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Detailed information for vg1003663158:

Variant ID: vg1003663158 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 3663158
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 128. )

Flanking Sequence (100 bp) in Reference Genome:


GTAATTAGTATTCCATAAAACAATAATCTCCAAAACTAAGTTTATCATTATAAAAAGGAAAAAATATGAATTAACCCCTGAACGGTTGCGATCATCCGAA[T/C]
TACACCTGTAATTTGAATACTAAACATTTAAGTTCCATCAACTATCTAAACTGGACAAACCGACTCAATCCCAAGAGGTTTTGGTCTAACGTGGCAGTTC

Reverse complement sequence

GAACTGCCACGTTAGACCAAAACCTCTTGGGATTGAGTCGGTTTGTCCAGTTTAGATAGTTGATGGAACTTAAATGTTTAGTATTCAAATTACAGGTGTA[A/G]
TTCGGATGATCGCAACCGTTCAGGGGTTAATTCATATTTTTTCCTTTTTATAATGATAAACTTAGTTTTGGAGATTATTGTTTTATGGAATACTAATTAC

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 95.00% 4.30% 0.78% 0.00% NA
All Indica  2759 91.40% 7.30% 1.34% 0.00% NA
All Japonica  1512 100.00% 0.00% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 81.70% 15.30% 3.03% 0.00% NA
Indica II  465 98.70% 0.90% 0.43% 0.00% NA
Indica III  913 94.00% 5.60% 0.44% 0.00% NA
Indica Intermediate  786 91.30% 7.00% 1.65% 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  90 100.00% 0.00% 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
vg1003663158 T -> C LOC_Os10g07010.1 upstream_gene_variant ; 1589.0bp to feature; MODIFIER silent_mutation Average:44.192; most accessible tissue: Zhenshan97 young leaf, score: 68.315 N N N N
vg1003663158 T -> C LOC_Os10g07010-LOC_Os10g07030 intergenic_region ; MODIFIER silent_mutation Average:44.192; most accessible tissue: Zhenshan97 young leaf, score: 68.315 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1003663158 2.04E-07 NA mr1547 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
vg1003663158 1.72E-06 NA mr1547 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
vg1003663158 1.07E-08 1.37E-06 mr1709 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
vg1003663158 5.74E-07 NA mr1709 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
vg1003663158 NA 7.01E-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
vg1003663158 NA 1.52E-06 mr1547_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
vg1003663158 1.19E-10 NA 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
vg1003663158 1.96E-07 NA mr1709_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