Search for Variation information by Variation ID:

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

Detailed information for vg0405224019:

Variant ID: vg0405224019 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 5224019
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CAACAGTCGCCGACTAATCGAACGAGGACTAGAGACAAGGTGAATGGCACTTGGTAAAATTCAACTAAACAAAACCCGATTGTGTTTGAGGATGTACAAA[G/A]
CTATTTATAGAGGAAAATAAAGCTATGGTTAAGTGCTAATTCATGGAGGTGGAGGGAGACACTTCCGAGATGGGCCTAGTCTAATTACATGGCCTAAGGC

Reverse complement sequence

GCCTTAGGCCATGTAATTAGACTAGGCCCATCTCGGAAGTGTCTCCCTCCACCTCCATGAATTAGCACTTAACCATAGCTTTATTTTCCTCTATAAATAG[C/T]
TTTGTACATCCTCAAACACAATCGGGTTTTGTTTAGTTGAATTTTACCAAGTGCCATTCACCTTGTCTCTAGTCCTCGTTCGATTAGTCGGCGACTGTTG

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	33.60%	0.40%	0.89%	65.07%	NA
All Indica	2759	8.40%	0.60%	1.34%	89.67%	NA
All Japonica	1512	86.40%	0.30%	0.26%	12.96%	NA
Aus	269	1.50%	0.00%	0.37%	98.14%	NA
Indica I	595	8.10%	2.40%	3.19%	86.39%	NA
Indica II	465	15.10%	0.20%	0.86%	83.87%	NA
Indica III	913	2.60%	0.00%	0.88%	96.50%	NA
Indica Intermediate	786	11.50%	0.10%	0.76%	87.66%	NA
Temperate Japonica	767	92.20%	0.70%	0.39%	6.78%	NA
Tropical Japonica	504	77.20%	0.00%	0.20%	22.62%	NA
Japonica Intermediate	241	87.60%	0.00%	0.00%	12.45%	NA
VI/Aromatic	96	8.30%	0.00%	0.00%	91.67%	NA
Intermediate	90	41.10%	0.00%	0.00%	58.89%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0405224019	G -> DEL	N	N	silent_mutation	Average:21.801; most accessible tissue: Minghui63 young leaf, score: 36.684	N	N	N	N
vg0405224019	G -> A	LOC_Os04g09740.1	upstream_gene_variant ; 504.0bp to feature; MODIFIER	silent_mutation	Average:21.801; most accessible tissue: Minghui63 young leaf, score: 36.684	N	N	N	N
vg0405224019	G -> A	LOC_Os04g09750.1	upstream_gene_variant ; 3051.0bp to feature; MODIFIER	silent_mutation	Average:21.801; most accessible tissue: Minghui63 young leaf, score: 36.684	N	N	N	N
vg0405224019	G -> A	LOC_Os04g09730.1	downstream_gene_variant ; 1542.0bp to feature; MODIFIER	silent_mutation	Average:21.801; most accessible tissue: Minghui63 young leaf, score: 36.684	N	N	N	N
vg0405224019	G -> A	LOC_Os04g09730-LOC_Os04g09740	intergenic_region ; MODIFIER	silent_mutation	Average:21.801; most accessible tissue: Minghui63 young leaf, score: 36.684	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0405224019	2.50E-06	5.37E-06	mr1717_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