Search for Variation information by Variation ID:

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

Detailed information for vg1215233068:

Variant ID: vg1215233068 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 15233068
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 232. )

Flanking Sequence (100 bp) in Reference Genome:

AATGTGTCTAAACAACGTGAGAAATATACTTGTTCATTTTGTGGAAAATATGGACATATTGTTGGTTTTTGTTTCAGATTAGCTCATAAACAGAAAAAGG[A/G]
GAGAGAGATTGCTTTTGCAAAATCAAAGTGGCAAAAATCTGGTTTTCCCTCGAGGAAACCGGTCAAACCGCAGTGGGTCCCACGGTCAGACCGGCGACCG

Reverse complement sequence

CGGTCGCCGGTCTGACCGTGGGACCCACTGCGGTTTGACCGGTTTCCTCGAGGGAAAACCAGATTTTTGCCACTTTGATTTTGCAAAAGCAATCTCTCTC[T/C]
CCTTTTTCTGTTTATGAGCTAATCTGAAACAAAAACCAACAATATGTCCATATTTTCCACAAAATGAACAAGTATATTTCTCACGTTGTTTAGACACATT

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	32.20%	17.50%	6.45%	43.82%	NA
All Indica	2759	15.40%	26.30%	8.08%	50.16%	NA
All Japonica	1512	66.60%	6.00%	1.92%	25.46%	NA
Aus	269	11.20%	0.00%	14.13%	74.72%	NA
Indica I	595	7.40%	7.90%	7.56%	77.14%	NA
Indica II	465	9.20%	54.80%	5.16%	30.75%	NA
Indica III	913	22.10%	20.90%	9.31%	47.65%	NA
Indica Intermediate	786	17.40%	29.60%	8.78%	44.15%	NA
Temperate Japonica	767	88.30%	4.80%	0.91%	6.00%	NA
Tropical Japonica	504	35.30%	9.90%	2.98%	51.79%	NA
Japonica Intermediate	241	63.10%	1.70%	2.90%	32.37%	NA
VI/Aromatic	96	17.70%	1.00%	10.42%	70.83%	NA
Intermediate	90	48.90%	8.90%	5.56%	36.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1215233068	A -> DEL	N	N	silent_mutation	Average:16.956; most accessible tissue: Minghui63 root, score: 31.271	N	N	N	N
vg1215233068	A -> G	LOC_Os12g26140.1	downstream_gene_variant ; 4363.0bp to feature; MODIFIER	silent_mutation	Average:16.956; most accessible tissue: Minghui63 root, score: 31.271	N	N	N	N
vg1215233068	A -> G	LOC_Os12g26150.1	intron_variant ; MODIFIER	silent_mutation	Average:16.956; most accessible tissue: Minghui63 root, score: 31.271	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1215233068	2.16E-06	2.16E-06	mr1938	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