Search for Variation information by Variation ID:

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

Detailed information for vg1208090350:

Variant ID: vg1208090350 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 8090350
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CTCCATCATAAAACCAGATGACTCCTGCCCTTCTTCCAGTATCATCTCCGTGACAATTCTAATGCTTCAGGAAAAACAATTCTAATGCTGGAAGTGATTC[A/G]
TGGCCAGCCTAGGCATAGGTTCCATGTTATTGTAAATGATTCTAGCTACATTATGATATTTTATATTATATAATAGAAATATAAAATATGTTTTGATAGT

Reverse complement sequence

ACTATCAAAACATATTTTATATTTCTATTATATAATATAAAATATCATAATGTAGCTAGAATCATTTACAATAACATGGAACCTATGCCTAGGCTGGCCA[T/C]
GAATCACTTCCAGCATTAGAATTGTTTTTCCTGAAGCATTAGAATTGTCACGGAGATGATACTGGAAGAAGGGCAGGAGTCATCTGGTTTTATGATGGAG

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	93.30%	1.00%	0.91%	4.80%	NA
All Indica	2759	91.30%	0.00%	0.58%	8.12%	NA
All Japonica	1512	95.10%	3.20%	1.72%	0.00%	NA
Aus	269	99.30%	0.00%	0.37%	0.37%	NA
Indica I	595	86.90%	0.00%	0.84%	12.27%	NA
Indica II	465	95.10%	0.00%	0.43%	4.52%	NA
Indica III	913	92.00%	0.00%	0.55%	7.45%	NA
Indica Intermediate	786	91.60%	0.00%	0.51%	7.89%	NA
Temperate Japonica	767	93.60%	3.70%	2.74%	0.00%	NA
Tropical Japonica	504	99.40%	0.00%	0.60%	0.00%	NA
Japonica Intermediate	241	90.90%	8.30%	0.83%	0.00%	NA
VI/Aromatic	96	99.00%	1.00%	0.00%	0.00%	NA
Intermediate	90	97.80%	0.00%	0.00%	2.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1208090350	A -> DEL	N	N	silent_mutation	Average:41.989; most accessible tissue: Zhenshan97 young leaf, score: 67.334	N	N	N	N
vg1208090350	A -> G	LOC_Os12g14240.1	upstream_gene_variant ; 3959.0bp to feature; MODIFIER	silent_mutation	Average:41.989; most accessible tissue: Zhenshan97 young leaf, score: 67.334	N	N	N	N
vg1208090350	A -> G	LOC_Os12g14230-LOC_Os12g14240	intergenic_region ; MODIFIER	silent_mutation	Average:41.989; most accessible tissue: Zhenshan97 young leaf, score: 67.334	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1208090350	1.77E-06	9.20E-08	mr1013	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
vg1208090350	2.16E-07	1.77E-09	mr1031	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
vg1208090350	NA	4.22E-06	mr1034	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
vg1208090350	4.84E-07	1.11E-08	mr1056	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