RiceVarMap2

Detailed information for vg0136517682:

Variant ID: vg0136517682 (JBrowse)

Variation Type: SNP

Chromosome: chr01

Position: 36517682

Reference Allele: A

Alternative Allele: T

Primary Allele: A

Secondary Allele: T

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 309. )

Flanking Sequence (100 bp) in Reference Genome:

CACCATATAGTTGAATACGTAAAAGCCACAGTCATCCCTGTATGTTTTTGAGAAAGTAGTGTCAGTACAAGCTTTGGGTTGGTTGTATTTCGTTTGTTTT[A/T]
GGAGTCACTCACCCGTTCTGCTGCTCTGGTATATTTTCAACTGTCTCAAAGTCCCAATTAAGTATGTCCATGTTCCACCCTGGAGATGCAAGACGCATGC

Reverse complement sequence

GCATGCGTCTTGCATCTCCAGGGTGGAACATGGACATACTTAATTGGGACTTTGAGACAGTTGAAAATATACCAGAGCAGCAGAACGGGTGAGTGACTCC[T/A]
AAAACAAACGAAATACAACCAACCCAAAGCTTGTACTGACACTACTTTCTCAAAAACATACAGGGATGACTGTGGCTTTTACGTATTCAACTATATGGTG

Allele Frequencies:

Search:

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	39.30%	12.60%	38.34%	9.75%	NA
All Indica	2759	7.40%	21.10%	55.74%	15.69%	NA
All Japonica	1512	97.20%	0.30%	1.46%	1.06%	NA
Aus	269	14.90%	0.40%	82.53%	2.23%	NA
Indica I	595	11.40%	2.00%	73.61%	12.94%	NA
Indica II	465	1.90%	25.40%	57.63%	15.05%	NA
Indica III	913	5.70%	33.00%	42.06%	19.28%	NA
Indica Intermediate	786	9.70%	19.30%	57.00%	13.99%	NA
Temperate Japonica	767	98.70%	0.10%	0.91%	0.26%	NA
Tropical Japonica	504	96.80%	0.20%	2.18%	0.79%	NA
Japonica Intermediate	241	92.90%	1.20%	1.66%	4.15%	NA
VI/Aromatic	96	92.70%	0.00%	6.25%	1.04%	NA
Intermediate	90	61.10%	6.70%	26.67%	5.56%	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
vg0136517682	A -> T	LOC_Os01g63030.1	downstream_gene_variant ; 1069.0bp to feature; MODIFIER	silent_mutation	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N
vg0136517682	A -> T	LOC_Os01g63040.1	intron_variant ; MODIFIER	silent_mutation	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N
vg0136517682	A -> DEL	N	N	silent_mutation	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N

Showing 1 to 3 of 3 entries

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Detailed information for vg0136517682:

Flanking Sequence (100 bp) in Reference Genome:

Reverse complement sequence

Allele Frequencies:

Allele Effect:

RiceVarMap v2.0

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