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Detailed information for vg1202831695:

Variant ID: vg1202831695 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 2831695
Reference Allele: AAlternative Allele: C
Primary Allele: ASecondary Allele: C

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, C: 0.00, others allele: 0.00, population size: 340. )

Flanking Sequence (100 bp) in Reference Genome:


CCAGGAATAACTGATGTATACAATAAGTTGGAGGAAATTTACCATGAGATGAGAAAGATTTCTCACAGAGCCAACACACAATGTGATCTGCATGATGTGC[A/C]
TGCTGACCAAAAAGAGGAGCTACTTAAACACCACAGTGAGAAACTAGCATTTGCTTTTGGTTTAATCAGCTTGCCCCCTAATATACCAATTACTATATAC

Reverse complement sequence

GTATATAGTAATTGGTATATTAGGGGGCAAGCTGATTAAACCAAAAGCAAATGCTAGTTTCTCACTGTGGTGTTTAAGTAGCTCCTCTTTTTGGTCAGCA[T/G]
GCACATCATGCAGATCACATTGTGTGTTGGCTCTGTGAGAAATCTTTCTCATCTCATGGTAAATTTCCTCCAACTTATTGTATACATCAGTTATTCCTGG

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of C(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 100.00% 0.00% 0.00% 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  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 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 96.30% 3.70% 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
vg1202831695 A -> C LOC_Os12g06070.1 missense_variant ; p.His551Pro; MODERATE nonsynonymous_codon ; H551P Average:55.925; most accessible tissue: Callus, score: 89.063 unknown unknown DELETERIOUS 0.02