Search for Variation information by Variation ID:

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

Detailed information for vg0331091486:

Variant ID: vg0331091486 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 31091486
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GGACGTCCATGGCAGAGCTGAAGGCGCCGGACCCTGGGAAGACGAGGCGGTCGGCGGCGAGGATGTCCTCCGGGCTACGCACGTCACAGATGCTGAAGCC[A/G]
AGGTGGCGGATGGCGTTCCGCACGCTGCGCACGTTGCCCGCGCCGTAGTCCAGCAGCGTCACGGCTGTCGCATCGAACCGACGGCGAAGCGGAGGAAAAG

Reverse complement sequence

CTTTTCCTCCGCTTCGCCGTCGGTTCGATGCGACAGCCGTGACGCTGCTGGACTACGGCGCGGGCAACGTGCGCAGCGTGCGGAACGCCATCCGCCACCT[T/C]
GGCTTCAGCATCTGTGACGTGCGTAGCCCGGAGGACATCCTCGCCGCCGACCGCCTCGTCTTCCCAGGGTCCGGCGCCTTCAGCTCTGCCATGGACGTCC

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	32.80%	21.20%	3.70%	42.34%	NA
All Indica	2759	2.00%	30.60%	5.40%	62.09%	NA
All Japonica	1512	91.70%	7.60%	0.33%	0.33%	NA
Aus	269	1.90%	0.00%	4.46%	93.68%	NA
Indica I	595	1.20%	1.70%	5.38%	91.76%	NA
Indica II	465	4.90%	28.20%	5.16%	61.72%	NA
Indica III	913	0.30%	59.10%	4.38%	36.14%	NA
Indica Intermediate	786	2.70%	20.60%	6.74%	69.97%	NA
Temperate Japonica	767	89.40%	9.80%	0.52%	0.26%	NA
Tropical Japonica	504	98.40%	1.20%	0.00%	0.40%	NA
Japonica Intermediate	241	85.10%	14.10%	0.41%	0.41%	NA
VI/Aromatic	96	67.70%	22.90%	1.04%	8.33%	NA
Intermediate	90	43.30%	22.20%	8.89%	25.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0331091486	A -> DEL	LOC_Os03g54230.1	N	frameshift_variant	Average:11.771; most accessible tissue: Callus, score: 53.973	N	N	N	N
vg0331091486	A -> G	LOC_Os03g54230.1	synonymous_variant ; p.Leu66Leu; LOW	synonymous_codon	Average:11.771; most accessible tissue: Callus, score: 53.973	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0331091486	NA	4.16E-08	mr1343	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
vg0331091486	NA	5.52E-08	mr1343	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
vg0331091486	NA	3.18E-10	mr1354	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
vg0331091486	NA	1.31E-08	mr1699	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
vg0331091486	1.76E-09	1.27E-18	mr1829	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
vg0331091486	3.84E-11	1.97E-24	mr1829	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
vg0331091486	1.68E-07	NA	mr1842	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
vg0331091486	2.60E-07	7.40E-16	mr1842	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
vg0331091486	NA	3.01E-13	mr1902	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
vg0331091486	NA	4.98E-06	mr1933	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
vg0331091486	NA	9.81E-06	mr1036_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
vg0331091486	NA	4.14E-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
vg0331091486	NA	5.86E-06	mr1169_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
vg0331091486	1.64E-06	2.19E-11	mr1699_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
vg0331091486	2.27E-08	4.19E-19	mr1829_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
vg0331091486	4.19E-09	2.10E-28	mr1829_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
vg0331091486	3.73E-07	NA	mr1842_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
vg0331091486	1.57E-06	6.52E-19	mr1842_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
vg0331091486	1.80E-06	6.30E-15	mr1902_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
vg0331091486	1.11E-06	1.77E-22	mr1902_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
vg0331091486	NA	8.67E-12	mr1933_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