rs3131968
1 754211 rs12184313 G A . PASS AF=0.037334 ES:SE:LP:AF:ID -0.000504493:0.00200865:0.09691:0.037334:rs12184313
1 754334 rs3131967 T C . PASS AF=0.868732 ES:SE:LP:AF:ID -0.000455057:0.00110549:0.167491:0.868732:rs3131967
1 754503 rs3115859 G A . PASS AF=0.8378 ES:SE:LP:AF:ID -1.95782e-05:0.00103028:0.00877392:0.8378:rs3115859
1 754629 rs10454459 A G . PASS AF=0.037347 ES:SE:LP:AF:ID -0.000464006:0.00201166:0.0861861:0.037347:rs10454459
1 754964 rs3131966 C T . PASS AF=0.838436 ES:SE:LP:AF:ID 2.93336e-05:0.00103317:0.00877392:0.838436:rs3131966
1 755775 rs3131965 A G . PASS AF=0.839574 ES:SE:LP:AF:ID -0.000166585:0.00104702:0.0604807:0.839574:rs3131965
1 755890 rs3115858 A T . PASS AF=0.869019 ES:SE:LP:AF:ID -0.000517554:0.00110406:0.19382:0.869019:rs3115858
1 756604 rs3131962 A G . PASS AF=0.868559 ES:SE:LP:AF:ID -0.000529782:0.00110128:0.200659:0.868559:rs3131962
1 757640 rs3115853 G A . PASS AF=0.867537 ES:SE:LP:AF:ID -0.00049081:0.00109948:0.180456:0.867537:rs3115853
1 757734 rs4951929 C T . PASS AF=0.868706 ES:SE:LP:AF:ID -0.000506517:0.00110221:0.187087:0.868706:rs4951929
1 757936 rs4951862 C A . PASS AF=0.868716 ES:SE:LP:AF:ID -0.00050443:0.00110229:0.187087:0.868716:rs4951862
1 758144 rs3131956 A G . PASS AF=0.868723 ES:SE:LP:AF:ID -0.000509439:0.00110231:0.19382:0.868723:rs3131956
1 758626 rs3131954 C T . PASS AF=0.869194 ES:SE:LP:AF:ID -0.000538281:0.00110529:0.200659:0.869194:rs3131954