Search for Variation information by Variation ID:

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

Detailed information for vg0128797257:

Variant ID: vg0128797257 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 28797257
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, others allele: 0.00, population size: 295. )

Flanking Sequence (100 bp) in Reference Genome:


GGCATCCTCGCCGGCCGCTGGCATTGAGTGCAGCGACGATCGTGCCCGACCGGCCGACGGTGGCGGTGACTTCGCAGCGATGGTGAGCGCCGCCGATGCC[G/A]
AGGGATTCGAAGGAGGATTTGGCGATCAGTTCTGTGCCGAGGATGCAGTTCATGGTGGCTTCGACATGGGTTCCGCTTCCGCCATGGTGGGTGACGACGA

Reverse complement sequence

TCGTCGTCACCCACCATGGCGGAAGCGGAACCCATGTCGAAGCCACCATGAACTGCATCCTCGGCACAGAACTGATCGCCAAATCCTCCTTCGAATCCCT[C/T]
GGCATCGGCGGCGCTCACCATCGCTGCGAAGTCACCGCCACCGTCGGCCGGTCGGGCACGATCGTCGCTGCACTCAATGCCAGCGGCCGGCGAGGATGCC

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 97.10% 2.90% 0.00% 0.00% NA
All Indica  2759 99.20% 0.80% 0.00% 0.00% NA
All Japonica  1512 92.80% 7.20% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 98.30% 1.70% 0.00% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 99.70% 0.30% 0.00% 0.00% NA
Indica Intermediate  786 98.70% 1.30% 0.00% 0.00% NA
Temperate Japonica  767 99.70% 0.30% 0.00% 0.00% NA
Tropical Japonica  504 80.40% 19.60% 0.00% 0.00% NA
Japonica Intermediate  241 96.70% 3.30% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 96.70% 3.30% 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
vg0128797257 G -> A LOC_Os01g50110.1 missense_variant ; p.Glu200Lys; MODERATE nonsynonymous_codon ; E200K Average:76.315; most accessible tissue: Zhenshan97 young leaf, score: 81.353 unknown unknown TOLERATED 0.42