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Detailed information for vg1102244084:

Variant ID: vg1102244084 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 2244084
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CTTACTGTTATCACCTACACATACTACGCAAAGTTACAGTTTTATGATGATTTCCTACGGTATAATTACAACAAACTGAAATATGATGCTAATGTTGCAG[C/T]
AAACTAATAGTTTTCTCACTATAATTACAGTTTTTCTAAAATTTACTTTTTTTTTCTCAGTTATTTGTAAGTAATTATTACATTTGAGTTTATAATATTA

Reverse complement sequence

TAATATTATAAACTCAAATGTAATAATTACTTACAAATAACTGAGAAAAAAAAAGTAAATTTTAGAAAAACTGTAATTATAGTGAGAAAACTATTAGTTT[G/A]
CTGCAACATTAGCATCATATTTCAGTTTGTTGTAATTATACCGTAGGAAATCATCATAAAACTGTAACTTTGCGTAGTATGTGTAGGTGATAACAGTAAG

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 98.00% 1.40% 0.59% 0.00% NA
All Indica  2759 100.00% 0.00% 0.04% 0.00% NA
All Japonica  1512 94.00% 4.20% 1.79% 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 99.90% 0.00% 0.13% 0.00% NA
Temperate Japonica  767 90.50% 6.60% 2.87% 0.00% NA
Tropical Japonica  504 99.80% 0.00% 0.20% 0.00% NA
Japonica Intermediate  241 92.90% 5.40% 1.66% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 98.90% 1.10% 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
vg1102244084 C -> T LOC_Os11g05110.1 upstream_gene_variant ; 585.0bp to feature; MODIFIER silent_mutation Average:64.519; most accessible tissue: Minghui63 panicle, score: 84.552 N N N N
vg1102244084 C -> T LOC_Os11g05110.3 upstream_gene_variant ; 585.0bp to feature; MODIFIER silent_mutation Average:64.519; most accessible tissue: Minghui63 panicle, score: 84.552 N N N N
vg1102244084 C -> T LOC_Os11g05110.2 upstream_gene_variant ; 480.0bp to feature; MODIFIER silent_mutation Average:64.519; most accessible tissue: Minghui63 panicle, score: 84.552 N N N N
vg1102244084 C -> T LOC_Os11g05100.1 downstream_gene_variant ; 4982.0bp to feature; MODIFIER silent_mutation Average:64.519; most accessible tissue: Minghui63 panicle, score: 84.552 N N N N
vg1102244084 C -> T LOC_Os11g05120.1 downstream_gene_variant ; 961.0bp to feature; MODIFIER silent_mutation Average:64.519; most accessible tissue: Minghui63 panicle, score: 84.552 N N N N
vg1102244084 C -> T LOC_Os11g05130.1 downstream_gene_variant ; 3622.0bp to feature; MODIFIER silent_mutation Average:64.519; most accessible tissue: Minghui63 panicle, score: 84.552 N N N N
vg1102244084 C -> T LOC_Os11g05130.2 downstream_gene_variant ; 3622.0bp to feature; MODIFIER silent_mutation Average:64.519; most accessible tissue: Minghui63 panicle, score: 84.552 N N N N
vg1102244084 C -> T LOC_Os11g05110-LOC_Os11g05120 intergenic_region ; MODIFIER silent_mutation Average:64.519; most accessible tissue: Minghui63 panicle, score: 84.552 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1102244084 2.24E-06 2.24E-06 mr1172_2 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