Search for Variation information by Variation ID:

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

Detailed information for vg1128321535:

Variant ID: vg1128321535 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 28321535
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CACAAATCTATACATATAATTTTTACATTTTCAAACTCAACAACTTGAGAGTTATTCATGATTTATATTCCTAAGGTTTGACTTAAACATTGTCCTAAAC[G/A]
ACTTTCTTTATGAGTATGGAGGGAGTATGATCGTGCCTGTTGGGCCGGGTCAATGAATTGAAGTCGTCGTTTGTCTCGTTTATTAATTTTACTCCAACGA

Reverse complement sequence

TCGTTGGAGTAAAATTAATAAACGAGACAAACGACGACTTCAATTCATTGACCCGGCCCAACAGGCACGATCATACTCCCTCCATACTCATAAAGAAAGT[C/T]
GTTTAGGACAATGTTTAAGTCAAACCTTAGGAATATAAATCATGAATAACTCTCAAGTTGTTGAGTTTGAAAATGTAAAAATTATATGTATAGATTTGTG

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	19.60%	1.60%	13.03%	65.72%	NA
All Indica	2759	23.30%	2.60%	19.50%	54.55%	NA
All Japonica	1512	14.90%	0.10%	2.65%	82.34%	NA
Aus	269	12.30%	0.40%	5.58%	81.78%	NA
Indica I	595	26.40%	0.30%	16.30%	56.97%	NA
Indica II	465	14.40%	0.00%	27.53%	58.06%	NA
Indica III	913	25.80%	4.20%	20.15%	49.84%	NA
Indica Intermediate	786	23.30%	4.20%	16.41%	56.11%	NA
Temperate Japonica	767	19.00%	0.00%	2.09%	78.88%	NA
Tropical Japonica	504	7.70%	0.20%	3.57%	88.49%	NA
Japonica Intermediate	241	16.60%	0.40%	2.49%	80.50%	NA
VI/Aromatic	96	6.20%	0.00%	2.08%	91.67%	NA
Intermediate	90	22.20%	1.10%	23.33%	53.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1128321535	G -> A	LOC_Os11g47110.1	upstream_gene_variant ; 191.0bp to feature; MODIFIER	silent_mutation	Average:14.97; most accessible tissue: Callus, score: 81.789	N	N	N	N
vg1128321535	G -> A	LOC_Os11g47100-LOC_Os11g47110	intergenic_region ; MODIFIER	silent_mutation	Average:14.97; most accessible tissue: Callus, score: 81.789	N	N	N	N
vg1128321535	G -> DEL	N	N	silent_mutation	Average:14.97; most accessible tissue: Callus, score: 81.789	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1128321535	2.51E-06	2.51E-06	mr1542_2	Jap_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