Search for Variation information by Variation ID:

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

Detailed information for vg0111822580:

Variant ID: vg0111822580 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 11822580
Reference Allele: T	Alternative Allele: A
Primary Allele: A	Secondary Allele: T

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 268. )

Flanking Sequence (100 bp) in Reference Genome:

TAGTATCTGGCCCCGATACTTTTCAGTCAAGAATTTCCCATCAATGCAGAGAACAGGACGACAGTTCACGAATGCCATCTTGCATGCATGTAGAGCTAAG[T/A]
ACGCCCTTTGCAGCACACTCTTGCCAGGATGTTCAATTGAGGGGAATTTCTTCACTGCGTAAGAGCTCCCAGGGTTTCTTTCTTCGATAACACCAAGCAG

Reverse complement sequence

CTGCTTGGTGTTATCGAAGAAAGAAACCCTGGGAGCTCTTACGCAGTGAAGAAATTCCCCTCAATTGAACATCCTGGCAAGAGTGTGCTGCAAAGGGCGT[A/T]
CTTAGCTCTACATGCATGCAAGATGGCATTCGTGAACTGTCGTCCTGTTCTCTGCATTGATGGGAAATTCTTGACTGAAAAGTATCGGGGCCAGATACTA

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	54.30%	22.80%	19.81%	3.11%	NA
All Indica	2759	63.50%	2.20%	30.77%	3.48%	NA
All Japonica	1512	34.00%	64.70%	1.12%	0.13%	NA
Aus	269	69.90%	0.70%	12.27%	17.10%	NA
Indica I	595	49.20%	1.80%	43.19%	5.71%	NA
Indica II	465	57.20%	3.90%	34.19%	4.73%	NA
Indica III	913	77.40%	1.00%	20.48%	1.10%	NA
Indica Intermediate	786	61.80%	3.10%	31.30%	3.82%	NA
Temperate Japonica	767	28.30%	70.90%	0.78%	0.00%	NA
Tropical Japonica	504	47.00%	51.00%	1.79%	0.20%	NA
Japonica Intermediate	241	24.90%	73.90%	0.83%	0.41%	NA
VI/Aromatic	96	72.90%	7.30%	18.75%	1.04%	NA
Intermediate	90	46.70%	30.00%	21.11%	2.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0111822580	T -> A	LOC_Os01g21200.1	downstream_gene_variant ; 2582.0bp to feature; MODIFIER	silent_mutation	Average:13.504; most accessible tissue: Minghui63 panicle, score: 25.313	N	N	N	N
vg0111822580	T -> A	LOC_Os01g21190.1	intron_variant ; MODIFIER	silent_mutation	Average:13.504; most accessible tissue: Minghui63 panicle, score: 25.313	N	N	N	N
vg0111822580	T -> DEL	N	N	silent_mutation	Average:13.504; most accessible tissue: Minghui63 panicle, score: 25.313	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0111822580	NA	2.36E-07	mr1162	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
vg0111822580	NA	4.39E-22	mr1163	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
vg0111822580	NA	1.03E-21	mr1010_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
vg0111822580	NA	1.17E-07	mr1030_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
vg0111822580	NA	5.58E-06	mr1164_2	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
vg0111822580	NA	6.30E-06	mr1355_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
vg0111822580	8.04E-08	1.48E-06	mr1400_2	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
vg0111822580	7.94E-07	7.94E-07	mr1400_2	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
vg0111822580	NA	3.46E-06	mr1555_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
vg0111822580	NA	5.22E-08	mr1576_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
vg0111822580	NA	5.30E-09	mr1709_2	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
vg0111822580	NA	2.77E-07	mr1748_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