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Detailed information for vg0333546429:

Variant ID: vg0333546429 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 33546429
Reference Allele: TAlternative Allele: A
Primary Allele: TSecondary Allele: A

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.94, A: 0.07, others allele: 0.00, population size: 204. )

Flanking Sequence (100 bp) in Reference Genome:


TTAATTATTGAATCTGTTGTTACAACTTTACACAACACCAATACTCTATACTAATCTAGCAACTGGAGTATATTTATCCACAACATTCAAGGAAACATGA[T/A]
ACTTGTATGCGTATATAGGGGTGGCGCACATGTATTTATACTGTATTTCTCGACAAAAATATTATATGTACGTACATTTCAAATTAATACGTATGAACAC

Reverse complement sequence

GTGTTCATACGTATTAATTTGAAATGTACGTACATATAATATTTTTGTCGAGAAATACAGTATAAATACATGTGCGCCACCCCTATATACGCATACAAGT[A/T]
TCATGTTTCCTTGAATGTTGTGGATAAATATACTCCAGTTGCTAGATTAGTATAGAGTATTGGTGTTGTGTAAAGTTGTAACAACAGATTCAATAATTAA

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 78.40% 21.60% 0.00% 0.00% NA
All Indica  2759 73.10% 26.90% 0.00% 0.00% NA
All Japonica  1512 100.00% 0.00% 0.00% 0.00% NA
Aus  269 1.50% 98.50% 0.00% 0.00% NA
Indica I  595 97.50% 2.50% 0.00% 0.00% NA
Indica II  465 80.40% 19.60% 0.00% 0.00% NA
Indica III  913 54.50% 45.50% 0.00% 0.00% NA
Indica Intermediate  786 72.00% 28.00% 0.00% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 83.30% 16.70% 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
vg0333546429 T -> A LOC_Os03g58910.2 upstream_gene_variant ; 1855.0bp to feature; MODIFIER silent_mutation Average:58.283; most accessible tissue: Callus, score: 87.436 N N N N
vg0333546429 T -> A LOC_Os03g58920.2 downstream_gene_variant ; 34.0bp to feature; MODIFIER silent_mutation Average:58.283; most accessible tissue: Callus, score: 87.436 N N N N
vg0333546429 T -> A LOC_Os03g58920.1 downstream_gene_variant ; 34.0bp to feature; MODIFIER silent_mutation Average:58.283; most accessible tissue: Callus, score: 87.436 N N N N
vg0333546429 T -> A LOC_Os03g58910-LOC_Os03g58920 intergenic_region ; MODIFIER silent_mutation Average:58.283; most accessible tissue: Callus, score: 87.436 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0333546429 NA 6.99E-07 Spikelet_length Ind_All YES Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg0333546429 NA 3.00E-09 mr1860_2 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