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Detailed information for vg0604973186:

Variant ID: vg0604973186 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 4973186
Reference Allele: TAlternative Allele: A
Primary Allele: TSecondary Allele: A

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, A: 0.00, others allele: 0.00, population size: 286. )

Flanking Sequence (100 bp) in Reference Genome:


ATTATACATTATTAGAATATAGTATAAGGTTAAGCGAAGTGTAGCTCAACTTGCCATTGTGGTGGAAACCTGCACGCCCACCCGGGTTAAAGTCCTACAC[T/A]
TGATACGGGTGTCCGCATTCATGGTGTTAGTGGTGTTCACATTTTGCAGTAGTAGACAATATACCAGTGGTGAATTCGTCAATTTCAAAATATGTCGATT

Reverse complement sequence

AATCGACATATTTTGAAATTGACGAATTCACCACTGGTATATTGTCTACTACTGCAAAATGTGAACACCACTAACACCATGAATGCGGACACCCGTATCA[A/T]
GTGTAGGACTTTAACCCGGGTGGGCGTGCAGGTTTCCACCACAATGGCAAGTTGAGCTACACTTCGCTTAACCTTATACTATATTCTAATAATGTATAAT

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 56.10% 43.80% 0.11% 0.00% NA
All Indica  2759 37.10% 62.80% 0.11% 0.00% NA
All Japonica  1512 85.60% 14.20% 0.13% 0.00% NA
Aus  269 99.60% 0.40% 0.00% 0.00% NA
Indica I  595 44.40% 55.10% 0.50% 0.00% NA
Indica II  465 36.30% 63.70% 0.00% 0.00% NA
Indica III  913 32.60% 67.40% 0.00% 0.00% NA
Indica Intermediate  786 37.20% 62.80% 0.00% 0.00% NA
Temperate Japonica  767 86.00% 13.70% 0.26% 0.00% NA
Tropical Japonica  504 88.10% 11.90% 0.00% 0.00% NA
Japonica Intermediate  241 79.30% 20.70% 0.00% 0.00% NA
VI/Aromatic  96 10.40% 89.60% 0.00% 0.00% NA
Intermediate  90 63.30% 36.70% 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
vg0604973186 T -> A LOC_Os06g09750.1 upstream_gene_variant ; 3952.0bp to feature; MODIFIER silent_mutation Average:50.919; most accessible tissue: Callus, score: 68.8 N N N N
vg0604973186 T -> A LOC_Os06g09770.1 upstream_gene_variant ; 1432.0bp to feature; MODIFIER silent_mutation Average:50.919; most accessible tissue: Callus, score: 68.8 N N N N
vg0604973186 T -> A LOC_Os06g09760.1 downstream_gene_variant ; 413.0bp to feature; MODIFIER silent_mutation Average:50.919; most accessible tissue: Callus, score: 68.8 N N N N
vg0604973186 T -> A LOC_Os06g09760-LOC_Os06g09770 intergenic_region ; MODIFIER silent_mutation Average:50.919; most accessible tissue: Callus, score: 68.8 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0604973186 8.97E-06 1.43E-07 mr1201 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
vg0604973186 9.70E-08 4.33E-16 mr1201 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
vg0604973186 2.86E-06 4.77E-08 mr1219 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
vg0604973186 3.87E-06 9.99E-15 mr1219 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
vg0604973186 3.73E-07 6.47E-08 mr1274 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
vg0604973186 9.68E-08 6.25E-15 mr1274 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
vg0604973186 1.17E-06 1.01E-08 mr1201_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
vg0604973186 2.29E-08 4.58E-16 mr1201_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
vg0604973186 NA 8.08E-08 mr1219_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
vg0604973186 2.73E-06 4.44E-13 mr1219_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
vg0604973186 3.98E-08 6.96E-10 mr1274_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
vg0604973186 1.16E-06 1.67E-14 mr1274_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