Version 2.16.1
Genome Detective Platform

NGS Details (SRR3458562_Metagenome_example): Peduovirus R18C

Assembly

1843 (9 contig(s))
17.3
348
22.45 rpm (after QC)
2
de novo + reference guided assembly
Bcf Tools

Coverage Map

Variant Tables

Assignment

Peduovirus R18C (Taxonomy ID: 2843959)
91.6759
91.3118
4
44

Alignment

2990.0 (NT) + 3550.0 (AA) = 6540.0
88.0334
Local, heuristic, nucleotide (BLASTN)

Alignment Detailed Statistics

BeginEndCoverageScoreConcordanceMatchesIdentitiesI/D/M/F*Stop Codons
NT2987278095.8%299083.3%1814 (98.4%)1663 (90.2%)0/29
Mutations:2987A>G, 2992C>T, 6866T>G, 6867C>T, 6870_6898delGTGCAGTTTCCTGACCTGTCACTGCCTGC, 6899A>G, 11218G>A, 11548G>K, 11600C>S, 11607A>T, 11625T>C, 16518G>A, 16535T>C, 16542T>C, 16546G>A, 16548C>A, 16554G>A, 16557T>A, 16563A>G, 16569T>C, 16570T>C, 16578T>C, 16587T>C, 16596C>T, 16599T>C, 16611C>A, 16614A>G, 16617T>C, 16620C>A, 16623A>T, 16630G>A, 16633A>G, 16638A>G, 16641C>T, 16643G>T, 16644A>G, 16648A>G, 16653C>T, 16659G>A, 16662T>A, 16668A>G, 16671A>G, 16678A>G, 16683T>A, 16685A>G, 16686A>T, 16688G>A, 16689T>G, 16692A>T, 16695A>G, 16701C>T, 16707T>A, 16713A>G, 16716G>A, 16722C>T, 16725C>G, 16728T>A, 16731C>A, 16734C>T, 16736A>C, 16742G>A, 16746T>C, 16758C>A, 16761G>A, 16764T>C, 16774G>A, 16780T>A, 16781C>A, 16783G>A, 16787G>A, 16791T>A, 16798T>G, 16800T>A, 16802A>G, 16803A>C, 16804C>A, 16806G>A, 16809G>T, 16810G>A, 16811G>A, 16812C>A, 16817C>A, 16818T>C, 16821A>T, 16827G>A, 16828C>A, 16829G>C, 16830G>A, 16836G>A, 16840T>G, 16841C>T, 16842T>G, 16848T>C, 16854T>G, 16855T>A, 16857T>A, 16860C>T, 16863G>A, 16866G>A, 16867G>A, 16869T>A, 16872C>T, 16875C>T, 16876T>C, 16881T>A, 16884A>G, 16887G>A, 16890T>C, 16894A>T, 16899A>G, 16902G>A, 16905A>T, 16908T>A, 16911G>A, 16914G>A, 16917G>T, 16921A>G, 16922A>G, 16923G>T, 16926T>A, 16932A>G, 16935C>T, 16940G>A, 16941G>A, 16944G>T, 16948T>G, 16950C>A, 16953G>A, 16957A>G, 16958G>C, 16959C>T, 16966A>G, 16968T>A, 16970G>A, 16972A>G, 16978A>G, 16979A>T, 16980C>A, 16985A>C, 16992T>C, 16995C>T, 16999G>A, 17000C>A, 17001A>C, 17004G>A, 21453A>G, 27222C>G, 27591T>C, 27601A>C, 27759G>A, 27761T>C, 27777G>A
CDS
14213.7%28496.9%42 (100%)41 (97.6%)0/0/0/00
379056.4%14854.4%44 (83.0%)44 (83.0%)0/9/1/10
Protein mutations:V54_P62del (6870_6898delGTGCAGTTTCCTGACCTGTCACTGCCTGC)
Codon mutations:GTT52GTG (6866T>G), CTG53TTG (6867C>T), GTG54_CCT62del (6870_6898delGTGCAGTTTCCTGACCTGTCACTGCCTGC), GCA63--G (6870_6898delGTGCAGTTTCCTGACCTGTCACTGCCTGC 6899A>G)
9311620.7%15395.0%24 (100%)24 (100%)0/0/0/01
115719.1%32979.5%58 (100%)54 (93.1%)0/0/2/00
3920974.0%96281.5%171 (100%)130 (76.0%)0/0/0/00
