Search for Variation information by Variation ID:

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

Detailed information for vg0409515435:

Variant ID: vg0409515435 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 9515435
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.98, C: 0.02, others allele: 0.00, population size: 254. )

Flanking Sequence (100 bp) in Reference Genome:


AATGCCTAGCAACTCGTTCCTTATCTCTGGTAACCTTAGCAAGGGCTCGTAAACGCGATTGAACCAAGTCCTCCCTCTCATCGGCCATAAGGTTATAATA[T/C]
TCATCGGCTATCAAACCGTCTTGCAATTCTATCCTTCTAGAGCCGATTCTAACTTCCCATGGCAAAACAGCTTCATGTCCATAAACAAGCTTATAAGGAG

Reverse complement sequence

CTCCTTATAAGCTTGTTTATGGACATGAAGCTGTTTTGCCATGGGAAGTTAGAATCGGCTCTAGAAGGATAGAATTGCAAGACGGTTTGATAGCCGATGA[A/G]
TATTATAACCTTATGGCCGATGAGAGGGAGGACTTGGTTCAATCGCGTTTACGAGCCCTTGCTAAGGTTACCAGAGATAAGGAACGAGTTGCTAGGCATT

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 89.40% 0.90% 2.18% 7.60% NA
All Indica  2759 98.30% 0.30% 1.41% 0.00% NA
All Japonica  1512 72.70% 2.10% 2.98% 22.29% 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 99.60% 0.00% 0.43% 0.00% NA
Indica III  913 95.30% 1.00% 3.72% 0.00% NA
Indica Intermediate  786 99.60% 0.00% 0.38% 0.00% NA
Temperate Japonica  767 98.40% 0.10% 0.13% 1.30% NA
Tropical Japonica  504 30.00% 6.00% 7.94% 56.15% NA
Japonica Intermediate  241 80.10% 0.00% 1.66% 18.26% NA
VI/Aromatic  96 61.50% 0.00% 16.67% 21.88% NA
Intermediate  90 94.40% 1.10% 3.33% 1.11% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0409515435 T -> C LOC_Os04g17380.1 synonymous_variant ; p.Glu57Glu; LOW synonymous_codon Average:21.307; most accessible tissue: Callus, score: 28.075 N N N N
vg0409515435 T -> DEL LOC_Os04g17380.1 N frameshift_variant Average:21.307; most accessible tissue: Callus, score: 28.075 N N N N