Version 2.16.1
Genome Detective Platform

NGS Details (SRR3458562_Metagenome_example): Rotavirus A (segment 9)

Assembly

1049 (1 contig(s))
8355.4
82946
5352.04 rpm (after QC)
0
de novo + reference guided assembly
Bcf Tools

Coverage Map

Variant Tables

Assignment

Rotavirus A (Taxonomy ID: 28875)
76.7398
86.2385
1
1

Alignment

segment 9
1122.0 (NT) + 2006.0 (AA) = 3128.0
72.0405
Global, seeded, nucleotide + amino acids (AGA)

Alignment Detailed Statistics

BeginEndCoverageScoreConcordanceMatchesIdentitiesI/D/M/F*Stop Codons
NT14106298.8%112253.5%1049 (100%)805 (76.7%)0/0
Mutations:73G>A, 80C>T, 84T>C, 85C>T, 89T>C, 98T>C, 99T>A, 100C>T, 103C>T, 105A>G, 111C>T, 114A>C, 115C>T, 117T>A, 124T>A, 129T>G, 143T>A, 160C>T, 162T>G, 163T>C, 168A>G, 169A>G, 171T>A, 177A>C, 181T>G, 183A>C, 184C>A, 186A>C, 187T>A, 189T>A, 190C>A, 192C>A, 194G>A, 195A>T, 198A>G, 204T>C, 210T>A, 211A>G, 213T>A, 217C>T, 219T>G, 225C>T, 231C>T, 234C>A, 240C>T, 246A>G, 249C>T, 252T>A, 255T>C, 258A>T, 261G>A, 265G>A, 266A>G, 267A>T, 270A>G, 271A>C, 276C>T, 277C>T, 279C>G, 282T>A, 285T>A, 288A>C, 294C>T, 295C>T, 297A>G, 306G>T, 307A>G, 308C>T, 315T>A, 316G>T, 318G>A, 320C>A, 321T>C, 328A>G, 329A>C, 330C>T, 335A>C, 337T>G, 338C>A, 348C>T, 351A>C, 352C>T, 354G>A, 363A>G, 366T>C, 367C>T, 369T>A, 372G>A, 378G>A, 387T>A, 393C>A, 396A>G, 399T>C, 412A>G, 415A>G, 417C>T, 420T>A, 423A>G, 424T>G, 426G>C, 432T>A, 435T>G, 438T>A, 441G>A, 447G>A, 450T>C, 462C>T, 463G>T, 468A>T, 469C>T, 484G>T, 486G>T, 489G>A, 490T>C, 491T>A, 492G>A, 493C>A, 496T>C, 498G>A, 507A>T, 511C>T, 513T>G, 516G>C, 522A>T, 528A>G, 531C>T, 538T>C, 543T>C, 555T>C, 558T>A, 561T>G, 564G>A, 579A>G, 585C>T, 588A>G, 591G>A, 615A>T, 618A>T, 621T>C, 624A>G, 625A>G, 633A>G, 640C>T, 642T>A, 654T>A, 660A>T, 669C>T, 670T>C, 672G>A, 674C>T, 679G>A, 682G>C, 684T>A, 685A>G, 686C>A, 687A>C, 690T>G, 697G>A, 698A>C, 709G>A, 711T>G, 714A>G, 717G>A, 720G>A, 723A>G, 729T>A, 732C>T, 735G>T, 738T>A, 744C>T, 747T>C, 750T>C, 753T>C, 756G>A, 757C>T, 759G>A, 760G>A, 762T>C, 771A>G, 780T>C, 783T>C, 786T>A, 787A>C, 789A>C, 798G>A, 801A>G, 804G>A, 813A>G, 816A>G, 825C>A, 828T>C, 834A>G, 837T>A, 840T>C, 843T>C, 844T>G, 846T>G, 847G>A, 852C>T, 853C>T, 855C>A, 858T>C, 861A>C, 864T>A, 876T>A, 880G>A, 894A>G, 895C>A, 897G>A, 909T>A, 912C>T, 933T>G, 939T>C, 942T>G, 948A>G, 951C>T, 954T>C, 957A>C, 958G>A, 963G>A, 969A>T, 972A>G, 973G>A, 974T>C, 975T>A, 990A>T, 996A>G, 999A>T, 1005A>G, 1006G>T, 1008A>G, 1011A>G, 1014T>C, 1017T>C, 1020C>T, 1032A>G, 1033T>C, 1035A>T, 1036C>G, 1041G>A, 1047A>G, 1053T>C, 1057G>A, 1058T>C
