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Detailed information for vg0902040540:

Variant ID: vg0902040540 (JBrowse)Variation Type: SNP
Chromosome: chr09Position: 2040540
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.97, T: 0.02, others allele: 0.00, population size: 286. )

Flanking Sequence (100 bp) in Reference Genome:


CTGAAGACGAAGTTAGAAGACTAAGGCTCAAACCCCAGTTGAGTTTTGCCTGTGGAGTGGAGTTGAAGCCCAGCTAGGATCGCCTTTTCCGCTGCTGCTG[C/T]
TTTCGTTTCGGTGTGAGGACTAAGTGCCTCTTCTGTAAGTATTTTACGCTTTATTTATGTTTGGATCTGTATATTAAGAGGCGGCATTCCAGATGCTGAA

Reverse complement sequence

TTCAGCATCTGGAATGCCGCCTCTTAATATACAGATCCAAACATAAATAAAGCGTAAAATACTTACAGAAGAGGCACTTAGTCCTCACACCGAAACGAAA[G/A]
CAGCAGCAGCGGAAAAGGCGATCCTAGCTGGGCTTCAACTCCACTCCACAGGCAAAACTCAACTGGGGTTTGAGCCTTAGTCTTCTAACTTCGTCTTCAG

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 92.60% 7.40% 0.00% 0.00% NA
All Indica  2759 95.40% 4.60% 0.00% 0.00% NA
All Japonica  1512 99.90% 0.10% 0.00% 0.00% NA
Aus  269 19.00% 81.00% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 93.30% 6.70% 0.00% 0.00% NA
Indica III  913 96.20% 3.80% 0.00% 0.00% NA
Indica Intermediate  786 92.40% 7.60% 0.00% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 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 96.90% 3.10% 0.00% 0.00% NA
Intermediate  90 98.90% 1.10% 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
vg0902040540 C -> T LOC_Os09g03960.1 upstream_gene_variant ; 3133.0bp to feature; MODIFIER silent_mutation Average:56.763; most accessible tissue: Zhenshan97 panicle, score: 77.482 N N N N
vg0902040540 C -> T LOC_Os09g03970.1 upstream_gene_variant ; 245.0bp to feature; MODIFIER silent_mutation Average:56.763; most accessible tissue: Zhenshan97 panicle, score: 77.482 N N N N
vg0902040540 C -> T LOC_Os09g03980.1 upstream_gene_variant ; 3161.0bp to feature; MODIFIER silent_mutation Average:56.763; most accessible tissue: Zhenshan97 panicle, score: 77.482 N N N N
vg0902040540 C -> T LOC_Os09g03960-LOC_Os09g03970 intergenic_region ; MODIFIER silent_mutation Average:56.763; most accessible tissue: Zhenshan97 panicle, score: 77.482 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0902040540 NA 1.00E-07 mr1193 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
vg0902040540 NA 4.71E-12 mr1471 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
vg0902040540 NA 1.00E-11 mr1722 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
vg0902040540 9.70E-06 4.17E-09 mr1808 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
vg0902040540 NA 1.79E-20 mr1855 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
vg0902040540 NA 5.01E-21 mr1855_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