Search for Variation information by Variation ID:

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

Detailed information for vg0801451645:

Variant ID: vg0801451645 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 1451645
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AGAGGAGATGAGGTAGCCCGGTCGATGACTAGGCGCAAGCTAGCGCATCTAAAAGTTATCCTATGCTTATTCACACAGTTGTTTAGTTATTTATGTAGTT[T/C]
ATAAACTCCTTATATAAGGTACTGGAATTTCTGTGGGATAGTAAATGAGATCTCCGCCTATGGTGTTCTTCTAGTGTTTGAACAGGTGCACTCACGAGGA

Reverse complement sequence

TCCTCGTGAGTGCACCTGTTCAAACACTAGAAGAACACCATAGGCGGAGATCTCATTTACTATCCCACAGAAATTCCAGTACCTTATATAAGGAGTTTAT[A/G]
AACTACATAAATAACTAAACAACTGTGTGAATAAGCATAGGATAACTTTTAGATGCGCTAGCTTGCGCCTAGTCATCGACCGGGCTACCTCATCTCCTCT

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	79.10%	20.80%	0.15%	0.00%	NA
All Indica	2759	68.00%	31.90%	0.14%	0.00%	NA
All Japonica	1512	99.30%	0.70%	0.00%	0.00%	NA
Aus	269	98.10%	1.90%	0.00%	0.00%	NA
Indica I	595	73.80%	26.10%	0.17%	0.00%	NA
Indica II	465	95.30%	4.70%	0.00%	0.00%	NA
Indica III	913	43.50%	56.30%	0.22%	0.00%	NA
Indica Intermediate	786	75.80%	24.00%	0.13%	0.00%	NA
Temperate Japonica	767	99.60%	0.40%	0.00%	0.00%	NA
Tropical Japonica	504	99.60%	0.40%	0.00%	0.00%	NA
Japonica Intermediate	241	97.90%	2.10%	0.00%	0.00%	NA
VI/Aromatic	96	17.70%	79.20%	3.12%	0.00%	NA
Intermediate	90	88.90%	11.10%	0.00%	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
vg0801451645	T -> C	LOC_Os08g03150.1	upstream_gene_variant ; 1151.0bp to feature; MODIFIER	silent_mutation	Average:70.331; most accessible tissue: Zhenshan97 panicle, score: 83.904	N	N	N	N
vg0801451645	T -> C	LOC_Os08g03160.1	downstream_gene_variant ; 2511.0bp to feature; MODIFIER	silent_mutation	Average:70.331; most accessible tissue: Zhenshan97 panicle, score: 83.904	N	N	N	N
vg0801451645	T -> C	LOC_Os08g03150-LOC_Os08g03160	intergenic_region ; MODIFIER	silent_mutation	Average:70.331; most accessible tissue: Zhenshan97 panicle, score: 83.904	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0801451645	NA	9.76E-07	mr1274	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
vg0801451645	2.39E-07	1.28E-20	mr1739	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
vg0801451645	2.70E-07	1.52E-18	mr1739	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
vg0801451645	NA	2.53E-07	mr1758	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
vg0801451645	NA	2.31E-15	mr1739_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
vg0801451645	NA	2.04E-13	mr1739_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