Genome Detective

NGS Details (SRR3458562_Metagenome_example): Carettavirus e142

Assembly

Coverage Length

214 (1 contig(s))

Depth Of Coverage

18.7

Number Of Reads

Reads Per Million

2.65 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

Carettavirus e142 (Taxonomy ID: 2955581)

Reference Genome

NC_055709.1

NT Identity (%)

94.3925

AA Identity (%)

91.6667

Number Of Stop Codons

Number Of CDS

194

Alignment

Alignment Score

380.0 (NT) + 455.0 (AA) = 835.0

Concordance (%)

92.6748

Alignment Method

Local, heuristic, nucleotide (BLASTN)

NT Alignment

Download alignment (FASTA)

Region Bam File

Download BAM file (.bam)

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	74995	75208	0.2%	380	88.8%	214 (100%)	202 (94.4%)	0/0
Mutations:	74997G>A, 74998C>G, 75000A>C, 75004T>C, 75007A>G, 75010C>T, 75186T>C, 75187T>G, 75188T>C, 75189T>G, 75195T>C, 75196A>T

^*: Inserts / Deletes / Misaligned / Frameshifts

Analysis details

This analysis was performed with panviral2.43