Search for Variation information by Variation ID:

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

Detailed information for vg0207033740:

Variant ID: vg0207033740 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 7033740
Reference Allele: T	Alternative Allele: A
Primary Allele: T	Secondary Allele: A

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.99, A: 0.01, others allele: 0.00, population size: 300. )

Flanking Sequence (100 bp) in Reference Genome:

CAACATGAAGACCTGAAATAGAGGCAAAACAATCATTGGCCAGTGAAAGCCATACAAGTAAATATTAGCAGTCCAAGTTCAGAGCAAAAGGTACACTAAC[T/A]
AGTAAGATTTAAAGAGGATTAAGTGTACTAAAATTAACACGCAGATTCATTCACTTGTCTAGTTGTCTTACCGCAAGGAAAGTTTGAACTTCATTGTTCA

Reverse complement sequence

TGAACAATGAAGTTCAAACTTTCCTTGCGGTAAGACAACTAGACAAGTGAATGAATCTGCGTGTTAATTTTAGTACACTTAATCCTCTTTAAATCTTACT[A/T]
GTTAGTGTACCTTTTGCTCTGAACTTGGACTGCTAATATTTACTTGTATGGCTTTCACTGGCCAATGATTGTTTTGCCTCTATTTCAGGTCTTCATGTTG

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	65.80%	34.10%	0.08%	0.00%	NA
All Indica	2759	43.80%	56.10%	0.07%	0.00%	NA
All Japonica	1512	97.80%	2.20%	0.00%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	51.10%	48.70%	0.17%	0.00%	NA
Indica II	465	33.80%	66.20%	0.00%	0.00%	NA
Indica III	913	34.70%	65.20%	0.11%	0.00%	NA
Indica Intermediate	786	54.80%	45.20%	0.00%	0.00%	NA
Temperate Japonica	767	98.40%	1.60%	0.00%	0.00%	NA
Tropical Japonica	504	97.00%	3.00%	0.00%	0.00%	NA
Japonica Intermediate	241	97.50%	2.50%	0.00%	0.00%	NA
VI/Aromatic	96	97.90%	2.10%	0.00%	0.00%	NA
Intermediate	90	65.60%	32.20%	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
vg0207033740	T -> A	LOC_Os02g13200.1	intron_variant ; MODIFIER	silent_mutation	Average:55.654; most accessible tissue: Callus, score: 75.191	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0207033740	NA	1.64E-06	mr1045	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