manhattan_plot
qq_plot
af_plot
pz_plot
beta_std_plot
{
"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-d-22601_31193034,TotalVariants=9855759,VariantsNotRead=0,HarmonisedVariants=9855759,VariantsNotHarmonised=0,SwitchedAlleles=208,StudyType=Continuous>",
"contig": "<ID=1,length=249250621,assembly=HG19/GRCh37>",
"contig.1": "<ID=2,length=243199373,assembly=HG19/GRCh37>",
"contig.2": "<ID=3,length=198022430,assembly=HG19/GRCh37>",
"contig.3": "<ID=4,length=191154276,assembly=HG19/GRCh37>",
"contig.4": "<ID=5,length=180915260,assembly=HG19/GRCh37>",
"contig.5": "<ID=6,length=171115067,assembly=HG19/GRCh37>",
"contig.6": "<ID=7,length=159138663,assembly=HG19/GRCh37>",
"contig.7": "<ID=8,length=146364022,assembly=HG19/GRCh37>",
"contig.8": "<ID=9,length=141213431,assembly=HG19/GRCh37>",
"contig.9": "<ID=10,length=135534747,assembly=HG19/GRCh37>",
"contig.10": "<ID=11,length=135006516,assembly=HG19/GRCh37>",
"contig.11": "<ID=12,length=133851895,assembly=HG19/GRCh37>",
"contig.12": "<ID=13,length=115169878,assembly=HG19/GRCh37>",
"contig.13": "<ID=14,length=107349540,assembly=HG19/GRCh37>",
"contig.14": "<ID=15,length=102531392,assembly=HG19/GRCh37>",
"contig.15": "<ID=16,length=90354753,assembly=HG19/GRCh37>",
"contig.16": "<ID=17,length=81195210,assembly=HG19/GRCh37>",
"contig.17": "<ID=18,length=78077248,assembly=HG19/GRCh37>",
"contig.18": "<ID=19,length=59128983,assembly=HG19/GRCh37>",
"contig.19": "<ID=20,length=63025520,assembly=HG19/GRCh37>",
"contig.20": "<ID=21,length=48129895,assembly=HG19/GRCh37>",
"contig.21": "<ID=22,length=51304566,assembly=HG19/GRCh37>",
"contig.22": "<ID=X,length=155270560,assembly=HG19/GRCh37>",
"contig.23": "<ID=Y,length=59373566,assembly=HG19/GRCh37>",
"contig.24": "<ID=MT,length=16569,assembly=HG19/GRCh37>",
"contig.25": "<ID=GL000207.1,length=4262,assembly=HG19/GRCh37>",
"contig.26": "<ID=GL000226.1,length=15008,assembly=HG19/GRCh37>",
"contig.27": "<ID=GL000229.1,length=19913,assembly=HG19/GRCh37>",
"contig.28": "<ID=GL000231.1,length=27386,assembly=HG19/GRCh37>",
"contig.29": "<ID=GL000210.1,length=27682,assembly=HG19/GRCh37>",
"contig.30": "<ID=GL000239.1,length=33824,assembly=HG19/GRCh37>",
"contig.31": "<ID=GL000235.1,length=34474,assembly=HG19/GRCh37>",
"contig.32": "<ID=GL000201.1,length=36148,assembly=HG19/GRCh37>",
"contig.33": "<ID=GL000247.1,length=36422,assembly=HG19/GRCh37>",
"contig.34": "<ID=GL000245.1,length=36651,assembly=HG19/GRCh37>",
"contig.35": "<ID=GL000197.1,length=37175,assembly=HG19/GRCh37>",
"contig.36": "<ID=GL000203.1,length=37498,assembly=HG19/GRCh37>",
"contig.37": "<ID=GL000246.1,length=38154,assembly=HG19/GRCh37>",
"contig.38": "<ID=GL000249.1,length=38502,assembly=HG19/GRCh37>",
"contig.39": "<ID=GL000196.1,length=38914,assembly=HG19/GRCh37>",
"contig.40": "<ID=GL000248.1,length=39786,assembly=HG19/GRCh37>",
"contig.41": "<ID=GL000244.1,length=39929,assembly=HG19/GRCh37>",
"contig.42": "<ID=GL000238.1,length=39939,assembly=HG19/GRCh37>",
"contig.43": "<ID=GL000202.1,length=40103,assembly=HG19/GRCh37>",
"contig.44": "<ID=GL000234.1,length=40531,assembly=HG19/GRCh37>",
"contig.45": "<ID=GL000232.1,length=40652,assembly=HG19/GRCh37>",
"contig.46": "<ID=GL000206.1,length=41001,assembly=HG19/GRCh37>",
"contig.47": "<ID=GL000240.1,length=41933,assembly=HG19/GRCh37>",
"contig.48": "<ID=GL000236.1,length=41934,assembly=HG19/GRCh37>",
"contig.49": "<ID=GL000241.1,length=42152,assembly=HG19/GRCh37>",
"contig.50": "<ID=GL000243.1,length=43341,assembly=HG19/GRCh37>",
"contig.51": "<ID=GL000242.1,length=43523,assembly=HG19/GRCh37>",
"contig.52": "<ID=GL000230.1,length=43691,assembly=HG19/GRCh37>",
"contig.53": "<ID=GL000237.1,length=45867,assembly=HG19/GRCh37>",
