Search for Variation information by Variation ID:

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

Detailed information for vg0903406771:

Variant ID: vg0903406771 (JBrowse)Variation Type: SNP
Chromosome: chr09Position: 3406771
Reference Allele: TAlternative Allele: G
Primary Allele: TSecondary Allele: G

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 263. )

Flanking Sequence (100 bp) in Reference Genome:


TCAAAGTCAAGTACATAATATCTGTCTCGCATATGTCAAATAATACAGTGCTGTAGGAAAAAAACAGAGATGGAGAGTTGGATACATACCACAAATTAGA[T/G]
CCTACCATTGGTTTAGCAAGGTCTCCATATTTACCAGGTTCAATAGGCGTGTAGCACTGTGATGTTTTTTCTTCCAGGGATTAACTCAGGAACAAATTAA

Reverse complement sequence

TTAATTTGTTCCTGAGTTAATCCCTGGAAGAAAAAACATCACAGTGCTACACGCCTATTGAACCTGGTAAATATGGAGACCTTGCTAAACCAATGGTAGG[A/C]
TCTAATTTGTGGTATGTATCCAACTCTCCATCTCTGTTTTTTTCCTACAGCACTGTATTATTTGACATATGCGAGACAGATATTATGTACTTGACTTTGA

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 99.80% 0.20% 0.02% 0.00% NA
All Indica  2759 99.60% 0.30% 0.04% 0.00% NA
All Japonica  1512 100.00% 0.00% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 99.80% 0.00% 0.17% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 99.50% 0.50% 0.00% 0.00% NA
Indica Intermediate  786 99.50% 0.50% 0.00% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 100.00% 0.00% 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
vg0903406771 T -> G LOC_Os09g07020.1 synonymous_variant ; p.Gly237Gly; LOW N Average:52.894; most accessible tissue: Callus, score: 78.358 N N N N
vg0903406771 T -> G LOC_Os09g07020.2 synonymous_variant ; p.Gly236Gly; LOW N Average:52.894; most accessible tissue: Callus, score: 78.358 N N N N
vg0903406771 T -> G LOC_Os09g07010.1 upstream_gene_variant ; 3662.0bp to feature; MODIFIER N Average:52.894; most accessible tissue: Callus, score: 78.358 N N N N
vg0903406771 T -> G LOC_Os09g07030.1 downstream_gene_variant ; 2109.0bp to feature; MODIFIER N Average:52.894; most accessible tissue: Callus, score: 78.358 N N N N