{
"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=ieu-a-52,TotalVariants=2214251,VariantsNotRead=0,HarmonisedVariants=2214251,VariantsNotHarmonised=0,SwitchedAlleles=0,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/ieu-a-import/processed/ieu-a-52/ieu-a-52_data.json --ref /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/QC/genomes/b37/human_g1k_v37.fasta; 1.1.1",
"file_date": "2020-02-04T08:21:00.127019",
"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/ieu-a-import/processed/ieu-a-52/ieu-a-52.vcf.gz -O z /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ieu-a-import/processed/ieu-a-52/ieu-a-52_data.vcf.gz; Date=Tue Feb 4 19:41:01 2020",
"bcftools_viewVersion": "1.9-74-g6af271c+htslib-1.9-64-g226b4a8",
"bcftools_viewCommand": "view -h /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/ieu-a-52/ieu-a-52.vcf.gz; Date=Sun May 10 12:01:45 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/ieu-a-import/processed/ieu-a-52/ieu-a-52.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/ieu-a-import/processed/ieu-a-52/ldsc.txt \
--w-ld-chr /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/reference/eur_w_ld_chr/
Beginning analysis at Wed Feb 5 11:08:42 2020
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ieu-a-import/processed/ieu-a-52/ieu-a-52.vcf.gz ...
Read summary statistics for 2214251 SNPs.
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, 1058281 SNPs remain.
After merging with regression SNP LD, 1058281 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.1747 (0.0125)
Lambda GC: 1.0368
Mean Chi^2: 1.0825
Intercept: 0.8834 (0.0083)
Ratio < 0 (usually indicates GC correction).
Analysis finished at Wed Feb 5 11:09:10 2020
Total time elapsed: 28.24s
{
"af_correlation": 0.9083,
"inflation_factor": 1.0475,
"mean_EFFECT": 0,
"n": 100384,
"n_snps": 2214251,
"n_clumped_hits": 20,
"n_p_sig": 405,
"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": 8685,
"n_miss_AF_reference": 17436,
"n_est": 98674.3461,
"ratio_se_n": 0.9914,
"mean_diff": -0,
"ratio_diff": 1.864,
"sd_y_est1": 1.4592,
"sd_y_est2": 1.4467,
"r2_sum1": 0.0118,
"r2_sum2": 0.0056,
"r2_sum3": 0.0057,
"r2_sum4": 0.0103,
"ldsc_nsnp_merge_refpanel_ld": 1058281,
"ldsc_nsnp_merge_regression_ld": 1058281,
"ldsc_observed_scale_h2_beta": 0.1747,
"ldsc_observed_scale_h2_se": 0.0125,
"ldsc_intercept_beta": 0.8834,
"ldsc_intercept_se": 0.0083,
"ldsc_lambda_gc": 1.0368,
"ldsc_mean_chisq": 1.0825,
"ldsc_ratio": -1.4133
}
name | value |
---|---|
af_correlation | FALSE |
inflation_factor | FALSE |
n | FALSE |
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 |
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 | 42 | 0 | 2214251 | 0 | 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 |
character | ALT | 0 | 1.0000000 | 1 | 1 | 0 | 4 | 0 | NA | NA | NA | NA | NA | NA | NA | NA |
numeric | CHROM | 0 | 1.0000000 | NA | NA | NA | NA | NA | 8.518331e+00 | 5.627839e+00 | 1.0000e+00 | 4.000000e+00 | 8.000000e+00 | 1.200000e+01 | 2.300000e+01 | ▇▅▅▂▂ |
