Search for Variation information by Variation ID:

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

Detailed information for vg0413763191:

Variant ID: vg0413763191 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 13763191
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ACATTGAGGCTGGTCCCAAAGATCAATATGCCATCGACATATAAGCACAAGATCACTCCTTCTCCCCCACTATAGCGATAGTACACACATTTGTCAGCTT[C/T]
GTTCACAACAAAGCCTGCAGATGTAAGCGTGGTGTCAAACTTCTCATGCCATTGCTTAGGTGCTTGCTTGAGGCCATACAAGGATTTCAACAGTTTACAC

Reverse complement sequence

GTGTAAACTGTTGAAATCCTTGTATGGCCTCAAGCAAGCACCTAAGCAATGGCATGAGAAGTTTGACACCACGCTTACATCTGCAGGCTTTGTTGTGAAC[G/A]
AAGCTGACAAATGTGTGTACTATCGCTATAGTGGGGGAGAAGGAGTGATCTTGTGCTTATATGTCGATGGCATATTGATCTTTGGGACCAGCCTCAATGT

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	92.20%	0.30%	5.56%	1.90%	NA
All Indica	2759	88.50%	0.40%	8.37%	2.65%	NA
All Japonica	1512	97.40%	0.00%	1.52%	1.12%	NA
Aus	269	99.30%	0.40%	0.37%	0.00%	NA
Indica I	595	91.90%	0.70%	3.03%	4.37%	NA
Indica II	465	86.50%	0.00%	12.69%	0.86%	NA
Indica III	913	88.20%	0.50%	8.87%	2.41%	NA
Indica Intermediate	786	87.70%	0.40%	9.29%	2.67%	NA
Temperate Japonica	767	98.80%	0.00%	0.78%	0.39%	NA
Tropical Japonica	504	97.80%	0.00%	1.39%	0.79%	NA
Japonica Intermediate	241	91.70%	0.00%	4.15%	4.15%	NA
VI/Aromatic	96	99.00%	0.00%	1.04%	0.00%	NA
Intermediate	90	91.10%	1.10%	7.78%	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
vg0413763191	C -> DEL	N	N	silent_mutation	Average:27.455; most accessible tissue: Zhenshan97 flower, score: 51.467	N	N	N	N
vg0413763191	C -> T	LOC_Os04g24090.1	upstream_gene_variant ; 2112.0bp to feature; MODIFIER	silent_mutation	Average:27.455; most accessible tissue: Zhenshan97 flower, score: 51.467	N	N	N	N
vg0413763191	C -> T	LOC_Os04g24100.1	intron_variant ; MODIFIER	silent_mutation	Average:27.455; most accessible tissue: Zhenshan97 flower, score: 51.467	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0413763191	NA	4.87E-06	mr1812	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