Version 2.16.3
Genome Detective Platform

NGS Details (SRR3458562_Metagenome_example): Salmonella phage epsilon34

Assembly

1346 (4 contig(s))
14.4
184
11.87 rpm (after QC)
0
de novo + reference guided assembly
Bcf Tools

Coverage Map

Variant Tables

Assignment

Salmonella phage epsilon34 (Taxonomy ID: 348058)
90.4903
87.8525
2
73

Alignment

2180.0 (NT) + 2686.0 (AA) = 4866.0
85.4434
Local, heuristic, nucleotide (BLASTN)

Alignment Detailed Statistics

BeginEndCoverageScoreConcordanceMatchesIdentitiesI/D/M/F*Stop Codons
NT11706420323.1%218081.0%1346 (100%)1218 (90.5%)0/0
Mutations:11716T>C, 11720T>G, 11722C>T, 11728A>G, 11731T>A, 11734T>C, 11735C>A, 11736A>T, 11740A>C, 11742G>A, 11749G>A, 11758C>G, 11759G>A, 11761G>T, 11770A>C, 11771A>C, 11782T>G, 11785T>A, 11786A>T, 11787G>C, 11788C>T, 11791T>C, 11801A>G, 11802T>A, 11803T>A, 11809A>G, 11812G>C, 11815G>T, 11817T>G, 11830G>T, 11836G>A, 11837C>A, 11840G>C, 11841T>C, 11845C>T, 11847A>T, 11854C>T, 11857G>T, 11858A>G, 11860G>A, 11863T>G, 11864A>C, 11869G>A, 11872G>A, 11875T>A, 11878T>G, 11881T>C, 11884G>C, 11891G>C, 11896C>T, 11900A>G, 11908T>C, 11917G>A, 11920C>T, 11934A>G, 11941T>C, 11945C>A, 11962G>A, 11971G>T, 11980A>C, 11981T>A, 11983A>C, 11984G>A, 11985T>C, 11986C>A, 11992A>T, 12004T>A, 12010C>A, 12051C>T, 12069C>T, 12088G>A, 12091G>A, 12092A>G, 12099C>G, 12100A>T, 12103G>A, 12114G>C, 12130G>T, 12132T>A, 12134T>C, 12135T>G, 12137A>C, 12138G>A, 12139C>A, 12140A>C, 12145A>C, 12146C>A, 12149T>G, 12151A>G, 12152A>T, 15913T>C, 15970G>A, 15977A>G, 15984A>C, 15994T>G, 16048G>A, 16147G>A, 16148A>C, 16153C>A, 16195T>C, 16202C>A, 16205G>A, 16207G>A, 16210G>A, 16215C>A, 16216C>A, 40432T>C, 40446G>A, 40454G>C, 40473C>G, 40475C>T, 40482C>A, 40513C>T, 40528A>G, 40531C>A, 40543A>G, 40550C>T, 40553C>T, 40562A>T, 40563G>A, 40615G>A, 40623A>T, 40632C>T, 40641C>T, 40665C>T, 40683C>T, 40704T>G, 40706G>A
CDS
34245024.2%60482.4%109 (100%)88 (80.7%)0/0/0/01
Protein mutations:S346A (11720T>G 11722C>T), Q351M (11735C>A 11736A>T), R353K (11742G>A), V359I (11759G>A 11761G>T), I373E (11801A>G 11802T>A 11803T>A), K377N (11815G>T), M378R (11817T>G), Q385K (11837C>A), V386P (11840G>C 11841T>C), Y388F (11847A>T), K392E (11858A>G 11860G>A), M394L (11864A>C), I398M (11878T>G), E400D (11884G>C), E403Q (11891G>C), N406D (11900A>G), D417G (11934A>G), Q421K (11945C>A), Q432H (11980A>C), S433T (11981T>A 11983A>C), V434T (11984G>A 11985T>C 11986C>A)
