Search for Variation information by Variation ID:

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

Detailed information for vg0825997865:

Variant ID: vg0825997865 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 25997865
Reference Allele: C	Alternative Allele: T
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AGCTCCGGGCAGCCGTGCATCTCGGCGCAGCCCAGCGTCGTCGCCACCGTCTCCACTGACACGCTCTCCCACAGCTTCTGGGCGCACATCAGCTTCAGCC[C/T]
GTCCAGCGCGTACCTGTCCGCCGCCGCGAGCAAACGCTGATGATGAAGCAGATGATCGCTCGTGCTCGCCGTCGTCGACGACGATGAGCCCTCGATGATC

Reverse complement sequence

GATCATCGAGGGCTCATCGTCGTCGACGACGGCGAGCACGAGCGATCATCTGCTTCATCATCAGCGTTTGCTCGCGGCGGCGGACAGGTACGCGCTGGAC[G/A]
GGCTGAAGCTGATGTGCGCCCAGAAGCTGTGGGAGAGCGTGTCAGTGGAGACGGTGGCGACGACGCTGGGCTGCGCCGAGATGCACGGCTGCCCGGAGCT

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	64.60%	35.30%	0.17%	0.02%	NA
All Indica	2759	98.40%	1.30%	0.25%	0.04%	NA
All Japonica	1512	3.00%	97.00%	0.00%	0.00%	NA
Aus	269	81.40%	18.60%	0.00%	0.00%	NA
Indica I	595	99.20%	0.50%	0.17%	0.17%	NA
Indica II	465	98.30%	1.50%	0.22%	0.00%	NA
Indica III	913	99.30%	0.40%	0.22%	0.00%	NA
Indica Intermediate	786	96.80%	2.80%	0.38%	0.00%	NA
Temperate Japonica	767	2.50%	97.50%	0.00%	0.00%	NA
Tropical Japonica	504	2.20%	97.80%	0.00%	0.00%	NA
Japonica Intermediate	241	6.60%	93.40%	0.00%	0.00%	NA
VI/Aromatic	96	21.90%	78.10%	0.00%	0.00%	NA
Intermediate	90	55.60%	43.30%	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
vg0825997865	C -> T	LOC_Os08g41150.1	missense_variant ; p.Gly279Arg; MODERATE	nonsynonymous_codon ; G279R	Average:70.712; most accessible tissue: Zhenshan97 panicle, score: 84.824	unknown	unknown	TOLERATED	1.00
vg0825997865	C -> DEL	LOC_Os08g41150.1	N	frameshift_variant	Average:70.712; most accessible tissue: Zhenshan97 panicle, score: 84.824	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0825997865	NA	6.32E-22	mr1021	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
vg0825997865	NA	4.92E-26	mr1024	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
vg0825997865	NA	8.77E-16	mr1323	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
vg0825997865	NA	1.69E-20	mr1477	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
vg0825997865	NA	2.22E-37	mr1601	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
vg0825997865	NA	2.73E-38	mr1689_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