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Detailed information for vg0323033808:

Variant ID: vg0323033808 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 23033808
Reference Allele: CAlternative Allele: T
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


ATCCCTGTATTTTCTCCCGAATCGAGTGGGATGCACATCCACAAATCAACATCCCAAATATTAAGTTACTTATACACACAGATCAAATACATCACAAATC[C/T]
TAAAAAACTATACACAAATTAAATAAATCACAGATTATACAAGATTATACATCTCAGATCCATGCAATGCAATGAATCACAAAATCTAAAAAAATTATAC

Reverse complement sequence

GTATAATTTTTTTAGATTTTGTGATTCATTGCATTGCATGGATCTGAGATGTATAATCTTGTATAATCTGTGATTTATTTAATTTGTGTATAGTTTTTTA[G/A]
GATTTGTGATGTATTTGATCTGTGTGTATAAGTAACTTAATATTTGGGATGTTGATTTGTGGATGTGCATCCCACTCGATTCGGGAGAAAATACAGGGAT

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 54.40% 43.00% 1.42% 1.14% NA
All Indica  2759 90.10% 6.30% 1.74% 1.92% NA
All Japonica  1512 0.70% 99.10% 0.13% 0.00% NA
Aus  269 14.10% 85.90% 0.00% 0.00% NA
Indica I  595 92.60% 5.20% 1.85% 0.34% NA
Indica II  465 92.50% 4.70% 1.29% 1.51% NA
Indica III  913 89.60% 6.60% 0.88% 2.96% NA
Indica Intermediate  786 87.30% 7.60% 2.93% 2.16% 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 0.40% 99.20% 0.41% 0.00% NA
VI/Aromatic  96 2.10% 84.40% 13.54% 0.00% NA
Intermediate  90 38.90% 55.60% 4.44% 1.11% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0323033808 C -> T LOC_Os03g41390.1 downstream_gene_variant ; 2420.0bp to feature; MODIFIER silent_mutation Average:53.322; most accessible tissue: Zhenshan97 flag leaf, score: 68.25 N N N N
vg0323033808 C -> T LOC_Os03g41380-LOC_Os03g41390 intergenic_region ; MODIFIER silent_mutation Average:53.322; most accessible tissue: Zhenshan97 flag leaf, score: 68.25 N N N N
vg0323033808 C -> DEL N N silent_mutation Average:53.322; most accessible tissue: Zhenshan97 flag leaf, score: 68.25 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0323033808 NA 8.92E-07 mr1074 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
vg0323033808 NA 6.26E-08 mr1081 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
vg0323033808 NA 3.44E-08 mr1130 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
vg0323033808 NA 8.08E-08 mr1148 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
vg0323033808 NA 6.14E-06 mr1254 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