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Detailed information for vg0613463494:

Variant ID: vg0613463494 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 13463494
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TCCCTTATCATATTCGATTCTGTTTCTGAGAAAATATTTCTAAATTTGTTTCCGTTTCTGAAATATTCCGACCGACATATTTCATTTTTGAAAATAGGTC[C/T]
GGAATCCAGAAAATTTTCGTACCGTTTTCATCCCTATACGAAATTAGGAAGGGCGCTCTAGTCGAAAGCGTCCTTAGGGCAGACACTGTTGGGGGGGCCT

Reverse complement sequence

AGGCCCCCCCAACAGTGTCTGCCCTAAGGACGCTTTCGACTAGAGCGCCCTTCCTAATTTCGTATAGGGATGAAAACGGTACGAAAATTTTCTGGATTCC[G/A]
GACCTATTTTCAAAAATGAAATATGTCGGTCGGAATATTTCAGAAACGGAAACAAATTTAGAAATATTTTCTCAGAAACAGAATCGAATATGATAAGGGA

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 93.50% 6.50% 0.02% 0.00% NA
All Indica  2759 97.90% 2.10% 0.00% 0.00% NA
All Japonica  1512 92.50% 7.50% 0.07% 0.00% NA
Aus  269 52.40% 47.60% 0.00% 0.00% NA
Indica I  595 96.50% 3.50% 0.00% 0.00% NA
Indica II  465 98.90% 1.10% 0.00% 0.00% NA
Indica III  913 99.90% 0.10% 0.00% 0.00% NA
Indica Intermediate  786 96.20% 3.80% 0.00% 0.00% NA
Temperate Japonica  767 99.70% 0.30% 0.00% 0.00% NA
Tropical Japonica  504 80.60% 19.20% 0.20% 0.00% NA
Japonica Intermediate  241 94.20% 5.80% 0.00% 0.00% NA
VI/Aromatic  96 97.90% 2.10% 0.00% 0.00% NA
Intermediate  90 92.20% 7.80% 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
vg0613463494 C -> T LOC_Os06g23090.1 upstream_gene_variant ; 531.0bp to feature; MODIFIER silent_mutation Average:69.772; most accessible tissue: Callus, score: 98.015 N N N N
vg0613463494 C -> T LOC_Os06g23080-LOC_Os06g23090 intergenic_region ; MODIFIER silent_mutation Average:69.772; most accessible tissue: Callus, score: 98.015 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0613463494 4.12E-11 NA mr1033 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
vg0613463494 7.31E-13 4.27E-17 mr1033 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
vg0613463494 1.30E-06 NA mr1176 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
vg0613463494 2.49E-07 3.58E-11 mr1176 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
vg0613463494 4.84E-16 NA mr1033_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
vg0613463494 1.55E-16 1.09E-22 mr1033_2 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
vg0613463494 2.68E-06 NA mr1536_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
vg0613463494 9.54E-08 2.99E-09 mr1536_2 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