Version 2.16.3
Genome Detective Platform

NGS Details (SRR3458562_Metagenome_example): Rotavirus A (segment 8)

Assembly

1059 (1 contig(s))
2133.2
20728
1337.46 rpm (after QC)
0
de novo + reference guided assembly
Bcf Tools

Coverage Map

Variant Tables

Assignment

Rotavirus A (Taxonomy ID: 28875)
80.2644
86.1635
1
1

Alignment

segment 8
1282.0 (NT) + 1912.0 (AA) = 3194.0
74.6785
Global, seeded, nucleotide + amino acids (AGA)

Alignment Detailed Statistics

BeginEndCoverageScoreConcordanceMatchesIdentitiesI/D/M/F*Stop Codons
NT11059100%128260.5%1059 (100%)850 (80.3%)0/0
Mutations:70C>T, 88T>C, 99A>G, 103T>C, 109T>A, 115T>C, 117A>G, 127T>A, 131G>T, 132C>G, 137C>T, 145T>A, 151A>G, 160G>A, 163C>T, 164A>C, 165T>A, 166G>A, 172G>A, 179G>A, 187T>A, 196A>T, 199A>T, 205G>A, 208T>G, 211T>A, 217T>C, 220G>A, 226G>T, 232T>C, 235T>G, 241T>C, 253C>A, 261T>A, 268A>T, 269A>C, 270T>C, 271T>A, 279C>A, 283G>A, 289T>G, 290A>G, 295G>A, 298A>T, 307T>G, 308C>T, 310A>G, 317T>A, 319G>T, 325G>T, 328G>T, 332G>T, 334A>T, 335A>G, 337C>T, 340C>T, 341T>G, 343T>G, 345A>G, 350T>C, 352A>T, 356C>A, 357G>A, 364A>T, 367A>T, 368A>G, 373G>A, 377T>C, 382A>G, 391G>A, 392A>C, 393T>G, 394A>G, 395C>A, 397T>A, 399A>G, 403A>G, 408C>A, 409A>T, 415T>C, 416A>G, 418T>G, 421A>T, 424T>C, 436T>G, 439A>G, 440C>T, 442T>G, 452A>G, 453C>T, 457G>A, 460T>A, 469A>T, 472G>C, 475T>A, 490T>G, 493A>T, 494A>G, 495T>C, 496A>C, 502A>T, 511A>G, 515A>G, 517T>A, 520A>T, 529C>T, 532T>A, 535C>T, 538C>T, 541C>A, 551C>T, 553A>G, 556T>A, 559T>C, 560T>C, 562A>G, 565A>G, 569C>A, 570A>G, 571A>C, 572T>C, 574G>A, 584C>T, 592G>A, 611G>A, 613T>A, 617T>A, 643T>A, 644G>T, 645T>C, 646T>A, 659T>C, 661A>G, 662G>A, 664C>T, 670A>G, 671C>T, 673T>G, 676A>G, 685T>C, 691G>A, 697T>A, 703C>T, 715G>A, 721T>C, 724T>C, 728A>G, 736G>A, 751T>G, 757C>T, 760T>A, 763C>T, 769A>T, 772T>C, 775A>T, 791G>A, 792T>A, 796A>G, 798C>A, 802A>G, 803G>A, 804T>A, 807A>T, 808T>G, 810A>T, 811T>A, 814T>G, 820C>T, 838T>A, 841T>A, 847A>G, 859A>G, 868A>T, 880G>A, 886T>C, 889A>T, 895C>A, 898G>A, 904A>G, 906G>A, 907G>A, 908T>C, 910G>A, 913T>G, 922A>G, 928A>G, 930C>G, 936A>G, 937A>T, 943A>G, 949A>G, 952G>A, 961G>T, 970A>G, 976C>T, 979A>G, 989G>A, 991T>A, 994C>A, 995G>A, 1005C>T, 1010A>G, 1018G>A, 1022A>G, 1023T>G, 1024G>C, 1028G>A, 1030T>A, 1031T>A
CDS
1318100%191288.6%318 (100%)274 (86.2%)0/0/0/01
Protein mutations:K18R (99A>G), N24S (117A>G), A29C (131G>T 132C>G), M40Q (164A>C 165T>A 166G>A), D45N (179G>A), F72Y (261T>A), I75P (269A>C 270T>C 271T>A), T78N (279C>A), M82V (290A>G), L91I (317T>A 319G>T), A96S (332G>T 334A>T), N97D (335A>G 337C>T), S99A (341T>G 343T>G), N100S (345A>G), R104K (356C>A 357G>A), I108V (368A>G), I116R (392A>C 393T>G 394A>G), K118R (399A>G), P121H (408C>A 409A>T), I124V (416A>G 418T>G), D130E (436T>G), T136V (452A>G 453C>T), Q142H (472G>C), I150A (494A>G 495T>C 496A>C), I157V (515A>G 517T>A), Q175S (569C>A 570A>G 571A>C), V189I (611G>A 613T>A), L191M (617T>A), D199E (643T>A), V200S (644G>T 645T>C 646T>A), V206I (662G>A 664C>T), I228V (728A>G), V249N (791G>A 792T>A), T251N (798C>A), V253N (803G>A 804T>A), N254M (807A>T 808T>G), N255I (810A>T 811T>A), D256E (814T>G), D283E (895C>A), R287K (906G>A 907G>A), P295R (930C>G), K297S (936A>G 937A>T), V315I (989G>A 991T>A), V317I (995G>A)
Codon mutations:TGC8TGT (70C>T), AAT14AAC (88T>C), AAA18AGA (99A>G), TTT19TTC (103T>C), CCT21CCA (109T>A), AAT23AAC (115T>C), AAT24AGT (117A>G), ATT27ATA (127T>A), GCT29TGT (131G>T 132C>G), CTG31TTG (137C>T), GCT33GCA (145T>A), GTA35GTG (151A>G), AAG38AAA (160G>A), GAC39GAT (163C>T), ATG40CAA (164A>C 165T>A 166G>A), AAG42AAA (172G>A), GAT45AAT (179G>A), ATT47ATA (187T>A), GGA50GGT (196A>T), ATA51ATT (199A>T), CCG53CCA (205G>A), CCT54CCG (208T>G), CCT55CCA (211T>A), TTT57TTC (217T>C), AAG58AAA (220G>A), CGG60CGT (226G>T), AAT62AAC (232T>C), ACT63ACG (235T>G), GAT65GAC (241T>C), GGC69GGA (253C>A), TTT72TAT (261T>A), ACA74ACT (268A>T), ATT75CCA (269A>C 270T>C 271T>A), ACT78AAT (279C>A), AAG79AAA (283G>A), GCT81GCG (289T>G), ATG82GTG (290A>G), TTG83TTA (295G>A), ATA84ATT (298A>T), GCT87GCG (307T>G), CTA88TTG (308C>T 310A>G), TTG91ATT (317T>A 319G>T), GTG93GTT (325G>T), ACG94ACT (328G>T), GCA96TCT (332G>T 334A>T), AAC97GAT (335A>G 337C>T), GTC98GTT (340C>T), TCT99GCG (341T>G 343T>G), AAT100AGT (345A>G), TTA102CTT (350T>C 352A>T), CGA104AAA (356C>A 357G>A), GTA106GTT (364A>T), TCA107TCT (367A>T), ATA108GTA (368A>G), AGG109AGA (373G>A), TTA111CTA (377T>C), GAA112GAG (382A>G), GTG115GTA (391G>A), ATA116CGG (392A>C 393T>G 394A>G), CGT117AGA (395C>A 397T>A), AAA118AGA (399A>G), GAA119GAG (403A>G), CCA121CAT (408C>A 409A>T), GAT123GAC (415T>C), ATT124GTG (416A>G 418T>G), CTA125CTT (421A>T), TTT126TTC (424T>C), GAT130GAG (436T>G), TTA131TTG (439A>G), CTT132TTG (440C>T 442T>G), ACA136GTA (452A>G 453C>T), CTG137CTA (457G>A), ATT138ATA (460T>A), GGA141GGT (469A>T), CAG142CAC (472G>C), TCT143TCA (475T>A), ACT148ACG (490T>G), ACA149ACT (493A>T), ATA150GCC (494A>G 495T>C 496A>C), GCA152GCT (502A>T), GGA155GGG (511A>G), ATT157GTA (515A>G 517T>A), GTA158GTT (520A>T), AAC161AAT (529C>T), GCT162GCA (532T>A), GCC163GCT (535C>T), TTC164TTT (538C>T), ACC165ACA (541C>A), CTA169TTG (551C>T 553A>G), ACT170ACA (556T>A), TAT171TAC (559T>C), TTA172CTG (560T>C 562A>G), GAA173GAG (565A>G), CAA175AGC (569C>A 570A>G 571A>C), TTG176CTA (572T>C 574G>A), CTG180TTG (584C>T), CAG182CAA (592G>A), GTT189ATA (611G>A 613T>A), TTG191ATG (617T>A), GAT199GAA (643T>A), GTT200TCA (644G>T 645T>C 646T>A), TTA205CTG (659T>C 661A>G), GTC206ATT (662G>A 664C>T), GAA208GAG (670A>G), CTT209TTG (671C>T 673T>G), CGA210CGG (676A>G), TAT213TAC (685T>C), AAG215AAA (691G>A), GCT217GCA (697T>A), ATC219ATT (703C>T), AAG223AAA (715G>A), CAT225CAC (721T>C), TAT226TAC (724T>C), ATT228GTT (728A>G), AAG230AAA (736G>A), GCT235GCG (751T>G), CAC237CAT (757C>T), GCT238GCA (760T>A), GAC239GAT (763C>T), GTA241GTT (769A>T), TAT242TAC (772T>C), GCA243GCT (775A>T), GTT249AAT (791G>A 792T>A), AAA250AAG (796A>G), ACT251AAT (798C>A), GGA252GGG (802A>G), GTT253AAT (803G>A 804T>A), AAT254ATG (807A>T 808T>G), AAT255ATA (810A>T 811T>A), GAT256GAG (814T>G), AAC258AAT (820C>T), ATT264ATA (838T>A), ATT265ATA (841T>A), CAA267CAG (847A>G), GCA271GCG (859A>G), TCA274TCT (868A>T), CAG278CAA (880G>A), AAT280AAC (886T>C), ACA281ACT (889A>T), GAC283GAA (895C>A), GTG284GTA (898G>A), AAA286AAG (904A>G), AGG287AAA (906G>A 907G>A), TTG288CTA (908T>C 910G>A), CTT289CTG (913T>G), AAA292AAG (922A>G), AAA294AAG (928A>G), CCA295CGA (930C>G), AAA297AGT (936A>G 937A>T), CCA299CCG (943A>G), AAA301AAG (949A>G), GGG302GGA (952G>A), ACG305ACT (961G>T), AAA308AAG (970A>G), GAC310GAT (976C>T), GAA311GAG (979A>G), GTT315ATA (989G>A 991T>A), GGC316GGA (994C>A), GTT317ATT (995G>A)
Proteins
1318100%191288.6%318 (100%)274 (86.2%)0/0/0/01
Protein mutations:K18R (99A>G), N24S (117A>G), A29C (131G>T 132C>G), M40Q (164A>C 165T>A 166G>A), D45N (179G>A), F72Y (261T>A), I75P (269A>C 270T>C 271T>A), T78N (279C>A), M82V (290A>G), L91I (317T>A 319G>T), A96S (332G>T 334A>T), N97D (335A>G 337C>T), S99A (341T>G 343T>G), N100S (345A>G), R104K (356C>A 357G>A), I108V (368A>G), I116R (392A>C 393T>G 394A>G), K118R (399A>G), P121H (408C>A 409A>T), I124V (416A>G 418T>G), D130E (436T>G), T136V (452A>G 453C>T), Q142H (472G>C), I150A (494A>G 495T>C 496A>C), I157V (515A>G 517T>A), Q175S (569C>A 570A>G 571A>C), V189I (611G>A 613T>A), L191M (617T>A), D199E (643T>A), V200S (644G>T 645T>C 646T>A), V206I (662G>A 664C>T), I228V (728A>G), V249N (791G>A 792T>A), T251N (798C>A), V253N (803G>A 804T>A), N254M (807A>T 808T>G), N255I (810A>T 811T>A), D256E (814T>G), D283E (895C>A), R287K (906G>A 907G>A), P295R (930C>G), K297S (936A>G 937A>T), V315I (989G>A 991T>A), V317I (995G>A)
Codon mutations:TGC8TGT (70C>T), AAT14AAC (88T>C), AAA18AGA (99A>G), TTT19TTC (103T>C), CCT21CCA (109T>A), AAT23AAC (115T>C), AAT24AGT (117A>G), ATT27ATA (127T>A), GCT29TGT (131G>T 132C>G), CTG31TTG (137C>T), GCT33GCA (145T>A), GTA35GTG (151A>G), AAG38AAA (160G>A), GAC39GAT (163C>T), ATG40CAA (164A>C 165T>A 166G>A), AAG42AAA (172G>A), GAT45AAT (179G>A), ATT47ATA (187T>A), GGA50GGT (196A>T), ATA51ATT (199A>T), CCG53CCA (205G>A), CCT54CCG (208T>G), CCT55CCA (211T>A), TTT57TTC (217T>C), AAG58AAA (220G>A), CGG60CGT (226G>T), AAT62AAC (232T>C), ACT63ACG (235T>G), GAT65GAC (241T>C), GGC69GGA (253C>A), TTT72TAT (261T>A), ACA74ACT (268A>T), ATT75CCA (269A>C 270T>C 271T>A), ACT78AAT (279C>A), AAG79AAA (283G>A), GCT81GCG (289T>G), ATG82GTG (290A>G), TTG83TTA (295G>A), ATA84ATT (298A>T), GCT87GCG (307T>G), CTA88TTG (308C>T 310A>G), TTG91ATT (317T>A 319G>T), GTG93GTT (325G>T), ACG94ACT (328G>T), GCA96TCT (332G>T 334A>T), AAC97GAT (335A>G 337C>T), GTC98GTT (340C>T), TCT99GCG (341T>G 343T>G), AAT100AGT (345A>G), TTA102CTT (350T>C 352A>T), CGA104AAA (356C>A 357G>A), GTA106GTT (364A>T), TCA107TCT (367A>T), ATA108GTA (368A>G), AGG109AGA (373G>A), TTA111CTA (377T>C), GAA112GAG (382A>G), GTG115GTA (391G>A), ATA116CGG (392A>C 393T>G 394A>G), CGT117AGA (395C>A 397T>A), AAA118AGA (399A>G), GAA119GAG (403A>G), CCA121CAT (408C>A 409A>T), GAT123GAC (415T>C), ATT124GTG (416A>G 418T>G), CTA125CTT (421A>T), TTT126TTC (424T>C), GAT130GAG (436T>G), TTA131TTG (439A>G), CTT132TTG (440C>T 442T>G), ACA136GTA (452A>G 453C>T), CTG137CTA (457G>A), ATT138ATA (460T>A), GGA141GGT (469A>T), CAG142CAC (472G>C), TCT143TCA (475T>A), ACT148ACG (490T>G), ACA149ACT (493A>T), ATA150GCC (494A>G 495T>C 496A>C), GCA152GCT (502A>T), GGA155GGG (511A>G), ATT157GTA (515A>G 517T>A), GTA158GTT (520A>T), AAC161AAT (529C>T), GCT162GCA (532T>A), GCC163GCT (535C>T), TTC164TTT (538C>T), ACC165ACA (541C>A), CTA169TTG (551C>T 553A>G), ACT170ACA (556T>A), TAT171TAC (559T>C), TTA172CTG (560T>C 562A>G), GAA173GAG (565A>G), CAA175AGC (569C>A 570A>G 571A>C), TTG176CTA (572T>C 574G>A), CTG180TTG (584C>T), CAG182CAA (592G>A), GTT189ATA (611G>A 613T>A), TTG191ATG (617T>A), GAT199GAA (643T>A), GTT200TCA (644G>T 645T>C 646T>A), TTA205CTG (659T>C 661A>G), GTC206ATT (662G>A 664C>T), GAA208GAG (670A>G), CTT209TTG (671C>T 673T>G), CGA210CGG (676A>G), TAT213TAC (685T>C), AAG215AAA (691G>A), GCT217GCA (697T>A), ATC219ATT (703C>T), AAG223AAA (715G>A), CAT225CAC (721T>C), TAT226TAC (724T>C), ATT228GTT (728A>G), AAG230AAA (736G>A), GCT235GCG (751T>G), CAC237CAT (757C>T), GCT238GCA (760T>A), GAC239GAT (763C>T), GTA241GTT (769A>T), TAT242TAC (772T>C), GCA243GCT (775A>T), GTT249AAT (791G>A 792T>A), AAA250AAG (796A>G), ACT251AAT (798C>A), GGA252GGG (802A>G), GTT253AAT (803G>A 804T>A), AAT254ATG (807A>T 808T>G), AAT255ATA (810A>T 811T>A), GAT256GAG (814T>G), AAC258AAT (820C>T), ATT264ATA (838T>A), ATT265ATA (841T>A), CAA267CAG (847A>G), GCA271GCG (859A>G), TCA274TCT (868A>T), CAG278CAA (880G>A), AAT280AAC (886T>C), ACA281ACT (889A>T), GAC283GAA (895C>A), GTG284GTA (898G>A), AAA286AAG (904A>G), AGG287AAA (906G>A 907G>A), TTG288CTA (908T>C 910G>A), CTT289CTG (913T>G), AAA292AAG (922A>G), AAA294AAG (928A>G), CCA295CGA (930C>G), AAA297AGT (936A>G 937A>T), CCA299CCG (943A>G), AAA301AAG (949A>G), GGG302GGA (952G>A), ACG305ACT (961G>T), AAA308AAG (970A>G), GAC310GAT (976C>T), GAA311GAG (979A>G), GTT315ATA (989G>A 991T>A), GGC316GGA (994C>A), GTT317ATT (995G>A)
*: Inserts / Deletes / Misaligned / Frameshifts

Analysis details

This analysis was performed with panviral2.43