Search for Variation information by Variation ID:

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

Detailed information for vg1224998737:

Variant ID: vg1224998737 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 24998737
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.99, C: 0.00, others allele: 0.00, population size: 318. )

Flanking Sequence (100 bp) in Reference Genome:

AGGCACGCACGCACAACCCAATCAGAAATCAGAATTCAGACATAGTCTAATACTGATGCAGAGCAAATAACAGCAAATTTCAGGACAATGAAACGATTGA[T/C]
TGTTTGGATTGGTTGTTTATTACCATGATCTCCAGTTTCTCTAAGCATGGGAAACACTTCAGAATCTGCTCTATCTCACGGGGCACTCTGTGACCCATAT

Reverse complement sequence

ATATGGGTCACAGAGTGCCCCGTGAGATAGAGCAGATTCTGAAGTGTTTCCCATGCTTAGAGAAACTGGAGATCATGGTAATAAACAACCAATCCAAACA[A/G]
TCAATCGTTTCATTGTCCTGAAATTTGCTGTTATTTGCTCTGCATCAGTATTAGACTATGTCTGAATTCTGATTTCTGATTGGGTTGTGCGTGCGTGCCT

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	91.50%	8.00%	0.51%	0.00%	NA
All Indica	2759	98.30%	1.40%	0.25%	0.00%	NA
All Japonica	1512	92.50%	6.90%	0.66%	0.00%	NA
Aus	269	23.40%	74.30%	2.23%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	99.60%	0.00%	0.43%	0.00%	NA
Indica III	913	98.80%	1.10%	0.11%	0.00%	NA
Indica Intermediate	786	95.70%	3.80%	0.51%	0.00%	NA
Temperate Japonica	767	99.20%	0.30%	0.52%	0.00%	NA
Tropical Japonica	504	88.10%	11.10%	0.79%	0.00%	NA
Japonica Intermediate	241	80.10%	19.10%	0.83%	0.00%	NA
VI/Aromatic	96	75.00%	24.00%	1.04%	0.00%	NA
Intermediate	90	87.80%	12.20%	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
vg1224998737	T -> C	LOC_Os12g40360.1	upstream_gene_variant ; 2276.0bp to feature; MODIFIER	silent_mutation	Average:54.516; most accessible tissue: Zhenshan97 flower, score: 65.164	N	N	N	N
vg1224998737	T -> C	LOC_Os12g40380.1	downstream_gene_variant ; 3229.0bp to feature; MODIFIER	silent_mutation	Average:54.516; most accessible tissue: Zhenshan97 flower, score: 65.164	N	N	N	N
vg1224998737	T -> C	LOC_Os12g40370.1	intron_variant ; MODIFIER	silent_mutation	Average:54.516; most accessible tissue: Zhenshan97 flower, score: 65.164	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1224998737	3.44E-07	NA	Grain_width	All	YES	Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg1224998737	NA	3.01E-07	mr1064_2	Jap_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
vg1224998737	NA	1.20E-06	mr1456_2	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
vg1224998737	NA	8.70E-06	mr1740_2	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