Search for Variation information by Variation ID:

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

Detailed information for vg0103668688:

Variant ID: vg0103668688 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 3668688
Reference Allele: T	Alternative Allele: C
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, T: 0.02, others allele: 0.00, population size: 268. )

Flanking Sequence (100 bp) in Reference Genome:

AATTCAAAAGTAATTTAAGGAAAAAATTTCTCTGTTTCCAAAGAAAAAGTGAGTAAGCATATAGAGAACACAAAAAACATACCCAATCAAGCACTCCTCC[T/C]
TTCTGATTCGCTAGCCTTCCAAAGTCCAATGCCTTCTGACCAGTGATCAACTCAACCAACAAAACTCCAAACCCAAAAACATCCGTCTTCTCCGATGACT

Reverse complement sequence

AGTCATCGGAGAAGACGGATGTTTTTGGGTTTGGAGTTTTGTTGGTTGAGTTGATCACTGGTCAGAAGGCATTGGACTTTGGAAGGCTAGCGAATCAGAA[A/G]
GGAGGAGTGCTTGATTGGGTATGTTTTTTGTGTTCTCTATATGCTTACTCACTTTTTCTTTGGAAACAGAGAAATTTTTTCCTTAAATTACTTTTGAATT

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	74.20%	25.80%	0.04%	0.00%	NA
All Indica	2759	99.40%	0.60%	0.00%	0.00%	NA
All Japonica	1512	24.50%	75.40%	0.13%	0.00%	NA
Aus	269	98.10%	1.90%	0.00%	0.00%	NA
Indica I	595	99.80%	0.20%	0.00%	0.00%	NA
Indica II	465	99.10%	0.90%	0.00%	0.00%	NA
Indica III	913	99.50%	0.50%	0.00%	0.00%	NA
Indica Intermediate	786	99.20%	0.80%	0.00%	0.00%	NA
Temperate Japonica	767	6.40%	93.40%	0.26%	0.00%	NA
Tropical Japonica	504	55.20%	44.80%	0.00%	0.00%	NA
Japonica Intermediate	241	17.80%	82.20%	0.00%	0.00%	NA
VI/Aromatic	96	71.90%	28.10%	0.00%	0.00%	NA
Intermediate	90	65.60%	34.40%	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
vg0103668688	T -> C	LOC_Os01g07630.1	synonymous_variant ; p.Lys516Lys; LOW	synonymous_codon	Average:55.716; most accessible tissue: Zhenshan97 panicle, score: 75.67	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0103668688	NA	9.45E-15	mr1575_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