Search for Variation information by Variation ID:

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

Detailed information for vg0825196323:

Variant ID: vg0825196323 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 25196323
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.93, A: 0.08, others allele: 0.00, population size: 236. )

Flanking Sequence (100 bp) in Reference Genome:

CGACGAAGCTGGATGACATAGTAGTAGAACCTTGAGCACCAAGTGCCCCTACCTGGCGCGCCACTGTCGACGGGTGATACCCGTAGACCGGATATAGAGG[A/G]
TATTGGGGTACGTTGGTACAGGATCTACGTAAGACGACATCAAGCAGACAAAAGACGAAGATTATACTGGTTCAGGCCCCTTGATAGGTAATAGCCCTAA

Reverse complement sequence

TTAGGGCTATTACCTATCAAGGGGCCTGAACCAGTATAATCTTCGTCTTTTGTCTGCTTGATGTCGTCTTACGTAGATCCTGTACCAACGTACCCCAATA[T/C]
CCTCTATATCCGGTCTACGGGTATCACCCGTCGACAGTGGCGCGCCAGGTAGGGGCACTTGGTGCTCAAGGTTCTACTACTATGTCATCCAGCTTCGTCG

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	68.70%	31.10%	0.13%	0.06%	NA
All Indica	2759	56.80%	43.00%	0.18%	0.11%	NA
All Japonica	1512	99.50%	0.50%	0.00%	0.00%	NA
Aus	269	6.70%	93.30%	0.00%	0.00%	NA
Indica I	595	65.90%	33.60%	0.34%	0.17%	NA
Indica II	465	75.90%	24.10%	0.00%	0.00%	NA
Indica III	913	39.20%	60.70%	0.00%	0.11%	NA
Indica Intermediate	786	58.90%	40.60%	0.38%	0.13%	NA
Temperate Japonica	767	99.50%	0.50%	0.00%	0.00%	NA
Tropical Japonica	504	99.60%	0.40%	0.00%	0.00%	NA
Japonica Intermediate	241	99.60%	0.40%	0.00%	0.00%	NA
VI/Aromatic	96	93.80%	6.20%	0.00%	0.00%	NA
Intermediate	90	77.80%	21.10%	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
vg0825196323	A -> G	LOC_Os08g39810.1	synonymous_variant ; p.Tyr448Tyr; LOW	synonymous_codon	Average:47.608; most accessible tissue: Minghui63 root, score: 58.187	N	N	N	N
vg0825196323	A -> DEL	LOC_Os08g39810.1	N	frameshift_variant	Average:47.608; most accessible tissue: Minghui63 root, score: 58.187	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0825196323	NA	2.70E-07	mr1545	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
vg0825196323	NA	2.13E-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
vg0825196323	NA	2.68E-06	mr1699	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
vg0825196323	2.45E-18	6.15E-43	mr1874	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
vg0825196323	3.27E-17	2.00E-24	mr1874	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
vg0825196323	NA	9.89E-08	mr1004_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
vg0825196323	NA	4.93E-18	mr1587_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
vg0825196323	8.90E-08	NA	mr1699_2	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
vg0825196323	1.27E-07	9.11E-11	mr1699_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
vg0825196323	7.81E-21	1.42E-63	mr1874_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
vg0825196323	5.34E-19	1.36E-32	mr1874_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