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Detailed information for vg1119272401:

Variant ID: vg1119272401 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 19272401
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, others allele: 0.00, population size: 259. )

Flanking Sequence (100 bp) in Reference Genome:


TCATAAGTGCCAGTTATTATTAAGAACCATTACATATGTAATGCCCATATGTGTCGATTCATGATAAAAACCGGTACATGTGACATCGCACTTATAGATG[C/T]
TGGTTTATTATAATAACTGGTACCTATGTATTGTGATGTGTATATGTATCGGTTTGTTATAAGAACAGTACCTATGAATTTGGGAGAATATTGGTGTCGG

Reverse complement sequence

CCGACACCAATATTCTCCCAAATTCATAGGTACTGTTCTTATAACAAACCGATACATATACACATCACAATACATAGGTACCAGTTATTATAATAAACCA[G/A]
CATCTATAAGTGCGATGTCACATGTACCGGTTTTTATCATGAATCGACACATATGGGCATTACATATGTAATGGTTCTTAATAATAACTGGCACTTATGA

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 99.30% 0.50% 0.19% 0.00% NA
All Indica  2759 99.90% 0.00% 0.07% 0.00% NA
All Japonica  1512 98.10% 1.50% 0.46% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 99.80% 0.00% 0.17% 0.00% NA
Indica II  465 99.80% 0.00% 0.22% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 100.00% 0.00% 0.00% 0.00% NA
Temperate Japonica  767 96.20% 2.90% 0.91% 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
vg1119272401 C -> T LOC_Os11g32640-LOC_Os11g32650 intergenic_region ; MODIFIER silent_mutation Average:36.927; most accessible tissue: Zhenshan97 young leaf, score: 53.969 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1119272401 NA 5.03E-08 mr1062 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
vg1119272401 2.56E-06 6.89E-10 mr1062_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