RiceVarMap2

Search for Variation information by Variation ID:

Detailed information for vg0213362833:

Variant ID: vg0213362833 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 13362833
Reference Allele: A	Alternative Allele: G
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.96, A: 0.04, others allele: 0.00, population size: 250. )

Flanking Sequence (100 bp) in Reference Genome:

TACATCACCTATGGCAATTGTAGATTGATGCATCCTTCCGCTGCTTGTACTCATGGTTCTGTTGAACCTTAGCTTGCTACTGCTTACAATTGAGCAAAGC[A/G]
TACCTCATCCAAGCTTGCTATCTTCTTTAACTCGAGAGCACTTAAATTAGTGGTATTCCCTACGGTGTTTGCCAGTAAATTAGAATTAGTTAACTCAAAC

Reverse complement sequence

GTTTGAGTTAACTAATTCTAATTTACTGGCAAACACCGTAGGGAATACCACTAATTTAAGTGCTCTCGAGTTAAAGAAGATAGCAAGCTTGGATGAGGTA[T/C]
GCTTTGCTCAATTGTAAGCAGTAGCAAGCTAAGGTTCAACAGAACCATGAGTACAAGCAGCGGAAGGATGCATCAATCTACAATTGCCATAGGTGATGTA

Allele Frequencies:

Search:

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	65.40%	34.60%	0.08%	0.00%	NA
All Indica	2759	99.00%	0.90%	0.14%	0.00%	NA
All Japonica	1512	1.70%	98.30%	0.00%	0.00%	NA
Aus	269	99.60%	0.40%	0.00%	0.00%	NA
Indica I	595	99.80%	0.20%	0.00%	0.00%	NA
Indica II	465	98.30%	1.50%	0.22%	0.00%	NA
Indica III	913	99.50%	0.40%	0.11%	0.00%	NA
Indica Intermediate	786	98.20%	1.50%	0.25%	0.00%	NA
Temperate Japonica	767	0.90%	99.10%	0.00%	0.00%	NA
Tropical Japonica	504	2.40%	97.60%	0.00%	0.00%	NA
Japonica Intermediate	241	2.90%	97.10%	0.00%	0.00%	NA
VI/Aromatic	96	25.00%	75.00%	0.00%	0.00%	NA
Intermediate	90	44.40%	55.60%	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
vg0213362833	A -> G	LOC_Os02g22374.1	5_prime_UTR_variant ; 998.0bp to feature; MODIFIER	silent_mutation	Average:42.847; most accessible tissue: Zhenshan97 flower, score: 65.596	N	N	N	N
vg0213362833	A -> G	LOC_Os02g22374.3	3_prime_UTR_variant ; 245.0bp to feature; MODIFIER	silent_mutation	Average:42.847; most accessible tissue: Zhenshan97 flower, score: 65.596	N	N	N	N
vg0213362833	A -> G	LOC_Os02g22380.1	upstream_gene_variant ; 4969.0bp to feature; MODIFIER	silent_mutation	Average:42.847; most accessible tissue: Zhenshan97 flower, score: 65.596	N	N	N	N
vg0213362833	A -> G	LOC_Os02g22374.4	upstream_gene_variant ; 1056.0bp to feature; MODIFIER	silent_mutation	Average:42.847; most accessible tissue: Zhenshan97 flower, score: 65.596	N	N	N	N
vg0213362833	A -> G	LOC_Os02g22370.1	downstream_gene_variant ; 2181.0bp to feature; MODIFIER	silent_mutation	Average:42.847; most accessible tissue: Zhenshan97 flower, score: 65.596	N	N	N	N
vg0213362833	A -> G	LOC_Os02g22370.3	downstream_gene_variant ; 4581.0bp to feature; MODIFIER	silent_mutation	Average:42.847; most accessible tissue: Zhenshan97 flower, score: 65.596	N	N	N	N
vg0213362833	A -> G	LOC_Os02g22370.2	downstream_gene_variant ; 3027.0bp to feature; MODIFIER	silent_mutation	Average:42.847; most accessible tissue: Zhenshan97 flower, score: 65.596	N	N	N	N
vg0213362833	A -> G	LOC_Os02g22374.2	downstream_gene_variant ; 154.0bp to feature; MODIFIER	silent_mutation	Average:42.847; most accessible tissue: Zhenshan97 flower, score: 65.596	N	N	N	N

Showing 1 to 8 of 8 entries

Search for Variation information by Variation ID:

Detailed information for vg0213362833:

Flanking Sequence (100 bp) in Reference Genome:

Reverse complement sequence

Allele Frequencies:

Allele Effect:

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