Version 2.16.3
Genome Detective Platform

NGS Details (SRR3458562_Metagenome_example): Rotavirus A (segment 11)

Assembly

667 (1 contig(s))
1171.6
7044
454.51 rpm (after QC)
0
de novo + reference guided assembly
Bcf Tools

Coverage Map

Variant Tables

Assignment

Rotavirus A (Taxonomy ID: 28875)
90.4048
91.0959
1
2

Alignment

segment 11
1078.0 (NT) + 1795.0 (AA) = 2873.0
87.4848
Global, seeded, nucleotide + amino acids (AGA)

Alignment Detailed Statistics

BeginEndCoverageScoreConcordanceMatchesIdentitiesI/D/M/F*Stop Codons
NT1667100%107880.8%667 (100%)603 (90.4%)0/0
Mutations:61C>T, 66A>T, 68C>G, 75T>C, 78G>A, 87G>A, 138G>A, 167A>G, 183G>A, 195G>A, 240T>C, 304G>A, 315A>G, 318T>A, 324T>C, 330C>T, 333A>G, 357A>T, 366C>A, 367T>A, 369A>T, 373G>A, 375A>G, 378A>C, 381T>G, 384T>C, 385T>C, 390C>T, 402A>C, 408T>A, 411G>T, 412G>A, 413A>T, 415A>T, 417T>G, 432A>C, 436C>A, 437A>G, 438A>C, 439A>G, 456G>A, 465A>T, 467G>A, 471T>A, 480G>A, 495T>C, 498T>C, 504G>C, 513A>T, 537G>A, 554A>G, 558A>G, 561C>T, 568T>C, 591C>T, 606T>C, 618A>G, 623G>A, 629G>A, 632A>G, 633C>G, 634A>T, 661T>C, 663T>C
CDS
1199100%117393.5%199 (100%)185 (93.0%)0/0/0/01
Protein mutations:P14S (61C>T), T16S (68C>G), N49S (167A>G), A95T (304G>A), L112F (357A>T), L116I (367T>A 369A>T), V118M (373G>A 375A>G), K119N (378A>C), D131I (412G>A 413A>T), T132S (415A>T 417T>G), Q139S (436C>A 437A>G 438A>C), N140D (439A>G), R149K (467G>A), K178R (554A>G)
Codon mutations:CCT14TCT (61C>T), TCA15TCT (66A>T), ACT16AGT (68C>G), TAT18TAC (75T>C), AAG19AAA (78G>A), TCG22TCA (87G>A), CAG39CAA (138G>A), AAT49AGT (167A>G), TCG54TCA (183G>A), GAG58GAA (195G>A), AGT73AGC (240T>C), GCA95ACA (304G>A), CGA98CGG (315A>G), CCT99CCA (318T>A), AGT101AGC (324T>C), GTC103GTT (330C>T), GGA104GGG (333A>G), TTA112TTT (357A>T), GGC115GGA (366C>A), TTA116ATT (367T>A 369A>T), GTA118ATG (373G>A 375A>G), AAA119AAC (378A>C), GCT120GCG (381T>G), AAT121AAC (384T>C), TTG122CTG (385T>C), GAC123GAT (390C>T), TCA127TCC (402A>C), TCT129TCA (408T>A), ACG130ACT (411G>T), GAT131ATT (412G>A 413A>T), ACT132TCG (415A>T 417T>G), TCA137TCC (432A>C), CAA139AGC (436C>A 437A>G 438A>C), AAC140GAC (439A>G), AAG145AAA (456G>A), CCA148CCT (465A>T), AGA149AAA (467G>A), ATT150ATA (471T>A), GAG153GAA (480G>A), GAT158GAC (495T>C), TAT159TAC (498T>C), CTG161CTC (504G>C), TCA164TCT (513A>T), AAG172AAA (537G>A), AAG178AGG (554A>G), AAA179AAG (558A>G), TAC180TAT (561C>T), TTA183CTA (568T>C), GTC190GTT (591C>T), ATT195ATC (606T>C), TAA199TAG (618A>G)
