RiceVarMap2

Detailed information for vg0431565338:

Variant ID: vg0431565338 (JBrowse)

Variation Type: SNP

Chromosome: chr04

Position: 31565338

Reference Allele: A

Alternative Allele: G

Primary Allele: A

Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CGCTAGCGCTAAAACAGCTGTTGAAAATTCCATCTAATATCATCCATTCTCTAAGAGAGCTAGTTATTTCTAACTGTCCTGATCTGGAGTTCGGTGGAGA[A/G]
GAGGGAGCCCTCCGAGGATACACCTCTCTTAAGTCCATTAAAGTTCAGGGTTGCCCCAAACTGATACCGTTGTTGGTGAGTGGTAAGATGGAGGTTGGAT

Reverse complement sequence

ATCCAACCTCCATCTTACCACTCACCAACAACGGTATCAGTTTGGGGCAACCCTGAACTTTAATGGACTTAAGAGAGGTGTATCCTCGGAGGGCTCCCTC[T/C]
TCTCCACCGAACTCCAGATCAGGACAGTTAGAAATAACTAGCTCTCTTAGAGAATGGATGATATTAGATGGAATTTTCAACAGCTGTTTTAGCGCTAGCG

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	97.50%	0.10%	2.03%	0.40%	NA
All Indica	2759	96.20%	0.00%	3.19%	0.62%	NA
All Japonica	1512	99.70%	0.10%	0.20%	0.07%	NA
Aus	269	99.60%	0.40%	0.00%	0.00%	NA
Indica I	595	99.20%	0.00%	0.84%	0.00%	NA
Indica II	465	97.20%	0.00%	2.15%	0.65%	NA
Indica III	913	94.20%	0.10%	4.49%	1.20%	NA
Indica Intermediate	786	95.50%	0.00%	4.07%	0.38%	NA
Temperate Japonica	767	99.60%	0.00%	0.26%	0.13%	NA
Tropical Japonica	504	99.80%	0.20%	0.00%	0.00%	NA
Japonica Intermediate	241	99.60%	0.00%	0.41%	0.00%	NA
VI/Aromatic	96	96.90%	0.00%	3.12%	0.00%	NA
Intermediate	90	96.70%	0.00%	2.22%	1.11%	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
vg0431565338	A -> DEL	LOC_Os04g53000.1	N	frameshift_variant	Average:50.413; most accessible tissue: Callus, score: 73.976	N	N	N	N
vg0431565338	A -> G	LOC_Os04g53000.1	synonymous_variant ; p.Glu65Glu; LOW	synonymous_codon	Average:50.413; most accessible tissue: Callus, score: 73.976	N	N	N	N

Showing 1 to 2 of 2 entries

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Detailed information for vg0431565338:

Flanking Sequence (100 bp) in Reference Genome:

Reverse complement sequence

Allele Frequencies:

Allele Effect:

RiceVarMap v2.0

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