Search for Variation information by Variation ID:

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

Detailed information for vg0102547155:

Variant ID: vg0102547155 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 2547155
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GAGGGAAGCAGGCGGCAAGTGGAACAACGGGCGGAGGGAGAGAGGAACGCCAGTGCGGTCGTGCGGAGGGAGAAAGAGAGAGAGAGAGAGGGGGAAGAGA[G/A]
GGGTAGGATAGGAAAGAAAGGAAGAGAAGAGAAATGAGCTTTTTTGGGTTGGAACATTCATTAGGCTATTCAAACATGGTCTGCATTGTAGAGGTGAGTA

Reverse complement sequence

TACTCACCTCTACAATGCAGACCATGTTTGAATAGCCTAATGAATGTTCCAACCCAAAAAAGCTCATTTCTCTTCTCTTCCTTTCTTTCCTATCCTACCC[C/T]
TCTCTTCCCCCTCTCTCTCTCTCTCTTTCTCCCTCCGCACGACCGCACTGGCGTTCCTCTCTCCCTCCGCCCGTTGTTCCACTTGCCGCCTGCTTCCCTC

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	68.10%	5.70%	1.84%	24.35%	NA
All Indica	2759	70.00%	0.60%	0.91%	28.49%	NA
All Japonica	1512	68.90%	16.70%	3.90%	10.52%	NA
Aus	269	29.70%	0.00%	0.74%	69.52%	NA
Indica I	595	34.80%	1.20%	1.85%	62.18%	NA
Indica II	465	91.00%	0.60%	0.65%	7.74%	NA
Indica III	913	78.80%	0.00%	0.77%	20.48%	NA
Indica Intermediate	786	74.00%	0.90%	0.51%	24.55%	NA
Temperate Japonica	767	63.00%	28.30%	5.61%	3.13%	NA
Tropical Japonica	504	79.40%	0.60%	0.79%	19.25%	NA
Japonica Intermediate	241	66.00%	13.30%	4.98%	15.77%	NA
VI/Aromatic	96	87.50%	0.00%	0.00%	12.50%	NA
Intermediate	90	88.90%	2.20%	1.11%	7.78%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0102547155	G -> A	LOC_Os01g05380.1	upstream_gene_variant ; 4423.0bp to feature; MODIFIER	silent_mutation	Average:44.29; most accessible tissue: Minghui63 panicle, score: 86.85	N	N	N	N
vg0102547155	G -> A	LOC_Os01g05390.1	upstream_gene_variant ; 760.0bp to feature; MODIFIER	silent_mutation	Average:44.29; most accessible tissue: Minghui63 panicle, score: 86.85	N	N	N	N
vg0102547155	G -> A	LOC_Os01g05400.1	upstream_gene_variant ; 3791.0bp to feature; MODIFIER	silent_mutation	Average:44.29; most accessible tissue: Minghui63 panicle, score: 86.85	N	N	N	N
vg0102547155	G -> A	LOC_Os01g05380-LOC_Os01g05390	intergenic_region ; MODIFIER	silent_mutation	Average:44.29; most accessible tissue: Minghui63 panicle, score: 86.85	N	N	N	N
vg0102547155	G -> DEL	N	N	silent_mutation	Average:44.29; most accessible tissue: Minghui63 panicle, score: 86.85	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0102547155	NA	3.97E-07	mr1092	Jap_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0102547155	2.04E-07	2.04E-07	mr1958_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