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Detailed information for vg0409081465:

Variant ID: vg0409081465 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 9081465
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TCTTCTGGCAACGACGGCAGTGCTCGCGAGCACGCGTGGATTCGACGAGGGTGGCTGCGGCGACGCTCGCGGACGCATTGGGGGTGACAGCAGCACTCGC[G/A]
GGCACATCCAACAATGGTGACGGATCTGCAACAGCGGCTGCGACAGCACTCACCGACAGATCTGGTGGGCATCATCACAAGGGTCTTATCTTCTTCGAGA

Reverse complement sequence

TCTCGAAGAAGATAAGACCCTTGTGATGATGCCCACCAGATCTGTCGGTGAGTGCTGTCGCAGCCGCTGTTGCAGATCCGTCACCATTGTTGGATGTGCC[C/T]
GCGAGTGCTGCTGTCACCCCCAATGCGTCCGCGAGCGTCGCCGCAGCCACCCTCGTCGAATCCACGCGTGCTCGCGAGCACTGCCGTCGTTGCCAGAAGA

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 98.10% 1.90% 0.04% 0.00% NA
All Indica  2759 100.00% 0.00% 0.00% 0.00% NA
All Japonica  1512 99.50% 0.50% 0.07% 0.00% 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  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 99.90% 0.10% 0.00% 0.00% NA
Temperate Japonica  767 99.90% 0.00% 0.13% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 97.10% 2.90% 0.00% 0.00% NA
VI/Aromatic  96 22.90% 76.00% 1.04% 0.00% NA
Intermediate  90 91.10% 8.90% 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
vg0409081465 G -> A LOC_Os04g16690.1 synonymous_variant ; p.Ala45Ala; LOW nonsynonymous_codon ; A45V Average:70.165; most accessible tissue: Zhenshan97 young leaf, score: 85.886 unknown unknown DELETERIOUS 0.00