Search for Variation information by Variation ID:

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

Detailed information for vg0726064673:

Variant ID: vg0726064673 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 26064673
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.76, G: 0.24, others allele: 0.00, population size: 68. )

Flanking Sequence (100 bp) in Reference Genome:

CCGAACCTGTATAAACCCCTTTGGTCTCATCGTCTTTGGGGGATTGAATCCCCTCAAAATCACACAGCTTTGCTCACCAAGTCCTCGAATCTCACCCGCT[A/G]
CCCCCGGCCGAACTCACAAAGGGGGGCCTCACGGTTCCCTGGTGGATGAGTTCATTCTCCGACATAATTATAATATAATCGTAGTGTAATTATATTGTAG

Reverse complement sequence

CTACAATATAATTACACTACGATTATATTATAATTATGTCGGAGAATGAACTCATCCACCAGGGAACCGTGAGGCCCCCCTTTGTGAGTTCGGCCGGGGG[T/C]
AGCGGGTGAGATTCGAGGACTTGGTGAGCAAAGCTGTGTGATTTTGAGGGGATTCAATCCCCCAAAGACGATGAGACCAAAGGGGTTTATACAGGTTCGG

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	39.20%	33.70%	0.59%	26.51%	NA
All Indica	2759	5.90%	54.40%	0.83%	38.82%	NA
All Japonica	1512	96.20%	0.10%	0.07%	3.57%	NA
Aus	269	30.50%	25.30%	0.74%	43.49%	NA
Indica I	595	9.20%	31.10%	0.67%	58.99%	NA
Indica II	465	9.20%	70.30%	1.29%	19.14%	NA
Indica III	913	1.40%	64.50%	0.44%	33.63%	NA
Indica Intermediate	786	6.60%	51.00%	1.15%	41.22%	NA
Temperate Japonica	767	97.10%	0.10%	0.00%	2.74%	NA
Tropical Japonica	504	95.20%	0.00%	0.20%	4.56%	NA
Japonica Intermediate	241	95.40%	0.40%	0.00%	4.15%	NA
VI/Aromatic	96	96.90%	2.10%	0.00%	1.04%	NA
Intermediate	90	66.70%	20.00%	2.22%	11.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0726064673	A -> DEL	N	N	silent_mutation	Average:31.979; most accessible tissue: Minghui63 flag leaf, score: 73.752	N	N	N	N
vg0726064673	A -> G	LOC_Os07g43570.1	upstream_gene_variant ; 1469.0bp to feature; MODIFIER	silent_mutation	Average:31.979; most accessible tissue: Minghui63 flag leaf, score: 73.752	N	N	N	N
vg0726064673	A -> G	LOC_Os07g43570-LOC_Os07g43580	intergenic_region ; MODIFIER	silent_mutation	Average:31.979; most accessible tissue: Minghui63 flag leaf, score: 73.752	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0726064673	2.05E-07	1.38E-13	mr1004_2	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
vg0726064673	NA	5.36E-07	mr1004_2	Ind_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
vg0726064673	NA	8.91E-06	mr1013_2	Ind_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