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Detailed information for vg0825998355:

Variant ID: vg0825998355 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 25998355
Reference Allele: AAlternative Allele: C
Primary Allele: ASecondary Allele: C

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.01, others allele: 0.00, population size: 281. )

Flanking Sequence (100 bp) in Reference Genome:


ATATGAATGTAGCCATGCCGTCGATCACATAAATCGACTCGAGATCGCTCCGTGTGATGAAGCGATGCCATCCAATGGAGCGATGCCATCCGATGAAACG[A/C]
TGCCATCCAAGGAAGCGGAAGCCGGAGGATGTTCCCCTAATTACATCTATAGAGCTATTCTTTGCACAGAGTGAAGATGGTTTACCATCTTTGTTCATCA

Reverse complement sequence

TGATGAACAAAGATGGTAAACCATCTTCACTCTGTGCAAAGAATAGCTCTATAGATGTAATTAGGGGAACATCCTCCGGCTTCCGCTTCCTTGGATGGCA[T/G]
CGTTTCATCGGATGGCATCGCTCCATTGGATGGCATCGCTTCATCACACGGAGCGATCTCGAGTCGATTTATGTGATCGACGGCATGGCTACATTCATAT

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 98.50% 1.50% 0.00% 0.00% NA
All Indica  2759 97.40% 2.60% 0.00% 0.00% NA
All Japonica  1512 100.00% 0.00% 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 93.30% 6.70% 0.00% 0.00% NA
Indica III  913 96.40% 3.60% 0.00% 0.00% NA
Indica Intermediate  786 99.00% 1.00% 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
vg0825998355 A -> C LOC_Os08g41150.1 missense_variant ; p.His115Gln; MODERATE nonsynonymous_codon ; H115Q Average:66.26; most accessible tissue: Zhenshan97 panicle, score: 78.302 unknown unknown TOLERATED 0.30