Search for Variation information by Variation ID:

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

Detailed information for vg1005451839:

Variant ID: vg1005451839 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 5451839
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.92, G: 0.08, others allele: 0.00, population size: 49. )

Flanking Sequence (100 bp) in Reference Genome:

TGTAAATTGCGAAACGAATCTTTTAAGCAATTGTGCCATGATTTAACAACGTGATGCTACAGTATTTGCTAATGACAGATTATTTGGGCTTAATAAATTC[A/G]
CCTCGCAGTTTCTAGGCGGAATCTGTAATTTGTTTTGTTATTAGTCCATGTTTAATATTTCAAATATATATGTGTATATCCGATGTGACACGCCAAAATT

Reverse complement sequence

AATTTTGGCGTGTCACATCGGATATACACATATATATTTGAAATATTAAACATGGACTAATAACAAAACAAATTACAGATTCCGCCTAGAAACTGCGAGG[T/C]
GAATTTATTAAGCCCAAATAATCTGTCATTAGCAAATACTGTAGCATCACGTTGTTAAATCATGGCACAATTGCTTAAAAGATTCGTTTCGCAATTTACA

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	66.30%	33.30%	0.34%	0.00%	NA
All Indica	2759	64.60%	35.10%	0.33%	0.00%	NA
All Japonica	1512	63.80%	35.80%	0.33%	0.00%	NA
Aus	269	99.60%	0.40%	0.00%	0.00%	NA
Indica I	595	92.10%	7.90%	0.00%	0.00%	NA
Indica II	465	77.00%	22.40%	0.65%	0.00%	NA
Indica III	913	37.50%	62.20%	0.33%	0.00%	NA
Indica Intermediate	786	67.90%	31.70%	0.38%	0.00%	NA
Temperate Japonica	767	74.60%	25.30%	0.13%	0.00%	NA
Tropical Japonica	504	52.40%	47.40%	0.20%	0.00%	NA
Japonica Intermediate	241	53.50%	45.20%	1.24%	0.00%	NA
VI/Aromatic	96	61.50%	38.50%	0.00%	0.00%	NA
Intermediate	90	67.80%	30.00%	2.22%	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
vg1005451839	A -> G	LOC_Os10g10030.1	upstream_gene_variant ; 2765.0bp to feature; MODIFIER	silent_mutation	Average:33.852; most accessible tissue: Minghui63 root, score: 67.149	N	N	N	N
vg1005451839	A -> G	LOC_Os10g10030-LOC_Os10g10040	intergenic_region ; MODIFIER	silent_mutation	Average:33.852; most accessible tissue: Minghui63 root, score: 67.149	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1005451839	NA	9.48E-06	mr1120	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
vg1005451839	NA	9.50E-06	mr1386	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
vg1005451839	2.53E-06	NA	mr1768	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
vg1005451839	4.62E-06	5.39E-09	mr1768	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
vg1005451839	3.15E-11	NA	mr1768_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
vg1005451839	1.20E-07	2.42E-10	mr1768_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