Search for Variation information by Variation ID:

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

Detailed information for vg0415147115:

Variant ID: vg0415147115 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 15147115
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 295. )

Flanking Sequence (100 bp) in Reference Genome:

TGATCATGGGTCTATTTTCTATGCTCAAAGACTGGACTATTTATTATTCCCCGTAAGGGTTATCAACTGAATACTTGCGCCAGTCGGGATTCAATTGTTA[C/T]
ATCTATTTTGGAGTATCCCAGAAGGGATAATCATTCAGATCAGAAGCTATTCATATGAGCTACATTTGGTCTATAATACCTGGAAGATCTATTACTCGGG

Reverse complement sequence

CCCGAGTAATAGATCTTCCAGGTATTATAGACCAAATGTAGCTCATATGAATAGCTTCTGATCTGAATGATTATCCCTTCTGGGATACTCCAAAATAGAT[G/A]
TAACAATTGAATCCCGACTGGCGCAAGTATTCAGTTGATAACCCTTACGGGGAATAATAAATAGTCCAGTCTTTGAGCATAGAAAATAGACCCATGATCA

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	86.90%	0.10%	8.48%	4.49%	NA
All Indica	2759	91.80%	0.00%	6.16%	2.03%	NA
All Japonica	1512	89.70%	0.30%	4.30%	5.69%	NA
Aus	269	14.50%	0.40%	59.48%	25.65%	NA
Indica I	595	96.80%	0.00%	0.50%	2.69%	NA
Indica II	465	88.20%	0.20%	6.88%	4.73%	NA
Indica III	913	91.10%	0.00%	8.65%	0.22%	NA
Indica Intermediate	786	90.80%	0.00%	7.12%	2.04%	NA
Temperate Japonica	767	82.10%	0.50%	8.08%	9.26%	NA
Tropical Japonica	504	97.80%	0.00%	0.60%	1.59%	NA
Japonica Intermediate	241	97.10%	0.00%	0.00%	2.90%	NA
VI/Aromatic	96	99.00%	1.00%	0.00%	0.00%	NA
Intermediate	90	92.20%	0.00%	6.67%	1.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0415147115	C -> DEL	N	N	silent_mutation	Average:27.378; most accessible tissue: Minghui63 panicle, score: 42.799	N	N	N	N
vg0415147115	C -> T	LOC_Os04g26030.1	downstream_gene_variant ; 997.0bp to feature; MODIFIER	silent_mutation	Average:27.378; most accessible tissue: Minghui63 panicle, score: 42.799	N	N	N	N
vg0415147115	C -> T	LOC_Os04g26040.1	downstream_gene_variant ; 1537.0bp to feature; MODIFIER	silent_mutation	Average:27.378; most accessible tissue: Minghui63 panicle, score: 42.799	N	N	N	N
vg0415147115	C -> T	LOC_Os04g26030-LOC_Os04g26040	intergenic_region ; MODIFIER	silent_mutation	Average:27.378; most accessible tissue: Minghui63 panicle, score: 42.799	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0415147115	7.33E-06	NA	mr1282	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
vg0415147115	8.41E-06	NA	mr1658	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
vg0415147115	NA	8.71E-07	mr1062_2	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