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-20531,TotalVariants=13571440,VariantsNotRead=0,HarmonisedVariants=13571440,VariantsNotHarmonised=0,SwitchedAlleles=229,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-20531/ukb-d-20531_data.json --ref /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/QC/genomes/b37/human_g1k_v37.fasta; 1.1.1",
"file_date": "2019-11-25T16:10:16.440843",
"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-20531/ukb-d-20531.vcf.gz -O z /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ukb-d-import/processed/ukb-d-20531/ukb-d-20531_data.vcf.gz; Date=Mon Nov 25 16:40:38 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-20531/ukb-d-20531.vcf.gz; Date=Sun May 10 23:21:48 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-20531/ukb-d-20531.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-20531/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 17:17:10 2019
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ukb-d-import/processed/ukb-d-20531/ukb-d-20531.vcf.gz ...
Read summary statistics for 13571440 SNPs.
Dropped 12692 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, 1283502 SNPs remain.
After merging with regression SNP LD, 1283502 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.0391 (0.0048)
Lambda GC: 1.0683
Mean Chi^2: 1.0836
Intercept: 0.9954 (0.0064)
Ratio < 0 (usually indicates GC correction).
Analysis finished at Mon Nov 25 17:19:30 2019
Total time elapsed: 2.0m:20.29s
{
"af_correlation": 0.9521,
"inflation_factor": 1.0422,
"mean_EFFECT": 0,
"n": 116671,
"n_snps": 13571440,
"n_clumped_hits": 1,
"n_p_sig": 3,
"n_mono": 0,
"n_ns": 1251336,
"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": 564553,
"n_est": 117096.1576,
"ratio_se_n": 1.0018,
"mean_diff": 0,
"ratio_diff": 43.7162,
"sd_y_est1": 0.3494,
"sd_y_est2": 0.3501,
"r2_sum1": 0,
"r2_sum2": 0.0003,
"r2_sum3": 0.0003,
"r2_sum4": 0.0003,
"ldsc_nsnp_merge_refpanel_ld": 1283502,
"ldsc_nsnp_merge_regression_ld": 1283502,
"ldsc_observed_scale_h2_beta": 0.0391,
"ldsc_observed_scale_h2_se": 0.0048,
"ldsc_intercept_beta": 0.9954,
"ldsc_intercept_se": 0.0064,
"ldsc_lambda_gc": 1.0683,
"ldsc_mean_chisq": 1.0836,
"ldsc_ratio": -0.055
}
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 | FALSE |
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 | 13559412 | 0 | NA | NA | NA | NA | NA | NA | NA | NA |
character | REF | 0 | 1.0000000 | 1 | 100 | 0 | 57054 | 0 | NA | NA | NA | NA | NA | NA | NA | NA |
character | ALT | 0 | 1.0000000 | 1 | 342 | 0 | 33331 | 0 | NA | NA | NA | NA | NA | NA | NA | NA |
numeric | CHROM | 0 | 1.0000000 | NA | NA | NA | NA | NA | 9.051431e+00 | 6.185060e+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 | 7.902502e+07 | 5.591566e+07 | 3.02000e+02 | 3.292807e+07 | 7.013925e+07 | 1.148583e+08 | 2.492309e+08 | ▇▆▅▂▁ |
numeric | EFFECT | 0 | 1.0000000 | NA | NA | NA | NA | NA | 2.450000e-05 | 8.454100e-03 | -9.66979e-02 | -2.293200e-03 | -3.500000e-06 | 2.281500e-03 | 1.103800e-01 | ▁▁▇▁▁ |
numeric | SE | 0 | 1.0000000 | NA | NA | NA | NA | NA | 6.060800e-03 | 5.842200e-03 | 1.19690e-03 | 1.729900e-03 | 3.183600e-03 | 8.702300e-03 | 2.908860e-02 | ▇▂▁▁▁ |
