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Detailed information for vg0114643712:

Variant ID: vg0114643712 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 14643712
Reference Allele: TAlternative Allele: C
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, T: 0.00, others allele: 0.00, population size: 259. )

Flanking Sequence (100 bp) in Reference Genome:


GGTACCACATTAAAGGTATTTAAGTATTGATATATGTACTTAGGTACTAAGGGTAAAAATATAGTTTCGCTAGTAGAGTGAAAAGGGTAGAATTGTCCTC[T/C]
AAATTATAATAGGTACCACAAAGGTACGACCGTATGCGTTAACATCTACACGGTATCAGCGCTTATGTGTTTTATTTGTGTCATTTTCTCTTTTGCGTGT

Reverse complement sequence

ACACGCAAAAGAGAAAATGACACAAATAAAACACATAAGCGCTGATACCGTGTAGATGTTAACGCATACGGTCGTACCTTTGTGGTACCTATTATAATTT[A/G]
GAGGACAATTCTACCCTTTTCACTCTACTAGCGAAACTATATTTTTACCCTTAGTACCTAAGTACATATATCAATACTTAAATACCTTTAATGTGGTACC

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 58.60% 41.30% 0.04% 0.00% NA
All Indica  2759 87.10% 12.90% 0.07% 0.00% NA
All Japonica  1512 5.30% 94.70% 0.00% 0.00% NA
Aus  269 65.80% 34.20% 0.00% 0.00% NA
Indica I  595 92.40% 7.40% 0.17% 0.00% NA
Indica II  465 96.10% 3.70% 0.22% 0.00% NA
Indica III  913 79.60% 20.40% 0.00% 0.00% NA
Indica Intermediate  786 86.30% 13.70% 0.00% 0.00% NA
Temperate Japonica  767 1.60% 98.40% 0.00% 0.00% NA
Tropical Japonica  504 11.90% 88.10% 0.00% 0.00% NA
Japonica Intermediate  241 3.30% 96.70% 0.00% 0.00% NA
VI/Aromatic  96 63.50% 36.50% 0.00% 0.00% NA
Intermediate  90 55.60% 44.40% 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
vg0114643712 T -> C LOC_Os01g25820-LOC_Os01g25839 intergenic_region ; MODIFIER silent_mutation Average:57.299; most accessible tissue: Zhenshan97 flag leaf, score: 73.475 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0114643712 5.72E-08 5.71E-08 mr1261_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
vg0114643712 NA 7.30E-06 mr1510_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