Search for Variation information by Variation ID:

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

Detailed information for vg0106778059:

Variant ID: vg0106778059 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 6778059
Reference Allele: T	Alternative Allele: A
Primary Allele: T	Secondary Allele: A

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 327. )

Flanking Sequence (100 bp) in Reference Genome:

TGGTACATTACTAGCACAAACGAAAACATTGGGAAAATTCACATAGAGGTAGGATAAGATGCAAACAGTCTATGCTAATTTAATGCAAAATTCTGTGATC[T/A]
TCAATGATGCAAGATATGCATTGTTGAACTGTATGCAATGTTTCATTCCACTTGAATGTAAAGTTTTCCATGTTAACAATGAAAGGAGTGCATGAAAACA

Reverse complement sequence

TGTTTTCATGCACTCCTTTCATTGTTAACATGGAAAACTTTACATTCAAGTGGAATGAAACATTGCATACAGTTCAACAATGCATATCTTGCATCATTGA[A/T]
GATCACAGAATTTTGCATTAAATTAGCATAGACTGTTTGCATCTTATCCTACCTCTATGTGAATTTTCCCAATGTTTTCGTTTGTGCTAGTAATGTACCA

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	97.90%	1.30%	0.72%	0.00%	NA
All Indica	2759	100.00%	0.00%	0.00%	0.00%	NA
All Japonica	1512	93.70%	4.20%	2.18%	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	100.00%	0.00%	0.00%	0.00%	NA
Temperate Japonica	767	89.40%	6.50%	4.04%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	93.80%	5.40%	0.83%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	98.90%	0.00%	1.11%	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
vg0106778059	T -> A	LOC_Os01g12400.2	upstream_gene_variant ; 254.0bp to feature; MODIFIER	silent_mutation	Average:37.035; most accessible tissue: Callus, score: 78.707	N	N	N	N
vg0106778059	T -> A	LOC_Os01g12410.1	downstream_gene_variant ; 3860.0bp to feature; MODIFIER	silent_mutation	Average:37.035; most accessible tissue: Callus, score: 78.707	N	N	N	N
vg0106778059	T -> A	LOC_Os01g12400-LOC_Os01g12410	intergenic_region ; MODIFIER	silent_mutation	Average:37.035; most accessible tissue: Callus, score: 78.707	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0106778059	8.72E-07	7.77E-07	mr1008_2	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