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Detailed information for vg0202539929:

Variant ID: vg0202539929 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 2539929
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.96, C: 0.05, others allele: 0.00, population size: 232. )

Flanking Sequence (100 bp) in Reference Genome:


ATACCGGAATCGCGACATCAAACGTCGACAATGGCGCGCTAGGTAGGGGGAGTTTGGTACTTCAAGGTTTCGACGAGATGGGTTCAAAAGATGGATTCTC[T/C]
GACAACAAGCTATTCGACGACTTCGCTGTGGGAAGATCCAACCCGACCGAAGTATGTCTCCCGACGAGATCGGAACCATCGTCATCAACAACTCGATCTC

Reverse complement sequence

GAGATCGAGTTGTTGATGACGATGGTTCCGATCTCGTCGGGAGACATACTTCGGTCGGGTTGGATCTTCCCACAGCGAAGTCGTCGAATAGCTTGTTGTC[A/G]
GAGAATCCATCTTTTGAACCCATCTCGTCGAAACCTTGAAGTACCAAACTCCCCCTACCTAGCGCGCCATTGTCGACGTTTGATGTCGCGATTCCGGTAT

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 95.80% 4.20% 0.00% 0.00% NA
All Indica  2759 96.90% 3.10% 0.00% 0.00% NA
All Japonica  1512 99.50% 0.50% 0.00% 0.00% NA
Aus  269 97.80% 2.20% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 98.70% 1.30% 0.00% 0.00% NA
Indica III  913 95.80% 4.20% 0.00% 0.00% NA
Indica Intermediate  786 94.70% 5.30% 0.00% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 99.80% 0.20% 0.00% 0.00% NA
Japonica Intermediate  241 97.50% 2.50% 0.00% 0.00% NA
VI/Aromatic  96 6.20% 93.80% 0.00% 0.00% NA
Intermediate  90 88.90% 11.10% 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
vg0202539929 T -> C LOC_Os02g05290.1 synonymous_variant ; p.Ser8Ser; LOW synonymous_codon Average:46.751; most accessible tissue: Minghui63 young leaf, score: 62.741 N N N N