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Detailed information for vg0235926582:

Variant ID: vg0235926582 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 35926582
Reference Allele: AAlternative Allele: T
Primary Allele: ASecondary Allele: T

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.99, T: 0.01, others allele: 0.00, population size: 123. )

Flanking Sequence (100 bp) in Reference Genome:


CATGCAATTAGCTAGCACCTCGTTTCCACTAAATTATTATTTTTTAAATCCTTGACACTCAAGATGTTTAGGTTGTGTTTAGTTCACACTGAAGTTTGGA[A/T]
GTTTGGTTGAAATTGGTACGACGTGATAGAAAAAGTTGTGTGTATGAAAGGTTTGATGTAATGAAAAGTTGGAAGTTTGGAAAAAAAACTTTGGAACTAA

Reverse complement sequence

TTAGTTCCAAAGTTTTTTTTCCAAACTTCCAACTTTTCATTACATCAAACCTTTCATACACACAACTTTTTCTATCACGTCGTACCAATTTCAACCAAAC[T/A]
TCCAAACTTCAGTGTGAACTAAACACAACCTAAACATCTTGAGTGTCAAGGATTTAAAAAATAATAATTTAGTGGAAACGAGGTGCTAGCTAATTGCATG

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 95.70% 3.60% 0.66% 0.00% NA
All Indica  2759 93.00% 5.80% 1.12% 0.00% NA
All Japonica  1512 99.70% 0.30% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 99.70% 0.00% 0.34% 0.00% NA
Indica II  465 72.70% 24.10% 3.23% 0.00% NA
Indica III  913 98.80% 1.10% 0.11% 0.00% NA
Indica Intermediate  786 93.40% 5.00% 1.65% 0.00% NA
Temperate Japonica  767 99.70% 0.30% 0.00% 0.00% NA
Tropical Japonica  504 99.80% 0.20% 0.00% 0.00% NA
Japonica Intermediate  241 99.60% 0.40% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 94.40% 5.60% 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
vg0235926582 A -> T LOC_Os02g58800.1 upstream_gene_variant ; 3220.0bp to feature; MODIFIER silent_mutation Average:43.02; most accessible tissue: Zhenshan97 panicle, score: 63.607 N N N N
vg0235926582 A -> T LOC_Os02g58790.1 intron_variant ; MODIFIER silent_mutation Average:43.02; most accessible tissue: Zhenshan97 panicle, score: 63.607 N N N N
vg0235926582 A -> T LOC_Os02g58790.2 intron_variant ; MODIFIER silent_mutation Average:43.02; most accessible tissue: Zhenshan97 panicle, score: 63.607 N N N N
vg0235926582 A -> T LOC_Os02g58790.3 intron_variant ; MODIFIER silent_mutation Average:43.02; most accessible tissue: Zhenshan97 panicle, score: 63.607 N N N N
vg0235926582 A -> T LOC_Os02g58790.4 intron_variant ; MODIFIER silent_mutation Average:43.02; most accessible tissue: Zhenshan97 panicle, score: 63.607 N N N N
vg0235926582 A -> T LOC_Os02g58790.5 intron_variant ; MODIFIER silent_mutation Average:43.02; most accessible tissue: Zhenshan97 panicle, score: 63.607 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0235926582 NA 1.33E-06 mr1002_2 Ind_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
vg0235926582 NA 4.70E-06 mr1133_2 Ind_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