Search for Variation information by Variation ID:

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

Detailed information for vg1205728884:

Variant ID: vg1205728884 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 5728884
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GTCAGCGCCAAGGTCCTCGATCGAGGCGGCGGCGCAGCGGGGATAGAGAGAAGAGATGGAAGATATGACATATGGGCCCAAGGGTATTTTAGAACTTTCA[C/T]
GCCATTTCTCTCTACTCTTCAACCGAAAATTATTATTTTAATCAGCACGATGTCTATTGCTAAATTACCATGTTTATAGAGTGTTTTCCCCCAAAAGTGA

Reverse complement sequence

TCACTTTTGGGGGAAAACACTCTATAAACATGGTAATTTAGCAATAGACATCGTGCTGATTAAAATAATAATTTTCGGTTGAAGAGTAGAGAGAAATGGC[G/A]
TGAAAGTTCTAAAATACCCTTGGGCCCATATGTCATATCTTCCATCTCTTCTCTCTATCCCCGCTGCGCCGCCGCCTCGATCGAGGACCTTGGCGCTGAC

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	77.30%	0.30%	1.65%	20.67%	NA
All Indica	2759	63.50%	0.50%	2.79%	33.16%	NA
All Japonica	1512	97.60%	0.10%	0.00%	2.31%	NA
Aus	269	91.40%	0.00%	0.37%	8.18%	NA
Indica I	595	13.90%	1.30%	8.74%	75.97%	NA
Indica II	465	83.70%	0.00%	0.86%	15.48%	NA
Indica III	913	85.70%	0.50%	0.77%	13.03%	NA
Indica Intermediate	786	63.40%	0.30%	1.78%	34.61%	NA
Temperate Japonica	767	96.00%	0.10%	0.00%	3.91%	NA
Tropical Japonica	504	99.40%	0.00%	0.00%	0.60%	NA
Japonica Intermediate	241	99.20%	0.00%	0.00%	0.83%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	94.40%	0.00%	0.00%	5.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1205728884	C -> DEL	N	N	silent_mutation	Average:12.772; most accessible tissue: Callus, score: 23.334	N	N	N	N
vg1205728884	C -> T	LOC_Os12g10690.1	upstream_gene_variant ; 215.0bp to feature; MODIFIER	silent_mutation	Average:12.772; most accessible tissue: Callus, score: 23.334	N	N	N	N
vg1205728884	C -> T	LOC_Os12g10700.1	upstream_gene_variant ; 3405.0bp to feature; MODIFIER	silent_mutation	Average:12.772; most accessible tissue: Callus, score: 23.334	N	N	N	N
vg1205728884	C -> T	LOC_Os12g10690-LOC_Os12g10700	intergenic_region ; MODIFIER	silent_mutation	Average:12.772; most accessible tissue: Callus, score: 23.334	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1205728884	NA	6.83E-06	mr1549	Ind_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