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Detailed information for vg0221167230:

Variant ID: vg0221167230 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 21167230
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 359. )

Flanking Sequence (100 bp) in Reference Genome:


GACTGTTGACCCTCGCTTGCCTGCTCTGTATAAAGATGCATCTGATCTTGTAGGCATTGATGGGCCAAAAATTGAGCTCATCAGGTGGCTAACAGAGGGC[G/A]
TGAGTGGCCCTGAACAGCAATTGAAGGTGGTTCCCATTGTTGGATCTGGAGGATTGGGCAAGACAACTCTTGCTAACCAGGTGTACCACAATCTTGAGGG

Reverse complement sequence

CCCTCAAGATTGTGGTACACCTGGTTAGCAAGAGTTGTCTTGCCCAATCCTCCAGATCCAACAATGGGAACCACCTTCAATTGCTGTTCAGGGCCACTCA[C/T]
GCCCTCTGTTAGCCACCTGATGAGCTCAATTTTTGGCCCATCAATGCCTACAAGATCAGATGCATCTTTATACAGAGCAGGCAAGCGAGGGTCAACAGTC

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 98.00% 1.80% 0.21% 0.00% NA
All Indica  2759 99.20% 0.70% 0.04% 0.00% NA
All Japonica  1512 99.80% 0.10% 0.07% 0.00% NA
Aus  269 74.70% 22.30% 2.97% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 99.40% 0.60% 0.00% 0.00% NA
Indica III  913 98.20% 1.80% 0.00% 0.00% NA
Indica Intermediate  786 99.70% 0.10% 0.13% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 99.60% 0.20% 0.20% 0.00% NA
Japonica Intermediate  241 99.60% 0.40% 0.00% 0.00% NA
VI/Aromatic  96 99.00% 1.00% 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
vg0221167230 G -> A LOC_Os02g35210.1 missense_variant ; p.Val185Met; MODERATE nonsynonymous_codon ; V185M Average:71.53; most accessible tissue: Minghui63 flag leaf, score: 84.42 unknown unknown TOLERATED 0.10