numeric | PVAL | 0 | 1.0000000 | NA | NA | NA | NA | NA | 4.931082e-01 | 2.904611e-01 | 0.00000e+00 | 2.401638e-01 | 4.910989e-01 | 7.445781e-01 | 1.000000e+00 | ▇▇▇▇▇ |
numeric | PVAL_ztest | 0 | 1.0000000 | NA | NA | NA | NA | NA | 4.931068e-01 | 2.904619e-01 | 0.00000e+00 | 2.401613e-01 | 4.910975e-01 | 7.445776e-01 | 9.999998e-01 | ▇▇▇▇▇ |
numeric | AF | 0 | 1.0000000 | NA | NA | NA | NA | NA | 1.909995e-01 | 2.544497e-01 | 1.00000e-03 | 7.483200e-03 | 6.026700e-02 | 2.956792e-01 | 9.990000e-01 | ▇▂▁▁▁ |
numeric | AF_reference | 564553 | 0.9584014 | NA | NA | NA | NA | NA | 1.964743e-01 | 2.471295e-01 | 0.00000e+00 | 5.790700e-03 | 8.446490e-02 | 3.083070e-01 | 1.000000e+00 | ▇▂▁▁▁ |
numeric | N | 0 | 1.0000000 | NA | NA | NA | NA | NA | 1.166710e+05 | 0.000000e+00 | 1.16671e+05 | 1.166710e+05 | 1.166710e+05 | 1.166710e+05 | 1.166710e+05 | ▁▁▇▁▁ |
CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
---|---|---|---|---|---|---|---|---|---|---|---|
1 | 692794 | rs530212009 | CA | C | 0.0058156 | 0.0025183 | 0.0209247 | 0.0209226 | 0.1117640 | 0.1894970 | 116671 |
1 | 693731 | rs12238997 | A | G | 0.0056749 | 0.0023848 | 0.0173325 | 0.0173307 | 0.1167870 | 0.1417730 | 116671 |
1 | 707522 | rs371890604 | G | C | 0.0062717 | 0.0026756 | 0.0190801 | 0.0190784 | 0.0984045 | 0.1293930 | 116671 |
1 | 717587 | rs144155419 | G | A | 0.0022287 | 0.0064033 | 0.7277982 | 0.7277978 | 0.0158098 | 0.0045926 | 116671 |
1 | 723329 | rs189787166 | A | T | 0.0143586 | 0.0187298 | 0.4433125 | 0.4433087 | 0.0017688 | 0.0003994 | 116671 |
1 | 730087 | rs148120343 | T | C | 0.0083217 | 0.0033178 | 0.0121361 | 0.0121346 | 0.0569652 | 0.0127796 | 116671 |
1 | 731718 | rs142557973 | T | C | 0.0048133 | 0.0022629 | 0.0334164 | 0.0334144 | 0.1227110 | 0.1543530 | 116671 |
1 | 732032 | rs61770163 | A | C | 0.0046893 | 0.0024114 | 0.0518239 | 0.0518220 | 0.1223360 | 0.1555510 | 116671 |
1 | 734349 | rs141242758 | T | C | 0.0048456 | 0.0022641 | 0.0323415 | 0.0323393 | 0.1219640 | 0.1525560 | 116671 |
1 | 740284 | rs61770167 | C | T | 0.0055912 | 0.0103665 | 0.5896401 | 0.5896402 | 0.0058416 | 0.0023962 | 116671 |
CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
---|---|---|---|---|---|---|---|---|---|---|---|
23 | 154923311 | rs141127553 | C | T | 0.0009777 | 0.0026603 | 0.7132372 | 0.7132371 | 0.0553982 | 0.0309934 | 116671 |
23 | 154923374 | rs111332691 | T | A | -0.0043412 | 0.0028998 | 0.1343869 | 0.1343848 | 0.0447326 | 0.0116556 | 116671 |
23 | 154925045 | rs509981 | C | T | 0.0022757 | 0.0013955 | 0.1029480 | 0.1029437 | 0.2447630 | 0.3634440 | 116671 |
23 | 154925895 | rs538470 | C | T | 0.0021054 | 0.0014270 | 0.1400990 | 0.1400968 | 0.2411910 | 0.3634440 | 116671 |
23 | 154927581 | rs644138 | G | A | 0.0023413 | 0.0013133 | 0.0746277 | 0.0746250 | 0.3005140 | 0.4635760 | 116671 |
23 | 154929412 | rs557132 | C | T | 0.0022723 | 0.0013959 | 0.1035481 | 0.1035456 | 0.2446370 | 0.3568210 | 116671 |
23 | 154929637 | rs35185538 | CT | C | 0.0029743 | 0.0014582 | 0.0413800 | 0.0413774 | 0.2288170 | 0.3011920 | 116671 |
