Search for Variation information by Variation ID:

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

Detailed information for vg0101692357:

Variant ID: vg0101692357 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 1692357
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AGATGATGTCGTTGACTTTTTCTCACATGTTTGACCATTCGTCTTATTTAAAAAATTTACATAATTATAATTTATTTTGTTATGAGTTGTTTTATCACTC[A/G]
TAGTACTTTAAGTGTGATTTATATCTTATACATTTGCATAAAATTTTTGAATAAGATGAATGGTCAAACATGTGAGAAAAAGTTAACGACGTCATCTATT

Reverse complement sequence

AATAGATGACGTCGTTAACTTTTTCTCACATGTTTGACCATTCATCTTATTCAAAAATTTTATGCAAATGTATAAGATATAAATCACACTTAAAGTACTA[T/C]
GAGTGATAAAACAACTCATAACAAAATAAATTATAATTATGTAAATTTTTTAAATAAGACGAATGGTCAAACATGTGAGAAAAAGTCAACGACATCATCT

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	95.00%	4.60%	0.36%	0.00%	NA
All Indica	2759	99.80%	0.20%	0.00%	0.00%	NA
All Japonica	1512	85.10%	13.80%	1.06%	0.00%	NA
Aus	269	99.60%	0.40%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	100.00%	0.00%	0.00%	0.00%	NA
Indica III	913	99.90%	0.10%	0.00%	0.00%	NA
Indica Intermediate	786	99.50%	0.50%	0.00%	0.00%	NA
Temperate Japonica	767	96.30%	3.10%	0.52%	0.00%	NA
Tropical Japonica	504	83.30%	16.50%	0.20%	0.00%	NA
Japonica Intermediate	241	53.10%	42.30%	4.56%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	96.70%	2.20%	1.11%	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
vg0101692357	A -> G	LOC_Os01g03940-LOC_Os01g03950	intergenic_region ; MODIFIER	silent_mutation	Average:26.437; most accessible tissue: Zhenshan97 root, score: 44.635	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0101692357	1.68E-06	6.26E-07	mr1209	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