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Detailed information for vg0220739821:

Variant ID: vg0220739821 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 20739821
Reference Allele: GAlternative Allele: T
Primary Allele: GSecondary Allele: T

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, others allele: 0.00, population size: 368. )

Flanking Sequence (100 bp) in Reference Genome:


ATGGCAAGTGTCCTTGCCATACTAATGTAGCATGAGAGTGAATCTTGCTTTGACGTCTCTACAGAACTTGACCTCCCTGCTATAAGTGATCTTGCAGACC[G/T]
TAAAAGATGTCGTTCTTCAGGTCTTGCCAAGTTGTGGTTGTGATCAGAGACCAGCCGGATAACCTTCCACTCCCCGTGGTTATTCACTCTGAAGCGAACC

Reverse complement sequence

GGTTCGCTTCAGAGTGAATAACCACGGGGAGTGGAAGGTTATCCGGCTGGTCTCTGATCACAACCACAACTTGGCAAGACCTGAAGAACGACATCTTTTA[C/A]
GGTCTGCAAGATCACTTATAGCAGGGAGGTCAAGTTCTGTAGAGACGTCAAAGCAAGATTCACTCTCATGCTACATTAGTATGGCAAGGACACTTGCCAT

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 78.10% 21.90% 0.04% 0.00% NA
All Indica  2759 63.40% 36.60% 0.07% 0.00% NA
All Japonica  1512 99.40% 0.60% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 28.60% 71.40% 0.00% 0.00% NA
Indica II  465 64.90% 34.80% 0.22% 0.00% NA
Indica III  913 81.30% 18.70% 0.00% 0.00% NA
Indica Intermediate  786 67.90% 31.90% 0.13% 0.00% NA
Temperate Japonica  767 99.20% 0.80% 0.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 98.80% 1.20% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 83.30% 16.70% 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
vg0220739821 G -> T LOC_Os02g34590.1 synonymous_variant ; p.Arg200Arg; LOW synonymous_codon Average:73.386; most accessible tissue: Zhenshan97 young leaf, score: 81.353 N N N N