Search for Variation information by Variation ID:

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

Detailed information for vg0809694186:

Variant ID: vg0809694186 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 9694186
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TCGCTTGCCAGATCAATCTAATCCGTTGAATCTTGGTCAACTCTATGTCAAGATTAATCTTAGTCGTCTAAAATCGATATAAATCCGTTCCCTCTTTTCA[A/G]
TGGCATATTATTTCTTTTTAATATATGTCATCTACCAAATATAATCTAATCTATTTCCGGAGGTTGTTTTTATCTTAGTTATAAATCATTTGTAAATGGT

Reverse complement sequence

ACCATTTACAAATGATTTATAACTAAGATAAAAACAACCTCCGGAAATAGATTAGATTATATTTGGTAGATGACATATATTAAAAAGAAATAATATGCCA[T/C]
TGAAAAGAGGGAACGGATTTATATCGATTTTAGACGACTAAGATTAATCTTGACATAGAGTTGACCAAGATTCAACGGATTAGATTGATCTGGCAAGCGA

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	83.70%	2.70%	10.58%	3.03%	NA
All Indica	2759	89.50%	0.90%	9.35%	0.25%	NA
All Japonica	1512	77.40%	6.60%	7.08%	8.86%	NA
Aus	269	75.50%	0.00%	24.54%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	65.60%	3.70%	30.11%	0.65%	NA
Indica III	913	93.10%	0.30%	6.24%	0.33%	NA
Indica Intermediate	786	91.50%	0.60%	7.76%	0.13%	NA
Temperate Japonica	767	95.80%	0.00%	2.09%	2.09%	NA
Tropical Japonica	504	49.40%	17.90%	13.29%	19.44%	NA
Japonica Intermediate	241	77.60%	4.10%	9.96%	8.30%	NA
VI/Aromatic	96	34.40%	2.10%	62.50%	1.04%	NA
Intermediate	90	87.80%	1.10%	10.00%	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
vg0809694186	A -> G	LOC_Os08g15900.1	downstream_gene_variant ; 4173.0bp to feature; MODIFIER	silent_mutation	Average:33.053; most accessible tissue: Zhenshan97 flag leaf, score: 62.519	N	N	N	N
vg0809694186	A -> G	LOC_Os08g15910.1	downstream_gene_variant ; 1645.0bp to feature; MODIFIER	silent_mutation	Average:33.053; most accessible tissue: Zhenshan97 flag leaf, score: 62.519	N	N	N	N
vg0809694186	A -> G	LOC_Os08g15920.1	intron_variant ; MODIFIER	silent_mutation	Average:33.053; most accessible tissue: Zhenshan97 flag leaf, score: 62.519	N	N	N	N
vg0809694186	A -> DEL	N	N	silent_mutation	Average:33.053; most accessible tissue: Zhenshan97 flag leaf, score: 62.519	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0809694186	9.21E-08	NA	mr1301_2	Jap_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