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:10003,TotalVariants=9851866,VariantsNotRead=0,HarmonisedVariants=9851866,VariantsNotHarmonised=0,SwitchedAlleles=9851866,TotalControls=460123,TotalCases=2810,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_1140862382.vcf.gz --id UKB-b:10003 --data /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/ukbiobank/raw-output/data.batch_20003_1140862382.txt.gz --cohort_cases 2810 --cohort_controls 460123 --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": "2019-09-12T17:53:21.482971",
"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-10003/mac_discard.txt -Oz /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-10003/UKB-b-10003_raw.vcf.gz; Date=Thu Oct 17 12:23:24 2019",
"bcftools_viewCommand.1": "view -h /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/ukb-b-10003/ukb-b-10003.vcf.gz; Date=Fri May 8 07:09:17 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-10003/UKB-b-10003_data.vcf.gz \
--ref-ld-chr ../reference/eur_w_ld_chr/ \
--out /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-10003/ldsc.txt \
--w-ld-chr ../reference/eur_w_ld_chr/
Beginning analysis at Thu Oct 17 14:40:18 2019
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-10003/UKB-b-10003_data.vcf.gz ...
Read summary statistics for 3897653 SNPs.
Dropped 709 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, 933270 SNPs remain.
After merging with regression SNP LD, 933270 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.0046 (0.0012)
Lambda GC: 1.0482
Mean Chi^2: 1.0536
Intercept: 1.0075 (0.0093)
Ratio: 0.1394 (0.1732)
Analysis finished at Thu Oct 17 14:41:05 2019
Total time elapsed: 46.85sQC metrics
Metrics
Metrics
{
"af_correlation": 0.8712,
"inflation_factor": 1.0475,
"mean_EFFECT": 1.4804e-07,
"n": "-Inf",
"n_snps": 9851866,
"n_clumped_hits": 3,
"n_p_sig": 395,
"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": 31715,
"n_est": "NA",
"ratio_se_n": "NA",
"mean_diff": "NaN",
"ratio_diff": "NaN",
"sd_y_est1": "NA",
"sd_y_est2": "NA",
"r2_sum1": 0,
"r2_sum2": 0,
"r2_sum3": 0,
"r2_sum4": 0,
"ldsc_nsnp_merge_refpanel_ld": 933270,
"ldsc_nsnp_merge_regression_ld": 933270,
"ldsc_observed_scale_h2_beta": 0.0046,
"ldsc_observed_scale_h2_se": 0.0012,
"ldsc_intercept_beta": 1.0075,
"ldsc_intercept_se": 0.0093,
"ldsc_lambda_gc": 1.0482,
"ldsc_mean_chisq": 1.0536,
"ldsc_ratio": 0.1399
}
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 | 3896947 | 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 | 3897653 | 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 | 8.660267e+00 | 5.767456e+00 | 1.0000000 | 4.000000e+00 | 8.000000e+00 | 1.300000e+01 | 2.200000e+01 | <U+2587><U+2585><U+2583><U+2582><U+2582> |
| numeric | POS | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 7.856901e+07 | 5.675543e+07 | 828.0000000 | 3.161707e+07 | 6.890829e+07 | 1.147152e+08 | 2.492385e+08 | <U+2587><U+2586><U+2585><U+2582><U+2581> |