numeric | POS | 0 | 1.0000000 | NA | NA | NA | NA | NA | 7.895998e+07 | 5.548620e+07 | 1.3034e+04 | 3.295025e+07 | 7.041318e+07 | 1.142107e+08 | 2.491747e+08 | ▇▇▅▂▁ |
numeric | EFFECT | 0 | 1.0000000 | NA | NA | NA | NA | NA | 1.750000e-05 | 9.814800e-03 | -9.6000e-02 | -5.700000e-03 | 0.000000e+00 | 5.800000e-03 | 1.000000e-01 | ▁▁▇▁▁ |
numeric | SE | 0 | 1.0000000 | NA | NA | NA | NA | NA | 9.073900e-03 | 3.560200e-03 | 4.7000e-03 | 6.800000e-03 | 7.700000e-03 | 1.000000e-02 | 4.900000e-02 | ▇▁▁▁▁ |
numeric | PVAL | 0 | 1.0000000 | NA | NA | NA | NA | NA | 4.935585e-01 | 2.915440e-01 | 0.0000e+00 | 2.399999e-01 | 4.899999e-01 | 7.499995e-01 | 1.000000e+00 | ▇▇▇▇▇ |
numeric | PVAL_ztest | 0 | 1.0000000 | NA | NA | NA | NA | NA | 4.935787e-01 | 2.912827e-01 | 0.0000e+00 | 2.394069e-01 | 4.917677e-01 | 7.459807e-01 | 1.000000e+00 | ▇▇▇▇▇ |
numeric | AF | 8685 | 0.9960777 | NA | NA | NA | NA | NA | 3.710231e-01 | 2.655606e-01 | 8.3000e-03 | 1.417000e-01 | 3.083000e-01 | 5.667000e-01 | 9.917000e-01 | ▇▆▃▃▂ |
numeric | AF_reference | 17436 | 0.9921256 | NA | NA | NA | NA | NA | 3.724409e-01 | 2.486544e-01 | 1.9970e-04 | 1.631390e-01 | 3.160940e-01 | 5.539140e-01 | 1.000000e+00 | ▇▇▅▃▂ |
numeric | N | 0 | 1.0000000 | NA | NA | NA | NA | NA | 5.806952e+04 | 8.187220e+03 | 5.0000e+04 | 5.696200e+04 | 5.758500e+04 | 5.762100e+04 | 1.003840e+05 | ▇▁▁▁▁ |
CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
---|---|---|---|---|---|---|---|---|---|---|---|
1 | 785050 | rs2905062 | G | A | -0.0150 | 0.0090 | 0.0929994 | 0.0955807 | NA | 0.626997 | 60461 |
1 | 1003629 | rs4075116 | C | T | 0.0018 | 0.0082 | 0.8300000 | 0.8262511 | 0.73730 | 0.720647 | 54170 |
1 | 1017170 | rs3766193 | C | G | -0.0020 | 0.0075 | 0.7899998 | 0.7897258 | 0.56670 | 0.575479 | 54766 |
1 | 1017197 | rs3766192 | C | T | -0.0007 | 0.0072 | 0.9199999 | 0.9225499 | 0.57630 | 0.511182 | 55052 |
1 | 1018562 | rs9442371 | C | T | -0.0016 | 0.0071 | 0.8200001 | 0.8217054 | 0.59170 | 0.530152 | 55081 |
1 | 1018704 | rs9442372 | A | G | -0.0014 | 0.0071 | 0.8400000 | 0.8436843 | 0.60170 | 0.611022 | 55076 |
1 | 1021415 | rs3737728 | A | G | 0.0015 | 0.0078 | 0.8499999 | 0.8475012 | 0.71670 | 0.812700 | 55353 |
1 | 1021695 | rs9442398 | A | G | -0.0002 | 0.0081 | 0.9800000 | 0.9803011 | 0.72500 | 0.727236 | 55211 |
1 | 1022037 | rs6701114 | C | T | -0.0052 | 0.0080 | 0.5199996 | 0.5156922 | 0.56670 | 0.586661 | 50155 |
1 | 1097335 | rs9442385 | T | G | -0.0019 | 0.0130 | 0.8900000 | 0.8837999 | 0.94167 | 0.834665 | 53942 |
CHROM | POS | ID | REF | ALT | EFFECT | SE | PVAL | PVAL_ztest | AF | AF_reference | N |
---|---|---|---|---|---|---|---|---|---|---|---|
22 | 51151350 | rs6009951 | C | T | 0.0063 | 0.0071 | 0.3700002 | 0.3749045 | 0.4000 | 0.5559110 | 57629 |
22 | 51151724 | rs6010061 | C | T | 0.0084 | 0.0072 | 0.2399999 | 0.2433450 | 0.3833 | 0.6098240 | 57453 |
22 | 51158017 | rs6010065 | G | C | 0.0022 | 0.0068 | 0.7499995 | 0.7462943 | 0.4417 | 0.5475240 | 55101 |