CDS
1327100%200689.4%327 (100%)282 (86.2%)0/0/0/01
Protein mutations:V9I (73G>A), T11I (80C>T), I14T (89T>C), I17T (98T>C 99T>A), L26I (124T>A), F32Y (143T>A), F39L (163T>C), I40M (168A>G), I41V (169A>G 171T>A), S45A (181T>G 183A>C), P46T (184C>A 186A>C), F47I (187T>A 189T>A), L48I (190C>A 192C>A), R49N (194G>A 195A>T), I55V (211A>G 213T>A), E73S (265G>A 266A>G 267A>T), T75P (271A>C), T87V (307A>G 308C>T), A90S (316G>T 318G>A), T91N (320C>A 321T>C), N94A (328A>G 329A>C 330C>T), N96T (335A>C), S97E (337T>G 338C>A), T122A (412A>G), N123D (415A>G 417C>T), S126A (424T>G 426G>C), D130E (438T>A), V139L (463G>T), A146S (484G>T 486G>T), L148Q (490T>C 491T>A 492G>A), Q149K (493C>A), I193V (625A>G), T209I (674C>T), D211N (679G>A), A212P (682G>C 684T>A), T213D (685A>G 686C>A 687A>C), E217T (697G>A 698A>C), A221T (709G>A 711T>G), D238N (760G>A 762T>C), S266A (844T>G 846T>G), D267N (847G>A), A278T (880G>A), D304N (958G>A), V309T (973G>A 974T>C 975T>A), A320S (1006G>T 1008A>G)
Codon mutations:GTT9ATT (73G>A), ACC11ATC (80C>T), TTT12TTC (84T>C), CTG13TTG (85C>T), ATA14ACA (89T>C), ATT17ACA (98T>C 99T>A), CTA18TTA (100C>T), CTA19TTG (103C>T 105A>G), TAC21TAT (111C>T), ATA22ATC (114A>C), CTT23TTA (115C>T 117T>A), TTA26ATA (124T>A), ACT27ACG (129T>G), TTT32TAT (143T>A), CTT38TTG (160C>T 162T>G), TTT39CTT (163T>C), ATA40ATG (168A>G), ATT41GTA (169A>G 171T>A), ATA43ATC (177A>C), TCA45GCC (181T>G 183A>C), CCA46ACC (184C>A 186A>C), TTT47ATA (187T>A 189T>A), CTC48ATA (190C>A 192C>A), AGA49AAT (194G>A 195A>T), GCA50GCG (198A>G), AAT52AAC (204T>C), GGT54GGA (210T>A), ATT55GTA (211A>G 213T>A), CTT57TTG (217C>T 219T>G), ATC59ATT (225C>T), GGC61GGT (231C>T), TCC62TCA (234C>A), GAC64GAT (240C>T), GCA66GCG (246A>G), TAC67TAT (249C>T), GCT68GCA (252T>A), AAT69AAC (255T>C), TCA70TCT (258A>T), ACG71ACA (261G>A), GAA73AGT (265G>A 266A>G 267A>T), GAA74GAG (270A>G), ACA75CCA (271A>C), TTC76TTT (276C>T), CTC77TTG (277C>T 279C>G), ACT78ACA (282T>A), TCT79TCA (285T>A), ACA80ACC (288A>C), TGC82TGT (294C>T), CTA83TTG (295C>T 297A>G), CCG86CCT (306G>T), ACT87GTT (307A>G 308C>T), GCT89GCA (315T>A), GCG90TCA (316G>T 318G>A), ACT91AAC (320C>A 321T>C), AAC94GCT (328A>G 329A>C 330C>T), AAT96ACT (335A>C), TCA97GAA (337T>G 338C>A), GAC100GAT (348C>T), ACA101ACC (351A>C), CTG102TTA (352C>T 354G>A), CTA105CTG (363A>G), TTT106TTC (366T>C), CTT107TTA (367C>T 369T>A), ACG108ACA (372G>A), GGG110GGA (378G>A), ACT113ACA (387T>A), TCC115TCA (393C>A), GTA116GTG (396A>G), TAT117TAC (399T>C), ACT122GCT (412A>G), AAC123GAT (415A>G 417C>T), ATT124ATA (420T>A), GCA125GCG (423A>G), TCG126GCC (424T>G 426G>C), TCT128TCA (432T>A), GTT129GTG (435T>G), GAT130GAA (438T>A), CCG131CCA (441G>A), TTG133TTA (447G>A), TAT134TAC (450T>C), AAC138AAT (462C>T), GTA139TTA (463G>T), GTA140GTT (468A>T), CTA141TTA (469C>T), GCG146TCT (484G>T 486G>T), ACG147ACA (489G>A), TTG148CAA (490T>C 491T>A 492G>A), CAA149AAA (493C>A), TTG150CTA (496T>C 498G>A), TCA153TCT (507A>T), CTT155TTG (511C>T 513T>G), GCG156GCC (516G>C), CTA158CTT (522A>T), TTA160TTG (528A>G), AAC161AAT (531C>T), TTG164CTG (538T>C), TGT165TGC (543T>C), GAT169GAC (555T>C), ATT170ATA (558T>A), ACT171ACG (561T>G), CTG172CTA (564G>A), CAA177CAG (579A>G), GAC179GAT (585C>T), GAA180GAG (588A>G), GCG181GCA (591G>A), TCA189TCT (615A>T), TCA190TCT (618A>T), TGT191TGC (621T>C), ACA192ACG (624A>G), ATT193GTT (625A>G), GTA195GTG (633A>G), CTT198TTA (640C>T 642T>A), ACT202ACA (654T>A), GGA204GGT (660A>T), TGC207TGT (669C>T), TTG208CTA (670T>C 672G>A), ACA209ATA (674C>T), GAT211AAT (679G>A), GCT212CCA (682G>C 684T>A), ACA213GAC (685A>G 686C>A 687A>C), ACT214ACG (690T>G), GAA217ACA (697G>A 698A>C), GCT221ACG (709G>A 711T>G), GAA222GAG (714A>G), AAG223AAA (717G>A), TTG224TTA (720G>A), GTA225GTG (723A>G), ACT227ACA (729T>A), GAC228GAT (732C>T), GTG229GTT (735G>T), GTT230GTA (738T>A), GGC232GGT (744C>T), GTT233GTC (747T>C), AAT234AAC (750T>C), CAT235CAC (753T>C), AAG236AAA (756G>A), CTG237TTA (757C>T 759G>A), GAT238AAC (760G>A 762T>C), ACA241ACG (771A>G), TGT244TGC (780T>C), ACT245ACC (783T>C), ATT246ATA (786T>A), AGA247CGC (787A>C 789A>C), AAG250AAA (798G>A), AAA251AAG (801A>G), TTG252TTA (804G>A), AGA255AGG (813A>G), GAA256GAG (816A>G), GCC259GCA (825C>A), GTT260GTC (828T>C), CAA262CAG (834A>G), GTT263GTA (837T>A), GGT264GGC (840T>C), GGT265GGC (843T>C), TCT266GCG (844T>G 846T>G), GAC267AAC (847G>A), ATC268ATT (852C>T), CTC269TTA (853C>T 855C>A), GAT270GAC (858T>C), ATA271ATC (861A>C), ACT272ACA (864T>A), ACT276ACA (876T>A), GCA278ACA (880G>A), GAA282GAG (894A>G), CGG283AGA (895C>A 897G>A), ATT287ATA (909T>A), AAC288AAT (912C>T), GTT295GTG (933T>G), TAT297TAC (939T>C), ACT298ACG (942T>G), GTA300GTG (948A>G), GAC301GAT (951C>T), TAT302TAC (954T>C), GTA303GTC (957A>C), GAT304AAT (958G>A), CAG305CAA (963G>A), ATA307ATT (969A>T), CAA308CAG (972A>G), GTT309ACA (973G>A 974T>C 975T>A), TCA314TCT (990A>T), TCA316TCG (996A>G), CTA317CTT (999A>T), TCA319TCG (1005A>G), GCA320TCG (1006G>T 1008A>G), GCA321GCG (1011A>G), TTT322TTC (1014T>C), TAT323TAC (1017T>C), TAC324TAT (1020C>T)
Proteins
1327100%200689.4%327 (100%)282 (86.2%)0/0/0/01
