Search for Variation information by Variation ID:

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

Detailed information for vg0822230941:

Variant ID: vg0822230941 (JBrowse)	Variation Type: INDEL
Chromosome: chr08	Position: 22230941
Reference Allele: C	Alternative Allele: T,CAT
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.79, T: 0.22, others allele: 0.00, population size: 200. )

Flanking Sequence (100 bp) in Reference Genome:

GTTACTCTTGGGGACTAAGGTCTCCTAGACGGCTAGGCGTCGCCGGTGAGCACCTAAGGTTGTGGTGTGCCACGGAAAGTTTGTGAAGGCTTCGATTTTG[C/T,CAT]
CTCCGCAAGGGAAGAAATCAAGAGTGAAACCGAGGAGTGCATTTGTGCAACCTCGTGAGGAAAGGGTTGAAATAGGCCTGGCCCTTGTGGCTCCTCAATG

Reverse complement sequence

CATTGAGGAGCCACAAGGGCCAGGCCTATTTCAACCCTTTCCTCACGAGGTTGCACAAATGCACTCCTCGGTTTCACTCTTGATTTCTTCCCTTGCGGAG[G/A,ATG]
CAAAATCGAAGCCTTCACAAACTTTCCGTGGCACACCACAACCTTAGGTGCTCACCGGCGACGCCTAGCCGTCTAGGAGACCTTAGTCCCCAAGAGTAAC

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	62.90%	36.70%	0.32%	0.06%	CAT: 0.02%
All Indica	2759	97.30%	2.20%	0.33%	0.11%	CAT: 0.04%
All Japonica	1512	1.30%	98.50%	0.20%	0.00%	NA
Aus	269	49.10%	50.90%	0.00%	0.00%	NA
Indica I	595	99.50%	0.00%	0.34%	0.17%	NA
Indica II	465	97.80%	1.50%	0.43%	0.22%	NA
Indica III	913	98.20%	1.40%	0.11%	0.11%	CAT: 0.11%
Indica Intermediate	786	94.30%	5.20%	0.51%	0.00%	NA
Temperate Japonica	767	1.20%	98.60%	0.26%	0.00%	NA
Tropical Japonica	504	1.00%	98.80%	0.20%	0.00%	NA
Japonica Intermediate	241	2.50%	97.50%	0.00%	0.00%	NA
VI/Aromatic	96	89.60%	10.40%	0.00%	0.00%	NA
Intermediate	90	53.30%	43.30%	3.33%	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
vg0822230941	C -> T	LOC_Os08g35220.1	upstream_gene_variant ; 3454.0bp to feature; MODIFIER	silent_mutation	Average:36.437; most accessible tissue: Zhenshan97 flag leaf, score: 53.034	N	N	N	N
vg0822230941	C -> T	LOC_Os08g35230.1	upstream_gene_variant ; 4018.0bp to feature; MODIFIER	silent_mutation	Average:36.437; most accessible tissue: Zhenshan97 flag leaf, score: 53.034	N	N	N	N
vg0822230941	C -> T	LOC_Os08g35220.2	upstream_gene_variant ; 3480.0bp to feature; MODIFIER	silent_mutation	Average:36.437; most accessible tissue: Zhenshan97 flag leaf, score: 53.034	N	N	N	N
vg0822230941	C -> T	LOC_Os08g35220-LOC_Os08g35230	intergenic_region ; MODIFIER	silent_mutation	Average:36.437; most accessible tissue: Zhenshan97 flag leaf, score: 53.034	N	N	N	N
vg0822230941	C -> DEL	N	N	silent_mutation	Average:36.437; most accessible tissue: Zhenshan97 flag leaf, score: 53.034	N	N	N	N
vg0822230941	C -> CAT	LOC_Os08g35220.1	upstream_gene_variant ; 3455.0bp to feature; MODIFIER	silent_mutation	Average:36.437; most accessible tissue: Zhenshan97 flag leaf, score: 53.034	N	N	N	N
vg0822230941	C -> CAT	LOC_Os08g35230.1	upstream_gene_variant ; 4017.0bp to feature; MODIFIER	silent_mutation	Average:36.437; most accessible tissue: Zhenshan97 flag leaf, score: 53.034	N	N	N	N
vg0822230941	C -> CAT	LOC_Os08g35220.2	upstream_gene_variant ; 3481.0bp to feature; MODIFIER	silent_mutation	Average:36.437; most accessible tissue: Zhenshan97 flag leaf, score: 53.034	N	N	N	N
vg0822230941	C -> CAT	LOC_Os08g35220-LOC_Os08g35230	intergenic_region ; MODIFIER	silent_mutation	Average:36.437; most accessible tissue: Zhenshan97 flag leaf, score: 53.034	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0822230941	2.50E-06	2.11E-26	mr1551	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
vg0822230941	NA	3.19E-10	mr1581	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
vg0822230941	NA	1.08E-06	mr1761	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