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:8172,TotalVariants=9851866,VariantsNotRead=0,HarmonisedVariants=9851866,VariantsNotHarmonised=0,SwitchedAlleles=9851866,TotalControls=461832,TotalCases=1101,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_20003_1141153026.vcf.gz --id UKB-b:8172 --data /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/ukbiobank/raw-output/data.batch_20003_1141153026.txt.gz --cohort_cases 1101 --cohort_controls 461832 --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": "2019-09-13T11:57:34.348333",
"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-8172/mac_discard.txt -Oz /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-8172/UKB-b-8172_raw.vcf.gz; Date=Thu Oct 17 12:20:23 2019",
"bcftools_viewCommand.1": "view -h /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/ukb-b-8172/ukb-b-8172.vcf.gz; Date=Sun May 10 11:46:39 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-8172/UKB-b-8172_data.vcf.gz \
--ref-ld-chr ../reference/eur_w_ld_chr/ \
--out /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-8172/ldsc.txt \
--w-ld-chr ../reference/eur_w_ld_chr/
Beginning analysis at Thu Oct 17 14:41:23 2019
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-8172/UKB-b-8172_data.vcf.gz ...
Read summary statistics for 1637457 SNPs.
Dropped 151 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, 422690 SNPs remain.
After merging with regression SNP LD, 422690 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.0018 (0.0013)
Lambda GC: 1.0104
Mean Chi^2: 1.0109
Intercept: 0.9902 (0.0118)
Ratio < 0 (usually indicates GC correction).
Analysis finished at Thu Oct 17 14:41:50 2019
Total time elapsed: 27.36sQC metrics
Metrics
Metrics
{
"af_correlation": 0.624,
"inflation_factor": 1,
"mean_EFFECT": 1.7206e-07,
"n": "-Inf",
"n_snps": 9851866,
"n_clumped_hits": 0,
"n_p_sig": 0,
"n_mono": 0,
"n_ns": 0,
"n_mac": 0,
"is_snpid_unique": true,
"n_miss_EFFECT": 0,
"n_miss_SE": 0,
"n_miss_PVAL": 0,
"n_miss_AF": 0,
"n_miss_AF_reference": 12996,
"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": 422690,
"ldsc_nsnp_merge_regression_ld": 422690,
"ldsc_observed_scale_h2_beta": 0.0018,
"ldsc_observed_scale_h2_se": 0.0013,
"ldsc_intercept_beta": 0.9902,
"ldsc_intercept_se": 0.0118,
"ldsc_lambda_gc": 1.0104,
"ldsc_mean_chisq": 1.0109,
"ldsc_ratio": -0.8991
}
Flags
| name | value |
|---|---|
| af_correlation | TRUE |
| 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 | 4 | 58 | 0 | 1637308 | 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 | 1637457 | 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 | 8.661609e+00 | 5.766043e+00 | 1.00000e+00 | 4.000000e+00 | 8.000000e+00 | 1.300000e+01 | 2.200000e+01 | ▇▅▅▂▂ |
| numeric | POS | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 7.857462e+07 | 5.655083e+07 | 1.23330e+04 | 3.176931e+07 | 6.914485e+07 | 1.145268e+08 | 2.491722e+08 | ▇▆▅▂▁ |
