Version 2.16.3
Genome Detective Platform

NGS Details (SRR3458562_Metagenome_example): Rotavirus A (segment 6)

Assembly

1356 (1 contig(s))
6806.4
84309
5439.99 rpm (after QC)
0
de novo + reference guided assembly
Bcf Tools

Coverage Map

Variant Tables

Assignment

Rotavirus A (Taxonomy ID: 28875)
87.9794
97.4874
1
1

Alignment

segment 6
2060.0 (NT) + 2722.0 (AA) = 4782.0
87.2628
Global, seeded, nucleotide + amino acids (AGA)

Alignment Detailed Statistics

BeginEndCoverageScoreConcordanceMatchesIdentitiesI/D/M/F*Stop Codons
NT11356100%206076.0%1356 (100%)1193 (88.0%)0/0
Mutations:35A>G, 41T>C, 50G>A, 62C>T, 92G>A, 95T>C, 98T>C, 101C>T, 104G>A, 158A>G, 161T>C, 176C>T, 183T>C, 185G>A, 188A>G, 197C>T, 207A>G, 212C>T, 215G>A, 231T>C, 233G>A, 234C>T, 236G>A, 239C>T, 240T>C, 245C>T, 251T>C, 254T>C, 257T>C, 266A>C, 267A>C, 269A>C, 272T>C, 287C>T, 290G>A, 311C>T, 320G>A, 341G>A, 344C>T, 356T>A, 365C>T, 368G>A, 371A>T, 378C>T, 380G>A, 385C>G, 395C>T, 413T>C, 419G>A, 422G>A, 434A>G, 452T>C, 461G>A, 464G>A, 467A>G, 473C>T, 476T>A, 497T>C, 509A>G, 515T>C, 521A>G, 524T>C, 536C>A, 548T>C, 557C>T, 560A>G, 567T>C, 569A>C, 572C>T, 575A>G, 581G>A, 590A>G, 602T>C, 608C>T, 617T>A, 620T>C, 623C>T, 626A>G, 637T>C, 653T>C, 654A>G, 659G>A, 661C>A, 662A>G, 689G>A, 699C>T, 707C>T, 710G>A, 716G>A, 737C>T, 752G>A, 755A>G, 766T>A, 767T>C, 785C>T, 788G>A, 791G>A, 806G>A, 809G>A, 818G>A, 821T>C, 824A>G, 836C>T, 842T>C, 860T>G, 864G>A, 884T>A, 887T>C, 891C>T, 893A>G, 899C>T, 905A>G, 920C>T, 932A>G, 938A>G, 940T>C, 941A>G, 942C>T, 947C>T, 950G>A, 965C>T, 974T>C, 983G>A, 987T>C, 989G>C, 992A>G, 1004G>A, 1019G>A, 1022T>A, 1025A>G, 1028C>T, 1034T>C, 1046T>A, 1047C>A, 1049A>G, 1050T>C, 1061A>G, 1067C>T, 1073G>A, 1079G>A, 1085A>G, 1103C>T, 1121C>T, 1133A>G, 1139C>T, 1142T>C, 1151G>A, 1157G>A, 1163C>T, 1166T>C, 1172A>G, 1175C>T, 1208C>T, 1209A>G, 1211T>C, 1231A>C, 1243A>G, 1265T>C, 1266A>G, 1301A>C, 1306C>T, 1337T>C, 1338A>G
CDS
1398100%272298.3%398 (100%)388 (97.5%)0/0/0/01
Protein mutations:N62D (207A>G), A121G (385C>G), I205T (637T>C), I211V (654A>G), P213Q (661C>A 662A>G), F248Y (766T>A 767T>C), V281I (864G>A), V306A (940T>C 941A>G), L342M (1047C>A 1049A>G), I396V (1209A>G 1211T>C)
Codon mutations:CTA4CTG (35A>G), TCT6TCC (41T>C), AAG9AAA (50G>A), GAC13GAT (62C>T), TTG23TTA (92G>A), TAT24TAC (95T>C), TCT25TCC (98T>C), AAC26AAT (101C>T), GTG27GTA (104G>A), GAA45GAG (158A>G), TTT46TTC (161T>C), ATC51ATT (176C>T), TTG54CTA (183T>C 185G>A), CCA55CCG (188A>G), AAC58AAT (197C>T), AAT62GAT (207A>G), TTC63TTT (212C>T), GGG64GGA (215G>A), TTG70CTA (231T>C 233G>A), CTG71TTA (234C>T 236G>A), AAC72AAT (239C>T), TTA73CTA (240T>C), GAC74GAT (245C>T), AAT76AAC (251T>C), TAT77TAC (254T>C), GTT78GTC (257T>C), GCA81GCC (266A>C), AGA82CGC (267A>C 269A>C), AAT83AAC (272T>C), TTC88TTT (287C>T), GTG89GTA (290G>A), TGC96TGT (311C>T), GAG99GAA (320G>A), AGG106AGA (341G>A), AAC107AAT (344C>T), CCT111CCA (356T>A), GAC114GAT (365C>T), TCG115TCA (368G>A), CTA116CTT (371A>T), CTG119TTA (378C>T 380G>A), GCC121GGC (385C>G), TTC124TTT (395C>T), GAT130GAC (413T>C), TCG132TCA (419G>A), TCG133TCA (422G>A), GAA137GAG (434A>G), AAT143AAC (452T>C), CAG146CAA (461G>A), AGG147AGA (464G>A), ACA148ACG (467A>G), TTC150TTT (473C>T), ACT151ACA (476T>A), TTT158TTC (497T>C), GCA162GCG (509A>G), TTT164TTC (515T>C), CTA166CTG (521A>G), AAT167AAC (524T>C), CCC171CCA (536C>A), AAT175AAC (548T>C), GGC178GGT (557C>T), ACA179ACG (560A>G), TTA182CTC (567T>C 569A>C), AAC183AAT (572C>T), GCA184GCG (575A>G), TCG186TCA (581G>A), CAA189CAG (590A>G), TTT193TTC (602T>C), TAC195TAT (608C>T), GCT198GCA (617T>A), ATT199ATC (620T>C), AAC200AAT (623C>T), GCA201GCG (626A>G), ATA205ACA (637T>C), CAT210CAC (653T>C), ATT211GTT (654A>G), GTG212GTA (659G>A), CCA213CAG (661C>A 662A>G), ACG222ACA (689G>A), CTA226TTA (699C>T), GAC228GAT (707C>T), GCG229GCA (710G>A), AGG231AGA (716G>A), ATC238ATT (737C>T), GGG243GGA (752G>A), GCA244GCG (755A>G), TTT248TAC (766T>A 767T>C), CTC254CTT (785C>T), AGG255AGA (788G>A), CCG256CCA (791G>A), GTG261GTA (806G>A), GAG262GAA (809G>A), TTG265TTA (818G>A), AAT266AAC (821T>C), GGA267GGG (824A>G), AAC271AAT (836C>T), TAT273TAC (842T>C), ACT279ACG (860T>G), GTA281ATA (864G>A), ACT287ACA (884T>A), ATT288ATC (887T>C), CTA290TTG (891C>T 893A>G), TTC292TTT (899C>T), TTA294TTG (905A>G), AAC299AAT (920C>T), GCA303GCG (932A>G), GCA305GCG (938A>G), GTA306GCG (940T>C 941A>G), CTA307TTA (942C>T), TTC308TTT (947C>T), CCG309CCA (950G>A), TTC314TTT (965C>T), CAT317CAC (974T>C), GTG320GTA (983G>A), TTG322CTC (987T>C 989G>C), ACA323ACG (992A>G), GAG327GAA (1004G>A), GAG332GAA (1019G>A), TCT333TCA (1022T>A), GTA334GTG (1025A>G), CTC335CTT (1028C>T), GAT337GAC (1034T>C), ACT341ACA (1046T>A), CTA342ATG (1047C>A 1049A>G), TTA343CTA (1050T>C), GTA346GTG (1061A>G), TCC348TCT (1067C>T), AGG350AGA (1073G>A), GAG352GAA (1079G>A), GCA354GCG (1085A>G), GTC360GTT (1103C>T), AAC366AAT (1121C>T), TTA370TTG (1133A>G), ACC372ACT (1139C>T), AAT373AAC (1142T>C), CCG376CCA (1151G>A), AGG378AGA (1157G>A), GAC380GAT (1163C>T), AAT381AAC (1166T>C), CAA383CAG (1172A>G), CGC384CGT (1175C>T), CTC395CTT (1208C>T), ATT396GTC (1209A>G 1211T>C)
Proteins
1398100%272298.3%398 (100%)388 (97.5%)0/0/0/01
Protein mutations:N62D (207A>G), A121G (385C>G), I205T (637T>C), I211V (654A>G), P213Q (661C>A 662A>G), F248Y (766T>A 767T>C), V281I (864G>A), V306A (940T>C 941A>G), L342M (1047C>A 1049A>G), I396V (1209A>G 1211T>C)
