changeset 1:6ff67d2860e1 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 30f10306f4283140f7e54cfe1b8bc1f76f4ef834
author iuc
date Fri, 24 May 2024 10:47:00 +0000
parents 05c1bcba20c9
children def7a82d23e1
files macro.xml test-data/amrfinderplus/AMRFinderPlus_Nucleotide_identified_sequences.fasta test-data/amrfinderplus/AMRFinderPlus_Point_mutation_report.tsv test-data/amrfinderplus/AMRFinderPlus_report.tsv test-data/summarize/amrfinderplus_output.json
diffstat 5 files changed, 304 insertions(+), 1 deletions(-) [+]
line wrap: on
line diff
--- a/macro.xml	Tue Apr 30 08:41:54 2024 +0000
+++ b/macro.xml	Fri May 24 10:47:00 2024 +0000
@@ -1,6 +1,6 @@
 <?xml version="1.0"?>
 <macros>
-    <token name="@TOOL_VERSION@">0.8.4.1</token>
+    <token name="@TOOL_VERSION@">0.8.5.0</token>
     <token name="@VERSION_SUFFIX@">0</token>
     <token name="@PROFILE@">21.05</token>
     <xml name="version_command">
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/amrfinderplus/AMRFinderPlus_Nucleotide_identified_sequences.fasta	Fri May 24 10:47:00 2024 +0000
@@ -0,0 +1,209 @@
+>contig_153_polypolish:4412-4645 strand:- merE broad-spectrum mercury transporter MerE
+ATGAACAGCCCAGAGCACTTGCCGTCTGAGACGCACAAACCGATCACCGGCTACTTGTGG
+GGCGCGCTGGCCGTGCTCACCTGTCCCTGCCATTTGCCGATTCTCGCCATTGTGCTAGCC
+GGCACGACGGCCGGCGCGTTCATCGGGGAGCACTGGGGTATTGCAGCCCTCACGCTGACC
+GGCTTGTTTGTCCTGTCTGTGACGCGGCTGCTGCGGGCCTTCAAGGGAAGATCA
+>contig_153_polypolish:7613-7846 strand:- merT mercuric transport protein MerT
+TCTGAACCACAAAACGGGCGCGGCGCGTTCTTCGCCGGTGGGCTGGCCGCCATTCTTGCG
+TCGGCCTGCTGCCCGGGGCCGCTGGTTTTGATCGCCTTGGGGTTCAGCGGGGCATGGATC
+GGCAACCTGACGGTGCTGGAACCCTATCGCCCGATCTTCATCGGCGCAGCGCTGGTCGCG
+CTGCTTTTCGCCCGGCGGCGCATCTACCGCCCGGCGCAAGCCTGCCAAACCGGG
+>contig_160_polypolish:86415-86654 strand:- fosA FosA5 family fosfomycin resistance glutathione transferase
+GCAGTCAGCCAGCTGGCGCCGAGCGTGGCGTTTTATCAGCAGCTGTTGGGCATGACGCTG
+CACGCCCGCTGGGACAGCGGCGCCTATCTCTCCTGCGGCGATTTGTGGCTGTGCCTGTCG
+CTGGATCCGCAGCGGCGCATCACCCCGCCGGAGGAGAGCGACTACACCCATTATGCGTTT
+AGCATTAGCGAGGCGGATTTCGCTAGCTTCGCCGCCCGCCTTGAGGTTGCCGGCGTCAGC
+>contig_30_polypolish:13708-14433 strand:+ blaCTX-M CTX-M family extended-spectrum class A beta-lactamase
+AAACTTGCCGAATTAGAGCGGCAGTCGGGAGGCAGACTGGGTGTGGCATTGATTAACACA
+GCAGATAATTCGCAAATACTTTATCGTGCTGATGAGCGCTTTGCGATGTGCAGCACCAGT
+AAAGTGATGGCCGCGGCCGCGGTGCTGAAGAAAAGTGAAAGCGAACCGAATCTGTTAAAT
+CAGCGAGTTGAGATCAAAAAATCTGACCTTGTTAACTATAATCCGATTGCGGAAAAGCAC
+GTCAATGGGACGATGTCACTGGCTGAGCTTAGCGCGGCCGCGCTACAGTACAGCGATAAC
+GTGGCGATGAATAAGCTGATTGCTCACGTTGGCGGCCCGGCTAGCGTCACCGCGTTCGCC
+CGACAGCTGGGAGACGAAACGTTCCGTCTCGACCGTACCGAGCCGACGTTAAACACCGCC
+ATTCCGGGCGATCCGCGTGATACCACTTCACCTCGGGCAATGGCGCAAACTCTGCGGAAT
+CTGACGCTGGGTAAAGCATTGGGCGACAGCCAACGGGCGCAGCTGGTGACATGGATGAAA
+GGCAATACCACCGGTGCAGCGAGCATTCAGGCTGGACTGCCTGCTTCCCGGGTTGTGGGG
+GATAAAACCGGCAGCGGTGGCTATGGCACCACCAACGATATCGCGGTGATCTGGCCAAAG
+ATCGTGCGCCGCTGATTCTGGTCACTTACTTCACCCAGCCTCAACCTAAGGCAGAAAGCC
+GTCGCG
+>contig_30_polypolish:17856-18287 strand:+ merR mercury resistance transcriptional regulator MerR
+ATGGAAAATAATTTGGAAAACCTGACCATTGGCGTTTTTGCCAAGGCGGCCGGGGTCAAC
+GTGGAGACAATCCGCTTCTATCAGCGCAAGGGCCTGTTGCGGGAACCGGACAAGCCTTAC
+GGCAGCATCCGCCGCTATGGGGAGGCGGACGTGGTTCGGGTGAAATTCGTGAAATCGGCA
+CAGCGGCTGGGGTTCAGTCTGGACGAGATTGCCGAGCTGTTGCGGCTCGACGATGGCACC
+CACTGCGAGGAGGCCAGCAGCCCGGCCGAACACAAGCTCAAGGACGTGCGCGAGAAGATG
+GCCGACTTGGCGCGCATGGAAACCGTGCTGTCTGAACTCGTGTGCGCCTGCCATGCACGC
+AAGGGGAATGTTTCCTGCCCGTTGATCGCGTCACTACAGGGCGAAGCAGGCCCGGCAAGG
+TCAGCTATGCCT
+>contig_30_polypolish:20698-21348 strand:+ catA1 type A-1 chloramphenicol O-acetyltransferase
+GAAAAAATCACTGGATATACCACCGTTGATATATCCCAATGGCATCGTAAAGAACATTTT
+GAGGCATTTCAGTCAGTTGCTCAATGTACCTATAACCAGACCGTTCAGCTGGATATTACG
+GCCTTTTTAAAGACCGTAAAGAAAAATAAGCACAAGTTTTATCCGGCCTTTATTCACATT
+CTTGCCCGCCTGATGAATGCTCATCCGGAATTCCGTATGGCAATGAAAGACGGTGAGCTG
+GTGATATGGGATAGTGTTCACCCTTGTTACACCGTTTTCCATGAGCAAACTGAAACGTTT
+TCATCGCTCTGGAGTGAATACCACGACGATTTCCGGCAGTTTCTACACATATATTCGCAA
+GATGTGGCGTGTTACGGTGAAAACCGGCCTATTTCCCTAAAGGGTTTATTGAGAATATGT
+TTTTCGTCTCAGCCAATCCCACGGGTGAGTTTCACCAGTTTTGATTTAAACGTGGCCAAT
+ATGGACAACTTCTTCGCCCCCGTTTTCACCATGGGCAAATATTATACGCAAGGCGACAAG
+GTGCTGATGCCGCTGGCGATTCAGGTTCATCATGCCGTTTGTGATGGCTTCCATGTCGGC
+AGAATGCTTAATGAATTACAACAGTACTGCGATGAGTGGCAGGGCGGGGCG
+>contig_30_polypolish:3018-3344 strand:+ merR mercury resistance transcriptional regulator MerR
+TTTGCCAAGGCGGCCGGGGTCAACGTGGAGACAATCCGCTTCTATCAGCGCAAGGGCCTG
+TTGCGGGAACCGGACAAGCCTTACGGCGGCATCCGCCGCTATGGGGAGGCGGACGTGGTT
+CGGGTGAAATTCGTGAAATCGGCACAGCGGCTGGGGTTCAGTCTGGACGAGATTGCCGAG
+CTGTTGCGGCTCGACGATGGCACCCACTGCGAGGAGGCCAGCAGCTTGGCCGAACACAAG
+CTCAAGGACGTGCGCGAGAAGATGGCCGACTTGGCGCGCATGGAAACCGTGCTGTCTGAA
+CTCGTGTGCGCCTGCCATGCACGAAGG
+>contig_30_polypolish:5821-6243 strand:+ catA1 type A-1 chloramphenicol O-acetyltransferase
+GAAAAAATCACTGGATATACCACCGTTGATATATCCCAATGGCATCGTAAAGAACATTTT
+GAGGCATTTCAGTCAGTTGCTCAATGTACCTATAACCAGACCGTTCAGCTGGATATTACG
+GCCTTTTTAAAGACCGTAAAGAAAAATAAGCACAAGTTTTATCCGGCCTTTATTCACATT
+CTTGCCCGCCTGATGAATGCTCATCCGGAATTCCGTATGGCAATGAAAGACGGTGAGCTG
+GTGATATGGGATAGTGTTCACCCTTGTTACACCGTTTTCCATGAGCAAACTGAAACGTTT
+TCATCGCTCTGGAGTGAATACCACGACGATTTCCGGCAGTTTCTACACATATATTCGCAA
+GATGTGGCGTGTTACGGTGAAAACACGGCCTATTTCCCTAAAGGGTTTATTGAGAATATG
+TTT
+>contig_35_polypolish:4787-5644 strand:- aac(3)-IIe aminoglycoside N-acetyltransferase AAC(3)-IIe
+ATGCATACGCGGAAGGCAATAACGGAGGCAATTCGAAAATTAGGAGTCCAAACCGGTGAC
+CTGTTGATGGTGCATGCCTCACTTAAAGCGATTGGTCCGGTCGAAGGAGGAGCGGAGACG
+GTCGTTGCCGCGTTACGCTCCGCGGTTGGGCCGACTGGCACTGTGATGGGATACGCGTCG
+TGGGACCGATCACCCTACGAGGAGACTCTGAATGGCGCTCGGTTGGATGACAAAGCCCGC
+CGTACCTGGCCGCCGTTCGATCCCGCAACGGCCGGGACTTACCGTGGGTTCGGCCTGCTG
+AATCAATTTCTGGTTCAAGCCCCCGGCGCGCGGCGCAGCGCGCACCCCGATGCATCGATG
+GTCGCGGTTGGTCCGCTAGCTGAAACGCTGACGGAGCCTCACGAACTCGGTCACGCCTTG
+GGGGAAGGGTCGCCCGTCGAGCGGTTCGTCCGCCTTGGCGGGAAGGCCCTGCTGTTGGGT
+GCGCCGCTAAACTCCGTTACCGCATTGCACTACGCCGAGGCGGTTGCGGATATCCCCAAC
+AAACGATGGGTGACGTATGAGATGCCGATGCTTGGAAGAAACGGTGAAGTCGCCTGGAAA
+ACGGCATCAGAATACGATTCAAACGGCATTCTCGATTGCTTTGCTATCGAAGGAAAGCCG
+GATGCGGTCGAAACTATAGCAAATGCTTACGTGAAGCTCGGTCGCCATCGAGAAGGTGTC
+GTGGGCTTTGCTCAGTGCTACCTGTTCGACGCGCAGGACATCGTGACGTTCGGCGTCACC
+TATCTTGAGAAGCACTTCGGAGCCACTCCGATCGTGCCAGCACACGAAGCCGCCCAGCGC
+TCTTGCGAGCCTTCCGGT
+>contig_36_polypolish:9168-9608 strand:+ blaSHV SHV family class A beta-lactamase
+ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACAC
+GCCAGCCCGCAGCCGCTTGAGCAAATTAAACAAAGCGAAAGCCAGCTGTCGGGCCGCGTA
+GGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCCGGCGCGCCGATGAA
+CGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTG
+GATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGAC
+TACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGCGCC
+GCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGC
+CCCGCAGGATTGACTGCCTTT
+>contig_36_polypolish:9587-10024 strand:+ blaSHV SHV family class A beta-lactamase
+CCCCGCAGGATTGACTGCCTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGC
+TGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCC
+AGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAA
+CGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTG
+CTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTAGCAAGCGGGGTGCGCGCGGG
+ATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGG
+GATACGCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTG
+ATCGAGCACTGGCAACGC
+>contig_37_polypolish:18-569 strand:+ aac(6')-Ib3 aminoglycoside N-acetyltransferase AAC(6')-Ib3
+GTGACCAACAGCAACGATTCCGTCACACTGCGCCTCATGACTGAGCATGACCTTGCGATG
+CTCTATGAGTGGCTAAATCGATCTCATATCGTCGAGTGGTGGGGCGGAGAAGAAGCACGC
+CCGACACTTGCTGACGTACAGGAACAGTACTTGCCAAGCGTTTTAGCGCAAGAGTCCGTC
+ACTCCATACATTGCAATGCTGAATGGAGAGCCGATTGGGTATGCCCAGTCGTACGTTGCT
+CTTGGAAGCGGGGACGGATGGTGGGAAGAAGAAACCGATCCAGGAGTACGCGGAATAGAC
+CAGTTACTGGCGAATGCATCACAACTGGGCAAAGGCTTGGGAACCAAGCTGGTTCGAGCT
+CTGGTTGAGTTGCTGTTCAATGATCCCGAGGTCACCAAGATCCAAACGGACCCGTCGCCG
+AGCAACTTGCGAGCGATCCGATGCTACGAGAAAGCGGGGTTTGAGAGGCAAGGTACCGTA
+ACCACCCCAGATGGTCCAGCCGTGTACATGGTTCAAACACGCCAGGCATTCGAGCGAACA
+CGCAGTGATGCC
+>contig_37_polypolish:3006-3863 strand:+ blaTEM-1 broad-spectrum class A beta-lactamase TEM-1
+ATGAGTATTCAACATTTTCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCT
+GTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCA
+CGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCC
+GAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCC
+CGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTG
+GTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTA
+TGCAGTGCTGCCATAACCATGAGTGATAACACTGCTGCCAACTTACTTCTGACAACGATC
+GGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTT
+GATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATG
+CCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCT
+TCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGC
+TCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCT
+CGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTAC
+ACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCC
+TCACTGATTAAGCATTGG
+>contig_37_polypolish:642-1424 strand:+ aadA1 ANT(3'')-Ia family aminoglycoside nucleotidyltransferase AadA1
+ATGAGGGAAGCGGTGATCGCCGAAGTATCGACTCAACTATCAGAGGTAGTTGGCGTCATC
+GAGCGCCATCTCGAACCGACGTTGCTGGCCGTACATTTGTACGGCTCCGCAGTGGATGGC
+GGCCTGAAGCCACACAGTGATATTGATTTGCTGGTTACGGTGACCGTAAGGCTTGATGAA
+ACAACGCGGCGAGCTTTGATCAACGACCTTTGGAAACTTCGGCTTCCCGGAGAGAGCGAG
+ATTCTCCGCGCTGTAGAAGTCACCATTGTTGTGCACGACGACATCATTCCGTGGCGTTAT
+CCAGCTAAGCGCGAACTGCAATTTGGAGAATGGCAGCGCAATGACATTCTTGCAGGTATC
+TTCGAGCCAGCCACGATCGACATTGATCTGGCTATCTTGCTGACAAAAGCAAGAGAACAT
+AGCGTTGCCTTGGTAGGTCCAGCGGCGGAGGAACTCTTTGATCCGGTTCCTGAACAGGAT
+CTATTTGAGGCGCTAAATGAAACCTTAACGCTATGGAACTCGCCGCCCGACTGGGCTGGC
+GATGAGCGAAATGTAGTGCTTACGTTGTCCCGCATTTGGTACAGCGCAGTAACCGGCAAA
+ATCGCGCCGAAGGATGTCGCTGCCGACTGGGCAATGGAGCGCCTGCCGGCCCAGTATCAG
+CCCGTCATACTTGAAGCTAGGCAGGCTTATCTTGGACAAGAAGATCGCTTGGCCTCGCGC
+GCAGATCAGTTGGAAGAATTTGTTCACTACGTGAAAGGCGAGATCACCAAGGTAGTCGGC
+AAA
+>contig_37_polypolish:8924-9133 strand:- merC organomercurial transporter MerC
+CTTGAGCCAGTACGAGGACTGTTCATCAGCCGCCTGCTGCCGCTGTTTGCCGCGCTGGCC
+TTCTCGGCGAACGCGCTGGGTTGGTTCAGTCATCGGCAATGGCTGCGCAGTCTGCTCGGC
+ATGATCGGCCCGGCCATCGTGTTTGCGGCCACGGTCTGGCTGCTCGGCAACTGGTGGACG
+GCGAACCTGATGTACGTCGGCACCGGCCTT
+>contig_39_polypolish:3496-3825 strand:- qacE quaternary ammonium compound efflux SMR transporter QacE
+ATGAAAGGCTGGCTTTTTCTTGTTATCGCAATAGTTGGCGAAGTAATCGCAACATCCGCA
+TTAAAATCTAGCGAGGGCTTTACTAAGCTTGCCCCTTCCGCCGTTGTCATAATCGGTTAT
+GGCATCGCATTTTATTTTCTTTCTCTGGTTCTGAAATCCATCCCTGTCGGTGTTGCTTAT
+GCAGTCTGGTCGGGACTCGGCGTCGTCATAATTACAGCCATTGCCTGGTTGCTTCATGGG
+CAAAAGCTTGATGCGTGGGGCTTTGTAGGTATGGGGCTCATAGTTAGTGGTGTAGTAGTT
+TTAAACTTGCTTTCCAAAGCAAGTGCCCAC
+>contig_39_polypolish:4010-4327 strand:- dfrA30 trimethoprim-resistant dihydrofolate reductase DfrA30
+GGGGCGCTCCCCAATAGGAAATACGCGGTCGTTACTCGCTCAGCTCGGACGGCCAATAAT
+GACAACGTAGTAGTATTCCCGTCGATCGAAGAGGCCATGGGCGGTCTAGCTAAACTCACC
+GGTCACGTTATAGTGTCTGGTGGCGGGGAGATTTACAGAGAAACGTTGCCCATGGCCTCT
+ACGCTCCATGTATCGACGATCGACATTGAGCCAGAAGGGGATGTTTTCTTCCCGAATATT
+CCCAACTTCTTCGAAGTTGTTTTTGAGCAACATTTTAGTTCAAACATTAACTATTGCTAT
+CAAATTTGGAAAAAGGGT
+>contig_40_polypolish:2574-3359 strand:+ aph(3'')-Ib aminoglycoside O-phosphotransferase APH(3'')-Ib
+ATATTTTTTGGTGAATCGCATTCTGACTGGTTGCCTGTCAGAGGCGGAGAATCTGGTGAT
+TTTGTTTTTCGACGTGGTGACGGGCATGCCTTCGCGAAAATCGCACCTGCTTCCCGCCGC
+GGTGAGCTCGCTGGAGAGCGTGACCGCCTCATTTGGCTCAAAGGTCGAGGTGTGGCTTGC
+CCCGAGGTGATCAACTGGCAGGAGGAACAGGAGGGTGCATGCTTGGTGATAACGGCAATT
+CCGGGAGTACCGGCGGCTGATCTGTCTGGAGCGGATTTGCTCAAAGCGTGGCCGTCAATG
+GGGCAGCAACTTGGCGCTGTTCACAGCCTATCGGTTGATCAATGTCCGTTTGAGCGCAGG
+CTGTCGCGAATGTTCGGACGCGCCGTTGATGTGGTGTCCCGCAATGCCGTCAATCCCGAC
+TTCTTACCGGACGAGGACAAGAGTACGCCGCAGCTCGATCTTTTGGCTCGTGTCGAACGA
+GAGCTACCGGTGCGGCTCGACCAAGAGCGCACCGATATGGTTGTTTGCCATGGTGATCCC
+TGCATGCCGAACTTCATGGTGGACCCTAAAACTCTTCAATGCACGGGTCTGATCGACCTT
+GGGCGGCTCGGAACAGCAGATCGCTATGCCGATTTGGCACTCATGATTGCTAACGCCGAA
+GAGAACTGGGCAGCGCCAGATGAAGCAGAGCGCGCCTTCGCTGTCCTATTCAATGTATTG
+GGGATCGAAGCCCCCGACCGCGAACGCCTTGCCTTCTATCTGCGATTGGACCCTCTGACT
+TGGGGT
+>contig_40_polypolish:3555-4103 strand:+ aph(6)-Id aminoglycoside O-phosphotransferase APH(6)-Id
+GGAGCAGTCCGGTTGCTCGGTCGTGAGAACAATCTGATGTTGCTCGAATATGCCGGGGAG
+CGAATGCTCTCTCACATCGTTGCCGAGCACGGCGACTACCGAGCGACCGAAATTGCAGCG
+GAACTAATGGCGAAGCTGTATGCCGCATCTGAGGAACCCCTGCCTTCTGCCCTTCTCCCG
+ATCCGGGATCGCTTTGCAGCTTTGTTTCAGCGGGCGCGCGATGATCAAAACGCAGGTTGT
+CAAACTGACTACGTCCACGCGGCGATTATAGCCGATCAAATGATGAGCAATGCCTCGGAA
+CTGCGTGGGCTACATGGCGATCTGCATCATGAAAACATCATGTTCTCCAGTCGCGGCTGG
+CTGGTGATAGATCCCGTCGGTCTGGTCGGTGAAGTGGGCTTTGGCGCCGCCAATATGTTC
+TACGATCCGGCTGACAGAGACGACCTTTGTCTCGATCCTAGACGCATTGCACAGATGGCG
+GACGCATTCTCTCGTGCGCTGGACGTCGATCCGCGTCGCCTGCTCGACCGTGCGTACGCT
+TATGGGTGC
+>contig_40_polypolish:632-1258 strand:+ aph(3')-Ia aminoglycoside O-phosphotransferase APH(3')-Ia
+ATGAGCCATATTCAACGGGAAACGTCTTGCTCGAGGCCGCGATTAAATTCCAACATGGAT
+GCTGATTTATATGGGTATAAATGGGCTCGCGATAATGTCGGGCAATCAGGTGCGACAATC
+TATCGATTGTATGGGAAGCCCGATGCGCCAGAGTTGTTTCTGAAACATGGCAAAGGTAGC
+GTTGCCAATGATGTTACAGATGAGATGGTCAGACTAAACTGGCTGACGGAATTTATGCCT
+CTTCCGACCATCAAGCATTTTATCCGTACTCCTGATGATGCATGGTTACTCACCACTGCG
+ATCCCCGGGAAAACAGCATTCCGGGTATTAGAAGAATATCCTGATTCAGGTGAAAATATT
+GTTGATGCGCTGGCAGTGTTCCTGCGCCGGTTGCATTCGATTCCTGTTTGTAATTGTCCT
+TTTAACAACGATCGCGTATTTCGTCTCGCTCAGGCGCAATCACGAATGAATAACGGTTTG
