Genome Detective

NGS Details (SRR3458562_Metagenome_example): Porcine circovirus 2

Assembly

Coverage Length

1768 (1 contig(s))

Depth Of Coverage

5154.9

Number Of Reads

96411

Reads Per Million

6220.87 rpm (after QC)

Ambiguities

Assembly Method

read mapping against reference + variant calling

Consensus Caller

Bcf Tools

Coverage Map

Map

Variant Tables

Consensus Variants

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Minority Variants

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SNP Variants Table

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Annotated Variants Table

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Assignment

Type

Porcine circovirus 2 (Taxonomy ID: 85708)

Reference Genome

NC_005148.1

NT Identity (%)

97.6244

AA Identity (%)

97.5535

Number Of Stop Codons

Number Of CDS

Alignment

Alignment Score

3368.0 (NT) + 4806.0 (AA) = 8174.0

Concordance (%)

96.9402

Alignment Method

Global, seeded, nucleotide + amino acids (AGA)

NT Alignment

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Region Bam File

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CDS Alignment

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Consensus Sequence

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Consensus Contigs

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Genome Region

Sequence starts at position 1 and ends at position 1768 relative to NC_005148.1 reference sequence.

NC_005148.1

SRR3458562_Metagenome_example-NC_005148.1-92-0

NC_005148.1

SRR3458562_Metagenome_example-NC_005148.1-92-0

NC_005148.1

SRR3458562_Metagenome_example-NC_005148.1-92-0

ACCAGCGCACTTCGGCAGCGGCAGCACCTCGGCAGCACCTCAGCAGCAACATGCCCAGCAAGAAGAATGGAAGAAGCGGACCCCAACCACACAAAAGGTGGGTGTTCACGCTGAATAATCCTTCCGAAGACGAGCGCAAGAAAATACGGGAGCTTCCAATCTCCCTTTTTGATTATTTTATTGTTGGCGAGGAGGGTAATGAGGAAGGACGAACACCCCACCTCCAGGGGTTCGCTAATTTTGTGAAGAAGCAAACATTTAATAAAGTGAAATGGTATTTCGGTGCCCGCTGCCACATCGAGAAAGCGAAAGGAACTGATCAGCAGAATAAAGAATACTGCAGTAAAGAAGGCAACTTACTGATGGAATGTGGAGCTCCTAGATCTCAAGGACAACGGAGTGACCTGTCTACTGCTGTGAGTACCTTGTTGGAGAGCGGGAGTCTGGTGACCGTTGCAGAGCAGCACCCTGTAACGTTTGTCAGAAATTTCCGCGGGCTGGCTGAACTTTTGAAAGTGAGCGGGAAAATGCAGAAGCGTGATTGGAAGACCAATGTACACGTCATTGTGGGGCCACCTGGGTGTGGTAAAAGCAAATGGGCTGCTAATTTTGCAGACCCGGAAACCACATACTGGAAACCACCTAGAAACAAGTGGTGGGACGGTTACCATGGTGAAGAAGTGGTTGTTATTGATGACTTTTATGGCTGGCTGCCGTGGGATGATCTACTGAGATTGTGTGATCGATATCCATTGACTGTAGAGACTAAAGGTGGAACTGTACCTTTTTTGGCCCGCAGTATTCTGATTACCAGCAATCAGACCCCGTTGGAATGGTACTCCTCAACTGCTGTCCCAGCTGTAGAAGCTCTCTATCGGAGGATTACTTCCTTGGTATTTTGGAAGAATGCTACAGAACAATCCACGGAGGAAGGGGGCCAGTTCGTCACCCTTTCCCCCCCATGCCCTGAATTTCCATATGAAATAAATTACTGAGTCTT

