Search for Variation information by Variation ID:

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

Detailed information for vg0221675215:

Variant ID: vg0221675215 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 21675215
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GTTAATTATTGGCCGAAGATGACTTTATTTTCCTATGGGTTATAATTTGATTAGCGTGAACCTTATATATTGGATTGGTTCAGCTAAATGCTATATATAT[G/A]
TATGCTTAGCCATGCTTAGAAACATTAGCTAATTAAAGGGATTAATTATAAACTATGTTATATTATTATTTTAATTATGGTTACATTAAATGGTAGCTCA

Reverse complement sequence

TGAGCTACCATTTAATGTAACCATAATTAAAATAATAATATAACATAGTTTATAATTAATCCCTTTAATTAGCTAATGTTTCTAAGCATGGCTAAGCATA[C/T]
ATATATATAGCATTTAGCTGAACCAATCCAATATATAAGGTTCACGCTAATCAAATTATAACCCATAGGAAAATAAAGTCATCTTCGGCCAATAATTAAC

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	64.40%	0.20%	15.45%	19.93%	NA
All Indica	2759	43.80%	0.30%	24.65%	31.24%	NA
All Japonica	1512	96.80%	0.00%	0.79%	2.45%	NA
Aus	269	78.40%	0.40%	11.52%	9.67%	NA
Indica I	595	48.40%	0.30%	9.24%	42.02%	NA
Indica II	465	28.40%	0.00%	31.61%	40.00%	NA
Indica III	913	46.80%	0.40%	34.06%	18.73%	NA
Indica Intermediate	786	45.90%	0.40%	21.25%	32.44%	NA
Temperate Japonica	767	99.20%	0.00%	0.00%	0.78%	NA
Tropical Japonica	504	92.50%	0.00%	2.18%	5.36%	NA
Japonica Intermediate	241	97.90%	0.00%	0.41%	1.66%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	73.30%	0.00%	7.78%	18.89%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0221675215	G -> A	LOC_Os02g36050.1	upstream_gene_variant ; 1614.0bp to feature; MODIFIER	silent_mutation	Average:19.568; most accessible tissue: Zhenshan97 panicle, score: 24.575	N	N	N	N
vg0221675215	G -> A	LOC_Os02g36060.1	downstream_gene_variant ; 1128.0bp to feature; MODIFIER	silent_mutation	Average:19.568; most accessible tissue: Zhenshan97 panicle, score: 24.575	N	N	N	N
vg0221675215	G -> A	LOC_Os02g36050-LOC_Os02g36060	intergenic_region ; MODIFIER	silent_mutation	Average:19.568; most accessible tissue: Zhenshan97 panicle, score: 24.575	N	N	N	N
vg0221675215	G -> DEL	N	N	silent_mutation	Average:19.568; most accessible tissue: Zhenshan97 panicle, score: 24.575	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0221675215	3.91E-06	2.60E-06	mr1761_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