RiceVarMap2

Detailed information for vg0431565239:

Variant ID: vg0431565239 (JBrowse)

Variation Type: SNP

Chromosome: chr04

Position: 31565239

Reference Allele: G

Alternative Allele: A

Primary Allele: G

Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AAGGAATGAAGGTGGCCAAGCTTTCGCAGTCTCCGCGCCACCGCAGTCTCCGCGCTGCACTGTGTGTACTGCCACTTTCGATGAGATTGACTCCATCTCC[G/A]
CTAGCGCTAAAACAGCTGTTGAAAATTCCATCTAATATCATCCATTCTCTAAGAGAGCTAGTTATTTCTAACTGTCCTGATCTGGAGTTCGGTGGAGAAG

Reverse complement sequence

CTTCTCCACCGAACTCCAGATCAGGACAGTTAGAAATAACTAGCTCTCTTAGAGAATGGATGATATTAGATGGAATTTTCAACAGCTGTTTTAGCGCTAG[C/T]
GGAGATGGAGTCAATCTCATCGAAAGTGGCAGTACACACAGTGCAGCGCGGAGACTGCGGTGGCGCGGAGACTGCGAAAGCTTGGCCACCTTCATTCCTT

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	95.80%	0.90%	2.07%	1.23%	NA
All Indica	2759	94.20%	1.50%	2.36%	1.92%	NA
All Japonica	1512	98.00%	0.00%	1.72%	0.26%	NA
Aus	269	99.60%	0.00%	0.37%	0.00%	NA
Indica I	595	98.70%	0.00%	1.01%	0.34%	NA
Indica II	465	89.20%	7.50%	2.80%	0.43%	NA
Indica III	913	94.00%	0.00%	2.96%	3.07%	NA
Indica Intermediate	786	94.10%	0.80%	2.42%	2.67%	NA
Temperate Japonica	767	98.60%	0.00%	0.91%	0.52%	NA
Tropical Japonica	504	97.00%	0.00%	2.98%	0.00%	NA
Japonica Intermediate	241	98.30%	0.00%	1.66%	0.00%	NA
VI/Aromatic	96	96.90%	0.00%	2.08%	1.04%	NA
Intermediate	90	94.40%	1.10%	4.44%	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
vg0431565239	G -> DEL	LOC_Os04g53000.1	N	frameshift_variant	Average:33.027; most accessible tissue: Callus, score: 85.988	N	N	N	N
vg0431565239	G -> A	LOC_Os04g53000.1	synonymous_variant ; p.Pro32Pro; LOW	synonymous_codon	Average:33.027; most accessible tissue: Callus, score: 85.988	N	N	N	N

Showing 1 to 2 of 2 entries

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Detailed information for vg0431565239:

Flanking Sequence (100 bp) in Reference Genome:

Reverse complement sequence

Allele Frequencies:

Allele Effect:

RiceVarMap v2.0

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