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Detailed information for vg0806090419:

Variant ID: vg0806090419 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 6090419
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 277. )

Flanking Sequence (100 bp) in Reference Genome:


TGTGAGGCTGGCATGTATTTGCAATGAGGAAAAACAACCTGAGAATGGATTACACCAAAACATGTGCATGCATGTAGACCTGCAAAAGAAAAACAAGTTT[A/G]
GCATATTTCATATTTCAATTTCTCTAGTCGGTAAACAAGTTTAGCATTCAGGTGCCTAGTTCATATCCATGCTACAAAGTCATGTCAGACATCATATTGC

Reverse complement sequence

GCAATATGATGTCTGACATGACTTTGTAGCATGGATATGAACTAGGCACCTGAATGCTAAACTTGTTTACCGACTAGAGAAATTGAAATATGAAATATGC[T/C]
AAACTTGTTTTTCTTTTGCAGGTCTACATGCATGCACATGTTTTGGTGTAATCCATTCTCAGGTTGTTTTTCCTCATTGCAAATACATGCCAGCCTCACA

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 97.20% 2.40% 0.38% 0.00% NA
All Indica  2759 100.00% 0.00% 0.00% 0.00% NA
All Japonica  1512 91.40% 7.40% 1.19% 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  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 100.00% 0.00% 0.00% 0.00% NA
Temperate Japonica  767 98.00% 0.30% 1.69% 0.00% NA
Tropical Japonica  504 80.20% 19.20% 0.60% 0.00% NA
Japonica Intermediate  241 93.80% 5.40% 0.83% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 98.90% 1.10% 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
vg0806090419 A -> G LOC_Os08g10380.1 downstream_gene_variant ; 4238.0bp to feature; MODIFIER silent_mutation Average:45.152; most accessible tissue: Minghui63 flag leaf, score: 61.847 N N N N
vg0806090419 A -> G LOC_Os08g10380-LOC_Os08g10390 intergenic_region ; MODIFIER silent_mutation Average:45.152; most accessible tissue: Minghui63 flag leaf, score: 61.847 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0806090419 6.25E-07 6.25E-07 mr1266 Jap_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