Search for Variation information by Variation ID:

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

Detailed information for vg0204059211:

Variant ID: vg0204059211 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 4059211
Reference Allele: TAlternative Allele: G
Primary Allele: TSecondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, T: 0.02, others allele: 0.00, population size: 259. )

Flanking Sequence (100 bp) in Reference Genome:


TGTATGTATGCATGGCAGCATGGGAATGAAGGGCAGAAAAGTGGATAGGTAAACTTCCCTGGTGCTTTATTTGAAAGGAGAAACTTGATGAAACTTCATG[T/G]
GAATTTGTTGGTGCAATTTAATTTGAATGCATATGCATGTGGATGCAACGCTTTTATTTTGTTAATTACCTCTAGTTGCTCATGTAGCCTTCTTTGCACC

Reverse complement sequence

GGTGCAAAGAAGGCTACATGAGCAACTAGAGGTAATTAACAAAATAAAAGCGTTGCATCCACATGCATATGCATTCAAATTAAATTGCACCAACAAATTC[A/C]
CATGAAGTTTCATCAAGTTTCTCCTTTCAAATAAAGCACCAGGGAAGTTTACCTATCCACTTTTCTGCCCTTCATTCCCATGCTGCCATGCATACATACA

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 58.60% 41.30% 0.06% 0.00% NA
All Indica  2759 35.60% 64.40% 0.04% 0.00% NA
All Japonica  1512 99.60% 0.40% 0.00% 0.00% NA
Aus  269 48.00% 51.30% 0.74% 0.00% NA
Indica I  595 33.30% 66.70% 0.00% 0.00% NA
Indica II  465 28.00% 72.00% 0.00% 0.00% NA
Indica III  913 40.70% 59.10% 0.11% 0.00% NA
Indica Intermediate  786 35.90% 64.10% 0.00% 0.00% NA
Temperate Japonica  767 99.60% 0.40% 0.00% 0.00% NA
Tropical Japonica  504 99.80% 0.20% 0.00% 0.00% NA
Japonica Intermediate  241 99.20% 0.80% 0.00% 0.00% NA
VI/Aromatic  96 94.80% 5.20% 0.00% 0.00% NA
Intermediate  90 67.80% 32.20% 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
vg0204059211 T -> G LOC_Os02g07770.1 intron_variant ; MODIFIER silent_mutation Average:42.632; most accessible tissue: Callus, score: 80.707 N N N N