RiceVarMap2

Search for Variation information by Variation ID:

Detailed information for vg0224963772:

Variant ID: vg0224963772 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 24963772
Reference Allele: A	Alternative Allele: T
Primary Allele: A	Secondary Allele: T

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.82, T: 0.18, others allele: 0.00, population size: 90. )

Flanking Sequence (100 bp) in Reference Genome:

TAATAAAAATGAATGGTCAAATGTTACAAGTAAAAAGTCAAAGCGACATTTATTATAAGACAGGGGTAGTAGTTATCAATGTCACGCATCCCAATCCCTT[A/T]
AAAAAATATATATTAAGAGCCTGCGAAACTCATTTATAGGCTAAAATGAGCCGTGGACCCACTTATTTTGAGCCATAAGCATCCCTTAGCTCCAAGGCTC

Reverse complement sequence

GAGCCTTGGAGCTAAGGGATGCTTATGGCTCAAAATAAGTGGGTCCACGGCTCATTTTAGCCTATAAATGAGTTTCGCAGGCTCTTAATATATATTTTTT[T/A]
AAGGGATTGGGATGCGTGACATTGATAACTACTACCCCTGTCTTATAATAAATGTCGCTTTGACTTTTTACTTGTAACATTTGACCATTCATTTTTATTA

Allele Frequencies:

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Populations	Population Size	Frequency of A(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	76.80%	23.20%	0.00%	0.00%	NA
All Indica	2759	93.90%	6.10%	0.00%	0.00%	NA
All Japonica	1512	43.70%	56.30%	0.00%	0.00%	NA
Aus	269	84.40%	15.60%	0.00%	0.00%	NA
Indica I	595	95.30%	4.70%	0.00%	0.00%	NA
Indica II	465	98.30%	1.70%	0.00%	0.00%	NA
Indica III	913	92.90%	7.10%	0.00%	0.00%	NA
Indica Intermediate	786	91.50%	8.50%	0.00%	0.00%	NA
Temperate Japonica	767	61.80%	38.20%	0.00%	0.00%	NA
Tropical Japonica	504	12.50%	87.50%	0.00%	0.00%	NA
Japonica Intermediate	241	51.50%	48.50%	0.00%	0.00%	NA
VI/Aromatic	96	96.90%	3.10%	0.00%	0.00%	NA
Intermediate	90	62.20%	37.80%	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
vg0224963772	A -> T	LOC_Os02g41610.1	downstream_gene_variant ; 3514.0bp to feature; MODIFIER	silent_mutation	Average:47.038; most accessible tissue: Callus, score: 75.123	N	N	N	N
vg0224963772	A -> T	LOC_Os02g41620.1	downstream_gene_variant ; 892.0bp to feature; MODIFIER	silent_mutation	Average:47.038; most accessible tissue: Callus, score: 75.123	N	N	N	N
vg0224963772	A -> T	LOC_Os02g41620-LOC_Os02g41630	intergenic_region ; MODIFIER	silent_mutation	Average:47.038; most accessible tissue: Callus, score: 75.123	N	N	N	N

Showing 1 to 3 of 3 entries

Putative Genotype-Phenotype Associations:

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Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0224963772	1.83E-07	NA	Spikelet_length	All	Not	Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg0224963772	3.09E-07	1.13E-13	Spikelet_length	Jap_All	YES	Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg0224963772	NA	7.49E-09	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

Showing 1 to 3 of 3 entries

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Search for Variation information by Variation ID:

Detailed information for vg0224963772:

Flanking Sequence (100 bp) in Reference Genome:

Reverse complement sequence

Allele Frequencies:

Allele Effect:

Putative Genotype-Phenotype Associations:

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