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Detailed information for vg1202830688:

Variant ID: vg1202830688 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 2830688
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, T: 0.00, others allele: 0.00, population size: 309. )

Flanking Sequence (100 bp) in Reference Genome:


TTGCCATCAAGCTTGCACTTGATTCTAGCAGTTTTGTTGGGACTGCATTTCTTGATGTTTATGCAAAGTGTAATATGATAAAGGATGCCTGCTGGGTTTT[C/T]
GAGAATATGCCTGAGAAAACTTCAGTTACATGGAGTTCATTATTTGCAGGATTTGTGCAGAATGGTCTCCATGAAGAGGTATTGTGTTTATTTCAGAGTA

Reverse complement sequence

TACTCTGAAATAAACACAATACCTCTTCATGGAGACCATTCTGCACAAATCCTGCAAATAATGAACTCCATGTAACTGAAGTTTTCTCAGGCATATTCTC[G/A]
AAAACCCAGCAGGCATCCTTTATCATATTACACTTTGCATAAACATCAAGAAATGCAGTCCCAACAAAACTGCTAGAATCAAGTGCAAGCTTGATGGCAA

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 99.80% 0.20% 0.00% 0.00% NA
All Indica  2759 99.80% 0.20% 0.00% 0.00% NA
All Japonica  1512 100.00% 0.00% 0.00% 0.00% NA
Aus  269 98.50% 1.50% 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 99.50% 0.50% 0.00% 0.00% NA
Indica Intermediate  786 100.00% 0.00% 0.00% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 100.00% 0.00% 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
vg1202830688 C -> T LOC_Os12g06070.1 synonymous_variant ; p.Phe215Phe; LOW N Average:55.118; most accessible tissue: Callus, score: 81.656 N N N N