Search for Variation information by Variation ID:

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

Detailed information for vg0500376514:

Variant ID: vg0500376514 (JBrowse)Variation Type: INDEL
Chromosome: chr05Position: 376514
Reference Allele: ACTAlternative Allele: A
Primary Allele: ACTSecondary Allele: A

Inferred Ancestral Allele : ACT (evidence from allele frequency in Oryza rufipogon: ACT: 0.98, A: 0.01, others allele: 0.00, population size: 277. )

Flanking Sequence (100 bp) in Reference Genome:


AGTTGCCCCCAAAAAATTCTGTACAGCTTCAAATCAATCTGTGAGTGTACACTGAGCTATTTAACTCCAGATTCAATTTGCCCATTTACTCTGCTTGTTA[ACT/A]
TCAGTCTTGACACCAAGCCATCCAAGATTCCATATATTTCTTGATTCTCAGGTTGCCTCTCCCTAAATTGATGAAGAATCTCGTTTAAGTTCACCAGGCG

Reverse complement sequence

CGCCTGGTGAACTTAAACGAGATTCTTCATCAATTTAGGGAGAGGCAACCTGAGAATCAAGAAATATATGGAATCTTGGATGGCTTGGTGTCAAGACTGA[AGT/T]
TAACAAGCAGAGTAAATGGGCAAATTGAATCTGGAGTTAAATAGCTCAGTGTACACTCACAGATTGATTTGAAGCTGTACAGAATTTTTTGGGGGCAACT

Allele Frequencies:

Populations Population SizeFrequency of ACT(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 86.60% 13.40% 0.02% 0.00% NA
All Indica  2759 84.10% 15.80% 0.04% 0.00% NA
All Japonica  1512 96.50% 3.50% 0.00% 0.00% NA
Aus  269 53.50% 46.50% 0.00% 0.00% NA
Indica I  595 85.70% 14.30% 0.00% 0.00% NA
Indica II  465 97.00% 3.00% 0.00% 0.00% NA
Indica III  913 83.10% 16.90% 0.00% 0.00% NA
Indica Intermediate  786 76.50% 23.40% 0.13% 0.00% NA
Temperate Japonica  767 93.60% 6.40% 0.00% 0.00% NA
Tropical Japonica  504 99.80% 0.20% 0.00% 0.00% NA
Japonica Intermediate  241 98.80% 1.20% 0.00% 0.00% NA
VI/Aromatic  96 93.80% 6.20% 0.00% 0.00% NA
Intermediate  90 88.90% 11.10% 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
vg0500376514 ACT -> A LOC_Os05g01635.1 frameshift_variant ; p.Lys539fs; HIGH frameshift_variant Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 N N N N