Version 2.22.2
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