193100%62289.4%93 (100%)81 (87.1%)0/0/0/00
Protein mutations:R3H (87G>A), S20N (138G>A), I30V (167A>G), R35Q (183G>A), R39K (195G>A), V54A (240T>C), D79G (315A>G), L80H (318T>A), V82A (324T>C), S84L (330C>T), D85G (333A>G), *93L (357A>T)
Codon mutations:CGT3CAT (87G>A), AGT20AAT (138G>A), ATA30GTA (167A>G), CGA35CAA (183G>A), AGG39AAG (195G>A), GTT54GCT (240T>C), CAG75CAA (304G>A), GAC79GGC (315A>G), CTT80CAT (318T>A), GTA82GCA (324T>C), TCG84TTG (330C>T), GAT85GGT (333A>G), TAA93TTA (357A>T)
Proteins
1199100%117393.5%199 (100%)185 (93.0%)0/0/0/01
Protein mutations:P14S (61C>T), T16S (68C>G), N49S (167A>G), A95T (304G>A), L112F (357A>T), L116I (367T>A 369A>T), V118M (373G>A 375A>G), K119N (378A>C), D131I (412G>A 413A>T), T132S (415A>T 417T>G), Q139S (436C>A 437A>G 438A>C), N140D (439A>G), R149K (467G>A), K178R (554A>G)
Codon mutations:CCT14TCT (61C>T), TCA15TCT (66A>T), ACT16AGT (68C>G), TAT18TAC (75T>C), AAG19AAA (78G>A), TCG22TCA (87G>A), CAG39CAA (138G>A), AAT49AGT (167A>G), TCG54TCA (183G>A), GAG58GAA (195G>A), AGT73AGC (240T>C), GCA95ACA (304G>A), CGA98CGG (315A>G), CCT99CCA (318T>A), AGT101AGC (324T>C), GTC103GTT (330C>T), GGA104GGG (333A>G), TTA112TTT (357A>T), GGC115GGA (366C>A), TTA116ATT (367T>A 369A>T), GTA118ATG (373G>A 375A>G), AAA119AAC (378A>C), GCT120GCG (381T>G), AAT121AAC (384T>C), TTG122CTG (385T>C), GAC123GAT (390C>T), TCA127TCC (402A>C), TCT129TCA (408T>A), ACG130ACT (411G>T), GAT131ATT (412G>A 413A>T), ACT132TCG (415A>T 417T>G), TCA137TCC (432A>C), CAA139AGC (436C>A 437A>G 438A>C), AAC140GAC (439A>G), AAG145AAA (456G>A), CCA148CCT (465A>T), AGA149AAA (467G>A), ATT150ATA (471T>A), GAG153GAA (480G>A), GAT158GAC (495T>C), TAT159TAC (498T>C), CTG161CTC (504G>C), TCA164TCT (513A>T), AAG172AAA (537G>A), AAG178AGG (554A>G), AAA179AAG (558A>G), TAC180TAT (561C>T), TTA183CTA (568T>C), GTC190GTT (591C>T), ATT195ATC (606T>C), TAA199TAG (618A>G)
193100%62289.4%93 (100%)81 (87.1%)0/0/0/00
Protein mutations:R3H (87G>A), S20N (138G>A), I30V (167A>G), R35Q (183G>A), R39K (195G>A), V54A (240T>C), D79G (315A>G), L80H (318T>A), V82A (324T>C), S84L (330C>T), D85G (333A>G), *93L (357A>T)
Codon mutations:CGT3CAT (87G>A), AGT20AAT (138G>A), ATA30GTA (167A>G), CGA35CAA (183G>A), AGG39AAG (195G>A), GTT54GCT (240T>C), CAG75CAA (304G>A), GAC79GGC (315A>G), CTT80CAT (318T>A), GTA82GCA (324T>C), TCG84TTG (330C>T), GAT85GGT (333A>G), TAA93TTA (357A>T)
*: Inserts / Deletes / Misaligned / Frameshifts

Analysis details

This analysis was performed with panviral2.43