Search for Variation information by Variation ID:

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

Detailed information for vg0507057510:

Variant ID: vg0507057510 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 7057510
Reference Allele: A	Alternative Allele: T
Primary Allele: A	Secondary Allele: T

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 286. )

Flanking Sequence (100 bp) in Reference Genome:

AGGCCATGCAAACCGATTGGGGAGGGGAATACCAGCACTTAAATACCTTCTTCCAGCGCATTGGCATTGAGCACCATGTCTCCTGCCCCTATGCGCATCA[A/T]
CAAAACGGTTCTGCCGAGCGCAAACACCGCCATATTGTTTGAAGTTGGCCTTTCCCTGCTAGCCCATGCGTCCATGCCTCTCAAGTTTTGGGATGAAGCT

Reverse complement sequence

AGCTTCATCCCAAAACTTGAGAGGCATGGACGCATGGGCTAGCAGGGAAAGGCCAACTTCAAACAATATGGCGGTGTTTGCGCTCGGCAGAACCGTTTTG[T/A]
TGATGCGCATAGGGGCAGGAGACATGGTGCTCAATGCCAATGCGCTGGAAGAAGGTATTTAAGTGCTGGTATTCCCCTCCCCAATCGGTTTGCATGGCCT

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	92.10%	7.70%	0.23%	0.00%	NA
All Indica	2759	87.20%	12.50%	0.33%	0.00%	NA
All Japonica	1512	99.30%	0.70%	0.07%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	88.90%	10.90%	0.17%	0.00%	NA
Indica II	465	77.40%	21.90%	0.65%	0.00%	NA
Indica III	913	90.50%	9.30%	0.22%	0.00%	NA
Indica Intermediate	786	87.90%	11.70%	0.38%	0.00%	NA
Temperate Japonica	767	98.80%	1.20%	0.00%	0.00%	NA
Tropical Japonica	504	99.80%	0.20%	0.00%	0.00%	NA
Japonica Intermediate	241	99.60%	0.00%	0.41%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	90.00%	8.90%	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
vg0507057510	A -> T	LOC_Os05g12300.1	upstream_gene_variant ; 4481.0bp to feature; MODIFIER	silent_mutation	Average:59.316; most accessible tissue: Zhenshan97 panicle, score: 81.135	N	N	N	N
vg0507057510	A -> T	LOC_Os05g12300.2	upstream_gene_variant ; 4481.0bp to feature; MODIFIER	silent_mutation	Average:59.316; most accessible tissue: Zhenshan97 panicle, score: 81.135	N	N	N	N
vg0507057510	A -> T	LOC_Os05g12300.3	upstream_gene_variant ; 4481.0bp to feature; MODIFIER	silent_mutation	Average:59.316; most accessible tissue: Zhenshan97 panicle, score: 81.135	N	N	N	N
vg0507057510	A -> T	LOC_Os05g12290.1	intron_variant ; MODIFIER	silent_mutation	Average:59.316; most accessible tissue: Zhenshan97 panicle, score: 81.135	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0507057510	7.99E-12	1.08E-10	mr1593	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
vg0507057510	1.94E-10	4.09E-11	mr1593	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
vg0507057510	3.23E-17	2.99E-14	mr1593_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
vg0507057510	6.96E-15	1.55E-16	mr1593_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
vg0507057510	1.90E-06	NA	mr1807_2	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