Version 2.16.3
Genome Detective Platform

NGS Details (SRR3458562_Metagenome_example): Enterobacteria phage ST104

Assembly

1326 (4 contig(s))
23.2
287
18.52 rpm (after QC)
0
de novo + reference guided assembly
Bcf Tools

Coverage Map

Variant Tables

Assignment

Enterobacteria phage ST104 (Taxonomy ID: 221029)
88.0
88.3408
2
62

Alignment

1995.0 (NT) + 2492.0 (AA) = 4487.0
81.5879
Local, heuristic, nucleotide (BLASTN)

Alignment Detailed Statistics

BeginEndCoverageScoreConcordanceMatchesIdentitiesI/D/M/F*Stop Codons
NT4765361983.2%199575.7%1324 (99.8%)1166 (87.9%)1/2
Mutations:4832_4833delGC, 4874C>G, 4967G>A, 5070G>A, 5101T>G, 5106T>G, 5112T>C, 5120_5121insT, 5148C>A, 5222G>T, 5226G>T, 5261G>A, 5263T>A, 5270C>A, 5273C>A, 5285T>C, 5288C>T, 5297C>A, 5423T>A, 5428C>G, 5429G>A, 5430T>G, 5431T>C, 5432T>G, 5472G>A, 5481C>T, 5489T>C, 5519G>A, 5537C>T, 5540T>A, 5549T>C, 5551T>C, 5555T>A, 5561A>C, 5569A>C, 5579A>C, 5588A>T, 5597A>T, 5660T>C, 5669A>G, 17871C>T, 35792G>C, 35795A>G, 35798T>C, 35799T>A, 35804G>T, 35807C>A, 35810G>T, 35813G>T, 35819G>T, 35825A>T, 35828C>T, 35829C>A, 35830G>A, 35831T>A, 35840G>A, 35849T>C, 35852T>C, 35853T>C, 35858G>T, 35864A>G, 35873A>G, 35875A>C, 35876T>A, 35891T>A, 35894C>T, 35895A>C, 35897G>T, 35900G>T, 35906A>T, 35909T>C, 35915A>G, 35928T>C, 35930A>G, 35936C>T, 35939G>C, 35940C>A, 35942T>A, 35945T>G, 35948T>A, 35950A>C, 35951T>G, 35954C>T, 35955A>G, 35956A>G, 35958G>A, 35960C>G, 35966G>T, 35969T>C, 35972A>C, 35973T>G, 35978C>T, 35983G>A, 35987A>G, 35990T>C, 35999T>A, 36001C>T, 36002T>A, 36006G>A, 36008T>C, 36009A>G, 36011C>G, 36014A>C, 36021G>A, 36026T>C, 36032G>C, 36035A>C, 36039G>T, 36047A>T, 36050A>T, 36053T>G, 36054C>G, 36056A>T, 36059G>A, 36062T>G, 36065G>A, 36068A>T, 36070G>A, 36071C>T, 36080C>T, 36085C>A, 36086G>A, 36099A>C, 36101C>T, 36110C>T, 36111G>T, 36113A>T, 36114A>G, 36115A>G, 36120G>T, 36121A>C, 36122T>A, 36123G>A, 36124C>T, 36126T>G, 36127C>A, 36128T>C, 36130C>A, 36134C>T, 36136A>G, 36137T>C, 36146T>A, 36149A>T, 36152G>T, 36155T>A, 36158C>T, 36159G>T, 36160G>C, 36161A>T, 36162G>T, 36167A>T, 36168A>T, 36169A>C, 36171C>T, 36172C>T, 36173G>T, 36176A>T, 36177A>C, 36189G>A, 36194C>T
CDS
17680.0%41374.1%76 (100%)74 (97.4%)0/0/1/10
195100%53176.4%95 (99.0%)90 (93.8%)1/0/1/11
Protein mutations:D2V (5263T>A), P3S (5261G>A), L16I (5222G>T), K40N (5148C>A), N49_K50insX (5120_5121insT), D56A (5101T>G)
Codon mutations:GAC2GTC (5263T>A), CCC3TCC (5261G>A), GCC14GCA (5226G>T), CTT16ATT (5222G>T), AAG40AAT (5148C>A), AAT49_AAA50insA-- (5120_5121insT), GCA52GCG (5112T>C), GCA54GCC (5106T>G), GAT56GCT (5101T>G), AGC66AGT (5070G>A)
12826438.6%64590.1%102 (100%)92 (90.2%)0/0/0/01
Protein mutations:D154E (5597A>T), F164V (5569A>C), K170E (5549T>C 5551T>C), S193N (5481C>T), A196V (5472G>A), N210A (5429G>A 5430T>G 5431T>C), E211Q (5428C>G), E212D (5423T>A), K263N (5270C>A)
