RiceVarMap2

Search for Variation information by Variation ID:

Detailed information for vg0224480548:

Variant ID: vg0224480548 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 24480548
Reference Allele: G	Alternative Allele: A
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.99, G: 0.02, others allele: 0.00, population size: 268. )

Flanking Sequence (100 bp) in Reference Genome:

CATGCCAAGCAGGCAAGGTACATCCGTACGCATCAGGAAATAAAGGCCATTTCCTAATCACTTTGTCAATTTTTTTGGCATAAACCTTTACATAAACCAA[G/A]
TGAATGATTATTTTTTGGCATTGCCAATTGTTTTGGCTTGGGTAAGTTTGGGTCTGTTTGGGGAAGCTTTTAGATTCTGAGAAGCAGCTGTTTGGTAGCC

Reverse complement sequence

GGCTACCAAACAGCTGCTTCTCAGAATCTAAAAGCTTCCCCAAACAGACCCAAACTTACCCAAGCCAAAACAATTGGCAATGCCAAAAAATAATCATTCA[C/T]
TTGGTTTATGTAAAGGTTTATGCCAAAAAAATTGACAAAGTGATTAGGAAATGGCCTTTATTTCCTGATGCGTACGGATGTACCTTGCCTGCTTGGCATG

Allele Frequencies:

Search:

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	84.40%	15.40%	0.13%	0.00%	NA
All Indica	2759	91.70%	8.30%	0.07%	0.00%	NA
All Japonica	1512	71.00%	28.70%	0.26%	0.00%	NA
Aus	269	87.40%	12.60%	0.00%	0.00%	NA
Indica I	595	98.80%	1.20%	0.00%	0.00%	NA
Indica II	465	95.10%	4.90%	0.00%	0.00%	NA
Indica III	913	87.30%	12.70%	0.00%	0.00%	NA
Indica Intermediate	786	89.30%	10.40%	0.25%	0.00%	NA
Temperate Japonica	767	66.00%	33.60%	0.39%	0.00%	NA
Tropical Japonica	504	78.40%	21.40%	0.20%	0.00%	NA
Japonica Intermediate	241	71.80%	28.20%	0.00%	0.00%	NA
VI/Aromatic	96	81.20%	18.80%	0.00%	0.00%	NA
Intermediate	90	82.20%	17.80%	0.00%	0.00%	NA

Showing 1 to 13 of 13 entries

Allele Effect:

Search:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0224480548	G -> A	LOC_Os02g40410.1	upstream_gene_variant ; 3225.0bp to feature; MODIFIER	silent_mutation	Average:58.662; most accessible tissue: Minghui63 panicle, score: 81.412	N	N	N	N
vg0224480548	G -> A	LOC_Os02g40410.2	upstream_gene_variant ; 4895.0bp to feature; MODIFIER	silent_mutation	Average:58.662; most accessible tissue: Minghui63 panicle, score: 81.412	N	N	N	N
vg0224480548	G -> A	LOC_Os02g40420.1	downstream_gene_variant ; 2442.0bp to feature; MODIFIER	silent_mutation	Average:58.662; most accessible tissue: Minghui63 panicle, score: 81.412	N	N	N	N
vg0224480548	G -> A	LOC_Os02g40410-LOC_Os02g40420	intergenic_region ; MODIFIER	silent_mutation	Average:58.662; most accessible tissue: Minghui63 panicle, score: 81.412	N	N	N	N

Showing 1 to 4 of 4 entries

Putative Genotype-Phenotype Associations:

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Search:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0224480548	1.90E-06	NA	mr1180	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
vg0224480548	NA	1.35E-06	mr1180	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
vg0224480548	5.48E-06	NA	mr1183	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
vg0224480548	NA	2.16E-07	mr1183	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
vg0224480548	5.43E-06	NA	mr1503	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
vg0224480548	NA	7.78E-08	mr1503	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
vg0224480548	3.55E-06	NA	mr1123_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
vg0224480548	NA	1.83E-07	mr1446_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

Showing 1 to 8 of 8 entries

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Search for Variation information by Variation ID:

Detailed information for vg0224480548:

Flanking Sequence (100 bp) in Reference Genome:

Reverse complement sequence

Allele Frequencies:

Allele Effect:

Putative Genotype-Phenotype Associations:

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