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Detailed information for vg1217404715:

Variant ID: vg1217404715 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 17404715
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TACTCCACACAAAATAAATTAAATTTCGATTACTATATGAATTTAGAGAATAGATTTATTTGTTATTTTAAAGTAACTTAATATATATAATTTTTGTAAA[C/T]
AAAATGCATTGTTTGACAGTTCTATTATATTTTTTAAACAAAATGCATCGTTTAACAATTCTATTATAAATCAAGTTAAAATTTGTATGTTAATCAGAAA

Reverse complement sequence

TTTCTGATTAACATACAAATTTTAACTTGATTTATAATAGAATTGTTAAACGATGCATTTTGTTTAAAAAATATAATAGAACTGTCAAACAATGCATTTT[G/A]
TTTACAAAAATTATATATATTAAGTTACTTTAAAATAACAAATAAATCTATTCTCTAAATTCATATAGTAATCGAAATTTAATTTATTTTGTGTGGAGTA

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 86.70% 13.20% 0.08% 0.00% NA
All Indica  2759 95.10% 4.90% 0.00% 0.00% NA
All Japonica  1512 78.80% 21.10% 0.13% 0.00% NA
Aus  269 41.30% 58.40% 0.37% 0.00% NA
Indica I  595 99.80% 0.20% 0.00% 0.00% NA
Indica II  465 82.20% 17.80% 0.00% 0.00% NA
Indica III  913 99.20% 0.80% 0.00% 0.00% NA
Indica Intermediate  786 94.40% 5.60% 0.00% 0.00% NA
Temperate Japonica  767 95.40% 4.60% 0.00% 0.00% NA
Tropical Japonica  504 58.10% 41.50% 0.40% 0.00% NA
Japonica Intermediate  241 68.90% 31.10% 0.00% 0.00% NA
VI/Aromatic  96 99.00% 1.00% 0.00% 0.00% NA
Intermediate  90 86.70% 12.20% 1.11% 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
vg1217404715 C -> T LOC_Os12g29340.1 downstream_gene_variant ; 1474.0bp to feature; MODIFIER silent_mutation Average:75.492; most accessible tissue: Zhenshan97 root, score: 89.337 N N N N
vg1217404715 C -> T LOC_Os12g29330-LOC_Os12g29340 intergenic_region ; MODIFIER silent_mutation Average:75.492; most accessible tissue: Zhenshan97 root, score: 89.337 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1217404715 NA 4.54E-08 mr1188 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
vg1217404715 NA 2.31E-06 mr1388 Jap_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
vg1217404715 3.52E-06 3.52E-06 mr1601 Jap_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
vg1217404715 1.49E-06 1.22E-07 mr1602 Jap_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
vg1217404715 NA 3.54E-07 mr1188_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
vg1217404715 NA 3.97E-06 mr1702_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