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Detailed information for vg0301280405:

Variant ID: vg0301280405 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 1280405
Reference Allele: CAlternative Allele: A
Primary Allele: CSecondary Allele: A

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, A: 0.01, others allele: 0.00, population size: 245. )

Flanking Sequence (100 bp) in Reference Genome:


ATATGTTTTTTTTTTAAAAAAAGAATGACTATTCTTAATTACACTGTATTCTTTTATGATGATAAAACAACTATTGTTGGTATATCAAAAAGACCAAGGA[C/A]
AAATGCCATAGAAAACGATAAATATGTTATCAAGCAATTTATCTTCAATTACCATGCCCAATAAAGATGAGACTACATCAAGACATGCAAAAGAACATGA

Reverse complement sequence

TCATGTTCTTTTGCATGTCTTGATGTAGTCTCATCTTTATTGGGCATGGTAATTGAAGATAAATTGCTTGATAACATATTTATCGTTTTCTATGGCATTT[G/T]
TCCTTGGTCTTTTTGATATACCAACAATAGTTGTTTTATCATCATAAAAGAATACAGTGTAATTAAGAATAGTCATTCTTTTTTTAAAAAAAAAACATAT

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 96.00% 3.70% 0.36% 0.00% NA
All Indica  2759 99.90% 0.10% 0.00% 0.00% NA
All Japonica  1512 87.80% 11.00% 1.12% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 99.70% 0.30% 0.00% 0.00% NA
Temperate Japonica  767 99.00% 0.10% 0.91% 0.00% NA
Tropical Japonica  504 66.30% 31.90% 1.79% 0.00% NA
Japonica Intermediate  241 97.50% 2.10% 0.41% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 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
vg0301280405 C -> A LOC_Os03g03080.1 downstream_gene_variant ; 3416.0bp to feature; MODIFIER silent_mutation Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 N N N N
vg0301280405 C -> A LOC_Os03g03080-LOC_Os03g03100 intergenic_region ; MODIFIER silent_mutation Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0301280405 NA 2.55E-10 mr1518 Jap_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
vg0301280405 NA 1.02E-09 mr1676 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
vg0301280405 NA 9.88E-13 mr1769 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
vg0301280405 NA 5.82E-06 mr1807 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
vg0301280405 NA 6.14E-09 mr1951 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
vg0301280405 NA 8.44E-11 mr1676_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
vg0301280405 NA 4.59E-14 mr1769_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