Version 2.16.3
Genome Detective Platform

NGS Details (SRR3458562_Metagenome_example): Rotavirus A (segment 7)

Assembly

1105 (1 contig(s))
6402.1
63051
4068.33 rpm (after QC)
0
de novo + reference guided assembly
Bcf Tools

Coverage Map

Variant Tables

Assignment

Rotavirus A (Taxonomy ID: 28875)
79.702
81.5287
1
1

Alignment

segment 7
1227.0 (NT) + 1715.0 (AA) = 2942.0
70.8745
Global, seeded, nucleotide + amino acids (AGA)

Alignment Detailed Statistics

BeginEndCoverageScoreConcordanceMatchesIdentitiesI/D/M/F*Stop Codons
NT11105100%122758.5%1074 (97.2%)856 (77.5%)0/31
Mutations:4A>T, 46G>A, 49A>G, 58C>T, 59G>A, 60T>G, 61C>T, 64A>G, 74T>A, 88T>C, 94T>C, 97A>T, 103A>C, 106C>T, 110G>A, 118G>A, 119A>C, 120A>T, 121T>C, 127A>C, 130A>T, 131G>C, 143C>A, 145G>T, 148T>A, 149A>G, 151A>T, 155T>A, 163A>T, 168A>G, 169T>C, 180T>A, 181T>C, 184G>A, 190C>T, 196T>A, 208T>C, 215A>T, 217T>G, 226A>G, 227A>G, 228T>C, 241A>G, 244T>A, 245T>C, 251A>G, 252A>G, 253T>A, 262A>T, 265T>A, 268T>A, 269A>G, 270T>C, 283C>T, 287C>A, 289T>G, 292T>C, 299T>A, 300C>G, 301T>A, 303G>C, 304A>T, 305G>A, 309C>A, 312A>G, 314T>C, 316G>A, 322G>A, 328A>G, 337A>T, 355A>T, 382T>A, 383T>C, 385A>T, 388C>T, 394C>T, 403A>G, 406A>G, 410A>G, 411T>C, 412A>T, 415T>A, 418A>T, 430T>A, 433T>A, 442C>T, 445A>T, 447A>G, 449T>C, 451G>A, 455C>A, 457T>A, 463A>G, 464T>A, 466G>T, 481T>C, 496A>G, 502G>T, 505T>A, 520G>T, 523T>C, 526C>A, 532C>T, 541G>T, 542C>A, 544C>G, 550G>A, 559G>A, 560C>A, 563A>C, 565G>A, 575T>C, 581T>C, 582C>A, 583C>A, 589A>G, 603A>C, 604T>A, 606A>G, 614T>C, 615T>A, 616G>A, 624G>A, 628A>G, 629A>G, 631G>A, 644C>T, 646T>C, 652T>C, 658T>C, 661C>T, 664C>A, 667T>A, 676A>G, 677G>A, 678C>G, 679A>C, 682T>G, 685A>T, 691G>T, 692C>T, 694T>A, 698G>A, 699T>A, 700G>T, 704A>T, 705A>G, 713C>T, 715A>G, 719C>G, 720G>T, 725T>C, 727G>A, 730A>G, 740G>A, 742A>T, 745C>A, 749A>G, 750C>T, 751T>G, 757G>A, 758A>G, 769T>C, 770T>C, 772A>G, 774G>A, 848T>A, 850G>T, 851C>A, 853C>T, 857T>A, 859T>A, 865C>T, 868A>T, 875G>C, 877A>G, 880A>C, 881C>A, 883T>A, 887T>A, 889G>T, 893T>C, 894C>T, 895T>C, 898T>C, 906A>G, 908T>A, 913C>T, 914C>T, 916T>A, 934A>G, 935C>A, 936A>G, 938A>C, 939G>A, 943T>C, 946T>C, 950C>G, 956T>A, 958A>G, 960T>A, 962_967delGGTTGC, 973A>G, 974C>T, 977T>C, 978T>A, 980_1004delTGATACATGTTGAACAATCAAATAC, 1006G>A, 1008G>A, 1010T>A, 1012G>T, 1015T>A, 1016G>A, 1019G>A, 1020T>C, 1026A>T, 1027T>C, 1028G>A, 1032A>G, 1103G>A
