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Detailed information for vg0526335257:

Variant ID: vg0526335257 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 26335257
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 350. )

Flanking Sequence (100 bp) in Reference Genome:


TAGAAATGAGACTGTTGCAAAAAGTTATGAGTAGGTTTGATATTCTTGTTATACAAGATTCTACATCCGAGTCCAAATCAAGTCACTGCACAGCCAATTG[C/T]
ATCAGAAAGTAATCATCAATATAGGAAACTTTCTACAAAGAACACGATAAGTACATGTATCATTTGATAGCACGAATACACGTGACAAAATGTAACAGTA

Reverse complement sequence

TACTGTTACATTTTGTCACGTGTATTCGTGCTATCAAATGATACATGTACTTATCGTGTTCTTTGTAGAAAGTTTCCTATATTGATGATTACTTTCTGAT[G/A]
CAATTGGCTGTGCAGTGACTTGATTTGGACTCGGATGTAGAATCTTGTATAACAAGAATATCAAACCTACTCATAACTTTTTGCAACAGTCTCATTTCTA

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 99.70% 0.20% 0.11% 0.00% NA
All Indica  2759 99.50% 0.30% 0.18% 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 99.50% 0.00% 0.50% 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 99.70% 0.10% 0.13% 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
vg0526335257 C -> T LOC_Os05g45390.1 upstream_gene_variant ; 3919.0bp to feature; MODIFIER N Average:46.626; most accessible tissue: Callus, score: 82.662 N N N N
vg0526335257 C -> T LOC_Os05g45400.1 intron_variant ; MODIFIER N Average:46.626; most accessible tissue: Callus, score: 82.662 N N N N