NGS Details (ERR138007_norovirus_amplicon_example): Simian immunodeficiency virus

Assembly

137 (1 contig(s))
1.7
2
4.26 rpm (after QC)
2
de novo + reference guided assembly
Bcf Tools

Coverage Map

Variant Tables

Assignment

Simian immunodeficiency virus (Taxonomy ID: 11723)
78.1022
84.4444
0
6

Alignment

158.0 (NT) + 576.0 (AA) = 734.0
78.0851
Global, seeded, nucleotide + amino acids (AGA)

Alignment Detailed Statistics

BeginEndCoverageScoreConcordanceMatchesIdentitiesI/D/M/F*Stop Codons
NT145915951.4%15857.7%137 (100%)107 (78.1%)0/0
Mutations:1466C>A, 1471T>C, 1472A>C, 1480A>G, 1481C>A, 1484T>C, 1487G>A, 1493A>T, 1500A>G, 1502T>G, 1503C>T, 1505T>G, 1514C>A, 1517T>C, 1523A>G, 1535G>R, 1541C>T, 1544G>A, 1547A>T, 1550C>T, 1551A>C, 1552G>C, 1557C>G, 1560G>A, 1561C>T, 1562T>G, 1565C>G, 1568G>R, 1575G>C, 1592C>T
CDS
1892333.1%28884.5%45 (100%)38 (84.4%)0/0/0/00
Protein mutations:V192A (1471T>C 1472A>C), D195G (1480A>G 1481C>A), I202V (1500A>G 1502T>G), R219P (1551A>C 1552G>C), P221A (1557C>G), A222M (1560G>A 1561C>T 1562T>G), A227P (1575G>C)
Codon mutations:CTC190CTA (1466C>A), GTA192GCC (1471T>C 1472A>C), GAC195GGA (1480A>G 1481C>A), CAT196CAC (1484T>C), CAG197CAA (1487G>A), GCA199GCT (1493A>T), ATT202GTG (1500A>G 1502T>G), CTT203TTG (1503C>T 1505T>G), GTC206GTA (1514C>A), ATT207ATC (1517T>C), GAA209GAG (1523A>G), GAG213GAR (1535G>R), GAC215GAT (1541C>T), AGG216AGA (1544G>A), ACA217ACT (1547A>T), CAC218CAT (1550C>T), AGA219CCA (1551A>C 1552G>C), CCA221GCA (1557C>G), GCT222ATG (1560G>A 1561C>T 1562T>G), GGC223GGG (1565C>G), CCG224CCR (1568G>R), GCA227CCA (1575G>C), GAC232GAT (1592C>T)
1892338.8%28884.5%45 (100%)38 (84.4%)0/0/0/00
Protein mutations:V192A (1471T>C 1472A>C), D195G (1480A>G 1481C>A), I202V (1500A>G 1502T>G), R219P (1551A>C 1552G>C), P221A (1557C>G), A222M (1560G>A 1561C>T 1562T>G), A227P (1575G>C)
Codon mutations:CTC190CTA (1466C>A), GTA192GCC (1471T>C 1472A>C), GAC195GGA (1480A>G 1481C>A), CAT196CAC (1484T>C), CAG197CAA (1487G>A), GCA199GCT (1493A>T), ATT202GTG (1500A>G 1502T>G), CTT203TTG (1503C>T 1505T>G), GTC206GTA (1514C>A), ATT207ATC (1517T>C), GAA209GAG (1523A>G), GAG213GAR (1535G>R), GAC215GAT (1541C>T), AGG216AGA (1544G>A), ACA217ACT (1547A>T), CAC218CAT (1550C>T), AGA219CCA (1551A>C 1552G>C), CCA221GCA (1557C>G), GCT222ATG (1560G>A 1561C>T 1562T>G), GGC223GGG (1565C>G), CCG224CCR (1568G>R), GCA227CCA (1575G>C), GAC232GAT (1592C>T)
Proteins
1892333.1%28884.5%45 (100%)38 (84.4%)0/0/0/00
Protein mutations:V192A (1471T>C 1472A>C), D195G (1480A>G 1481C>A), I202V (1500A>G 1502T>G), R219P (1551A>C 1552G>C), P221A (1557C>G), A222M (1560G>A 1561C>T 1562T>G), A227P (1575G>C)
Codon mutations:CTC190CTA (1466C>A), GTA192GCC (1471T>C 1472A>C), GAC195GGA (1480A>G 1481C>A), CAT196CAC (1484T>C), CAG197CAA (1487G>A), GCA199GCT (1493A>T), ATT202GTG (1500A>G 1502T>G), CTT203TTG (1503C>T 1505T>G), GTC206GTA (1514C>A), ATT207ATC (1517T>C), GAA209GAG (1523A>G), GAG213GAR (1535G>R), GAC215GAT (1541C>T), AGG216AGA (1544G>A), ACA217ACT (1547A>T), CAC218CAT (1550C>T), AGA219CCA (1551A>C 1552G>C), CCA221GCA (1557C>G), GCT222ATG (1560G>A 1561C>T 1562T>G), GGC223GGG (1565C>G), CCG224CCR (1568G>R), GCA227CCA (1575G>C), GAC232GAT (1592C>T)
1892338.8%28884.5%45 (100%)38 (84.4%)0/0/0/00
Protein mutations:V192A (1471T>C 1472A>C), D195G (1480A>G 1481C>A), I202V (1500A>G 1502T>G), R219P (1551A>C 1552G>C), P221A (1557C>G), A222M (1560G>A 1561C>T 1562T>G), A227P (1575G>C)
Codon mutations:CTC190CTA (1466C>A), GTA192GCC (1471T>C 1472A>C), GAC195GGA (1480A>G 1481C>A), CAT196CAC (1484T>C), CAG197CAA (1487G>A), GCA199GCT (1493A>T), ATT202GTG (1500A>G 1502T>G), CTT203TTG (1503C>T 1505T>G), GTC206GTA (1514C>A), ATT207ATC (1517T>C), GAA209GAG (1523A>G), GAG213GAR (1535G>R), GAC215GAT (1541C>T), AGG216AGA (1544G>A), ACA217ACT (1547A>T), CAC218CAT (1550C>T), AGA219CCA (1551A>C 1552G>C), CCA221GCA (1557C>G), GCT222ATG (1560G>A 1561C>T 1562T>G), GGC223GGG (1565C>G), CCG224CCR (1568G>R), GCA227CCA (1575G>C), GAC232GAT (1592C>T)
*: Inserts / Deletes / Misaligned / Frameshifts

Analysis details

This analysis was performed with panviral2.43