Search for Variation information by Variation ID:

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

Detailed information for vg0808279708:

Variant ID: vg0808279708 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 8279708
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GCTGTGGGCGGTGATGGCAGGGACGGCAGTAGGTAGAGTGTAGAGGTCCCCACGACTATTGCAACGAAGAATCACGCGCTGGGTTTGAAGGTCCTTCACA[A/G]
AGAAACCAAACTCGTCAAATTCAATTGAGCATTTGTTGTCGCGGGTAAATTGACGAACAGAAAGTAAGTTTCGAACCAAGGAGGGAGCGACAAGGATGTT

Reverse complement sequence

AACATCCTTGTCGCTCCCTCCTTGGTTCGAAACTTACTTTCTGTTCGTCAATTTACCCGCGACAACAAATGCTCAATTGAATTTGACGAGTTTGGTTTCT[T/C]
TGTGAAGGACCTTCAAACCCAGCGCGTGATTCTTCGTTGCAATAGTCGTGGGGACCTCTACACTCTACCTACTGCCGTCCCTGCCATCACCGCCCACAGC

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	28.90%	24.20%	23.38%	23.47%	NA
All Indica	2759	3.80%	26.10%	37.04%	33.06%	NA
All Japonica	1512	81.60%	8.10%	1.72%	8.60%	NA
Aus	269	0.40%	79.20%	9.67%	10.78%	NA
Indica I	595	5.40%	18.00%	43.53%	33.11%	NA
Indica II	465	5.20%	13.50%	34.19%	47.10%	NA
Indica III	913	1.20%	37.70%	32.20%	28.92%	NA
Indica Intermediate	786	5.00%	26.10%	39.44%	29.52%	NA
Temperate Japonica	767	93.50%	4.30%	0.26%	1.96%	NA
Tropical Japonica	504	75.40%	3.80%	2.78%	18.06%	NA
Japonica Intermediate	241	56.80%	29.00%	4.15%	9.96%	NA
VI/Aromatic	96	0.00%	79.20%	9.38%	11.46%	NA
Intermediate	90	27.80%	17.80%	24.44%	30.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0808279708	A -> G	LOC_Os08g13870.1	downstream_gene_variant ; 3254.0bp to feature; MODIFIER	silent_mutation	Average:9.806; most accessible tissue: Callus, score: 34.609	N	N	N	N
vg0808279708	A -> G	LOC_Os08g13860.1	intron_variant ; MODIFIER	silent_mutation	Average:9.806; most accessible tissue: Callus, score: 34.609	N	N	N	N
vg0808279708	A -> DEL	N	N	silent_mutation	Average:9.806; most accessible tissue: Callus, score: 34.609	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0808279708	2.03E-06	6.51E-09	mr1829	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
vg0808279708	1.73E-07	NA	mr1842	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
vg0808279708	6.91E-08	4.31E-11	mr1829_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
vg0808279708	3.37E-09	3.46E-17	mr1842_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