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Detailed information for vg0512019746:

Variant ID: vg0512019746 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 12019746
Reference Allele: TAlternative Allele: A
Primary Allele: TSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GACTTTTAAAATTATTTCTAAAAATTCCATTTAAACAACAATTTATAAATTTTAAAATTTTCAGGGTGTGACAAACCTACCCCCCTTAAACAGAATCTCG[T/A]
CCTCGAGATTCGGAAGAACTGGCGAACAGGTGCGGATGAGCTGACTTCAATTCATCTTCTCGTTCCCAAGTTGATTCTTCTTCCGAGTGATTACTCCATT

Reverse complement sequence

AATGGAGTAATCACTCGGAAGAAGAATCAACTTGGGAACGAGAAGATGAATTGAAGTCAGCTCATCCGCACCTGTTCGCCAGTTCTTCCGAATCTCGAGG[A/T]
CGAGATTCTGTTTAAGGGGGGTAGGTTTGTCACACCCTGAAAATTTTAAAATTTATAAATTGTTGTTTAAATGGAATTTTTAGAAATAATTTTAAAAGTC

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 98.50% 0.00% 1.48% 0.00% NA
All Indica  2759 97.70% 0.10% 2.25% 0.00% NA
All Japonica  1512 100.00% 0.00% 0.00% 0.00% NA
Aus  269 97.00% 0.00% 2.97% 0.00% NA
Indica I  595 93.40% 0.00% 6.55% 0.00% NA
Indica II  465 99.80% 0.00% 0.22% 0.00% NA
Indica III  913 99.60% 0.20% 0.22% 0.00% NA
Indica Intermediate  786 97.50% 0.00% 2.54% 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
vg0512019746 T -> A LOC_Os05g20480.1 synonymous_variant ; p.Gly1239Gly; LOW synonymous_codon Average:13.49; most accessible tissue: Zhenshan97 flower, score: 22.37 N N N N