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Detailed information for vg1002797270:

Variant ID: vg1002797270 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 2797270
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, A: 0.01, others allele: 0.00, population size: 123. )

Flanking Sequence (100 bp) in Reference Genome:


ATTTTATATTATGGGGTTGTTCAGATTATAGTCAAAATAAACCTCACTAAATTTTGGCAATACAAAAAATTTAGTAAGTTGACAATATTACCAAAATTTT[G/A]
GCATTATTTCTTACACATTTATGAAAGTTTGGCAAAAAGATTTTGGCATTATTTCTTACGCATTTATGAAAGTTTGGCAAAAAGTTAAATGTATGTACAT

Reverse complement sequence

ATGTACATACATTTAACTTTTTGCCAAACTTTCATAAATGCGTAAGAAATAATGCCAAAATCTTTTTGCCAAACTTTCATAAATGTGTAAGAAATAATGC[C/T]
AAAATTTTGGTAATATTGTCAACTTACTAAATTTTTTGTATTGCCAAAATTTAGTGAGGTTTATTTTGACTATAATCTGAACAACCCCATAATATAAAAT

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 99.80% 0.20% 0.06% 0.00% NA
All Indica  2759 99.60% 0.30% 0.11% 0.00% NA
All Japonica  1512 100.00% 0.00% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 99.30% 0.30% 0.34% 0.00% NA
Indica II  465 99.10% 0.90% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 99.60% 0.30% 0.13% 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  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 100.00% 0.00% 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
vg1002797270 G -> A LOC_Os10g05600.1 upstream_gene_variant ; 592.0bp to feature; MODIFIER N Average:32.564; most accessible tissue: Callus, score: 66.454 N N N N
vg1002797270 G -> A LOC_Os10g05610.1 upstream_gene_variant ; 4658.0bp to feature; MODIFIER N Average:32.564; most accessible tissue: Callus, score: 66.454 N N N N
vg1002797270 G -> A LOC_Os10g05600-LOC_Os10g05610 intergenic_region ; MODIFIER N Average:32.564; most accessible tissue: Callus, score: 66.454 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1002797270 NA 3.66E-06 mr1165 Ind_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