Version 2.22.2
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