Codon mutations:ACT130ACC (5669A>G), GCA133GCG (5660T>C), GAT154GAA (5597A>T), CTT157CTA (5588A>T), GGT160GGG (5579A>C), TTT164GTT (5569A>C), CTT166CTG (5561A>C), GCA168GCT (5555T>A), AAA170GAG (5549T>C 5551T>C), ATA173ATT (5540T>A), GCG174GCA (5537C>T), CCC180CCT (5519G>A), CTA190CTG (5489T>C), AGC193AAC (5481C>T), GCA196GTA (5472G>A), CCA209CCC (5432T>G), AAC210GCT (5429G>A 5430T>G 5431T>C), GAA211CAA (5428C>G), GAA212GAT (5423T>A), CCG254CCT (5297C>A), GAG257GAA (5288C>T), CCA258CCG (5285T>C), GTG262GTT (5273C>A), AAG263AAT (5270C>A)
8712023.3%19487.4%34 (100%)32 (94.1%)0/0/0/00
Protein mutations:P87L (17871C>T)
Codon mutations:CCT87CTT (17871C>T)
23136828.8%70977.9%138 (100%)106 (76.8%)0/0/0/00
Protein mutations:S235T (35799T>A), R245K (35829C>A 35830G>A 35831T>A), N260T (35875A>C 35876T>A), N285T (35950A>C 35951T>G), N287G (35955A>G 35956A>G), G288R (35958G>A 35960C>G), S293A (35973T>G), S296N (35983G>A), T302I (36001C>T 36002T>A), D304N (36006G>A 36008T>C), N305E (36009A>G 36011C>G), V309I (36021G>A), A315S (36039G>T), P320A (36054C>G 36056A>T), S325N (36070G>A 36071C>T), A330E (36085C>A 36086G>A), I335L (36099A>C 36101C>T), A339S (36111G>T 36113A>T), N340G (36114A>G 36115A>G), D342S (36120G>T 36121A>C 36122T>A), A343I (36123G>A 36124C>T), S344D (36126T>G 36127C>A 36128T>C), A345D (36130C>A), D347G (36136A>G 36137T>C), M352I (36152G>T), G355S (36159G>T 36160G>C 36161A>T), A356S (36162G>T), N358S (36168A>T 36169A>C), P359F (36171C>T 36172C>T 36173G>T), I361L (36177A>C), V365I (36189G>A)
Codon mutations:TCG232TCC (35792G>C), CTA233CTG (35795A>G), CGT234CGC (35798T>C), TCT235ACT (35799T>A), GCG236GCT (35804G>T), GGC237GGA (35807C>A), GGG238GGT (35810G>T), GCG239GCT (35813G>T), CCG241CCT (35819G>T), TCA243TCT (35825A>T), GTC244GTT (35828C>T), CGT245AAA (35829C>A 35830G>A 35831T>A), CAG248CAA (35840G>A), AAT251AAC (35849T>C), AGT252AGC (35852T>C), TTG253CTG (35853T>C), TCG254TCT (35858G>T), GAA256GAG (35864A>G), AAA259AAG (35873A>G), AAT260ACA (35875A>C 35876T>A), CGT265CGA (35891T>A), GGC266GGT (35894C>T), AGG267CGT (35895A>C 35897G>T), CCG268CCT (35900G>T), GCA270GCT (35906A>T), GGT271GGC (35909T>C), GAA273GAG (35915A>G), TTA278CTG (35928T>C 35930A>G), GAC280GAT (35936C>T), GGG281GGC (35939G>C), CGT282AGA (35940C>A 35942T>A), ACT283ACG (35945T>G), GTT284GTA (35948T>A), AAT285ACG (35950A>C 35951T>G), GTC286GTT (35954C>T), AAT287GGT (35955A>G 35956A>G), GGC288AGG (35958G>A 35960C>G), CTG290CTT (35966G>T), CAT291CAC (35969T>C), GGA292GGC (35972A>C), TCT293GCT (35973T>G), GGC294GGT (35978C>T), AGT296AAT (35983G>A), GCA297GCG (35987A>G), TTT298TTC (35990T>C), GGT301GGA (35999T>A), ACT302ATA (36001C>T 36002T>A), GAT304AAC (36006G>A 36008T>C), AAC305GAG (36009A>G 36011C>G), GGA306GGC (36014A>C), GTT309ATT (36021G>A), CGT310CGC (36026T>C), CCG312CCC (36032G>C), GCA313GCC (36035A>C), GCT315TCT (36039G>T), GCA317GCT (36047A>T), GCA318GCT (36050A>T), CCT319CCG (36053T>G), CCA320GCT (36054C>G 36056A>T), ACG321ACA (36059G>A), TCT322TCG (36062T>G), GCG323GCA (36065G>A), GCA324GCT (36068A>T), AGC325AAT (36070G>A 36071C>T), AAC328AAT (36080C>T), GCG330GAA (36085C>A 36086G>A), ATC335CTT (36099A>C 36101C>T), ATC338ATT (36110C>T), GCA339TCT (36111G>T 36113A>T), AAC340GGC (36114A>G 36115A>G), GAT342TCA (36120G>T 36121A>C 36122T>A), GCT343ATT (36123G>A 36124C>T), TCT344GAC (36126T>G 36127C>A 36128T>C), GCT345GAT (36130C>A), CTC346CTT (36134C>T), GAT347GGC (36136A>G 36137T>C), ACT350ACA (36146T>A), GGA351GGT (36149A>T), ATG352ATT (36152G>T), ACT353ACA (36155T>A), GGC354GGT (36158C>T), GGA355TCT (36159G>T 36160G>C 36161A>T), GCA356TCA (36162G>T), GGA357GGT (36167A>T), AAT358TCT (36168A>T 36169A>C), CCG359TTT (36171C>T 36172C>T 36173G>T), GCA360GCT (36176A>T), ATT361CTT (36177A>C), GTT365ATT (36189G>A), CGC366CGT (36194C>T)
Proteins
17680.0%41374.1%76 (100%)74 (97.4%)0/0/1/10
Protein mutations:none
Codon mutations:GTC8GTT (4967G>A), CGG39CGC (4874C>G), CGC53C-- (4832_4833delGC)
195100%53176.4%95 (99.0%)90 (93.8%)1/0/1/11
Protein mutations:D2V (5263T>A), P3S (5261G>A), L16I (5222G>T), K40N (5148C>A), N49_K50insX (5120_5121insT), D56A (5101T>G)
Codon mutations:GAC2GTC (5263T>A), CCC3TCC (5261G>A), GCC14GCA (5226G>T), CTT16ATT (5222G>T), AAG40AAT (5148C>A), AAT49_AAA50insA-- (5120_5121insT), GCA52GCG (5112T>C), GCA54GCC (5106T>G), GAT56GCT (5101T>G), AGC66AGT (5070G>A)
12826438.6%64590.1%102 (100%)92 (90.2%)0/0/0/01
Protein mutations:D154E (5597A>T), F164V (5569A>C), K170E (5549T>C 5551T>C), S193N (5481C>T), A196V (5472G>A), N210A (5429G>A 5430T>G 5431T>C), E211Q (5428C>G), E212D (5423T>A), K263N (5270C>A)
Codon mutations:ACT130ACC (5669A>G), GCA133GCG (5660T>C), GAT154GAA (5597A>T), CTT157CTA (5588A>T), GGT160GGG (5579A>C), TTT164GTT (5569A>C), CTT166CTG (5561A>C), GCA168GCT (5555T>A), AAA170GAG (5549T>C 5551T>C), ATA173ATT (5540T>A), GCG174GCA (5537C>T), CCC180CCT (5519G>A), CTA190CTG (5489T>C), AGC193AAC (5481C>T), GCA196GTA (5472G>A), CCA209CCC (5432T>G), AAC210GCT (5429G>A 5430T>G 5431T>C), GAA211CAA (5428C>G), GAA212GAT (5423T>A), CCG254CCT (5297C>A), GAG257GAA (5288C>T), CCA258CCG (5285T>C), GTG262GTT (5273C>A), AAG263AAT (5270C>A)
8712023.3%19487.4%34 (100%)32 (94.1%)0/0/0/00
Protein mutations:P87L (17871C>T)
Codon mutations:CCT87CTT (17871C>T)
23136828.8%70977.9%138 (100%)106 (76.8%)0/0/0/00
