Genome Detective

NGS Details (SRR3458562_Metagenome_example): Limestonevirus RC2014

Assembly

Coverage Length

137632 (39 contig(s))

Depth Of Coverage

388.3

Number Of Reads

498422

Reads Per Million

32160.40 rpm (after QC)

Ambiguities

Assembly Method

read mapping against reference + variant calling

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

Limestonevirus RC2014 (Taxonomy ID: 2169973)

Reference Genome

NC_025452.1

NT Identity (%)

99.9869

AA Identity (%)

99.922

Number Of Stop Codons

183

Number Of CDS

196

Alignment

Alignment Score

275192.0 (NT) + 280627.0 (AA) = 555819.0

Concordance (%)

99.9829

Alignment Method

Local, heuristic, nucleotide (BLASTN)

NT Alignment

Download alignment (FASTA)

Region Bam File

Download BAM zip file

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	20	155346	88.6%	275192	99.9%	137632 (100%)	137614 (99.9%)	0/0
Mutations:	18683T>C 25555A>C 26335C>T 40756C>G 69946G>T 80439A>G 83101C>A 85545A>G 85548G>A 85641G>A 86315A>G 117492T>C 118556G>A 132068A>G 132079C>T 146049A>G 146065T>C 151445T>C

^*: Inserts / Deletes / Misaligned / Frameshifts

Analysis details

This analysis was performed with panviral2.43