CDS
1316100%171583.6%314 (99.4%)256 (81.0%)0/2/0/01
Protein mutations:V12S (59G>A 60T>G 61C>T), S17T (74T>A), A29T (110G>A), N32L (119A>C 120A>T 121T>C), E36Q (131G>C), Q40N (143C>A 145G>T), D41E (148T>A), I42V (149A>G 151A>T), S44T (155T>A), N48S (168A>G 169T>C), F52Y (180T>A 181T>C), I64L (215A>T 217T>G), I68A (227A>G 228T>C), N76G (251A>G 252A>G 253T>A), I82A (269A>G 270T>C), L88M (287C>A 289T>G), S92R (299T>A 300C>G 301T>A), R93T (303G>C 304A>T), A94T (305G>A), A95D (309C>A), K96R (312A>G), I129A (410A>G 411T>C 412A>T), K141R (447A>G), L147I (464T>A 466G>T), D160E (505T>A), Q179K (560C>A), S186Q (581T>C 582C>A 583C>A), N193T (603A>C 604T>A), N194S (606A>G), L197Q (614T>C 615T>A 616G>A), R200K (624G>A), M202V (629A>G 631G>A), H207Y (644C>T 646T>C), A218S (677G>A 678C>G 679A>C), H219Q (682T>G), E222D (691G>T), V225N (698G>A 699T>A 700G>T), N227C (704A>T 705A>G), R232V (719C>G 720G>T), G239S (740G>A 742A>T), T242V (749A>G 750C>T 751T>G), I245V (758A>G), R250K (774G>A), L275I (848T>A 850G>T), H276N (851C>A 853C>T), F278I (857T>A 859T>A), L281F (868A>T), V284L (875G>C 877A>G), L288I (887T>A 889G>T), S290L (893T>C 894C>T 895T>C), K294R (906A>G), L295I (908T>A), I303M (934A>G), Q304R (935C>A 936A>G), R305Q (938A>C 939G>A), Q309E (950C>G), S311T (956T>A 958A>G), F312Y (960T>A), G313_C314del (962_967delGGTTGC)
Codon mutations:ACG7ACA (46G>A), CAA8CAG (49A>G), GCC11GCT (58C>T), GTC12AGT (59G>A 60T>G 61C>T), TCA13TCG (64A>G), TCT17ACT (74T>A), GCT21GCC (88T>C), GTT23GTC (94T>C), GTA24GTT (97A>T), GCA26GCC (103A>C), ACC27ACT (106C>T), GCT29ACT (110G>A), GAG31GAA (118G>A), AAT32CTC (119A>C 120A>T 121T>C), GGA34GGC (127A>C), ATA35ATT (130A>T), GAA36CAA (131G>C), CAG40AAT (143C>A 145G>T), GAT41GAA (148T>A), ATA42GTT (149A>G 151A>T), TCT44ACT (155T>A), GTA46GTT (163A>T), AAT48AGC (168A>G 169T>C), TTT52TAC (180T>A 181T>C), GTG53GTA (184G>A), GAC55GAT (190C>T), TCT57TCA (196T>A), AAT61AAC (208T>C), ATT64TTG (215A>T 217T>G), GCA67GCG (226A>G), ATA68GCA (227A>G 228T>C), CAA72CAG (241A>G), GCT73GCA (244T>A), TTG74CTG (245T>C), AAT76GGA (251A>G 252A>G 253T>A), GGA79GGT (262A>T), TCT80TCA (265T>A), GCT81GCA (268T>A), ATA82GCA (269A>G 270T>C), AAC86AAT (283C>T), CTT88ATG (287C>A 289T>G), GCT89GCC (292T>C), TCT92AGA (299T>A 300C>G 301T>A), AGA93ACT (303G>C 