Search for Variation information by Variation ID:

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

Detailed information for vg0805182138:

Variant ID: vg0805182138 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 5182138
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.92, T: 0.08, others allele: 0.00, population size: 97. )

Flanking Sequence (100 bp) in Reference Genome:

TAGGGCTAGGGCGGCAGAGGCTGTGAGAGGGCGGCCAAGATCAATTTGAGTGGCGGGAGGCCACGTTTGAATACTTACCGGCGAAGGATTGGCTTGACCG[C/T]
GTGCGAATTCGGCTGGTGACGTGTTGGCGCCAATCCAAGCGCGACGCGTGGCGGCGGCGATGGTGAAAACGGCCGACTCGGGGGTGAATGGTTTGAATTG

Reverse complement sequence

CAATTCAAACCATTCACCCCCGAGTCGGCCGTTTTCACCATCGCCGCCGCCACGCGTCGCGCTTGGATTGGCGCCAACACGTCACCAGCCGAATTCGCAC[G/A]
CGGTCAAGCCAATCCTTCGCCGGTAAGTATTCAAACGTGGCCTCCCGCCACTCAAATTGATCTTGGCCGCCCTCTCACAGCCTCTGCCGCCCTAGCCCTA

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	81.10%	16.40%	0.59%	1.82%	NA
All Indica	2759	83.30%	12.90%	0.91%	2.90%	NA
All Japonica	1512	73.20%	26.70%	0.07%	0.00%	NA
Aus	269	98.90%	0.00%	0.37%	0.74%	NA
Indica I	595	94.30%	5.70%	0.00%	0.00%	NA
Indica II	465	68.60%	30.50%	0.00%	0.86%	NA
Indica III	913	81.90%	10.00%	2.19%	5.91%	NA
Indica Intermediate	786	85.40%	11.20%	0.64%	2.80%	NA
Temperate Japonica	767	88.70%	11.30%	0.00%	0.00%	NA
Tropical Japonica	504	54.40%	45.40%	0.20%	0.00%	NA
Japonica Intermediate	241	63.50%	36.50%	0.00%	0.00%	NA
VI/Aromatic	96	94.80%	1.00%	1.04%	3.12%	NA
Intermediate	90	80.00%	18.90%	0.00%	1.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0805182138	C -> T	LOC_Os08g08910.1	upstream_gene_variant ; 617.0bp to feature; MODIFIER	silent_mutation	Average:55.756; most accessible tissue: Zhenshan97 panicle, score: 79.071	N	N	N	N
vg0805182138	C -> T	LOC_Os08g08920.1	upstream_gene_variant ; 4737.0bp to feature; MODIFIER	silent_mutation	Average:55.756; most accessible tissue: Zhenshan97 panicle, score: 79.071	N	N	N	N
vg0805182138	C -> T	LOC_Os08g08900.1	downstream_gene_variant ; 3863.0bp to feature; MODIFIER	silent_mutation	Average:55.756; most accessible tissue: Zhenshan97 panicle, score: 79.071	N	N	N	N
vg0805182138	C -> T	LOC_Os08g08910-LOC_Os08g08920	intergenic_region ; MODIFIER	silent_mutation	Average:55.756; most accessible tissue: Zhenshan97 panicle, score: 79.071	N	N	N	N
vg0805182138	C -> DEL	N	N	silent_mutation	Average:55.756; most accessible tissue: Zhenshan97 panicle, score: 79.071	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0805182138	2.12E-06	2.11E-06	mr1197_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
vg0805182138	NA	4.36E-06	mr1646_2	Jap_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