Search for Variation information by Variation ID:

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

Detailed information for vg0821781292:

Variant ID: vg0821781292 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 21781292
Reference Allele: C	Alternative Allele: T
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.80, T: 0.20, others allele: 0.00, population size: 173. )

Flanking Sequence (100 bp) in Reference Genome:

TATCCACCTTGCCTTCGAAATCGCGCAATCTAGAAAACCGATTTTGCTCGGGGGGCAAGACATTAATATGCTCGTGAAGAAACCAAGAGAAGATGAACGG[C/T]
GATGGATACAACATCACATCTTTGAGCCGCCGTTTGTTGGATGCTAAGGCAAGGTATGGGTTTGTTGTGTTCAACATTATATTATATGCCTATGCCATGA

Reverse complement sequence

TCATGGCATAGGCATATAATATAATGTTGAACACAACAAACCCATACCTTGCCTTAGCATCCAACAAACGGCGGCTCAAAGATGTGATGTTGTATCCATC[G/A]
CCGTTCATCTTCTCTTGGTTTCTTCACGAGCATATTAATGTCTTGCCCCCCGAGCAAAATCGGTTTTCTAGATTGCGCGATTTCGAAGGCAAGGTGGATA

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	71.10%	28.00%	0.66%	0.23%	NA
All Indica	2759	97.80%	0.80%	1.05%	0.40%	NA
All Japonica	1512	17.20%	82.70%	0.07%	0.00%	NA
Aus	269	99.30%	0.70%	0.00%	0.00%	NA
Indica I	595	98.80%	0.20%	0.34%	0.67%	NA
Indica II	465	98.50%	1.30%	0.22%	0.00%	NA
Indica III	913	96.10%	0.50%	2.63%	0.77%	NA
Indica Intermediate	786	98.50%	1.30%	0.25%	0.00%	NA
Temperate Japonica	767	11.30%	88.70%	0.00%	0.00%	NA
Tropical Japonica	504	12.90%	87.10%	0.00%	0.00%	NA
Japonica Intermediate	241	44.80%	54.80%	0.41%	0.00%	NA
VI/Aromatic	96	90.60%	9.40%	0.00%	0.00%	NA
Intermediate	90	53.30%	45.60%	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
vg0821781292	C -> T	LOC_Os08g34670.1	downstream_gene_variant ; 570.0bp to feature; MODIFIER	silent_mutation	Average:29.069; most accessible tissue: Minghui63 flower, score: 40.98	N	N	N	N
vg0821781292	C -> T	LOC_Os08g34680.1	downstream_gene_variant ; 2873.0bp to feature; MODIFIER	silent_mutation	Average:29.069; most accessible tissue: Minghui63 flower, score: 40.98	N	N	N	N
vg0821781292	C -> T	LOC_Os08g34670-LOC_Os08g34680	intergenic_region ; MODIFIER	silent_mutation	Average:29.069; most accessible tissue: Minghui63 flower, score: 40.98	N	N	N	N
vg0821781292	C -> DEL	N	N	silent_mutation	Average:29.069; most accessible tissue: Minghui63 flower, score: 40.98	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0821781292	4.40E-06	NA	mr1103	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
vg0821781292	8.23E-07	1.42E-06	mr1246	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
vg0821781292	NA	2.15E-06	mr1510	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
vg0821781292	NA	2.72E-07	mr1804	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