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Detailed information for vg1101903575:

Variant ID: vg1101903575 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 1903575
Reference Allele: TAlternative Allele: A
Primary Allele: TSecondary Allele: A

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 309. )

Flanking Sequence (100 bp) in Reference Genome:


GGGCTCCCCTTTCGTCCAGTTAATCAACTAGTACGAAATCACTCAAAGCGAGAAGGAGATGTTGTAGCTGAGAAGGAGATCTTGTCCATGCAGATGGTGG[T/A]
ATTATCTTGCTCATTGTATTATGATTGATGACAAATGTGAGAACGATGTATATCAAAACACATTCAATGTTATATTTAATGAAACTAATTTAGTGTAATT

Reverse complement sequence

AATTACACTAAATTAGTTTCATTAAATATAACATTGAATGTGTTTTGATATACATCGTTCTCACATTTGTCATCAATCATAATACAATGAGCAAGATAAT[A/T]
CCACCATCTGCATGGACAAGATCTCCTTCTCAGCTACAACATCTCCTTCTCGCTTTGAGTGATTTCGTACTAGTTGATTAACTGGACGAAAGGGGAGCCC

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 98.70% 0.80% 0.51% 0.00% NA
All Indica  2759 100.00% 0.00% 0.00% 0.00% NA
All Japonica  1512 96.00% 2.60% 1.46% 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  786 100.00% 0.00% 0.00% 0.00% NA
Temperate Japonica  767 92.30% 5.10% 2.61% 0.00% NA
Tropical Japonica  504 99.60% 0.00% 0.40% 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 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
vg1101903575 T -> A LOC_Os11g04530.1 upstream_gene_variant ; 1131.0bp to feature; MODIFIER silent_mutation Average:40.563; most accessible tissue: Zhenshan97 root, score: 71.691 N N N N
vg1101903575 T -> A LOC_Os11g04520.1 downstream_gene_variant ; 4682.0bp to feature; MODIFIER silent_mutation Average:40.563; most accessible tissue: Zhenshan97 root, score: 71.691 N N N N
vg1101903575 T -> A LOC_Os11g04520.3 downstream_gene_variant ; 4689.0bp to feature; MODIFIER silent_mutation Average:40.563; most accessible tissue: Zhenshan97 root, score: 71.691 N N N N
vg1101903575 T -> A LOC_Os11g04520.2 intron_variant ; MODIFIER silent_mutation Average:40.563; most accessible tissue: Zhenshan97 root, score: 71.691 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1101903575 NA 6.23E-06 mr1496 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
vg1101903575 NA 8.94E-06 mr1515 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
vg1101903575 1.34E-06 7.02E-07 mr1917 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
vg1101903575 3.11E-06 4.64E-07 mr1936 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