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Detailed information for vg0405209631:

Variant ID: vg0405209631 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 5209631
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


AATTGTTATTTGATGTTAAATCAGTGGGTTCTGTCAAGTTAGCTATAGGTTGTGTCATATCAACGATTTCTATGGAAGGTAATAAGATATTATCTTCAGC[A/G]
GTTATGTATCTAGGACCTTTGACAAAAATTGATGCGTTTCTAACTCCACAAAGATTACTTCTCAATATAATTTCTTTCAAATTTAGTAAAATTTCTTTTA

Reverse complement sequence

TAAAAGAAATTTTACTAAATTTGAAAGAAATTATATTGAGAAGTAATCTTTGTGGAGTTAGAAACGCATCAATTTTTGTCAAAGGTCCTAGATACATAAC[T/C]
GCTGAAGATAATATCTTATTACCTTCCATAGAAATCGTTGATATGACACAACCTATAGCTAACTTGACAGAACCCACTGATTTAACATCAAATAACAATT

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 92.20% 7.80% 0.02% 0.00% NA
All Indica  2759 98.00% 2.00% 0.00% 0.00% NA
All Japonica  1512 79.70% 20.20% 0.07% 0.00% NA
Aus  269 99.60% 0.40% 0.00% 0.00% NA
Indica I  595 96.80% 3.20% 0.00% 0.00% NA
Indica II  465 98.70% 1.30% 0.00% 0.00% NA
Indica III  913 98.70% 1.30% 0.00% 0.00% NA
Indica Intermediate  786 97.60% 2.40% 0.00% 0.00% NA
Temperate Japonica  767 94.30% 5.70% 0.00% 0.00% NA
Tropical Japonica  504 56.30% 43.50% 0.20% 0.00% NA
Japonica Intermediate  241 82.20% 17.80% 0.00% 0.00% NA
VI/Aromatic  96 99.00% 1.00% 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
vg0405209631 A -> G LOC_Os04g09710.1 upstream_gene_variant ; 3806.0bp to feature; MODIFIER silent_mutation Average:36.945; most accessible tissue: Zhenshan97 panicle, score: 57.341 N N N N
vg0405209631 A -> G LOC_Os04g09720.2 downstream_gene_variant ; 341.0bp to feature; MODIFIER silent_mutation Average:36.945; most accessible tissue: Zhenshan97 panicle, score: 57.341 N N N N
vg0405209631 A -> G LOC_Os04g09720.1 intron_variant ; MODIFIER silent_mutation Average:36.945; most accessible tissue: Zhenshan97 panicle, score: 57.341 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0405209631 NA 1.67E-18 mr1301 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
vg0405209631 NA 1.82E-06 mr1602 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
vg0405209631 6.49E-07 NA mr1631 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