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Detailed information for vg0704593047:

Variant ID: vg0704593047 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 4593047
Reference Allele: TAlternative Allele: A
Primary Allele: ASecondary Allele: T

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:


ACAGGATGTGTACTTTGGCCAGCCCGCCCGACTGACTATACATAATTCAACAATTACAGCTTGCACCTATTTATTCCATTCTAAAACTATAAAATTTGCT[T/A]
AAAACAAATTTTTTACCATGTAGACCACAAAAGCATTTATAAACTATTATATTGAAGCCACATCAGAGTGTTCTATTATAGCTGCAAGTAGTCTTGGCAT

Reverse complement sequence

ATGCCAAGACTACTTGCAGCTATAATAGAACACTCTGATGTGGCTTCAATATAATAGTTTATAAATGCTTTTGTGGTCTACATGGTAAAAAATTTGTTTT[A/T]
AGCAAATTTTATAGTTTTAGAATGGAATAAATAGGTGCAAGCTGTAATTGTTGAATTATGTATAGTCAGTCGGGCGGGCTGGCCAAAGTACACATCCTGT

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 81.00% 18.80% 0.15% 0.00% NA
All Indica  2759 99.40% 0.50% 0.04% 0.00% NA
All Japonica  1512 43.60% 56.00% 0.40% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 99.70% 0.20% 0.17% 0.00% NA
Indica II  465 99.10% 0.90% 0.00% 0.00% NA
Indica III  913 99.80% 0.20% 0.00% 0.00% NA
Indica Intermediate  786 99.00% 1.00% 0.00% 0.00% NA
Temperate Japonica  767 55.10% 44.20% 0.65% 0.00% NA
Tropical Japonica  504 35.30% 64.70% 0.00% 0.00% NA
Japonica Intermediate  241 24.10% 75.50% 0.41% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 70.00% 30.00% 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
vg0704593047 T -> A LOC_Os07g08850.1 downstream_gene_variant ; 2381.0bp to feature; MODIFIER silent_mutation Average:50.681; most accessible tissue: Zhenshan97 panicle, score: 80.486 N N N N
vg0704593047 T -> A LOC_Os07g08860.1 downstream_gene_variant ; 47.0bp to feature; MODIFIER silent_mutation Average:50.681; most accessible tissue: Zhenshan97 panicle, score: 80.486 N N N N
vg0704593047 T -> A LOC_Os07g08870.1 downstream_gene_variant ; 3359.0bp to feature; MODIFIER silent_mutation Average:50.681; most accessible tissue: Zhenshan97 panicle, score: 80.486 N N N N
vg0704593047 T -> A LOC_Os07g08850-LOC_Os07g08860 intergenic_region ; MODIFIER silent_mutation Average:50.681; most accessible tissue: Zhenshan97 panicle, score: 80.486 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0704593047 NA 3.24E-14 mr1905 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
vg0704593047 NA 1.64E-07 mr1623_2 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