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Detailed information for vg0915670603:

Variant ID: vg0915670603 (JBrowse)Variation Type: SNP
Chromosome: chr09Position: 15670603
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 119. )

Flanking Sequence (100 bp) in Reference Genome:


TCGCCGTCGTTACTTGAAGCCACTGTCATTGTCGTTGCCGTCGACCTCGTTCTCGTCAGTGTCATGGGGACGAAGGGGGCTAGGGGCGGCTGGATTCGCC[C/T]
GTTCCTGTCACCATCGCCGGAGCCAGATCAGCTGCCACGATGCCTCCTTTCTACCGGATCCGCCGCCACCGCGCCTCCCCACTACCCGATCCTCCGCCGC

Reverse complement sequence

GCGGCGGAGGATCGGGTAGTGGGGAGGCGCGGTGGCGGCGGATCCGGTAGAAAGGAGGCATCGTGGCAGCTGATCTGGCTCCGGCGATGGTGACAGGAAC[G/A]
GGCGAATCCAGCCGCCCCTAGCCCCCTTCGTCCCCATGACACTGACGAGAACGAGGTCGACGGCAACGACAATGACAGTGGCTTCAAGTAACGACGGCGA

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 91.60% 7.70% 0.70% 0.00% NA
All Indica  2759 85.90% 12.90% 1.20% 0.00% NA
All Japonica  1512 99.80% 0.20% 0.00% 0.00% NA
Aus  269 99.60% 0.40% 0.00% 0.00% NA
Indica I  595 98.70% 1.00% 0.34% 0.00% NA
Indica II  465 57.00% 38.10% 4.95% 0.00% NA
Indica III  913 91.70% 8.20% 0.11% 0.00% NA
Indica Intermediate  786 86.60% 12.50% 0.89% 0.00% NA
Temperate Japonica  767 99.70% 0.30% 0.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 99.60% 0.40% 0.00% 0.00% NA
VI/Aromatic  96 99.00% 1.00% 0.00% 0.00% NA
Intermediate  90 94.40% 5.60% 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
vg0915670603 C -> T LOC_Os09g26050-LOC_Os09g26060 intergenic_region ; MODIFIER silent_mutation Average:63.415; most accessible tissue: Zhenshan97 young leaf, score: 83.623 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0915670603 NA 5.24E-06 mr1319 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
vg0915670603 NA 9.29E-07 mr1593 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
vg0915670603 1.55E-06 NA mr1655 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
vg0915670603 5.74E-06 5.74E-06 mr1655 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