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Detailed information for vg0724248659:

Variant ID: vg0724248659 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 24248659
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.68, A: 0.33, others allele: 0.00, population size: 90. )

Flanking Sequence (100 bp) in Reference Genome:


GCAAAACGAGGTGAGCCATTAGCTCATGATTAATTGAGTATTAATTATTTTAAATTTTAAAAATAGATTAATATGATTTTTTAAAGCAAATTTTCTATAG[G/A]
AAATTTTTGTAAAAAACACACCGTTTAGTAGTTTGGAAAGCGTGCGCGCGGAAAATGAGTTGTTATCTCCCTCAATGTTACCCGAACGAACGTAGCCTTA

Reverse complement sequence

TAAGGCTACGTTCGTTCGGGTAACATTGAGGGAGATAACAACTCATTTTCCGCGCGCACGCTTTCCAAACTACTAAACGGTGTGTTTTTTACAAAAATTT[C/T]
CTATAGAAAATTTGCTTTAAAAAATCATATTAATCTATTTTTAAAATTTAAAATAATTAATACTCAATTAATCATGAGCTAATGGCTCACCTCGTTTTGC

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 87.70% 12.00% 0.38% 0.00% NA
All Indica  2759 80.60% 19.40% 0.07% 0.00% NA
All Japonica  1512 97.80% 1.50% 0.73% 0.00% NA
Aus  269 98.10% 0.40% 1.49% 0.00% NA
Indica I  595 98.70% 1.30% 0.00% 0.00% NA
Indica II  465 82.20% 17.80% 0.00% 0.00% NA
Indica III  913 66.00% 33.80% 0.11% 0.00% NA
Indica Intermediate  786 82.80% 17.00% 0.13% 0.00% NA
Temperate Japonica  767 98.70% 0.50% 0.78% 0.00% NA
Tropical Japonica  504 96.20% 3.40% 0.40% 0.00% NA
Japonica Intermediate  241 97.90% 0.80% 1.24% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 91.10% 7.80% 1.11% 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
vg0724248659 G -> A LOC_Os07g40470.1 upstream_gene_variant ; 1397.0bp to feature; MODIFIER silent_mutation Average:55.552; most accessible tissue: Minghui63 panicle, score: 79.811 N N N N
vg0724248659 G -> A LOC_Os07g40460.1 downstream_gene_variant ; 1185.0bp to feature; MODIFIER silent_mutation Average:55.552; most accessible tissue: Minghui63 panicle, score: 79.811 N N N N
vg0724248659 G -> A LOC_Os07g40480.1 downstream_gene_variant ; 4264.0bp to feature; MODIFIER silent_mutation Average:55.552; most accessible tissue: Minghui63 panicle, score: 79.811 N N N N
vg0724248659 G -> A LOC_Os07g40460.2 downstream_gene_variant ; 3219.0bp to feature; MODIFIER silent_mutation Average:55.552; most accessible tissue: Minghui63 panicle, score: 79.811 N N N N
vg0724248659 G -> A LOC_Os07g40460.3 downstream_gene_variant ; 1185.0bp to feature; MODIFIER silent_mutation Average:55.552; most accessible tissue: Minghui63 panicle, score: 79.811 N N N N
vg0724248659 G -> A LOC_Os07g40460-LOC_Os07g40470 intergenic_region ; MODIFIER silent_mutation Average:55.552; most accessible tissue: Minghui63 panicle, score: 79.811 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0724248659 NA 4.57E-06 mr1721 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