Search for Variation information by Variation ID:

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

Detailed information for vg1124078519:

Variant ID: vg1124078519 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 24078519
Reference Allele: C	Alternative Allele: T
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CATCAAAATGGTTTCTGGGAGCAGTTTGGGCTTTGAAGCCAGCAGGTACATACAGTACCATGATAAGCAATTTGACACTGTGTATGCCTTTTGAAGCTCA[C/T]
CTGTAAGAGCTTTTTCATCCACCAGAAACGATGATAATCTTGACATTGTTGTTAAGTTGATTTTATGGTCATTGGCAAGCTTGATCTCACATAGGCTTGT

Reverse complement sequence

ACAAGCCTATGTGAGATCAAGCTTGCCAATGACCATAAAATCAACTTAACAACAATGTCAAGATTATCATCGTTTCTGGTGGATGAAAAAGCTCTTACAG[G/A]
TGAGCTTCAAAAGGCATACACAGTGTCAAATTGCTTATCATGGTACTGTATGTACCTGCTGGCTTCAAAGCCCAAACTGCTCCCAGAAACCATTTTGATG

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	37.70%	17.80%	1.02%	43.50%	NA
All Indica	2759	32.70%	2.90%	1.45%	62.92%	NA
All Japonica	1512	45.80%	40.70%	0.46%	13.03%	NA
Aus	269	23.40%	45.00%	0.37%	31.23%	NA
Indica I	595	4.70%	2.20%	1.68%	91.43%	NA
Indica II	465	26.70%	2.40%	1.29%	69.68%	NA
Indica III	913	54.70%	1.00%	0.88%	43.48%	NA
Indica Intermediate	786	32.10%	6.00%	2.04%	59.92%	NA
Temperate Japonica	767	39.10%	53.30%	0.39%	7.17%	NA
Tropical Japonica	504	52.80%	33.50%	0.40%	13.29%	NA
Japonica Intermediate	241	52.70%	15.40%	0.83%	31.12%	NA
VI/Aromatic	96	86.50%	1.00%	0.00%	12.50%	NA
Intermediate	90	44.40%	25.60%	0.00%	30.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1124078519	C -> T	LOC_Os11g40390.1	missense_variant ; p.Gly226Asp; MODERATE	nonsynonymous_codon ; G226D	Average:14.703; most accessible tissue: Callus, score: 80.918	unknown	unknown	TOLERATED	1.00
vg1124078519	C -> DEL	LOC_Os11g40390.1	N	frameshift_variant	Average:14.703; most accessible tissue: Callus, score: 80.918	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1124078519	3.55E-06	2.03E-06	mr1050_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
vg1124078519	5.62E-07	5.90E-07	mr1131_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
vg1124078519	2.79E-07	7.68E-07	mr1199_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
vg1124078519	2.77E-06	NA	mr1208_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
vg1124078519	NA	2.94E-06	mr1212_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
vg1124078519	7.44E-06	4.13E-06	mr1272_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
vg1124078519	NA	2.69E-06	mr1407_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
vg1124078519	1.12E-06	3.29E-07	mr1609_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
vg1124078519	1.52E-06	NA	mr1763_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
vg1124078519	6.26E-07	6.26E-07	mr1852_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
vg1124078519	3.22E-06	3.22E-06	mr1853_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
vg1124078519	NA	6.90E-06	mr1888_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
vg1124078519	2.33E-07	5.03E-07	mr1909_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
vg1124078519	NA	9.37E-06	mr1942_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