RiceVarMap2

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Detailed information for vg0213362965:

Variant ID: vg0213362965 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 13362965
Reference Allele: C	Alternative Allele: A
Primary Allele: C	Secondary Allele: A

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

Flanking Sequence (100 bp) in Reference Genome:

TCGAGAGCACTTAAATTAGTGGTATTCCCTACGGTGTTTGCCAGTAAATTAGAATTAGTTAACTCAAACAGTACATGATATATAGTGAAGAAATCACAAG[C/A]
TTAAAAGCTGTTACATACCATCGATCTGTATAAATTAATTTCAGAGATATACAATTAGCAATTAACTGGCAGCGGCATAACAGCTTTGCAAAAGAAGCGA

Reverse complement sequence

TCGCTTCTTTTGCAAAGCTGTTATGCCGCTGCCAGTTAATTGCTAATTGTATATCTCTGAAATTAATTTATACAGATCGATGGTATGTAACAGCTTTTAA[G/T]
CTTGTGATTTCTTCACTATATATCATGTACTGTTTGAGTTAACTAATTCTAATTTACTGGCAAACACCGTAGGGAATACCACTAATTTAAGTGCTCTCGA

Allele Frequencies:

Search:

Populations	Population Size	Frequency of C(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	96.70%	2.50%	0.68%	0.21%	NA
All Indica	2759	98.20%	1.80%	0.00%	0.00%	NA
All Japonica	1512	97.20%	0.00%	2.12%	0.66%	NA
Aus	269	75.50%	24.50%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	99.10%	0.90%	0.00%	0.00%	NA
Indica III	913	97.90%	2.10%	0.00%	0.00%	NA
Indica Intermediate	786	96.60%	3.40%	0.00%	0.00%	NA
Temperate Japonica	767	94.90%	0.00%	3.78%	1.30%	NA
Tropical Japonica	504	99.40%	0.00%	0.60%	0.00%	NA
Japonica Intermediate	241	100.00%	0.00%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	100.00%	0.00%	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
vg0213362965	C -> A	LOC_Os02g22380.1	upstream_gene_variant ; 4837.0bp to feature; MODIFIER	silent_mutation	Average:51.174; most accessible tissue: Zhenshan97 flower, score: 71.071	N	N	N	N
vg0213362965	C -> A	LOC_Os02g22374.4	upstream_gene_variant ; 1188.0bp to feature; MODIFIER	silent_mutation	Average:51.174; most accessible tissue: Zhenshan97 flower, score: 71.071	N	N	N	N
vg0213362965	C -> A	LOC_Os02g22370.1	downstream_gene_variant ; 2313.0bp to feature; MODIFIER	silent_mutation	Average:51.174; most accessible tissue: Zhenshan97 flower, score: 71.071	N	N	N	N
vg0213362965	C -> A	LOC_Os02g22370.3	downstream_gene_variant ; 4713.0bp to feature; MODIFIER	silent_mutation	Average:51.174; most accessible tissue: Zhenshan97 flower, score: 71.071	N	N	N	N
vg0213362965	C -> A	LOC_Os02g22370.2	downstream_gene_variant ; 3159.0bp to feature; MODIFIER	silent_mutation	Average:51.174; most accessible tissue: Zhenshan97 flower, score: 71.071	N	N	N	N
vg0213362965	C -> A	LOC_Os02g22374.2	downstream_gene_variant ; 22.0bp to feature; MODIFIER	silent_mutation	Average:51.174; most accessible tissue: Zhenshan97 flower, score: 71.071	N	N	N	N
vg0213362965	C -> A	LOC_Os02g22374.1	intron_variant ; MODIFIER	silent_mutation	Average:51.174; most accessible tissue: Zhenshan97 flower, score: 71.071	N	N	N	N
vg0213362965	C -> A	LOC_Os02g22374.3	intron_variant ; MODIFIER	silent_mutation	Average:51.174; most accessible tissue: Zhenshan97 flower, score: 71.071	N	N	N	N
vg0213362965	C -> DEL	N	N	silent_mutation	Average:51.174; most accessible tissue: Zhenshan97 flower, score: 71.071	N	N	N	N

Showing 1 to 9 of 9 entries

Search for Variation information by Variation ID:

Detailed information for vg0213362965:

Flanking Sequence (100 bp) in Reference Genome:

Reverse complement sequence

Allele Frequencies:

Allele Effect:

RiceVarMap v2.0

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