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Detailed information for vg0520264655:

Variant ID: vg0520264655 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 20264655
Reference Allele: TAlternative Allele: A
Primary Allele: TSecondary Allele: A

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.96, A: 0.05, others allele: 0.00, population size: 191. )

Flanking Sequence (100 bp) in Reference Genome:


AAGCTAGGTAATGAAGATGAAACAACTGGCTAATGGTTTCTGGTAATTCTAAAATATCTGACTCACTAAGATCAAGAACACGCAAGTTCTTAAATTCAGA[T/A]
AGAAATTTACTAGGAAGATGACTCAATGACAACGAAGAGCTTCTAAGAACTAATAATGTCCGTAGCCTTTCCAACTTACACTTACTCTTGAGCTGTGGAA

Reverse complement sequence

TTCCACAGCTCAAGAGTAAGTGTAAGTTGGAAAGGCTACGGACATTATTAGTTCTTAGAAGCTCTTCGTTGTCATTGAGTCATCTTCCTAGTAAATTTCT[A/T]
TCTGAATTTAAGAACTTGCGTGTTCTTGATCTTAGTGAGTCAGATATTTTAGAATTACCAGAAACCATTAGCCAGTTGTTTCATCTTCATTACCTAGCTT

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 93.40% 6.60% 0.00% 0.00% NA
All Indica  2759 97.70% 2.30% 0.00% 0.00% NA
All Japonica  1512 99.90% 0.10% 0.00% 0.00% NA
Aus  269 10.40% 89.60% 0.00% 0.00% NA
Indica I  595 99.70% 0.30% 0.00% 0.00% NA
Indica II  465 98.90% 1.10% 0.00% 0.00% NA
Indica III  913 98.80% 1.20% 0.00% 0.00% NA
Indica Intermediate  786 94.30% 5.70% 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 99.60% 0.40% 0.00% 0.00% NA
VI/Aromatic  96 97.90% 2.10% 0.00% 0.00% NA
Intermediate  90 94.40% 5.60% 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
vg0520264655 T -> A LOC_Os05g34230.1 synonymous_variant ; p.Leu569Leu; LOW synonymous_codon Average:73.073; most accessible tissue: Minghui63 flag leaf, score: 86.315 N N N N