"contig.54": "<ID=GL000233.1,length=45941,assembly=HG19/GRCh37>",
"contig.55": "<ID=GL000204.1,length=81310,assembly=HG19/GRCh37>",
"contig.56": "<ID=GL000198.1,length=90085,assembly=HG19/GRCh37>",
"contig.57": "<ID=GL000208.1,length=92689,assembly=HG19/GRCh37>",
"contig.58": "<ID=GL000191.1,length=106433,assembly=HG19/GRCh37>",
"contig.59": "<ID=GL000227.1,length=128374,assembly=HG19/GRCh37>",
"contig.60": "<ID=GL000228.1,length=129120,assembly=HG19/GRCh37>",
"contig.61": "<ID=GL000214.1,length=137718,assembly=HG19/GRCh37>",
"contig.62": "<ID=GL000221.1,length=155397,assembly=HG19/GRCh37>",
"contig.63": "<ID=GL000209.1,length=159169,assembly=HG19/GRCh37>",
"contig.64": "<ID=GL000218.1,length=161147,assembly=HG19/GRCh37>",
"contig.65": "<ID=GL000220.1,length=161802,assembly=HG19/GRCh37>",
"contig.66": "<ID=GL000213.1,length=164239,assembly=HG19/GRCh37>",
"contig.67": "<ID=GL000211.1,length=166566,assembly=HG19/GRCh37>",
"contig.68": "<ID=GL000199.1,length=169874,assembly=HG19/GRCh37>",
"contig.69": "<ID=GL000217.1,length=172149,assembly=HG19/GRCh37>",
"contig.70": "<ID=GL000216.1,length=172294,assembly=HG19/GRCh37>",
"contig.71": "<ID=GL000215.1,length=172545,assembly=HG19/GRCh37>",
"contig.72": "<ID=GL000205.1,length=174588,assembly=HG19/GRCh37>",
"contig.73": "<ID=GL000219.1,length=179198,assembly=HG19/GRCh37>",
"contig.74": "<ID=GL000224.1,length=179693,assembly=HG19/GRCh37>",
"contig.75": "<ID=GL000223.1,length=180455,assembly=HG19/GRCh37>",
"contig.76": "<ID=GL000195.1,length=182896,assembly=HG19/GRCh37>",
"contig.77": "<ID=GL000212.1,length=186858,assembly=HG19/GRCh37>",
"contig.78": "<ID=GL000222.1,length=186861,assembly=HG19/GRCh37>",
"contig.79": "<ID=GL000200.1,length=187035,assembly=HG19/GRCh37>",
"contig.80": "<ID=GL000193.1,length=189789,assembly=HG19/GRCh37>",
"contig.81": "<ID=GL000194.1,length=191469,assembly=HG19/GRCh37>",
"contig.82": "<ID=GL000225.1,length=211173,assembly=HG19/GRCh37>",
"contig.83": "<ID=GL000192.1,length=547496,assembly=HG19/GRCh37>",
"gwas_harmonisation_command": "--json /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ukb-d-import/processed/ukb-d-22601_31193034/ukb-d-22601_31193034_data.json --ref /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/QC/genomes/b37/human_g1k_v37.fasta; 1.1.1",
"file_date": "2019-11-25T13:52:19.672482",
"bcftools_annotateVersion": "1.9-74-g6af271c+htslib-1.9-64-g226b4a8",
"bcftools_annotateCommand": "annotate -a /mnt/storage/home/gh13047/mr-eve/vcf-reference-datasets/dbsnp/dbsnp.v153.b37.vcf.gz -c ID -o /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ukb-d-import/processed/ukb-d-22601_31193034/ukb-d-22601_31193034.vcf.gz -O z /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ukb-d-import/processed/ukb-d-22601_31193034/ukb-d-22601_31193034_data.vcf.gz; Date=Mon Nov 25 14:40:22 2019",
"bcftools_viewVersion": "1.9-74-g6af271c+htslib-1.9-64-g226b4a8",
"bcftools_viewCommand": "view -h /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/ukb-d-22601_31193034/ukb-d-22601_31193034.vcf.gz; Date=Sun May 10 01:57:41 2020"
}
*********************************************************************
* 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/dev/ukb-d-import/processed/ukb-d-22601_31193034/ukb-d-22601_31193034.vcf.gz \
--ref-ld-chr /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/reference/eur_w_ld_chr/ \
--out /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ukb-d-import/processed/ukb-d-22601_31193034/ldsc.txt \
--w-ld-chr /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/reference/eur_w_ld_chr/
Beginning analysis at Mon Nov 25 15:33:46 2019
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ukb-d-import/processed/ukb-d-22601_31193034/ukb-d-22601_31193034.vcf.gz ...
