Search for Variation information by Variation ID:

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

Detailed information for vg0515200431:

Variant ID: vg0515200431 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 15200431
Reference Allele: T	Alternative Allele: G
Primary Allele: T	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GTTTGTGTATATTATTGATCATGAGAAGTACGTGAAAATTTTCAATTCCCGGGAAGCATAGGCCCAGGAGGAATCAAGTGGGAGTTCAGGGACATGCAAC[T/G]
GAGAATCTGCTGAGGTTTTCTCTGACATGATACGGTAAGATTGCCTTTCTTTGATGTTCTGATGAAAATGGAGAAGTTTTGTGCCACACATAGATCTGTT

Reverse complement sequence

AACAGATCTATGTGTGGCACAAAACTTCTCCATTTTCATCAGAACATCAAAGAAAGGCAATCTTACCGTATCATGTCAGAGAAAACCTCAGCAGATTCTC[A/C]
GTTGCATGTCCCTGAACTCCCACTTGATTCCTCCTGGGCCTATGCTTCCCGGGAATTGAAAATTTTCACGTACTTCTCATGATCAATAATATACACAAAC

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	66.10%	21.10%	2.50%	10.26%	NA
All Indica	2759	52.20%	29.40%	3.81%	14.57%	NA
All Japonica	1512	97.40%	0.90%	0.33%	1.32%	NA
Aus	269	27.10%	61.00%	0.74%	11.15%	NA
Indica I	595	64.40%	24.40%	6.89%	4.37%	NA
Indica II	465	64.10%	22.40%	2.80%	10.75%	NA
Indica III	913	45.30%	27.60%	1.97%	25.08%	NA
Indica Intermediate	786	44.00%	39.40%	4.20%	12.34%	NA
Temperate Japonica	767	97.40%	0.00%	0.39%	2.22%	NA
Tropical Japonica	504	97.60%	2.20%	0.20%	0.00%	NA
Japonica Intermediate	241	97.10%	1.20%	0.41%	1.24%	NA
VI/Aromatic	96	67.70%	1.00%	3.12%	28.12%	NA
Intermediate	90	80.00%	10.00%	3.33%	6.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0515200431	T -> DEL	N	N	silent_mutation	Average:38.614; most accessible tissue: Callus, score: 69.114	N	N	N	N
vg0515200431	T -> G	LOC_Os05g26130.1	upstream_gene_variant ; 3040.0bp to feature; MODIFIER	silent_mutation	Average:38.614; most accessible tissue: Callus, score: 69.114	N	N	N	N
vg0515200431	T -> G	LOC_Os05g26130-LOC_Os05g26140	intergenic_region ; MODIFIER	silent_mutation	Average:38.614; most accessible tissue: Callus, score: 69.114	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0515200431	5.31E-07	1.14E-07	mr1413	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
vg0515200431	7.95E-07	7.95E-07	mr1413	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
vg0515200431	NA	2.84E-06	mr1574	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
vg0515200431	NA	3.52E-07	mr1764	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
vg0515200431	NA	4.94E-06	mr1831	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