Codon mutations:CTA4CTG (35A>G), TCT6TCC (41T>C), AAG9AAA (50G>A), GAC13GAT (62C>T), TTG23TTA (92G>A), TAT24TAC (95T>C), TCT25TCC (98T>C), AAC26AAT (101C>T), GTG27GTA (104G>A), GAA45GAG (158A>G), TTT46TTC (161T>C), ATC51ATT (176C>T), TTG54CTA (183T>C 185G>A), CCA55CCG (188A>G), AAC58AAT (197C>T), AAT62GAT (207A>G), TTC63TTT (212C>T), GGG64GGA (215G>A), TTG70CTA (231T>C 233G>A), CTG71TTA (234C>T 236G>A), AAC72AAT (239C>T), TTA73CTA (240T>C), GAC74GAT (245C>T), AAT76AAC (251T>C), TAT77TAC (254T>C), GTT78GTC (257T>C), GCA81GCC (266A>C), AGA82CGC (267A>C 269A>C), AAT83AAC (272T>C), TTC88TTT (287C>T), GTG89GTA (290G>A), TGC96TGT (311C>T), GAG99GAA (320G>A), AGG106AGA (341G>A), AAC107AAT (344C>T), CCT111CCA (356T>A), GAC114GAT (365C>T), TCG115TCA (368G>A), CTA116CTT (371A>T), CTG119TTA (378C>T 380G>A), GCC121GGC (385C>G), TTC124TTT (395C>T), GAT130GAC (413T>C), TCG132TCA (419G>A), TCG133TCA (422G>A), GAA137GAG (434A>G), AAT143AAC (452T>C), CAG146CAA (461G>A), AGG147AGA (464G>A), ACA148ACG (467A>G), TTC150TTT (473C>T), ACT151ACA (476T>A), TTT158TTC (497T>C), GCA162GCG (509A>G), TTT164TTC (515T>C), CTA166CTG (521A>G), AAT167AAC (524T>C), CCC171CCA (536C>A), AAT175AAC (548T>C), GGC178GGT (557C>T), ACA179ACG (560A>G), TTA182CTC (567T>C 569A>C), AAC183AAT (572C>T), GCA184GCG (575A>G), TCG186TCA (581G>A), CAA189CAG (590A>G), TTT193TTC (602T>C), TAC195TAT (608C>T), GCT198GCA (617T>A), ATT199ATC (620T>C), AAC200AAT (623C>T), GCA201GCG (626A>G), ATA205ACA (637T>C), CAT210CAC (653T>C), ATT211GTT (654A>G), GTG212GTA (659G>A), CCA213CAG (661C>A 662A>G), ACG222ACA (689G>A), CTA226TTA (699C>T), GAC228GAT (707C>T), GCG229GCA (710G>A), AGG231AGA (716G>A), ATC238ATT (737C>T), GGG243GGA (752G>A), GCA244GCG (755A>G), TTT248TAC (766T>A 767T>C), CTC254CTT (785C>T), AGG255AGA (788G>A), CCG256CCA (791G>A), GTG261GTA (806G>A), GAG262GAA (809G>A), TTG265TTA (818G>A), AAT266AAC (821T>C), GGA267GGG (824A>G), AAC271AAT (836C>T), TAT273TAC (842T>C), ACT279ACG (860T>G), GTA281ATA (864G>A), ACT287ACA (884T>A), ATT288ATC (887T>C), CTA290TTG (891C>T 893A>G), TTC292TTT (899C>T), TTA294TTG (905A>G), AAC299AAT (920C>T), GCA303GCG (932A>G), GCA305GCG (938A>G), GTA306GCG (940T>C 941A>G), CTA307TTA (942C>T), TTC308TTT (947C>T), CCG309CCA (950G>A), TTC314TTT (965C>T), CAT317CAC (974T>C), GTG320GTA (983G>A), TTG322CTC (987T>C 989G>C), ACA323ACG (992A>G), GAG327GAA (1004G>A), GAG332GAA (1019G>A), TCT333TCA (1022T>A), GTA334GTG (1025A>G), CTC335CTT (1028C>T), GAT337GAC (1034T>C), ACT341ACA (1046T>A), CTA342ATG (1047C>A 1049A>G), TTA343CTA (1050T>C), GTA346GTG (1061A>G), TCC348TCT (1067C>T), AGG350AGA (1073G>A), GAG352GAA (1079G>A), GCA354GCG (1085A>G), GTC360GTT (1103C>T), AAC366AAT (1121C>T), TTA370TTG (1133A>G), ACC372ACT (1139C>T), AAT373AAC (1142T>C), CCG376CCA (1151G>A), AGG378AGA (1157G>A), GAC380GAT (1163C>T), AAT381AAC (1166T>C), CAA383CAG (1172A>G), CGC384CGT (1175C>T), CTC395CTT (1208C>T), ATT396GTC (1209A>G 1211T>C)
*: Inserts / Deletes / Misaligned / Frameshifts

Analysis details

This analysis was performed with panviral2.43