Search for Variation information by Variation ID:

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

Detailed information for vg0224219685:

Variant ID: vg0224219685 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 24219685
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.85, C: 0.16, others allele: 0.00, population size: 94. )

Flanking Sequence (100 bp) in Reference Genome:

TTGAAATCTAGGGTATTTTCAGGTGACCAAAATTTACAAGTCCTATATCTCAAATGCTTGTTTTGAAGTTATACGGTACTCGGTGCTTATGATACTACTT[C/T]
CATTTCAAGTTATAAGACGTTTTGACTTTGGTCAAAGTCAAGCTGCTTCAAGTTTGTAGAAAAAATAACAATATTTTCAGCCCAAGATAAATTTATTATG

Reverse complement sequence

CATAATAAATTTATCTTGGGCTGAAAATATTGTTATTTTTTCTACAAACTTGAAGCAGCTTGACTTTGACCAAAGTCAAAACGTCTTATAACTTGAAATG[G/A]
AAGTAGTATCATAAGCACCGAGTACCGTATAACTTCAAAACAAGCATTTGAGATATAGGACTTGTAAATTTTGGTCACCTGAAAATACCCTAGATTTCAA

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	59.90%	39.60%	0.47%	0.02%	NA
All Indica	2759	43.70%	55.80%	0.51%	0.04%	NA
All Japonica	1512	90.60%	8.90%	0.46%	0.00%	NA
Aus	269	48.00%	52.00%	0.00%	0.00%	NA
Indica I	595	39.80%	59.30%	0.84%	0.00%	NA
Indica II	465	58.70%	40.90%	0.22%	0.22%	NA
Indica III	913	30.10%	69.70%	0.22%	0.00%	NA
Indica Intermediate	786	53.40%	45.80%	0.76%	0.00%	NA
Temperate Japonica	767	89.40%	9.80%	0.78%	0.00%	NA
Tropical Japonica	504	92.10%	7.70%	0.20%	0.00%	NA
Japonica Intermediate	241	91.30%	8.70%	0.00%	0.00%	NA
VI/Aromatic	96	58.30%	41.70%	0.00%	0.00%	NA
Intermediate	90	78.90%	20.00%	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
vg0224219685	C -> T	LOC_Os02g40010.1	upstream_gene_variant ; 3620.0bp to feature; MODIFIER	silent_mutation	Average:34.059; most accessible tissue: Zhenshan97 panicle, score: 67.02	N	N	N	N
vg0224219685	C -> T	LOC_Os02g40010.2	upstream_gene_variant ; 3620.0bp to feature; MODIFIER	silent_mutation	Average:34.059; most accessible tissue: Zhenshan97 panicle, score: 67.02	N	N	N	N
vg0224219685	C -> T	LOC_Os02g40010.3	upstream_gene_variant ; 3620.0bp to feature; MODIFIER	silent_mutation	Average:34.059; most accessible tissue: Zhenshan97 panicle, score: 67.02	N	N	N	N
vg0224219685	C -> T	LOC_Os02g40010.4	upstream_gene_variant ; 3620.0bp to feature; MODIFIER	silent_mutation	Average:34.059; most accessible tissue: Zhenshan97 panicle, score: 67.02	N	N	N	N
vg0224219685	C -> T	LOC_Os02g40000-LOC_Os02g40010	intergenic_region ; MODIFIER	silent_mutation	Average:34.059; most accessible tissue: Zhenshan97 panicle, score: 67.02	N	N	N	N
vg0224219685	C -> DEL	N	N	silent_mutation	Average:34.059; most accessible tissue: Zhenshan97 panicle, score: 67.02	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0224219685	1.52E-06	1.52E-06	mr1470	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