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Detailed information for vg1104329073:

Variant ID: vg1104329073 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 4329073
Reference Allele: CAlternative Allele: A
Primary Allele: CSecondary Allele: A

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 245. )

Flanking Sequence (100 bp) in Reference Genome:


GAGTCACGTACACATTAGGTCAGCCCCAGCCACTTGCACCTCTTGCAAAGTCAACAAGGTAGGAAGATATGACGCCTCCCCTGCTCCTCGCAATACGTCT[C/A]
CATGTCATGGGACTAGTGTAGAAACTAGGGGGCTTTTATTTTTGTCAAGCCTTATGAATGTTAATTGGCAAGACGTTTCATTTAAATACTGCAAACCAAA

Reverse complement sequence

TTTGGTTTGCAGTATTTAAATGAAACGTCTTGCCAATTAACATTCATAAGGCTTGACAAAAATAAAAGCCCCCTAGTTTCTACACTAGTCCCATGACATG[G/T]
AGACGTATTGCGAGGAGCAGGGGAGGCGTCATATCTTCCTACCTTGTTGACTTTGCAAGAGGTGCAAGTGGCTGGGGCTGACCTAATGTGTACGTGACTC

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 90.80% 9.20% 0.08% 0.00% NA
All Indica  2759 84.40% 15.40% 0.14% 0.00% NA
All Japonica  1512 99.80% 0.20% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 86.20% 13.60% 0.17% 0.00% NA
Indica II  465 93.50% 6.50% 0.00% 0.00% NA
Indica III  913 77.90% 22.00% 0.11% 0.00% NA
Indica Intermediate  786 85.20% 14.50% 0.25% 0.00% NA
Temperate Japonica  767 99.60% 0.40% 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 95.60% 4.40% 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
vg1104329073 C -> A LOC_Os11g08230.1 upstream_gene_variant ; 3528.0bp to feature; MODIFIER silent_mutation Average:58.639; most accessible tissue: Callus, score: 86.12 N N N N
vg1104329073 C -> A LOC_Os11g08260.1 upstream_gene_variant ; 991.0bp to feature; MODIFIER silent_mutation Average:58.639; most accessible tissue: Callus, score: 86.12 N N N N
vg1104329073 C -> A LOC_Os11g08235.1 downstream_gene_variant ; 3489.0bp to feature; MODIFIER silent_mutation Average:58.639; most accessible tissue: Callus, score: 86.12 N N N N
vg1104329073 C -> A LOC_Os11g08240.1 downstream_gene_variant ; 2709.0bp to feature; MODIFIER silent_mutation Average:58.639; most accessible tissue: Callus, score: 86.12 N N N N
vg1104329073 C -> A LOC_Os11g08250.1 downstream_gene_variant ; 975.0bp to feature; MODIFIER silent_mutation Average:58.639; most accessible tissue: Callus, score: 86.12 N N N N
vg1104329073 C -> A LOC_Os11g08250-LOC_Os11g08260 intergenic_region ; MODIFIER silent_mutation Average:58.639; most accessible tissue: Callus, score: 86.12 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1104329073 NA 7.74E-06 mr1561_2 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
vg1104329073 NA 4.53E-06 mr1996_2 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