304A>T), GCA94ACA (305G>A), GCT95GAT (309C>A), AAA96AGA (312A>G), TTG97CTA (314T>C 316G>A), GAG99GAA (322G>A), GTA101GTG (328A>G), CTA104CTT (337A>T), TCA110TCT (355A>T), GTT119GTA (382T>A), TTA120CTT (383T>C 385A>T), AAC121AAT (388C>T), TGC123TGT (394C>T), GTA126GTG (403A>G), AAA127AAG (406A>G), ATA129GCT (410A>G 411T>C 412A>T), CCT130CCA (415T>A), GGA131GGT (418A>T), TCT135TCA (430T>A), ATT136ATA (433T>A), TGC139TGT (442C>T), ACA140ACT (445A>T), AAA141AGA (447A>G), TTG142CTA (449T>C 451G>A), CGT144AGA (455C>A 457T>A), AAA146AAG (463A>G), TTG147ATT (464T>A 466G>T), GTT152GTC (481T>C), TCA157TCG (496A>G), GTG159GTT (502G>T), GAT160GAA (505T>A), GTG165GTT (520G>T), GAT166GAC (523T>C), ACC167ACA (526C>A), GAC169GAT (532C>T), TCG172TCT (541G>T), CGC173AGG (542C>A 544C>G), GAG175GAA (550G>A), GAG178GAA (559G>A), CAA179AAA (560C>A), AGG180CGA (563A>C 565G>A), TTG184CTG (575T>C), TCC186CAA (581T>C 582C>A 583C>A), GTA188GTG (589A>G), AAT193ACA (603A>C 604T>A), AAT194AGT (606A>G), TTG197CAA (614T>C 615T>A 616G>A), AGA200AAA (624G>A), AAA201AAG (628A>G), ATG202GTA (629A>G 631G>A), CAT207TAC (644C>T 646T>C), CTT209CTC (652T>C), AAT211AAC (658T>C), GTC212GTT (661C>T), ATC213ATA (664C>A), TCT214TCA (667T>A), CAA217CAG (676A>G), GCA218AGC (677G>A 678C>G 679A>C), CAT219CAG (682T>G), ATA220ATT (685A>T), GAG222GAT (691G>T), CTT223TTA (692C>T 694T>A), GTG225AAT (698G>A 699T>A 700G>T), AAT227TGT (704A>T 705A>G), CTA230TTG (713C>T 715A>G), CGT232GTT (719C>G 720G>T), TTG234CTA (725T>C 727G>A), CAA235CAG (730A>G), GGA239AGT (740G>A 742A>T), TCC240TCA (745C>A), ACT242GTG (749A>G 750C>T 751T>G), TCG244TCA (757G>A), ATT245GTT (758A>G), TAT248TAC (769T>C), TTA249CTG (770T>C 772A>G), AGA250AAA (774G>A), TTG275ATT (848T>A 850G>T), CAC276AAT (851C>A 853C>T), TTT278ATA (857T>A 859T>A), GAC280GAT (865C>T), TTA281TTT (868A>T), GTA284CTG (875G>C 877A>G), ATA285ATC (880A>C), CGT286AGA (881C>A 883T>A), TTG288ATT (887T>A 889G>T), TCT290CTC (893T>C 894C>T 895T>C), GAT291GAC (898T>C), AAA294AGA (906A>G), TTA295ATA (908T>A), TTC296TTT (913C>T), CTT297TTA (914C>T 916T>A), ATA303ATG (934A>G), CAG304AGG (935C>A 936A>G), AGA305CAA (938A>C 939G>A), TGT306TGC (943T>C), AAT307AAC (946T>C), CAA309GAA (950C>G), TCA311ACG (956T>A 958A>G), TTT312TAT (960T>A), GGT313_TGC314del (962_967delGGTTGC), TAA316TAG (973A>G)
Proteins
