Search for Variation information by Variation ID:

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

Detailed information for vg0623683404:

Variant ID: vg0623683404 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 23683404
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GTGAAACATTTTCGATCTACTTAGTGAAACAATTCCGATATACCTGGTGAAACATCGTGCAACATTTAAAAATAATTTAATAATAAGCTAATTTTTTTTC[G/A]
TCGGAATATATCCATGTGTGGTCTTGTTTTGAAGATTTAATTGCAACGAATTTAATGGTGCAATCGGATCATGATTTGGATAAGTAATTTAAGAGAAAAT

Reverse complement sequence

ATTTTCTCTTAAATTACTTATCCAAATCATGATCCGATTGCACCATTAAATTCGTTGCAATTAAATCTTCAAAACAAGACCACACATGGATATATTCCGA[C/T]
GAAAAAAAATTAGCTTATTATTAAATTATTTTTAAATGTTGCACGATGTTTCACCAGGTATATCGGAATTGTTTCACTAAGTAGATCGAAAATGTTTCAC

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	94.30%	0.60%	0.34%	4.78%	NA
All Indica	2759	91.60%	0.90%	0.43%	7.07%	NA
All Japonica	1512	99.50%	0.10%	0.00%	0.40%	NA
Aus	269	90.00%	0.70%	1.49%	7.81%	NA
Indica I	595	94.80%	0.00%	0.50%	4.71%	NA
Indica II	465	86.90%	1.90%	0.00%	11.18%	NA
Indica III	913	93.00%	0.90%	0.33%	5.81%	NA
Indica Intermediate	786	90.30%	1.00%	0.76%	7.89%	NA
Temperate Japonica	767	99.50%	0.10%	0.00%	0.39%	NA
Tropical Japonica	504	99.80%	0.00%	0.00%	0.20%	NA
Japonica Intermediate	241	99.20%	0.00%	0.00%	0.83%	NA
VI/Aromatic	96	96.90%	1.00%	0.00%	2.08%	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
vg0623683404	G -> A	LOC_Os06g39870.1	upstream_gene_variant ; 1775.0bp to feature; MODIFIER	silent_mutation	Average:22.023; most accessible tissue: Zhenshan97 panicle, score: 59.59	N	N	N	N
vg0623683404	G -> A	LOC_Os06g39860-LOC_Os06g39870	intergenic_region ; MODIFIER	silent_mutation	Average:22.023; most accessible tissue: Zhenshan97 panicle, score: 59.59	N	N	N	N
vg0623683404	G -> DEL	N	N	silent_mutation	Average:22.023; most accessible tissue: Zhenshan97 panicle, score: 59.59	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0623683404	6.10E-06	NA	mr1829_2	Ind_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
vg0623683404	3.57E-06	NA	mr1902_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