Genome Detective

NGS Details (SRR3458562_Metagenome_example): Bovine alphaherpesvirus 1

Assembly

Coverage Length

67956 (248 contig(s))

Depth Of Coverage

22.2

Number Of Reads

14789

Reads Per Million

954.25 rpm (after QC)

Ambiguities

Assembly Method

read mapping against reference + variant calling

Consensus Caller

Bcf Tools

Coverage Map

Map

Variant Tables

Consensus Variants

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Minority Variants

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SNP Variants Table

Download SNP mutations table (csv)

Annotated Variants Table

Download annotated variants table (csv)

Assignment

Type

Bovine alphaherpesvirus 1 (Taxonomy ID: 10320)

Reference Genome

NC_063268.1

NT Identity (%)

99.9456

AA Identity (%)

99.0897

Number Of Stop Codons

Number Of CDS

Alignment

Alignment Score

135758.0 (NT) + 133538.0 (AA) = 269296.0

Concordance (%)

99.8488

Alignment Method

Local, heuristic, nucleotide (BLASTN)

NT Alignment

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Region Bam File

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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	71	134071	50.4%	135758	99.9%	67956 (99.9%)	67920 (99.9%)	1/0
Mutations:	1224T>G 7418A>G 7424T>G 12161G>A 12724C>A 19861G>T 23113T>A 23117G>C 23300T>G 23877G>A 25550_25551insT 26284C>T 26288T>C 37977G>A 37983A>C 40007T>G 41796G>A 46107T>C 48218G>T 57456C>G 60386G>T 66755C>A 67181T>A 68737C>G 71500A>G 79670G>T 80237T>C 90950G>T 91355A>G 94002A>G 97891C>T 97896C>T 100118G>T 100676A>G 114890C>A 117493G>C 121424G>T

^*: Inserts / Deletes / Misaligned / Frameshifts

Analysis details

This analysis was performed with panviral2.43