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Detailed information for vg0206284604:

Variant ID: vg0206284604 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 6284604
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.56, C: 0.44, others allele: 0.00, population size: 84. )

Flanking Sequence (100 bp) in Reference Genome:


CTATTTATCCAAAAAATACGTTACGTCTCCCTATTTATGAAAATTGCCGTTTACATTTGGTTGCATCTTATAGTCTTTTGCTTCAGTTTGCGCCTTGGGA[T/C]
TGGATAGGACAGCATCTGGCAGACTAGCACATAGACCTATTTAGCTCTTCCATTAAAATTTCTTGATAAACACCATTGCTAAATTTTATTTTATTTTAAG

Reverse complement sequence

CTTAAAATAAAATAAAATTTAGCAATGGTGTTTATCAAGAAATTTTAATGGAAGAGCTAAATAGGTCTATGTGCTAGTCTGCCAGATGCTGTCCTATCCA[A/G]
TCCCAAGGCGCAAACTGAAGCAAAAGACTATAAGATGCAACCAAATGTAAACGGCAATTTTCATAAATAGGGAGACGTAACGTATTTTTTGGATAAATAG

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 81.70% 10.30% 0.76% 7.28% NA
All Indica  2759 79.30% 16.20% 0.22% 4.28% NA
All Japonica  1512 97.60% 1.70% 0.26% 0.53% NA
Aus  269 30.50% 0.00% 7.81% 61.71% NA
Indica I  595 93.30% 6.70% 0.00% 0.00% NA
Indica II  465 65.20% 26.50% 0.22% 8.17% NA
Indica III  913 76.60% 19.60% 0.33% 3.50% NA
Indica Intermediate  786 80.20% 13.50% 0.25% 6.11% NA
Temperate Japonica  767 98.60% 0.90% 0.52% 0.00% NA
Tropical Japonica  504 96.20% 3.00% 0.00% 0.79% NA
Japonica Intermediate  241 97.10% 1.20% 0.00% 1.66% NA
VI/Aromatic  96 44.80% 8.30% 3.12% 43.75% NA
Intermediate  90 80.00% 6.70% 2.22% 11.11% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0206284604 T -> DEL N N silent_mutation Average:27.365; most accessible tissue: Minghui63 flower, score: 34.612 N N N N
vg0206284604 T -> C LOC_Os02g12100-LOC_Os02g12110 intergenic_region ; MODIFIER silent_mutation Average:27.365; most accessible tissue: Minghui63 flower, score: 34.612 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0206284604 NA 4.29E-06 mr1004 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
vg0206284604 NA 2.36E-08 mr1006 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
vg0206284604 NA 4.92E-08 mr1007 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
vg0206284604 NA 8.74E-06 mr1007 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
vg0206284604 NA 5.11E-06 mr1037 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
vg0206284604 NA 5.00E-08 mr1052 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
vg0206284604 NA 2.92E-13 mr1004_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
vg0206284604 NA 2.36E-07 mr1004_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
vg0206284604 NA 1.79E-07 mr1006_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