Search for Variation information by Variation ID:

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

Detailed information for vg0817676420:

Variant ID: vg0817676420 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 17676420
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.99, G: 0.02, others allele: 0.00, population size: 213. )

Flanking Sequence (100 bp) in Reference Genome:

GCATTCACGTGACACTAAACATCATGTTACGTGGTATGTGAGAGTTGCAGTATGTATGTGTTGGGCTTTTTGTTGTACAAAATATGGTCACGATGAAGAT[A/G]
TTACACTCATACTATAAATGGCTTAATATATATTGCAAACTTTACATCTTCGTGAGTCACGGTTTATGGTTGTCGCCGCCATAACGCCATTGCAAGTCCC

Reverse complement sequence

GGGACTTGCAATGGCGTTATGGCGGCGACAACCATAAACCGTGACTCACGAAGATGTAAAGTTTGCAATATATATTAAGCCATTTATAGTATGAGTGTAA[T/C]
ATCTTCATCGTGACCATATTTTGTACAACAAAAAGCCCAACACATACATACTGCAACTCTCACATACCACGTAACATGATGTTTAGTGTCACGTGAATGC

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	60.40%	39.10%	0.25%	0.23%	NA
All Indica	2759	42.70%	56.70%	0.33%	0.36%	NA
All Japonica	1512	83.40%	16.40%	0.20%	0.00%	NA
Aus	269	99.30%	0.70%	0.00%	0.00%	NA
Indica I	595	74.50%	25.00%	0.17%	0.34%	NA
Indica II	465	12.00%	87.70%	0.22%	0.00%	NA
Indica III	913	35.80%	63.50%	0.33%	0.33%	NA
Indica Intermediate	786	44.70%	54.20%	0.51%	0.64%	NA
Temperate Japonica	767	97.00%	3.00%	0.00%	0.00%	NA
Tropical Japonica	504	64.10%	35.50%	0.40%	0.00%	NA
Japonica Intermediate	241	80.50%	19.10%	0.41%	0.00%	NA
VI/Aromatic	96	99.00%	1.00%	0.00%	0.00%	NA
Intermediate	90	62.20%	36.70%	0.00%	1.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0817676420	A -> G	LOC_Os08g28900.1	upstream_gene_variant ; 1490.0bp to feature; MODIFIER	silent_mutation	Average:53.29; most accessible tissue: Minghui63 root, score: 66.549	N	N	N	N
vg0817676420	A -> G	LOC_Os08g28890.1	downstream_gene_variant ; 2036.0bp to feature; MODIFIER	silent_mutation	Average:53.29; most accessible tissue: Minghui63 root, score: 66.549	N	N	N	N
vg0817676420	A -> G	LOC_Os08g28890-LOC_Os08g28900	intergenic_region ; MODIFIER	silent_mutation	Average:53.29; most accessible tissue: Minghui63 root, score: 66.549	N	N	N	N
vg0817676420	A -> DEL	N	N	silent_mutation	Average:53.29; most accessible tissue: Minghui63 root, score: 66.549	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0817676420	NA	1.79E-16	Grain_length	All	Not	Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg0817676420	NA	2.70E-06	mr1040	Jap_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
vg0817676420	NA	8.79E-06	mr1336	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
vg0817676420	1.59E-07	NA	mr1533	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
vg0817676420	NA	1.13E-08	mr1533	Jap_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
vg0817676420	NA	1.49E-06	mr1836	Jap_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
vg0817676420	1.05E-08	NA	mr1980	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
vg0817676420	NA	5.04E-06	mr1980	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
vg0817676420	NA	8.68E-11	mr1980	Jap_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
vg0817676420	NA	2.64E-09	mr1174_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
vg0817676420	NA	7.05E-11	mr1347_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
vg0817676420	NA	1.73E-06	mr1362_2	Jap_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
vg0817676420	1.70E-06	NA	mr1533_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
vg0817676420	NA	4.10E-11	mr1533_2	Jap_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
vg0817676420	NA	6.12E-06	mr1836_2	Jap_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