+GTTGATGCGAGTGATTTTGATGACGAGCGTAATGGCTGGCCTGTTGAACAAGTCTGGAAA
+GAAATGCATAAGCTTTTGCCATTCTCACCGGATTCAGTCGTCACTCATGGTGATTTCTCA
+CTTGATAACCTTATTTTTGACGAGGGA
+>contig_41_polypolish:100023-100541 strand:- terD tellurium resistance membrane protein TerD
+ATGAGCGTTTCACTATCTAAAGGCGGCAACGTTTCCCTGAGCAAAACCGCGCCAAGCATG
+AAAAACGTGCTGGTTGGCCTTGGCTGGGATGCACGTTCTACGGACGGTCAGGACTTTGAC
+CTCGATGCTTCCGCATTTCTGCTGGCAGCCAATGGCAAGGTTCGTGGCGATGCAGATTTC
+ATTTTCTATAACAACCTGAAATCTGCTGATGGTTCCGTTACTCATACCGGTGATAACCGT
+ACCGGTGAAGGTGATGGCGACGATGAATCCCTCAAAATCAAACTGGACGCGGTACACGGG
+GATGTCGACAAAATTATTTTCGTTGTCACTATCCATGATGCTCAGGCTCGTCGCCAGAGC
+TTCGGTCAGGTTTCCGGCGCATTTATCCGTCTGGTGAATGATGACAATCAGACTGAAGTT
+GCTCGCTACGATCTGACAGAAGACGCTTCTACTGAAACTGCCATGCTGTTTGGGGAGCTG
+TATCGTCACAACGGAGAATGGAAATTCCGTGCGGTTGGC
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/amrfinderplus/AMRFinderPlus_Point_mutation_report.tsv	Fri May 24 10:47:00 2024 +0000
@@ -0,0 +1,35 @@
+Protein identifier	Contig id	Start	Stop	Strand	Gene symbol	Sequence name	Scope	Element type	Element subtype	Class	Subclass	Method	Target length	Reference sequence length	% Coverage of reference sequence	% Identity to reference sequence	Alignment length	Accession of closest sequence	Name of closest sequence	HMM id	HMM description	Hierarchy node
+NA	contig_107_polypolish	5	861	-	23S_A2074A	Campylobacter 23S ribosomal RNA [WILDTYPE]	core	AMR	POINT	MACROLIDE	MACROLIDE	POINTN	857	2912	29.36	81.82	869	NC_022347.1:1040292-1037381	23S ribosomal RNA	NA	NA	NA
+NA	contig_107_polypolish	5	861	-	23S_A2074A	Campylobacter 23S ribosomal RNA [WILDTYPE]	core	AMR	POINT	MACROLIDE	MACROLIDE	POINTN	857	2912	29.36	81.95	870	NC_002163.1:396449-399360	23S ribosomal RNA	NA	NA	NA
+NA	contig_107_polypolish	5	861	-	23S_A2075A	Campylobacter 23S ribosomal RNA [WILDTYPE]	core	AMR	POINT	MACROLIDE	MACROLIDE	POINTN	857	2912	29.36	81.82	869	NC_022347.1:1040292-1037381	23S ribosomal RNA	NA	NA	NA
+NA	contig_107_polypolish	5	861	-	23S_A2075A	Campylobacter 23S ribosomal RNA [WILDTYPE]	core	AMR	POINT	MACROLIDE	MACROLIDE	POINTN	857	2912	29.36	81.95	870	NC_002163.1:396449-399360	23S ribosomal RNA	NA	NA	NA
+NA	contig_107_polypolish	5	861	-	23S_C2627C	Campylobacter 23S ribosomal RNA [WILDTYPE]	core	AMR	POINT	MACROLIDE	MACROLIDE	POINTN	857	2912	29.36	81.82	869	NC_022347.1:1040292-1037381	23S ribosomal RNA	NA	NA	NA
+NA	contig_107_polypolish	5	861	-	23S_C2627C	Campylobacter 23S ribosomal RNA [WILDTYPE]	core	AMR	POINT	MACROLIDE	MACROLIDE	POINTN	857	2912	29.36	81.95	870	NC_002163.1:396449-399360	23S ribosomal RNA	NA	NA	NA
+NA	contig_10_polypolish	345	1334	-	23S_A2074A	Campylobacter 23S ribosomal RNA [WILDTYPE]	core	AMR	POINT	MACROLIDE	MACROLIDE	POINTN	990	2912	33.93	80.56	1003	NC_002163.1:396449-399360	23S ribosomal RNA	NA	NA	NA
+NA	contig_10_polypolish	345	1334	-	23S_A2075A	Campylobacter 23S ribosomal RNA [WILDTYPE]	core	AMR	POINT	MACROLIDE	MACROLIDE	POINTN	990	2912	33.93	80.56	1003	NC_002163.1:396449-399360	23S ribosomal RNA	NA	NA	NA
+NA	contig_10_polypolish	345	1334	-	23S_C2627C	Campylobacter 23S ribosomal RNA [WILDTYPE]	core	AMR	POINT	MACROLIDE	MACROLIDE	POINTN	990	2912	33.93	80.56	1003	NC_002163.1:396449-399360	23S ribosomal RNA	NA	NA	NA
+NA	contig_10_polypolish	416	1334	-	23S_A2074A	Campylobacter 23S ribosomal RNA [WILDTYPE]	core	AMR	POINT	MACROLIDE	MACROLIDE	POINTN	919	2912	31.49	81.10	931	NC_022347.1:1040292-1037381	23S ribosomal RNA	NA	NA	NA
+NA	contig_10_polypolish	416	1334	-	23S_A2075A	Campylobacter 23S ribosomal RNA [WILDTYPE]	core	AMR	POINT	MACROLIDE	MACROLIDE	POINTN	919	2912	31.49	81.10	931	NC_022347.1:1040292-1037381	23S ribosomal RNA	NA	NA	NA
+NA	contig_10_polypolish	416	1334	-	23S_C2627C	Campylobacter 23S ribosomal RNA [WILDTYPE]	core	AMR	POINT	MACROLIDE	MACROLIDE	POINTN	919	2912	31.49	81.10	931	NC_022347.1:1040292-1037381	23S ribosomal RNA	NA	NA	NA
+NA	contig_11_polypolish	1319	2308	-	23S_A2074A	Campylobacter 23S ribosomal RNA [WILDTYPE]	core	AMR	POINT	MACROLIDE	MACROLIDE	POINTN	990	2912	33.93	80.56	1003	NC_002163.1:396449-399360	23S ribosomal RNA	NA	NA	NA
+NA	contig_11_polypolish	1319	2308	-	23S_A2075A	Campylobacter 23S ribosomal RNA [WILDTYPE]	core	AMR	POINT	MACROLIDE	MACROLIDE	POINTN	990	2912	33.93	80.56	1003	NC_002163.1:396449-399360	23S ribosomal RNA	NA	NA	NA
+NA	contig_11_polypolish	1319	2308	-	23S_C2627C	Campylobacter 23S ribosomal RNA [WILDTYPE]	core	AMR	POINT	MACROLIDE	MACROLIDE	POINTN	990	2912	33.93	80.56	1003	NC_002163.1:396449-399360	23S ribosomal RNA	NA	NA	NA
+NA	contig_11_polypolish	1390	2308	-	23S_A2074A	Campylobacter 23S ribosomal RNA [WILDTYPE]	core	AMR	POINT	MACROLIDE	MACROLIDE	POINTN	919	2912	31.49	81.10	931	NC_022347.1:1040292-1037381	23S ribosomal RNA	NA	NA	NA
+NA	contig_11_polypolish	1390	2308	-	23S_A2075A	Campylobacter 23S ribosomal RNA [WILDTYPE]	core	AMR	POINT	MACROLIDE	MACROLIDE	POINTN	919	2912	31.49	81.10	931	NC_022347.1:1040292-1037381	23S ribosomal RNA	NA	NA	NA
+NA	contig_11_polypolish	1390	2308	-	23S_C2627C	Campylobacter 23S ribosomal RNA [WILDTYPE]	core	AMR	POINT	MACROLIDE	MACROLIDE	POINTN	919	2912	31.49	81.10	931	NC_022347.1:1040292-1037381	23S ribosomal RNA	NA	NA	NA
+NA	contig_12_polypolish	61	472	-	23S_A2074A	Campylobacter 23S ribosomal RNA [WILDTYPE]	core	AMR	POINT	MACROLIDE	MACROLIDE	POINTN	412	2912	14.08	82.01	417	NC_022347.1:1040292-1037381	23S ribosomal RNA	NA	NA	NA
+NA	contig_12_polypolish	61	472	-	23S_A2074A	Campylobacter 23S ribosomal RNA [WILDTYPE]	core	AMR	POINT	MACROLIDE	MACROLIDE	POINTN	412	2912	14.08	82.30	418	NC_002163.1:396449-399360	23S ribosomal RNA	NA	NA	NA
+NA	contig_12_polypolish	61	472	-	23S_A2075A	Campylobacter 23S ribosomal RNA [WILDTYPE]	core	AMR	POINT	MACROLIDE	MACROLIDE	POINTN	412	2912	14.08	82.01	417	NC_022347.1:1040292-1037381	23S ribosomal RNA	NA	NA	NA
+NA	contig_12_polypolish	61	472	-	23S_A2075A	Campylobacter 23S ribosomal RNA [WILDTYPE]	core	AMR	POINT	MACROLIDE	MACROLIDE	POINTN	412	2912	14.08	82.30	418	NC_002163.1:396449-399360	23S ribosomal RNA	NA	NA	NA
+NA	contig_7_polypolish	39847	40836	-	23S_A2074A	Campylobacter 23S ribosomal RNA [WILDTYPE]	core	AMR	POINT	MACROLIDE	MACROLIDE	POINTN	990	2912	33.93	80.56	1003	NC_002163.1:396449-399360	23S ribosomal RNA	NA	NA	NA
+NA	contig_7_polypolish	39847	40836	-	23S_A2075A	Campylobacter 23S ribosomal RNA [WILDTYPE]	core	AMR	POINT	MACROLIDE	MACROLIDE	POINTN	990	2912	33.93	80.56	1003	NC_002163.1:396449-399360	23S ribosomal RNA	NA	NA	NA
+NA	contig_7_polypolish	39847	40836	-	23S_C2627C	Campylobacter 23S ribosomal RNA [WILDTYPE]	core	AMR	POINT	MACROLIDE	MACROLIDE	POINTN	990	2912	33.93	80.56	1003	NC_002163.1:396449-399360	23S ribosomal RNA	NA	NA	NA
+NA	contig_7_polypolish	39918	40836	-	23S_A2074A	Campylobacter 23S ribosomal RNA [WILDTYPE]	core	AMR	POINT	MACROLIDE	MACROLIDE	POINTN	919	2912	31.49	81.10	931	NC_022347.1:1040292-1037381	23S ribosomal RNA	NA	NA	NA
+NA	contig_7_polypolish	39918	40836	-	23S_A2075A	Campylobacter 23S ribosomal RNA [WILDTYPE]	core	AMR	POINT	MACROLIDE	MACROLIDE	POINTN	919	2912	31.49	81.10	931	NC_022347.1:1040292-1037381	23S ribosomal RNA	NA	NA	NA
+NA	contig_7_polypolish	39918	40836	-	23S_C2627C	Campylobacter 23S ribosomal RNA [WILDTYPE]	core	AMR	POINT	MACROLIDE	MACROLIDE	POINTN	919	2912	31.49	81.10	931	NC_022347.1:1040292-1037381	23S ribosomal RNA	NA	NA	NA
+NA	contig_82_polypolish	31069	31987	+	23S_A2074A	Campylobacter 23S ribosomal RNA [WILDTYPE]	core	AMR	POINT	MACROLIDE	MACROLIDE	POINTN	919	2912	31.49	81.10	931	NC_022347.1:1040292-1037381	23S ribosomal RNA	NA	NA	NA
+NA	contig_82_polypolish	31069	31987	+	23S_A2075A	Campylobacter 23S ribosomal RNA [WILDTYPE]	core	AMR	POINT	MACROLIDE	MACROLIDE	POINTN	919	2912	31.49	81.10	931	NC_022347.1:1040292-1037381	23S ribosomal RNA	NA	NA	NA
+NA	contig_82_polypolish	31069	31987	+	23S_C2627C	Campylobacter 23S ribosomal RNA [WILDTYPE]	core	AMR	POINT	MACROLIDE	MACROLIDE	POINTN	919	2912	31.49	81.10	931	NC_022347.1:1040292-1037381	23S ribosomal RNA	NA	NA	NA
+NA	contig_82_polypolish	31069	32058	+	23S_A2074A	Campylobacter 23S ribosomal RNA [WILDTYPE]	core	AMR	POINT	MACROLIDE	MACROLIDE	POINTN	990	2912	33.93	80.56	1003	NC_002163.1:396449-399360	23S ribosomal RNA	NA	NA	NA
+NA	contig_82_polypolish	31069	32058	+	23S_A2075A	Campylobacter 23S ribosomal RNA [WILDTYPE]	core	AMR	POINT	MACROLIDE	MACROLIDE	POINTN	990	2912	33.93	80.56	1003	NC_002163.1:396449-399360	23S ribosomal RNA	NA	NA	NA
+NA	contig_82_polypolish	31069	32058	+	23S_C2627C	Campylobacter 23S ribosomal RNA [WILDTYPE]	core	AMR	POINT	MACROLIDE	MACROLIDE	POINTN	990	2912	33.93	80.56	1003	NC_002163.1:396449-399360	23S ribosomal RNA	NA	NA	NA
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/amrfinderplus/AMRFinderPlus_report.tsv	Fri May 24 10:47:00 2024 +0000
@@ -0,0 +1,58 @@
+Protein identifier	Contig id	Start	Stop	Strand	Gene symbol	Sequence name	Scope	Element type	Element subtype	Class	Subclass	Method	Target length	Reference sequence length	% Coverage of reference sequence	% Identity to reference sequence	Alignment length	Accession of closest sequence	Name of closest sequence	HMM id	HMM description	Hierarchy node
+NA	contig_153_polypolish	4412	4645	-	merE	broad-spectrum mercury transporter MerE	plus	STRESS	METAL	MERCURY	MERCURY	BLASTX	78	78	100.00	96.15	78	AAC38236.1	broad-spectrum mercury transporter MerE	NA	NA	merE
+NA	contig_153_polypolish	7613	7846	-	merT	mercuric transport protein MerT	plus	STRESS	METAL	MERCURY	MERCURY	PARTIALX	78	116	67.24	92.31	78	CAA70196.1	mercuric transport protein MerT	NA	NA	merT
+NA	contig_160_polypolish	86415	86654	-	fosA	FosA5 family fosfomycin resistance glutathione transferase	core	AMR	AMR	FOSFOMYCIN	FOSFOMYCIN	PARTIALX	80	139	57.55	98.75	80	WP_114473955.1	fosfomycin resistance glutathione transferase FosA9	NA	NA	fosA5_fam
+NA	contig_30_polypolish	3018	3344	+	merR	mercury resistance transcriptional regulator MerR	plus	STRESS	METAL	MERCURY	MERCURY	PARTIALX	109	144	75.69	93.58	109	BAA20334.1	mercury resistance transcriptional regulator MerR	NA	NA	merR_Ps
+NA	contig_30_polypolish	5821	6243	+	catA1	type A-1 chloramphenicol O-acetyltransferase	core	AMR	AMR	PHENICOL	CHLORAMPHENICOL	PARTIALX	141	219	64.38	98.58	141	WP_000412211.1	type A-1 chloramphenicol O-acetyltransferase	NA	NA	catA1
+NA	contig_30_polypolish	5821	6243	+	catA1	type A-1 chloramphenicol O-acetyltransferase	core	AMR	AMR	PHENICOL	CHLORAMPHENICOL	PARTIALX	141	219	64.38	98.58	141	WP_063843217.1	type A-1 chloramphenicol O-acetyltransferase	NA	NA	catA1
+NA	contig_30_polypolish	13708	14433	+	blaCTX-M	CTX-M family extended-spectrum class A beta-lactamase	core	AMR	AMR	BETA-LACTAM	CEPHALOSPORIN	INTERNAL_STOP	242	291	84.54	90.24	246	WP_063860025.1	extended-spectrum class A beta-lactamase CTX-M-179	NA	NA	blaCTX-M
+NA	contig_30_polypolish	17856	18287	+	merR	mercury resistance transcriptional regulator MerR	plus	STRESS	METAL	MERCURY	MERCURY	BLASTX	144	144	100.00	92.36	144	CAA77320.1	mercury resistance transcriptional regulator MerR	NA	NA	merR_Ps
+NA	contig_30_polypolish	20698	21348	+	catA1	type A-1 chloramphenicol O-acetyltransferase	core	AMR	AMR	PHENICOL	CHLORAMPHENICOL	BLASTX	217	219	99.09	92.17	217	WP_000412211.1	type A-1 chloramphenicol O-acetyltransferase	NA	NA	catA1
+NA	contig_35_polypolish	4787	5644	-	aac(3)-IIe	aminoglycoside N-acetyltransferase AAC(3)-IIe	core	AMR	AMR	AMINOGLYCOSIDE	GENTAMICIN	EXACTX	286	286	100.00	100.00	286	WP_000557452.1	aminoglycoside N-acetyltransferase AAC(3)-IIe	NA	NA	aac(3)-IIe
+NA	contig_36_polypolish	9168	9608	+	blaSHV	SHV family class A beta-lactamase	core	AMR	AMR	BETA-LACTAM	BETA-LACTAM	PARTIALX	147	286	51.40	99.32	147	WP_002904004.1	extended-spectrum class A beta-lactamase SHV-12	NA	NA	blaSHV
+NA	contig_36_polypolish	9168	9608	+	blaSHV	SHV family class A beta-lactamase	core	AMR	AMR	BETA-LACTAM	BETA-LACTAM	PARTIALX	147	286	51.40	99.32	147	WP_004176269.1	broad-spectrum class A beta-lactamase SHV-11	NA	NA	blaSHV
+NA	contig_36_polypolish	9168	9608	+	blaSHV	SHV family class A beta-lactamase	core	AMR	AMR	BETA-LACTAM	BETA-LACTAM	PARTIALX	147	286	51.40	99.32	147	WP_004183952.1	broad-spectrum class A beta-lactamase SHV-60	NA	NA	blaSHV
+NA	contig_36_polypolish	9168	9608	+	blaSHV	SHV family class A beta-lactamase	core	AMR	AMR	BETA-LACTAM	BETA-LACTAM	PARTIALX	147	286	51.40	99.32	147	WP_032488413.1	extended-spectrum class A beta-lactamase SHV-2a	NA	NA	blaSHV
+NA	contig_36_polypolish	9168	9608	+	blaSHV	SHV family class A beta-lactamase	core	AMR	AMR	BETA-LACTAM	BETA-LACTAM	PARTIALX	147	286	51.40	99.32	147	WP_032494802.1	extended-spectrum class A beta-lactamase SHV-129	NA	NA	blaSHV
+NA	contig_36_polypolish	9168	9608	+	blaSHV	SHV family class A beta-lactamase	core	AMR	AMR	BETA-LACTAM	BETA-LACTAM	PARTIALX	147	286	51.40	99.32	147	WP_063864610.1	inhibitor-resistant broad-spectrum class A beta-lactamase SHV-107	NA	NA	blaSHV
+NA	contig_36_polypolish	9168	9608	+	blaSHV	SHV family class A beta-lactamase	core	AMR	AMR	BETA-LACTAM	BETA-LACTAM	PARTIALX	147	286	51.40	99.32	147	WP_063864613.1	class A beta-lactamase SHV-110	NA	NA	blaSHV
+NA	contig_36_polypolish	9168	9608	+	blaSHV	SHV family class A beta-lactamase	core	AMR	AMR	BETA-LACTAM	BETA-LACTAM	PARTIALX	147	286	51.40	99.32	147	WP_063864619.1	extended-spectrum class A beta-lactamase SHV-13	NA	NA	blaSHV
+NA	contig_36_polypolish	9168	9608	+	blaSHV	SHV family class A beta-lactamase	core	AMR	AMR	BETA-LACTAM	BETA-LACTAM	PARTIALX	147	286	51.40	99.32	147	WP_063864622.1	extended-spectrum class A beta-lactamase SHV-134	NA	NA	blaSHV