Read summary statistics for 9855759 SNPs.
Dropped 7533 SNPs with duplicated rs numbers.
Reading reference panel LD Score from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/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 /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/reference/eur_w_ld_chr/[1-22] ...
Read regression weight LD Scores for 1290028 SNPs.
After merging with reference panel LD, 1276989 SNPs remain.
After merging with regression SNP LD, 1276989 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: -0.0015 (0.0043)
Lambda GC: 0.9994
Mean Chi^2: 1.0015
Intercept: 1.0042 (0.0055)
Ratio: 2.7954 (3.6374)
Analysis finished at Mon Nov 25 15:35:25 2019
Total time elapsed: 1.0m:38.63s
{
"af_correlation": 0.9409,
"inflation_factor": 1.0024,
"mean_EFFECT": 1.2825e-06,
"n": 89866,
"n_snps": 9855759,
"n_clumped_hits": 2,
"n_p_sig": 2,
"n_mono": 0,
"n_ns": 1073888,
"n_mac": 0,
"is_snpid_unique": false,
"n_miss_EFFECT": 0,
"n_miss_SE": 0,
"n_miss_PVAL": 0,
"n_miss_AF": 0,
"n_miss_AF_reference": 195513,
"n_est": 89862.4794,
"ratio_se_n": 1,
"mean_diff": 7.6584e-06,
"ratio_diff": 5.5695,
"sd_y_est1": 0.1243,
"sd_y_est2": 0.1243,
"r2_sum1": 0,
"r2_sum2": 0.0007,
"r2_sum3": 0.0007,
"r2_sum4": 0.0007,
"ldsc_nsnp_merge_refpanel_ld": 1276989,
"ldsc_nsnp_merge_regression_ld": 1276989,
"ldsc_observed_scale_h2_beta": "NA",
"ldsc_observed_scale_h2_se": "NA",
"ldsc_intercept_beta": 1.0042,
"ldsc_intercept_se": 0.0055,
"ldsc_lambda_gc": 0.9994,
"ldsc_mean_chisq": 1.0015,
"ldsc_ratio": 2.8
}
name | value |
---|---|
af_correlation | FALSE |
inflation_factor | FALSE |
n | FALSE |
is_snpid_non_unique | TRUE |
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 |
General metrics
af_correlation
: Correlation coefficient between AF
and AF_reference
.inflation_factor
(lambda
): Genomic inflation factor.mean_EFFECT
: Mean of EFFECT
size.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 below 5e-8
.n_mono
: Number of monomorphic (MAF == 1
or MAF == 0
) SNPs.n_ns
: Number of SNPs with nonsense values:
A, C, G or T
.< 0
or > 1
.<= 0
or = Infinity
).< 0
or > 1
.n_mac
: Number of cases where MAC
(\(2 \times N \times MAF\)) is less than 6
.is_snpid_unique
: true
if the combination of ID
REF
ALT
is unique and therefore no duplication in snpid.n_miss_<*>
: Number of NA
observations 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 expect ratio_se_n
to 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.
ratio_diff
: \(\texttt{ratio_diff} = |\frac{\texttt{mean_diff}}{\texttt{mean_diff2}}|\), absolute ratio between the mean of diff
and the mean of diff2
(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.
