Search for Variation information by Variation ID:

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

Detailed information for vg1124625149:

Variant ID: vg1124625149 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 24625149
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.98, C: 0.01, others allele: 0.00, population size: 236. )

Flanking Sequence (100 bp) in Reference Genome:

AAATAAACTCTCCAAAGTTTTATTTTATTTTGTTTATTTAGTATACTCAGTTGCCCGCACTTATTTTAATTATTTTATTTGTGAACACTCACGCGTCTAT[T/C]
TGAGTGGCCCTAATAGAAGCATGTACTTTGTTTAACACAATATAACCGGTCGATAGTTCGATCTACTAAAGCTTAACTTATCTTGTGCCATCCATTTATT

Reverse complement sequence

AATAAATGGATGGCACAAGATAAGTTAAGCTTTAGTAGATCGAACTATCGACCGGTTATATTGTGTTAAACAAAGTACATGCTTCTATTAGGGCCACTCA[A/G]
ATAGACGCGTGAGTGTTCACAAATAAAATAATTAAAATAAGTGCGGGCAACTGAGTATACTAAATAAACAAAATAAAATAAAACTTTGGAGAGTTTATTT

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	57.80%	40.00%	1.57%	0.63%	NA
All Indica	2759	37.00%	59.30%	2.57%	1.05%	NA
All Japonica	1512	94.90%	5.00%	0.07%	0.00%	NA
Aus	269	71.00%	28.60%	0.37%	0.00%	NA
Indica I	595	34.80%	59.00%	6.22%	0.00%	NA
Indica II	465	9.70%	89.90%	0.43%	0.00%	NA
Indica III	913	51.40%	45.00%	0.66%	2.96%	NA
Indica Intermediate	786	38.30%	58.10%	3.31%	0.25%	NA
Temperate Japonica	767	96.50%	3.50%	0.00%	0.00%	NA
Tropical Japonica	504	94.20%	5.60%	0.20%	0.00%	NA
Japonica Intermediate	241	91.30%	8.70%	0.00%	0.00%	NA
VI/Aromatic	96	34.40%	64.60%	0.00%	1.04%	NA
Intermediate	90	55.60%	43.30%	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
vg1124625149	T -> DEL	N	N	silent_mutation	Average:44.152; most accessible tissue: Zhenshan97 flower, score: 60.838	N	N	N	N
vg1124625149	T -> C	LOC_Os11g41110.1	upstream_gene_variant ; 3863.0bp to feature; MODIFIER	silent_mutation	Average:44.152; most accessible tissue: Zhenshan97 flower, score: 60.838	N	N	N	N
vg1124625149	T -> C	LOC_Os11g41100-LOC_Os11g41110	intergenic_region ; MODIFIER	silent_mutation	Average:44.152; most accessible tissue: Zhenshan97 flower, score: 60.838	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1124625149	NA	7.57E-08	mr1285	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
vg1124625149	NA	1.12E-06	mr1377	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