Genome Detective

NGS Details (SRR3458562_Metagenome_example): Agtrevirus SKML39

Assembly

Coverage Length

125 (1 contig(s))

Depth Of Coverage

62.3

Number Of Reads

107

Reads Per Million

6.90 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

Download minority variants (vcf)

SNP Variants Table

Download SNP mutations table (csv)

Annotated Variants Table

Download annotated variants table (csv)

Assignment

Type

Agtrevirus SKML39 (Taxonomy ID: 2169690)

Reference Genome

NC_019910.1

NT Identity (%)

100.0

AA Identity (%)

100.0

Number Of Stop Codons

Number Of CDS

208

Alignment

Alignment Score

250.0 (NT) + 268.0 (AA) = 518.0

Concordance (%)

100.0

Alignment Method

Local, heuristic, nucleotide (BLASTN)

NT Alignment

Download alignment (FASTA)

Region Bam File

Download BAM file (.bam)

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	24501	24625	0.1%	250	100%	125 (100%)	125 (100%)	0/0
Mutations:	none

^*: Inserts / Deletes / Misaligned / Frameshifts

Analysis details

This analysis was performed with panviral2.43