\

Search for Variation information by Variation ID:

Please input a variation ID (e.g., vg0722097923 , STR0500036000 ).

Detailed information for vg1115442463:

Variant ID: vg1115442463 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 15442463
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GGTCCATCACCGCAAATACTCTCCCGAGGCATCGAGTTAGCAAACAACAGTATTACATACGTATAGTATCCATCTAGAAGCCATAATCATGAAATAATCA[C/T]
GGATATCCAAACAAACAACCCGAAACCGAAACCGACACAGCGTCGGTCGGTCAGACCGTGAGCTGGCCGGTCCGACCGCTCGACCACCGCCGGTCTGACC

Reverse complement sequence

GGTCAGACCGGCGGTGGTCGAGCGGTCGGACCGGCCAGCTCACGGTCTGACCGACCGACGCTGTGTCGGTTTCGGTTTCGGGTTGTTTGTTTGGATATCC[G/A]
TGATTATTTCATGATTATGGCTTCTAGATGGATACTATACGTATGTAATACTGTTGTTTGCTAACTCGATGCCTCGGGAGAGTATTTGCGGTGATGGACC

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 96.30% 3.70% 0.00% 0.00% NA
All Indica  2759 93.80% 6.20% 0.00% 0.00% NA
All Japonica  1512 99.90% 0.10% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 81.50% 18.50% 0.00% 0.00% NA
Indica II  465 99.80% 0.20% 0.00% 0.00% NA
Indica III  913 97.90% 2.10% 0.00% 0.00% NA
Indica Intermediate  786 94.90% 5.10% 0.00% 0.00% NA
Temperate Japonica  767 99.90% 0.10% 0.00% 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 93.30% 6.70% 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
vg1115442463 C -> T LOC_Os11g26860.1 downstream_gene_variant ; 2418.0bp to feature; MODIFIER silent_mutation Average:45.953; most accessible tissue: Zhenshan97 flag leaf, score: 68.25 N N N N
vg1115442463 C -> T LOC_Os11g26870.1 downstream_gene_variant ; 1331.0bp to feature; MODIFIER silent_mutation Average:45.953; most accessible tissue: Zhenshan97 flag leaf, score: 68.25 N N N N
vg1115442463 C -> T LOC_Os11g26880.1 downstream_gene_variant ; 2428.0bp to feature; MODIFIER silent_mutation Average:45.953; most accessible tissue: Zhenshan97 flag leaf, score: 68.25 N N N N
vg1115442463 C -> T LOC_Os11g26890.1 downstream_gene_variant ; 4712.0bp to feature; MODIFIER silent_mutation Average:45.953; most accessible tissue: Zhenshan97 flag leaf, score: 68.25 N N N N
vg1115442463 C -> T LOC_Os11g26890.2 downstream_gene_variant ; 4712.0bp to feature; MODIFIER silent_mutation Average:45.953; most accessible tissue: Zhenshan97 flag leaf, score: 68.25 N N N N
vg1115442463 C -> T LOC_Os11g26860-LOC_Os11g26870 intergenic_region ; MODIFIER silent_mutation Average:45.953; most accessible tissue: Zhenshan97 flag leaf, score: 68.25 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1115442463 1.05E-06 1.04E-06 mr1102 Ind_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
vg1115442463 3.28E-08 1.79E-09 mr1097_2 Ind_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
vg1115442463 4.00E-08 4.22E-08 mr1154_2 Ind_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
vg1115442463 4.19E-06 1.41E-07 mr1223_2 Ind_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