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Detailed information for vg1010488113:

Variant ID: vg1010488113 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 10488113
Reference Allele: AAlternative Allele: T
Primary Allele: ASecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


ATATCTATTGTGTACGTAATTATATAGGAGTTGTGTACGTATGTAGAGACAGATCATATGGTTTTTTAGGACAGATGGATTACTTTCATATATCTAATTT[A/T]
ATTTAATGGTTGAAAATAATGGATCATCGGTTTAAGTGTAAATTGATGGATATATGCTTACTTTTTTATATAACTTTTCGTAGATTCTTTCTAATTTATT

Reverse complement sequence

AATAAATTAGAAAGAATCTACGAAAAGTTATATAAAAAAGTAAGCATATATCCATCAATTTACACTTAAACCGATGATCCATTATTTTCAACCATTAAAT[T/A]
AAATTAGATATATGAAAGTAATCCATCTGTCCTAAAAAACCATATGATCTGTCTCTACATACGTACACAACTCCTATATAATTACGTACACAATAGATAT

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 93.80% 6.00% 0.19% 0.00% NA
All Indica  2759 99.70% 0.20% 0.04% 0.00% NA
All Japonica  1512 81.50% 18.00% 0.53% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 99.70% 0.20% 0.17% 0.00% NA
Indica II  465 99.80% 0.20% 0.00% 0.00% NA
Indica III  913 99.60% 0.40% 0.00% 0.00% NA
Indica Intermediate  786 100.00% 0.00% 0.00% 0.00% NA
Temperate Japonica  767 69.20% 29.90% 0.91% 0.00% NA
Tropical Japonica  504 96.40% 3.60% 0.00% 0.00% NA
Japonica Intermediate  241 89.20% 10.40% 0.41% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 92.20% 7.80% 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
vg1010488113 A -> T LOC_Os10g20710.1 upstream_gene_variant ; 2177.0bp to feature; MODIFIER silent_mutation Average:15.406; most accessible tissue: Callus, score: 35.831 N N N N
vg1010488113 A -> T LOC_Os10g20710-LOC_Os10g20720 intergenic_region ; MODIFIER silent_mutation Average:15.406; most accessible tissue: Callus, score: 35.831 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1010488113 1.11E-06 2.88E-11 mr1768_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