Version 2.22.2
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