Search for Variation information by Variation ID:

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

Detailed information for vg0405051916:

Variant ID: vg0405051916 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 5051916
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: 236. )

Flanking Sequence (100 bp) in Reference Genome:

TTAGCAAGATGATGTTTACGAATAAAAATCAAAAGCTTGCAACATGAGATACATATACGGTTATGTAATGGTTATATGGGCATTAAAATTGGATGAAGAT[A/G]
GATCGCTTTAAAGGTGTGATGTGCGATTTGATTATATGACCGACGTTATGATTGTCCTAACTATTTGATCAAAGGGCATATTTTCCTAGTTAACATAGGA

Reverse complement sequence

TCCTATGTTAACTAGGAAAATATGCCCTTTGATCAAATAGTTAGGACAATCATAACGTCGGTCATATAATCAAATCGCACATCACACCTTTAAAGCGATC[T/C]
ATCTTCATCCAATTTTAATGCCCATATAACCATTACATAACCGTATATGTATCTCATGTTGCAAGCTTTTGATTTTTATTCGTAAACATCATCTTGCTAA

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	90.80%	7.10%	0.17%	1.97%	NA
All Indica	2759	86.80%	11.60%	0.14%	1.45%	NA
All Japonica	1512	96.10%	0.30%	0.13%	3.44%	NA
Aus	269	99.60%	0.00%	0.37%	0.00%	NA
Indica I	595	97.30%	2.20%	0.17%	0.34%	NA
Indica II	465	92.70%	2.20%	0.22%	4.95%	NA
Indica III	913	73.20%	26.60%	0.11%	0.11%	NA
Indica Intermediate	786	91.10%	7.00%	0.13%	1.78%	NA
Temperate Japonica	767	99.60%	0.30%	0.00%	0.13%	NA
Tropical Japonica	504	89.10%	0.40%	0.40%	10.12%	NA
Japonica Intermediate	241	99.60%	0.40%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	88.90%	8.90%	1.11%	1.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0405051916	A -> DEL	N	N	silent_mutation	Average:25.547; most accessible tissue: Zhenshan97 flag leaf, score: 66.824	N	N	N	N
vg0405051916	A -> G	LOC_Os04g09430-LOC_Os04g09450	intergenic_region ; MODIFIER	silent_mutation	Average:25.547; most accessible tissue: Zhenshan97 flag leaf, score: 66.824	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0405051916	2.91E-06	7.40E-08	mr1798_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