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Detailed information for vg0216160886:

Variant ID: vg0216160886 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 16160886
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CGATGGGCACAGGATCAATGGTACCTTCTTCCGGCGAGTACAAGCGGAGGCCGGGCTTGAAGAAGCCATGGGGGCCGCGACCAGTCCTTGGCTACCACCC[G/A]
TCATGGCCTCCCCGCCGCACTTGGTTGCCTCCTGCCGTCGCCTCGCCACCGCAGTTGCTTGCCTCCCGCCGTCGCCTCGCCGCCGCGGAGCTCACCGCTG

Reverse complement sequence

CAGCGGTGAGCTCCGCGGCGGCGAGGCGACGGCGGGAGGCAAGCAACTGCGGTGGCGAGGCGACGGCAGGAGGCAACCAAGTGCGGCGGGGAGGCCATGA[C/T]
GGGTGGTAGCCAAGGACTGGTCGCGGCCCCCATGGCTTCTTCAAGCCCGGCCTCCGCTTGTACTCGCCGGAAGAAGGTACCATTGATCCTGTGCCCATCG

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 96.40% 3.60% 0.00% 0.00% NA
All Indica  2759 97.40% 2.60% 0.00% 0.00% NA
All Japonica  1512 99.30% 0.70% 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 98.90% 1.10% 0.00% 0.00% NA
Indica III  913 94.70% 5.30% 0.00% 0.00% NA
Indica Intermediate  786 97.70% 2.30% 0.00% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 98.60% 1.40% 0.00% 0.00% NA
Japonica Intermediate  241 98.30% 1.70% 0.00% 0.00% NA
VI/Aromatic  96 16.70% 83.30% 0.00% 0.00% NA
Intermediate  90 88.90% 11.10% 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
vg0216160886 G -> A LOC_Os02g27430.1 missense_variant ; p.Thr2Met; MODERATE nonsynonymous_codon ; T2M Average:64.184; most accessible tissue: Zhenshan97 young leaf, score: 87.153 unknown unknown DELETERIOUS 0.00