| numeric | EFFECT | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 2.000000e-07 | 1.048000e-04 | -5.04000e-04 | -7.080000e-05 | 3.000000e-07 | 7.070000e-05 | 5.239000e-04 | ▁▂▇▂▁ |
| numeric | SE | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 1.042000e-04 | 3.100000e-06 | 9.77000e-05 | 1.020000e-04 | 1.035000e-04 | 1.058000e-04 | 1.984000e-04 | ▇▁▁▁▁ |
| numeric | PVAL | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 4.978632e-01 | 2.896963e-01 | 2.60000e-06 | 2.399999e-01 | 5.000000e-01 | 7.499995e-01 | 1.000000e+00 | ▇▇▇▇▇ |
| numeric | PVAL_ztest | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 4.978651e-01 | 2.896693e-01 | 2.60000e-06 | 2.442750e-01 | 4.968475e-01 | 7.498083e-01 | 9.999996e-01 | ▇▇▇▇▇ |
| numeric | AF | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 4.789689e-01 | 1.045363e-01 | 3.17893e-01 | 3.873090e-01 | 4.684730e-01 | 5.653230e-01 | 6.821070e-01 | ▇▇▆▅▅ |
| numeric | AF_reference | 12996 | 0.9920633 | NA | NA | NA | NA | NA | NA | NA | 4.577208e-01 | 1.492786e-01 | 1.99700e-04 | 3.452480e-01 | 4.508790e-01 | 5.646960e-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 | 0.0000343 | 0.0001798 | 0.8499999 | 0.8485700 | 0.623763 | 0.782149 | NA |
| 1 | 54676 | rs2462492 | C | T | 0.0000572 | 0.0001781 | 0.7499995 | 0.7482527 | 0.400401 | NA | NA |
| 1 | 91536 | rs6702460 | G | T | 0.0000754 | 0.0001754 | 0.6700003 | 0.6673591 | 0.456851 | 0.420727 | NA |
| 1 | 706368 | rs55727773 | A | G | -0.0000572 | 0.0001244 | 0.6499995 | 0.6456130 | 0.515650 | 0.275160 | NA |
| 1 | 814495 | rs74461805 | C | A | 0.0000295 | 0.0001705 | 0.8600001 | 0.8628515 | 0.340397 | NA | NA |
| 1 | 840753 | rs4970382 | T | C | -0.0001565 | 0.0001033 | 0.1299999 | 0.1299145 | 0.400106 | 0.468850 | NA |
| 1 | 843405 | rs11516185 | A | G | -0.0000418 | 0.0001283 | 0.7400005 | 0.7447187 | 0.362599 | 0.375399 | NA |
| 1 | 850218 | rs6664536 | T | A | 0.0000757 | 0.0001030 | 0.4600002 | 0.4627324 | 0.590333 | 0.345248 | NA |
| 1 | 850371 | rs6679046 | G | T | 0.0000696 | 0.0001036 | 0.5000000 | 0.5018975 | 0.603726 | 0.508786 | NA |
| 1 | 850780 | rs6657440 | C | T | 0.0000648 | 0.0001036 | 0.5300002 | 0.5315003 | 0.603944 | 0.560304 | NA |
| CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 22 | 51158499 | rs8136930 | T | G | -0.0001940 | 0.0001017 | 0.0560003 | 0.0563376 | 0.461648 | 0.544728 | NA |
| 22 | 51161019 | rs5770994 | C | T | 0.0001576 | 0.0001013 | 0.1199999 | 0.1198566 | 0.482193 | 0.425719 | NA |
| 22 | 51163039 | rs715584 | G | T | -0.0001515 | 0.0001029 | 0.1400000 | 0.1409296 | 0.426984 | 0.473642 | NA |
| 22 | 51164109 | rs5770995 | G | C | -0.0001391 | 0.0001023 | 0.1700000 | 0.1738390 | 0.452716 | 0.510982 | NA |
| 22 | 51164115 | rs5770996 | C | T | -0.0001605 | 0.0001022 | 0.1199999 | 0.1163802 | 0.456928 | 0.514776 | NA |
| 22 | 51174048 | rs9628245 | G | C | -0.0001921 | 0.0001155 | 0.0959997 | 0.0963433 | 0.380130 | 0.433107 | NA |
