Search for Variation information by Variation ID:

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

Detailed information for vg0222613010:

Variant ID: vg0222613010 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 22613010
Reference Allele: C	Alternative Allele: T
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 241. )

Flanking Sequence (100 bp) in Reference Genome:

TCCCGATGTTCCGGTGTACTTTGAAATAGTCGTCGAGGTTCCTCCAGGAGCATAGCAAGGCAAGTCATGCTTGTCACTTGAACATATTGATCCTATATTG[C/T]
AAATGCTCTATCATTTTCCTTTAAGTACTGCATCATTTTATAATGTTACTGCTCTATCGTTTTTCACTTGAACATGTTTTCCTTTAAGTACGGCCAGTGA

Reverse complement sequence

TCACTGGCCGTACTTAAAGGAAAACATGTTCAAGTGAAAAACGATAGAGCAGTAACATTATAAAATGATGCAGTACTTAAAGGAAAATGATAGAGCATTT[G/A]
CAATATAGGATCAATATGTTCAAGTGACAAGCATGACTTGCCTTGCTATGCTCCTGGAGGAACCTCGACGACTATTTCAAAGTACACCGGAACATCGGGA

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	52.90%	46.70%	0.17%	0.25%	NA
All Indica	2759	84.00%	15.40%	0.18%	0.36%	NA
All Japonica	1512	3.40%	96.30%	0.13%	0.13%	NA
Aus	269	36.40%	63.60%	0.00%	0.00%	NA
Indica I	595	80.80%	18.20%	0.50%	0.50%	NA
Indica II	465	92.50%	6.90%	0.22%	0.43%	NA
Indica III	913	85.20%	14.70%	0.00%	0.11%	NA
Indica Intermediate	786	80.00%	19.30%	0.13%	0.51%	NA
Temperate Japonica	767	0.70%	99.10%	0.13%	0.13%	NA
Tropical Japonica	504	8.50%	91.10%	0.20%	0.20%	NA
Japonica Intermediate	241	1.70%	98.30%	0.00%	0.00%	NA
VI/Aromatic	96	1.00%	99.00%	0.00%	0.00%	NA
Intermediate	90	32.20%	66.70%	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
vg0222613010	C -> T	LOC_Os02g37450.1	upstream_gene_variant ; 927.0bp to feature; MODIFIER	silent_mutation	Average:40.629; most accessible tissue: Minghui63 panicle, score: 53.77	N	N	N	N
vg0222613010	C -> T	LOC_Os02g37460.1	upstream_gene_variant ; 1281.0bp to feature; MODIFIER	silent_mutation	Average:40.629; most accessible tissue: Minghui63 panicle, score: 53.77	N	N	N	N
vg0222613010	C -> T	LOC_Os02g37470.1	upstream_gene_variant ; 4493.0bp to feature; MODIFIER	silent_mutation	Average:40.629; most accessible tissue: Minghui63 panicle, score: 53.77	N	N	N	N
vg0222613010	C -> T	LOC_Os02g37440.1	downstream_gene_variant ; 3802.0bp to feature; MODIFIER	silent_mutation	Average:40.629; most accessible tissue: Minghui63 panicle, score: 53.77	N	N	N	N
vg0222613010	C -> T	LOC_Os02g37450-LOC_Os02g37460	intergenic_region ; MODIFIER	silent_mutation	Average:40.629; most accessible tissue: Minghui63 panicle, score: 53.77	N	N	N	N
vg0222613010	C -> DEL	N	N	silent_mutation	Average:40.629; most accessible tissue: Minghui63 panicle, score: 53.77	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0222613010	1.24E-06	4.25E-15	mr1188	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
vg0222613010	NA	2.44E-06	mr1188	Ind_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
vg0222613010	NA	8.39E-07	mr1045_2	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
vg0222613010	3.43E-06	1.27E-15	mr1188_2	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
vg0222613010	NA	3.26E-07	mr1968_2	Ind_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