| numeric | EFFECT | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 1.000000e-07 | 1.944000e-04 | -0.0013494 | -1.276000e-04 | -4.000000e-07 | 1.271000e-04 | 1.580200e-03 | <U+2581><U+2582><U+2587><U+2581><U+2581> |
| numeric | SE | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 1.874000e-04 | 2.430000e-05 | 0.0001558 | 1.663000e-04 | 1.795000e-04 | 2.042000e-04 | 5.698000e-04 | <U+2587><U+2581><U+2581><U+2581><U+2581> |
| numeric | PVAL | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 4.933834e-01 | 2.907843e-01 | 0.0000000 | 2.399999e-01 | 4.899999e-01 | 7.499995e-01 | 1.000000e+00 | <U+2587><U+2587><U+2587><U+2587><U+2587> |
| numeric | PVAL_ztest | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 4.933836e-01 | 2.907588e-01 | 0.0000000 | 2.404420e-01 | 4.914419e-01 | 7.452283e-01 | 1.000000e+00 | <U+2587><U+2587><U+2587><U+2587><U+2587> |
| numeric | AF | 0 | 1.0000000 | NA | NA | NA | NA | NA | NA | NA | 3.984855e-01 | 2.094935e-01 | 0.1245560 | 2.157480e-01 | 3.525560e-01 | 5.545980e-01 | 8.754440e-01 | <U+2587><U+2585><U+2583><U+2583><U+2582> |
| numeric | AF_reference | 31715 | 0.9918631 | NA | NA | NA | NA | NA | NA | NA | 3.869357e-01 | 2.146118e-01 | 0.0000000 | 2.104630e-01 | 3.484420e-01 | 5.423320e-01 | 1.000000e+00 | <U+2585><U+2587><U+2585><U+2583><U+2581> |
Head and tail
| CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 | 49298 | rs200943160 | T | C | 0.0000092 | 0.0002867 | 0.9699999 | 0.9745272 | 0.623763 | 0.782149 | NA |
| 1 | 54676 | rs2462492 | C | T | -0.0005534 | 0.0002840 | 0.0510000 | 0.0513868 | 0.400401 | NA | NA |
| 1 | 91536 | rs6702460 | G | T | 0.0003550 | 0.0002797 | 0.2000000 | 0.2043812 | 0.456851 | 0.420727 | NA |
| 1 | 534192 | rs6680723 | C | T | 0.0002127 | 0.0003195 | 0.5099998 | 0.5055606 | 0.240960 | NA | NA |
| 1 | 706368 | rs55727773 | A | G | -0.0000287 | 0.0001983 | 0.8800001 | 0.8848533 | 0.515650 | 0.275160 | NA |
| 1 | 729679 | rs4951859 | C | G | -0.0001424 | 0.0002320 | 0.5400003 | 0.5393879 | 0.843212 | 0.639976 | NA |
| 1 | 736289 | rs79010578 | T | A | 0.0001591 | 0.0002504 | 0.5300002 | 0.5252447 | 0.132330 | 0.139577 | NA |
| 1 | 752566 | rs3094315 | G | A | -0.0001347 | 0.0002247 | 0.5500004 | 0.5488130 | 0.838951 | 0.718251 | NA |
| 1 | 752721 | rs3131972 | A | G | -0.0001149 | 0.0002244 | 0.6100002 | 0.6087114 | 0.838580 | 0.653355 | NA |
| 1 | 753405 | rs3115860 | C | A | -0.0000532 | 0.0002408 | 0.8300000 | 0.8251369 | 0.869781 | 0.751797 | NA |
| CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 22 | 51197266 | rs61290853 | A | G | -0.0000521 | 0.0001747 | 0.7700005 | 0.7656415 | 0.386333 | 0.4229230 | NA |
| 22 | 51198027 | rs34939255 | A | G | -0.0000857 | 0.0001978 | 0.6600001 | 0.6648123 | 0.254557 | 0.0984425 | NA |
| 22 | 51210289 | rs112565862 | C | T | -0.0000945 | 0.0002633 | 0.7199992 | 0.7196517 | 0.129955 | 0.1018370 | NA |
| 22 | 51211106 | rs9628250 | T | C | -0.0002393 | 0.0001961 | 0.2200002 | 0.2223666 | 0.271547 | 0.1671330 | NA |
| 22 | 51211392 | rs3888396 | T | C | -0.0001299 | 0.0002609 | 0.6200004 | 0.6187060 | 0.132635 | 0.1641370 | NA |