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.
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.
r2 metrics
Sum of variance explained, calculated from the clumped top hits sample.
r2_sum<*>
: r2
statistics under various assumptions
1
: \(r^2 = \sum_j{\frac{2 \times \beta_j^2 \times {MAF}_j \times (1 - {MAF}_j)}{\texttt{var1}}}\), \(\texttt{var1} = 1\).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
: NOT is_snpid_unique
.mean_EFFECT_nonfinite
: mean(EFFECT)
is NA
, NaN
, or Inf
.mean_EFFECT_05
: abs(mean(EFFECT))
> 0.5.mean_EFFECT_01
: abs(mean(EFFECT))
> 0.1.mean_chisq
: ldsc_mean_chisq
> 1.3 or ldsc_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<*>
> 0.5Plots
skim_type | skim_variable | n_missing | complete_rate | character.min | character.max | character.empty | character.n_unique | character.whitespace | numeric.mean | numeric.sd | numeric.p0 | numeric.p25 | numeric.p50 | numeric.p75 | numeric.p100 | numeric.hist |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
character | ID | 0 | 1.0000000 | 3 | 94 | 0 | 9848773 | 0 | NA | NA | NA | NA | NA | NA | NA | NA |
character | REF | 0 | 1.0000000 | 1 | 98 | 0 | 47679 | 0 | NA | NA | NA | NA | NA | NA | NA | NA |
character | ALT | 0 | 1.0000000 | 1 | 342 | 0 | 29935 | 0 | NA | NA | NA | NA | NA | NA | NA | NA |
numeric | CHROM | 0 | 1.0000000 | NA | NA | NA | NA | NA | 9.080095e+00 | 6.176579e+00 | 1.00000e+00 | 4.000000e+00 | 8.000000e+00 | 1.300000e+01 | 2.300000e+01 | ▇▅▅▂▂ |
numeric | POS | 0 | 1.0000000 | NA | NA | NA | NA | NA | 7.875032e+07 | 5.609887e+07 | 3.02000e+02 | 3.245476e+07 | 6.964884e+07 | 1.147409e+08 | 2.492297e+08 | ▇▆▅▂▁ |
numeric | EFFECT | 0 | 1.0000000 | NA | NA | NA | NA | NA | 1.300000e-06 | 1.365800e-03 | -1.21554e-02 | -6.496000e-04 | -1.120000e-05 | 6.320000e-04 | 1.558740e-02 | ▁▂▇▁▁ |
numeric | SE | 0 | 1.0000000 | NA | NA | NA | NA | NA | 1.179600e-03 | 6.962000e-04 | 4.84900e-04 | 6.441000e-04 | 8.688000e-04 | 1.519100e-03 | 3.888500e-03 | ▇▂▁▁▁ |
numeric | PVAL | 0 | 1.0000000 | NA | NA | NA | NA | NA | 4.996939e-01 | 2.884345e-01 | 0.00000e+00 | 2.502770e-01 | 4.994822e-01 | 7.494989e-01 | 1.000000e+00 | ▇▇▇▇▇ |
numeric | PVAL_ztest | 0 | 1.0000000 | NA | NA | NA | NA | NA | 4.996922e-01 | 2.884356e-01 | 0.00000e+00 | 2.502740e-01 | 4.994801e-01 | 7.494986e-01 | 9.999999e-01 | ▇▇▇▇▇ |
numeric | AF | 0 | 1.0000000 | NA | NA | NA | NA | NA | 2.578968e-01 | 2.629296e-01 | 8.91580e-03 | 4.104100e-02 | 1.542520e-01 | 4.108930e-01 | 9.910840e-01 | ▇▂▂▁▁ |
numeric | AF_reference | 195513 | 0.9801626 | NA | NA | NA | NA | NA | 2.574820e-01 | 2.537487e-01 | 0.00000e+00 | 4.612620e-02 | 1.697280e-01 | 4.069490e-01 | 1.000000e+00 | ▇▃▂▁▁ |
numeric | N | 0 | 1.0000000 | NA | NA | NA | NA | NA | 8.986600e+04 | 0.000000e+00 | 8.98660e+04 | 8.986600e+04 | 8.986600e+04 | 8.986600e+04 | 8.986600e+04 | ▁▁▇▁▁ |
CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
---|---|---|---|---|---|---|---|---|---|---|---|
1 | 692794 | rs530212009 | CA | C | 0.0011659 | 0.0010244 | 0.2550721 | 0.2550669 | 0.1114870 | 0.1894970 | 89866 |
1 | 693731 | rs12238997 | A | G | 0.0001687 | 0.0009704 | 0.8619850 | 0.8619845 | 0.1164980 | 0.1417730 | 89866 |
1 | 707522 | rs371890604 | G | C | 0.0007492 | 0.0010909 | 0.4922435 | 0.4922426 | 0.0978285 | 0.1293930 | 89866 |
1 | 717587 | rs144155419 | G | A | 0.0014640 | 0.0025986 | 0.5731786 | 0.5731779 | 0.0158090 | 0.0045926 | 89866 |
1 | 730087 | rs148120343 | T | C | 0.0005507 | 0.0013456 | 0.6823717 | 0.6823703 | 0.0569661 | 0.0127796 | 89866 |
1 | 731718 | rs142557973 | T | C | 0.0002444 | 0.0009209 | 0.7907132 | 0.7907137 | 0.1223780 | 0.1543530 | 89866 |
1 | 732032 | rs61770163 | A | C | 0.0003941 | 0.0009817 | 0.6881086 | 0.6881081 | 0.1220530 | 0.1555510 | 89866 |
1 | 734349 | rs141242758 | T | C | 0.0002610 | 0.0009215 | 0.7770393 | 0.7770388 | 0.1216170 | 0.1525560 | 89866 |
1 | 749963 | rs529266287 | T | TAA | -0.0003278 | 0.0009067 | 0.7176736 | 0.7176722 | 0.8689590 | 0.7641770 | 89866 |
1 | 751343 | rs28544273 | T | A | 0.0003408 | 0.0008988 | 0.7045681 | 0.7045671 | 0.1236780 | 0.2426120 | 89866 |
CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
---|---|---|---|---|---|---|---|---|---|---|---|
23 | 154923311 | rs141127553 | C | T | 0.0006627 | 0.0010778 | 0.5386703 | 0.5386661 | 0.0553576 | 0.0309934 | 89866 |
23 | 154923374 | rs111332691 | T | A | -0.0005514 | 0.0011734 | 0.6384193 | 0.6384198 | 0.0449113 | 0.0116556 | 89866 |
23 | 154925045 | rs509981 | C | T | 0.0002897 | 0.0005659 | 0.6086519 | 0.6086510 | 0.2444280 | 0.3634440 | 89866 |
23 | 154925895 | rs538470 | C | T | 0.0001363 | 0.0005787 | 0.8138360 | 0.8138351 | 0.2408760 | 0.3634440 | 89866 |
23 | 154927581 | rs644138 | G | A | 0.0003924 | 0.0005323 | 0.4610542 | 0.4610525 | 0.3001910 | 0.4635760 | 89866 |
23 | 154929412 | rs557132 | C | T | 0.0002990 | 0.0005661 | 0.5973433 | 0.5973413 | 0.2442750 | 0.3568210 | 89866 |
23 | 154929637 | rs35185538 | CT | C | 0.0005081 | 0.0005911 | 0.3900336 | 0.3900325 | 0.2286930 | 0.3011920 | 89866 |
23 | 154929952 | rs4012982 | CAA | C | 0.0002385 | 0.0005957 | 0.6889505 | 0.6889498 | 0.2381980 | 0.3165560 | 89866 |
23 | 154930230 | rs781880 | A | G | 0.0002729 | 0.0005659 | 0.6296526 | 0.6296518 | 0.2447120 | 0.3618540 | 89866 |
23 | 154930487 | rs781879 | T | A | 0.0001910 | 0.0019197 | 0.9207319 | 0.9207323 | 0.0196791 | 0.1263580 | 89866 |
1 692794 rs530212009 CA C . PASS AF=0.111487 ES:SE:LP:AF:SS:ID 0.00116591:0.00102441:0.593337:0.111487:89866:1_692794_CA_C
1 693731 rs12238997 A G . PASS AF=0.116498 ES:SE:LP:AF:SS:ID 0.000168703:0.000970402:0.0645003:0.116498:89866:rs12238997
1 707522 rs371890604 G C . PASS AF=0.0978285 ES:SE:LP:AF:SS:ID 0.000749199:0.00109094:0.30782:0.0978285:89866:rs371890604
