Search for Variation information by Variation ID:

Please input a variation ID (e.g., vg0722097923 , STR0500036000 ).

Detailed information for vg0725460660:

Variant ID: vg0725460660 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 25460660
Reference Allele: TAlternative Allele: C
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.97, C: 0.02, others allele: 0.00, population size: 81. )

Flanking Sequence (100 bp) in Reference Genome:


GGCTTGCCCATAACCGAGGGCGCGGTTATTCGAATAGATTATACTCTGATCAGAGGTGTACATCTTTACCCACAAGACACATCTTCCTCACGTGTAACCA[T/C]
GTGCCACATACCACCACGGTATATGGATGGAAGATGTGACATAGTTTCCAACCCATCCTAGCCATAGACAAGAGTACCGACCCAACCCCACCTACGGCCG

Reverse complement sequence

CGGCCGTAGGTGGGGTTGGGTCGGTACTCTTGTCTATGGCTAGGATGGGTTGGAAACTATGTCACATCTTCCATCCATATACCGTGGTGGTATGTGGCAC[A/G]
TGGTTACACGTGAGGAAGATGTGTCTTGTGGGTAAAGATGTACACCTCTGATCAGAGTATAATCTATTCGAATAACCGCGCCCTCGGTTATGGGCAAGCC

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 57.20% 38.90% 3.75% 0.17% NA
All Indica  2759 91.80% 6.00% 2.10% 0.11% NA
All Japonica  1512 0.10% 99.90% 0.00% 0.00% NA
Aus  269 49.40% 5.60% 43.12% 1.86% NA
Indica I  595 87.70% 9.20% 2.86% 0.17% NA
Indica II  465 92.30% 7.30% 0.43% 0.00% NA
Indica III  913 96.30% 1.10% 2.63% 0.00% NA
Indica Intermediate  786 89.30% 8.50% 1.91% 0.25% NA
Temperate Japonica  767 0.10% 99.90% 0.00% 0.00% NA
Tropical Japonica  504 0.00% 100.00% 0.00% 0.00% NA
Japonica Intermediate  241 0.40% 99.60% 0.00% 0.00% NA
VI/Aromatic  96 4.20% 95.80% 0.00% 0.00% NA
Intermediate  90 33.30% 63.30% 3.33% 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
vg0725460660 T -> DEL N N silent_mutation Average:21.188; most accessible tissue: Minghui63 young leaf, score: 27.355 N N N N
vg0725460660 T -> C LOC_Os07g42550.1 upstream_gene_variant ; 989.0bp to feature; MODIFIER silent_mutation Average:21.188; most accessible tissue: Minghui63 young leaf, score: 27.355 N N N N
vg0725460660 T -> C LOC_Os07g42540.1 downstream_gene_variant ; 2737.0bp to feature; MODIFIER silent_mutation Average:21.188; most accessible tissue: Minghui63 young leaf, score: 27.355 N N N N
vg0725460660 T -> C LOC_Os07g42550-LOC_Os07g42560 intergenic_region ; MODIFIER silent_mutation Average:21.188; most accessible tissue: Minghui63 young leaf, score: 27.355 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0725460660 NA 1.24E-14 mr1751 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
vg0725460660 NA 1.07E-06 mr1751 Ind_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