22 | 51163138 | rs715586 | C | T | -0.0007 | 0.0074 | 0.9199999 | 0.9246368 | 0.1500 | 0.0902556 | 92526 |
22 | 51165664 | rs8137951 | G | A | 0.0060 | 0.0053 | 0.2599998 | 0.2576027 | 0.2750 | 0.4063500 | 98101 |
22 | 51178090 | rs2285395 | G | A | -0.0021 | 0.0100 | 0.8400000 | 0.8336677 | 0.0667 | 0.0666933 | 92634 |
23 | 35921591 | rs2204667 | C | G | -0.0140 | 0.0088 | 0.1100001 | 0.1116300 | 0.1667 | NA | 57597 |
23 | 51666786 | rs14115 | A | G | 0.0032 | 0.0140 | 0.8200001 | 0.8192020 | 0.0250 | NA | 52169 |
23 | 70163799 | rs1626496 | A | C | -0.0009 | 0.0130 | 0.9400001 | 0.9448059 | 0.0750 | NA | 57601 |
23 | 118495837 | rs12882977 | G | A | -0.0062 | 0.0064 | 0.3300000 | 0.3326699 | 0.5167 | 0.2307280 | 57618 |
1 785050 rs2905062 G A . PASS . ES:SE:LP:SS:ID -0.015:0.009:1.03152:60461:rs2905062
1 1003629 rs4075116 C T . PASS AF=0.7373 ES:SE:LP:AF:SS:ID 0.0018:0.0082:0.0809219:0.7373:54170:rs4075116
1 1017170 rs3766193 C G . PASS AF=0.5667 ES:SE:LP:AF:SS:ID -0.002:0.0075:0.102373:0.5667:54766:rs3766193
1 1017197 rs3766192 C T . PASS AF=0.5763 ES:SE:LP:AF:SS:ID -0.0007:0.0072:0.0362122:0.5763:55052:rs3766192
1 1018562 rs9442371 C T . PASS AF=0.5917 ES:SE:LP:AF:SS:ID -0.0016:0.0071:0.0861861:0.5917:55081:rs9442371
1 1018704 rs9442372 A G . PASS AF=0.6017 ES:SE:LP:AF:SS:ID -0.0014:0.0071:0.0757207:0.6017:55076:rs9442372
1 1021415 rs3737728 A G . PASS AF=0.7167 ES:SE:LP:AF:SS:ID 0.0015:0.0078:0.0705811:0.7167:55353:rs3737728
1 1021695 rs9442398 A G . PASS AF=0.725 ES:SE:LP:AF:SS:ID -0.0002:0.0081:0.00877392:0.725:55211:rs9442398
1 1022037 rs6701114 C T . PASS AF=0.5667 ES:SE:LP:AF:SS:ID -0.0052:0.008:0.283997:0.5667:50155:rs6701114
1 1097335 rs9442385 T G . PASS AF=0.94167 ES:SE:LP:AF:SS:ID -0.0019:0.013:0.05061:0.94167:53942:rs9442385
1 1099342 rs9660710 A C . PASS AF=0.94068 ES:SE:LP:AF:SS:ID -0.0005:0.013:0.0132283:0.94068:54765:rs9660710
1 1100217 rs1891905 C T . PASS AF=0.95833 ES:SE:LP:AF:SS:ID -0.0037:0.018:0.0809219:0.95833:54003:rs1891905
1 1124663 rs6684820 G A . PASS AF=0.2667 ES:SE:LP:AF:SS:ID -0.011:0.0083:0.744727:0.2667:54518:rs6684820
1 1125553 rs10907174 A T . PASS AF=0.225 ES:SE:LP:AF:SS:ID -0.0079:0.0087:0.443698:0.225:55855:rs10907174
1 1130727 rs10907175 A C . PASS AF=0.1 ES:SE:LP:AF:SS:ID -0.0074:0.012:0.267606:0.1:56099:rs10907175
1 1135242 rs9729550 A C . PASS AF=0.275 ES:SE:LP:AF:SS:ID -0.01:0.0081:0.69897:0.275:54478:rs9729550
1 1138913 rs3819001 T C . PASS AF=0.0431 ES:SE:LP:AF:SS:ID -0.02:0.018:0.568636:0.0431:52579:rs3819001
1 1140435 rs1815606 G T . PASS AF=0.3103 ES:SE:LP:AF:SS:ID -0.0082:0.0062:0.744727:0.3103:76828:rs1815606
1 1143657 rs3753348 C G . PASS AF=0.03333 ES:SE:LP:AF:SS:ID -0.023:0.02:0.619789:0.03333:53189:rs3753348
1 1152631 rs11721 C A . PASS AF=0.08333 ES:SE:LP:AF:SS:ID -0.023:0.013:1.16749:0.08333:53180:rs11721
1 1158277 rs3813199 G A . PASS AF=0.1 ES:SE:LP:AF:SS:ID -0.0076:0.011:0.29243:0.1:56975:rs3813199