23 | 154929952 | rs4012982 | CAA | C | 0.0025954 | 0.0014692 | 0.0773108 | 0.0773083 | 0.2386790 | 0.3165560 | 116671 |
23 | 154930230 | rs781880 | A | G | 0.0021788 | 0.0013954 | 0.1184459 | 0.1184422 | 0.2450490 | 0.3618540 | 116671 |
23 | 154930487 | rs781879 | T | A | -0.0021523 | 0.0047466 | 0.6502285 | 0.6502264 | 0.0196771 | 0.1263580 | 116671 |
1 692794 rs530212009 CA C . PASS AF=0.111764 ES:SE:LP:AF:SS:ID 0.00581564:0.00251827:1.67934:0.111764:116671:1_692794_CA_C
1 693731 rs12238997 A G . PASS AF=0.116787 ES:SE:LP:AF:SS:ID 0.00567493:0.00238481:1.76114:0.116787:116671:rs12238997
1 707522 rs371890604 G C . PASS AF=0.0984045 ES:SE:LP:AF:SS:ID 0.00627169:0.00267564:1.71942:0.0984045:116671:rs371890604
1 717587 rs144155419 G A . PASS AF=0.0158098 ES:SE:LP:AF:SS:ID 0.00222871:0.0064033:0.137989:0.0158098:116671:rs144155419
1 723329 rs189787166 A T . PASS AF=0.00176879 ES:SE:LP:AF:SS:ID 0.0143586:0.0187298:0.35329:0.00176879:116671:rs189787166
1 730087 rs148120343 T C . PASS AF=0.0569652 ES:SE:LP:AF:SS:ID 0.0083217:0.00331779:1.91592:0.0569652:116671:rs148120343
1 731718 rs58276399 T C . PASS AF=0.122711 ES:SE:LP:AF:SS:ID 0.00481328:0.00226287:1.47604:0.122711:116671:rs58276399
1 732032 rs61770163 A C . PASS AF=0.122336 ES:SE:LP:AF:SS:ID 0.00468929:0.00241143:1.28547:0.122336:116671:rs61770163
1 734349 rs141242758 T C . PASS AF=0.121964 ES:SE:LP:AF:SS:ID 0.00484565:0.00226412:1.49024:0.121964:116671:rs141242758
1 740284 rs61770167 C T . PASS AF=0.00584163 ES:SE:LP:AF:SS:ID 0.00559125:0.0103665:0.229413:0.00584163:116671:rs61770167
1 742813 rs112573343 C T . PASS AF=0.00184013 ES:SE:LP:AF:SS:ID 0.012509:0.0197882:0.277946:0.00184013:116671:rs112573343
1 749963 rs529266287 T TAA . PASS AF=0.868961 ES:SE:LP:AF:SS:ID -0.00535937:0.00223067:1.78831:0.868961:116671:rs529266287
1 750230 rs190826124 G C . PASS AF=0.00159334 ES:SE:LP:AF:SS:ID -0.020068:0.0197884:0.507906:0.00159334:116671:rs190826124
1 751343 rs28544273 T A . PASS AF=0.12375 ES:SE:LP:AF:SS:ID 0.00615349:0.00221015:2.27027:0.12375:116671:rs28544273
1 751488 rs200141114 G GA . PASS AF=0.143417 ES:SE:LP:AF:SS:ID 0.00706:0.00218556:2.90765:0.143417:116671:rs200141114
1 751756 rs28527770 T C . PASS AF=0.123871 ES:SE:LP:AF:SS:ID 0.00616343:0.00220709:2.28148:0.123871:116671:rs28527770
1 753405 rs3115860 C A . PASS AF=0.869725 ES:SE:LP:AF:SS:ID -0.00584619:0.00214954:2.1848:0.869725:116671:rs3115860
1 753425 rs3131970 T C . PASS AF=0.874521 ES:SE:LP:AF:SS:ID -0.00587852:0.00218564:2.14541:0.874521:116671:rs3131970
1 753541 rs2073813 G A . PASS AF=0.129734 ES:SE:LP:AF:SS:ID 0.00601575:0.00215552:2.27921:0.129734:116671:rs2073813
1 754105 rs12184325 C T . PASS AF=0.0365044 ES:SE:LP:AF:SS:ID 0.00223284:0.00391676:0.245171:0.0365044:116671:rs12184325
1 754182 rs3131969 A G . PASS AF=0.86932 ES:SE:LP:AF:SS:ID -0.00585852:0.00214747:2.1958:0.86932:116671:rs3131969
1 754192 rs3131968 A G . PASS AF=0.869388 ES:SE:LP:AF:SS:ID -0.00575331:0.00214826:2.13049:0.869388:116671:rs3131968
1 754334 rs3131967 T C . PASS AF=0.86932 ES:SE:LP:AF:SS:ID -0.00586379:0.00214742:2.19912:0.86932:116671:rs3131967
1 754433 rs150578204 G A . PASS AF=0.00511436 ES:SE:LP:AF:SS:ID 0.0232865:0.010986:1.46804:0.00511436:116671:rs150578204
