Search for Variation information by Variation ID:

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

Detailed information for vg1214380715:

Variant ID: vg1214380715 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 14380715
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.85, A: 0.15, others allele: 0.00, population size: 96. )

Flanking Sequence (100 bp) in Reference Genome:

TTAATTATATTCACCGGAAAAGGATCATGATCAAGCTTCATCTTGGAGCCATCGGTGAACTTCAATCGTCCTTCATCTATGGCCGATTGAACCTGTCGTC[A/G]
AAACACATTGCAATCATTAGTGGAATGAGAATGAGAATCATGCCATTTACAATAAGCTCGACGTTTCAATTCTTCTTGAGATGGTATGATATGGCCTTTA

Reverse complement sequence

TAAAGGCCATATCATACCATCTCAAGAAGAATTGAAACGTCGAGCTTATTGTAAATGGCATGATTCTCATTCTCATTCCACTAATGATTGCAATGTGTTT[T/C]
GACGACAGGTTCAATCGGCCATAGATGAAGGACGATTGAAGTTCACCGATGGCTCCAAGATGAAGCTTGATCATGATCCTTTTCCGGTGAATATAATTAA

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	26.80%	12.60%	1.71%	58.89%	NA
All Indica	2759	16.80%	19.80%	2.61%	60.82%	NA
All Japonica	1512	49.90%	2.80%	0.26%	46.96%	NA
Aus	269	5.20%	0.40%	1.12%	93.31%	NA
Indica I	595	22.20%	1.80%	1.68%	74.29%	NA
Indica II	465	13.80%	35.30%	3.87%	47.10%	NA
Indica III	913	16.50%	22.90%	2.85%	57.72%	NA
Indica Intermediate	786	14.80%	20.60%	2.29%	62.34%	NA
Temperate Japonica	767	79.00%	5.10%	0.13%	15.78%	NA
Tropical Japonica	504	13.30%	0.00%	0.60%	86.11%	NA
Japonica Intermediate	241	34.00%	1.70%	0.00%	64.32%	NA
VI/Aromatic	96	4.20%	1.00%	1.04%	93.75%	NA
Intermediate	90	35.60%	3.30%	1.11%	60.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1214380715	A -> DEL	N	N	silent_mutation	Average:6.922; most accessible tissue: Callus, score: 22.25	N	N	N	N
vg1214380715	A -> G	LOC_Os12g25050.1	intron_variant ; MODIFIER	silent_mutation	Average:6.922; most accessible tissue: Callus, score: 22.25	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1214380715	9.48E-06	NA	mr1326	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