Search for Variation information by Variation ID:

Please input a variation ID (e.g., vg0722097923 , STR0500036000 ).

Detailed information for vg0207449651:

Variant ID: vg0207449651 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 7449651
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 123. )

Flanking Sequence (100 bp) in Reference Genome:

CCGGTGCAATATAGGTCTCATGGCGTTTTGGACGGCGGTTTTAGCTTACGTGGCGCCTACGTGGCTAAATTGACCCGGTCTTCATCTGACGTGGCATAGA[T/C]
GTGGCATTGACGTGGCAATTTGATTTGGAAATTAATAAAAAAAGAGTGACCCCACATGTCAGCTACACCAAAAGAATTAATTAAAAAATGGTGGGTCCTA

Reverse complement sequence

TAGGACCCACCATTTTTTAATTAATTCTTTTGGTGTAGCTGACATGTGGGGTCACTCTTTTTTTATTAATTTCCAAATCAAATTGCCACGTCAATGCCAC[A/G]
TCTATGCCACGTCAGATGAAGACCGGGTCAATTTAGCCACGTAGGCGCCACGTAAGCTAAAACCGCCGTCCAAAACGCCATGAGACCTATATTGCACCGG

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	95.60%	0.20%	0.57%	3.62%	NA
All Indica	2759	92.80%	0.20%	0.91%	6.13%	NA
All Japonica	1512	99.90%	0.00%	0.07%	0.07%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	98.20%	0.00%	1.85%	0.00%	NA
Indica II	465	91.20%	0.60%	0.65%	7.53%	NA
Indica III	913	89.80%	0.20%	0.22%	9.75%	NA
Indica Intermediate	786	93.00%	0.10%	1.15%	5.73%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	99.80%	0.00%	0.00%	0.20%	NA
Japonica Intermediate	241	99.60%	0.00%	0.41%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	95.60%	2.20%	1.11%	1.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0207449651	T -> DEL	N	N	silent_mutation	Average:62.267; most accessible tissue: Zhenshan97 root, score: 79.962	N	N	N	N
vg0207449651	T -> C	LOC_Os02g13790.1	upstream_gene_variant ; 88.0bp to feature; MODIFIER	silent_mutation	Average:62.267; most accessible tissue: Zhenshan97 root, score: 79.962	N	N	N	N
vg0207449651	T -> C	LOC_Os02g13785-LOC_Os02g13790	intergenic_region ; MODIFIER	silent_mutation	Average:62.267; most accessible tissue: Zhenshan97 root, score: 79.962	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0207449651	NA	2.63E-17	mr1870	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