Version 2.22.2
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