Protein mutations:V9I (73G>A), T11I (80C>T), I14T (89T>C), I17T (98T>C 99T>A), L26I (124T>A), F32Y (143T>A), F39L (163T>C), I40M (168A>G), I41V (169A>G 171T>A), S45A (181T>G 183A>C), P46T (184C>A 186A>C), F47I (187T>A 189T>A), L48I (190C>A 192C>A), R49N (194G>A 195A>T), I55V (211A>G 213T>A), E73S (265G>A 266A>G 267A>T), T75P (271A>C), T87V (307A>G 308C>T), A90S (316G>T 318G>A), T91N (320C>A 321T>C), N94A (328A>G 329A>C 330C>T), N96T (335A>C), S97E (337T>G 338C>A), T122A (412A>G), N123D (415A>G 417C>T), S126A (424T>G 426G>C), D130E (438T>A), V139L (463G>T), A146S (484G>T 486G>T), L148Q (490T>C 491T>A 492G>A), Q149K (493C>A), I193V (625A>G), T209I (674C>T), D211N (679G>A), A212P (682G>C 684T>A), T213D (685A>G 686C>A 687A>C), E217T (697G>A 698A>C), A221T (709G>A 711T>G), D238N (760G>A 762T>C), S266A (844T>G 846T>G), D267N (847G>A), A278T (880G>A), D304N (958G>A), V309T (973G>A 974T>C 975T>A), A320S (1006G>T 1008A>G)
Codon mutations:GTT9ATT (73G>A), ACC11ATC (80C>T), TTT12TTC (84T>C), CTG13TTG (85C>T), ATA14ACA (89T>C), ATT17ACA (98T>C 99T>A), CTA18TTA (100C>T), CTA19TTG (103C>T 105A>G), TAC21TAT (111C>T), ATA22ATC (114A>C), CTT23TTA (115C>T 117T>A), TTA26ATA (124T>A), ACT27ACG (129T>G), TTT32TAT (143T>A), CTT38TTG (160C>T 162T>G), TTT39CTT (163T>C), ATA40ATG (168A>G), ATT41GTA (169A>G 171T>A), ATA43ATC (177A>C), TCA45GCC (181T>G 183A>C), CCA46ACC (184C>A 186A>C), TTT47ATA (187T>A 189T>A), CTC48ATA (190C>A 192C>A), AGA49AAT (194G>A 195A>T), GCA50GCG (198A>G), AAT52AAC (204T>C), GGT54GGA (210T>A), ATT55GTA (211A>G 213T>A), CTT57TTG (217C>T 219T>G), ATC59ATT (225C>T), GGC61GGT (231C>T), TCC62TCA (234C>A), GAC64GAT (240C>T), GCA66GCG (246A>G), TAC67TAT (249C>T), GCT68GCA (252T>A), AAT69AAC (255T>C), TCA70TCT (258A>T), ACG71ACA (261G>A), GAA73AGT (265G>A 266A>G 267A>T), GAA74GAG (270A>G), ACA75CCA (271A>C), TTC76TTT (276C>T), CTC77TTG (277C>T 279C>G), ACT78ACA (282T>A), TCT79TCA (285T>A), ACA80ACC (288A>C), TGC82TGT (294C>T), CTA83TTG (295C>T 297A>G), CCG86CCT (306G>T), ACT87GTT (307A>G 308C>T), GCT89GCA (315T>A), GCG90TCA (316G>T 318G>A), ACT91AAC (320C>A 321T>C), AAC94GCT (328A>G 329A>C 330C>T), AAT96ACT (335A>C), TCA97GAA (337T>G 338C>A), GAC100GAT (348C>T), ACA101ACC (351A>C), CTG102TTA (352C>T 354G>A), CTA105CTG (363A>G), TTT106TTC (366T>C), CTT107TTA (367C>T 369T>A), ACG108ACA (372G>A), GGG110GGA (378G>A), ACT113ACA (387T>A), TCC115TCA (393C>A), GTA116GTG (396A>G), TAT117TAC (399T>C), ACT122GCT (412A>G), AAC123GAT (415A>G 417C>T), ATT124ATA (420T>A), GCA125GCG (423A>G), TCG126GCC (424T>G 426G>C), TCT128TCA (432T>A), GTT129GTG (435T>G), GAT130GAA (438T>A), CCG131CCA (441G>A), TTG133TTA (447G>A), TAT134TAC (450T>C), AAC138AAT (462C>T), GTA139TTA (463G>T), GTA140GTT (468A>T), CTA141TTA (469C>T), GCG146TCT (484G>T 486G>T), ACG147ACA (489G>A), TTG148CAA (490T>C 491T>A 492G>A), CAA149AAA (493C>A), TTG150CTA (496T>C 498G>A), TCA153TCT (507A>T), CTT155TTG (511C>T 513T>G), GCG156GCC (516G>C), CTA158CTT (522A>T), TTA160TTG (528A>G), AAC161AAT (531C>T), TTG164CTG (538T>C), TGT165TGC (543T>C), GAT169GAC (555T>C), ATT170ATA (558T>A), ACT171ACG (561T>G), CTG172CTA (564G>A), CAA177CAG (579A>G), GAC179GAT (585C>T), GAA180GAG (588A>G), GCG181GCA (591G>A), TCA189TCT (615A>T), TCA190TCT (618A>T), TGT191TGC (621T>C), ACA192ACG (624A>G), ATT193GTT (625A>G), GTA195GTG (633A>G), CTT198TTA (640C>T 642T>A), ACT202ACA (654T>A), GGA204GGT (660A>T), TGC207TGT (669C>T), TTG208CTA (670T>C 672G>A), ACA209ATA (674C>T), GAT211AAT (679G>A), GCT212CCA (682G>C 684T>A), ACA213GAC (685A>G 686C>A 687A>C), ACT214ACG (690T>G), GAA217ACA (697G>A 698A>C), GCT221ACG (709G>A 711T>G), GAA222GAG (714A>G), AAG223AAA (717G>A), TTG224TTA (720G>A), GTA225GTG (723A>G), ACT227ACA (729T>A), GAC228GAT (732C>T), GTG229GTT (735G>T), GTT230GTA (738T>A), GGC232GGT (744C>T), GTT233GTC (747T>C), AAT234AAC (750T>C), CAT235CAC (753T>C), AAG236AAA (756G>A), CTG237TTA (757C>T 759G>A), GAT238AAC (760G>A 762T>C), ACA241ACG (771A>G), TGT244TGC (780T>C), ACT245ACC (783T>C), ATT246ATA (786T>A), AGA247CGC (787A>C 789A>C), AAG250AAA (798G>A), AAA251AAG (801A>G), TTG252TTA (804G>A), AGA255AGG (813A>G), GAA256GAG (816A>G), GCC259GCA (825C>A), GTT260GTC (828T>C), CAA262CAG (834A>G), GTT263GTA (837T>A), GGT264GGC (840T>C), GGT265GGC (843T>C), TCT266GCG (844T>G 846T>G), GAC267AAC (847G>A), ATC268ATT (852C>T), CTC269TTA (853C>T 855C>A), GAT270GAC (858T>C), ATA271ATC (861A>C), ACT272ACA (864T>A), ACT276ACA (876T>A), GCA278ACA (880G>A), GAA282GAG (894A>G), CGG283AGA (895C>A 897G>A), ATT287ATA (909T>A), AAC288AAT (912C>T), GTT295GTG (933T>G), TAT297TAC (939T>C), ACT298ACG (942T>G), GTA300GTG (948A>G), GAC301GAT (951C>T), TAT302TAC (954T>C), GTA303GTC (957A>C), GAT304AAT (958G>A), CAG305CAA (963G>A), ATA307ATT (969A>T), CAA308CAG (972A>G), GTT309ACA (973G>A 974T>C 975T>A), TCA314TCT (990A>T), TCA316TCG (996A>G), CTA317CTT (999A>T), TCA319TCG (1005A>G), GCA320TCG (1006G>T 1008A>G), GCA321GCG (1011A>G), TTT322TTC (1014T>C), TAT323TAC (1017T>C), TAC324TAT (1020C>T)
*: Inserts / Deletes / Misaligned / Frameshifts

Analysis details

This analysis was performed with panviral2.43