Search for Variation information by Variation ID:

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

Detailed information for vg0602342015:

Variant ID: vg0602342015 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 2342015
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.93, C: 0.06, others allele: 0.00, population size: 213. )

Flanking Sequence (100 bp) in Reference Genome:

ATAATATTAGAATATTAATGTATATATGTTCTCTGTGGATATATATATTTGTTCGTATATATGTCACTGAATGCGGGCCTGGCCAGCTTTATATGGGGAC[T/C]
CTTTATCAAGATTGTTCATATATTACACCGTAAGTGACGACTCTTCATCAGCGCGGCTGATGATCGATATATACTATAGCTAATACATGGGGATTAAGGT

Reverse complement sequence

ACCTTAATCCCCATGTATTAGCTATAGTATATATCGATCATCAGCCGCGCTGATGAAGAGTCGTCACTTACGGTGTAATATATGAACAATCTTGATAAAG[A/G]
GTCCCCATATAAAGCTGGCCAGGCCCGCATTCAGTGACATATATACGAACAAATATATATATCCACAGAGAACATATATACATTAATATTCTAATATTAT

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	96.50%	2.40%	1.12%	0.00%	NA
All Indica	2759	99.70%	0.20%	0.07%	0.00%	NA
All Japonica	1512	90.00%	6.70%	3.31%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	99.40%	0.40%	0.22%	0.00%	NA
Indica III	913	100.00%	0.00%	0.00%	0.00%	NA
Indica Intermediate	786	99.40%	0.50%	0.13%	0.00%	NA
Temperate Japonica	767	86.30%	9.40%	4.30%	0.00%	NA
Tropical Japonica	504	95.60%	3.00%	1.39%	0.00%	NA
Japonica Intermediate	241	90.00%	5.80%	4.15%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	91.10%	7.80%	1.11%	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
vg0602342015	T -> C	LOC_Os06g05209.1	upstream_gene_variant ; 3826.0bp to feature; MODIFIER	silent_mutation	Average:73.691; most accessible tissue: Callus, score: 90.505	N	N	N	N
vg0602342015	T -> C	LOC_Os06g05230.1	upstream_gene_variant ; 1522.0bp to feature; MODIFIER	silent_mutation	Average:73.691; most accessible tissue: Callus, score: 90.505	N	N	N	N
vg0602342015	T -> C	LOC_Os06g05220.1	intron_variant ; MODIFIER	silent_mutation	Average:73.691; most accessible tissue: Callus, score: 90.505	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0602342015	NA	5.06E-07	mr1712	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
vg0602342015	1.90E-06	1.90E-06	mr1770	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