Search for Variation information by Variation ID:

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

Detailed information for vg1207220776:

Variant ID: vg1207220776 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 7220776
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, others allele: 0.00, population size: 286. )

Flanking Sequence (100 bp) in Reference Genome:

GCAGCTTCCAAAATTCCCCAAGTCTGAAAGAGAGCTCAATGATACATCCATTCAGAACATTCAGGCGGACATGTGCTACTTCATCCACCGTGAGTGCGCA[C/T]
ATCAGCCTGGGCGGTTTTTCGACAACGAAGGAGTCTTAGCCCTGCCGGAGAACGAATCCCTGTCTAACTGGACCAGGCATATAATATAGCTAGGGTTTTG

Reverse complement sequence

CAAAACCCTAGCTATATTATATGCCTGGTCCAGTTAGACAGGGATTCGTTCTCCGGCAGGGCTAAGACTCCTTCGTTGTCGAAAAACCGCCCAGGCTGAT[G/A]
TGCGCACTCACGGTGGATGAAGTAGCACATGTCCGCCTGAATGTTCTGAATGGATGTATCATTGAGCTCTCTTTCAGACTTGGGGAATTTTGGAAGCTGC

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	92.60%	6.40%	0.99%	0.00%	NA
All Indica	2759	88.70%	9.70%	1.59%	0.00%	NA
All Japonica	1512	99.80%	0.20%	0.00%	0.00%	NA
Aus	269	88.10%	10.80%	1.12%	0.00%	NA
Indica I	595	99.50%	0.50%	0.00%	0.00%	NA
Indica II	465	61.70%	33.50%	4.73%	0.00%	NA
Indica III	913	96.80%	2.70%	0.44%	0.00%	NA
Indica Intermediate	786	86.90%	10.80%	2.29%	0.00%	NA
Temperate Japonica	767	99.70%	0.30%	0.00%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	99.60%	0.40%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	97.80%	2.20%	0.00%	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
vg1207220776	C -> T	LOC_Os12g13020.1	missense_variant ; p.His864Tyr; MODERATE	nonsynonymous_codon ; H864Y	Average:16.843; most accessible tissue: Minghui63 young leaf, score: 24.836	unknown	unknown	DELETERIOUS	0.00

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1207220776	1.58E-06	5.12E-11	mr1024_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
vg1207220776	3.23E-06	1.76E-13	mr1565_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