Search for Variation information by Variation ID:

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

Detailed information for vg0709265984:

Variant ID: vg0709265984 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 9265984
Reference Allele: T	Alternative Allele: A
Primary Allele: T	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CGTATGTTAAAATTGATTTTCGTAGGCCGGTAACATTTTTAATAACTTTGATGGAAACAACCGTTATTATAAAATGTTGTTTTAACCCCGCAAAAAAAAA[T/A]
GTTGTTCTACAATCGTAACTGCTTGTGTTATGGAAAGTAGGCATGGCTTTTCTTTTTAGAAAAAGTACGAATTACCCCCCGAACTATCGCGGTCGACCGA

Reverse complement sequence

TCGGTCGACCGCGATAGTTCGGGGGGTAATTCGTACTTTTTCTAAAAAGAAAAGCCATGCCTACTTTCCATAACACAAGCAGTTACGATTGTAGAACAAC[A/T]
TTTTTTTTTGCGGGGTTAAAACAACATTTTATAATAACGGTTGTTTCCATCAAAGTTATTAAAAATGTTACCGGCCTACGAAAATCAATTTTAACATACG

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	97.80%	2.10%	0.11%	0.00%	NA
All Indica	2759	100.00%	0.00%	0.00%	0.00%	NA
All Japonica	1512	93.10%	6.50%	0.33%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	100.00%	0.00%	0.00%	0.00%	NA
Indica III	913	100.00%	0.00%	0.00%	0.00%	NA
Indica Intermediate	786	100.00%	0.00%	0.00%	0.00%	NA
Temperate Japonica	767	89.80%	9.50%	0.65%	0.00%	NA
Tropical Japonica	504	99.80%	0.20%	0.00%	0.00%	NA
Japonica Intermediate	241	89.60%	10.40%	0.00%	0.00%	NA
VI/Aromatic	96	99.00%	1.00%	0.00%	0.00%	NA
Intermediate	90	98.90%	1.10%	0.00%	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
vg0709265984	T -> A	LOC_Os07g15940.1	upstream_gene_variant ; 3154.0bp to feature; MODIFIER	silent_mutation	Average:42.967; most accessible tissue: Callus, score: 59.686	N	N	N	N
vg0709265984	T -> A	LOC_Os07g15950.1	downstream_gene_variant ; 227.0bp to feature; MODIFIER	silent_mutation	Average:42.967; most accessible tissue: Callus, score: 59.686	N	N	N	N
vg0709265984	T -> A	LOC_Os07g15940-LOC_Os07g15950	intergenic_region ; MODIFIER	silent_mutation	Average:42.967; most accessible tissue: Callus, score: 59.686	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0709265984	9.50E-07	9.50E-07	mr1081_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
vg0709265984	8.72E-06	8.72E-06	mr1256_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
vg0709265984	7.23E-06	7.23E-06	mr1889_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