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Detailed information for vg1109924691:

Variant ID: vg1109924691 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 9924691
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.02, others allele: 0.00, population size: 55. )

Flanking Sequence (100 bp) in Reference Genome:


GTCATTTATATAGCCATGGGAGCCCGGGATCGAGTCCACATCGACGGGAAAAACTCTGGAAAGTTTGGGATCTTCGCCGGAAAAAGGAAAGATTGAACCG[T/C]
GAAATTGGAAAGGATTTCCATAGAAACTTTTGGGGATTTCTTGGGGAAATTGTAGAGGAGATTGAGAGGATTCCGTTCTCGCAACTAATTTGGAAAAAGG

Reverse complement sequence

CCTTTTTCCAAATTAGTTGCGAGAACGGAATCCTCTCAATCTCCTCTACAATTTCCCCAAGAAATCCCCAAAAGTTTCTATGGAAATCCTTTCCAATTTC[A/G]
CGGTTCAATCTTTCCTTTTTCCGGCGAAGATCCCAAACTTTCCAGAGTTTTTCCCGTCGATGTGGACTCGATCCCGGGCTCCCATGGCTATATAAATGAC

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 40.90% 0.80% 0.13% 58.17% NA
All Indica  2759 13.70% 1.40% 0.18% 84.70% NA
All Japonica  1512 95.80% 0.00% 0.00% 4.17% NA
Aus  269 17.10% 0.00% 0.00% 82.90% NA
Indica I  595 22.50% 0.00% 0.84% 76.64% NA
Indica II  465 8.80% 3.40% 0.00% 87.74% NA
Indica III  913 2.40% 1.90% 0.00% 95.73% NA
Indica Intermediate  786 23.00% 0.80% 0.00% 76.21% NA
Temperate Japonica  767 97.00% 0.00% 0.00% 3.00% NA
Tropical Japonica  504 94.40% 0.00% 0.00% 5.56% NA
Japonica Intermediate  241 95.00% 0.00% 0.00% 4.98% NA
VI/Aromatic  96 19.80% 0.00% 0.00% 80.21% NA
Intermediate  90 44.40% 0.00% 1.11% 54.44% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1109924691 T -> DEL N N silent_mutation Average:20.716; most accessible tissue: Callus, score: 90.572 N N N N
vg1109924691 T -> C LOC_Os11g17760.1 intron_variant ; MODIFIER silent_mutation Average:20.716; most accessible tissue: Callus, score: 90.572 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1109924691 NA 4.52E-14 mr1361 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