1 717587 rs144155419 G A . PASS AF=0.015809 ES:SE:LP:AF:SS:ID 0.00146397:0.00259856:0.24171:0.015809:89866:rs144155419
1 730087 rs148120343 T C . PASS AF=0.0569661 ES:SE:LP:AF:SS:ID 0.000550661:0.0013456:0.165979:0.0569661:89866:rs148120343
1 731718 rs58276399 T C . PASS AF=0.122378 ES:SE:LP:AF:SS:ID 0.000244382:0.000920862:0.101981:0.122378:89866:rs58276399
1 732032 rs61770163 A C . PASS AF=0.122053 ES:SE:LP:AF:SS:ID 0.000394095:0.000981743:0.162343:0.122053:89866:rs61770163
1 734349 rs141242758 T C . PASS AF=0.121617 ES:SE:LP:AF:SS:ID 0.000260964:0.000921548:0.109557:0.121617:89866:rs141242758
1 749963 rs529266287 T TAA . PASS AF=0.868959 ES:SE:LP:AF:SS:ID -0.000327824:0.000906664:0.144073:0.868959:89866:rs529266287
1 751343 rs28544273 T A . PASS AF=0.123678 ES:SE:LP:AF:SS:ID 0.000340802:0.000898828:0.152077:0.123678:89866:rs28544273
1 751488 rs200141114 G GA . PASS AF=0.143191 ES:SE:LP:AF:SS:ID 0.000382081:0.00088989:0.175442:0.143191:89866:rs200141114
1 751756 rs28527770 T C . PASS AF=0.123813 ES:SE:LP:AF:SS:ID 0.000336157:0.000897531:0.149962:0.123813:89866:rs28527770
1 753405 rs3115860 C A . PASS AF=0.869927 ES:SE:LP:AF:SS:ID -0.000126901:0.000874516:0.0532408:0.869927:89866:rs3115860
1 753425 rs3131970 T C . PASS AF=0.87461 ES:SE:LP:AF:SS:ID -9.6502e-05:0.000888774:0.0392739:0.87461:89866:rs3131970
1 753541 rs2073813 G A . PASS AF=0.12951 ES:SE:LP:AF:SS:ID 0.000160831:0.00087719:0.0682752:0.12951:89866:rs2073813
1 754105 rs12184325 C T . PASS AF=0.0357365 ES:SE:LP:AF:SS:ID 0.00212536:0.00160481:0.731928:0.0357365:89866:rs12184325
1 754182 rs3131969 A G . PASS AF=0.869574 ES:SE:LP:AF:SS:ID -6.3726e-05:0.000873746:0.0260141:0.869574:89866:rs3131969
1 754192 rs3131968 A G . PASS AF=0.869652 ES:SE:LP:AF:SS:ID -7.534e-05:0.000874135:0.0309025:0.869652:89866:rs3131968
1 754334 rs3131967 T C . PASS AF=0.86957 ES:SE:LP:AF:SS:ID -6.16998e-05:0.000873711:0.0251651:0.86957:89866:rs3131967
1 755890 rs3115858 A T . PASS AF=0.869566 ES:SE:LP:AF:SS:ID -7.81734e-06:0.000871979:0.00311767:0.869566:89866:rs3115858
1 756434 rs61768170 G C . PASS AF=0.126879 ES:SE:LP:AF:SS:ID 0.000213854:0.000890154:0.0914394:0.126879:89866:rs61768170
1 756604 rs3131962 A G . PASS AF=0.869094 ES:SE:LP:AF:SS:ID 1.11721e-05:0.000869718:0.00447405:0.869094:89866:rs3131962
1 757640 rs3115853 G A . PASS AF=0.868498 ES:SE:LP:AF:SS:ID -6.39852e-05:0.000869186:0.0262641:0.868498:89866:rs3115853
1 757734 rs4951929 C T . PASS AF=0.869245 ES:SE:LP:AF:SS:ID -9.96459e-06:0.000870513:0.00398464:0.869245:89866:rs4951929
1 757936 rs4951862 C A . PASS AF=0.869251 ES:SE:LP:AF:SS:ID -1.23173e-05:0.000870572:0.00493019:0.869251:89866:rs4951862
1 758144 rs3131956 A G . PASS AF=0.869252 ES:SE:LP:AF:SS:ID -8.33805e-06:0.000870578:0.00333162:0.869252:89866:rs3131956
