Search for Variation information by Variation ID:

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

Detailed information for vg0104838836:

Variant ID: vg0104838836 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 4838836
Reference Allele: TAlternative Allele: G
Primary Allele: GSecondary Allele: T

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, others allele: 0.00, population size: 309. )

Flanking Sequence (100 bp) in Reference Genome:


CTTTAGTTTGGGTCAAGTGCATGCCCCCCACTAGTTTAAGTCTGAAGAAGTAGCTTCAATTAATTATCAACTGGAGAGAGTCCCCATCATTTGAATTTTT[T/G]
AAGTGGCTATGTGATCCCCTGATCTTGATGCTACTTTTGTAGCTAAATTAAGCAGATTCTACTCCTGACCTGATGAAGATGAACACATGACTTCTGGCAC

Reverse complement sequence

GTGCCAGAAGTCATGTGTTCATCTTCATCAGGTCAGGAGTAGAATCTGCTTAATTTAGCTACAAAAGTAGCATCAAGATCAGGGGATCACATAGCCACTT[A/C]
AAAAATTCAAATGATGGGGACTCTCTCCAGTTGATAATTAATTGAAGCTACTTCTTCAGACTTAAACTAGTGGGGGGCATGCACTTGACCCAAACTAAAG

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 90.90% 8.80% 0.30% 0.00% NA
All Indica  2759 99.50% 0.50% 0.00% 0.00% NA
All Japonica  1512 72.90% 26.30% 0.79% 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 97.60% 2.40% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 99.70% 0.30% 0.00% 0.00% NA
Temperate Japonica  767 50.80% 47.70% 1.43% 0.00% NA
Tropical Japonica  504 99.40% 0.60% 0.00% 0.00% NA
Japonica Intermediate  241 88.00% 11.60% 0.41% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 90.00% 7.80% 2.22% 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
vg0104838836 T -> G LOC_Os01g09480.1 upstream_gene_variant ; 621.0bp to feature; MODIFIER silent_mutation Average:63.335; most accessible tissue: Callus, score: 92.775 N N N N
vg0104838836 T -> G LOC_Os01g09490.1 upstream_gene_variant ; 1518.0bp to feature; MODIFIER silent_mutation Average:63.335; most accessible tissue: Callus, score: 92.775 N N N N
vg0104838836 T -> G LOC_Os01g09480-LOC_Os01g09490 intergenic_region ; MODIFIER silent_mutation Average:63.335; most accessible tissue: Callus, score: 92.775 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0104838836 NA 8.10E-08 mr1446_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
vg0104838836 4.12E-06 NA mr1923_2 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