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Detailed information for vg0202540565:

Variant ID: vg0202540565 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 2540565
Reference Allele: TAlternative Allele: C
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.98, T: 0.02, others allele: 0.00, population size: 263. )

Flanking Sequence (100 bp) in Reference Genome:


TTCTCTGCTATATATCTTGCCTTCTAGAAAGTATTTTTCAGGAACAATTGAGCACTTGAGTAGGATGTGGTCGAGTACACTGCATTATCAAGAACGTTCT[T/C]
GACAAATGCAGAGTCGTCGCGCCCAACCAACCAACGAAGACCGACGACCTATCTCATACACCGGCCATGGCTGGACTACTCGAGAAAAGGTTGTTAACGG

Reverse complement sequence

CCGTTAACAACCTTTTCTCGAGTAGTCCAGCCATGGCCGGTGTATGAGATAGGTCGTCGGTCTTCGTTGGTTGGTTGGGCGCGACGACTCTGCATTTGTC[A/G]
AGAACGTTCTTGATAATGCAGTGTACTCGACCACATCCTACTCAAGTGCTCAATTGTTCCTGAAAAATACTTTCTAGAAGGCAAGATATATAGCAGAGAA

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 80.90% 19.10% 0.02% 0.00% NA
All Indica  2759 99.40% 0.50% 0.04% 0.00% NA
All Japonica  1512 43.40% 56.60% 0.00% 0.00% NA
Aus  269 96.70% 3.30% 0.00% 0.00% NA
Indica I  595 99.80% 0.20% 0.00% 0.00% NA
Indica II  465 98.90% 1.10% 0.00% 0.00% NA
Indica III  913 99.70% 0.30% 0.00% 0.00% NA
Indica Intermediate  786 99.10% 0.80% 0.13% 0.00% NA
Temperate Japonica  767 8.60% 91.40% 0.00% 0.00% NA
Tropical Japonica  504 90.10% 9.90% 0.00% 0.00% NA
Japonica Intermediate  241 56.40% 43.60% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 74.40% 25.60% 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
vg0202540565 T -> C LOC_Os02g05270.1 upstream_gene_variant ; 4390.0bp to feature; MODIFIER silent_mutation Average:58.062; most accessible tissue: Minghui63 panicle, score: 73.225 N N N N
vg0202540565 T -> C LOC_Os02g05280.1 downstream_gene_variant ; 1895.0bp to feature; MODIFIER silent_mutation Average:58.062; most accessible tissue: Minghui63 panicle, score: 73.225 N N N N
vg0202540565 T -> C LOC_Os02g05300.1 downstream_gene_variant ; 1525.0bp to feature; MODIFIER silent_mutation Average:58.062; most accessible tissue: Minghui63 panicle, score: 73.225 N N N N
vg0202540565 T -> C LOC_Os02g05290.1 intron_variant ; MODIFIER silent_mutation Average:58.062; most accessible tissue: Minghui63 panicle, score: 73.225 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0202540565 NA 5.16E-10 mr1712 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
vg0202540565 NA 3.89E-06 mr1826 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