Search for Variation information by Variation ID:

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

Detailed information for vg0428951624:

Variant ID: vg0428951624 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 28951624
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 241. )

Flanking Sequence (100 bp) in Reference Genome:

CGTGTAACCACGTGCCACATACCACCACGGCATACGGACGAAAGACGTGATATAGTTCCCAACCCATCCTAGCCATAAACAAGAGTACCGACCCAACCCC[G/A]
CCTACGGCCGGAACCCCCGAGACAGGTAGGCAGTAGGGATGAAAACGGAGCGGATAGTTTCCGTCCGCTCCGGACAAAAACGGATACGGATACCTTTCGG

Reverse complement sequence

CCGAAAGGTATCCGTATCCGTTTTTGTCCGGAGCGGACGGAAACTATCCGCTCCGTTTTCATCCCTACTGCCTACCTGTCTCGGGGGTTCCGGCCGTAGG[C/T]
GGGGTTGGGTCGGTACTCTTGTTTATGGCTAGGATGGGTTGGGAACTATATCACGTCTTTCGTCCGTATGCCGTGGTGGTATGTGGCACGTGGTTACACG

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	77.90%	21.90%	0.23%	0.00%	NA
All Indica	2759	87.20%	12.50%	0.33%	0.00%	NA
All Japonica	1512	67.90%	32.00%	0.07%	0.00%	NA
Aus	269	60.60%	39.00%	0.37%	0.00%	NA
Indica I	595	97.50%	2.00%	0.50%	0.00%	NA
Indica II	465	96.10%	3.70%	0.22%	0.00%	NA
Indica III	913	73.80%	25.60%	0.55%	0.00%	NA
Indica Intermediate	786	89.70%	10.30%	0.00%	0.00%	NA
Temperate Japonica	767	86.20%	13.80%	0.00%	0.00%	NA
Tropical Japonica	504	54.00%	45.80%	0.20%	0.00%	NA
Japonica Intermediate	241	39.00%	61.00%	0.00%	0.00%	NA
VI/Aromatic	96	18.80%	81.20%	0.00%	0.00%	NA
Intermediate	90	75.60%	24.40%	0.00%	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
vg0428951624	G -> A	LOC_Os04g48570.1	downstream_gene_variant ; 2287.0bp to feature; MODIFIER	silent_mutation	Average:46.439; most accessible tissue: Minghui63 young leaf, score: 63.571	N	N	N	N
vg0428951624	G -> A	LOC_Os04g48580.1	intron_variant ; MODIFIER	silent_mutation	Average:46.439; most accessible tissue: Minghui63 young leaf, score: 63.571	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0428951624	NA	3.98E-07	mr1226	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
vg0428951624	NA	5.13E-06	mr1807	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
vg0428951624	7.92E-07	7.92E-07	mr1193_2	Jap_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
vg0428951624	NA	3.36E-06	mr1318_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
vg0428951624	NA	1.58E-07	mr1521_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
vg0428951624	NA	4.65E-06	mr1531_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
vg0428951624	NA	2.12E-06	mr1680_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
vg0428951624	NA	1.80E-06	mr1788_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
vg0428951624	NA	1.29E-07	mr1788_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
vg0428951624	NA	3.41E-06	mr1976_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