| 22 | 51186143 | rs2879914 | T | C | -0.0002464 | 0.0001089 | 0.0239999 | 0.0236315 | 0.381826 | 0.273363 | NA |
| 22 | 51186228 | rs3865766 | C | T | -0.0001948 | 0.0001061 | 0.0659994 | 0.0663358 | 0.451063 | 0.453275 | NA |
| 22 | 51197266 | rs61290853 | A | G | -0.0001214 | 0.0001096 | 0.2700001 | 0.2677205 | 0.386333 | 0.422923 | NA |
| 22 | 51212875 | rs2238837 | A | C | -0.0001940 | 0.0001168 | 0.0969996 | 0.0967701 | 0.331455 | 0.372404 | NA |
bcf preview
1 49298 rs10399793 T C . PASS AF=0.623763 ES:SE:LP:AF:ID 3.43299e-05:0.000179791:0.0705811:0.623763:rs10399793
1 54676 rs2462492 C T . PASS AF=0.400401 ES:SE:LP:AF:ID 5.71653e-05:0.000178116:0.124939:0.400401:rs2462492
1 91536 rs6702460 G T . PASS AF=0.456851 ES:SE:LP:AF:ID 7.5374e-05:0.00017538:0.173925:0.456851:rs6702460
1 706368 rs12029736 A G . PASS AF=0.51565 ES:SE:LP:AF:ID -5.71893e-05:0.000124361:0.187087:0.51565:rs12029736
1 814495 rs74461805 C A . PASS AF=0.340397 ES:SE:LP:AF:ID 2.94569e-05:0.000170522:0.0655015:0.340397:rs74461805
1 840753 rs4970382 T C . PASS AF=0.400106 ES:SE:LP:AF:ID -0.000156487:0.00010333:0.886057:0.400106:rs4970382
1 843405 rs11516185 A G . PASS AF=0.362599 ES:SE:LP:AF:ID -4.17671e-05:0.000128273:0.130768:0.362599:rs11516185
1 850218 rs6664536 T A . PASS AF=0.590333 ES:SE:LP:AF:ID 7.56584e-05:0.000103027:0.337242:0.590333:rs6664536
1 850371 rs6679046 G T . PASS AF=0.603726 ES:SE:LP:AF:ID 6.95715e-05:0.000103605:0.30103:0.603726:rs6679046
1 850780 rs6657440 C T . PASS AF=0.603944 ES:SE:LP:AF:ID 6.48187e-05:0.000103591:0.275724:0.603944:rs6657440
1 852037 rs4970463 G A . PASS AF=0.589688 ES:SE:LP:AF:ID 5.86243e-05:0.000103194:0.244125:0.589688:rs4970463
1 852063 rs28436996 G A . PASS AF=0.589667 ES:SE:LP:AF:ID 5.83265e-05:0.000103148:0.244125:0.589667:rs28436996
1 852875 rs13303369 C T . PASS AF=0.607674 ES:SE:LP:AF:ID 7.49384e-05:0.000103822:0.327902:0.607674:rs13303369
1 853954 rs1806509 C A . PASS AF=0.607833 ES:SE:LP:AF:ID 7.32246e-05:0.000103836:0.318759:0.607833:rs1806509
1 854777 rs13303019 A G . PASS AF=0.610318 ES:SE:LP:AF:ID 9.07371e-05:0.000103938:0.420216:0.610318:rs13303019
1 854978 rs13303057 A C . PASS AF=0.603286 ES:SE:LP:AF:ID 6.80864e-05:0.000103631:0.29243:0.603286:rs13303057
1 855075 rs6673914 C G . PASS AF=0.610338 ES:SE:LP:AF:ID 9.1785e-05:0.00010394:0.420216:0.610338:rs6673914
1 856099 rs28534711 T G . PASS AF=0.389935 ES:SE:LP:AF:ID -8.12672e-05:0.00010396:0.366532:0.389935:rs28534711
1 856108 rs28742275 A G . PASS AF=0.389918 ES:SE:LP:AF:ID -8.11951e-05:0.000103965:0.366532:0.389918:rs28742275
1 856476 rs4040605 A G . PASS AF=0.350351 ES:SE:LP:AF:ID -0.000135081:0.000106802:0.677781:0.350351:rs4040605
1 866893 rs2880024 T C . PASS AF=0.610554 ES:SE:LP:AF:ID 0.000152357:0.000104524:0.853872:0.610554:rs2880024
1 875770 rs4970379 A G . PASS AF=0.600084 ES:SE:LP:AF:ID 0.000140114:0.000105393:0.744727:0.600084:rs4970379
1 881627 rs2272757 G A . PASS AF=0.65239 ES:SE:LP:AF:ID 0.000165633:0.000106465:0.920819:0.65239:rs2272757
