Search for Variation information by Variation ID:

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

Detailed information for vg0622581640:

Variant ID: vg0622581640 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 22581640
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AGGGGAATCACATTAATGCATAGACTTTGATTATTGGCATAGCTTTGGAATAGAGCCACCGCAATGGTGTTAGTTAATTAAAATACACTATATGGTGGGC[T/C]
GTGGGTGCATGGTTTTGCTATTTGTGCCCATGGCGATTAAGGACCAGTTCGCGGGATGCCCTGGAAGAACTTATCATACTTACCACAAGCCAACGTGGGC

Reverse complement sequence

GCCCACGTTGGCTTGTGGTAAGTATGATAAGTTCTTCCAGGGCATCCCGCGAACTGGTCCTTAATCGCCATGGGCACAAATAGCAAAACCATGCACCCAC[A/G]
GCCCACCATATAGTGTATTTTAATTAACTAACACCATTGCGGTGGCTCTATTCCAAAGCTATGCCAATAATCAAAGTCTATGCATTAATGTGATTCCCCT

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	14.10%	1.40%	3.41%	81.17%	NA
All Indica	2759	1.90%	1.80%	3.59%	92.64%	NA
All Japonica	1512	38.90%	0.30%	2.18%	58.60%	NA
Aus	269	3.70%	1.90%	6.69%	87.73%	NA
Indica I	595	1.80%	1.30%	1.85%	94.96%	NA
Indica II	465	1.90%	1.90%	5.59%	90.54%	NA
Indica III	913	1.30%	2.30%	3.72%	92.66%	NA
Indica Intermediate	786	2.70%	1.70%	3.56%	92.11%	NA
Temperate Japonica	767	63.60%	0.00%	0.39%	35.98%	NA
Tropical Japonica	504	8.10%	1.00%	5.56%	85.32%	NA
Japonica Intermediate	241	24.50%	0.00%	0.83%	74.69%	NA
VI/Aromatic	96	0.00%	1.00%	6.25%	92.71%	NA
Intermediate	90	15.60%	2.20%	5.56%	76.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0622581640	T -> C	LOC_Os06g38130.1	downstream_gene_variant ; 3449.0bp to feature; MODIFIER	silent_mutation	Average:13.587; most accessible tissue: Minghui63 young leaf, score: 27.355	N	N	N	N
vg0622581640	T -> C	LOC_Os06g38130-LOC_Os06g38140	intergenic_region ; MODIFIER	silent_mutation	Average:13.587; most accessible tissue: Minghui63 young leaf, score: 27.355	N	N	N	N
vg0622581640	T -> DEL	N	N	silent_mutation	Average:13.587; most accessible tissue: Minghui63 young leaf, score: 27.355	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0622581640	4.49E-06	4.49E-06	mr1412	Ind_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