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Detailed information for vg0614961483:

Variant ID: vg0614961483 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 14961483
Reference Allele: TAlternative Allele: A
Primary Allele: TSecondary Allele: A

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.01, others allele: 0.00, population size: 363. )

Flanking Sequence (100 bp) in Reference Genome:


GTACACGTGGAGCCCAAAGTGCGCCTGCTAGCTGTCCCCGTCGAGTCAACCTGTGAAGAGAGGTAAATTGTATGGCTCGATGATGTAATTATCATAAAAA[T/A]
TTAGAAATGAACAATCCGAACTCACGAGTGGTCGGCAGGGGGGACGGTCGGCTGCACGTTGCCGGGAAACACCTGCCTAAGTCCGAACTGTCTCATCACA

Reverse complement sequence

TGTGATGAGACAGTTCGGACTTAGGCAGGTGTTTCCCGGCAACGTGCAGCCGACCGTCCCCCCTGCCGACCACTCGTGAGTTCGGATTGTTCATTTCTAA[A/T]
TTTTTATGATAATTACATCATCGAGCCATACAATTTACCTCTCTTCACAGGTTGACTCGACGGGGACAGCTAGCAGGCGCACTTTGGGCTCCACGTGTAC

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 46.90% 0.00% 40.46% 12.63% NA
All Indica  2759 40.30% 0.00% 43.02% 16.60% NA
All Japonica  1512 53.60% 0.00% 39.75% 6.61% NA
Aus  269 65.40% 0.00% 23.42% 11.15% NA
Indica I  595 28.10% 0.00% 61.34% 10.59% NA
Indica II  465 46.20% 0.00% 41.29% 12.47% NA
Indica III  913 44.90% 0.10% 31.00% 23.99% NA
Indica Intermediate  786 40.80% 0.00% 44.15% 15.01% NA
Temperate Japonica  767 47.20% 0.00% 51.63% 1.17% NA
Tropical Japonica  504 56.50% 0.00% 26.79% 16.67% NA
Japonica Intermediate  241 68.00% 0.00% 29.05% 2.90% NA
VI/Aromatic  96 75.00% 0.00% 22.92% 2.08% NA
Intermediate  90 47.80% 1.10% 43.33% 7.78% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0614961483 T -> A LOC_Os06g25580.1 intron_variant ; MODIFIER silent_mutation Average:5.508; most accessible tissue: Callus, score: 15.921 N N N N
vg0614961483 T -> DEL N N silent_mutation Average:5.508; most accessible tissue: Callus, score: 15.921 N N N N