Search for Variation information by Variation ID:

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

Detailed information for vg0316144275:

Variant ID: vg0316144275 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 16144275
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ACGCTCTAAAACCGCGACATGGCACTCCTACAAACGCTCTCAAGTCACCACATGGCACAGTCTAATCTTACCGTCGATTTTCACTTAAATTGGTGGACCC[G/A]
TTATTTTACACTATTAGATTAAATTTATTATTAAATATAATAGCTTCCTCCTCTATGGACGATACAAACGGTACCACTGTTCCCCCTGCGTACGTACGTA

Reverse complement sequence

TACGTACGTACGCAGGGGGAACAGTGGTACCGTTTGTATCGTCCATAGAGGAGGAAGCTATTATATTTAATAATAAATTTAATCTAATAGTGTAAAATAA[C/T]
GGGTCCACCAATTTAAGTGAAAATCGACGGTAAGATTAGACTGTGCCATGTGGTGACTTGAGAGCGTTTGTAGGAGTGCCATGTCGCGGTTTTAGAGCGT

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	93.70%	6.20%	0.11%	0.00%	NA
All Indica	2759	99.90%	0.10%	0.00%	0.00%	NA
All Japonica	1512	83.30%	16.70%	0.00%	0.00%	NA
Aus	269	96.30%	1.90%	1.86%	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	99.60%	0.40%	0.00%	0.00%	NA
Temperate Japonica	767	84.70%	15.30%	0.00%	0.00%	NA
Tropical Japonica	504	94.60%	5.40%	0.00%	0.00%	NA
Japonica Intermediate	241	55.20%	44.80%	0.00%	0.00%	NA
VI/Aromatic	96	74.00%	26.00%	0.00%	0.00%	NA
Intermediate	90	93.30%	6.70%	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
vg0316144275	G -> A	LOC_Os03g28080-LOC_Os03g28090	intergenic_region ; MODIFIER	silent_mutation	Average:41.533; most accessible tissue: Minghui63 panicle, score: 66.554	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0316144275	4.26E-06	4.26E-06	mr1717	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