Version 2.22.2
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