+NA	contig_36_polypolish	9168	9608	+	blaSHV	SHV family class A beta-lactamase	core	AMR	AMR	BETA-LACTAM	BETA-LACTAM	PARTIALX	147	286	51.40	99.32	147	WP_063864638.1	extended-spectrum class A beta-lactamase SHV-152	NA	NA	blaSHV
+NA	contig_36_polypolish	9168	9608	+	blaSHV	SHV family class A beta-lactamase	core	AMR	AMR	BETA-LACTAM	BETA-LACTAM	PARTIALX	147	286	51.40	99.32	147	WP_063864641.1	class A beta-lactamase SHV-155	NA	NA	blaSHV
+NA	contig_36_polypolish	9168	9608	+	blaSHV	SHV family class A beta-lactamase	core	AMR	AMR	BETA-LACTAM	BETA-LACTAM	PARTIALX	147	286	51.40	99.32	147	WP_063864645.1	class A beta-lactamase SHV-159	NA	NA	blaSHV
+NA	contig_36_polypolish	9168	9608	+	blaSHV	SHV family class A beta-lactamase	core	AMR	AMR	BETA-LACTAM	BETA-LACTAM	PARTIALX	147	286	51.40	99.32	147	WP_063864654.1	class A beta-lactamase SHV-172	NA	NA	blaSHV
+NA	contig_36_polypolish	9168	9608	+	blaSHV	SHV family class A beta-lactamase	core	AMR	AMR	BETA-LACTAM	BETA-LACTAM	PARTIALX	147	286	51.40	99.32	147	WP_063864656.1	class A beta-lactamase SHV-178	NA	NA	blaSHV
+NA	contig_36_polypolish	9168	9608	+	blaSHV	SHV family class A beta-lactamase	core	AMR	AMR	BETA-LACTAM	BETA-LACTAM	PARTIALX	147	286	51.40	99.32	147	WP_063864666.1	class A beta-lactamase SHV-190	NA	NA	blaSHV
+NA	contig_36_polypolish	9168	9608	+	blaSHV	SHV family class A beta-lactamase	core	AMR	AMR	BETA-LACTAM	BETA-LACTAM	PARTIALX	147	286	51.40	99.32	147	WP_063864674.1	extended-spectrum class A beta-lactamase SHV-31	NA	NA	blaSHV
+NA	contig_36_polypolish	9168	9608	+	blaSHV	SHV family class A beta-lactamase	core	AMR	AMR	BETA-LACTAM	BETA-LACTAM	PARTIALX	147	286	51.40	99.32	147	WP_063864681.1	broad-spectrum class A beta-lactamase SHV-40	NA	NA	blaSHV
+NA	contig_36_polypolish	9168	9608	+	blaSHV	SHV family class A beta-lactamase	core	AMR	AMR	BETA-LACTAM	BETA-LACTAM	PARTIALX	147	286	51.40	99.32	147	WP_063864693.1	inhibitor-resistant broad-spectrum class A beta-lactamase SHV-56	NA	NA	blaSHV
+NA	contig_36_polypolish	9168	9608	+	blaSHV	SHV family class A beta-lactamase	core	AMR	AMR	BETA-LACTAM	BETA-LACTAM	PARTIALX	147	286	51.40	99.32	147	WP_063864709.1	broad-spectrum class A beta-lactamase SHV-79	NA	NA	blaSHV
+NA	contig_36_polypolish	9168	9608	+	blaSHV	SHV family class A beta-lactamase	core	AMR	AMR	BETA-LACTAM	BETA-LACTAM	PARTIALX	147	286	51.40	99.32	147	WP_063864718.1	class A beta-lactamase SHV-96	NA	NA	blaSHV
+NA	contig_36_polypolish	9168	9608	+	blaSHV	SHV family class A beta-lactamase	core	AMR	AMR	BETA-LACTAM	BETA-LACTAM	PARTIALX	147	286	51.40	99.32	147	WP_096807447.1	class A beta-lactamase SHV-200	NA	NA	blaSHV
+NA	contig_36_polypolish	9168	9608	+	blaSHV	SHV family class A beta-lactamase	core	AMR	AMR	BETA-LACTAM	BETA-LACTAM	PARTIALX	147	286	51.40	99.32	147	WP_122630870.1	class A beta-lactamase SHV-215	NA	NA	blaSHV
+NA	contig_36_polypolish	9168	9608	+	blaSHV	SHV family class A beta-lactamase	core	AMR	AMR	BETA-LACTAM	BETA-LACTAM	PARTIALX	147	286	51.40	99.32	147	WP_122630880.1	class A beta-lactamase SHV-228	NA	NA	blaSHV
+NA	contig_36_polypolish	9587	10024	+	blaSHV	SHV family class A beta-lactamase	core	AMR	AMR	BETA-LACTAM	BETA-LACTAM	PARTIALX	146	286	51.05	95.89	146	WP_002904004.1	extended-spectrum class A beta-lactamase SHV-12	NA	NA	blaSHV
+NA	contig_36_polypolish	9587	10024	+	blaSHV	SHV family class A beta-lactamase	core	AMR	AMR	BETA-LACTAM	BETA-LACTAM	PARTIALX	146	286	51.05	95.89	146	WP_011117369.1	extended-spectrum class A beta-lactamase SHV-5	NA	NA	blaSHV
+NA	contig_36_polypolish	9587	10024	+	blaSHV	SHV family class A beta-lactamase	core	AMR	AMR	BETA-LACTAM	BETA-LACTAM	PARTIALX	146	286	51.05	95.89	146	WP_020316986.1	extended-spectrum class A beta-lactamase SHV-7	NA	NA	blaSHV
+NA	contig_36_polypolish	9587	10024	+	blaSHV	SHV family class A beta-lactamase	core	AMR	AMR	BETA-LACTAM	BETA-LACTAM	PARTIALX	146	286	51.05	95.89	146	WP_063864635.1	extended-spectrum class A beta-lactamase SHV-15	NA	NA	blaSHV
+NA	contig_36_polypolish	9587	10024	+	blaSHV	SHV family class A beta-lactamase	core	AMR	AMR	BETA-LACTAM	BETA-LACTAM	PARTIALX	146	286	51.05	95.89	146	WP_063864640.1	extended-spectrum class A beta-lactamase SHV-154	NA	NA	blaSHV
+NA	contig_36_polypolish	9587	10024	+	blaSHV	SHV family class A beta-lactamase	core	AMR	AMR	BETA-LACTAM	BETA-LACTAM	PARTIALX	146	286	51.05	95.89	146	WP_063864647.1	extended-spectrum class A beta-lactamase SHV-160	NA	NA	blaSHV
+NA	contig_36_polypolish	9587	10024	+	blaSHV	SHV family class A beta-lactamase	core	AMR	AMR	BETA-LACTAM	BETA-LACTAM	PARTIALX	146	286	51.05	95.89	146	WP_063864652.1	extended-spectrum class A beta-lactamase SHV-165	NA	NA	blaSHV
+NA	contig_36_polypolish	9587	10024	+	blaSHV	SHV family class A beta-lactamase	core	AMR	AMR	BETA-LACTAM	BETA-LACTAM	PARTIALX	146	286	51.05	95.89	146	WP_063864692.1	extended-spectrum class A beta-lactamase SHV-55	NA	NA	blaSHV
+NA	contig_36_polypolish	9587	10024	+	blaSHV	SHV family class A beta-lactamase	core	AMR	AMR	BETA-LACTAM	BETA-LACTAM	PARTIALX	146	286	51.05	95.89	146	WP_063864698.1	extended-spectrum class A beta-lactamase SHV-64	NA	NA	blaSHV
+NA	contig_36_polypolish	9587	10024	+	blaSHV	SHV family class A beta-lactamase	core	AMR	AMR	BETA-LACTAM	BETA-LACTAM	PARTIALX	146	286	51.05	95.89	146	WP_063864700.1	extended-spectrum class A beta-lactamase SHV-66	NA	NA	blaSHV
+NA	contig_36_polypolish	9587	10024	+	blaSHV	SHV family class A beta-lactamase	core	AMR	AMR	BETA-LACTAM	BETA-LACTAM	PARTIALX	146	286	51.05	95.89	146	WP_268871888.1	class A beta-lactamase SHV-230	NA	NA	blaSHV
+NA	contig_37_polypolish	18	569	+	aac(6')-Ib3	aminoglycoside N-acetyltransferase AAC(6')-Ib3	core	AMR	AMR	AMINOGLYCOSIDE	AMIKACIN/KANAMYCIN/TOBRAMYCIN	ALLELEX	184	184	100.00	100.00	184	WP_032488579.1	aminoglycoside N-acetyltransferase AAC(6')-Ib3	NA	NA	aac(6')-Ib3
+NA	contig_37_polypolish	642	1424	+	aadA1	ANT(3'')-Ia family aminoglycoside nucleotidyltransferase AadA1	core	AMR	AMR	AMINOGLYCOSIDE	STREPTOMYCIN	BLASTX	261	262	100.00	97.71	262	WP_001206315.1	ANT(3'')-Ia family aminoglycoside nucleotidyltransferase AadA1	NA	NA	aadA1
+NA	contig_37_polypolish	3006	3863	+	blaTEM-1	broad-spectrum class A beta-lactamase TEM-1	core	AMR	AMR	BETA-LACTAM	BETA-LACTAM	ALLELEX	286	286	100.00	100.00	286	WP_000027057.1	broad-spectrum class A beta-lactamase TEM-1	NA	NA	blaTEM-1
+NA	contig_37_polypolish	8924	9133	-	merC	organomercurial transporter MerC	plus	STRESS	METAL	MERCURY	ORGANOMERCURY	PARTIALX	70	140	50.00	90.00	70	AAC33908.1	organomercurial transporter MerC	NA	NA	merC
+NA	contig_39_polypolish	3496	3825	-	qacE	quaternary ammonium compound efflux SMR transporter QacE	core	STRESS	BIOCIDE	QUATERNARY AMMONIUM	QUATERNARY AMMONIUM	EXACTX	110	110	100.00	100.00	110	WP_010890145.1	quaternary ammonium compound efflux SMR transporter QacE	NA	NA	qacE
+NA	contig_39_polypolish	4010	4327	-	dfrA30	trimethoprim-resistant dihydrofolate reductase DfrA30	core	AMR	AMR	TRIMETHOPRIM	TRIMETHOPRIM	PARTIALX	106	157	67.52	98.11	106	WP_063844408.1	trimethoprim-resistant dihydrofolate reductase DfrA30	NA	NA	dfrA30
+NA	contig_40_polypolish	632	1258	+	aph(3')-Ia	aminoglycoside O-phosphotransferase APH(3')-Ia	core	AMR	AMR	AMINOGLYCOSIDE	KANAMYCIN	PARTIALX	209	271	77.12	99.04	209	WP_000018329.1	aminoglycoside O-phosphotransferase APH(3')-Ia	NA	NA	aph(3')-Ia
+NA	contig_40_polypolish	632	1258	+	aph(3')-Ia	aminoglycoside O-phosphotransferase APH(3')-Ia	core	AMR	AMR	AMINOGLYCOSIDE	KANAMYCIN	PARTIALX	209	271	77.12	99.04	209	WP_063842148.1	aminoglycoside O-phosphotransferase APH(3')-Ia	NA	NA	aph(3')-Ia
+NA	contig_40_polypolish	2574	3359	+	aph(3'')-Ib	aminoglycoside O-phosphotransferase APH(3'')-Ib	core	AMR	AMR	AMINOGLYCOSIDE	STREPTOMYCIN	BLASTX	262	267	98.13	100.00	262	WP_001082319.1	aminoglycoside O-phosphotransferase APH(3'')-Ib	NA	NA	aph(3'')-Ib
+NA	contig_40_polypolish	3555	4103	+	aph(6)-Id	aminoglycoside O-phosphotransferase APH(6)-Id	core	AMR	AMR	AMINOGLYCOSIDE	STREPTOMYCIN	PARTIALX	183	278	65.83	98.91	183	WP_000480968.1	aminoglycoside O-phosphotransferase APH(6)-Id	NA	NA	aph(6)-Id
+NA	contig_40_polypolish	3555	4103	+	aph(6)-Id	aminoglycoside O-phosphotransferase APH(6)-Id	core	AMR	AMR	AMINOGLYCOSIDE	STREPTOMYCIN	PARTIALX	183	278	65.83	98.91	183	WP_000480972.1	aminoglycoside O-phosphotransferase APH(6)-Id	NA	NA	aph(6)-Id
+NA	contig_40_polypolish	3555	4103	+	aph(6)-Id	aminoglycoside O-phosphotransferase APH(6)-Id	core	AMR	AMR	AMINOGLYCOSIDE	STREPTOMYCIN	PARTIALX	183	278	65.83	98.91	183	WP_063842183.1	aminoglycoside O-phosphotransferase APH(6)-Id	NA	NA	aph(6)-Id
+NA	contig_41_polypolish	100023	100541	-	terD	tellurium resistance membrane protein TerD	plus	STRESS	METAL	TELLURIUM	TELLURIUM	BLASTX	173	192	90.10	98.84	173	AAA98292.1	tellurium resistance membrane protein TerD	NA	NA	terD
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/summarize/amrfinderplus_output.json	Fri May 24 10:47:00 2024 +0000
@@ -0,0 +1,1 @@
+[{"analysis_software_version": "3.11.26", "reference_database_version": "v3.11-2023-04-17.1", "analysis_software_name": "amrfinderplus", "results": [{"name": "amrfinderplus_report", "file_path": "tests/data/dummy/amrfinderplus/AMRFinderPlus_report.tsv", "hid": "12345", "galaxy_id": null, "content": [{"Protein identifier": null, "Contig id": "contig_153_polypolish", "Start": 4412, "Stop": 4645, "Strand": "-", "Gene symbol": "merE", "Sequence name": "broad-spectrum mercury transporter MerE", "Scope": "plus", "Element type": "STRESS", "Element subtype": "METAL", "Class": "MERCURY", "Subclass": "MERCURY", "Method": "BLASTX", "Target length": 78, "Reference sequence length": 78, "% Coverage of reference sequence": 100.0, "% Identity to reference sequence": 96.15, "Alignment length": 78, "Accession of closest sequence": "AAC38236.1", "Name of closest sequence": "broad-spectrum mercury transporter MerE", "HMM id": null, "HMM description": null, "Hierarchy node": "merE"}, {"Protein identifier": null, "Contig id": "contig_153_polypolish", "Start": 7613, "Stop": 7846, "Strand": "-", "Gene symbol": "merT", "Sequence name": "mercuric transport protein MerT", "Scope": "plus", "Element type": "STRESS", "Element subtype": "METAL", "Class": "MERCURY", "Subclass": "MERCURY", "Method": "PARTIALX", "Target length": 78, "Reference sequence length": 116, "% Coverage of reference sequence": 67.24, "% Identity to reference sequence": 92.31, "Alignment length": 78, "Accession of closest sequence": "CAA70196.1", "Name of closest sequence": "mercuric transport protein MerT", "HMM id": null, "HMM description": null, "Hierarchy node": "merT"}, {"Protein identifier": null, "Contig id": "contig_160_polypolish", "Start": 86415, "Stop": 86654, "Strand": "-", "Gene symbol": "fosA", "Sequence name": "FosA5 family fosfomycin resistance glutathione transferase", "Scope": "core", "Element type": "AMR", "Element subtype": "AMR", "Class": "FOSFOMYCIN", "Subclass": "FOSFOMYCIN", "Method": "PARTIALX", "Target length": 80, "Reference sequence length": 139, "% Coverage of reference sequence": 57.55, "% Identity to reference sequence": 98.75, "Alignment length": 80, "Accession of closest sequence": "WP_114473955.1", "Name of closest sequence": "fosfomycin resistance glutathione transferase FosA9", "HMM id": null, "HMM description": null, "Hierarchy node": "fosA5_fam"}, {"Protein identifier": null, "Contig id": "contig_30_polypolish", "Start": 3018, "Stop": 3344, "Strand": "+", "Gene symbol": "merR", "Sequence name": "mercury resistance transcriptional regulator MerR", "Scope": "plus", "Element type": "STRESS", "Element subtype": "METAL", "Class": "MERCURY", "Subclass": "MERCURY", "Method": "PARTIALX", "Target length": 109, "Reference sequence length": 144, "% Coverage of reference sequence": 75.69, "% Identity to reference sequence": 93.58, "Alignment length": 109, "Accession of closest sequence": "BAA20334.1", "Name of closest sequence": "mercury resistance transcriptional regulator MerR", "HMM id": null, "HMM description": null, "Hierarchy node": "merR_Ps"}, {"Protein identifier": null, "Contig id": "contig_30_polypolish", "Start": 5821, "Stop": 6243, "Strand": "+", "Gene symbol": "catA1", "Sequence name": "type A-1 chloramphenicol O-acetyltransferase", "Scope": "core", "Element type": "AMR", "Element subtype": "AMR", "Class": "PHENICOL", "Subclass": "CHLORAMPHENICOL", "Method": "PARTIALX", "Target length": 141, "Reference sequence length": 219, "% Coverage of reference sequence": 64.38, "% Identity to reference sequence": 98.58, "Alignment length": 141, "Accession of closest sequence": "WP_000412211.1", "Name of closest sequence": "type A-1 chloramphenicol O-acetyltransferase", "HMM id": null, "HMM description": null, "Hierarchy node": "catA1"}, {"Protein identifier": null, "Contig id": "contig_30_polypolish", "Start": 5821, "Stop": 6243, "Strand": "+", "Gene symbol": "catA1", "Sequence name": "type A-1 chloramphenicol O-acetyltransferase", "Scope": "core", "Element type": "AMR", "Element subtype": "AMR", "Class": "PHENICOL", "Subclass": "CHLORAMPHENICOL", "Method": "PARTIALX", "Target length": 141, "Reference sequence length": 219, "% Coverage of reference sequence": 64.38, "% Identity to reference sequence": 98.58, "Alignment length": 141, "Accession of closest sequence": "WP_063843217.1", "Name of closest