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Detailed information for vg0200486470:

Variant ID: vg0200486470 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 486470
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, T: 0.00, others allele: 0.00, population size: 313. )

Flanking Sequence (100 bp) in Reference Genome:


TGTGCAGAGGATATTGTCACAGCCTCTATTCGGGTACTTTCCAGTATCGCGACGCATGGTAGACATGATGTTGAGGCTTTGTCTTGTGGGTACAGTGGTA[C/T]
ACCTCTGGCCAGAGTAAAACTATTCGAATAGCCGTGCCCGCGGTCATGGGCGGGTTGAGCAATGTTTCTTGTGATTAGTCTCACACCTCTCACAATAATT

Reverse complement sequence

AATTATTGTGAGAGGTGTGAGACTAATCACAAGAAACATTGCTCAACCCGCCCATGACCGCGGGCACGGCTATTCGAATAGTTTTACTCTGGCCAGAGGT[G/A]
TACCACTGTACCCACAAGACAAAGCCTCAACATCATGTCTACCATGCGTCGCGATACTGGAAAGTACCCGAATAGAGGCTGTGACAATATCCTCTGCACA

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 90.40% 9.60% 0.02% 0.00% NA
All Indica  2759 83.60% 16.30% 0.04% 0.00% NA
All Japonica  1512 100.00% 0.00% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 98.80% 1.20% 0.00% 0.00% NA
Indica II  465 89.20% 10.80% 0.00% 0.00% NA
Indica III  913 72.60% 27.40% 0.00% 0.00% NA
Indica Intermediate  786 81.60% 18.30% 0.13% 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 95.60% 4.40% 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
vg0200486470 C -> T LOC_Os02g01890.1 upstream_gene_variant ; 2443.0bp to feature; MODIFIER silent_mutation Average:57.826; most accessible tissue: Minghui63 young leaf, score: 78.443 N N N N
vg0200486470 C -> T LOC_Os02g01900.1 upstream_gene_variant ; 4982.0bp to feature; MODIFIER silent_mutation Average:57.826; most accessible tissue: Minghui63 young leaf, score: 78.443 N N N N
vg0200486470 C -> T LOC_Os02g01870.1 downstream_gene_variant ; 2501.0bp to feature; MODIFIER silent_mutation Average:57.826; most accessible tissue: Minghui63 young leaf, score: 78.443 N N N N
vg0200486470 C -> T LOC_Os02g01880.1 intron_variant ; MODIFIER silent_mutation Average:57.826; most accessible tissue: Minghui63 young leaf, score: 78.443 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0200486470 NA 8.15E-07 mr1200 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
vg0200486470 4.12E-06 4.12E-06 mr1293 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
vg0200486470 NA 5.19E-08 mr1458 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