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Detailed information for vg0220738772:

Variant ID: vg0220738772 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 20738772
Reference Allele: AAlternative Allele: C
Primary Allele: ASecondary Allele: C

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.99, others allele: 0.00, population size: 363. )

Flanking Sequence (100 bp) in Reference Genome:


AATTGAGTTGCATTGTCATCATATCAAAATGAACTGTGCAGACTCTTGATCCTCGCCCTTGCATTGTCATCTCAAATTGATATCTGTTATTGTCTTCGCA[A/C]
TGAAGCTCCTTGAATTTTGTGGCTCCACATCCATCAAGAAAATACGTCTCAAACAACTTGTAGATTCTGTATGTATAAACTTTTGCTGCATGATTCAAAA

Reverse complement sequence

TTTTGAATCATGCAGCAAAAGTTTATACATACAGAATCTACAAGTTGTTTGAGACGTATTTTCTTGATGGATGTGGAGCCACAAAATTCAAGGAGCTTCA[T/G]
TGCGAAGACAATAACAGATATCAATTTGAGATGACAATGCAAGGGCGAGGATCAAGAGTCTGCACAGTTCATTTTGATATGATGACAATGCAACTCAATT

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 99.20% 0.70% 0.11% 0.00% NA
All Indica  2759 99.70% 0.30% 0.04% 0.00% NA
All Japonica  1512 98.10% 1.60% 0.26% 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 99.00% 0.90% 0.11% 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 94.60% 4.80% 0.60% 0.00% NA
Japonica Intermediate  241 99.60% 0.00% 0.41% 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
vg0220738772 A -> C LOC_Os02g34590.1 missense_variant ; p.His549Gln; MODERATE nonsynonymous_codon ; H549Q Average:52.182; most accessible tissue: Callus, score: 81.423 benign -0.094 TOLERATED 0.64