Genome Detective

NGS Details (SRR3458562_Metagenome_example): Libanvirus ptim40

Assembly

Coverage Length

131 (1 contig(s))

Depth Of Coverage

12.4

Number Of Reads

Reads Per Million

1.03 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

Libanvirus ptim40 (Taxonomy ID: 2734115)

Reference Genome

NC_028663.1

NT Identity (%)

75.5725

AA Identity (%)

81.8182

Number Of Stop Codons

Number Of CDS

235

Alignment

Alignment Score

134.0 (NT) + 303.0 (AA) = 437.0

Concordance (%)

72.1122

Alignment Method

Local, heuristic, nucleotide (BLASTN)

NT Alignment

Download alignment (FASTA)

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	19493	19623	0.1%	134	51.1%	131 (100%)	99 (75.6%)	0/0
Mutations:	19502T>A 19505C>T 19508C>T 19514C>T 19520A>T 19538C>T 19542C>T 19547C>A 19553A>C 19566T>C 19568G>T 19569G>T 19574A>T 19576T>A 19580C>T 19581A>C 19583A>T 19586T>C 19587C>G 19590C>T 19592T>G 19595C>T 19597T>A 19599G>A 19602A>C 19604C>A 19605G>A 19611C>T 19613T>G 19616A>T 19619A>C 19622G>A

^*: Inserts / Deletes / Misaligned / Frameshifts

Analysis details

This analysis was performed with panviral2.43