Search for Variation information by Variation ID:

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

Detailed information for vg0118123199:

Variant ID: vg0118123199 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 18123199
Reference Allele: CAlternative Allele: A
Primary Allele: CSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


ATCTCAGTTCAGACTATCCGATCACATAGAACTATCCGACCTGATATCAGACAATCCGACCCTGTTTTGTTTTAGCTTCCGCATTTATTTTAAAAATCAC[C/A]
TATTCACCCCCCTCTAGGCGACATCAAGGTCCTTTCAGTTATAATAGTTAACATTTAATTAATCGTGTGCTACTGAGCTTTATCGTTTCGGTTTTTAAAA

Reverse complement sequence

TTTTAAAAACCGAAACGATAAAGCTCAGTAGCACACGATTAATTAAATGTTAACTATTATAACTGAAAGGACCTTGATGTCGCCTAGAGGGGGGTGAATA[G/T]
GTGATTTTTAAAATAAATGCGGAAGCTAAAACAAAACAGGGTCGGATTGTCTGATATCAGGTCGGATAGTTCTATGTGATCGGATAGTCTGAACTGAGAT

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 98.60% 1.40% 0.06% 0.00% NA
All Indica  2759 97.60% 2.30% 0.11% 0.00% NA
All Japonica  1512 100.00% 0.00% 0.00% 0.00% NA
Aus  269 99.60% 0.40% 0.00% 0.00% NA
Indica I  595 99.50% 0.50% 0.00% 0.00% NA
Indica II  465 89.50% 10.10% 0.43% 0.00% NA
Indica III  913 99.90% 0.00% 0.11% 0.00% NA
Indica Intermediate  786 98.30% 1.70% 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
vg0118123199 C -> A LOC_Os01g33000.1 upstream_gene_variant ; 1730.0bp to feature; MODIFIER silent_mutation Average:65.78; most accessible tissue: Callus, score: 81.157 N N N N
vg0118123199 C -> A LOC_Os01g32990.1 downstream_gene_variant ; 2050.0bp to feature; MODIFIER silent_mutation Average:65.78; most accessible tissue: Callus, score: 81.157 N N N N
vg0118123199 C -> A LOC_Os01g32990-LOC_Os01g33000 intergenic_region ; MODIFIER silent_mutation Average:65.78; most accessible tissue: Callus, score: 81.157 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0118123199 NA 2.09E-08 mr1711_2 Ind_All YES Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251