1 891059 rs13303065 C T . PASS AF=0.652428 ES:SE:LP:AF:ID 0.000169896:0.000106448:0.958607:0.652428:rs13303065
1 891945 rs13303106 A G . PASS AF=0.65249 ES:SE:LP:AF:ID 0.000170301:0.000106572:0.958607:0.65249:rs13303106
1 903245 rs28690976 A G . PASS AF=0.566937 ES:SE:LP:AF:ID 0.000231977:0.00010585:1.55284:0.566937:rs28690976
1 909073 rs3892467 C T . PASS AF=0.386683 ES:SE:LP:AF:ID -8.27868e-05:0.000105562:0.366532:0.386683:rs3892467
1 909238 rs3829740 G C . PASS AF=0.571412 ES:SE:LP:AF:ID -0.000131378:0.000102233:0.69897:0.571412:rs3829740
1 910394 rs28477686 C T . PASS AF=0.324456 ES:SE:LP:AF:ID -0.000121542:0.00011081:0.568636:0.324456:rs28477686
1 912049 rs7367995 T C . PASS AF=0.58525 ES:SE:LP:AF:ID 8.14856e-05:0.00010327:0.366532:0.58525:rs7367995
1 913889 rs2340596 G A . PASS AF=0.599213 ES:SE:LP:AF:ID 0.000115814:0.000103438:0.585027:0.599213:rs2340596
1 914333 rs13302979 C G . PASS AF=0.602521 ES:SE:LP:AF:ID 0.000106735:0.000103752:0.522879:0.602521:rs13302979
1 914852 rs13303368 G C . PASS AF=0.600078 ES:SE:LP:AF:ID 0.000104329:0.000103552:0.508638:0.600078:rs13303368
1 914940 rs13303033 T C . PASS AF=0.584292 ES:SE:LP:AF:ID 7.59556e-05:0.000102971:0.337242:0.584292:rs13303033
1 916834 rs6694632 G A . PASS AF=0.589106 ES:SE:LP:AF:ID 9.09343e-05:0.000103129:0.420216:0.589106:rs6694632
1 918384 rs13303118 G T . PASS AF=0.584205 ES:SE:LP:AF:ID 7.82626e-05:0.000102923:0.346787:0.584205:rs13303118
1 918573 rs2341354 A G . PASS AF=0.589331 ES:SE:LP:AF:ID 8.76564e-05:0.00010305:0.408935:0.589331:rs2341354
1 919501 rs4970414 G T . PASS AF=0.583932 ES:SE:LP:AF:ID 6.29328e-05:0.000106571:0.259637:0.583932:rs4970414
1 921716 rs13303278 C A . PASS AF=0.567888 ES:SE:LP:AF:ID 3.17811e-05:0.000102838:0.119186:0.567888:rs13303278
1 924528 rs34712273 C A . PASS AF=0.578492 ES:SE:LP:AF:ID 7.58978e-05:0.000103133:0.337242:0.578492:rs34712273
1 930533 rs3128110 C G . PASS AF=0.386078 ES:SE:LP:AF:ID -7.03735e-05:0.000104451:0.30103:0.386078:rs3128110
1 930567 rs3121574 A G . PASS AF=0.38612 ES:SE:LP:AF:ID -7.15932e-05:0.000104453:0.309804:0.38612:rs3121574
1 930751 rs3128111 C G . PASS AF=0.385075 ES:SE:LP:AF:ID -7.70802e-05:0.000104517:0.337242:0.385075:rs3128111
1 931166 rs2710880 A G . PASS AF=0.386762 ES:SE:LP:AF:ID -6.8748e-05:0.00010447:0.29243:0.386762:rs2710880
1 931362 rs2799060 G A . PASS AF=0.385568 ES:SE:LP:AF:ID -7.36515e-05:0.000104521:0.318759:0.385568:rs2799060
1 933790 rs9442392 G A . PASS AF=0.578607 ES:SE:LP:AF:ID 6.57925e-05:0.000103098:0.283997:0.578607:rs9442392
1 936111 rs1936360 C T . PASS AF=0.573546 ES:SE:LP:AF:ID 5.98362e-05:0.000103073:0.251812:0.573546:rs1936360
1 940005 rs2799056 A G . PASS AF=0.399259 ES:SE:LP:AF:ID -6.3311e-05:0.000104089:0.267606:0.399259:rs2799056
1 940096 rs4503294 C T . PASS AF=0.565311 ES:SE:LP:AF:ID 6.23943e-05:0.000102778:0.267606:0.565311:rs4503294
1 941284 rs3128116 C T . PASS AF=0.397393 ES:SE:LP:AF:ID -6.92817e-05:0.000104111:0.29243:0.397393:rs3128116