Version 2.16.1
Genome Detective Platform

NGS Details (SRR3458562_Metagenome_example): Porcine circovirus 2

Assembly

1768 (1 contig(s))
5154.9
96411
6220.87 rpm (after QC)
0
read mapping against reference + variant calling
Bcf Tools

Coverage Map

Variant Tables

Assignment

Porcine circovirus 2 (Taxonomy ID: 85708)
97.6244
97.5535
3
3

Alignment

3368.0 (NT) + 4806.0 (AA) = 8174.0
96.9402
Global, seeded, nucleotide + amino acids (AGA)

Alignment Detailed Statistics

BeginEndCoverageScoreConcordanceMatchesIdentitiesI/D/M/F*Stop Codons
NT11768100%336895.2%1768 (100%)1726 (97.6%)0/0
Mutations:92C>T, 155T>C, 167T>A, 218C>T, 257A>T, 272A>G, 281C>G, 308G>C, 338C>T, 362G>T, 365G>T, 381A>C, 662C>T, 735T>C, 1137G>A, 1165T>C, 1167C>G, 1168T>A, 1178T>C, 1183T>G, 1187C>A, 1232A>G, 1316G>T, 1329T>A, 1344A>G, 1355G>A, 1369T>C, 1374C>G, 1379T>G, 1382A>C, 1391G>A, 1406C>G, 1510G>T, 1511A>T, 1522G>T, 1547G>T, 1548C>G, 1625G>A, 1631A>G, 1706C>T, 1709T>G, 1737C>G
CDS
1315100%230899.4%315 (100%)313 (99.4%)0/0/0/01
Protein mutations:F77L (281C>G), M105I (365G>T)
Codon mutations:CAC14CAT (92C>T), CTT35CTC (155T>C), CTT39CTA (167T>A), CCC56CCT (218C>T), ACA69ACT (257A>T), AAA74AAG (272A>G), TTC77TTG (281C>G), GCG86GCC (308G>C), TAC96TAT (338C>T), CTG104CTT (362G>T), ATG105ATT (365G>T), AGA111CGA (381A>C), GAC204GAT (662C>T), TTG229CTG (735T>C)
1105100%78197.0%105 (100%)102 (97.1%)0/0/0/01
Protein mutations:V4I (662C>T), H103N (365G>T), Q104K (362G>T)
Codon mutations:GTC4ATC (662C>T), TCT97TCG (381A>C), CAT103AAT (365G>T), CAG104AAG (362G>T)
1234100%171797.0%234 (100%)223 (95.3%)0/0/0/01
Protein mutations:S63T (1547G>T 1548C>G), L72M (1522G>T), N75K (1511A>T), L76I (1510G>T), S121T (1374C>G), I123V (1369T>C), I131T (1344A>G), Q136L (1329T>A), M185L (1183T>G), R191G (1165T>C), T200I (1137G>A)
Codon mutations:CGA9CGC (1709T>G), AGG10AGA (1706C>T), CGT35CGC (1631A>G), CGC37CGT (1625G>A), AGC63ACA (1547G>T 1548C>G), CTG72ATG (1522G>T), AAT75AAA (1511A>T), CTT76ATT (1510G>T), CCG110CCC (1406C>G), GAC115GAT (1391G>A), GTT118GTG (1382A>C), GGA119GGC (1379T>G), AGT121ACT (1374C>G), ATT123GTT (1369T>C), GAC127GAT (1355G>A), ATA131ACA (1344A>G), CAA136CTA (1329T>A), CCC140CCA (1316G>T), GAT168GAC (1232A>G), CTG183CTT (1187C>A), ATG185CTG (1183T>G), AGA186AGG (1178T>C), AGT190TCT (1167C>G 1168T>A), AGA191GGA (1165T>C), ACT200ATT (1137G>A)
Proteins
1315100%230899.4%315 (100%)313 (99.4%)0/0/0/01
Protein mutations:F77L (281C>G), M105I (365G>T)
Codon mutations:CAC14CAT (92C>T), CTT35CTC (155T>C), CTT39CTA (167T>A), CCC56CCT (218C>T), ACA69ACT (257A>T), AAA74AAG (272A>G), TTC77TTG (281C>G), GCG86GCC (308G>C), TAC96TAT (338C>T), CTG104CTT (362G>T), ATG105ATT (365G>T), AGA111CGA (381A>C), GAC204GAT (662C>T), TTG229CTG (735T>C)
1105100%78197.0%105 (100%)102 (97.1%)0/0/0/01
Protein mutations:V4I (662C>T), H103N (365G>T), Q104K (362G>T)
Codon mutations:GTC4ATC (662C>T), TCT97TCG (381A>C), CAT103AAT (365G>T), CAG104AAG (362G>T)
1234100%171797.0%234 (100%)223 (95.3%)0/0/0/01
Protein mutations:S63T (1547G>T 1548C>G), L72M (1522G>T), N75K (1511A>T), L76I (1510G>T), S121T (1374C>G), I123V (1369T>C), I131T (1344A>G), Q136L (1329T>A), M185L (1183T>G), R191G (1165T>C), T200I (1137G>A)
Codon mutations:CGA9CGC (1709T>G), AGG10AGA (1706C>T), CGT35CGC (1631A>G), CGC37CGT (1625G>A), AGC63ACA (1547G>T 1548C>G), CTG72ATG (1522G>T), AAT75AAA (1511A>T), CTT76ATT (1510G>T), CCG110CCC (1406C>G), GAC115GAT (1391G>A), GTT118GTG (1382A>C), GGA119GGC (1379T>G), AGT121ACT (1374C>G), ATT123GTT (1369T>C), GAC127GAT (1355G>A), ATA131ACA (1344A>G), CAA136CTA (1329T>A), CCC140CCA (1316G>T), GAT168GAC (1232A>G), CTG183CTT (1187C>A), ATG185CTG (1183T>G), AGA186AGG (1178T>C), AGT190TCT (1167C>G 1168T>A), AGA191GGA (1165T>C), ACT200ATT (1137G>A)
*: Inserts / Deletes / Misaligned / Frameshifts

Analysis details

This analysis was performed with panviral2.43