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Detailed information for vg1108453091:

Variant ID: vg1108453091 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 8453091
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GATTACAACTTTAGAAGATCGTAACTGGGAAAATGGAAAAAATATACCACCACCCACACACCGACAACACCGACACACAGATCCAGGAGAAGGCTAGCAT[C/T]
GAACCGGCCACCGCTAAGCGTGGCCGACCGCCGTAGGTCAACAAAGGAACACAAACAAGAACGCCCAATAAACGCCCTTACAACCAACACAAAGCCCAAC

Reverse complement sequence

GTTGGGCTTTGTGTTGGTTGTAAGGGCGTTTATTGGGCGTTCTTGTTTGTGTTCCTTTGTTGACCTACGGCGGTCGGCCACGCTTAGCGGTGGCCGGTTC[G/A]
ATGCTAGCCTTCTCCTGGATCTGTGTGTCGGTGTTGTCGGTGTGTGGGTGGTGGTATATTTTTTCCATTTTCCCAGTTACGATCTTCTAAAGTTGTAATC

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 99.30% 0.30% 0.44% 0.00% NA
All Indica  2759 100.00% 0.00% 0.00% 0.00% NA
All Japonica  1512 97.70% 0.90% 1.39% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 100.00% 0.00% 0.00% 0.00% NA
Temperate Japonica  767 96.20% 1.70% 2.09% 0.00% NA
Tropical Japonica  504 99.40% 0.00% 0.60% 0.00% NA
Japonica Intermediate  241 98.80% 0.40% 0.83% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 100.00% 0.00% 0.00% 0.00% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1108453091 C -> T LOC_Os11g15010.1 upstream_gene_variant ; 3511.0bp to feature; MODIFIER silent_mutation Average:70.069; most accessible tissue: Zhenshan97 young leaf, score: 84.431 N N N N
vg1108453091 C -> T LOC_Os11g15030.1 upstream_gene_variant ; 4044.0bp to feature; MODIFIER silent_mutation Average:70.069; most accessible tissue: Zhenshan97 young leaf, score: 84.431 N N N N
vg1108453091 C -> T LOC_Os11g15020.1 downstream_gene_variant ; 735.0bp to feature; MODIFIER silent_mutation Average:70.069; most accessible tissue: Zhenshan97 young leaf, score: 84.431 N N N N
vg1108453091 C -> T LOC_Os11g15010-LOC_Os11g15020 intergenic_region ; MODIFIER silent_mutation Average:70.069; most accessible tissue: Zhenshan97 young leaf, score: 84.431 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1108453091 NA 1.80E-06 mr1280 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
vg1108453091 3.87E-06 1.14E-07 mr1563_2 Jap_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