sequence": "type A-1 chloramphenicol O-acetyltransferase", "HMM id": null, "HMM description": null, "Hierarchy node": "catA1"}, {"Protein identifier": null, "Contig id": "contig_30_polypolish", "Start": 13708, "Stop": 14433, "Strand": "+", "Gene symbol": "blaCTX-M", "Sequence name": "CTX-M family extended-spectrum class A beta-lactamase", "Scope": "core", "Element type": "AMR", "Element subtype": "AMR", "Class": "BETA-LACTAM", "Subclass": "CEPHALOSPORIN", "Method": "INTERNAL_STOP", "Target length": 242, "Reference sequence length": 291, "% Coverage of reference sequence": 84.54, "% Identity to reference sequence": 90.24, "Alignment length": 246, "Accession of closest sequence": "WP_063860025.1", "Name of closest sequence": "extended-spectrum class A beta-lactamase CTX-M-179", "HMM id": null, "HMM description": null, "Hierarchy node": "blaCTX-M"}, {"Protein identifier": null, "Contig id": "contig_30_polypolish", "Start": 17856, "Stop": 18287, "Strand": "+", "Gene symbol": "merR", "Sequence name": "mercury resistance transcriptional regulator MerR", "Scope": "plus", "Element type": "STRESS", "Element subtype": "METAL", "Class": "MERCURY", "Subclass": "MERCURY", "Method": "BLASTX", "Target length": 144, "Reference sequence length": 144, "% Coverage of reference sequence": 100.0, "% Identity to reference sequence": 92.36, "Alignment length": 144, "Accession of closest sequence": "CAA77320.1", "Name of closest sequence": "mercury resistance transcriptional regulator MerR", "HMM id": null, "HMM description": null, "Hierarchy node": "merR_Ps"}, {"Protein identifier": null, "Contig id": "contig_30_polypolish", "Start": 20698, "Stop": 21348, "Strand": "+", "Gene symbol": "catA1", "Sequence name": "type A-1 chloramphenicol O-acetyltransferase", "Scope": "core", "Element type": "AMR", "Element subtype": "AMR", "Class": "PHENICOL", "Subclass": "CHLORAMPHENICOL", "Method": "BLASTX", "Target length": 217, "Reference sequence length": 219, "% Coverage of reference sequence": 99.09, "% Identity to reference sequence": 92.17, "Alignment length": 217, "Accession of closest sequence": "WP_000412211.1", "Name of closest sequence": "type A-1 chloramphenicol O-acetyltransferase", "HMM id": null, "HMM description": null, "Hierarchy node": "catA1"}, {"Protein identifier": null, "Contig id": "contig_35_polypolish", "Start": 4787, "Stop": 5644, "Strand": "-", "Gene symbol": "aac(3)-IIe", "Sequence name": "aminoglycoside N-acetyltransferase AAC(3)-IIe", "Scope": "core", "Element type": "AMR", "Element subtype": "AMR", "Class": "AMINOGLYCOSIDE", "Subclass": "GENTAMICIN", "Method": "EXACTX", "Target length": 286, "Reference sequence length": 286, "% Coverage of reference sequence": 100.0, "% Identity to reference sequence": 100.0, "Alignment length": 286, "Accession of closest sequence": "WP_000557452.1", "Name of closest sequence": "aminoglycoside N-acetyltransferase AAC(3)-IIe", "HMM id": null, "HMM description": null, "Hierarchy node": "aac(3)-IIe"}, {"Protein identifier": null, "Contig id": "contig_36_polypolish", "Start": 9168, "Stop": 9608, "Strand": "+", "Gene symbol": "blaSHV", "Sequence name": "SHV family class A beta-lactamase", "Scope": "core", "Element type": "AMR", "Element subtype": "AMR", "Class": "BETA-LACTAM", "Subclass": "BETA-LACTAM", "Method": "PARTIALX", "Target length": 147, "Reference sequence length": 286, "% Coverage of reference sequence": 51.4, "% Identity to reference sequence": 99.32, "Alignment length": 147, "Accession of closest sequence": "WP_002904004.1", "Name of closest sequence": "extended-spectrum class A beta-lactamase SHV-12", "HMM id": null, "HMM description": null, "Hierarchy node": "blaSHV"}, {"Protein identifier": null, "Contig id": "contig_36_polypolish", "Start": 9168, "Stop": 9608, "Strand": "+", "Gene symbol": "blaSHV", "Sequence name": "SHV family class A beta-lactamase", "Scope": "core", "Element type": "AMR", "Element subtype": "AMR", "Class": "BETA-LACTAM", "Subclass": "BETA-LACTAM", "Method": "PARTIALX", "Target length": 147, "Reference sequence length": 286, "% Coverage of reference sequence": 51.4, "% Identity to reference sequence": 99.32, "Alignment length": 147, "Accession of closest sequence": "WP_004176269.1", "Name of closest sequence": "broad-spectrum class A beta-lactamase SHV-11", "HMM id": null, "HMM description": null, "Hierarchy node": "blaSHV"}, {"Protein identifier": null, "Contig id": "contig_36_polypolish", "Start": 9168, "Stop": 9608, "Strand": "+", "Gene symbol": "blaSHV", "Sequence name": "SHV family class A beta-lactamase", "Scope": "core", "Element type": "AMR", "Element subtype": "AMR", "Class": "BETA-LACTAM", "Subclass": "BETA-LACTAM", "Method": "PARTIALX", "Target length": 147, "Reference sequence length": 286, "% Coverage of reference sequence": 51.4, "% Identity to reference sequence": 99.32, "Alignment length": 147, "Accession of closest sequence": "WP_004183952.1", "Name of closest sequence": "broad-spectrum class A beta-lactamase SHV-60", "HMM id": null, "HMM description": null, "Hierarchy node": "blaSHV"}, {"Protein identifier": null, "Contig id": "contig_36_polypolish", "Start": 9168, "Stop": 9608, "Strand": "+", "Gene symbol": "blaSHV", "Sequence name": "SHV family class A beta-lactamase", "Scope": "core", "Element type": "AMR", "Element subtype": "AMR", "Class": "BETA-LACTAM", "Subclass": "BETA-LACTAM", "Method": "PARTIALX", "Target length": 147, "Reference sequence length": 286, "% Coverage of reference sequence": 51.4, "% Identity to reference sequence": 99.32, "Alignment length": 147, "Accession of closest sequence": "WP_032488413.1", "Name of closest sequence": "extended-spectrum class A beta-lactamase SHV-2a", "HMM id": null, "HMM description": null, "Hierarchy node": "blaSHV"}, {"Protein identifier": null, "Contig id": "contig_36_polypolish", "Start": 9168, "Stop": 9608, "Strand": "+", "Gene symbol": "blaSHV", "Sequence name": "SHV family class A beta-lactamase", "Scope": "core", "Element type": "AMR", "Element subtype": "AMR", "Class": "BETA-LACTAM", "Subclass": "BETA-LACTAM", "Method": "PARTIALX", "Target length": 147, "Reference sequence length": 286, "% Coverage of reference sequence": 51.4, "% Identity to reference sequence": 99.32, "Alignment length": 147, "Accession of closest sequence": "WP_032494802.1", "Name of closest sequence": "extended-spectrum class A beta-lactamase SHV-129", "HMM id": null, "HMM description": null, "Hierarchy node": "blaSHV"}, {"Protein identifier": null, "Contig id": "contig_36_polypolish", "Start": 9168, "Stop": 9608, "Strand": "+", "Gene symbol": "blaSHV", "Sequence name": "SHV family class A beta-lactamase", "Scope": "core", "Element type": "AMR", "Element subtype": "AMR", "Class": "BETA-LACTAM", "Subclass": "BETA-LACTAM", "Method": "PARTIALX", "Target length": 147, "Reference sequence length": 286, "% Coverage of reference sequence": 51.4, "% Identity to reference sequence": 99.32, "Alignment length": 147, "Accession of closest sequence": "WP_063864610.1", "Name of closest sequence": "inhibitor-resistant broad-spectrum class A beta-lactamase SHV-107", "HMM id": null, "HMM description": null, "Hierarchy node": "blaSHV"}, {"Protein identifier": null, "Contig id": "contig_36_polypolish", "Start": 9168, "Stop": 9608, "Strand": "+", "Gene symbol": "blaSHV", "Sequence name": "SHV family class A beta-lactamase", "Scope": "core", "Element type": "AMR", "Element subtype": "AMR", "Class": "BETA-LACTAM", "Subclass": "BETA-LACTAM", "Method": "PARTIALX", "Target length": 147, "Reference sequence length": 286, "% Coverage of reference sequence": 51.4, "% Identity to reference sequence": 99.32, "Alignment length": 147, "Accession of closest sequence": "WP_063864613.1", "Name of closest sequence": "class A beta-lactamase SHV-110", "HMM id": null, "HMM description": null, "Hierarchy node": "blaSHV"}, {"Protein identifier": null, "Contig id": "contig_36_polypolish", "Start": 9168, "Stop": 9608, "Strand": "+", "Gene symbol": "blaSHV", "Sequence name": "SHV family class A beta-lactamase", "Scope": "core", "Element type": "AMR", "Element subtype": "AMR", "Class": "BETA-LACTAM", "Subclass": "BETA-LACTAM", "Method": "PARTIALX", "Target length": 147, "Reference sequence length": 286, "% Coverage of reference sequence": 51.4, "% Identity to reference sequence": 99.32, "Alignment length": 147, "Accession of closest sequence": "WP_063864619.1", "Name of closest sequence": "extended-spectrum class A beta-lactamase SHV-13", "HMM id": null, "HMM description": null, "Hierarchy node": "blaSHV"}, {"Protein identifier": null, "Contig id": "contig_36_polypolish", "Start": 9168, "Stop": 9608, "Strand": "+", "Gene symbol": "blaSHV", "Sequence name": "SHV family class A beta-lactamase", "Scope": "core", "Element type": "AMR", "Element subtype": "AMR", "Class": "BETA-LACTAM", "Subclass": "BETA-LACTAM", "Method": "PARTIALX", "Target length": 147, "Reference sequence length": 286, "% Coverage of reference sequence": 51.4, "% Identity to reference sequence": 99.32, "Alignment length": 147, "Accession of closest sequence": "WP_063864622.1", "Name of closest sequence": "extended-spectrum class A beta-lactamase SHV-134", "HMM id": null, "HMM description": null, "Hierarchy node": "blaSHV"}, {"Protein identifier": null, "Contig id": "contig_36_polypolish", "Start": 9168, "Stop": 9608, "Strand": "+", "Gene symbol": "blaSHV", "Sequence name": "SHV family class A beta-lactamase", "Scope": "core", "Element type": "AMR", "Element subtype": "AMR", "Class": "BETA-LACTAM", "Subclass": "BETA-LACTAM", "Method": "PARTIALX", "Target length": 147, "Reference sequence length": 286, "% Coverage of reference sequence": 51.4, "% Identity to reference sequence": 99.32, "Alignment length": 147, "Accession of closest sequence": "WP_063864638.1", "Name of closest sequence": "extended-spectrum class A beta-lactamase SHV-152", "HMM id": null, "HMM description": null, "Hierarchy node": "blaSHV"}, {"Protein identifier": null, "Contig id": "contig_36_polypolish", "Start": 9168, "Stop": 9608, "Strand": "+", "Gene symbol": "blaSHV", "Sequence name": "SHV family class A beta-lactamase", "Scope": "core", "Element type": "AMR", "Element subtype": "AMR", "Class": "BETA-LACTAM", "Subclass": "BETA-LACTAM", "Method": "PARTIALX", "Target length": 147, "Reference sequence length": 286, "% Coverage of reference sequence": 51.4, "% Identity to reference sequence": 99.32, "Alignment length": 147, "Accession of closest sequence": "WP_063864641.1", "Name of closest sequence": "class A beta-lactamase SHV-155", "HMM id": null, "HMM description": null, "Hierarchy node": "blaSHV"}, {"Protein identifier": null, "Contig id": "contig_36_polypolish", "Start": 9168, "Stop": 9608, "Strand": "+", "Gene symbol": "blaSHV", "Sequence name": "SHV family class A beta-lactamase", "Scope": "core", "Element type": "AMR", "Element subtype": "AMR", "Class": "BETA-LACTAM", "Subclass": "BETA-LACTAM", "Method": "PARTIALX", "Target length": 147, "Reference sequence length": 286, "% Coverage of reference sequence": 51.4, "% Identity to reference sequence": 99.32, "Alignment length": 147, "Accession of closest sequence": "WP_063864645.1", "Name of closest sequence": "class A beta-lactamase SHV-159", "HMM id": null, "HMM description": null, "Hierarchy node": "blaSHV"}, {"Protein identifier": null, "Contig id": "contig_36_polypolish", "Start": 9168, "Stop": 9608, "Strand": "+", "Gene symbol": "blaSHV", "Sequence name": "SHV family class A beta-lactamase", "Scope": "core", "Element type": "AMR", "Element subtype": "AMR", "Class": "BETA-LACTAM", "Subclass": "BETA-LACTAM", "Method": "PARTIALX", "Target length": 147, "Reference sequence length": 286, "% Coverage of reference sequence": 51.4, "% Identity to reference sequence": 99.32, "Alignment length": 147, "Accession of closest sequence": "WP_063864654.1", "Name of closest sequence": "class A beta-lactamase SHV-172", "HMM id": null, "HMM description": null, "Hierarchy node": "blaSHV"}, {"Protein identifier": null, "Contig id": "contig_36_polypolish", "Start": 9168, "Stop": 9608, "Strand": "+", "Gene symbol": "blaSHV", "Sequence name": "SHV family class A beta-lactamase", "Scope": "core", "Element type": "AMR", "Element subtype": "AMR", "Class": "BETA-LACTAM", "Subclass": "BETA-LACTAM", "Method": "PARTIALX", "Target length": 147, "Reference sequence length": 286, "% Coverage of reference sequence": 51.4, "% Identity to reference sequence": 99.32, "Alignment length": 147, "Accession of closest sequence": "WP_063864656.1", "Name of closest sequence": "class A beta-lactamase SHV-178", "HMM id": null, "HMM description": null, "Hierarchy node": "blaSHV"}, {"Protein identifier": null, "Contig id": "contig_36_polypolish", "Start": 9168, "Stop": 9608, "Strand": "+", "Gene symbol": "blaSHV", "Sequence name": "SHV family class A beta-lactamase", "Scope": "core", "Element type": "AMR", "Element subtype": "AMR", "Class": "BETA-LACTAM", "Subclass": "BETA-LACTAM", "Method": "PARTIALX", "Target length": 147, "Reference sequence length": 286, "% Coverage of reference sequence": 51.4, "% Identity to reference sequence": 99.32, "Alignment length": 147, "Accession of closest sequence": "WP_063864666.1", "Name of closest sequence": "class A beta-lactamase