Search for Variation information by Variation ID:

Please input a variation ID (e.g., vg0722097923 , STR0500036000 ).

Detailed information for vg1123253205:

Variant ID: vg1123253205 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 23253205
Reference Allele: CAlternative Allele: G
Primary Allele: CSecondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


AAGACCGGCCATTGCACCCTCTCGAACGCCAGGATGGAGTCGACGTACCCCTGCGCCAATAATGGCGCAACGGCGGCTGGCTTCTGCGGCTCGCCGGCGG[C/G]
GGTGGCGGCCGCCGCCGCCGTCGTCTTCTTTGCCTCGTCGGCTGATGCCACCGCAGAGGCGTCCATGGATGATGGATCAGTATTCACTTGGAGTGCGTAT

Reverse complement sequence

ATACGCACTCCAAGTGAATACTGATCCATCATCCATGGACGCCTCTGCGGTGGCATCAGCCGACGAGGCAAAGAAGACGACGGCGGCGGCGGCCGCCACC[G/C]
CCGCCGGCGAGCCGCAGAAGCCAGCCGCCGTTGCGCCATTATTGGCGCAGGGGTACGTCGACTCCATCCTGGCGTTCGAGAGGGTGCAATGGCCGGTCTT

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 97.30% 2.70% 0.02% 0.00% NA
All Indica  2759 95.50% 4.50% 0.04% 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 84.50% 15.30% 0.17% 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 95.80% 4.20% 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 97.80% 2.20% 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
vg1123253205 C -> G LOC_Os11g39060.1 missense_variant ; p.Ala23Pro; MODERATE nonsynonymous_codon ; A23P Average:69.249; most accessible tissue: Callus, score: 82.581 unknown unknown TOLERATED 0.07