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Detailed information for vg0605481649:

Variant ID: vg0605481649 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 5481649
Reference Allele: AAlternative Allele: C
Primary Allele: ASecondary Allele: C

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.99, C: 0.01, others allele: 0.00, population size: 116. )

Flanking Sequence (100 bp) in Reference Genome:


CCATCGGTTTAATATACATCTTAAACTGTTTATTTGATAGGTACACAATATAATTGTGTAAACTTTATTTTAAAATAGTGCATTATTTGAAAATAATAGT[A/C]
AAAATAATGAGTACACATGTTTAAGTGGAAACTATATTACATTATTAATTTAATGGTCACATATAATGGTTTAAATTTTATTTTCAAAAATTGTAGAGCT

Reverse complement sequence

AGCTCTACAATTTTTGAAAATAAAATTTAAACCATTATATGTGACCATTAAATTAATAATGTAATATAGTTTCCACTTAAACATGTGTACTCATTATTTT[T/G]
ACTATTATTTTCAAATAATGCACTATTTTAAAATAAAGTTTACACAATTATATTGTGTACCTATCAAATAAACAGTTTAAGATGTATATTAAACCGATGG

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 98.20% 0.30% 1.52% 0.00% NA
All Indica  2759 97.50% 0.40% 2.07% 0.00% NA
All Japonica  1512 100.00% 0.00% 0.00% 0.00% NA
Aus  269 95.20% 0.00% 4.83% 0.00% NA
Indica I  595 99.70% 0.30% 0.00% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 94.70% 0.90% 4.38% 0.00% NA
Indica Intermediate  786 97.70% 0.10% 2.16% 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 99.00% 1.00% 0.00% 0.00% NA
Intermediate  90 97.80% 0.00% 2.22% 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
vg0605481649 A -> C LOC_Os06g10580-LOC_Os06g10590 intergenic_region ; MODIFIER silent_mutation Average:16.808; most accessible tissue: Minghui63 panicle, score: 25.313 N N N N