Search for Variation information by Variation ID:

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

Detailed information for vg1004990336:

Variant ID: vg1004990336 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 4990336
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CGAACAACGGTTTAAACGTTGAACTTTTCTGTGTTTGTTCCAATTTTCCTCGAAATATACTAATTTGAAACTCGGGACATTACAAGTATAGGGCTCCACC[A/G]
ACATGTGTTTAATTCCAAGTCAAAGTATGCAGGTGAGCATGCATTAAATTCTCCATTAATCATGTTATATATAATTAAGAGAATTTCCTAAATTAAAATA

Reverse complement sequence

TATTTTAATTTAGGAAATTCTCTTAATTATATATAACATGATTAATGGAGAATTTAATGCATGCTCACCTGCATACTTTGACTTGGAATTAAACACATGT[T/C]
GGTGGAGCCCTATACTTGTAATGTCCCGAGTTTCAAATTAGTATATTTCGAGGAAAATTGGAACAAACACAGAAAAGTTCAACGTTTAAACCGTTGTTCG

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 96.50% 0.80% 1.82% 0.93% NA
All Indica  2759 95.90% 0.00% 2.75% 1.38% NA
All Japonica  1512 97.50% 2.40% 0.13% 0.00% NA
Aus  269 95.90% 0.00% 1.86% 2.23% NA
Indica I  595 95.80% 0.00% 2.69% 1.51% NA
Indica II  465 95.30% 0.00% 3.01% 1.72% NA
Indica III  913 95.60% 0.00% 2.96% 1.42% NA
Indica Intermediate  786 96.60% 0.00% 2.42% 1.02% NA
Temperate Japonica  767 95.00% 4.70% 0.26% 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 99.00% 0.00% 1.04% 0.00% NA
Intermediate  90 97.80% 0.00% 2.22% 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
vg1004990336 A -> G LOC_Os10g09220.1 upstream_gene_variant ; 3771.0bp to feature; MODIFIER silent_mutation Average:30.003; most accessible tissue: Callus, score: 54.125 N N N N
vg1004990336 A -> G LOC_Os10g09240.1 downstream_gene_variant ; 4162.0bp to feature; MODIFIER silent_mutation Average:30.003; most accessible tissue: Callus, score: 54.125 N N N N
vg1004990336 A -> G LOC_Os10g09220-LOC_Os10g09240 intergenic_region ; MODIFIER silent_mutation Average:30.003; most accessible tissue: Callus, score: 54.125 N N N N
vg1004990336 A -> DEL N N silent_mutation Average:30.003; most accessible tissue: Callus, score: 54.125 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1004990336 3.54E-06 1.16E-07 mr1300 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
vg1004990336 7.70E-06 3.60E-07 mr1310 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
vg1004990336 NA 7.76E-06 mr1959 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