Codon mutations:TAT344TAC (11716T>C), TCC346GCT (11720T>G 11722C>T), CAA348CAG (11728A>G), CGT349CGA (11731T>A), ATT350ATC (11734T>C), CAG351ATG (11735C>A 11736A>T), GGA352GGC (11740A>C), AGA353AAA (11742G>A), CAG355CAA (11749G>A), GGC358GGG (11758C>G), GTG359ATT (11759G>A 11761G>T), GCA362GCC (11770A>C), AGA363CGA (11771A>C), GGT366GGG (11782T>G), GCT367GCA (11785T>A), AGC368TCT (11786A>T 11787G>C 11788C>T), GGT369GGC (11791T>C), ATT373GAA (11801A>G 11802T>A 11803T>A), GAA375GAG (11809A>G), GCG376GCC (11812G>C), AAG377AAT (11815G>T), ATG378AGG (11817T>G), GGG382GGT (11830G>T), CCG384CCA (11836G>A), CAG385AAG (11837C>A), GTT386CCT (11840G>C 11841T>C), GAC387GAT (11845C>T), TAC388TTC (11847A>T), AGC390AGT (11854C>T), CCG391CCT (11857G>T), AAG392GAA (11858A>G 11860G>A), GCT393GCG (11863T>G), ATG394CTG (11864A>C), CAG395CAA (11869G>A), CAG396CAA (11872G>A), TCT397TCA (11875T>A), ATT398ATG (11878T>G), CGT399CGC (11881T>C), GAG400GAC (11884G>C), GAA403CAA (11891G>C), TAC404TAT (11896C>T), AAC406GAC (11900A>G), TAT408TAC (11908T>C), CAG411CAA (11917G>A), TAC412TAT (11920C>T), GAT417GGT (11934A>G), GGT419GGC (11941T>C), CAG421AAG (11945C>A), CAG426CAA (11962G>A), GCG429GCT (11971G>T), CAA432CAC (11980A>C), TCA433ACC (11981T>A 11983A>C), GTC434ACA (11984G>A 11985T>C 11986C>A), GGA436GGT (11992A>T), TCT440TCA (12004T>A), TCC442TCA (12010C>A)
1446.2%22175.9%44 (100%)32 (72.7%)0/0/0/00
Protein mutations:E20K (12088G>A), D21S (12091G>A 12092A>G), T24S (12100A>T), A25T (12103G>A), E28D (12114G>C), A34S (12130G>T 12132T>A), V35A (12134T>C 12135T>G), Q36P (12137A>C 12138G>A), Q37T (12139C>A 12140A>C), T39Q (12145A>C 12146C>A), V40G (12149T>G), N41V (12151A>G 12152A>T)
Codon mutations:AAC7AAT (12051C>T), TTC13TTT (12069C>T), GAA20AAA (12088G>A), GAT21AGT (12091G>A 12092A>G), GGC23GGG (12099C>G), ACC24TCC (12100A>T), GCC25ACC (12103G>A), GAG28GAC (12114G>C), GCT34TCA (12130G>T 12132T>A), GTT35GCG (12134T>C 12135T>G), CAG36CCA (12137A>C 12138G>A), CAA37ACA (12139C>A 12140A>C), ACA39CAA (12145A>C 12146C>A), GTT40GGT (12149T>G), AAT41GTT (12151A>G 12152A>T)
5020652.2%103496.5%157 (100%)151 (96.2%)0/0/0/00
Protein mutations:K124E (15977A>G), E126A (15984A>C), K181Q (16148A>C), Q199K (16202C>A), E200K (16205G>A 16207G>A), T203K (16215C>A 16216C>A)
Codon mutations:CGT102CGC (15913T>C), ACG121ACA (15970G>A), AAG124GAG (15977A>G), GAA126GCA (15984A>C), CGT129CGG (15994T>G), CTG147CTA (16048G>A), CCG180CCA (16147G>A), AAA181CAA (16148A>C), GCC182GCA (16153C>A), ATT196ATC (16195T>C), CAA199AAA (16202C>A), GAG200AAA (16205G>A 16207G>A), AAG201AAA (16210G>A), ACC203AAA (16215C>A 16216C>A)
14415910.1%7982.3%16 (100%)14 (87.5%)0/0/0/01
Protein mutations:R154K (40446G>A), E157Q (40454G>C)
Codon mutations:GCT149GCC (40432T>C), AGA154AAA (40446G>A), GAG157CAG (40454G>C)
19162.3%50487.7%91 (100%)81 (89.0%)0/0/0/00