SHV-190", "HMM id": null, "HMM description": null, "Hierarchy node": "blaSHV"}, {"Protein identifier": null, "Contig id": "contig_36_polypolish", "Start": 9168, "Stop": 9608, "Strand": "+", "Gene symbol": "blaSHV", "Sequence name": "SHV family class A beta-lactamase", "Scope": "core", "Element type": "AMR", "Element subtype": "AMR", "Class": "BETA-LACTAM", "Subclass": "BETA-LACTAM", "Method": "PARTIALX", "Target length": 147, "Reference sequence length": 286, "% Coverage of reference sequence": 51.4, "% Identity to reference sequence": 99.32, "Alignment length": 147, "Accession of closest sequence": "WP_063864674.1", "Name of closest sequence": "extended-spectrum class A beta-lactamase SHV-31", "HMM id": null, "HMM description": null, "Hierarchy node": "blaSHV"}, {"Protein identifier": null, "Contig id": "contig_36_polypolish", "Start": 9168, "Stop": 9608, "Strand": "+", "Gene symbol": "blaSHV", "Sequence name": "SHV family class A beta-lactamase", "Scope": "core", "Element type": "AMR", "Element subtype": "AMR", "Class": "BETA-LACTAM", "Subclass": "BETA-LACTAM", "Method": "PARTIALX", "Target length": 147, "Reference sequence length": 286, "% Coverage of reference sequence": 51.4, "% Identity to reference sequence": 99.32, "Alignment length": 147, "Accession of closest sequence": "WP_063864681.1", "Name of closest sequence": "broad-spectrum class A beta-lactamase SHV-40", "HMM id": null, "HMM description": null, "Hierarchy node": "blaSHV"}, {"Protein identifier": null, "Contig id": "contig_36_polypolish", "Start": 9168, "Stop": 9608, "Strand": "+", "Gene symbol": "blaSHV", "Sequence name": "SHV family class A beta-lactamase", "Scope": "core", "Element type": "AMR", "Element subtype": "AMR", "Class": "BETA-LACTAM", "Subclass": "BETA-LACTAM", "Method": "PARTIALX", "Target length": 147, "Reference sequence length": 286, "% Coverage of reference sequence": 51.4, "% Identity to reference sequence": 99.32, "Alignment length": 147, "Accession of closest sequence": "WP_063864693.1", "Name of closest sequence": "inhibitor-resistant broad-spectrum class A beta-lactamase SHV-56", "HMM id": null, "HMM description": null, "Hierarchy node": "blaSHV"}, {"Protein identifier": null, "Contig id": "contig_36_polypolish", "Start": 9168, "Stop": 9608, "Strand": "+", "Gene symbol": "blaSHV", "Sequence name": "SHV family class A beta-lactamase", "Scope": "core", "Element type": "AMR", "Element subtype": "AMR", "Class": "BETA-LACTAM", "Subclass": "BETA-LACTAM", "Method": "PARTIALX", "Target length": 147, "Reference sequence length": 286, "% Coverage of reference sequence": 51.4, "% Identity to reference sequence": 99.32, "Alignment length": 147, "Accession of closest sequence": "WP_063864709.1", "Name of closest sequence": "broad-spectrum class A beta-lactamase SHV-79", "HMM id": null, "HMM description": null, "Hierarchy node": "blaSHV"}, {"Protein identifier": null, "Contig id": "contig_36_polypolish", "Start": 9168, "Stop": 9608, "Strand": "+", "Gene symbol": "blaSHV", "Sequence name": "SHV family class A beta-lactamase", "Scope": "core", "Element type": "AMR", "Element subtype": "AMR", "Class": "BETA-LACTAM", "Subclass": "BETA-LACTAM", "Method": "PARTIALX", "Target length": 147, "Reference sequence length": 286, "% Coverage of reference sequence": 51.4, "% Identity to reference sequence": 99.32, "Alignment length": 147, "Accession of closest sequence": "WP_063864718.1", "Name of closest sequence": "class A beta-lactamase SHV-96", "HMM id": null, "HMM description": null, "Hierarchy node": "blaSHV"}, {"Protein identifier": null, "Contig id": "contig_36_polypolish", "Start": 9168, "Stop": 9608, "Strand": "+", "Gene symbol": "blaSHV", "Sequence name": "SHV family class A beta-lactamase", "Scope": "core", "Element type": "AMR", "Element subtype": "AMR", "Class": "BETA-LACTAM", "Subclass": "BETA-LACTAM", "Method": "PARTIALX", "Target length": 147, "Reference sequence length": 286, "% Coverage of reference sequence": 51.4, "% Identity to reference sequence": 99.32, "Alignment length": 147, "Accession of closest sequence": "WP_096807447.1", "Name of closest sequence": "class A beta-lactamase SHV-200", "HMM id": null, "HMM description": null, "Hierarchy node": "blaSHV"}, {"Protein identifier": null, "Contig id": "contig_36_polypolish", "Start": 9168, "Stop": 9608, "Strand": "+", "Gene symbol": "blaSHV", "Sequence name": "SHV family class A beta-lactamase", "Scope": "core", "Element type": "AMR", "Element subtype": "AMR", "Class": "BETA-LACTAM", "Subclass": "BETA-LACTAM", "Method": "PARTIALX", "Target length": 147, "Reference sequence length": 286, "% Coverage of reference sequence": 51.4, "% Identity to reference sequence": 99.32, "Alignment length": 147, "Accession of closest sequence": "WP_122630870.1", "Name of closest sequence": "class A beta-lactamase SHV-215", "HMM id": null, "HMM description": null, "Hierarchy node": "blaSHV"}, {"Protein identifier": null, "Contig id": "contig_36_polypolish", "Start": 9168, "Stop": 9608, "Strand": "+", "Gene symbol": "blaSHV", "Sequence name": "SHV family class A beta-lactamase", "Scope": "core", "Element type": "AMR", "Element subtype": "AMR", "Class": "BETA-LACTAM", "Subclass": "BETA-LACTAM", "Method": "PARTIALX", "Target length": 147, "Reference sequence length": 286, "% Coverage of reference sequence": 51.4, "% Identity to reference sequence": 99.32, "Alignment length": 147, "Accession of closest sequence": "WP_122630880.1", "Name of closest sequence": "class A beta-lactamase SHV-228", "HMM id": null, "HMM description": null, "Hierarchy node": "blaSHV"}, {"Protein identifier": null, "Contig id": "contig_36_polypolish", "Start": 9587, "Stop": 10024, "Strand": "+", "Gene symbol": "blaSHV", "Sequence name": "SHV family class A beta-lactamase", "Scope": "core", "Element type": "AMR", "Element subtype": "AMR", "Class": "BETA-LACTAM", "Subclass": "BETA-LACTAM", "Method": "PARTIALX", "Target length": 146, "Reference sequence length": 286, "% Coverage of reference sequence": 51.05, "% Identity to reference sequence": 95.89, "Alignment length": 146, "Accession of closest sequence": "WP_002904004.1", "Name of closest sequence": "extended-spectrum class A beta-lactamase SHV-12", "HMM id": null, "HMM description": null, "Hierarchy node": "blaSHV"}, {"Protein identifier": null, "Contig id": "contig_36_polypolish", "Start": 9587, "Stop": 10024, "Strand": "+", "Gene symbol": "blaSHV", "Sequence name": "SHV family class A beta-lactamase", "Scope": "core", "Element type": "AMR", "Element subtype": "AMR", "Class": "BETA-LACTAM", "Subclass": "BETA-LACTAM", "Method": "PARTIALX", "Target length": 146, "Reference sequence length": 286, "% Coverage of reference sequence": 51.05, "% Identity to reference sequence": 95.89, "Alignment length": 146, "Accession of closest sequence": "WP_011117369.1", "Name of closest sequence": "extended-spectrum class A beta-lactamase SHV-5", "HMM id": null, "HMM description": null, "Hierarchy node": "blaSHV"}, {"Protein identifier": null, "Contig id": "contig_36_polypolish", "Start": 9587, "Stop": 10024, "Strand": "+", "Gene symbol": "blaSHV", "Sequence name": "SHV family class A beta-lactamase", "Scope": "core", "Element type": "AMR", "Element subtype": "AMR", "Class": "BETA-LACTAM", "Subclass": "BETA-LACTAM", "Method": "PARTIALX", "Target length": 146, "Reference sequence length": 286, "% Coverage of reference sequence": 51.05, "% Identity to reference sequence": 95.89, "Alignment length": 146, "Accession of closest sequence": "WP_020316986.1", "Name of closest sequence": "extended-spectrum class A beta-lactamase SHV-7", "HMM id": null, "HMM description": null, "Hierarchy node": "blaSHV"}, {"Protein identifier": null, "Contig id": "contig_36_polypolish", "Start": 9587, "Stop": 10024, "Strand": "+", "Gene symbol": "blaSHV", "Sequence name": "SHV family class A beta-lactamase", "Scope": "core", "Element type": "AMR", "Element subtype": "AMR", "Class": "BETA-LACTAM", "Subclass": "BETA-LACTAM", "Method": "PARTIALX", "Target length": 146, "Reference sequence length": 286, "% Coverage of reference sequence": 51.05, "% Identity to reference sequence": 95.89, "Alignment length": 146, "Accession of closest sequence": "WP_063864635.1", "Name of closest sequence": "extended-spectrum class A beta-lactamase SHV-15", "HMM id": null, "HMM description": null, "Hierarchy node": "blaSHV"}, {"Protein identifier": null, "Contig id": "contig_36_polypolish", "Start": 9587, "Stop": 10024, "Strand": "+", "Gene symbol": "blaSHV", "Sequence name": "SHV family class A beta-lactamase", "Scope": "core", "Element type": "AMR", "Element subtype": "AMR", "Class": "BETA-LACTAM", "Subclass": "BETA-LACTAM", "Method": "PARTIALX", "Target length": 146, "Reference sequence length": 286, "% Coverage of reference sequence": 51.05, "% Identity to reference sequence": 95.89, "Alignment length": 146, "Accession of closest sequence": "WP_063864640.1", "Name of closest sequence": "extended-spectrum class A beta-lactamase SHV-154", "HMM id": null, "HMM description": null, "Hierarchy node": "blaSHV"}, {"Protein identifier": null, "Contig id": "contig_36_polypolish", "Start": 9587, "Stop": 10024, "Strand": "+", "Gene symbol": "blaSHV", "Sequence name": "SHV family class A beta-lactamase", "Scope": "core", "Element type": "AMR", "Element subtype": "AMR", "Class": "BETA-LACTAM", "Subclass": "BETA-LACTAM", "Method": "PARTIALX", "Target length": 146, "Reference sequence length": 286, "% Coverage of reference sequence": 51.05, "% Identity to reference sequence": 95.89, "Alignment length": 146, "Accession of closest sequence": "WP_063864647.1", "Name of closest sequence": "extended-spectrum class A beta-lactamase SHV-160", "HMM id": null, "HMM description": null, "Hierarchy node": "blaSHV"}, {"Protein identifier": null, "Contig id": "contig_36_polypolish", "Start": 9587, "Stop": 10024, "Strand": "+", "Gene symbol": "blaSHV", "Sequence name": "SHV family class A beta-lactamase", "Scope": "core", "Element type": "AMR", "Element subtype": "AMR", "Class": "BETA-LACTAM", "Subclass": "BETA-LACTAM", "Method": "PARTIALX", "Target length": 146, "Reference sequence length": 286, "% Coverage of reference sequence": 51.05, "% Identity to reference sequence": 95.89, "Alignment length": 146, "Accession of closest sequence": "WP_063864652.1", "Name of closest sequence": "extended-spectrum class A beta-lactamase SHV-165", "HMM id": null, "HMM description": null, "Hierarchy node": "blaSHV"}, {"Protein identifier": null, "Contig id": "contig_36_polypolish", "Start": 9587, "Stop": 10024, "Strand": "+", "Gene symbol": "blaSHV", "Sequence name": "SHV family class A beta-lactamase", "Scope": "core", "Element type": "AMR", "Element subtype": "AMR", "Class": "BETA-LACTAM", "Subclass": "BETA-LACTAM", "Method": "PARTIALX", "Target length": 146, "Reference sequence length": 286, "% Coverage of reference sequence": 51.05, "% Identity to reference sequence": 95.89, "Alignment length": 146, "Accession of closest sequence": "WP_063864692.1", "Name of closest sequence": "extended-spectrum class A beta-lactamase SHV-55", "HMM id": null, "HMM description": null, "Hierarchy node": "blaSHV"}, {"Protein identifier": null, "Contig id": "contig_36_polypolish", "Start": 9587, "Stop": 10024, "Strand": "+", "Gene symbol": "blaSHV", "Sequence name": "SHV family class A beta-lactamase", "Scope": "core", "Element type": "AMR", "Element subtype": "AMR", "Class": "BETA-LACTAM", "Subclass": "BETA-LACTAM", "Method": "PARTIALX", "Target length": 146, "Reference sequence length": 286, "% Coverage of reference sequence": 51.05, "% Identity to reference sequence": 95.89, "Alignment length": 146, "Accession of closest sequence": "WP_063864698.1", "Name of closest sequence": "extended-spectrum class A beta-lactamase SHV-64", "HMM id": null, "HMM description": null, "Hierarchy node": "blaSHV"}, {"Protein identifier": null, "Contig id": "contig_36_polypolish", "Start": 9587, "Stop": 10024, "Strand": "+", "Gene symbol": "blaSHV", "Sequence name": "SHV family class A beta-lactamase", "Scope": "core", "Element type": "AMR", "Element subtype": "AMR", "Class": "BETA-LACTAM", "Subclass": "BETA-LACTAM", "Method": "PARTIALX", "Target length": 146, "Reference sequence length": 286, "% Coverage of reference sequence": 51.05, "% Identity to reference sequence": 95.89, "Alignment length": 146, "Accession of closest sequence": "WP_063864700.1", "Name of closest sequence": "extended-spectrum class A beta-lactamase SHV-66", "HMM id": null, "HMM description": null, "Hierarchy node": "blaSHV"}, {"Protein identifier": null, "Contig id": "contig_36_polypolish", "Start": 9587, "Stop": 10024, "Strand": "+", "Gene symbol": "blaSHV", "Sequence name": "SHV family class A beta-lactamase", "Scope": "core", "Element type": "AMR", "Element subtype": "AMR", "Class": "BETA-LACTAM", "Subclass": "BETA-LACTAM", "Method": "PARTIALX", "Target length": 146, "Reference sequence length": 286, "% Coverage of reference sequence": 51.05, "% Identity to reference sequence": 95.89, "Alignment length": 146, "Accession of closest sequence": "WP_268871888.1", "Name of closest sequence": "class A beta-lactamase SHV-230", "HMM id": null, "HMM description": null, "Hierarchy node": "blaSHV"}, {"Protein