Search for Variation information by Variation ID:

Please input a variation ID (e.g., vg0722097923 , STR0500036000 ).

Detailed information for vg0602403184:

Variant ID: vg0602403184 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 2403184
Reference Allele: CAlternative Allele: T
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.95, T: 0.05, others allele: 0.00, population size: 119. )

Flanking Sequence (100 bp) in Reference Genome:


GCCTCCAGCTAGCAGGGGCGGATCTAGGAGGGGCTAAATAAACTATACAAAACTACAGCCTCTCTTCTAATGGATGTATGACAAAAAATTTTAATGGTGA[C/T]
TTCATGGGGCTCCCATGGTTACAACGTTGGTAGTGGGGCCTCAAAGACCCCGGAGCCCCATGGTGGATCCGCCACTGCCAGCTAGCTAATAAAATGTTGA

Reverse complement sequence

TCAACATTTTATTAGCTAGCTGGCAGTGGCGGATCCACCATGGGGCTCCGGGGTCTTTGAGGCCCCACTACCAACGTTGTAACCATGGGAGCCCCATGAA[G/A]
TCACCATTAAAATTTTTTGTCATACATCCATTAGAAGAGAGGCTGTAGTTTTGTATAGTTTATTTAGCCCCTCCTAGATCCGCCCCTGCTAGCTGGAGGC

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 59.30% 40.60% 0.04% 0.00% NA
All Indica  2759 87.70% 12.30% 0.04% 0.00% NA
All Japonica  1512 1.10% 98.90% 0.07% 0.00% NA
Aus  269 95.50% 4.50% 0.00% 0.00% NA
Indica I  595 99.00% 1.00% 0.00% 0.00% NA
Indica II  465 53.30% 46.50% 0.22% 0.00% NA
Indica III  913 98.10% 1.90% 0.00% 0.00% NA
Indica Intermediate  786 87.40% 12.60% 0.00% 0.00% NA
Temperate Japonica  767 0.40% 99.60% 0.00% 0.00% NA
Tropical Japonica  504 1.40% 98.40% 0.20% 0.00% NA
Japonica Intermediate  241 2.50% 97.50% 0.00% 0.00% NA
VI/Aromatic  96 79.20% 20.80% 0.00% 0.00% NA
Intermediate  90 38.90% 61.10% 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
vg0602403184 C -> T LOC_Os06g05330.1 upstream_gene_variant ; 4372.0bp to feature; MODIFIER silent_mutation Average:59.969; most accessible tissue: Callus, score: 87.53 N N N N
vg0602403184 C -> T LOC_Os06g05340.1 upstream_gene_variant ; 594.0bp to feature; MODIFIER silent_mutation Average:59.969; most accessible tissue: Callus, score: 87.53 N N N N
vg0602403184 C -> T LOC_Os06g05350.1 upstream_gene_variant ; 2225.0bp to feature; MODIFIER silent_mutation Average:59.969; most accessible tissue: Callus, score: 87.53 N N N N
vg0602403184 C -> T LOC_Os06g05340-LOC_Os06g05350 intergenic_region ; MODIFIER silent_mutation Average:59.969; most accessible tissue: Callus, score: 87.53 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0602403184 NA 2.34E-06 mr1044 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
vg0602403184 NA 5.27E-13 mr1069 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
vg0602403184 2.09E-28 6.58E-109 mr1141 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
vg0602403184 9.60E-22 2.30E-46 mr1141 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
vg0602403184 NA 5.42E-14 mr1149 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
vg0602403184 NA 3.79E-23 mr1150 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
vg0602403184 NA 3.45E-06 mr1192 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
vg0602403184 NA 8.10E-15 mr1441 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
vg0602403184 NA 5.69E-06 mr1598 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
vg0602403184 NA 6.59E-14 mr1982 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
vg0602403184 7.00E-24 1.74E-117 mr1141_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
vg0602403184 3.29E-16 1.96E-43 mr1141_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
vg0602403184 NA 1.43E-26 mr1149_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
vg0602403184 NA 6.34E-31 mr1150_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
vg0602403184 NA 4.43E-09 mr1222_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
vg0602403184 NA 4.19E-27 mr1441_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