1316100%171583.6%314 (99.4%)256 (81.0%)0/2/0/01
Protein mutations:V12S (59G>A 60T>G 61C>T), S17T (74T>A), A29T (110G>A), N32L (119A>C 120A>T 121T>C), E36Q (131G>C), Q40N (143C>A 145G>T), D41E (148T>A), I42V (149A>G 151A>T), S44T (155T>A), N48S (168A>G 169T>C), F52Y (180T>A 181T>C), I64L (215A>T 217T>G), I68A (227A>G 228T>C), N76G (251A>G 252A>G 253T>A), I82A (269A>G 270T>C), L88M (287C>A 289T>G), S92R (299T>A 300C>G 301T>A), R93T (303G>C 304A>T), A94T (305G>A), A95D (309C>A), K96R (312A>G), I129A (410A>G 411T>C 412A>T), K141R (447A>G), L147I (464T>A 466G>T), D160E (505T>A), Q179K (560C>A), S186Q (581T>C 582C>A 583C>A), N193T (603A>C 604T>A), N194S (606A>G), L197Q (614T>C 615T>A 616G>A), R200K (624G>A), M202V (629A>G 631G>A), H207Y (644C>T 646T>C), A218S (677G>A 678C>G 679A>C), H219Q (682T>G), E222D (691G>T), V225N (698G>A 699T>A 700G>T), N227C (704A>T 705A>G), R232V (719C>G 720G>T), G239S (740G>A 742A>T), T242V (749A>G 750C>T 751T>G), I245V (758A>G), R250K (774G>A), L275I (848T>A 850G>T), H276N (851C>A 853C>T), F278I (857T>A 859T>A), L281F (868A>T), V284L (875G>C 877A>G), L288I (887T>A 889G>T), S290L (893T>C 894C>T 895T>C), K294R (906A>G), L295I (908T>A), I303M (934A>G), Q304R (935C>A 936A>G), R305Q (938A>C 939G>A), Q309E (950C>G), S311T (956T>A 958A>G), F312Y (960T>A), G313_C314del (962_967delGGTTGC)
Codon mutations:ACG7ACA (46G>A), CAA8CAG (49A>G), GCC11GCT (58C>T), GTC12AGT (59G>A 60T>G 61C>T), TCA13TCG (64A>G), TCT17ACT (74T>A), GCT21GCC (88T>C), GTT23GTC (94T>C), GTA24GTT (97A>T), GCA26GCC (103A>C), ACC27ACT (106C>T), GCT29ACT (110G>A), GAG31GAA (118G>A), AAT32CTC (119A>C 120A>T 121T>C), GGA34GGC (127A>C), ATA35ATT (130A>T), GAA36CAA (131G>C), CAG40AAT (143C>A 145G>T), GAT41GAA (148T>A), ATA42GTT (149A>G 151A>T), TCT44ACT (155T>A), GTA46GTT (163A>T), AAT48AGC (168A>G 169T>C), TTT52TAC (180T>A 181T>C), GTG53GTA (184G>A), GAC55GAT (190C>T), TCT57TCA (196T>A), AAT61AAC (208T>C), ATT64TTG (215A>T 217T>G), GCA67GCG (226A>G), ATA68GCA (227A>G 228T>C), CAA72CAG (241A>G), GCT73GCA (244T>A), TTG74CTG (245T>C), AAT76GGA (251A>G 252A>G 253T>A), GGA79GGT (262A>T), TCT80TCA (265T>A), GCT81GCA (268T>A), ATA82GCA (269A>G 270T>C), AAC86AAT (283C>T), CTT88ATG (287C>A 289T>G), GCT89GCC (292T>C), TCT92AGA (299T>A 300C>G 301T>A), AGA93ACT (303G>C 304A>T), GCA94ACA (305G>A), GCT95GAT (309C>A), AAA96AGA (312A>G), TTG97CTA (314T>C 