Protein mutations:A6V (40475C>T), N24D (40528A>G), H25N (40531C>A), N29D (40543A>G), T31I (40550C>T), A32V (40553C>T), E35V (40562A>T 40563G>A), D53N (40615G>A), R83H (40706G>A)
Codon mutations:ACC5ACG (40473C>G), GCG6GTG (40475C>T), ATC8ATA (40482C>A), CTG19TTG (40513C>T), AAT24GAT (40528A>G), CAT25AAT (40531C>A), AAC29GAC (40543A>G), ACC31ATC (40550C>T), GCC32GTC (40553C>T), GAG35GTA (40562A>T 40563G>A), GAT53AAT (40615G>A), GCA55GCT (40623A>T), GAC58GAT (40632C>T), TAC61TAT (40641C>T), AAC69AAT (40665C>T), CTC75CTT (40683C>T), GGT82GGG (40704T>G), CGT83CAT (40706G>A)
12438.7%12386.6%24 (100%)20 (83.3%)0/0/0/00
Protein mutations:T3M (40665C>T), S9F (40683C>T), V16G (40704T>G), V17I (40706G>A)
Codon mutations:ACG3ATG (40665C>T), TCC9TTC (40683C>T), GTC16GGC (40704T>G), GTA17ATA (40706G>A)
12024.7%12196.8%20 (100%)19 (95.0%)0/0/0/00
Proteins
34245024.2%60482.4%109 (100%)88 (80.7%)0/0/0/01
Protein mutations:S346A (11720T>G 11722C>T), Q351M (11735C>A 11736A>T), R353K (11742G>A), V359I (11759G>A 11761G>T), I373E (11801A>G 11802T>A 11803T>A), K377N (11815G>T), M378R (11817T>G), Q385K (11837C>A), V386P (11840G>C 11841T>C), Y388F (11847A>T), K392E (11858A>G 11860G>A), M394L (11864A>C), I398M (11878T>G), E400D (11884G>C), E403Q (11891G>C), N406D (11900A>G), D417G (11934A>G), Q421K (11945C>A), Q432H (11980A>C), S433T (11981T>A 11983A>C), V434T (11984G>A 11985T>C 11986C>A)
Codon mutations:TAT344TAC (11716T>C), TCC346GCT (11720T>G 11722C>T), CAA348CAG (11728A>G), CGT349CGA (11731T>A), ATT350ATC (11734T>C), CAG351ATG (11735C>A 11736A>T), GGA352GGC (11740A>C), AGA353AAA (11742G>A), CAG355CAA (11749G>A), GGC358GGG (11758C>G), GTG359ATT (11759G>A 11761G>T), GCA362GCC (11770A>C), AGA363CGA (11771A>C), GGT366GGG (11782T>G), GCT367GCA (11785T>A), AGC368TCT (11786A>T 11787G>C 11788C>T), GGT369GGC (11791T>C), ATT373GAA (11801A>G 11802T>A 11803T>A), GAA375GAG (11809A>G), GCG376GCC (11812G>C), AAG377AAT (11815G>T), ATG378AGG (11817T>G), GGG382GGT (11830G>T), CCG384CCA (11836G>A), CAG385AAG (11837C>A), GTT386CCT (11840G>C 11841T>C), GAC387GAT (11845C>T), TAC388TTC (11847A>T), AGC390AGT (11854C>T), CCG391CCT (11857G>T), AAG392GAA (11858A>G 11860G>A), GCT393GCG (11863T>G), ATG394CTG (11864A>C), CAG395CAA (11869G>A), CAG396CAA (11872G>A), TCT397TCA (11875T>A), ATT398ATG (11878T>G), CGT399CGC (11881T>C), GAG400GAC (11884G>C), GAA403CAA (11891G>C), TAC404TAT (11896C>T), AAC406GAC (11900A>G), TAT408TAC (11908T>C), CAG411CAA (11917G>A), TAC412TAT (11920C>T), GAT417GGT (11934A>G), GGT419GGC (11941T>C), CAG421AAG (11945C>A), CAG426CAA (11962G>A), GCG429GCT (11971G>T), CAA432CAC (11980A>C), TCA433ACC (11981T>A 11983A>C), GTC434ACA (11984G>A 11985T>C 11986C>A), GGA436GGT (11992A>T), TCT440TCA (12004T>A), TCC442TCA (12010C>A)
