Search for Variation information by Variation ID:

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

Detailed information for vg0610205177:

Variant ID: vg0610205177 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 10205177
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.97, T: 0.03, others allele: 0.00, population size: 119. )

Flanking Sequence (100 bp) in Reference Genome:

CAAATCCATCATAATAATAATGTTACATATTTACAAAAGAAAAGAAAATAGCAGCAGATAAACGGTCTAGCGATGGCATCATATCCACTCCCACAGGCAG[C/T]
TTAATTGGGGTATAAGCCAAACGTCTTCTGCTTCGAATCTTTTCTTCAACTGGGGTTTAATTGATTATTGCAAAGTGAGTACATGGAATACTCCGCAAGC

Reverse complement sequence

GCTTGCGGAGTATTCCATGTACTCACTTTGCAATAATCAATTAAACCCCAGTTGAAGAAAAGATTCGAAGCAGAAGACGTTTGGCTTATACCCCAATTAA[G/A]
CTGCCTGTGGGAGTGGATATGATGCCATCGCTAGACCGTTTATCTGCTGCTATTTTCTTTTCTTTTGTAAATATGTAACATTATTATTATGATGGATTTG

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	91.00%	5.00%	0.17%	3.75%	NA
All Indica	2759	88.10%	6.50%	0.25%	5.22%	NA
All Japonica	1512	97.80%	0.80%	0.00%	1.46%	NA
Aus	269	84.40%	15.20%	0.00%	0.37%	NA
Indica I	595	99.80%	0.20%	0.00%	0.00%	NA
Indica II	465	91.60%	2.60%	0.86%	4.95%	NA
Indica III	913	76.50%	12.80%	0.22%	10.51%	NA
Indica Intermediate	786	90.60%	6.10%	0.13%	3.18%	NA
Temperate Japonica	767	97.80%	0.80%	0.00%	1.43%	NA
Tropical Japonica	504	99.40%	0.00%	0.00%	0.60%	NA
Japonica Intermediate	241	94.20%	2.50%	0.00%	3.32%	NA
VI/Aromatic	96	87.50%	4.20%	1.04%	7.29%	NA
Intermediate	90	93.30%	3.30%	0.00%	3.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0610205177	C -> T	LOC_Os06g17580.1	upstream_gene_variant ; 2242.0bp to feature; MODIFIER	silent_mutation	Average:27.62; most accessible tissue: Zhenshan97 young leaf, score: 49.329	N	N	N	N
vg0610205177	C -> T	LOC_Os06g17590.1	upstream_gene_variant ; 3978.0bp to feature; MODIFIER	silent_mutation	Average:27.62; most accessible tissue: Zhenshan97 young leaf, score: 49.329	N	N	N	N
vg0610205177	C -> T	LOC_Os06g17580-LOC_Os06g17590	intergenic_region ; MODIFIER	silent_mutation	Average:27.62; most accessible tissue: Zhenshan97 young leaf, score: 49.329	N	N	N	N
vg0610205177	C -> DEL	N	N	silent_mutation	Average:27.62; most accessible tissue: Zhenshan97 young leaf, score: 49.329	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0610205177	1.31E-07	NA	mr1695	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
vg0610205177	2.36E-07	NA	mr1165_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
vg0610205177	1.90E-10	NA	mr1695_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