Protein mutations:S235T (35799T>A), R245K (35829C>A 35830G>A 35831T>A), N260T (35875A>C 35876T>A), N285T (35950A>C 35951T>G), N287G (35955A>G 35956A>G), G288R (35958G>A 35960C>G), S293A (35973T>G), S296N (35983G>A), T302I (36001C>T 36002T>A), D304N (36006G>A 36008T>C), N305E (36009A>G 36011C>G), V309I (36021G>A), A315S (36039G>T), P320A (36054C>G 36056A>T), S325N (36070G>A 36071C>T), A330E (36085C>A 36086G>A), I335L (36099A>C 36101C>T), A339S (36111G>T 36113A>T), N340G (36114A>G 36115A>G), D342S (36120G>T 36121A>C 36122T>A), A343I (36123G>A 36124C>T), S344D (36126T>G 36127C>A 36128T>C), A345D (36130C>A), D347G (36136A>G 36137T>C), M352I (36152G>T), G355S (36159G>T 36160G>C 36161A>T), A356S (36162G>T), N358S (36168A>T 36169A>C), P359F (36171C>T 36172C>T 36173G>T), I361L (36177A>C), V365I (36189G>A)
Codon mutations:TCG232TCC (35792G>C), CTA233CTG (35795A>G), CGT234CGC (35798T>C), TCT235ACT (35799T>A), GCG236GCT (35804G>T), GGC237GGA (35807C>A), GGG238GGT (35810G>T), GCG239GCT (35813G>T), CCG241CCT (35819G>T), TCA243TCT (35825A>T), GTC244GTT (35828C>T), CGT245AAA (35829C>A 35830G>A 35831T>A), CAG248CAA (35840G>A), AAT251AAC (35849T>C), AGT252AGC (35852T>C), TTG253CTG (35853T>C), TCG254TCT (35858G>T), GAA256GAG (35864A>G), AAA259AAG (35873A>G), AAT260ACA (35875A>C 35876T>A), CGT265CGA (35891T>A), GGC266GGT (35894C>T), AGG267CGT (35895A>C 35897G>T), CCG268CCT (35900G>T), GCA270GCT (35906A>T), GGT271GGC (35909T>C), GAA273GAG (35915A>G), TTA278CTG (35928T>C 35930A>G), GAC280GAT (35936C>T), GGG281GGC (35939G>C), CGT282AGA (35940C>A 35942T>A), ACT283ACG (35945T>G), GTT284GTA (35948T>A), AAT285ACG (35950A>C 35951T>G), GTC286GTT (35954C>T), AAT287GGT (35955A>G 35956A>G), GGC288AGG (35958G>A 35960C>G), CTG290CTT (35966G>T), CAT291CAC (35969T>C), GGA292GGC (35972A>C), TCT293GCT (35973T>G), GGC294GGT (35978C>T), AGT296AAT (35983G>A), GCA297GCG (35987A>G), TTT298TTC (35990T>C), GGT301GGA (35999T>A), ACT302ATA (36001C>T 36002T>A), GAT304AAC (36006G>A 36008T>C), AAC305GAG (36009A>G 36011C>G), GGA306GGC (36014A>C), GTT309ATT (36021G>A), CGT310CGC (36026T>C), CCG312CCC (36032G>C), GCA313GCC (36035A>C), GCT315TCT (36039G>T), GCA317GCT (36047A>T), GCA318GCT (36050A>T), CCT319CCG (36053T>G), CCA320GCT (36054C>G 36056A>T), ACG321ACA (36059G>A), TCT322TCG (36062T>G), GCG323GCA (36065G>A), GCA324GCT (36068A>T), AGC325AAT (36070G>A 36071C>T), AAC328AAT (36080C>T), GCG330GAA (36085C>A 36086G>A), ATC335CTT (36099A>C 36101C>T), ATC338ATT (36110C>T), GCA339TCT (36111G>T 36113A>T), AAC340GGC (36114A>G 36115A>G), GAT342TCA (36120G>T 36121A>C 36122T>A), GCT343ATT (36123G>A 36124C>T), TCT344GAC (36126T>G 36127C>A 36128T>C), GCT345GAT (36130C>A), CTC346CTT (36134C>T), GAT347GGC (36136A>G 36137T>C), ACT350ACA (36146T>A), GGA351GGT (36149A>T), ATG352ATT (36152G>T), ACT353ACA (36155T>A), GGC354GGT (36158C>T), GGA355TCT (36159G>T 36160G>C 36161A>T), GCA356TCA (36162G>T), GGA357GGT (36167A>T), AAT358TCT (36168A>T 36169A>C), CCG359TTT (36171C>T 36172C>T 36173G>T), GCA360GCT (36176A>T), ATT361CTT (36177A>C), GTT365ATT (36189G>A), CGC366CGT (36194C>T)
*: Inserts / Deletes / Misaligned / Frameshifts

Analysis details

This analysis was performed with panviral2.43