TTTTATCACTTCGTAATGGTTTTTATTATTCATTTAGGGTTTAAGTGGGGGGTCTTTAAGATTAAATTCTCTGAATTGTACATACATGGTTACACGGATATTGTAGTCCTGGTCGTATTTACTGTTTTCGAACGCAGTGCCGAGGCCTACGTGGTCCACATTTCTACTGGTTTGTAGTCTCATCCACAGCTGATTCCTTTTGTTATTTGGTTGGAAGTAATCAATAGTGGAATCAAGAACAGGTTTGGGTGTGAAGTAACGGGAGTGGTAGGAGAAGGGTTGGGGGATTGTATGGCGGGAGGAGTAGTTTACATAGGGGTCATAGGTTTGGGCTGTGGCCTTTATTACAAAGTTGTCATCTAGAATAATAGCACTGGATCCAACTCCCCTGTCACCCTGGGTGATCGGGGAGCAGGGCCAGAATTCAACCTTAACCTTTCTTATTCTGTAGTATTCAAAGGGTATAGAGATTTTGTTGGTCCCCCCTCCCGGGGGAACAAAGTCGTCAAGATTAAATCTCAGCATGTCCACCGCCCAGGAGGGCGTGCTGACTGTGGTAGCCTTGACAGTATATCCGAAGGTGCGGGAGAGGCGGGCGTTGAAGATGCCATTTTTCCTTCTCCAGCGGTAACGGTGGCGGGGGTGGACGAGCCAGGGGCGGCGGCGGAGGATCTGGCCAAGATGGCTGCGGGGGCGGTGTCTTCTCCTTCGGTAACGCCTCCTTGGATACGTCATACCTGAAAACGAAAGAAGTGCGCTGTAAGTATT

ACCAGCGCACTTCGGCAGCGGCAGCACCTCGGCAGCACCTCAGCAGCAACATGCCCAGCAAGAAGAATGGAAGAAGCGGACCCCAACCACATAAAAGGTGGGTGTTCACGCTGAATAATCCTTCCGAAGACGAGCGCAAGAAAATACGGGAGCTCCCAATCTCCCTATTTGATTATTTTATTGTTGGCGAGGAGGGTAATGAGGAAGGACGAACACCTCACCTCCAGGGGTTCGCTAATTTTGTGAAGAAGCAAACTTTTAATAAAGTGAAGTGGTATTTGGGTGCCCGCTGCCACATCGAGAAAGCCAAAGGAACTGATCAGCAGAATAAAGAATATTGCAGTAAAGAAGGCAACTTACTTATTGAATGTGGAGCTCCTCGATCTCAAGGACAACGGAGTGACCTGTCTACTGCTGTGAGTACCTTGTTGGAGAGCGGGAGTCTGGTGACCGTTGCAGAGCAGCACCCTGTAACGTTTGTCAGAAATTTCCGCGGGCTGGCTGAACTTTTGAAAGTGAGCGGGAAAATGCAGAAGCGTGATTGGAAGACCAATGTACACGTCATTGTGGGGCCACCTGGGTGTGGTAAAAGCAAATGGGCTGCTAATTTTGCAGACCCGGAAACCACATACTGGAAACCACCTAGAAACAAGTGGTGGGATGGTTACCATGGTGAAGAAGTGGTTGTTATTGATGACTTTTATGGCTGGCTGCCGTGGGATGATCTACTGAGACTGTGTGATCGATATCCATTGACTGTAGAGACTAAAGGTGGAACTGTACCTTTTTTGGCCCGCAGTATTCTGATTACCAGCAATCAGACCCCGTTGGAATGGTACTCCTCAACTGCTGTCCCAGCTGTAGAAGCTCTCTATCGGAGGATTACTTCCTTGGTATTTTGGAAGAATGCTACAGAACAATCCACGGAGGAAGGGGGCCAGTTCGTCACCCTTTCCCCCCCATGCCCTGAATTTCCATATGAAATAAATTACTGAGTCTT

TTTTATCACTTCGTAATGGTTTTTATTATTCATTTAGGGTTTAAGTGGGGGGTCTTTAAGATTAAATTCTCTGAATTGTACATACATGGTTACACGGATATTGTAGTCCTGGTCGTATTTACTGTTTTCGAACGCAATGCCGAGGCCTACGTGGTCCACATTTCCAGAGGTTTGTAGCCTCAGCCAAAGCTGATTCCTTTTGTTATTTGGTTGGAAGTAATCAATAGTGGAGTCAAGAACAGGTTTGGGTGTGAAGTAACGGGAGTGGTAGGAGAAGGGTTGGGGGATTGTATGGCGGGAGGAGTAGTTTACATATGGGTCATAGGTTAGGGCTGTGGCCTTTGTTACAAAGTTATCATCTAGAATAACAGCAGTGGAGCCCACTCCCCTATCACCCTGGGTGATGGGGGAGCAGGGCCAGAATTCAACCTTAACCTTTCTTATTCTGTAGTATTCAAAGGGTATAGAGATTTTGTTGGTCCCCCCTCCCGGGGGAACAAAGTCGTCAATTTTAAATCTCATCATGTCCACCGCCCAGGAGGGCGTTGTGACTGTGGTAGCCTTGACAGTATATCCGAAGGTGCGGGAGAGGCGGGCGTTGAAGATGCCATTTTTCCTTCTCCAACGGTAGCGGTGGCGGGGGTGGACGAGCCAGGGGCGGCGGCGGAGGATCTGGCCAAGATGGCTGCGGGGGCGGTGTCTTCTTCTGCGGTAACGCCTCCTTGGATACGTCATAGCTGAAAACGAAAGAAGTGCGCTGTAAGTATT

