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Detailed information for vg0802960649:

Variant ID: vg0802960649 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 2960649
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: 263. )

Flanking Sequence (100 bp) in Reference Genome:


ACCACTTAGTCCCGCTTAGATGTAAACTCGTCTATCACCACTATAGATTATCATTGTCTTGAAAGGAATTGTATTTGTACCATCAAAATAAGCCTAACAT[A/G]
TCATTAATACAATAAAAAAATCATGCACACTTCACACATAAGTGTTCATGTCTTACTTATGTTTAAATTTATGTATAAATACACTAAAAATACCGTTTCT

Reverse complement sequence

AGAAACGGTATTTTTAGTGTATTTATACATAAATTTAAACATAAGTAAGACATGAACACTTATGTGTGAAGTGTGCATGATTTTTTTATTGTATTAATGA[T/C]
ATGTTAGGCTTATTTTGATGGTACAAATACAATTCCTTTCAAGACAATGATAATCTATAGTGGTGATAGACGAGTTTACATCTAAGCGGGACTAAGTGGT

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 98.70% 1.20% 0.08% 0.00% NA
All Indica  2759 100.00% 0.00% 0.00% 0.00% NA
All Japonica  1512 96.00% 3.70% 0.26% 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  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 89.50% 9.70% 0.79% 0.00% NA
Japonica Intermediate  241 97.10% 2.90% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 100.00% 0.00% 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
vg0802960649 A -> G LOC_Os08g05530.1 upstream_gene_variant ; 4709.0bp to feature; MODIFIER silent_mutation Average:32.844; most accessible tissue: Minghui63 flag leaf, score: 41.254 N N N N
vg0802960649 A -> G LOC_Os08g05520-LOC_Os08g05530 intergenic_region ; MODIFIER silent_mutation Average:32.844; most accessible tissue: Minghui63 flag leaf, score: 41.254 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0802960649 NA 1.13E-07 mr1136 Jap_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
vg0802960649 NA 1.33E-07 mr1188 Jap_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
vg0802960649 NA 5.53E-08 mr1136_2 Jap_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
vg0802960649 NA 1.10E-08 mr1188_2 Jap_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
vg0802960649 8.00E-07 7.99E-07 mr1448_2 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