1446.2%22175.9%44 (100%)32 (72.7%)0/0/0/00
Protein mutations:E20K (12088G>A), D21S (12091G>A 12092A>G), T24S (12100A>T), A25T (12103G>A), E28D (12114G>C), A34S (12130G>T 12132T>A), V35A (12134T>C 12135T>G), Q36P (12137A>C 12138G>A), Q37T (12139C>A 12140A>C), T39Q (12145A>C 12146C>A), V40G (12149T>G), N41V (12151A>G 12152A>T)
Codon mutations:AAC7AAT (12051C>T), TTC13TTT (12069C>T), GAA20AAA (12088G>A), GAT21AGT (12091G>A 12092A>G), GGC23GGG (12099C>G), ACC24TCC (12100A>T), GCC25ACC (12103G>A), GAG28GAC (12114G>C), GCT34TCA (12130G>T 12132T>A), GTT35GCG (12134T>C 12135T>G), CAG36CCA (12137A>C 12138G>A), CAA37ACA (12139C>A 12140A>C), ACA39CAA (12145A>C 12146C>A), GTT40GGT (12149T>G), AAT41GTT (12151A>G 12152A>T)
5020652.2%103496.5%157 (100%)151 (96.2%)0/0/0/00
Protein mutations:K124E (15977A>G), E126A (15984A>C), K181Q (16148A>C), Q199K (16202C>A), E200K (16205G>A 16207G>A), T203K (16215C>A 16216C>A)
Codon mutations:CGT102CGC (15913T>C), ACG121ACA (15970G>A), AAG124GAG (15977A>G), GAA126GCA (15984A>C), CGT129CGG (15994T>G), CTG147CTA (16048G>A), CCG180CCA (16147G>A), AAA181CAA (16148A>C), GCC182GCA (16153C>A), ATT196ATC (16195T>C), CAA199AAA (16202C>A), GAG200AAA (16205G>A 16207G>A), AAG201AAA (16210G>A), ACC203AAA (16215C>A 16216C>A)
14415910.1%7982.3%16 (100%)14 (87.5%)0/0/0/01
Protein mutations:R154K (40446G>A), E157Q (40454G>C)
Codon mutations:GCT149GCC (40432T>C), AGA154AAA (40446G>A), GAG157CAG (40454G>C)
19162.3%50487.7%91 (100%)81 (89.0%)0/0/0/00
Protein mutations:A6V (40475C>T), N24D (40528A>G), H25N (40531C>A), N29D (40543A>G), T31I (40550C>T), A32V (40553C>T), E35V (40562A>T 40563G>A), D53N (40615G>A), R83H (40706G>A)
Codon mutations:ACC5ACG (40473C>G), GCG6GTG (40475C>T), ATC8ATA (40482C>A), CTG19TTG (40513C>T), AAT24GAT (40528A>G), CAT25AAT (40531C>A), AAC29GAC (40543A>G), ACC31ATC (40550C>T), GCC32GTC (40553C>T), GAG35GTA (40562A>T 40563G>A), GAT53AAT (40615G>A), GCA55GCT (40623A>T), GAC58GAT (40632C>T), TAC61TAT (40641C>T), AAC69AAT (40665C>T), CTC75CTT (40683C>T), GGT82GGG (40704T>G), CGT83CAT (40706G>A)
12438.7%12386.6%24 (100%)20 (83.3%)0/0/0/00
Protein mutations:T3M (40665C>T), S9F (40683C>T), V16G (40704T>G), V17I (40706G>A)
Codon mutations:ACG3ATG (40665C>T), TCC9TTC (40683C>T), GTC16GGC (40704T>G), GTA17ATA (40706G>A)
12024.7%12196.8%20 (100%)19 (95.0%)0/0/0/00
Protein mutations:none
Codon mutations:none
*: Inserts / Deletes / Misaligned / Frameshifts

Analysis details

This analysis was performed with panviral2.43