Search for Variation information by Variation ID:

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

Detailed information for vg0524661216:

Variant ID: vg0524661216 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 24661216
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, others allele: 0.00, population size: 254. )

Flanking Sequence (100 bp) in Reference Genome:

GGCCCGGGTGGCCGGTTGAAAAGCTGTTGGCCGGGTGCCAATCTTGTGTCATTTCTAAAGACTGATACATTGCACATACTCCGACCGGACGAGACGCACT[G/A]
TCTCATCCGCGTCGTTTGAGAAGCACTCACCTAGTTGTTTTTAGAAAAGAGTTCAAATAAAATCAATTGCAAAAACAACAGCCTTTCCTTGAAGCCTGCA

Reverse complement sequence

TGCAGGCTTCAAGGAAAGGCTGTTGTTTTTGCAATTGATTTTATTTGAACTCTTTTCTAAAAACAACTAGGTGAGTGCTTCTCAAACGACGCGGATGAGA[C/T]
AGTGCGTCTCGTCCGGTCGGAGTATGTGCAATGTATCAGTCTTTAGAAATGACACAAGATTGGCACCCGGCCAACAGCTTTTCAACCGGCCACCCGGGCC

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	99.80%	0.20%	0.04%	0.00%	NA
All Indica	2759	99.70%	0.30%	0.04%	0.00%	NA
All Japonica	1512	100.00%	0.00%	0.00%	0.00%	NA
Aus	269	99.30%	0.40%	0.37%	0.00%	NA
Indica I	595	99.20%	0.70%	0.17%	0.00%	NA
Indica II	465	99.80%	0.20%	0.00%	0.00%	NA
Indica III	913	100.00%	0.00%	0.00%	0.00%	NA
Indica Intermediate	786	99.60%	0.40%	0.00%	0.00%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	100.00%	0.00%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	100.00%	0.00%	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
vg0524661216	G -> A	LOC_Os05g42170.1	upstream_gene_variant ; 2381.0bp to feature; MODIFIER	N	Average:36.505; most accessible tissue: Minghui63 root, score: 69.344	N	N	N	N
vg0524661216	G -> A	LOC_Os05g42180.1	upstream_gene_variant ; 2698.0bp to feature; MODIFIER	N	Average:36.505; most accessible tissue: Minghui63 root, score: 69.344	N	N	N	N
vg0524661216	G -> A	LOC_Os05g42170-LOC_Os05g42180	intergenic_region ; MODIFIER	N	Average:36.505; most accessible tissue: Minghui63 root, score: 69.344	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0524661216	9.20E-07	2.02E-06	mr1758	Ind_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