1 1162435 rs3766186 C A . PASS AF=0.1 ES:SE:LP:AF:SS:ID -0.0078:0.012:0.30103:0.1:56964:rs3766186
1 1163804 rs7515488 C T . PASS AF=0.15 ES:SE:LP:AF:SS:ID -0.021:0.01:1.42022:0.15:56927:rs7515488
1 1165310 rs11260562 G A . PASS AF=0.05172 ES:SE:LP:AF:SS:ID -0.033:0.016:1.36653:0.05172:51893:rs11260562
1 1176597 rs6675798 T C . PASS AF=0.1083 ES:SE:LP:AF:SS:ID -0.028:0.013:1.56864:0.1083:52589:rs6675798
1 1181751 rs6603783 T C . PASS AF=0.1 ES:SE:LP:AF:SS:ID -0.026:0.013:1.39794:0.1:52569:rs6603783
1 1192515 rs7524470 A G . PASS AF=0.05833 ES:SE:LP:AF:SS:ID -0.0072:0.019:0.154902:0.05833:52134:rs7524470
1 1194804 rs11804831 T C . PASS AF=0.2083 ES:SE:LP:AF:SS:ID -0.028:0.0093:2.63827:0.2083:55264:rs11804831
1 1198618 rs12563338 T A . PASS AF=0.04167 ES:SE:LP:AF:SS:ID -0.03:0.019:0.958607:0.04167:56308:rs12563338
1 1206343 rs6667923 C A . PASS AF=0.05833 ES:SE:LP:AF:SS:ID -0.012:0.018:0.29243:0.05833:56683:rs6667923
1 1206619 rs6668223 C A . PASS AF=0.0339 ES:SE:LP:AF:SS:ID -0.018:0.021:0.39794:0.0339:54836:rs6668223
1 1211292 rs6685064 C T . PASS AF=0.1 ES:SE:LP:AF:SS:ID -0.014:0.013:0.568636:0.1:55074:rs6685064
1 1474304 rs1571150 C A . PASS AF=0.3 ES:SE:LP:AF:SS:ID 0.0011:0.007:0.0555173:0.3:57604:rs1571150
1 1478153 rs3766180 T C . PASS AF=0.2417 ES:SE:LP:AF:SS:ID 0.0021:0.0072:0.113509:0.2417:57503:rs3766180
1 1478180 rs3766178 T C . PASS AF=0.2667 ES:SE:LP:AF:SS:ID 0.0018:0.0072:0.09691:0.2667:57580:rs3766178
1 1481348 rs3766177 T C . PASS . ES:SE:LP:SS:ID 0.0043:0.0078:0.236572:57408:rs3766177
1 1483010 rs7517401 G A . PASS AF=0.2833 ES:SE:LP:AF:SS:ID 0.0004:0.0072:0.0177288:0.2833:57205:rs7517401
1 1486834 rs3128342 C A . PASS AF=0.3333 ES:SE:LP:AF:SS:ID 0.0001:0.0074:0.00436481:0.3333:52786:rs3128342
1 1489670 rs7531530 C T . PASS AF=0.25 ES:SE:LP:AF:SS:ID 0.005:0.0075:0.29243:0.25:57616:rs7531530
1 1489928 rs7366884 T C . PASS AF=0.25 ES:SE:LP:AF:SS:ID 0.005:0.0077:0.283997:0.25:57612:rs7366884
1 1497201 rs3766169 A C . PASS AF=0.2458 ES:SE:LP:AF:SS:ID 0.0017:0.0072:0.091515:0.2458:57613:rs3766169
1 1499298 rs9439468 A G . PASS AF=0.3103 ES:SE:LP:AF:SS:ID 0.0009:0.0068:0.05061:0.3103:57629:rs9439468
1 1500941 rs6603791 A G . PASS AF=0.3 ES:SE:LP:AF:SS:ID 0.001:0.0068:0.0555173:0.3:57616:rs6603791
1 1501064 rs6656541 T G . PASS AF=0.3 ES:SE:LP:AF:SS:ID 0.0005:0.0069:0.0268721:0.3:57622:rs6656541
1 1505255 rs6603793 C T . PASS AF=0.3 ES:SE:LP:AF:SS:ID 0.0007:0.0069:0.0362122:0.3:57611:rs6603793
1 1509034 rs7520996 T C . PASS AF=0.2797 ES:SE:LP:AF:SS:ID -0.0033:0.0071:0.19382:0.2797:57292:rs7520996
1 1510801 rs7519837 C T . PASS AF=0.2917 ES:SE:LP:AF:SS:ID -0.0042:0.0071:0.259637:0.2917:57211:rs7519837
1 1706136 rs6603811 T C . PASS AF=0.97458 ES:SE:LP:AF:SS:ID -0.01:0.01:0.481486:0.97458:85551:rs6603811
1 1706160 rs7531583 A G . PASS AF=0.7833 ES:SE:LP:AF:SS:ID -0.0042:0.0057:0.337242:0.7833:97676:rs7531583
1 1708801 rs12044597 A G . PASS AF=0.5169 ES:SE:LP:AF:SS:ID 0.0089:0.0049:1.17393:0.5169:98150:rs12044597