| 22 | 51212875 | rs2238837 | A | C | 0.0001606 | 0.0001863 | 0.3900004 | 0.3887435 | 0.331455 | 0.3724040 | NA |
| 22 | 51213613 | rs34726907 | C | T | 0.0001966 | 0.0002455 | 0.4199997 | 0.4231280 | 0.127816 | 0.1727240 | NA |
| 22 | 51216564 | rs9616970 | T | C | 0.0002090 | 0.0002444 | 0.3900004 | 0.3925475 | 0.128330 | 0.1563500 | NA |
| 22 | 51219006 | rs28729663 | G | A | 0.0001904 | 0.0002392 | 0.4299995 | 0.4261888 | 0.137953 | 0.2052720 | NA |
| 22 | 51237063 | rs3896457 | T | C | 0.0000506 | 0.0001907 | 0.7899998 | 0.7907438 | 0.297971 | 0.2050720 | NA |
bcf preview
1 49298 rs10399793 T C . PASS AF=0.623763 ES:SE:LP:AF:ID 9.15481e-06:0.000286707:0.0132283:0.623763:rs10399793
1 54676 rs2462492 C T . PASS AF=0.400401 ES:SE:LP:AF:ID -0.000553371:0.000284037:1.29243:0.400401:rs2462492
1 91536 rs6702460 G T . PASS AF=0.456851 ES:SE:LP:AF:ID 0.000354952:0.000279673:0.69897:0.456851:rs6702460
1 534192 rs6680723 C T . PASS AF=0.24096 ES:SE:LP:AF:ID 0.000212683:0.000319456:0.29243:0.24096:rs6680723
1 706368 rs12029736 A G . PASS AF=0.51565 ES:SE:LP:AF:ID -2.87199e-05:0.000198315:0.0555173:0.51565:rs12029736
1 729679 rs4951859 C G . PASS AF=0.843212 ES:SE:LP:AF:ID -0.000142396:0.000232014:0.267606:0.843212:rs4951859
1 736289 rs79010578 T A . PASS AF=0.13233 ES:SE:LP:AF:ID 0.000159079:0.000250407:0.275724:0.13233:rs79010578
1 752566 rs3094315 G A . PASS AF=0.838951 ES:SE:LP:AF:ID -0.00013471:0.000224689:0.259637:0.838951:rs3094315
1 752721 rs3131972 A G . PASS AF=0.83858 ES:SE:LP:AF:ID -0.000114898:0.000224448:0.21467:0.83858:rs3131972
1 753405 rs3115860 C A . PASS AF=0.869781 ES:SE:LP:AF:ID -5.32121e-05:0.000240841:0.0809219:0.869781:rs3115860
1 753541 rs2073813 G A . PASS AF=0.129871 ES:SE:LP:AF:ID 4.80475e-05:0.000241334:0.0757207:0.129871:rs2073813
1 754182 rs3131969 A G . PASS AF=0.869123 ES:SE:LP:AF:ID -3.33667e-05:0.000240369:0.05061:0.869123:rs3131969
1 754192 rs3131968 A G . PASS AF=0.869221 ES:SE:LP:AF:ID -3.72779e-05:0.000240465:0.0555173:0.869221:rs3131968
1 754334 rs3131967 T C . PASS AF=0.869126 ES:SE:LP:AF:ID -2.23526e-05:0.000240365:0.0315171:0.869126:rs3131967
1 754503 rs3115859 G A . PASS AF=0.838033 ES:SE:LP:AF:ID -8.62832e-05:0.000223824:0.154902:0.838033:rs3115859
1 754964 rs3131966 C T . PASS AF=0.838664 ES:SE:LP:AF:ID -8.2844e-05:0.000224453:0.148742:0.838664:rs3131966
1 755775 rs3131965 A G . PASS AF=0.839777 ES:SE:LP:AF:ID -0.000100581:0.000227489:0.180456:0.839777:rs3131965
1 755890 rs3115858 A T . PASS AF=0.869405 ES:SE:LP:AF:ID -4.06565e-05:0.000240087:0.0604807:0.869405:rs3115858
1 756604 rs3131962 A G . PASS AF=0.868952 ES:SE:LP:AF:ID -3.8294e-05:0.000239483:0.0604807:0.868952:rs3131962
1 757640 rs3115853 G A . PASS AF=0.867905 ES:SE:LP:AF:ID -2.8546e-05:0.000239024:0.0457575:0.867905:rs3115853
1 757734 rs4951929 C T . PASS AF=0.869095 ES:SE:LP:AF:ID -4.20584e-05:0.000239679:0.0655015:0.869095:rs4951929
1 757936 rs4951862 C A . PASS AF=0.869104 ES:SE:LP:AF:ID -4.2097e-05:0.000239697:0.0655015:0.869104:rs4951862
