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Detailed information for vg0204059965:

Variant ID: vg0204059965 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 4059965
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


ATCGAGGAACAAGCTAAGCTAGGAGAAAACCCTAGCTAGCTAAGGTGTGGTTAGCTAGCTAGGTTACCTGGAGATGGCTCTTGAGGTGGTAGAGGGTGAG[G/A]
CCCTTCACTCCCATCACCCTCATGATCGTCTTGGGCGTCGCCTCTGCGACGACAAGACGATCATCAATTCATCGTAAGAAAGAAGAGATTAATTCTTGTT

Reverse complement sequence

AACAAGAATTAATCTCTTCTTTCTTACGATGAATTGATGATCGTCTTGTCGTCGCAGAGGCGACGCCCAAGACGATCATGAGGGTGATGGGAGTGAAGGG[C/T]
CTCACCCTCTACCACCTCAAGAGCCATCTCCAGGTAACCTAGCTAGCTAACCACACCTTAGCTAGCTAGGGTTTTCTCCTAGCTTAGCTTGTTCCTCGAT

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% 0.00% 0.00% NA
All Indica  2759 96.70% 3.30% 0.00% 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  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 97.80% 2.20% 0.00% 0.00% NA
Indica III  913 93.10% 6.90% 0.00% 0.00% NA
Indica Intermediate  786 97.80% 2.20% 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 98.90% 1.10% 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
vg0204059965 G -> A LOC_Os02g07770.1 synonymous_variant ; p.Gly55Gly; LOW synonymous_codon Average:61.112; most accessible tissue: Minghui63 panicle, score: 85.556 N N N N