Search for Variation information by Variation ID:

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

Detailed information for vg0114207760:

Variant ID: vg0114207760 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 14207760
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CTGCTTAACTCCAGTGCAGGTCCAAAAGCTTGCCTTTAGGTGTAGGAGCGTGCCAGTTGATTTGATACTGCAATCAACAAGAAATAAAGACAAAGAAACC[G/A]
CGGTTAAATCCATAAACGATAGCCGATCGGCTAGTTGCCGATGACGTATCATTTATCTTTGAGCCGATATCATATGTAGATCGATCGGCAGTATTGAATA

Reverse complement sequence

TATTCAATACTGCCGATCGATCTACATATGATATCGGCTCAAAGATAAATGATACGTCATCGGCAACTAGCCGATCGGCTATCGTTTATGGATTTAACCG[C/T]
GGTTTCTTTGTCTTTATTTCTTGTTGATTGCAGTATCAAATCAACTGGCACGCTCCTACACCTAAAGGCAAGCTTTTGGACCTGCACTGGAGTTAAGCAG

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	41.00%	1.30%	12.87%	44.90%	NA
All Indica	2759	12.60%	2.10%	18.16%	67.09%	NA
All Japonica	1512	95.60%	0.10%	1.06%	3.24%	NA
Aus	269	13.40%	0.00%	29.00%	57.62%	NA
Indica I	595	9.90%	0.00%	13.45%	76.64%	NA
Indica II	465	10.80%	10.80%	17.42%	61.08%	NA
Indica III	913	14.60%	0.10%	21.80%	63.53%	NA
Indica Intermediate	786	13.50%	1.00%	17.94%	67.56%	NA
Temperate Japonica	767	98.40%	0.00%	0.39%	1.17%	NA
Tropical Japonica	504	90.30%	0.00%	2.38%	7.34%	NA
Japonica Intermediate	241	97.90%	0.40%	0.41%	1.24%	NA
VI/Aromatic	96	57.30%	0.00%	3.12%	39.58%	NA
Intermediate	90	56.70%	0.00%	11.11%	32.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0114207760	G -> A	LOC_Os01g25160.1	downstream_gene_variant ; 2719.0bp to feature; MODIFIER	silent_mutation	Average:11.573; most accessible tissue: Callus, score: 31.173	N	N	N	N
vg0114207760	G -> A	LOC_Os01g25150-LOC_Os01g25160	intergenic_region ; MODIFIER	silent_mutation	Average:11.573; most accessible tissue: Callus, score: 31.173	N	N	N	N
vg0114207760	G -> DEL	N	N	silent_mutation	Average:11.573; most accessible tissue: Callus, score: 31.173	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0114207760	1.49E-06	1.49E-06	mr1848_2	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