Protein mutations:V50A (16535T>C), V54I (16546G>A 16548C>A), S62P (16570T>C), D82N (16630G>A), I83V (16633A>G), G86V (16643G>T 16644A>G), N88D (16648A>G), K98E (16678A>G), N99K (16683T>A), K100S (16685A>G 16686A>T), G101E (16688G>A 16689T>G), H114Q (16728T>A), N117T (16736A>C), S119N (16742G>A), D124E (16758C>A), V130I (16774G>A), S132N (16780T>A 16781C>A), V133I (16783G>A), S134N (16787G>A), S138A (16798T>G 16800T>A), K139S (16802A>G 16803A>C), Q140K (16804C>A 16806G>A), G142K (16810G>A 16811G>A 16812C>A), T144N (16817C>A 16818T>C), E145D (16821A>T), R148T (16828C>A 16829G>C 16830G>A), S152V (16840T>G 16841C>T 16842T>G), S157T (16855T>A 16857T>A), V161I (16867G>A 16869T>A), M170L (16894A>T), M177I (16917G>T), K179G (16921A>G 16922A>G 16923G>T), R185K (16940G>A 16941G>A), S188A (16948T>G 16950C>A), S191A (16957A>G 16958G>C 16959C>T), I194V (16966A>G 16968T>A), R195K (16970G>A), T196A (16972A>G), N198V (16978A>G 16979A>T 16980C>A), N200T (16985A>C), A205N (16999G>A 17000C>A 17001A>C)
Codon mutations:AGG44AGA (16518G>A), GTT50GCT (16535T>C), CCT52CCC (16542T>C), GTC54ATA (16546G>A 16548C>A), GTG56GTA (16554G>A), ACT57ACA (16557T>A), GAA59GAG (16563A>G), AAT61AAC (16569T>C), TCT62CCT (16570T>C), GCT64GCC (16578T>C), TAT67TAC (16587T>C), ATC70ATT (16596C>T), AAT71AAC (16599T>C), ACC75ACA (16611C>A), GGA76GGG (16614A>G), AAT77AAC (16617T>C), GCC78GCA (16620C>A), CCA79CCT (16623A>T), GAT82AAT (16630G>A), ATT83GTT (16633A>G), GAA84GAG (16638A>G), GTC85GTT (16641C>T), GGA86GTG (16643G>T 16644A>G), AAT88GAT (16648A>G), CCC89CCT (16653C>T), CTG91CTA (16659G>A), GTT92GTA (16662T>A), GCA94GCG (16668A>G), GAA95GAG (16671A>G), AAA98GAA (16678A>G), AAT99AAA (16683T>A), AAA100AGT (16685A>G 16686A>T), GGT101GAG (16688G>A 16689T>G), ATA102ATT (16692A>T), CCA103CCG (16695A>G), AGC105AGT (16701C>T), GTT107GTA (16707T>A), GTA109GTG (16713A>G), TTG110TTA (16716G>A), AAC112AAT (16722C>T), GGC113GGG (16725C>G), CAT114CAA (16728T>A), TCC115TCA (16731C>A), CTC116CTT (16734C>T), AAC117ACC (16736A>C), AGT119AAT (16742G>A), CTT120CTC (16746T>C), GAC124GAA (16758C>A), CAG125CAA (16761G>A), ATT126ATC (16764T>C), GTT130ATT (16774G>A), TCT132AAT (16780T>A 16781C>A), GTT133ATT (16783G>A), AGT134AAT (16787G>A), ATT135ATA (16791T>A), TCT138GCA (16798T>G 16800T>A), AAA139AGC (16802A>G 16803A>C), CAG140AAA (16804C>A 16806G>A), CCG141CCT (16809G>T), GGC142AAA (16810G>A 16811G>A 16812C>A), ACT144AAC (16817C>A 16818T>C), GAA145GAT (16821A>T), GAG147GAA (16827G>A), CGG148ACA (16828C>A 16829G>C 16830G>A), GAG150GAA (16836G>A), TCT152GTG (16840T>G 16841C>T 16842T>G), GAT154GAC (16848T>C), GCT156GCG (16854T>G), TCT157ACA (16855T>A 16857T>A), TTC158TTT (16860C>T), GAG159GAA (16863G>A), GGG160GGA (16866G>A), GTT161ATA (16867G>A 16869T>A), AGC162AGT (16872C>T), TAC163TAT (16875C>T), TTA164CTA (16876T>C), GGT165GGA (16881T>A), GCA166GCG (16884A>G), AGG167AGA (16887G>A), AGT168AGC (16890T>C), ATG170TTG (16894A>T), ACA171ACG (16899A>G), CAG172CAA (16902G>A), ATA173ATT (16905A>T), GCT174GCA (16908T>A), GAG175GAA (16911G>A), CAG176CAA (16914G>A), ATG177ATT (16917G>T), AAG179GGT (16921A>G 16922A>G 16923G>T), ATT180ATA (16926T>A), GAA182GAG (16932A>G), GAC183GAT (16935C>T), AGG185AAA (16940G>A 16941G>A), CCG186CCT (16944G>T), TCC188GCA (16948T>G 16950C>A), CAG189CAA (16953G>A), AGC191GCT (16957A>G 16958G>C 16959C>T), ATT194GTA (16966A>G 16968T>A), AGA195AAA (16970G>A), ACA196GCA (16972A>G), AAC198GTA (16978A>G 16979A>T 16980C>A), AAT200ACT (16985A>C), AGT202AGC (16992T>C), GAC203GAT (16995C>T), GCA205AAC (16999G>A 17000C>A 17001A>C), GAG206GAA (17004G>A)