identifier": null, "Contig id": "contig_37_polypolish", "Start": 18, "Stop": 569, "Strand": "+", "Gene symbol": "aac(6')-Ib3", "Sequence name": "aminoglycoside N-acetyltransferase AAC(6')-Ib3", "Scope": "core", "Element type": "AMR", "Element subtype": "AMR", "Class": "AMINOGLYCOSIDE", "Subclass": "AMIKACIN/KANAMYCIN/TOBRAMYCIN", "Method": "ALLELEX", "Target length": 184, "Reference sequence length": 184, "% Coverage of reference sequence": 100.0, "% Identity to reference sequence": 100.0, "Alignment length": 184, "Accession of closest sequence": "WP_032488579.1", "Name of closest sequence": "aminoglycoside N-acetyltransferase AAC(6')-Ib3", "HMM id": null, "HMM description": null, "Hierarchy node": "aac(6')-Ib3"}, {"Protein identifier": null, "Contig id": "contig_37_polypolish", "Start": 642, "Stop": 1424, "Strand": "+", "Gene symbol": "aadA1", "Sequence name": "ANT(3'')-Ia family aminoglycoside nucleotidyltransferase AadA1", "Scope": "core", "Element type": "AMR", "Element subtype": "AMR", "Class": "AMINOGLYCOSIDE", "Subclass": "STREPTOMYCIN", "Method": "BLASTX", "Target length": 261, "Reference sequence length": 262, "% Coverage of reference sequence": 100.0, "% Identity to reference sequence": 97.71, "Alignment length": 262, "Accession of closest sequence": "WP_001206315.1", "Name of closest sequence": "ANT(3'')-Ia family aminoglycoside nucleotidyltransferase AadA1", "HMM id": null, "HMM description": null, "Hierarchy node": "aadA1"}, {"Protein identifier": null, "Contig id": "contig_37_polypolish", "Start": 3006, "Stop": 3863, "Strand": "+", "Gene symbol": "blaTEM-1", "Sequence name": "broad-spectrum class A beta-lactamase TEM-1", "Scope": "core", "Element type": "AMR", "Element subtype": "AMR", "Class": "BETA-LACTAM", "Subclass": "BETA-LACTAM", "Method": "ALLELEX", "Target length": 286, "Reference sequence length": 286, "% Coverage of reference sequence": 100.0, "% Identity to reference sequence": 100.0, "Alignment length": 286, "Accession of closest sequence": "WP_000027057.1", "Name of closest sequence": "broad-spectrum class A beta-lactamase TEM-1", "HMM id": null, "HMM description": null, "Hierarchy node": "blaTEM-1"}, {"Protein identifier": null, "Contig id": "contig_37_polypolish", "Start": 8924, "Stop": 9133, "Strand": "-", "Gene symbol": "merC", "Sequence name": "organomercurial transporter MerC", "Scope": "plus", "Element type": "STRESS", "Element subtype": "METAL", "Class": "MERCURY", "Subclass": "ORGANOMERCURY", "Method": "PARTIALX", "Target length": 70, "Reference sequence length": 140, "% Coverage of reference sequence": 50.0, "% Identity to reference sequence": 90.0, "Alignment length": 70, "Accession of closest sequence": "AAC33908.1", "Name of closest sequence": "organomercurial transporter MerC", "HMM id": null, "HMM description": null, "Hierarchy node": "merC"}, {"Protein identifier": null, "Contig id": "contig_39_polypolish", "Start": 3496, "Stop": 3825, "Strand": "-", "Gene symbol": "qacE", "Sequence name": "quaternary ammonium compound efflux SMR transporter QacE", "Scope": "core", "Element type": "STRESS", "Element subtype": "BIOCIDE", "Class": "QUATERNARY AMMONIUM", "Subclass": "QUATERNARY AMMONIUM", "Method": "EXACTX", "Target length": 110, "Reference sequence length": 110, "% Coverage of reference sequence": 100.0, "% Identity to reference sequence": 100.0, "Alignment length": 110, "Accession of closest sequence": "WP_010890145.1", "Name of closest sequence": "quaternary ammonium compound efflux SMR transporter QacE", "HMM id": null, "HMM description": null, "Hierarchy node": "qacE"}, {"Protein identifier": null, "Contig id": "contig_39_polypolish", "Start": 4010, "Stop": 4327, "Strand": "-", "Gene symbol": "dfrA30", "Sequence name": "trimethoprim-resistant dihydrofolate reductase DfrA30", "Scope": "core", "Element type": "AMR", "Element subtype": "AMR", "Class": "TRIMETHOPRIM", "Subclass": "TRIMETHOPRIM", "Method": "PARTIALX", "Target length": 106, "Reference sequence length": 157, "% Coverage of reference sequence": 67.52, "% Identity to reference sequence": 98.11, "Alignment length": 106, "Accession of closest sequence": "WP_063844408.1", "Name of closest sequence": "trimethoprim-resistant dihydrofolate reductase DfrA30", "HMM id": null, "HMM description": null, "Hierarchy node": "dfrA30"}, {"Protein identifier": null, "Contig id": "contig_40_polypolish", "Start": 632, "Stop": 1258, "Strand": "+", "Gene symbol": "aph(3')-Ia", "Sequence name": "aminoglycoside O-phosphotransferase APH(3')-Ia", "Scope": "core", "Element type": "AMR", "Element subtype": "AMR", "Class": "AMINOGLYCOSIDE", "Subclass": "KANAMYCIN", "Method": "PARTIALX", "Target length": 209, "Reference sequence length": 271, "% Coverage of reference sequence": 77.12, "% Identity to reference sequence": 99.04, "Alignment length": 209, "Accession of closest sequence": "WP_000018329.1", "Name of closest sequence": "aminoglycoside O-phosphotransferase APH(3')-Ia", "HMM id": null, "HMM description": null, "Hierarchy node": "aph(3')-Ia"}, {"Protein identifier": null, "Contig id": "contig_40_polypolish", "Start": 632, "Stop": 1258, "Strand": "+", "Gene symbol": "aph(3')-Ia", "Sequence name": "aminoglycoside O-phosphotransferase APH(3')-Ia", "Scope": "core", "Element type": "AMR", "Element subtype": "AMR", "Class": "AMINOGLYCOSIDE", "Subclass": "KANAMYCIN", "Method": "PARTIALX", "Target length": 209, "Reference sequence length": 271, "% Coverage of reference sequence": 77.12, "% Identity to reference sequence": 99.04, "Alignment length": 209, "Accession of closest sequence": "WP_063842148.1", "Name of closest sequence": "aminoglycoside O-phosphotransferase APH(3')-Ia", "HMM id": null, "HMM description": null, "Hierarchy node": "aph(3')-Ia"}, {"Protein identifier": null, "Contig id": "contig_40_polypolish", "Start": 2574, "Stop": 3359, "Strand": "+", "Gene symbol": "aph(3'')-Ib", "Sequence name": "aminoglycoside O-phosphotransferase APH(3'')-Ib", "Scope": "core", "Element type": "AMR", "Element subtype": "AMR", "Class": "AMINOGLYCOSIDE", "Subclass": "STREPTOMYCIN", "Method": "BLASTX", "Target length": 262, "Reference sequence length": 267, "% Coverage of reference sequence": 98.13, "% Identity to reference sequence": 100.0, "Alignment length": 262, "Accession of closest sequence": "WP_001082319.1", "Name of closest sequence": "aminoglycoside O-phosphotransferase APH(3'')-Ib", "HMM id": null, "HMM description": null, "Hierarchy node": "aph(3'')-Ib"}, {"Protein identifier": null, "Contig id": "contig_40_polypolish", "Start": 3555, "Stop": 4103, "Strand": "+", "Gene symbol": "aph(6)-Id", "Sequence name": "aminoglycoside O-phosphotransferase APH(6)-Id", "Scope": "core", "Element type": "AMR", "Element subtype": "AMR", "Class": "AMINOGLYCOSIDE", "Subclass": "STREPTOMYCIN", "Method": "PARTIALX", "Target length": 183, "Reference sequence length": 278, "% Coverage of reference sequence": 65.83, "% Identity to reference sequence": 98.91, "Alignment length": 183, "Accession of closest sequence": "WP_000480968.1", "Name of closest sequence": "aminoglycoside O-phosphotransferase APH(6)-Id", "HMM id": null, "HMM description": null, "Hierarchy node": "aph(6)-Id"}, {"Protein identifier": null, "Contig id": "contig_40_polypolish", "Start": 3555, "Stop": 4103, "Strand": "+", "Gene symbol": "aph(6)-Id", "Sequence name": "aminoglycoside O-phosphotransferase APH(6)-Id", "Scope": "core", "Element type": "AMR", "Element subtype": "AMR", "Class": "AMINOGLYCOSIDE", "Subclass": "STREPTOMYCIN", "Method": "PARTIALX", "Target length": 183, "Reference sequence length": 278, "% Coverage of reference sequence": 65.83, "% Identity to reference sequence": 98.91, "Alignment length": 183, "Accession of closest sequence": "WP_000480972.1", "Name of closest sequence": "aminoglycoside O-phosphotransferase APH(6)-Id", "HMM id": null, "HMM description": null, "Hierarchy node": "aph(6)-Id"}, {"Protein identifier": null, "Contig id": "contig_40_polypolish", "Start": 3555, "Stop": 4103, "Strand": "+", "Gene symbol": "aph(6)-Id", "Sequence name": "aminoglycoside O-phosphotransferase APH(6)-Id", "Scope": "core", "Element type": "AMR", "Element subtype": "AMR", "Class": "AMINOGLYCOSIDE", "Subclass": "STREPTOMYCIN", "Method": "PARTIALX", "Target length": 183, "Reference sequence length": 278, "% Coverage of reference sequence": 65.83, "% Identity to reference sequence": 98.91, "Alignment length": 183, "Accession of closest sequence": "WP_063842183.1", "Name of closest sequence": "aminoglycoside O-phosphotransferase APH(6)-Id", "HMM id": null, "HMM description": null, "Hierarchy node": "aph(6)-Id"}, {"Protein identifier": null, "Contig id": "contig_41_polypolish", "Start": 100023, "Stop": 100541, "Strand": "-", "Gene symbol": "terD", "Sequence name": "tellurium resistance membrane protein TerD", "Scope": "plus", "Element type": "STRESS", "Element subtype": "METAL", "Class": "TELLURIUM", "Subclass": "TELLURIUM", "Method": "BLASTX", "Target length": 173, "Reference sequence length": 192, "% Coverage of reference sequence": 90.1, "% Identity to reference sequence": 98.84, "Alignment length": 173, "Accession of closest sequence": "AAA98292.1", "Name of closest sequence": "tellurium resistance membrane protein TerD", "HMM id": null, "HMM description": null, "Hierarchy node": "terD"}]}, {"name": "point_mutation_report", "file_path": "tests/data/dummy/amrfinderplus/AMRFinderPlus_Point_mutation_report.tsv", "hid": "12345", "galaxy_id": null, "content": [{"Protein identifier": null, "Contig id": "contig_107_polypolish", "Start": 5, "Stop": 861, "Strand": "-", "Gene symbol": "23S_A2074A", "Sequence name": "Campylobacter 23S ribosomal RNA [WILDTYPE]", "Scope": "core", "Element type": "AMR", "Element subtype": "POINT", "Class": "MACROLIDE", "Subclass": "MACROLIDE", "Method": "POINTN", "Target length": 857, "Reference sequence length": 2912, "% Coverage of reference sequence": 29.36, "% Identity to reference sequence": 81.82, "Alignment length": 869, "Accession of closest sequence": "NC_022347.1:1040292-1037381", "Name of closest sequence": "23S ribosomal RNA", "HMM id": null, "HMM description": null, "Hierarchy node": null}, {"Protein identifier": null, "Contig id": "contig_107_polypolish", "Start": 5, "Stop": 861, "Strand": "-", "Gene symbol": "23S_A2074A", "Sequence name": "Campylobacter 23S ribosomal RNA [WILDTYPE]", "Scope": "core", "Element type": "AMR", "Element subtype": "POINT", "Class": "MACROLIDE", "Subclass": "MACROLIDE", "Method": "POINTN", "Target length": 857, "Reference sequence length": 2912, "% Coverage of reference sequence": 29.36, "% Identity to reference sequence": 81.95, "Alignment length": 870, "Accession of closest sequence": "NC_002163.1:396449-399360", "Name of closest sequence": "23S ribosomal RNA", "HMM id": null, "HMM description": null, "Hierarchy node": null}, {"Protein identifier": null, "Contig id": "contig_107_polypolish", "Start": 5, "Stop": 861, "Strand": "-", "Gene symbol": "23S_A2075A", "Sequence name": "Campylobacter 23S ribosomal RNA [WILDTYPE]", "Scope": "core", "Element type": "AMR", "Element subtype": "POINT", "Class": "MACROLIDE", "Subclass": "MACROLIDE", "Method": "POINTN", "Target length": 857, "Reference sequence length": 2912, "% Coverage of reference sequence": 29.36, "% Identity to reference sequence": 81.82, "Alignment length": 869, "Accession of closest sequence": "NC_022347.1:1040292-1037381", "Name of closest sequence": "23S ribosomal RNA", "HMM id": null, "HMM description": null, "Hierarchy node": null}, {"Protein identifier": null, "Contig id": "contig_107_polypolish", "Start": 5, "Stop": 861, "Strand": "-", "Gene symbol": "23S_A2075A", "Sequence name": "Campylobacter 23S ribosomal RNA [WILDTYPE]", "Scope": "core", "Element type": "AMR", "Element subtype": "POINT", "Class": "MACROLIDE", "Subclass": "MACROLIDE", "Method": "POINTN", "Target length": 857, "Reference sequence length": 2912, "% Coverage of reference sequence": 29.36, "% Identity to reference sequence": 81.95, "Alignment length": 870, "Accession of closest sequence": "NC_002163.1:396449-399360", "Name of closest sequence": "23S ribosomal RNA", "HMM id": null, "HMM description": null, "Hierarchy node": null}, {"Protein identifier": null, "Contig id": "contig_107_polypolish", "Start": 5, "Stop": 861, "Strand": "-", "Gene symbol": "23S_C2627C", "Sequence name": "Campylobacter 23S ribosomal RNA [WILDTYPE]", "Scope": "core", "Element type": "AMR", "Element subtype": "POINT", "Class": "MACROLIDE", "Subclass": "MACROLIDE", "Method": "POINTN", "Target length": 857, "Reference sequence length": 2912, "% Coverage of reference sequence": 29.36, "% Identity to reference sequence": 81.82, "Alignment length": 869, "Accession of closest sequence": "NC_022347.1:1040292-1037381", "Name of closest sequence": "23S ribosomal RNA", "HMM id": null, "HMM description": null, "Hierarchy node": null}, {"Protein identifier": null, "Contig id": "contig_107_polypolish", "Start": 5, "Stop": 861, "Strand": "-", "Gene symbol": "23S_C2627C", "Sequence name": "Campylobacter 23S ribosomal RNA [WILDTYPE]", "Scope": "core", "Element type": "AMR", "Element subtype": "POINT", "Class": "MACROLIDE", "Subclass": "MACROLIDE", "Method": "POINTN", "Target length": 857, "Reference