RiceVarMap2

Detailed information for vg0223953133:

Variant ID: vg0223953133 (JBrowse)

Variation Type: SNP

Chromosome: chr02

Position: 23953133

Reference Allele: C

Alternative Allele: T

Primary Allele: C

Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CGAGTTCAAGGATGCCATCGGCGACGATCCGGCGGGCGTCCTGAGCTCCTGGAACAAAACCACCCCTTTCTGCCGGTGGAATGGCGTGAAATGCGGCCGC[C/T]
GGGAGCATCGCGTCACGGCGCTCGAGCTCGCCGGCCAGAACTTGACCGGTCGACTCGCCGCCGCTTCTCTCGGGAATCTGAGTTACCTTCACCTGCTTGA

Reverse complement sequence

TCAAGCAGGTGAAGGTAACTCAGATTCCCGAGAGAAGCGGCGGCGAGTCGACCGGTCAAGTTCTGGCCGGCGAGCTCGAGCGCCGTGACGCGATGCTCCC[G/A]
GCGGCCGCATTTCACGCCATTCCACCGGCAGAAAGGGGTGGTTTTGTTCCAGGAGCTCAGGACGCCCGCCGGATCGTCGCCGATGGCATCCTTGAACTCG

Allele Frequencies:

Search:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	80.80%	2.70%	0.40%	16.08%	NA
All Indica	2759	70.70%	4.60%	0.58%	24.14%	NA
All Japonica	1512	98.40%	0.00%	0.00%	1.59%	NA
Aus	269	81.40%	0.00%	1.12%	17.47%	NA
Indica I	595	85.20%	0.20%	0.17%	14.45%	NA
Indica II	465	80.90%	9.00%	0.22%	9.89%	NA
Indica III	913	52.60%	7.60%	0.77%	39.10%	NA
Indica Intermediate	786	74.70%	1.90%	0.89%	22.52%	NA
Temperate Japonica	767	99.10%	0.00%	0.00%	0.91%	NA
Tropical Japonica	504	97.40%	0.00%	0.00%	2.58%	NA
Japonica Intermediate	241	98.30%	0.00%	0.00%	1.66%	NA
VI/Aromatic	96	81.20%	0.00%	0.00%	18.75%	NA
Intermediate	90	94.40%	0.00%	0.00%	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
vg0223953133	C -> T	LOC_Os02g39660.1	missense_variant ; p.Arg70Trp; MODERATE	nonsynonymous_codon ; R70W	Average:68.797; most accessible tissue: Zhenshan97 young leaf, score: 86.383	unknown	unknown	TOLERATED	0.08
vg0223953133	C -> DEL	LOC_Os02g39660.1	N	frameshift_variant	Average:68.797; most accessible tissue: Zhenshan97 young leaf, score: 86.383	N	N	N	N

Showing 1 to 2 of 2 entries

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Detailed information for vg0223953133:

Flanking Sequence (100 bp) in Reference Genome:

Reverse complement sequence

Allele Frequencies:

Allele Effect:

RiceVarMap v2.0

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