Search for Variation information by Variation ID:

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

Detailed information for vg0528755805:

Variant ID: vg0528755805 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 28755805
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, A: 0.02, others allele: 0.00, population size: 63. )

Flanking Sequence (100 bp) in Reference Genome:

GGAGGAGATGGAACGAGGAGGGAGAACGGAGGGAGGCACTACCGTGCGGGGGTGATGGGGCGCAGTGACGAGAGGCCGACGGCGCGGGAGTGATCTCTCC[G/A]
GCCTCGGGCCGGGGAAGAGGAAGAAGACGAGTGCCCGGAGTCCCCTTCCGCGTCCACGAATGCACCGGCTCTCCCGGTGCTTGGCGATGAACGGCGGAGG

Reverse complement sequence

CCTCCGCCGTTCATCGCCAAGCACCGGGAGAGCCGGTGCATTCGTGGACGCGGAAGGGGACTCCGGGCACTCGTCTTCTTCCTCTTCCCCGGCCCGAGGC[C/T]
GGAGAGATCACTCCCGCGCCGTCGGCCTCTCGTCACTGCGCCCCATCACCCCCGCACGGTAGTGCCTCCCTCCGTTCTCCCTCCTCGTTCCATCTCCTCC

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	48.10%	31.60%	17.10%	3.17%	NA
All Indica	2759	15.80%	53.30%	27.26%	3.62%	NA
All Japonica	1512	99.70%	0.10%	0.13%	0.07%	NA
Aus	269	66.50%	1.50%	15.61%	16.36%	NA
Indica I	595	6.10%	43.70%	42.35%	7.90%	NA
Indica II	465	14.60%	49.00%	32.90%	3.44%	NA
Indica III	913	20.50%	61.70%	16.87%	0.99%	NA
Indica Intermediate	786	18.40%	53.40%	24.55%	3.56%	NA
Temperate Japonica	767	99.60%	0.10%	0.13%	0.13%	NA
Tropical Japonica	504	99.60%	0.20%	0.20%	0.00%	NA
Japonica Intermediate	241	100.00%	0.00%	0.00%	0.00%	NA
VI/Aromatic	96	95.80%	2.10%	1.04%	1.04%	NA
Intermediate	90	65.60%	17.80%	12.22%	4.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0528755805	G -> DEL	N	N	silent_mutation	Average:38.173; most accessible tissue: Minghui63 young leaf, score: 69.4	N	N	N	N
vg0528755805	G -> A	LOC_Os05g50170.1	upstream_gene_variant ; 3996.0bp to feature; MODIFIER	silent_mutation	Average:38.173; most accessible tissue: Minghui63 young leaf, score: 69.4	N	N	N	N
vg0528755805	G -> A	LOC_Os05g50170.2	upstream_gene_variant ; 3996.0bp to feature; MODIFIER	silent_mutation	Average:38.173; most accessible tissue: Minghui63 young leaf, score: 69.4	N	N	N	N
vg0528755805	G -> A	LOC_Os05g50180.1	downstream_gene_variant ; 2099.0bp to feature; MODIFIER	silent_mutation	Average:38.173; most accessible tissue: Minghui63 young leaf, score: 69.4	N	N	N	N
vg0528755805	G -> A	LOC_Os05g50190.1	downstream_gene_variant ; 4347.0bp to feature; MODIFIER	silent_mutation	Average:38.173; most accessible tissue: Minghui63 young leaf, score: 69.4	N	N	N	N
vg0528755805	G -> A	LOC_Os05g50170-LOC_Os05g50180	intergenic_region ; MODIFIER	silent_mutation	Average:38.173; most accessible tissue: Minghui63 young leaf, score: 69.4	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0528755805	4.88E-06	4.88E-06	mr1273_2	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