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Detailed information for vg0815172680:

Variant ID: vg0815172680 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 15172680
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CTGAAAAAGTTATCAACAACAAAGTTGAATAAAACATCAAGATCTAAAACTTTTATTTTGATCATTTCTTCATCTGATAAAATGTTAGTAACATTGTTCA[C/T]
AAATTTTATATATATGTGTTATAGTTTATAAAACCAGATAAGAGATATGTCAATTTTGTGAACAATGTTACTATTACTTTATCAGATGAAGAAATGACCA

Reverse complement sequence

TGGTCATTTCTTCATCTGATAAAGTAATAGTAACATTGTTCACAAAATTGACATATCTCTTATCTGGTTTTATAAACTATAACACATATATATAAAATTT[G/A]
TGAACAATGTTACTAACATTTTATCAGATGAAGAAATGATCAAAATAAAAGTTTTAGATCTTGATGTTTTATTCAACTTTGTTGTTGATAACTTTTTCAG

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 98.40% 1.40% 0.25% 0.00% NA
All Indica  2759 98.10% 1.60% 0.29% 0.00% NA
All Japonica  1512 99.10% 0.90% 0.07% 0.00% NA
Aus  269 98.50% 0.70% 0.74% 0.00% NA
Indica I  595 99.30% 0.70% 0.00% 0.00% NA
Indica II  465 99.10% 0.60% 0.22% 0.00% NA
Indica III  913 97.00% 2.70% 0.22% 0.00% NA
Indica Intermediate  786 97.70% 1.70% 0.64% 0.00% NA
Temperate Japonica  767 99.90% 0.10% 0.00% 0.00% NA
Tropical Japonica  504 97.40% 2.40% 0.20% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 97.90% 2.10% 0.00% 0.00% NA
Intermediate  90 96.70% 2.20% 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
vg0815172680 C -> T LOC_Os08g25010-LOC_Os08g25020 intergenic_region ; MODIFIER N Average:17.351; most accessible tissue: Callus, score: 27.339 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0815172680 2.47E-06 2.68E-07 mr1334 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
vg0815172680 4.76E-06 NA mr1750 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
vg0815172680 2.41E-06 NA mr1935 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
vg0815172680 7.31E-06 NA mr1935 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
vg0815172680 6.15E-07 NA mr1987 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
vg0815172680 5.96E-06 5.96E-06 mr1987 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