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Detailed information for vg1218191046:

Variant ID: vg1218191046 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 18191046
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.98, T: 0.01, others allele: 0.00, population size: 222. )

Flanking Sequence (100 bp) in Reference Genome:


GACCTTGGCAGTAGCAGAAATCCCTAGGTCCAAAACACATTTGATGGGTCTGGATCAGTAAGAGCAAGTTTAATAGTATAGCCAACTACTAGCTGCAATT[C/T]
ATCTATAGCTAATCTAATAGCTTATTCATATAATATATAGTTACATACTACACTATTAATACATGATCCCACCTATCATACACACATTGCGTCTTGGAGT

Reverse complement sequence

ACTCCAAGACGCAATGTGTGTATGATAGGTGGGATCATGTATTAATAGTGTAGTATGTAACTATATATTATATGAATAAGCTATTAGATTAGCTATAGAT[G/A]
AATTGCAGCTAGTAGTTGGCTATACTATTAAACTTGCTCTTACTGATCCAGACCCATCAAATGTGTTTTGGACCTAGGGATTTCTGCTACTGCCAAGGTC

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 87.50% 7.60% 0.15% 4.72% NA
All Indica  2759 95.50% 3.80% 0.04% 0.65% NA
All Japonica  1512 80.00% 12.30% 0.33% 7.41% NA
Aus  269 56.90% 22.30% 0.37% 20.45% NA
Indica I  595 99.30% 0.70% 0.00% 0.00% NA
Indica II  465 89.70% 9.20% 0.00% 1.08% NA
Indica III  913 97.40% 2.50% 0.00% 0.11% NA
Indica Intermediate  786 94.00% 4.30% 0.13% 1.53% NA
Temperate Japonica  767 87.20% 0.40% 0.26% 12.13% NA
Tropical Japonica  504 76.00% 23.60% 0.20% 0.20% NA
Japonica Intermediate  241 65.10% 26.60% 0.83% 7.47% NA
VI/Aromatic  96 60.40% 6.20% 0.00% 33.33% NA
Intermediate  90 87.80% 5.60% 0.00% 6.67% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1218191046 C -> DEL N N silent_mutation Average:55.654; most accessible tissue: Zhenshan97 root, score: 71.174 N N N N
vg1218191046 C -> T LOC_Os12g30310.1 downstream_gene_variant ; 1387.0bp to feature; MODIFIER silent_mutation Average:55.654; most accessible tissue: Zhenshan97 root, score: 71.174 N N N N
vg1218191046 C -> T LOC_Os12g30310-LOC_Os12g30320 intergenic_region ; MODIFIER silent_mutation Average:55.654; most accessible tissue: Zhenshan97 root, score: 71.174 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1218191046 NA 5.34E-06 mr1048 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1218191046 NA 2.74E-07 mr1058 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1218191046 5.73E-06 NA mr1060 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1218191046 NA 1.05E-06 mr1230 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1218191046 8.87E-06 2.38E-07 mr1266 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1218191046 8.76E-06 8.75E-06 mr1267 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1218191046 2.17E-06 2.17E-06 mr1299 Jap_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1218191046 NA 1.43E-06 mr1345 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1218191046 4.81E-07 3.51E-07 mr1364 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1218191046 NA 2.92E-06 mr1364 Jap_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1218191046 NA 1.14E-07 mr1382 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1218191046 NA 3.40E-06 mr1398 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1218191046 NA 9.93E-07 mr1408 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1218191046 NA 1.26E-06 mr1427 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1218191046 NA 5.61E-06 mr1427 Jap_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1218191046 1.78E-07 1.70E-07 mr1443 All YES Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1218191046 NA 8.65E-07 mr1443 Jap_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1218191046 4.63E-06 4.63E-06 mr1564 Jap_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1218191046 6.59E-06 NA mr1693 Jap_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1218191046 NA 2.39E-06 mr1697 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1218191046 NA 6.09E-06 mr1743 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1218191046 8.19E-07 NA mr1819 All YES Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1218191046 NA 2.28E-07 mr1819 Jap_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1218191046 8.07E-06 NA mr1845 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1218191046 NA 6.55E-06 mr1884 Jap_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1218191046 4.83E-06 4.83E-06 mr1948 Jap_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251