RiceVarMap2

Detailed information for vg0224434814:

Variant ID: vg0224434814 (JBrowse)

Variation Type: SNP

Chromosome: chr02

Position: 24434814

Reference Allele: G

Alternative Allele: A

Primary Allele: A

Secondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.70, G: 0.29, others allele: 0.00, population size: 78. )

Flanking Sequence (100 bp) in Reference Genome:

CCAACTCGAACTTAATAAATAATCATGGGCAGGTTAGACATAGAGATTTGAGTGATTGTTATGCACGAATCCAACCGTACAGTAGCAGAATGAAGAAAGT[G/A]
GGAGCCTCTCAAGCGTGTGCGTACCGGGATCGCCGTCGCCGAAGCGCCGCTCTCCCGTCGTGAGCAGTCGGAGAGAATATTGTTGTTCCGGAGACGGAGG

Reverse complement sequence

CCTCCGTCTCCGGAACAACAATATTCTCTCCGACTGCTCACGACGGGAGAGCGGCGCTTCGGCGACGGCGATCCCGGTACGCACACGCTTGAGAGGCTCC[C/T]
ACTTTCTTCATTCTGCTACTGTACGGTTGGATTCGTGCATAACAATCACTCAAATCTCTATGTCTAACCTGCCCATGATTATTTATTAAGTTCGAGTTGG

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	55.40%	24.70%	0.40%	19.55%	NA
All Indica	2759	58.10%	25.60%	0.29%	16.06%	NA
All Japonica	1512	48.20%	22.90%	0.60%	28.31%	NA
Aus	269	71.70%	16.70%	0.00%	11.52%	NA
Indica I	595	45.70%	18.50%	0.34%	35.46%	NA
Indica II	465	76.30%	19.60%	0.22%	3.87%	NA
Indica III	913	52.20%	32.20%	0.11%	15.44%	NA
Indica Intermediate	786	63.40%	26.80%	0.51%	9.29%	NA
Temperate Japonica	767	39.90%	23.20%	0.78%	36.11%	NA
Tropical Japonica	504	63.30%	24.80%	0.40%	11.51%	NA
Japonica Intermediate	241	43.20%	17.80%	0.41%	38.59%	NA
VI/Aromatic	96	41.70%	51.00%	2.08%	5.21%	NA
Intermediate	90	57.80%	23.30%	0.00%	18.89%	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
vg0224434814	G -> A	LOC_Os02g40350.1	downstream_gene_variant ; 1125.0bp to feature; MODIFIER	silent_mutation	Average:67.181; most accessible tissue: Zhenshan97 flower, score: 83.812	N	N	N	N
vg0224434814	G -> A	LOC_Os02g40340.1	intron_variant ; MODIFIER	silent_mutation	Average:67.181; most accessible tissue: Zhenshan97 flower, score: 83.812	N	N	N	N
vg0224434814	G -> A	LOC_Os02g40340.2	intron_variant ; MODIFIER	silent_mutation	Average:67.181; most accessible tissue: Zhenshan97 flower, score: 83.812	N	N	N	N
vg0224434814	G -> DEL	N	N	silent_mutation	Average:67.181; most accessible tissue: Zhenshan97 flower, score: 83.812	N	N	N	N

Showing 1 to 4 of 4 entries

Contact

Address: Room B111, National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural university, Wuhan, 430070, China

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Detailed information for vg0224434814:

Flanking Sequence (100 bp) in Reference Genome:

Reverse complement sequence

Allele Frequencies:

Allele Effect:

RiceVarMap v2.0

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