sequence length": 2912, "% Coverage of reference sequence": 29.36, "% Identity to reference sequence": 81.95, "Alignment length": 870, "Accession of closest sequence": "NC_002163.1:396449-399360", "Name of closest sequence": "23S ribosomal RNA", "HMM id": null, "HMM description": null, "Hierarchy node": null}, {"Protein identifier": null, "Contig id": "contig_10_polypolish", "Start": 345, "Stop": 1334, "Strand": "-", "Gene symbol": "23S_A2074A", "Sequence name": "Campylobacter 23S ribosomal RNA [WILDTYPE]", "Scope": "core", "Element type": "AMR", "Element subtype": "POINT", "Class": "MACROLIDE", "Subclass": "MACROLIDE", "Method": "POINTN", "Target length": 990, "Reference sequence length": 2912, "% Coverage of reference sequence": 33.93, "% Identity to reference sequence": 80.56, "Alignment length": 1003, "Accession of closest sequence": "NC_002163.1:396449-399360", "Name of closest sequence": "23S ribosomal RNA", "HMM id": null, "HMM description": null, "Hierarchy node": null}, {"Protein identifier": null, "Contig id": "contig_10_polypolish", "Start": 345, "Stop": 1334, "Strand": "-", "Gene symbol": "23S_A2075A", "Sequence name": "Campylobacter 23S ribosomal RNA [WILDTYPE]", "Scope": "core", "Element type": "AMR", "Element subtype": "POINT", "Class": "MACROLIDE", "Subclass": "MACROLIDE", "Method": "POINTN", "Target length": 990, "Reference sequence length": 2912, "% Coverage of reference sequence": 33.93, "% Identity to reference sequence": 80.56, "Alignment length": 1003, "Accession of closest sequence": "NC_002163.1:396449-399360", "Name of closest sequence": "23S ribosomal RNA", "HMM id": null, "HMM description": null, "Hierarchy node": null}, {"Protein identifier": null, "Contig id": "contig_10_polypolish", "Start": 345, "Stop": 1334, "Strand": "-", "Gene symbol": "23S_C2627C", "Sequence name": "Campylobacter 23S ribosomal RNA [WILDTYPE]", "Scope": "core", "Element type": "AMR", "Element subtype": "POINT", "Class": "MACROLIDE", "Subclass": "MACROLIDE", "Method": "POINTN", "Target length": 990, "Reference sequence length": 2912, "% Coverage of reference sequence": 33.93, "% Identity to reference sequence": 80.56, "Alignment length": 1003, "Accession of closest sequence": "NC_002163.1:396449-399360", "Name of closest sequence": "23S ribosomal RNA", "HMM id": null, "HMM description": null, "Hierarchy node": null}, {"Protein identifier": null, "Contig id": "contig_10_polypolish", "Start": 416, "Stop": 1334, "Strand": "-", "Gene symbol": "23S_A2074A", "Sequence name": "Campylobacter 23S ribosomal RNA [WILDTYPE]", "Scope": "core", "Element type": "AMR", "Element subtype": "POINT", "Class": "MACROLIDE", "Subclass": "MACROLIDE", "Method": "POINTN", "Target length": 919, "Reference sequence length": 2912, "% Coverage of reference sequence": 31.49, "% Identity to reference sequence": 81.1, "Alignment length": 931, "Accession of closest sequence": "NC_022347.1:1040292-1037381", "Name of closest sequence": "23S ribosomal RNA", "HMM id": null, "HMM description": null, "Hierarchy node": null}, {"Protein identifier": null, "Contig id": "contig_10_polypolish", "Start": 416, "Stop": 1334, "Strand": "-", "Gene symbol": "23S_A2075A", "Sequence name": "Campylobacter 23S ribosomal RNA [WILDTYPE]", "Scope": "core", "Element type": "AMR", "Element subtype": "POINT", "Class": "MACROLIDE", "Subclass": "MACROLIDE", "Method": "POINTN", "Target length": 919, "Reference sequence length": 2912, "% Coverage of reference sequence": 31.49, "% Identity to reference sequence": 81.1, "Alignment length": 931, "Accession of closest sequence": "NC_022347.1:1040292-1037381", "Name of closest sequence": "23S ribosomal RNA", "HMM id": null, "HMM description": null, "Hierarchy node": null}, {"Protein identifier": null, "Contig id": "contig_10_polypolish", "Start": 416, "Stop": 1334, "Strand": "-", "Gene symbol": "23S_C2627C", "Sequence name": "Campylobacter 23S ribosomal RNA [WILDTYPE]", "Scope": "core", "Element type": "AMR", "Element subtype": "POINT", "Class": "MACROLIDE", "Subclass": "MACROLIDE", "Method": "POINTN", "Target length": 919, "Reference sequence length": 2912, "% Coverage of reference sequence": 31.49, "% Identity to reference sequence": 81.1, "Alignment length": 931, "Accession of closest sequence": "NC_022347.1:1040292-1037381", "Name of closest sequence": "23S ribosomal RNA", "HMM id": null, "HMM description": null, "Hierarchy node": null}, {"Protein identifier": null, "Contig id": "contig_11_polypolish", "Start": 1319, "Stop": 2308, "Strand": "-", "Gene symbol": "23S_A2074A", "Sequence name": "Campylobacter 23S ribosomal RNA [WILDTYPE]", "Scope": "core", "Element type": "AMR", "Element subtype": "POINT", "Class": "MACROLIDE", "Subclass": "MACROLIDE", "Method": "POINTN", "Target length": 990, "Reference sequence length": 2912, "% Coverage of reference sequence": 33.93, "% Identity to reference sequence": 80.56, "Alignment length": 1003, "Accession of closest sequence": "NC_002163.1:396449-399360", "Name of closest sequence": "23S ribosomal RNA", "HMM id": null, "HMM description": null, "Hierarchy node": null}, {"Protein identifier": null, "Contig id": "contig_11_polypolish", "Start": 1319, "Stop": 2308, "Strand": "-", "Gene symbol": "23S_A2075A", "Sequence name": "Campylobacter 23S ribosomal RNA [WILDTYPE]", "Scope": "core", "Element type": "AMR", "Element subtype": "POINT", "Class": "MACROLIDE", "Subclass": "MACROLIDE", "Method": "POINTN", "Target length": 990, "Reference sequence length": 2912, "% Coverage of reference sequence": 33.93, "% Identity to reference sequence": 80.56, "Alignment length": 1003, "Accession of closest sequence": "NC_002163.1:396449-399360", "Name of closest sequence": "23S ribosomal RNA", "HMM id": null, "HMM description": null, "Hierarchy node": null}, {"Protein identifier": null, "Contig id": "contig_11_polypolish", "Start": 1319, "Stop": 2308, "Strand": "-", "Gene symbol": "23S_C2627C", "Sequence name": "Campylobacter 23S ribosomal RNA [WILDTYPE]", "Scope": "core", "Element type": "AMR", "Element subtype": "POINT", "Class": "MACROLIDE", "Subclass": "MACROLIDE", "Method": "POINTN", "Target length": 990, "Reference sequence length": 2912, "% Coverage of reference sequence": 33.93, "% Identity to reference sequence": 80.56, "Alignment length": 1003, "Accession of closest sequence": "NC_002163.1:396449-399360", "Name of closest sequence": "23S ribosomal RNA", "HMM id": null, "HMM description": null, "Hierarchy node": null}, {"Protein identifier": null, "Contig id": "contig_11_polypolish", "Start": 1390, "Stop": 2308, "Strand": "-", "Gene symbol": "23S_A2074A", "Sequence name": "Campylobacter 23S ribosomal RNA [WILDTYPE]", "Scope": "core", "Element type": "AMR", "Element subtype": "POINT", "Class": "MACROLIDE", "Subclass": "MACROLIDE", "Method": "POINTN", "Target length": 919, "Reference sequence length": 2912, "% Coverage of reference sequence": 31.49, "% Identity to reference sequence": 81.1, "Alignment length": 931, "Accession of closest sequence": "NC_022347.1:1040292-1037381", "Name of closest sequence": "23S ribosomal RNA", "HMM id": null, "HMM description": null, "Hierarchy node": null}, {"Protein identifier": null, "Contig id": "contig_11_polypolish", "Start": 1390, "Stop": 2308, "Strand": "-", "Gene symbol": "23S_A2075A", "Sequence name": "Campylobacter 23S ribosomal RNA [WILDTYPE]", "Scope": "core", "Element type": "AMR", "Element subtype": "POINT", "Class": "MACROLIDE", "Subclass": "MACROLIDE", "Method": "POINTN", "Target length": 919, "Reference sequence length": 2912, "% Coverage of reference sequence": 31.49, "% Identity to reference sequence": 81.1, "Alignment length": 931, "Accession of closest sequence": "NC_022347.1:1040292-1037381", "Name of closest sequence": "23S ribosomal RNA", "HMM id": null, "HMM description": null, "Hierarchy node": null}, {"Protein identifier": null, "Contig id": "contig_11_polypolish", "Start": 1390, "Stop": 2308, "Strand": "-", "Gene symbol": "23S_C2627C", "Sequence name": "Campylobacter 23S ribosomal RNA [WILDTYPE]", "Scope": "core", "Element type": "AMR", "Element subtype": "POINT", "Class": "MACROLIDE", "Subclass": "MACROLIDE", "Method": "POINTN", "Target length": 919, "Reference sequence length": 2912, "% Coverage of reference sequence": 31.49, "% Identity to reference sequence": 81.1, "Alignment length": 931, "Accession of closest sequence": "NC_022347.1:1040292-1037381", "Name of closest sequence": "23S ribosomal RNA", "HMM id": null, "HMM description": null, "Hierarchy node": null}, {"Protein identifier": null, "Contig id": "contig_12_polypolish", "Start": 61, "Stop": 472, "Strand": "-", "Gene symbol": "23S_A2074A", "Sequence name": "Campylobacter 23S ribosomal RNA [WILDTYPE]", "Scope": "core", "Element type": "AMR", "Element subtype": "POINT", "Class": "MACROLIDE", "Subclass": "MACROLIDE", "Method": "POINTN", "Target length": 412, "Reference sequence length": 2912, "% Coverage of reference sequence": 14.08, "% Identity to reference sequence": 82.01, "Alignment length": 417, "Accession of closest sequence": "NC_022347.1:1040292-1037381", "Name of closest sequence": "23S ribosomal RNA", "HMM id": null, "HMM description": null, "Hierarchy node": null}, {"Protein identifier": null, "Contig id": "contig_12_polypolish", "Start": 61, "Stop": 472, "Strand": "-", "Gene symbol": "23S_A2074A", "Sequence name": "Campylobacter 23S ribosomal RNA [WILDTYPE]", "Scope": "core", "Element type": "AMR", "Element subtype": "POINT", "Class": "MACROLIDE", "Subclass": "MACROLIDE", "Method": "POINTN", "Target length": 412, "Reference sequence length": 2912, "% Coverage of reference sequence": 14.08, "% Identity to reference sequence": 82.3, "Alignment length": 418, "Accession of closest sequence": "NC_002163.1:396449-399360", "Name of closest sequence": "23S ribosomal RNA", "HMM id": null, "HMM description": null, "Hierarchy node": null}, {"Protein identifier": null, "Contig id": "contig_12_polypolish", "Start": 61, "Stop": 472, "Strand": "-", "Gene symbol": "23S_A2075A", "Sequence name": "Campylobacter 23S ribosomal RNA [WILDTYPE]", "Scope": "core", "Element type": "AMR", "Element subtype": "POINT", "Class": "MACROLIDE", "Subclass": "MACROLIDE", "Method": "POINTN", "Target length": 412, "Reference sequence length": 2912, "% Coverage of reference sequence": 14.08, "% Identity to reference sequence": 82.01, "Alignment length": 417, "Accession of closest sequence": "NC_022347.1:1040292-1037381", "Name of closest sequence": "23S ribosomal RNA", "HMM id": null, "HMM description": null, "Hierarchy node": null}, {"Protein identifier": null, "Contig id": "contig_12_polypolish", "Start": 61, "Stop": 472, "Strand": "-", "Gene symbol": "23S_A2075A", "Sequence name": "Campylobacter 23S ribosomal RNA [WILDTYPE]", "Scope": "core", "Element type": "AMR", "Element subtype": "POINT", "Class": "MACROLIDE", "Subclass": "MACROLIDE", "Method": "POINTN", "Target length": 412, "Reference sequence length": 2912, "% Coverage of reference sequence": 14.08, "% Identity to reference sequence": 82.3, "Alignment length": 418, "Accession of closest sequence": "NC_002163.1:396449-399360", "Name of closest sequence": "23S ribosomal RNA", "HMM id": null, "HMM description": null, "Hierarchy node": null}, {"Protein identifier": null, "Contig id": "contig_7_polypolish", "Start": 39847, "Stop": 40836, "Strand": "-", "Gene symbol": "23S_A2074A", "Sequence name": "Campylobacter 23S ribosomal RNA [WILDTYPE]", "Scope": "core", "Element type": "AMR", "Element subtype": "POINT", "Class": "MACROLIDE", "Subclass": "MACROLIDE", "Method": "POINTN", "Target length": 990, "Reference sequence length": 2912, "% Coverage of reference sequence": 33.93, "% Identity to reference sequence": 80.56, "Alignment length": 1003, "Accession of closest sequence": "NC_002163.1:396449-399360", "Name of closest sequence": "23S ribosomal RNA", "HMM id": null, "HMM description": null, "Hierarchy node": null}, {"Protein identifier": null, "Contig id": "contig_7_polypolish", "Start": 39847, "Stop": 40836, "Strand": "-", "Gene symbol": "23S_A2075A", "Sequence name": "Campylobacter 23S ribosomal RNA [WILDTYPE]", "Scope": "core", "Element type": "AMR", "Element subtype": "POINT", "Class": "MACROLIDE", "Subclass": "MACROLIDE", "Method": "POINTN", "Target length": 990, "Reference sequence length": 2912, "% Coverage of reference sequence": 33.93, "% Identity to reference sequence": 80.56, "Alignment length": 1003, "Accession of closest sequence": "NC_002163.1:396449-399360", "Name of closest sequence": "23S ribosomal RNA", "HMM id": null, "HMM description": null, "Hierarchy node": null}, {"Protein identifier": null, "Contig id": "contig_7_polypolish", "Start": 39847, "Stop": 40836, "Strand": "-", "Gene symbol": "23S_C2627C", "Sequence name": "Campylobacter 23S ribosomal RNA [WILDTYPE]", "Scope": "core", "Element type": "AMR", "Element subtype": "POINT", "Class": "MACROLIDE", "Subclass": "MACROLIDE", "Method": "POINTN", "Target length": 990, "Reference sequence length": 2912, "% Coverage of reference sequence": 33.93, "% Identity to reference sequence": 80.56, "Alignment length": 1003, "Accession of closest sequence": "NC_002163.1:396449-399360", "Name of closest sequence": "23S ribosomal RNA", "HMM