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Detailed information for vg0135984170:

Variant ID: vg0135984170 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 35984170
Reference Allele: AAlternative Allele: T
Primary Allele: ASecondary Allele: T

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 309. )

Flanking Sequence (100 bp) in Reference Genome:


TCGAGCACAGTAACCATGTAGCAACATGTTTCTGCTCAAAGACGAGCCAGTTTCCAAATTGTCTTCAGTATACAGCCGCCATGTTTTGACGTAGTACTAC[A/T]
TACATTTACTTCGGCCTGGTTTGGAATTTGAATGGTATTCTTTATAGCTAAGTTGCTTAATAATGTTTGACTAATTTCAGAATACTTGCTATCAAAACCG

Reverse complement sequence

CGGTTTTGATAGCAAGTATTCTGAAATTAGTCAAACATTATTAAGCAACTTAGCTATAAAGAATACCATTCAAATTCCAAACCAGGCCGAAGTAAATGTA[T/A]
GTAGTACTACGTCAAAACATGGCGGCTGTATACTGAAGACAATTTGGAAACTGGCTCGTCTTTGAGCAGAAACATGTTGCTACATGGTTACTGTGCTCGA

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 97.90% 2.10% 0.00% 0.00% NA
All Indica  2759 96.50% 3.50% 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 90.90% 9.10% 0.00% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 98.00% 2.00% 0.00% 0.00% NA
Indica Intermediate  786 96.80% 3.20% 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 96.70% 3.30% 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
vg0135984170 A -> T LOC_Os01g62160.1 3_prime_UTR_variant ; 217.0bp to feature; MODIFIER silent_mutation Average:67.671; most accessible tissue: Zhenshan97 flower, score: 83.392 N N N N