Genome Detective

NGS Details (SRR3458562_Metagenome_example): Ahtivirus sagseatwo

Assembly

Coverage Length

236 (1 contig(s))

Depth Of Coverage

8.1

Number Of Reads

Reads Per Million

1.42 rpm (after QC)

Ambiguities

Assembly Method

de novo + reference guided assembly

Consensus Caller

Bcf Tools

Coverage Map

Map

Variant Tables

Consensus Variants

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Minority Variants

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SNP Variants Table

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Annotated Variants Table

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Assignment

Type

Ahtivirus sagseatwo (Taxonomy ID: 2734079)

Reference Genome

NC_015281.1

NT Identity (%)

75.0

AA Identity (%)

84.8101

Number Of Stop Codons

Number Of CDS

230

Alignment

Alignment Score

236.0 (NT) + 514.0 (AA) = 750.0

Concordance (%)

71.7017

Alignment Method

Local, heuristic, nucleotide (BLASTN)

NT Alignment

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Region Bam File

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CDS Alignment

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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	169495	169730	0.1%	236	50.0%	236 (100%)	177 (75.0%)	0/0
Mutations:	169504A>T 169511G>A 169513C>T 169514G>A 169515C>G 169517A>T 169519G>A 169521G>C 169525C>T 169528A>G 169529C>T 169532C>T 169534C>G 169537G>A 169549A>T 169561C>A 169567C>T 169568G>A 169569T>C 169573C>T 169588T>G 169594C>G 169599A>C 169600C>T 169606A>T 169609A>T 169612T>C 169618T>A 169621A>T 169626C>G 169627A>C 169628T>C 169630G>A 169633T>A 169643C>T 169645T>A 169646A>C 169648G>T 169651G>A 169654T>C 169657A>G 169658T>C 169660G>T 169663A>T 169666T>A 169667C>T 169668T>C 169670A>G 169673G>C 169674G>A 169675C>A 169676A>T 169678C>G 169679C>A 169681T>A 169693T>A 169696T>C 169711T>A 169720A>T

^*: Inserts / Deletes / Misaligned / Frameshifts

Analysis details

This analysis was performed with panviral2.43