Search for Variation information by Variation ID:

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

Detailed information for vg1120155107:

Variant ID: vg1120155107 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 20155107
Reference Allele: CAlternative Allele: G,A
Primary Allele: CSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GTATTTGCAAGAGAGAAAAATAAATATATACTATTCTCCCGGAGAAAATATACGTATGTTTATATGCATGTACAGGAGACTATTATTTGCAAAAAAAAAA[C/G,A]
ATGAATATGTACGTACATAAAAAAAATATTAACCATGTCCTTCTAACCCTTAAATTAGAAAGTTTATACATGATCAGTCTACCCTCTGCTGTGGCTCCTT

Reverse complement sequence

AAGGAGCCACAGCAGAGGGTAGACTGATCATGTATAAACTTTCTAATTTAAGGGTTAGAAGGACATGGTTAATATTTTTTTTATGTACGTACATATTCAT[G/C,T]
TTTTTTTTTTGCAAATAATAGTCTCCTGTACATGCATATAAACATACGTATATTTTCTCCGGGAGAATAGTATATATTTATTTTTCTCTCTTGCAAATAC

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 96.70% 2.00% 1.31% 0.00% G: 0.02%
All Indica  2759 99.40% 0.20% 0.40% 0.00% G: 0.04%
All Japonica  1512 91.50% 5.60% 2.84% 0.00% NA
Aus  269 98.10% 0.00% 1.86% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 99.60% 0.20% 0.00% 0.00% G: 0.22%
Indica III  913 99.50% 0.20% 0.33% 0.00% NA
Indica Intermediate  786 98.70% 0.30% 1.02% 0.00% NA
Temperate Japonica  767 96.90% 1.20% 1.96% 0.00% NA
Tropical Japonica  504 80.60% 14.70% 4.76% 0.00% NA
Japonica Intermediate  241 97.50% 0.80% 1.66% 0.00% NA
VI/Aromatic  96 95.80% 1.00% 3.12% 0.00% NA
Intermediate  90 97.80% 2.20% 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
vg1120155107 C -> A LOC_Os11g34390.1 upstream_gene_variant ; 1085.0bp to feature; MODIFIER silent_mutation Average:48.949; most accessible tissue: Minghui63 root, score: 68.289 N N N N
vg1120155107 C -> A LOC_Os11g34410.1 upstream_gene_variant ; 3400.0bp to feature; MODIFIER silent_mutation Average:48.949; most accessible tissue: Minghui63 root, score: 68.289 N N N N
vg1120155107 C -> A LOC_Os11g34400.1 downstream_gene_variant ; 2083.0bp to feature; MODIFIER silent_mutation Average:48.949; most accessible tissue: Minghui63 root, score: 68.289 N N N N
vg1120155107 C -> A LOC_Os11g34390-LOC_Os11g34400 intergenic_region ; MODIFIER silent_mutation Average:48.949; most accessible tissue: Minghui63 root, score: 68.289 N N N N
vg1120155107 C -> G LOC_Os11g34390.1 upstream_gene_variant ; 1085.0bp to feature; MODIFIER silent_mutation Average:48.949; most accessible tissue: Minghui63 root, score: 68.289 N N N N
vg1120155107 C -> G LOC_Os11g34410.1 upstream_gene_variant ; 3400.0bp to feature; MODIFIER silent_mutation Average:48.949; most accessible tissue: Minghui63 root, score: 68.289 N N N N
vg1120155107 C -> G LOC_Os11g34400.1 downstream_gene_variant ; 2083.0bp to feature; MODIFIER silent_mutation Average:48.949; most accessible tissue: Minghui63 root, score: 68.289 N N N N
vg1120155107 C -> G LOC_Os11g34390-LOC_Os11g34400 intergenic_region ; MODIFIER silent_mutation Average:48.949; most accessible tissue: Minghui63 root, score: 68.289 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1120155107 1.36E-07 NA mr1301_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