6146595.6%31693.5%46 (100%)45 (97.8%)0/0/0/00
981003.0%847.1%3 (100%)2 (66.7%)0/0/0/01
Protein mutations:S99R (27222C>G)
Codon mutations:AGC99AGG (27222C>G)
175100%538100%75 (100%)75 (100%)0/0/0/01
192100%60099.0%92 (100%)91 (98.9%)0/0/0/01
Protein mutations:L48S (27591T>C)
Codon mutations:TTA48TCA (27591T>C), CTA51CTC (27601A>C)
1324.2%21297.2%32 (100%)30 (93.8%)0/0/0/00
Protein mutations:A16T (27759G>A 27761T>C), A22T (27777G>A)
Codon mutations:GCT16ACC (27759G>A 27761T>C), GCG22ACG (27777G>A)
Proteins
14213.7%28496.9%42 (100%)41 (97.6%)0/0/0/00
Protein mutations:none
Codon mutations:none
379056.4%14854.4%44 (83.0%)44 (83.0%)0/9/1/10
Protein mutations:V54_P62del (6870_6898delGTGCAGTTTCCTGACCTGTCACTGCCTGC)
Codon mutations:GTT52GTG (6866T>G), CTG53TTG (6867C>T), GTG54_CCT62del (6870_6898delGTGCAGTTTCCTGACCTGTCACTGCCTGC), GCA63--G (6870_6898delGTGCAGTTTCCTGACCTGTCACTGCCTGC 6899A>G)
9311620.7%15395.0%24 (100%)24 (100%)0/0/0/01
Protein mutations:none
Codon mutations:none
115719.1%32979.5%58 (100%)54 (93.1%)0/0/2/00
Protein mutations:none
Codon mutations:GAT13A.. (11218G>A), GAT123KAT (11548G>K), TCG140TSG (11600C>S), GGA142GGT (11607A>T), GGT148GGC (11625T>C)
3920974.0%96281.5%171 (100%)130 (76.0%)0/0/0/00
Protein mutations:V50A (16535T>C), V54I (16546G>A 16548C>A), S62P (16570T>C), D82N (16630G>A), I83V (16633A>G), G86V (16643G>T 16644A>G), N88D (16648A>G), K98E (16678A>G), N99K (16683T>A), K100S (16685A>G 16686A>T), G101E (16688G>A 16689T>G), H114Q (16728T>A), N117T (16736A>C), S119N (16742G>A), D124E (16758C>A), V130I (16774G>A), S132N (16780T>A 16781C>A), V133I (16783G>A), S134N (16787G>A), S138A (16798T>G 16800T>A), K139S (16802A>G 16803A>C), Q140K (16804C>A 16806G>A), G142K (16810G>A 16811G>A 16812C>A), T144N (16817C>A 16818T>C), E145D (16821A>T), R148T (16828C>A 16829G>C 16830G>A), S152V (16840T>G 16841C>T 16842T>G), S157T (16855T>A 16857T>A), V161I (16867G>A 16869T>A), M170L (16894A>T), M177I (16917G>T), K179G (16921A>G 16922A>G 16923G>T), R185K (16940G>A 16941G>A), S188A (16948T>G 16950C>A), S191A (16957A>G 16958G>C 16959C>T), I194V (16966A>G 16968T>A), R195K (16970G>A), T196A (16972A>G), N198V (16978A>G 16979A>T 16980C>A), N200T (16985A>C), A205N (16999G>A 17000C>A 17001A>C)
