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Detailed information for vg0515261196:

Variant ID: vg0515261196 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 15261196
Reference Allele: AAlternative Allele: C
Primary Allele: ASecondary Allele: C

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 200. )

Flanking Sequence (100 bp) in Reference Genome:


AGATATACCTAAGACAGCTTTTACCACTAGGTATGGGTTGTTTGAATGTACTGTTATGTCTTTTGGACTTACCAATGCCCCCGCTTTCTTCATGAACCTA[A/C]
TGAATAAGGTGTTTATGGAATACCTAGACAAGTTCGTGGTGGTCTTTATTGATGACATTCTTATCTACTCTCGAACCAAAGAAGAGCATGAAGAACATCT

Reverse complement sequence

AGATGTTCTTCATGCTCTTCTTTGGTTCGAGAGTAGATAAGAATGTCATCAATAAAGACCACCACGAACTTGTCTAGGTATTCCATAAACACCTTATTCA[T/G]
TAGGTTCATGAAGAAAGCGGGGGCATTGGTAAGTCCAAAAGACATAACAGTACATTCAAACAACCCATACCTAGTGGTAAAAGCTGTCTTAGGTATATCT

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 99.30% 0.40% 0.32% 0.00% NA
All Indica  2759 98.80% 0.70% 0.51% 0.00% NA
All Japonica  1512 99.90% 0.00% 0.07% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 97.50% 2.00% 0.50% 0.00% NA
Indica II  465 99.60% 0.40% 0.00% 0.00% NA
Indica III  913 99.60% 0.00% 0.44% 0.00% NA
Indica Intermediate  786 98.30% 0.80% 0.89% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 99.80% 0.00% 0.20% 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  90 100.00% 0.00% 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
vg0515261196 A -> C LOC_Os05g26230.1 missense_variant ; p.Met673Leu; MODERATE N Average:11.936; most accessible tissue: Zhenshan97 panicle, score: 24.575 N N N N
vg0515261196 A -> C LOC_Os05g26220.1 downstream_gene_variant ; 2288.0bp to feature; MODIFIER N Average:11.936; most accessible tissue: Zhenshan97 panicle, score: 24.575 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0515261196 NA 6.92E-06 mr1011 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
vg0515261196 1.04E-06 1.05E-06 mr1012 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