Genome Detective

NGS Details (SRR3458562_Metagenome_example): Agtrevirus EM4

Assembly

Coverage Length

71386 (299 contig(s))

Depth Of Coverage

22.4

Number Of Reads

18788

Reads Per Million

1212.29 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

Agtrevirus EM4 (Taxonomy ID: 2844121)

Reference Genome

NC_049384.1

NT Identity (%)

99.9398

AA Identity (%)

99.0257

Number Of Stop Codons

111

Number Of CDS

219

Alignment

Alignment Score

142582.0 (NT) + 143097.0 (AA) = 285679.0

Concordance (%)

99.929

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	116	160338	44.4%	142582	99.9%	71385 (99.9%)	71343 (99.9%)	1/1
Mutations:	953A>G 974T>C 1029A>C 14141A>G 18863A>C 64221A>G 64324C>T 64342C>T 80250C>T 80283C>T 80295A>G 88119T>C 88149T>C 88191T>C 93648C>T 97073G>A 97088T>C 97115C>T 127031T>C 127405C>T 127462T>C 127546C>T 129523A>G 142140T>C 142194T>C 148332C>T 148429T>C 148435A>T 149906A>G 149927G>A 150016T>C 150062A>T 150080delT 150395A>G 153129C>T 153165T>C 153261_153262insG 153297G>C 155339A>G 155340G>C 155349G>C 160165A>G 160170C>T 160181C>T

^*: Inserts / Deletes / Misaligned / Frameshifts

Analysis details

This analysis was performed with panviral2.43