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Detailed information for vg1202830937:

Variant ID: vg1202830937 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 2830937
Reference Allele: TAlternative Allele: G
Primary Allele: TSecondary Allele: G

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 359. )

Flanking Sequence (100 bp) in Reference Genome:


TCAGCACATGTGCAAGCTTAGCATTGATAATTGAAGGAACACAGGTGCATGCAGTTATTGTTAAGCATGGTTTTCATAGGAACCTCTTTGTAGCAACATC[T/G]
CTTGTGGATGTCTATGCAAAGTGTGGTCAGATTGAAAAATCATATGAAGTATTTGCTGATATGGAAGAAAAGAATGTTGTCTTATGGAATGCAATGATTG

Reverse complement sequence

CAATCATTGCATTCCATAAGACAACATTCTTTTCTTCCATATCAGCAAATACTTCATATGATTTTTCAATCTGACCACACTTTGCATAGACATCCACAAG[A/C]
GATGTTGCTACAAAGAGGTTCCTATGAAAACCATGCTTAACAATAACTGCATGCACCTGTGTTCCTTCAATTATCAATGCTAAGCTTGCACATGTGCTGA

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 99.70% 0.30% 0.00% 0.00% NA
All Indica  2759 99.60% 0.40% 0.00% 0.00% NA
All Japonica  1512 100.00% 0.00% 0.00% 0.00% NA
Aus  269 99.30% 0.70% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 99.40% 0.60% 0.00% 0.00% NA
Indica III  913 99.90% 0.10% 0.00% 0.00% NA
Indica Intermediate  786 99.20% 0.80% 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 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
vg1202830937 T -> G LOC_Os12g06070.1 synonymous_variant ; p.Ser298Ser; LOW N Average:48.925; most accessible tissue: Callus, score: 84.964 N N N N