Search for Variation information by Variation ID:

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

Detailed information for vg0131616560:

Variant ID: vg0131616560 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 31616560
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ATTTTTGCATCACTTCTCAGGCAGCTATGTACACGGGAGAAGCAATTCATCATAGCAAAAAATATTGCACTTCCATTTGCACATCAACAAAAGGGCCCCT[G/A]
TGTGAATTCGGTGAAGGCATCCAAACCATATTAGTAGAATTTAGCCATGTGTAATATAGTTTTATAGTCCTATACTCCTATGTGCTCTGTTTCAATGCTA

Reverse complement sequence

TAGCATTGAAACAGAGCACATAGGAGTATAGGACTATAAAACTATATTACACATGGCTAAATTCTACTAATATGGTTTGGATGCCTTCACCGAATTCACA[C/T]
AGGGGCCCTTTTGTTGATGTGCAAATGGAAGTGCAATATTTTTTGCTATGATGAATTGCTTCTCCCGTGTACATAGCTGCCTGAGAAGTGATGCAAAAAT

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	95.80%	2.80%	1.35%	0.00%	NA
All Indica	2759	100.00%	0.00%	0.00%	0.00%	NA
All Japonica	1512	87.20%	8.70%	4.10%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	100.00%	0.00%	0.00%	0.00%	NA
Indica III	913	100.00%	0.00%	0.00%	0.00%	NA
Indica Intermediate	786	100.00%	0.00%	0.00%	0.00%	NA
Temperate Japonica	767	88.80%	9.00%	2.22%	0.00%	NA
Tropical Japonica	504	95.40%	3.00%	1.59%	0.00%	NA
Japonica Intermediate	241	65.10%	19.50%	15.35%	0.00%	NA
VI/Aromatic	96	97.90%	1.00%	1.04%	0.00%	NA
Intermediate	90	97.80%	1.10%	1.11%	0.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0131616560	G -> A	LOC_Os01g54969.1	downstream_gene_variant ; 4427.0bp to feature; MODIFIER	silent_mutation	Average:34.267; most accessible tissue: Zhenshan97 root, score: 72.188	N	N	N	N
vg0131616560	G -> A	LOC_Os01g54980.1	downstream_gene_variant ; 1916.0bp to feature; MODIFIER	silent_mutation	Average:34.267; most accessible tissue: Zhenshan97 root, score: 72.188	N	N	N	N
vg0131616560	G -> A	LOC_Os01g54990.1	downstream_gene_variant ; 607.0bp to feature; MODIFIER	silent_mutation	Average:34.267; most accessible tissue: Zhenshan97 root, score: 72.188	N	N	N	N
vg0131616560	G -> A	LOC_Os01g54980.2	downstream_gene_variant ; 1917.0bp to feature; MODIFIER	silent_mutation	Average:34.267; most accessible tissue: Zhenshan97 root, score: 72.188	N	N	N	N
vg0131616560	G -> A	LOC_Os01g54980-LOC_Os01g54990	intergenic_region ; MODIFIER	silent_mutation	Average:34.267; most accessible tissue: Zhenshan97 root, score: 72.188	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0131616560	6.73E-07	8.78E-11	mr1062	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