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Detailed information for vg0135986518:

Variant ID: vg0135986518 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 35986518
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: 291. )

Flanking Sequence (100 bp) in Reference Genome:


AACCCAATCCCCTCACGTGTTTCCTTTAAAAAAAAATATTAACAGCCAATCGGATGATGAAATTGGGGAAACTACCTGTGAACAGATGAGCTAATTACTT[A/T]
AAAAAAACGCATATGCTACACTTTACAATTCTGGACTGAACAGGCAAAGCAATTCGATGGCAAGTACAGACTAATTGTTCTCCGGGAGATGTTGTTTTCC

Reverse complement sequence

GGAAAACAACATCTCCCGGAGAACAATTAGTCTGTACTTGCCATCGAATTGCTTTGCCTGTTCAGTCCAGAATTGTAAAGTGTAGCATATGCGTTTTTTT[T/A]
AAGTAATTAGCTCATCTGTTCACAGGTAGTTTCCCCAATTTCATCATCCGATTGGCTGTTAATATTTTTTTTTAAAGGAAACACGTGAGGGGATTGGGTT

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 99.80% 0.10% 0.08% 0.00% NA
All Indica  2759 99.90% 0.00% 0.04% 0.00% NA
All Japonica  1512 100.00% 0.00% 0.00% 0.00% NA
Aus  269 96.70% 2.20% 1.12% 0.00% NA
Indica I  595 99.80% 0.00% 0.17% 0.00% NA
Indica II  465 99.80% 0.20% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 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  504 100.00% 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
vg0135986518 A -> T LOC_Os01g62160.1 intron_variant ; MODIFIER silent_mutation Average:47.906; most accessible tissue: Callus, score: 74.913 N N N N