1 758626 rs3131954 C T . PASS AF=0.869724 ES:SE:LP:AF:SS:ID -1.52678e-05:0.000872893:0.00610326:0.869724:89866:rs3131954
1 759293 rs10157329 T A . PASS AF=0.0991203 ES:SE:LP:AF:SS:ID 0.000350423:0.00101619:0.136549:0.0991203:89866:rs10157329
1 759837 rs3115851 T A . PASS AF=0.873732 ES:SE:LP:AF:SS:ID -0.000100312:0.00088586:0.0410335:0.873732:89866:rs3115851
1 761732 rs2286139 C T . PASS AF=0.863116 ES:SE:LP:AF:SS:ID -0.000403338:0.000868892:0.192122:0.863116:89866:rs2286139
1 761752 rs1057213 C T . PASS AF=0.868511 ES:SE:LP:AF:SS:ID -0.000185431:0.000877573:0.0795354:0.868511:89866:rs1057213
1 762273 rs3115849 G A . PASS AF=0.86539 ES:SE:LP:AF:SS:ID -0.000107304:0.000877702:0.044458:0.86539:89866:rs3115849
1 762485 rs12095200 C A . PASS AF=0.0994301 ES:SE:LP:AF:SS:ID -0.000381362:0.00105105:0.144647:0.0994301:89866:rs12095200
1 762589 rs3115848 G C . PASS AF=0.870696 ES:SE:LP:AF:SS:ID -0.000157339:0.000887798:0.0658385:0.870696:89866:rs3115848
1 762592 rs3131950 C G . PASS AF=0.870695 ES:SE:LP:AF:SS:ID -0.000157329:0.000887798:0.065834:0.870695:89866:rs3131950
1 762601 rs3131949 T C . PASS AF=0.870693 ES:SE:LP:AF:SS:ID -0.000156934:0.000887801:0.0656571:0.870693:89866:rs3131949
1 762632 rs3131948 T A . PASS AF=0.871061 ES:SE:LP:AF:SS:ID -0.000183538:0.00088822:0.0776405:0.871061:89866:rs3131948
1 764191 rs7515915 T G . PASS AF=0.126484 ES:SE:LP:AF:SS:ID 0.000230694:0.000889117:0.0994816:0.126484:89866:rs7515915
1 766007 rs61768174 A C . PASS AF=0.106022 ES:SE:LP:AF:SS:ID 0.000129712:0.000966544:0.0490299:0.106022:89866:rs61768174
1 766105 rs2519015 T A . PASS AF=0.854451 ES:SE:LP:AF:SS:ID -0.000361805:0.000868685:0.169381:0.854451:89866:rs2519015
1 768116 rs376645387 A AGTTTT . PASS AF=0.839008 ES:SE:LP:AF:SS:ID -0.00059329:0.000858168:0.31038:0.839008:89866:rs376645387
1 768253 rs2977608 A C . PASS AF=0.76317 ES:SE:LP:AF:SS:ID -0.000387767:0.000689963:0.241006:0.76317:89866:rs2977608
1 768448 rs12562034 G A . PASS AF=0.10519 ES:SE:LP:AF:SS:ID 0.000369074:0.000950876:0.156199:0.10519:89866:rs12562034
1 769138 rs59306077 CAT C . PASS AF=0.129876 ES:SE:LP:AF:SS:ID 0.000249895:0.000876663:0.11036:0.129876:89866:rs762168062
1 769223 rs60320384 C G . PASS AF=0.129602 ES:SE:LP:AF:SS:ID 0.000200042:0.000875516:0.0865729:0.129602:89866:rs60320384
1 769963 rs7518545 G A . PASS AF=0.104469 ES:SE:LP:AF:SS:ID 0.000418446:0.000958208:0.178924:0.104469:89866:rs7518545
1 770181 rs146076599 A G . PASS AF=0.00900456 ES:SE:LP:AF:SS:ID 0.00313252:0.00338134:0.45071:0.00900456:89866:rs146076599
1 770886 rs371458725 G A . PASS AF=0.103468 ES:SE:LP:AF:SS:ID 0.000449312:0.000966522:0.19245:0.103468:89866:rs371458725
1 771410 rs2519006 C T . PASS AF=0.829371 ES:SE:LP:AF:SS:ID -0.000348795:0.00085457:0.165476:0.829371:89866:rs2519006
1 771823 rs2977605 T C . PASS AF=0.869112 ES:SE:LP:AF:SS:ID -0.000145318:0.000871292:0.0617105:0.869112:89866:rs2977605