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Detailed information for vg0905620923:

Variant ID: vg0905620923 (JBrowse)Variation Type: SNP
Chromosome: chr09Position: 5620923
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.01, others allele: 0.00, population size: 254. )

Flanking Sequence (100 bp) in Reference Genome:


CGAGGCACTAATCCTGCCTTGCGTCGGAGCGAAGAGATGGATCTTCTTCCTCTGGAATAGCTGGCAACGATCTAACGAGGCACTAATCCCGCCTTGCGTC[G/A]
AAGCGAAGAGATGGATCTTCTTCCTCTGGAATAGCTGGCTCTCTTTCTTCTGGATCTTCCTCCTCTGGGGTAGCTGACGGCGGTGCTTCTCCCTTGAGCT

Reverse complement sequence

AGCTCAAGGGAGAAGCACCGCCGTCAGCTACCCCAGAGGAGGAAGATCCAGAAGAAAGAGAGCCAGCTATTCCAGAGGAAGAAGATCCATCTCTTCGCTT[C/T]
GACGCAAGGCGGGATTAGTGCCTCGTTAGATCGTTGCCAGCTATTCCAGAGGAAGAAGATCCATCTCTTCGCTCCGACGCAAGGCAGGATTAGTGCCTCG

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 98.80% 1.20% 0.00% 0.00% NA
All Indica  2759 99.70% 0.30% 0.00% 0.00% NA
All Japonica  1512 100.00% 0.00% 0.00% 0.00% NA
Aus  269 83.30% 16.70% 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 99.30% 0.70% 0.00% 0.00% NA
Indica Intermediate  786 99.60% 0.40% 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 99.00% 1.00% 0.00% 0.00% NA
Intermediate  90 100.00% 0.00% 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
vg0905620923 G -> A LOC_Os09g10310.1 synonymous_variant ; p.Phe202Phe; LOW nonsynonymous_codon ; F202S Average:49.638; most accessible tissue: Zhenshan97 flag leaf, score: 66.824 unknown unknown TOLERATED 1.00