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Detailed information for vg0802234736:

Variant ID: vg0802234736 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 2234736
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.01, others allele: 0.00, population size: 254. )

Flanking Sequence (100 bp) in Reference Genome:


GCATGCTATGTTGGGGGTCAAACGTGGTCAAATAACGATTAGACCGGGAGTGGTACATTAAACCAAGTTCACGGATCTAAATGTGTAATTTTCAAGTTCA[C/T]
GGACCTAAATAATATTACTCTGCAAGTTTAAGTACCGGCTATGTATCTCACTCTTTAATGAAAATGAATCTCCTATTAATTAGGAGAGGCCTAAGAAAAC

Reverse complement sequence

GTTTTCTTAGGCCTCTCCTAATTAATAGGAGATTCATTTTCATTAAAGAGTGAGATACATAGCCGGTACTTAAACTTGCAGAGTAATATTATTTAGGTCC[G/A]
TGAACTTGAAAATTACACATTTAGATCCGTGAACTTGGTTTAATGTACCACTCCCGGTCTAATCGTTATTTGACCACGTTTGACCCCCAACATAGCATGC

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 96.20% 3.80% 0.00% 0.00% NA
All Indica  2759 93.70% 6.30% 0.00% 0.00% NA
All Japonica  1512 99.90% 0.10% 0.00% 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 96.60% 3.40% 0.00% 0.00% NA
Indica III  913 87.60% 12.40% 0.00% 0.00% NA
Indica Intermediate  786 94.10% 5.90% 0.00% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 99.80% 0.20% 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 97.80% 2.20% 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
vg0802234736 C -> T LOC_Os08g04520.1 upstream_gene_variant ; 1337.0bp to feature; MODIFIER silent_mutation Average:52.696; most accessible tissue: Minghui63 young leaf, score: 68.745 N N N N
vg0802234736 C -> T LOC_Os08g04530.1 upstream_gene_variant ; 3845.0bp to feature; MODIFIER silent_mutation Average:52.696; most accessible tissue: Minghui63 young leaf, score: 68.745 N N N N
vg0802234736 C -> T LOC_Os08g04520-LOC_Os08g04530 intergenic_region ; MODIFIER silent_mutation Average:52.696; most accessible tissue: Minghui63 young leaf, score: 68.745 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0802234736 NA 3.01E-06 Grain_weight Ind_All Not 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
vg0802234736 2.69E-06 2.69E-06 mr1957_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