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Detailed information for vg0233354900:

Variant ID: vg0233354900 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 33354900
Reference Allele: GAlternative Allele: T
Primary Allele: GSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CACGGCGTCCTCCTCCTTGTCCAGGCTGCACATCACGAAGCGGACGTCGATGGCGGCGCGCCGCGGCGGCGGCTGGAGCGCGTACGCCATGCGGAGCAGC[G/T]
CGCGCCGCTCGTAGAAGTCGGGGCGGGTGAGGATGCCGAAGAACATGCGGAAGTCGACGTCGTCGTCCGCCGCCGCCGCCGCCGCGACGCTCTTGCTGGC

Reverse complement sequence

GCCAGCAAGAGCGTCGCGGCGGCGGCGGCGGCGGACGACGACGTCGACTTCCGCATGTTCTTCGGCATCCTCACCCGCCCCGACTTCTACGAGCGGCGCG[C/A]
GCTGCTCCGCATGGCGTACGCGCTCCAGCCGCCGCCGCGGCGCGCCGCCATCGACGTCCGCTTCGTGATGTGCAGCCTGGACAAGGAGGAGGACGCCGTG

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 99.80% 0.10% 0.08% 0.00% NA
All Indica  2759 100.00% 0.00% 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  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 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 90.60% 5.20% 4.17% 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
vg0233354900 G -> T LOC_Os02g54450.1 missense_variant ; p.Ala73Glu; MODERATE nonsynonymous_codon ; A73E Average:67.361; most accessible tissue: Zhenshan97 root, score: 82.17 benign 1.454 TOLERATED 0.25