1 758144 rs3131956 A G . PASS AF=0.869112 ES:SE:LP:AF:ID -4.22934e-05:0.000239703:0.0655015:0.869112:rs3131956
1 758626 rs3131954 C T . PASS AF=0.869589 ES:SE:LP:AF:ID -3.15876e-05:0.000240361:0.0457575:0.869589:rs3131954
1 760912 rs1048488 C T . PASS AF=0.838313 ES:SE:LP:AF:ID -9.71751e-05:0.0002234:0.180456:0.838313:rs1048488
1 761147 rs3115850 T C . PASS AF=0.838434 ES:SE:LP:AF:ID -8.63432e-05:0.000223558:0.154902:0.838434:rs3115850
1 761732 rs2286139 C T . PASS AF=0.862261 ES:SE:LP:AF:ID -5.48894e-05:0.000238836:0.0861861:0.862261:rs2286139
1 763394 rs3115847 G A . PASS AF=0.706753 ES:SE:LP:AF:ID 1.70253e-05:0.000232505:0.0268721:0.706753:rs3115847
1 768253 rs2977608 A C . PASS AF=0.761304 ES:SE:LP:AF:ID 1.8191e-06:0.000189765:0.00436481:0.761304:rs2977608
1 769223 rs60320384 C G . PASS AF=0.129576 ES:SE:LP:AF:ID 5.00345e-05:0.00024119:0.0757207:0.129576:rs60320384
1 771823 rs2977605 T C . PASS AF=0.868911 ES:SE:LP:AF:ID -4.6954e-05:0.000239902:0.0757207:0.868911:rs2977605
1 771967 rs59066358 G A . PASS AF=0.129677 ES:SE:LP:AF:ID 5.72648e-05:0.000241034:0.091515:0.129677:rs59066358
1 772755 rs2905039 A C . PASS AF=0.868921 ES:SE:LP:AF:ID -5.1382e-05:0.000239906:0.0809219:0.868921:rs2905039
1 776546 rs12124819 A G . PASS AF=0.26539 ES:SE:LP:AF:ID -0.000134296:0.000211971:0.275724:0.26539:rs12124819
1 777122 rs2980319 A T . PASS AF=0.870044 ES:SE:LP:AF:ID -6.92425e-05:0.000240396:0.113509:0.870044:rs2980319
1 778745 rs1055606 A G . PASS AF=0.128576 ES:SE:LP:AF:ID 8.74483e-05:0.000241345:0.142668:0.128576:rs1055606
1 779322 rs4040617 A G . PASS AF=0.128873 ES:SE:LP:AF:ID 9.85895e-05:0.000240935:0.167491:0.128873:rs4040617
1 780785 rs2977612 T A . PASS AF=0.868786 ES:SE:LP:AF:ID -7.11468e-05:0.000239755:0.113509:0.868786:rs2977612
1 782981 rs6594026 C T . PASS AF=0.129513 ES:SE:LP:AF:ID 6.989e-05:0.000240858:0.113509:0.129513:rs6594026
1 785050 rs2905062 G A . PASS AF=0.868539 ES:SE:LP:AF:ID -7.52283e-05:0.000239699:0.124939:0.868539:rs2905062
1 785989 rs2980300 T C . PASS AF=0.86848 ES:SE:LP:AF:ID -7.20845e-05:0.000239848:0.119186:0.86848:rs2980300
1 787399 rs2905055 G T . PASS AF=0.86078 ES:SE:LP:AF:ID -0.000107225:0.000239684:0.187087:0.86078:rs2905055
1 787606 rs3863622 G T . PASS AF=0.128461 ES:SE:LP:AF:ID 7.26092e-05:0.000242156:0.119186:0.128461:rs3863622
1 787685 rs2905054 G T . PASS AF=0.861493 ES:SE:LP:AF:ID -8.24006e-05:0.000239842:0.136677:0.861493:rs2905054
1 787844 rs2905053 C T . PASS AF=0.869229 ES:SE:LP:AF:ID -5.69178e-05:0.000240725:0.091515:0.869229:rs2905053
1 791191 rs111818025 G A . PASS AF=0.127879 ES:SE:LP:AF:ID 6.62169e-05:0.000243707:0.102373:0.127879:rs111818025
1 795988 rs59380221 C T . PASS AF=0.143051 ES:SE:LP:AF:ID -2.16351e-05:0.000248604:0.0315171:0.143051:rs59380221
1 798400 rs10900604 A G . PASS AF=0.20658 ES:SE:LP:AF:ID -2.69083e-05:0.000202444:0.05061:0.20658:rs10900604
1 798959 rs11240777 G A . PASS AF=0.206409 ES:SE:LP:AF:ID -2.95488e-05:0.000202531:0.0555173:0.206409:rs11240777
1 808631 rs11240779 G A . PASS AF=0.772626 ES:SE:LP:AF:ID 0.000123686:0.000192661:0.283997:0.772626:rs11240779