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ORF1

MPSKKNGRSGPQPHKRWVFTLNNPSEDERKKIRELPISLFDYFIVGEEGNEEGRTPHLQGFANFVKKQTFNKVKWYFGARCHIEKAKGTDQQNKEYCSKEGNLLMECGAPRSQGQRSDLSTAVSTLLESGSLVTVAEQHPVTFVRNFRGLAELLKVSGKMQKRDWKTNVHVIVGPPGCGKSKWAANFADPETTYWKPPRNKWWDGYHGEEVVVIDDFYGWLPWDDLLRLCDRYPLTVETKGGTVPFLARSILITSNQTPLEWYSSTAVPAVEALYRRITSLVFWKNATEQSTEEGGQFVTLSPPCPEFPYEINY*

MPSKKNGRSGPQPHKRWVFTLNNPSEDERKKIRELPISLFDYFIVGEEGNEEGRTPHLQGFANFVKKQTFNKVKWYLGARCHIEKAKGTDQQNKEYCSKEGNLLIECGAPRSQGQRSDLSTAVSTLLESGSLVTVAEQHPVTFVRNFRGLAELLKVSGKMQKRDWKTNVHVIVGPPGCGKSKWAANFADPETTYWKPPRNKWWDGYHGEEVVVIDDFYGWLPWDDLLRLCDRYPLTVETKGGTVPFLARSILITSNQTPLEWYSSTAVPAVEALYRRITSLVFWKNATEQSTEEGGQFVTLSPPCPEFPYEINY*

ORF3

*QHFTSSRSRLSLPTVQRSSHTGQQLAPTQHGNCLLVRYRKDSIEAPQSFKQFHAPFHLLTIPLGIYVDNHPWRPTTFAFPSSIKCVRFGCVPFWRSVLPPVTVM

*KNFTSSRSRLSLPTVQRSSHTGQQLAPTQHGNCLLVRYRKDSIEAPQSFKQFHAPFHLLTIPLGIYVDNHPWRPTTFAFPSSIKCVRFGCVPFWRSVLPPITVM

ORF2

*PKLPPDKLNFERFQVYMTVRINYDQDYKSNEFATGLGVHDVNRSTQLRMWLQNRKNNPQFYDITSDLVPKPTFYRSHYSFPQPITHRSSYNVYPDYTQATAKIVFNDDLIIASSGVGRDGQTIPSCPWFEVKVKRIRYYEFPISIKNTGGGPPVFDDLNFRLMDVAWSPTSVTTAKVTYGFTRSLRANFIGNKRRWRYRHRPHVLWPRRRLIQGLHSRPRHRRRRYRRRPYTM

*PKLPPDKLNFERFQVYMTVRINYDQDYKSNEFAIGLGVHDVNGSTQLRLWLQNRKNNPQFYDITSDLVPKPTFYRSHYSFPQPITHRSSYNVYPDYTLATAKTVFNDDLIVATSGVGRDGQTIPSCPWFEVKVKRIRYYEFPISIKNTGGGPPVFDDIKFRMMDVAWSPTTVTTAKVTYGFTRSLRANFIGNKRRWRYRHRPHVLWPRRRLIQGLHSRPRHRRRRYRRRPYTM

Alignment Detailed Statistics


	Begin	End	Coverage	Score	Concordance	Matches	Identities	I/D/M/F^*	Stop Codons
NT	1	1768	100%	3368	95.2%	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

ORF1	1	315	100%	2308	99.4%	315 (100%)	313 (99.4%)	0/0/0/0	1
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)
ORF3	1	105	100%	781	97.0%	105 (100%)	102 (97.1%)	0/0/0/0	1
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)
ORF2	1	234	100%	1717	97.0%	234 (100%)	223 (95.3%)	0/0/0/0	1
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

replicase (NP_937956.1)	1	315	100%	2308	99.4%	315 (100%)	313 (99.4%)	0/0/0/0	1
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)
ORF3 protein (YP_006355434.1)	1	105	100%	781	97.0%	105 (100%)	102 (97.1%)	0/0/0/0	1
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)
capsid protein (NP_937957.1)	1	234	100%	1717	97.0%	234 (100%)	223 (95.3%)	0/0/0/0	1
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