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Detailed information for vg0118743986:

Variant ID: vg0118743986 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 18743986
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.99, others allele: 0.00, population size: 126. )

Flanking Sequence (100 bp) in Reference Genome:


CTTTTATTTTAATTTTTTAAACTACTGGGCGGCGCCTGGTAGTATTTCTACTAAAAAACAATTATGTAACAATGCAGAACAAGTTTGTCAGGGTTATGGA[T/C]
ACCACATACATAATAGTAGTCGACTAAATCTCGGCAGGACCCACCACTTACCATGTCCTATACGGAAACAACCTGCGGATATAGGAGGAGTTCTGGATAA

Reverse complement sequence

TTATCCAGAACTCCTCCTATATCCGCAGGTTGTTTCCGTATAGGACATGGTAAGTGGTGGGTCCTGCCGAGATTTAGTCGACTACTATTATGTATGTGGT[A/G]
TCCATAACCCTGACAAACTTGTTCTGCATTGTTACATAATTGTTTTTTAGTAGAAATACTACCAGGCGCCGCCCAGTAGTTTAAAAAATTAAAATAAAAG

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 94.80% 2.60% 2.60% 0.00% NA
All Indica  2759 91.30% 4.50% 4.20% 0.00% NA
All Japonica  1512 100.00% 0.00% 0.00% 0.00% NA
Aus  269 98.10% 0.00% 1.86% 0.00% NA
Indica I  595 70.80% 15.00% 14.29% 0.00% NA
Indica II  465 98.70% 0.90% 0.43% 0.00% NA
Indica III  913 99.80% 0.00% 0.22% 0.00% NA
Indica Intermediate  786 92.70% 3.80% 3.44% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 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 96.70% 1.10% 2.22% 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
vg0118743986 T -> C LOC_Os01g34040.1 upstream_gene_variant ; 2261.0bp to feature; MODIFIER silent_mutation Average:52.325; most accessible tissue: Minghui63 flag leaf, score: 66.556 N N N N
vg0118743986 T -> C LOC_Os01g34040-LOC_Os01g34050 intergenic_region ; MODIFIER silent_mutation Average:52.325; most accessible tissue: Minghui63 flag leaf, score: 66.556 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0118743986 1.26E-06 NA mr1519 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
vg0118743986 6.98E-08 2.59E-08 mr1519 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
vg0118743986 5.06E-06 9.55E-09 mr1519_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
vg0118743986 NA 6.04E-06 mr1547_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
vg0118743986 NA 3.38E-08 mr1709_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