Search for Variation information by Variation ID:

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

Detailed information for vg0710573623:

Variant ID: vg0710573623 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 10573623
Reference Allele: A	Alternative Allele: G
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.94, A: 0.07, others allele: 0.00, population size: 204. )

Flanking Sequence (100 bp) in Reference Genome:

CGCGGAGATCGACGGTCTTGTGTAGTCGATGGCGCCGCTTGCCGAGAAGGTTTTCTGCTCCATGCATTGGCGTTGGCCGTCCTGGTAGCTTTTGTATCCT[A/G]
TAGAAAAATATCTCAAGGAAGCATGTAATATACTTTGAAGTATTTGTGACTTGTAAGAAATACTTGTAAAATATAAATGGAATCTATCTAAGTTTTCTTA

Reverse complement sequence

TAAGAAAACTTAGATAGATTCCATTTATATTTTACAAGTATTTCTTACAAGTCACAAATACTTCAAAGTATATTACATGCTTCCTTGAGATATTTTTCTA[T/C]
AGGATACAAAAGCTACCAGGACGGCCAACGCCAATGCATGGAGCAGAAAACCTTCTCGGCAAGCGGCGCCATCGACTACACAAGACCGTCGATCTCCGCG

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	87.50%	9.80%	2.71%	0.00%	NA
All Indica	2759	98.70%	1.20%	0.14%	0.00%	NA
All Japonica	1512	69.50%	23.50%	7.01%	0.00%	NA
Aus	269	92.20%	6.70%	1.12%	0.00%	NA
Indica I	595	99.50%	0.30%	0.17%	0.00%	NA
Indica II	465	98.10%	1.50%	0.43%	0.00%	NA
Indica III	913	98.60%	1.40%	0.00%	0.00%	NA
Indica Intermediate	786	98.50%	1.40%	0.13%	0.00%	NA
Temperate Japonica	767	56.70%	33.10%	10.17%	0.00%	NA
Tropical Japonica	504	86.70%	11.30%	1.98%	0.00%	NA
Japonica Intermediate	241	74.30%	18.30%	7.47%	0.00%	NA
VI/Aromatic	96	41.70%	47.90%	10.42%	0.00%	NA
Intermediate	90	81.10%	13.30%	5.56%	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
vg0710573623	A -> G	LOC_Os07g17870.1	upstream_gene_variant ; 3001.0bp to feature; MODIFIER	silent_mutation	Average:46.961; most accessible tissue: Minghui63 flag leaf, score: 67.099	N	N	N	N
vg0710573623	A -> G	LOC_Os07g17860.1	downstream_gene_variant ; 76.0bp to feature; MODIFIER	silent_mutation	Average:46.961; most accessible tissue: Minghui63 flag leaf, score: 67.099	N	N	N	N
vg0710573623	A -> G	LOC_Os07g17860-LOC_Os07g17870	intergenic_region ; MODIFIER	silent_mutation	Average:46.961; most accessible tissue: Minghui63 flag leaf, score: 67.099	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0710573623	7.14E-07	2.35E-08	mr1955	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