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Detailed information for vg0609897017:

Variant ID: vg0609897017 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 9897017
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.84, T: 0.15, others allele: 0.00, population size: 97. )

Flanking Sequence (100 bp) in Reference Genome:


ACAACATTTACAAGTACTAGATGATTTCAACTGAAATAATCATCAACAACAAAGTTGTATAACTCATCAATATCTATAGCTTTTATTTGGGTCATTTCTT[C/T]
ATCTGACAAAGTGATTTGTAATATTGTTCACAAAATTTACATCTCTCTCTTATAGTTTATAAACTATACAAGAGATATGTACATTTTGTGGGCCAGTTGT

Reverse complement sequence

ACAACTGGCCCACAAAATGTACATATCTCTTGTATAGTTTATAAACTATAAGAGAGAGATGTAAATTTTGTGAACAATATTACAAATCACTTTGTCAGAT[G/A]
AAGAAATGACCCAAATAAAAGCTATAGATATTGATGAGTTATACAACTTTGTTGTTGATGATTATTTCAGTTGAAATCATCTAGTACTTGTAAATGTTGT

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 88.30% 11.70% 0.06% 0.00% NA
All Indica  2759 81.10% 18.80% 0.11% 0.00% NA
All Japonica  1512 99.30% 0.70% 0.00% 0.00% NA
Aus  269 98.50% 1.50% 0.00% 0.00% NA
Indica I  595 97.50% 2.50% 0.00% 0.00% NA
Indica II  465 77.60% 22.40% 0.00% 0.00% NA
Indica III  913 70.80% 28.90% 0.33% 0.00% NA
Indica Intermediate  786 82.80% 17.20% 0.00% 0.00% NA
Temperate Japonica  767 99.10% 0.90% 0.00% 0.00% NA
Tropical Japonica  504 99.60% 0.40% 0.00% 0.00% NA
Japonica Intermediate  241 99.20% 0.80% 0.00% 0.00% NA
VI/Aromatic  96 92.70% 7.30% 0.00% 0.00% NA
Intermediate  90 87.80% 12.20% 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
vg0609897017 C -> T LOC_Os06g17070.1 upstream_gene_variant ; 1849.0bp to feature; MODIFIER silent_mutation Average:36.14; most accessible tissue: Callus, score: 61.089 N N N N
vg0609897017 C -> T LOC_Os06g17070-LOC_Os06g17080 intergenic_region ; MODIFIER silent_mutation Average:36.14; most accessible tissue: Callus, score: 61.089 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0609897017 NA 4.61E-06 mr1122 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
vg0609897017 1.83E-09 NA mr1695 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
vg0609897017 8.48E-09 NA mr1695 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
vg0609897017 1.13E-07 NA mr1695_2 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
vg0609897017 2.20E-08 NA mr1695_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