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Detailed information for vg1113567989:

Variant ID: vg1113567989 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 13567989
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TCAGCGTCATGCCAAAAGACGTCTTCGACAAGCTCAACTTCACGGTGTTGGCGCCAACACCGATGCCCCATCAATTGGCTAACTCGTCAGTCTGTTACCC[G/A]
GCAGAGATAGCGGAGGATGTGCCAGTCAAGATACGGGATTTCTTCATCCCGGTTGACTTTGTGGTGCTGGACATGGACATAGGAAAAGAGACGCCGCTCA

Reverse complement sequence

TGAGCGGCGTCTCTTTTCCTATGTCCATGTCCAGCACCACAAAGTCAACCGGGATGAAGAAATCCCGTATCTTGACTGGCACATCCTCCGCTATCTCTGC[C/T]
GGGTAACAGACTGACGAGTTAGCCAATTGATGGGGCATCGGTGTTGGCGCCAACACCGTGAAGTTGAGCTTGTCGAAGACGTCTTTTGGCATGACGCTGA

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 98.30% 1.70% 0.00% 0.00% NA
All Indica  2759 97.00% 3.00% 0.00% 0.00% NA
All Japonica  1512 100.00% 0.00% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 99.40% 0.60% 0.00% 0.00% NA
Indica III  913 91.30% 8.70% 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
vg1113567989 G -> A LOC_Os11g23950.1 synonymous_variant ; p.Pro31Pro; LOW synonymous_codon Average:33.332; most accessible tissue: Zhenshan97 flag leaf, score: 47.303 N N N N