316G>A), GAG99GAA (322G>A), GTA101GTG (328A>G), CTA104CTT (337A>T), TCA110TCT (355A>T), GTT119GTA (382T>A), TTA120CTT (383T>C 385A>T), AAC121AAT (388C>T), TGC123TGT (394C>T), GTA126GTG (403A>G), AAA127AAG (406A>G), ATA129GCT (410A>G 411T>C 412A>T), CCT130CCA (415T>A), GGA131GGT (418A>T), TCT135TCA (430T>A), ATT136ATA (433T>A), TGC139TGT (442C>T), ACA140ACT (445A>T), AAA141AGA (447A>G), TTG142CTA (449T>C 451G>A), CGT144AGA (455C>A 457T>A), AAA146AAG (463A>G), TTG147ATT (464T>A 466G>T), GTT152GTC (481T>C), TCA157TCG (496A>G), GTG159GTT (502G>T), GAT160GAA (505T>A), GTG165GTT (520G>T), GAT166GAC (523T>C), ACC167ACA (526C>A), GAC169GAT (532C>T), TCG172TCT (541G>T), CGC173AGG (542C>A 544C>G), GAG175GAA (550G>A), GAG178GAA (559G>A), CAA179AAA (560C>A), AGG180CGA (563A>C 565G>A), TTG184CTG (575T>C), TCC186CAA (581T>C 582C>A 583C>A), GTA188GTG (589A>G), AAT193ACA (603A>C 604T>A), AAT194AGT (606A>G), TTG197CAA (614T>C 615T>A 616G>A), AGA200AAA (624G>A), AAA201AAG (628A>G), ATG202GTA (629A>G 631G>A), CAT207TAC (644C>T 646T>C), CTT209CTC (652T>C), AAT211AAC (658T>C), GTC212GTT (661C>T), ATC213ATA (664C>A), TCT214TCA (667T>A), CAA217CAG (676A>G), GCA218AGC (677G>A 678C>G 679A>C), CAT219CAG (682T>G), ATA220ATT (685A>T), GAG222GAT (691G>T), CTT223TTA (692C>T 694T>A), GTG225AAT (698G>A 699T>A 700G>T), AAT227TGT (704A>T 705A>G), CTA230TTG (713C>T 715A>G), CGT232GTT (719C>G 720G>T), TTG234CTA (725T>C 727G>A), CAA235CAG (730A>G), GGA239AGT (740G>A 742A>T), TCC240TCA (745C>A), ACT242GTG (749A>G 750C>T 751T>G), TCG244TCA (757G>A), ATT245GTT (758A>G), TAT248TAC (769T>C), TTA249CTG (770T>C 772A>G), AGA250AAA (774G>A), TTG275ATT (848T>A 850G>T), CAC276AAT (851C>A 853C>T), TTT278ATA (857T>A 859T>A), GAC280GAT (865C>T), TTA281TTT (868A>T), GTA284CTG (875G>C 877A>G), ATA285ATC (880A>C), CGT286AGA (881C>A 883T>A), TTG288ATT (887T>A 889G>T), TCT290CTC (893T>C 894C>T 895T>C), GAT291GAC (898T>C), AAA294AGA (906A>G), TTA295ATA (908T>A), TTC296TTT (913C>T), CTT297TTA (914C>T 916T>A), ATA303ATG (934A>G), CAG304AGG (935C>A 936A>G), AGA305CAA (938A>C 939G>A), TGT306TGC (943T>C), AAT307AAC (946T>C), CAA309GAA (950C>G), TCA311ACG (956T>A 958A>G), TTT312TAT (960T>A), GGT313_TGC314del (962_967delGGTTGC), TAA316TAG (973A>G)
*: Inserts / Deletes / Misaligned / Frameshifts

Analysis details

This analysis was performed with panviral2.43