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Detailed information for vg0409082049:

Variant ID: vg0409082049 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 9082049
Reference Allele: GAlternative Allele: T
Primary Allele: TSecondary Allele: G

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.90, G: 0.10, others allele: 0.00, population size: 254. )

Flanking Sequence (100 bp) in Reference Genome:


GATGTAATGGTCCAGTAAGCGTGAGGGTTGCTTGTAAACATCCCAGGGAGCTGCACTTCTCAAACTATGTTGTATATCAACTGGGTTGGTTACTTGATTA[G/T]
ATTGTAGAAAGAGCTACCCTACATATGAGAATAGACAAAACCAACCTGTTGATGGCGATGACATGGATGATAAAAAGGATGATGGAGAGGAAGACATAAT

Reverse complement sequence

ATTATGTCTTCCTCTCCATCATCCTTTTTATCATCCATGTCATCGCCATCAACAGGTTGGTTTTGTCTATTCTCATATGTAGGGTAGCTCTTTCTACAAT[C/A]
TAATCAAGTAACCAACCCAGTTGATATACAACATAGTTTGAGAAGTGCAGCTCCCTGGGATGTTTACAAGCAACCCTCACGCTTACTGGACCATTACATC

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 65.10% 34.90% 0.02% 0.00% NA
All Indica  2759 99.00% 1.00% 0.00% 0.00% NA
All Japonica  1512 1.10% 98.90% 0.07% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 99.80% 0.20% 0.00% 0.00% NA
Indica II  465 97.80% 2.20% 0.00% 0.00% NA
Indica III  913 99.60% 0.40% 0.00% 0.00% NA
Indica Intermediate  786 98.50% 1.50% 0.00% 0.00% NA
Temperate Japonica  767 0.50% 99.50% 0.00% 0.00% NA
Tropical Japonica  504 1.40% 98.40% 0.20% 0.00% NA
Japonica Intermediate  241 2.10% 97.90% 0.00% 0.00% NA
VI/Aromatic  96 14.60% 85.40% 0.00% 0.00% NA
Intermediate  90 50.00% 50.00% 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
vg0409082049 G -> T LOC_Os04g16690.1 splice_acceptor_variant&intron_variant ; HIGH splice_acceptor_variant Average:55.455; most accessible tissue: Zhenshan97 young leaf, score: 81.102 N N N N