Search for Variation information by Variation ID:

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

Detailed information for vg0705168219:

Variant ID: vg0705168219 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 5168219
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.93, T: 0.07, others allele: 0.00, population size: 86. )

Flanking Sequence (100 bp) in Reference Genome:

CGGGTACGGCTATTCGAATAGTTTACTCTGATCAGAGGTGTACCACTGTACCCACAAGACACAGCTCCACAACATGTCACCATGCGCCTTAGTACCACCA[C/T]
GGTACCTTGGAAAGGAACTGTGACAATACCTCTCACACTGTCACATCCTGATTTTTGTTTCAGGATTTATAAATTATTTAATAAATTATTATTAGAATTT

Reverse complement sequence

AAATTCTAATAATAATTTATTAAATAATTTATAAATCCTGAAACAAAAATCAGGATGTGACAGTGTGAGAGGTATTGTCACAGTTCCTTTCCAAGGTACC[G/A]
TGGTGGTACTAAGGCGCATGGTGACATGTTGTGGAGCTGTGTCTTGTGGGTACAGTGGTACACCTCTGATCAGAGTAAACTATTCGAATAGCCGTACCCG

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	51.50%	47.00%	1.46%	0.08%	NA
All Indica	2759	27.40%	70.60%	1.78%	0.14%	NA
All Japonica	1512	99.70%	0.30%	0.00%	0.00%	NA
Aus	269	7.10%	86.60%	6.32%	0.00%	NA
Indica I	595	8.60%	88.90%	2.52%	0.00%	NA
Indica II	465	11.80%	86.70%	1.51%	0.00%	NA
Indica III	913	48.40%	50.20%	1.20%	0.22%	NA
Indica Intermediate	786	26.60%	71.10%	2.04%	0.25%	NA
Temperate Japonica	767	99.90%	0.10%	0.00%	0.00%	NA
Tropical Japonica	504	99.60%	0.40%	0.00%	0.00%	NA
Japonica Intermediate	241	99.20%	0.80%	0.00%	0.00%	NA
VI/Aromatic	96	96.90%	3.10%	0.00%	0.00%	NA
Intermediate	90	62.20%	34.40%	3.33%	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
vg0705168219	C -> DEL	N	N	silent_mutation	Average:29.543; most accessible tissue: Minghui63 panicle, score: 59.629	N	N	N	N
vg0705168219	C -> T	LOC_Os07g09710.1	upstream_gene_variant ; 1153.0bp to feature; MODIFIER	silent_mutation	Average:29.543; most accessible tissue: Minghui63 panicle, score: 59.629	N	N	N	N
vg0705168219	C -> T	LOC_Os07g09700.1	downstream_gene_variant ; 4717.0bp to feature; MODIFIER	silent_mutation	Average:29.543; most accessible tissue: Minghui63 panicle, score: 59.629	N	N	N	N
vg0705168219	C -> T	LOC_Os07g09710-LOC_Os07g09720	intergenic_region ; MODIFIER	silent_mutation	Average:29.543; most accessible tissue: Minghui63 panicle, score: 59.629	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0705168219	3.30E-06	NA	mr1794	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