Search for Variation information by Variation ID:

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

Detailed information for vg0625359035:

Variant ID: vg0625359035 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 25359035
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 277. )

Flanking Sequence (100 bp) in Reference Genome:

TATGATGCTAACAATCAATTACTACCTCTTGCATTTGCTATTGTGGAGAAGGAAGATAGTGCAAACTGGGGGTGGTTTATGAGATGGCTACGAAGTAAGG[T/C]
AATAGGCTATGGAAAGTTTATGTGTGTTATATCTGATCGACATAAAGCCATAAAATGGTTGTTTAAGCAGCCCCACATTGGATGGAATGAGAGCGTCGGT

Reverse complement sequence

ACCGACGCTCTCATTCCATCCAATGTGGGGCTGCTTAAACAACCATTTTATGGCTTTATGTCGATCAGATATAACACACATAAACTTTCCATAGCCTATT[A/G]
CCTTACTTCGTAGCCATCTCATAAACCACCCCCAGTTTGCACTATCTTCCTTCTCCACAATAGCAAATGCAAGAGGTAGTAATTGATTGTTAGCATCATA

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	92.20%	1.60%	6.20%	0.00%	NA
All Indica	2759	87.00%	2.60%	10.37%	0.00%	NA
All Japonica	1512	100.00%	0.00%	0.00%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	94.30%	0.00%	5.71%	0.00%	NA
Indica II	465	86.20%	2.80%	10.97%	0.00%	NA
Indica III	913	83.50%	4.40%	12.16%	0.00%	NA
Indica Intermediate	786	86.10%	2.40%	11.45%	0.00%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	100.00%	0.00%	0.00%	0.00%	NA
VI/Aromatic	96	99.00%	0.00%	1.04%	0.00%	NA
Intermediate	90	90.00%	3.30%	6.67%	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
vg0625359035	T -> C	LOC_Os06g42230.1	splice_donor_variant&intron_variant ; HIGH	splice_donor_variant	Average:23.717; most accessible tissue: Callus, score: 43.12	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0625359035	2.44E-06	3.67E-06	mr1010_2	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