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Detailed information for vg1208090350:

Variant ID: vg1208090350 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 8090350
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CTCCATCATAAAACCAGATGACTCCTGCCCTTCTTCCAGTATCATCTCCGTGACAATTCTAATGCTTCAGGAAAAACAATTCTAATGCTGGAAGTGATTC[A/G]
TGGCCAGCCTAGGCATAGGTTCCATGTTATTGTAAATGATTCTAGCTACATTATGATATTTTATATTATATAATAGAAATATAAAATATGTTTTGATAGT

Reverse complement sequence

ACTATCAAAACATATTTTATATTTCTATTATATAATATAAAATATCATAATGTAGCTAGAATCATTTACAATAACATGGAACCTATGCCTAGGCTGGCCA[T/C]
GAATCACTTCCAGCATTAGAATTGTTTTTCCTGAAGCATTAGAATTGTCACGGAGATGATACTGGAAGAAGGGCAGGAGTCATCTGGTTTTATGATGGAG

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 93.30% 1.00% 0.91% 4.80% NA
All Indica  2759 91.30% 0.00% 0.58% 8.12% NA
All Japonica  1512 95.10% 3.20% 1.72% 0.00% NA
Aus  269 99.30% 0.00% 0.37% 0.37% NA
Indica I  595 86.90% 0.00% 0.84% 12.27% NA
Indica II  465 95.10% 0.00% 0.43% 4.52% NA
Indica III  913 92.00% 0.00% 0.55% 7.45% NA
Indica Intermediate  786 91.60% 0.00% 0.51% 7.89% NA
Temperate Japonica  767 93.60% 3.70% 2.74% 0.00% NA
Tropical Japonica  504 99.40% 0.00% 0.60% 0.00% NA
Japonica Intermediate  241 90.90% 8.30% 0.83% 0.00% NA
VI/Aromatic  96 99.00% 1.00% 0.00% 0.00% NA
Intermediate  90 97.80% 0.00% 0.00% 2.22% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1208090350 A -> DEL N N silent_mutation Average:41.989; most accessible tissue: Zhenshan97 young leaf, score: 67.334 N N N N
vg1208090350 A -> G LOC_Os12g14240.1 upstream_gene_variant ; 3959.0bp to feature; MODIFIER silent_mutation Average:41.989; most accessible tissue: Zhenshan97 young leaf, score: 67.334 N N N N
vg1208090350 A -> G LOC_Os12g14230-LOC_Os12g14240 intergenic_region ; MODIFIER silent_mutation Average:41.989; most accessible tissue: Zhenshan97 young leaf, score: 67.334 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1208090350 1.77E-06 9.20E-08 mr1013 Jap_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1208090350 2.16E-07 1.77E-09 mr1031 Jap_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
vg1208090350 NA 4.22E-06 mr1034 Jap_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1208090350 4.84E-07 1.11E-08 mr1056 Jap_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