1 754458 rs142682604 G T . PASS AF=0.00508319 ES:SE:LP:AF:SS:ID 0.0229991:0.0110104:1.43507:0.00508319:116671:rs142682604
1 755435 rs184270342 T G . PASS AF=0.00567226 ES:SE:LP:AF:SS:ID -0.00823176:0.0106069:0.358819:0.00567226:116671:rs184270342
1 755890 rs3115858 A T . PASS AF=0.869393 ES:SE:LP:AF:SS:ID -0.0057355:0.0021435:2.12744:0.869393:116671:rs3115858
1 756434 rs61768170 G C . PASS AF=0.127006 ES:SE:LP:AF:SS:ID 0.00623828:0.00218805:2.36072:0.127006:116671:rs61768170
1 756604 rs3131962 A G . PASS AF=0.868922 ES:SE:LP:AF:SS:ID -0.0058002:0.00213794:2.17594:0.868922:116671:rs3131962
1 757640 rs3115853 G A . PASS AF=0.868312 ES:SE:LP:AF:SS:ID -0.00591398:0.00213703:2.24782:0.868312:116671:rs3115853
1 757734 rs4951929 C T . PASS AF=0.869102 ES:SE:LP:AF:SS:ID -0.00573499:0.00213999:2.13282:0.869102:116671:rs4951929
1 757936 rs4951862 C A . PASS AF=0.869109 ES:SE:LP:AF:SS:ID -0.00574066:0.00214014:2.13601:0.869109:116671:rs4951862
1 758144 rs3131956 A G . PASS AF=0.869111 ES:SE:LP:AF:SS:ID -0.00573747:0.00214015:2.13406:0.869111:116671:rs3131956
1 758626 rs3131954 C T . PASS AF=0.869547 ES:SE:LP:AF:SS:ID -0.00576359:0.00214561:2.14101:0.869547:116671:rs3131954
1 759293 rs10157329 T A . PASS AF=0.0996286 ES:SE:LP:AF:SS:ID 0.00544401:0.00249419:1.53668:0.0996286:116671:rs10157329
1 759600 rs545998451 AGT A . PASS AF=0.00653587 ES:SE:LP:AF:SS:ID -0.00502195:0.00962283:0.22058:0.00653587:116671:1_759600_AGT_A
1 759837 rs3115851 T A . PASS AF=0.873604 ES:SE:LP:AF:SS:ID -0.00596735:0.00217843:2.21056:0.873604:116671:rs3115851
1 761732 rs2286139 C T . PASS AF=0.862894 ES:SE:LP:AF:SS:ID -0.00664321:0.0021366:2.72673:0.862894:116671:rs2286139
1 761752 rs1057213 C T . PASS AF=0.868289 ES:SE:LP:AF:SS:ID -0.00593035:0.00215713:2.22364:0.868289:116671:rs1057213
1 762273 rs3115849 G A . PASS AF=0.865301 ES:SE:LP:AF:SS:ID -0.00571926:0.00215739:2.0955:0.865301:116671:rs3115849
1 762485 rs12095200 C A . PASS AF=0.0998268 ES:SE:LP:AF:SS:ID 0.00699855:0.00257709:2.17947:0.0998268:116671:rs12095200
1 762589 rs3115848 G C . PASS AF=0.87059 ES:SE:LP:AF:SS:ID -0.00585303:0.00218275:2.13487:0.87059:116671:rs3115848
1 762592 rs3131950 C G . PASS AF=0.87059 ES:SE:LP:AF:SS:ID -0.00585315:0.00218275:2.13494:0.87059:116671:rs3131950
1 762601 rs3131949 T C . PASS AF=0.870588 ES:SE:LP:AF:SS:ID -0.00585493:0.00218275:2.136:0.870588:116671:rs3131949
1 762632 rs3131948 T A . PASS AF=0.870908 ES:SE:LP:AF:SS:ID -0.00587892:0.00218364:2.14886:0.870908:116671:rs3131948
1 764191 rs7515915 T G . PASS AF=0.126614 ES:SE:LP:AF:SS:ID 0.00616506:0.00218544:2.31977:0.126614:116671:rs7515915
1 766007 rs61768174 A C . PASS AF=0.106349 ES:SE:LP:AF:SS:ID 0.00573575:0.0023757:1.8023:0.106349:116671:rs61768174
1 766105 rs2519015 T A . PASS AF=0.854325 ES:SE:LP:AF:SS:ID -0.00587441:0.00213598:2.22501:0.854325:116671:rs2519015
1 767393 rs538667473 A C . PASS AF=0.00168058 ES:SE:LP:AF:SS:ID 0.0112587:0.0188138:0.259988:0.00168058:116671:rs538667473
1 768116 rs376645387 A AGTTTT . PASS AF=0.839027 ES:SE:LP:AF:SS:ID 0.00091161:0.00211679:0.176058:0.839027:116671:rs376645387