Genome Detective

NGS Details (SRR3458562_Metagenome_example): Tefnutvirus siom18

Assembly

Coverage Length

136 (1 contig(s))

Depth Of Coverage

7.3

Number Of Reads

Reads Per Million

0.58 rpm (after QC)

Ambiguities

Assembly Method

de novo + reference guided assembly

Consensus Caller

Bcf Tools

Coverage Map

Map

Variant Tables

Consensus Variants

Download consensus variants (vcf)

Minority Variants

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SNP Variants Table

Download SNP mutations table (csv)

Annotated Variants Table

Download annotated variants table (csv)

Assignment

Type

Tefnutvirus siom18 (Taxonomy ID: 2734147)

Reference Genome

NC_021536.1

NT Identity (%)

78.6765

AA Identity (%)

86.6667

Number Of Stop Codons

Number Of CDS

209

Alignment

Alignment Score

156.0 (NT) + 269.0 (AA) = 425.0

Concordance (%)

76.7148

Alignment Method

Local, heuristic, nucleotide (BLASTN)

NT Alignment

Download alignment (FASTA)

Region Bam File

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CDS Alignment

Download CDS alignment (FASTA)

Consensus Sequence

Download consensus sequence (FASTA) (Including IUPAC ambiguity codes)

Consensus Contigs

Download consensus contigs (FASTA)

Genome Region

Select a protein in the search box or a mutation in the table below to see the alignment details. Duplicated protein names are extended with "- CDS name".

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Alignment Detailed Statistics


	Begin	End	Coverage	Score	Concordance	Matches	Identities	I/D/M/F^*	Stop Codons
NT	153164	153299	0.1%	156	57.4%	136 (100%)	107 (78.7%)	0/0
Mutations:	153166A>C 153172A>G 153174C>A 153175A>G 153177T>C 153183T>A 153189C>G 153192T>C 153195T>A 153201T>C 153204C>T 153207T>C 153210T>C 153213A>T 153219A>G 153225C>T 153226A>C 153228G>C 153231G>A 153232T>G 153234A>G 153255G>T 153261T>C 153264G>C 153273C>T 153276T>C 153279G>A 153289C>A 153294T>C

^*: Inserts / Deletes / Misaligned / Frameshifts

Analysis details

This analysis was performed with panviral2.43