Search for Variation information by Variation ID:

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

Detailed information for vg1226936545:

Variant ID: vg1226936545 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 26936545
Reference Allele: G	Alternative Allele: A
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TATCATAAATATTTAAATAACACATCGAAAATAAGATGACGTCCCTCGATGGGTAAAATGACTTTTGTCCTGAGCATACTATTCTTCGCGGGGAGACCGC[G/A]
CCAAGCTGGTCATCGTGCACACAAGCATACTATATCATTGTCATCTCTGCTGCTTCTATCGATCTTTTATTATTTGTGTATCCATGCATGCTAGGGACTG

Reverse complement sequence

CAGTCCCTAGCATGCATGGATACACAAATAATAAAAGATCGATAGAAGCAGCAGAGATGACAATGATATAGTATGCTTGTGTGCACGATGACCAGCTTGG[C/T]
GCGGTCTCCCCGCGAAGAATAGTATGCTCAGGACAAAAGTCATTTTACCCATCGAGGGACGTCATCTTATTTTCGATGTGTTATTTAAATATTTATGATA

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	47.30%	12.40%	0.91%	39.31%	NA
All Indica	2759	78.30%	3.00%	0.43%	18.30%	NA
All Japonica	1512	1.90%	14.00%	1.59%	82.61%	NA
Aus	269	1.10%	96.70%	0.00%	2.23%	NA
Indica I	595	37.80%	5.70%	1.51%	54.96%	NA
Indica II	465	94.40%	1.10%	0.00%	4.52%	NA
Indica III	913	91.90%	1.20%	0.11%	6.79%	NA
Indica Intermediate	786	83.50%	4.20%	0.25%	12.09%	NA
Temperate Japonica	767	1.60%	25.70%	2.35%	70.40%	NA
Tropical Japonica	504	2.00%	1.40%	0.79%	95.83%	NA
Japonica Intermediate	241	2.50%	2.90%	0.83%	93.78%	NA
VI/Aromatic	96	4.20%	19.80%	4.17%	71.88%	NA
Intermediate	90	47.80%	16.70%	3.33%	32.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1226936545	G -> DEL	N	N	silent_mutation	Average:35.716; most accessible tissue: Callus, score: 79.837	N	N	N	N
vg1226936545	G -> A	LOC_Os12g43410.1	upstream_gene_variant ; 3253.0bp to feature; MODIFIER	silent_mutation	Average:35.716; most accessible tissue: Callus, score: 79.837	N	N	N	N
vg1226936545	G -> A	LOC_Os12g43410-LOC_Os12g43440	intergenic_region ; MODIFIER	silent_mutation	Average:35.716; most accessible tissue: Callus, score: 79.837	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1226936545	NA	3.69E-06	mr1662	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
vg1226936545	NA	1.26E-06	mr1041_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
vg1226936545	NA	8.07E-06	mr1050_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
vg1226936545	NA	4.23E-06	mr1245_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
vg1226936545	NA	1.61E-06	mr1293_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
vg1226936545	NA	4.78E-06	mr1373_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
vg1226936545	NA	1.25E-06	mr1373_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
vg1226936545	NA	3.38E-06	mr1497_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
vg1226936545	NA	8.13E-07	mr1508_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
vg1226936545	NA	9.84E-06	mr1508_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
vg1226936545	NA	4.29E-06	mr1543_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
vg1226936545	NA	5.97E-06	mr1655_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
vg1226936545	NA	6.48E-08	mr1662_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
vg1226936545	6.31E-06	6.31E-06	mr1697_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
vg1226936545	NA	4.24E-07	mr1745_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
vg1226936545	2.24E-06	2.24E-06	mr1832_2	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
vg1226936545	1.31E-06	1.30E-06	mr1833_2	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
vg1226936545	1.76E-06	1.76E-06	mr1843_2	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
vg1226936545	NA	4.80E-10	mr1851_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