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Detailed information for vg0204059356:

Variant ID: vg0204059356 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 4059356
Reference Allele: GAlternative Allele: T
Primary Allele: GSecondary Allele: T

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.86, G: 0.14, others allele: 0.00, population size: 232. )

Flanking Sequence (100 bp) in Reference Genome:


GCAACGCTTTTATTTTGTTAATTACCTCTAGTTGCTCATGTAGCCTTCTTTGCACCTCCATCTGCATTCTGATGGCATCGTTCACGTTGCGGCTGAGAGA[G/T]
AGAATTTCACACACAAGCAAACACAAAAATGGAGTTAGGAAAGAACAAAAAAAAAGAGTAACTGAACAAGGACTAAGAAAGAAATTAAAATCTTAAACCG

Reverse complement sequence

CGGTTTAAGATTTTAATTTCTTTCTTAGTCCTTGTTCAGTTACTCTTTTTTTTTGTTCTTTCCTAACTCCATTTTTGTGTTTGCTTGTGTGTGAAATTCT[C/A]
TCTCTCAGCCGCAACGTGAACGATGCCATCAGAATGCAGATGGAGGTGCAAAGAAGGCTACATGAGCAACTAGAGGTAATTAACAAAATAAAAGCGTTGC

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 58.70% 41.20% 0.08% 0.00% NA
All Indica  2759 35.70% 64.30% 0.07% 0.00% NA
All Japonica  1512 99.70% 0.30% 0.00% 0.00% NA
Aus  269 48.70% 50.60% 0.74% 0.00% NA
Indica I  595 33.10% 66.90% 0.00% 0.00% NA
Indica II  465 28.00% 71.80% 0.22% 0.00% NA
Indica III  913 41.00% 58.90% 0.11% 0.00% NA
Indica Intermediate  786 36.00% 64.00% 0.00% 0.00% NA
Temperate Japonica  767 99.70% 0.30% 0.00% 0.00% NA
Tropical Japonica  504 99.80% 0.20% 0.00% 0.00% NA
Japonica Intermediate  241 99.20% 0.80% 0.00% 0.00% NA
VI/Aromatic  96 94.80% 5.20% 0.00% 0.00% NA
Intermediate  90 66.70% 33.30% 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
vg0204059356 G -> T LOC_Os02g07770.1 intron_variant ; MODIFIER silent_mutation Average:39.874; most accessible tissue: Callus, score: 60.214 N N N N