Search for Variation information by Variation ID:

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

Detailed information for vg0331267762:

Variant ID: vg0331267762 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 31267762
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AAGGCTGCCCCAGGCGCCACATGGCCCTCCCCCGAGGAGGGATCGGGCCCGAGGTCAGACGGCGGCGGCCCCCTCCCGTGACTAGGGGTCGGGCTCCCCC[G/A]
ACCCCCTCTCTAGGTCACCACGTACAGGTGCCCACCTACCCGCATTTATGGCGACCCGAGCGGTCGCTGCGGCGTGCAATGTACTCAACCGATCTGTGAC

Reverse complement sequence

GTCACAGATCGGTTGAGTACATTGCACGCCGCAGCGACCGCTCGGGTCGCCATAAATGCGGGTAGGTGGGCACCTGTACGTGGTGACCTAGAGAGGGGGT[C/T]
GGGGGAGCCCGACCCCTAGTCACGGGAGGGGGCCGCCGCCGTCTGACCTCGGGCCCGATCCCTCCTCGGGGGAGGGCCATGTGGCGCCTGGGGCAGCCTT

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	93.60%	0.20%	2.07%	4.13%	NA
All Indica	2759	89.20%	0.30%	3.55%	6.92%	NA
All Japonica	1512	99.90%	0.00%	0.00%	0.07%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	86.10%	0.20%	7.06%	6.72%	NA
Indica II	465	81.50%	0.40%	6.88%	11.18%	NA
Indica III	913	92.10%	0.20%	0.55%	7.12%	NA
Indica Intermediate	786	92.90%	0.40%	2.42%	4.33%	NA
Temperate Japonica	767	99.90%	0.00%	0.00%	0.13%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	100.00%	0.00%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	96.70%	0.00%	0.00%	3.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0331267762	G -> A	LOC_Os03g54990.1	downstream_gene_variant ; 1365.0bp to feature; MODIFIER	silent_mutation	Average:64.783; most accessible tissue: Zhenshan97 panicle, score: 83.41	N	N	N	N
vg0331267762	G -> A	LOC_Os03g54980-LOC_Os03g54990	intergenic_region ; MODIFIER	silent_mutation	Average:64.783; most accessible tissue: Zhenshan97 panicle, score: 83.41	N	N	N	N
vg0331267762	G -> DEL	N	N	silent_mutation	Average:64.783; most accessible tissue: Zhenshan97 panicle, score: 83.41	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0331267762	2.23E-06	7.06E-06	mr1873	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