Search for Variation information by Variation ID:

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

Detailed information for vg1204011153:

Variant ID: vg1204011153 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 4011153
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GACCCAGTCTTCGTCCTGCGTGTCCTCAACGTGTCGCTTACGTGGCATTAGAGTAAAAAAAATTGTGGGACCAACATATCATTCACACACAAAAAAAAAT[A/G]
GTGGAACCCACCGACATGGGGCCCACATTTCATCCTCACCTCTCCCCCTCTCTCTCTCATTTTTGTCTCTCTTACATTCCATCAGCCGGCCGAAACACGA

Reverse complement sequence

TCGTGTTTCGGCCGGCTGATGGAATGTAAGAGAGACAAAAATGAGAGAGAGAGGGGGAGAGGTGAGGATGAAATGTGGGCCCCATGTCGGTGGGTTCCAC[T/C]
ATTTTTTTTTGTGTGTGAATGATATGTTGGTCCCACAATTTTTTTTACTCTAATGCCACGTAAGCGACACGTTGAGGACACGCAGGACGAAGACTGGGTC

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	27.60%	6.60%	0.23%	65.59%	NA
All Indica	2759	7.10%	0.50%	0.25%	92.10%	NA
All Japonica	1512	62.80%	19.10%	0.07%	18.06%	NA
Aus	269	10.40%	0.00%	0.74%	88.85%	NA
Indica I	595	1.70%	0.20%	0.67%	97.48%	NA
Indica II	465	17.60%	0.90%	0.22%	81.29%	NA
Indica III	913	4.80%	0.10%	0.00%	95.07%	NA
Indica Intermediate	786	7.80%	1.00%	0.25%	90.97%	NA
Temperate Japonica	767	83.60%	11.70%	0.13%	4.56%	NA
Tropical Japonica	504	42.10%	26.40%	0.00%	31.55%	NA
Japonica Intermediate	241	39.80%	27.40%	0.00%	32.78%	NA
VI/Aromatic	96	85.40%	0.00%	0.00%	14.58%	NA
Intermediate	90	54.40%	7.80%	1.11%	36.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1204011153	A -> DEL	N	N	silent_mutation	Average:18.947; most accessible tissue: Callus, score: 69.366	N	N	N	N
vg1204011153	A -> G	LOC_Os12g07900.1	upstream_gene_variant ; 362.0bp to feature; MODIFIER	silent_mutation	Average:18.947; most accessible tissue: Callus, score: 69.366	N	N	N	N
vg1204011153	A -> G	LOC_Os12g07910.1	upstream_gene_variant ; 1131.0bp to feature; MODIFIER	silent_mutation	Average:18.947; most accessible tissue: Callus, score: 69.366	N	N	N	N
vg1204011153	A -> G	LOC_Os12g07900-LOC_Os12g07910	intergenic_region ; MODIFIER	silent_mutation	Average:18.947; most accessible tissue: Callus, score: 69.366	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1204011153	NA	1.81E-06	mr1345	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
vg1204011153	6.12E-06	NA	mr1653	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
vg1204011153	NA	5.36E-06	mr1653	Jap_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