Search for Variation information by Variation ID:

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

Detailed information for vg0713636558:

Variant ID: vg0713636558 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 13636558
Reference Allele: C	Alternative Allele: T
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CGGTGGATTCGGCCATTGTCATCGTGGTCGGTGTTAGAGTTTGTGTCGAATATGTGTAGGTCTCGACTGAACTCCGTTATCAAATATCGTGCCTCGGTGT[C/T]
GTCATCGTGTTTGGATCTCCTATGACGTTTCTTCCGCGTTTGATCTCCGATGTGATTTTGAGGCCGGTTTTATAACAGTCGGCATCCGGTGGATCCGGCC

Reverse complement sequence

GGCCGGATCCACCGGATGCCGACTGTTATAAAACCGGCCTCAAAATCACATCGGAGATCAAACGCGGAAGAAACGTCATAGGAGATCCAAACACGATGAC[G/A]
ACACCGAGGCACGATATTTGATAACGGAGTTCAGTCGAGACCTACACATATTCGACACAAACTCTAACACCGACCACGATGACAATGGCCGAATCCACCG

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	63.20%	34.80%	0.19%	1.78%	NA
All Indica	2759	94.80%	5.10%	0.11%	0.04%	NA
All Japonica	1512	2.60%	96.90%	0.00%	0.46%	NA
Aus	269	95.20%	0.70%	1.12%	2.97%	NA
Indica I	595	97.10%	2.50%	0.34%	0.00%	NA
Indica II	465	95.50%	4.50%	0.00%	0.00%	NA
Indica III	913	99.80%	0.20%	0.00%	0.00%	NA
Indica Intermediate	786	86.80%	13.00%	0.13%	0.13%	NA
Temperate Japonica	767	1.00%	98.80%	0.00%	0.13%	NA
Tropical Japonica	504	4.40%	95.20%	0.00%	0.40%	NA
Japonica Intermediate	241	4.10%	94.20%	0.00%	1.66%	NA
VI/Aromatic	96	27.10%	3.10%	3.12%	66.67%	NA
Intermediate	90	55.60%	40.00%	0.00%	4.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0713636558	C -> DEL	N	N	silent_mutation	Average:59.498; most accessible tissue: Zhenshan97 flower, score: 76.539	N	N	N	N
vg0713636558	C -> T	LOC_Os07g24050.1	upstream_gene_variant ; 1710.0bp to feature; MODIFIER	silent_mutation	Average:59.498; most accessible tissue: Zhenshan97 flower, score: 76.539	N	N	N	N
vg0713636558	C -> T	LOC_Os07g24030-LOC_Os07g24050	intergenic_region ; MODIFIER	silent_mutation	Average:59.498; most accessible tissue: Zhenshan97 flower, score: 76.539	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0713636558	4.33E-06	NA	mr1004	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
vg0713636558	NA	3.57E-09	mr1005	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
vg0713636558	8.37E-07	NA	mr1005	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
vg0713636558	2.78E-06	NA	mr1011	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
vg0713636558	NA	1.37E-28	mr1075	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
vg0713636558	NA	4.51E-23	mr1888	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
vg0713636558	NA	4.01E-09	mr1222_2	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