Codon mutations:AGG44AGA (16518G>A), GTT50GCT (16535T>C), CCT52CCC (16542T>C), GTC54ATA (16546G>A 16548C>A), GTG56GTA (16554G>A), ACT57ACA (16557T>A), GAA59GAG (16563A>G), AAT61AAC (16569T>C), TCT62CCT (16570T>C), GCT64GCC (16578T>C), TAT67TAC (16587T>C), ATC70ATT (16596C>T), AAT71AAC (16599T>C), ACC75ACA (16611C>A), GGA76GGG (16614A>G), AAT77AAC (16617T>C), GCC78GCA (16620C>A), CCA79CCT (16623A>T), GAT82AAT (16630G>A), ATT83GTT (16633A>G), GAA84GAG (16638A>G), GTC85GTT (16641C>T), GGA86GTG (16643G>T 16644A>G), AAT88GAT (16648A>G), CCC89CCT (16653C>T), CTG91CTA (16659G>A), GTT92GTA (16662T>A), GCA94GCG (16668A>G), GAA95GAG (16671A>G), AAA98GAA (16678A>G), AAT99AAA (16683T>A), AAA100AGT (16685A>G 16686A>T), GGT101GAG (16688G>A 16689T>G), ATA102ATT (16692A>T), CCA103CCG (16695A>G), AGC105AGT (16701C>T), GTT107GTA (16707T>A), GTA109GTG (16713A>G), TTG110TTA (16716G>A), AAC112AAT (16722C>T), GGC113GGG (16725C>G), CAT114CAA (16728T>A), TCC115TCA (16731C>A), CTC116CTT (16734C>T), AAC117ACC (16736A>C), AGT119AAT (16742G>A), CTT120CTC (16746T>C), GAC124GAA (16758C>A), CAG125CAA (16761G>A), ATT126ATC (16764T>C), GTT130ATT (16774G>A), TCT132AAT (16780T>A 16781C>A), GTT133ATT (16783G>A), AGT134AAT (16787G>A), ATT135ATA (16791T>A), TCT138GCA (16798T>G 16800T>A), AAA139AGC (16802A>G 16803A>C), CAG140AAA (16804C>A 16806G>A), CCG141CCT (16809G>T), GGC142AAA (16810G>A 16811G>A 16812C>A), ACT144AAC (16817C>A 16818T>C), GAA145GAT (16821A>T), GAG147GAA (16827G>A), CGG148ACA (16828C>A 16829G>C 16830G>A), GAG150GAA (16836G>A), TCT152GTG (16840T>G 16841C>T 16842T>G), GAT154GAC (16848T>C), GCT156GCG (16854T>G), TCT157ACA (16855T>A 16857T>A), TTC158TTT (16860C>T), GAG159GAA (16863G>A), GGG160GGA (16866G>A), GTT161ATA (16867G>A 16869T>A), AGC162AGT (16872C>T), TAC163TAT (16875C>T), TTA164CTA (16876T>C), GGT165GGA (16881T>A), GCA166GCG (16884A>G), AGG167AGA (16887G>A), AGT168AGC (16890T>C), ATG170TTG (16894A>T), ACA171ACG (16899A>G), CAG172CAA (16902G>A), ATA173ATT (16905A>T), GCT174GCA (16908T>A), GAG175GAA (16911G>A), CAG176CAA (16914G>A), ATG177ATT (16917G>T), AAG179GGT (16921A>G 16922A>G 16923G>T), ATT180ATA (16926T>A), GAA182GAG (16932A>G), GAC183GAT (16935C>T), AGG185AAA (16940G>A 16941G>A), CCG186CCT (16944G>T), TCC188GCA (16948T>G 16950C>A), CAG189CAA (16953G>A), AGC191GCT (16957A>G 16958G>C 16959C>T), ATT194GTA (16966A>G 16968T>A), AGA195AAA (16970G>A), ACA196GCA (16972A>G), AAC198GTA (16978A>G 16979A>T 16980C>A), AAT200ACT (16985A>C), AGT202AGC (16992T>C), GAC203GAT (16995C>T), GCA205AAC (16999G>A 17000C>A 17001A>C), GAG206GAA (17004G>A)
6146595.6%31693.5%46 (100%)45 (97.8%)0/0/0/00
Protein mutations:none
Codon mutations:GAA639GAG (21453A>G)
981003.0%847.1%3 (100%)2 (66.7%)0/0/0/01
Protein mutations:S99R (27222C>G)
Codon mutations:AGC99AGG (27222C>G)
175100%538100%75 (100%)75 (100%)0/0/0/01
Protein mutations:none
Codon mutations:none
192100%60099.0%92 (100%)91 (98.9%)0/0/0/01
Protein mutations:L48S (27591T>C)
Codon mutations:TTA48TCA (27591T>C), CTA51CTC (27601A>C)
1324.2%21297.2%32 (100%)30 (93.8%)0/0/0/00
Protein mutations:A16T (27759G>A 27761T>C), A22T (27777G>A)
Codon mutations:GCT16ACC (27759G>A 27761T>C), GCG22ACG (27777G>A)
*: Inserts / Deletes / Misaligned / Frameshifts

Analysis details

This analysis was performed with panviral2.43