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Detailed information for vg0234310894:

Variant ID: vg0234310894 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 34310894
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, A: 0.00, others allele: 0.00, population size: 295. )

Flanking Sequence (100 bp) in Reference Genome:


CCTATGAAGATAATATACCTATACCTATGGAATTCCTCTACTTATTCTACTGTAGTTGGTAATTTTCTTCATTTTTTTTAAGATAATGAAATAACATTCC[G/A]
GCTTTTGCTCAACGAGATACAACCAATTATTACAAAGTCCACACACGAACAAACTCAGCACACACTGACATAATGTAAAGAAAACATAAACTAAAAGACA

Reverse complement sequence

TGTCTTTTAGTTTATGTTTTCTTTACATTATGTCAGTGTGTGCTGAGTTTGTTCGTGTGTGGACTTTGTAATAATTGGTTGTATCTCGTTGAGCAAAAGC[C/T]
GGAATGTTATTTCATTATCTTAAAAAAAATGAAGAAAATTACCAACTACAGTAGAATAAGTAGAGGAATTCCATAGGTATAGGTATATTATCTTCATAGG

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 97.50% 2.50% 0.00% 0.00% NA
All Indica  2759 99.50% 0.50% 0.00% 0.00% NA
All Japonica  1512 99.80% 0.20% 0.00% 0.00% NA
Aus  269 64.70% 35.30% 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 99.20% 0.80% 0.00% 0.00% NA
Indica Intermediate  786 99.00% 1.00% 0.00% 0.00% NA
Temperate Japonica  767 99.70% 0.30% 0.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 99.60% 0.40% 0.00% 0.00% NA
VI/Aromatic  96 93.80% 6.20% 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
vg0234310894 G -> A LOC_Os02g56040.1 upstream_gene_variant ; 3165.0bp to feature; MODIFIER silent_mutation Average:36.789; most accessible tissue: Callus, score: 59.39 N N N N
vg0234310894 G -> A LOC_Os02g56060.1 upstream_gene_variant ; 1812.0bp to feature; MODIFIER silent_mutation Average:36.789; most accessible tissue: Callus, score: 59.39 N N N N
vg0234310894 G -> A LOC_Os02g56050.1 intron_variant ; MODIFIER silent_mutation Average:36.789; most accessible tissue: Callus, score: 59.39 N N N N