Search for Variation information by Variation ID:

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

Detailed information for vg0900355549:

Variant ID: vg0900355549 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 355549
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: 331. )

Flanking Sequence (100 bp) in Reference Genome:

AGGAGCTGGTACCAGCTTCGGACTTTTTGCTTGGGGACTTTCCAACTCCATCTCCAGAAGGTATAGGCACATCATGGGACCCCACTTTGATAGTAATTAC[T/C]
TCCGAAGTCCTCTCTTCCACCTTGACGCGCTTTCCTTCCCTCTTTTCTTCATTAGCCCGATTTTTACCATAAAATCGGCTATTGTTTGGTGAAGACAAAT

Reverse complement sequence

ATTTGTCTTCACCAAACAATAGCCGATTTTATGGTAAAAATCGGGCTAATGAAGAAAAGAGGGAAGGAAAGCGCGTCAAGGTGGAAGAGAGGACTTCGGA[A/G]
GTAATTACTATCAAAGTGGGGTCCCATGATGTGCCTATACCTTCTGGAGATGGAGTTGGAAAGTCCCCAAGCAAAAAGTCCGAAGCTGGTACCAGCTCCT

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	86.10%	0.10%	3.98%	9.80%	NA
All Indica	2759	85.60%	0.10%	6.05%	8.23%	NA
All Japonica	1512	87.30%	0.10%	0.33%	12.30%	NA
Aus	269	77.30%	0.40%	5.58%	16.73%	NA
Indica I	595	71.60%	0.00%	12.10%	16.30%	NA
Indica II	465	87.30%	0.40%	6.02%	6.24%	NA
Indica III	913	94.90%	0.20%	1.31%	3.61%	NA
Indica Intermediate	786	84.40%	0.00%	7.00%	8.65%	NA
Temperate Japonica	767	76.40%	0.00%	0.65%	22.95%	NA
Tropical Japonica	504	99.40%	0.20%	0.00%	0.40%	NA
Japonica Intermediate	241	96.70%	0.00%	0.00%	3.32%	NA
VI/Aromatic	96	99.00%	1.00%	0.00%	0.00%	NA
Intermediate	90	93.30%	0.00%	1.11%	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
vg0900355549	T -> DEL	LOC_Os09g01480.1	N	frameshift_variant	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N
vg0900355549	T -> C	LOC_Os09g01480.1	synonymous_variant ; p.Glu303Glu; LOW	synonymous_codon	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0900355549	2.27E-06	2.35E-07	mr1274_2	Jap_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