id": null, "HMM description": null, "Hierarchy node": null}, {"Protein identifier": null, "Contig id": "contig_7_polypolish", "Start": 39918, "Stop": 40836, "Strand": "-", "Gene symbol": "23S_A2074A", "Sequence name": "Campylobacter 23S ribosomal RNA [WILDTYPE]", "Scope": "core", "Element type": "AMR", "Element subtype": "POINT", "Class": "MACROLIDE", "Subclass": "MACROLIDE", "Method": "POINTN", "Target length": 919, "Reference sequence length": 2912, "% Coverage of reference sequence": 31.49, "% Identity to reference sequence": 81.1, "Alignment length": 931, "Accession of closest sequence": "NC_022347.1:1040292-1037381", "Name of closest sequence": "23S ribosomal RNA", "HMM id": null, "HMM description": null, "Hierarchy node": null}, {"Protein identifier": null, "Contig id": "contig_7_polypolish", "Start": 39918, "Stop": 40836, "Strand": "-", "Gene symbol": "23S_A2075A", "Sequence name": "Campylobacter 23S ribosomal RNA [WILDTYPE]", "Scope": "core", "Element type": "AMR", "Element subtype": "POINT", "Class": "MACROLIDE", "Subclass": "MACROLIDE", "Method": "POINTN", "Target length": 919, "Reference sequence length": 2912, "% Coverage of reference sequence": 31.49, "% Identity to reference sequence": 81.1, "Alignment length": 931, "Accession of closest sequence": "NC_022347.1:1040292-1037381", "Name of closest sequence": "23S ribosomal RNA", "HMM id": null, "HMM description": null, "Hierarchy node": null}, {"Protein identifier": null, "Contig id": "contig_7_polypolish", "Start": 39918, "Stop": 40836, "Strand": "-", "Gene symbol": "23S_C2627C", "Sequence name": "Campylobacter 23S ribosomal RNA [WILDTYPE]", "Scope": "core", "Element type": "AMR", "Element subtype": "POINT", "Class": "MACROLIDE", "Subclass": "MACROLIDE", "Method": "POINTN", "Target length": 919, "Reference sequence length": 2912, "% Coverage of reference sequence": 31.49, "% Identity to reference sequence": 81.1, "Alignment length": 931, "Accession of closest sequence": "NC_022347.1:1040292-1037381", "Name of closest sequence": "23S ribosomal RNA", "HMM id": null, "HMM description": null, "Hierarchy node": null}, {"Protein identifier": null, "Contig id": "contig_82_polypolish", "Start": 31069, "Stop": 31987, "Strand": "+", "Gene symbol": "23S_A2074A", "Sequence name": "Campylobacter 23S ribosomal RNA [WILDTYPE]", "Scope": "core", "Element type": "AMR", "Element subtype": "POINT", "Class": "MACROLIDE", "Subclass": "MACROLIDE", "Method": "POINTN", "Target length": 919, "Reference sequence length": 2912, "% Coverage of reference sequence": 31.49, "% Identity to reference sequence": 81.1, "Alignment length": 931, "Accession of closest sequence": "NC_022347.1:1040292-1037381", "Name of closest sequence": "23S ribosomal RNA", "HMM id": null, "HMM description": null, "Hierarchy node": null}, {"Protein identifier": null, "Contig id": "contig_82_polypolish", "Start": 31069, "Stop": 31987, "Strand": "+", "Gene symbol": "23S_A2075A", "Sequence name": "Campylobacter 23S ribosomal RNA [WILDTYPE]", "Scope": "core", "Element type": "AMR", "Element subtype": "POINT", "Class": "MACROLIDE", "Subclass": "MACROLIDE", "Method": "POINTN", "Target length": 919, "Reference sequence length": 2912, "% Coverage of reference sequence": 31.49, "% Identity to reference sequence": 81.1, "Alignment length": 931, "Accession of closest sequence": "NC_022347.1:1040292-1037381", "Name of closest sequence": "23S ribosomal RNA", "HMM id": null, "HMM description": null, "Hierarchy node": null}, {"Protein identifier": null, "Contig id": "contig_82_polypolish", "Start": 31069, "Stop": 31987, "Strand": "+", "Gene symbol": "23S_C2627C", "Sequence name": "Campylobacter 23S ribosomal RNA [WILDTYPE]", "Scope": "core", "Element type": "AMR", "Element subtype": "POINT", "Class": "MACROLIDE", "Subclass": "MACROLIDE", "Method": "POINTN", "Target length": 919, "Reference sequence length": 2912, "% Coverage of reference sequence": 31.49, "% Identity to reference sequence": 81.1, "Alignment length": 931, "Accession of closest sequence": "NC_022347.1:1040292-1037381", "Name of closest sequence": "23S ribosomal RNA", "HMM id": null, "HMM description": null, "Hierarchy node": null}, {"Protein identifier": null, "Contig id": "contig_82_polypolish", "Start": 31069, "Stop": 32058, "Strand": "+", "Gene symbol": "23S_A2074A", "Sequence name": "Campylobacter 23S ribosomal RNA [WILDTYPE]", "Scope": "core", "Element type": "AMR", "Element subtype": "POINT", "Class": "MACROLIDE", "Subclass": "MACROLIDE", "Method": "POINTN", "Target length": 990, "Reference sequence length": 2912, "% Coverage of reference sequence": 33.93, "% Identity to reference sequence": 80.56, "Alignment length": 1003, "Accession of closest sequence": "NC_002163.1:396449-399360", "Name of closest sequence": "23S ribosomal RNA", "HMM id": null, "HMM description": null, "Hierarchy node": null}, {"Protein identifier": null, "Contig id": "contig_82_polypolish", "Start": 31069, "Stop": 32058, "Strand": "+", "Gene symbol": "23S_A2075A", "Sequence name": "Campylobacter 23S ribosomal RNA [WILDTYPE]", "Scope": "core", "Element type": "AMR", "Element subtype": "POINT", "Class": "MACROLIDE", "Subclass": "MACROLIDE", "Method": "POINTN", "Target length": 990, "Reference sequence length": 2912, "% Coverage of reference sequence": 33.93, "% Identity to reference sequence": 80.56, "Alignment length": 1003, "Accession of closest sequence": "NC_002163.1:396449-399360", "Name of closest sequence": "23S ribosomal RNA", "HMM id": null, "HMM description": null, "Hierarchy node": null}, {"Protein identifier": null, "Contig id": "contig_82_polypolish", "Start": 31069, "Stop": 32058, "Strand": "+", "Gene symbol": "23S_C2627C", "Sequence name": "Campylobacter 23S ribosomal RNA [WILDTYPE]", "Scope": "core", "Element type": "AMR", "Element subtype": "POINT", "Class": "MACROLIDE", "Subclass": "MACROLIDE", "Method": "POINTN", "Target length": 990, "Reference sequence length": 2912, "% Coverage of reference sequence": 33.93, "% Identity to reference sequence": 80.56, "Alignment length": 1003, "Accession of closest sequence": "NC_002163.1:396449-399360", "Name of closest sequence": "23S ribosomal RNA", "HMM id": null, "HMM description": null, "Hierarchy node": null}]}, {"name": "nucleotide_sequence", "file_path": "tests/data/dummy/amrfinderplus/AMRFinderPlus_Nucleotide_identified_sequences.fasta", "hid": "12345", "galaxy_id": null, "content": [{"Name": "contig_153_polypolish:4412-4645", "Contig id": "contig_153_polypolish", "Start": "4412", "Stop": "4645", "Strand": "-", "Gene symbol": "merE", "Sequence name": "broad-spectrum mercury transporter MerE", "Length": 234, "Sequence": "ATGAACAGCCCAGAGCACTTGCCGTCTGAGACGCACAAACCGATCACCGGCTACTTGTGGGGCGCGCTGGCCGTGCTCACCTGTCCCTGCCATTTGCCGATTCTCGCCATTGTGCTAGCCGGCACGACGGCCGGCGCGTTCATCGGGGAGCACTGGGGTATTGCAGCCCTCACGCTGACCGGCTTGTTTGTCCTGTCTGTGACGCGGCTGCTGCGGGCCTTCAAGGGAAGATCA"}, {"Name": "contig_153_polypolish:7613-7846", "Contig id": "contig_153_polypolish", "Start": "7613", "Stop": "7846", "Strand": "-", "Gene symbol": "merT", "Sequence name": "mercuric transport protein MerT", "Length": 234, "Sequence": "TCTGAACCACAAAACGGGCGCGGCGCGTTCTTCGCCGGTGGGCTGGCCGCCATTCTTGCGTCGGCCTGCTGCCCGGGGCCGCTGGTTTTGATCGCCTTGGGGTTCAGCGGGGCATGGATCGGCAACCTGACGGTGCTGGAACCCTATCGCCCGATCTTCATCGGCGCAGCGCTGGTCGCGCTGCTTTTCGCCCGGCGGCGCATCTACCGCCCGGCGCAAGCCTGCCAAACCGGG"}, {"Name": "contig_160_polypolish:86415-86654", "Contig id": "contig_160_polypolish", "Start": "86415", "Stop": "86654", "Strand": "-", "Gene symbol": "fosA", "Sequence name": "FosA5 family fosfomycin resistance glutathione transferase", "Length": 240, "Sequence": "GCAGTCAGCCAGCTGGCGCCGAGCGTGGCGTTTTATCAGCAGCTGTTGGGCATGACGCTGCACGCCCGCTGGGACAGCGGCGCCTATCTCTCCTGCGGCGATTTGTGGCTGTGCCTGTCGCTGGATCCGCAGCGGCGCATCACCCCGCCGGAGGAGAGCGACTACACCCATTATGCGTTTAGCATTAGCGAGGCGGATTTCGCTAGCTTCGCCGCCCGCCTTGAGGTTGCCGGCGTCAGC"}, {"Name": "contig_30_polypolish:13708-14433", "Contig id": "contig_30_polypolish", "Start": "13708", "Stop": "14433", "Strand": "+", "Gene symbol": "blaCTX-M", "Sequence name": "CTX-M family extended-spectrum class A beta-lactamase", "Length": 726, "Sequence": "AAACTTGCCGAATTAGAGCGGCAGTCGGGAGGCAGACTGGGTGTGGCATTGATTAACACAGCAGATAATTCGCAAATACTTTATCGTGCTGATGAGCGCTTTGCGATGTGCAGCACCAGTAAAGTGATGGCCGCGGCCGCGGTGCTGAAGAAAAGTGAAAGCGAACCGAATCTGTTAAATCAGCGAGTTGAGATCAAAAAATCTGACCTTGTTAACTATAATCCGATTGCGGAAAAGCACGTCAATGGGACGATGTCACTGGCTGAGCTTAGCGCGGCCGCGCTACAGTACAGCGATAACGTGGCGATGAATAAGCTGATTGCTCACGTTGGCGGCCCGGCTAGCGTCACCGCGTTCGCCCGACAGCTGGGAGACGAAACGTTCCGTCTCGACCGTACCGAGCCGACGTTAAACACCGCCATTCCGGGCGATCCGCGTGATACCACTTCACCTCGGGCAATGGCGCAAACTCTGCGGAATCTGACGCTGGGTAAAGCATTGGGCGACAGCCAACGGGCGCAGCTGGTGACATGGATGAAAGGCAATACCACCGGTGCAGCGAGCATTCAGGCTGGACTGCCTGCTTCCCGGGTTGTGGGGGATAAAACCGGCAGCGGTGGCTATGGCACCACCAACGATATCGCGGTGATCTGGCCAAAGATCGTGCGCCGCTGATTCTGGTCACTTACTTCACCCAGCCTCAACCTAAGGCAGAAAGCCGTCGCG"}, {"Name": "contig_30_polypolish:17856-18287", "Contig id": "contig_30_polypolish", "Start": "17856", "Stop": "18287", "Strand": "+", "Gene symbol": "merR", "Sequence name": "mercury resistance transcriptional regulator MerR", "Length": 432, "Sequence": "ATGGAAAATAATTTGGAAAACCTGACCATTGGCGTTTTTGCCAAGGCGGCCGGGGTCAACGTGGAGACAATCCGCTTCTATCAGCGCAAGGGCCTGTTGCGGGAACCGGACAAGCCTTACGGCAGCATCCGCCGCTATGGGGAGGCGGACGTGGTTCGGGTGAAATTCGTGAAATCGGCACAGCGGCTGGGGTTCAGTCTGGACGAGATTGCCGAGCTGTTGCGGCTCGACGATGGCACCCACTGCGAGGAGGCCAGCAGCCCGGCCGAACACAAGCTCAAGGACGTGCGCGAGAAGATGGCCGACTTGGCGCGCATGGAAACCGTGCTGTCTGAACTCGTGTGCGCCTGCCATGCACGCAAGGGGAATGTTTCCTGCCCGTTGATCGCGTCACTACAGGGCGAAGCAGGCCCGGCAAGGTCAGCTATGCCT"}, {"Name": "contig_30_polypolish:20698-21348", "Contig id": "contig_30_polypolish", "Start": "20698", "Stop": "21348", "Strand": "+", "Gene symbol": "catA1", "Sequence name": "type A-1 chloramphenicol O-acetyltransferase", "Length": 651, "Sequence": "GAAAAAATCACTGGATATACCACCGTTGATATATCCCAATGGCATCGTAAAGAACATTTTGAGGCATTTCAGTCAGTTGCTCAATGTACCTATAACCAGACCGTTCAGCTGGATATTACGGCCTTTTTAAAGACCGTAAAGAAAAATAAGCACAAGTTTTATCCGGCCTTTATTCACATTCTTGCCCGCCTGATGAATGCTCATCCGGAATTCCGTATGGCAATGAAAGACGGTGAGCTGGTGATATGGGATAGTGTTCACCCTTGTTACACCGTTTTCCATGAGCAAACTGAAACGTTTTCATCGCTCTGGAGTGAATACCACGACGATTTCCGGCAGTTTCTACACATATATTCGCAAGATGTGGCGTGTTACGGTGAAAACCGGCCTATTTCCCTAAAGGGTTTATTGAGAATATGTTTTTCGTCTCAGCCAATCCCACGGGTGAGTTTCACCAGTTTTGATTTAAACGTGGCCAATATGGACAACTTCTTCGCCCCCGTTTTCACCATGGGCAAATATTATACGCAAGGCGACAAGGTGCTGATGCCGCTGGCGATTCAGGTTCATCATGCCGTTTGTGATGGCTTCCATGTCGGCAGAATGCTTAATGAATTACAACAGTACTGCGATGAGTGGCAGGGCGGGGCG"}, {"Name": "contig_30_polypolish:3018-3344", "Contig id": "contig_30_polypolish", "Start": "3018", "Stop": "3344", "Strand": "+", "Gene symbol": "merR", "Sequence name": "mercury resistance transcriptional regulator MerR", "Length": 327, "Sequence": "TTTGCCAAGGCGGCCGGGGTCAACGTGGAGACAATCCGCTTCTATCAGCGCAAGGGCCTGTTGCGGGAACCGGACAAGCCTTACGGCGGCATCCGCCGCTATGGGGAGGCGGACGTGGTTCGGGTGAAATTCGTGAAATCGGCACAGCGGCTGGGGTTCAGTCTGGACGAGATTGCCGAGCTGTTGCGGCTCGACGATGGCACCCACTGCGAGGAGGCCAGCAGCTTGGCCGAACACAAGCTCAAGGACGTGCGCGAGAAGATGGCCGACTTGGCGCGCATGGAAACCGTGCTGTCTGAACTCGTGTGCGCCTGCCATGCACGAAGG"}, {"Name": "contig_30_polypolish:5821-6243", "Contig id": "contig_30_polypolish", "Start": "5821", "Stop": "6243", "Strand": "+", "Gene symbol": "catA1", "Sequence name": "type A-1 chloramphenicol O-acetyltransferase", "Length": 423, "Sequence": "GAAAAAATCACTGGATATACCACCGTTGATATATCCCAATGGCATCGTAAAGAACATTTTGAGGCATTTCAGTCAGTTGCTCAATGTACCTATAACCAGACCGTTCAGCTGGATATTACGGCCTTTTTAAAGACCGTAAAGAAAAATAAGCACAAGTTTTATCCGGCCTTTATTCACATTCTTGCCCGCCTGATGAATGCTCATCCGGAATTCCGTATGGCAATGAAAGACGGTGAGCTGGTGATATGGGATAGTGTTCACCCTTGTTACACCGTTTTCCATGAGCAAACTGAAACGTTTTCATCGCTCTGGAGTGAATACCACGACGATTTCCGGCAGTTTCTACACATATATTCGCAAGATGTGGCGTGTTACGGTGAAAACACGGCCTATTTCCCTAAAGGGTTTATTGAGAATATGTTT"}, {"Name": "contig_35_polypolish:4787-5644", "Contig id": "contig_35_polypolish", "Start": "4787", "Stop": "5644", "Strand": "-", "Gene symbol": "aac(3)-IIe", "Sequence name": "aminoglycoside N-acetyltransferase AAC(3)-IIe", "Length": 858, "Sequence": "ATGCATACGCGGAAGGCAATAACGGAGGCAATTCGAAAATTAGGAGTCCAAACCGGTGACCTGTTGATGGTGCATGCCTCACTTAAAGCGATTGGTCCGGTCGAAGGAGGAGCGGAGACGGTCGTTGCCGCGTTACGCTCCGCGGTTGGGCCGACTGGCACTGTGATGGGATACGCGTCGTGGGACCGATCACCCTACGAGGAGACTCTGAATGGCGCTCGGTTGGATGACAAAGCCCGCCGTACCTGGCCGCCGTTCGATCCCGCAACGGCCGGGACTTACCGTGGGTTCGGCCTGCTGAATCAATTTCTGGTTCAAGCCCCCGGCGCGCGGCGCAGCGCGCACCCCGATGCATCGATGGTCGCGGTTGGTCCGCTAGCTGAAACGCTGACGGAGCCTCACGAACTCGGTCACGCCTTGGGGGAAGGGTCGCCCGTCGAGCGGTTCGTCCGCCTTGGCGGGAAGGCCCTGCTGTTGGGTGCGCCGCTAAACTCCGTTACCGCATTGCACTACGCCGAGGCGGTTGCGGATATCCCCAACAAACGATGGGTGACGTATGAGATGCCGATGCTTGGAAGAAACGGTGAAGTCGCCTGGAAAACGGCATCAGAATACGATTCAAACGGCATTCTCGATTGCTTTGCTATCGAAGGAAAGCCGGATGCGGTCGAAACTATAGCAAATGCTTACGTGAAGCTCGGTCGCCATCGAGAAGGTGTCGTGGGCTTTGCTCAGTGCTACCTGTTCGACGCGCAGGACATCGTGACGTTCGGCGTCACCTATCTTGAGAAGCACTTCGGAGCCACTCCGATCGTGCCAGCACACGAAGCCGCCCAGCGCTCTTGCGAGCCTTCCGGT"}, {"Name": "contig_36_polypolish:9168-9608", "Contig id": "contig_36_polypolish", "Start": "9168", "Stop": "9608", "Strand": "+", "Gene symbol": "blaSHV", "Sequence name": "SHV family class A beta-lactamase", "Length": 441, "Sequence": "ATGCGTTATATTCGCCTGTGTATTATCTCCCTGTTAGCCACCCTGCCGCTGGCGGTACACGCCAGCCCGCAGCCGCTTGAGCAAATTAAACAAAGCGAAAGCCAGCTGTCGGGCCGCGTAGGCATGATAGAAATGGATCTGGCCAGCGGCCGCACGCTGACCGCCCGGCGCGCCGATGAACGCTTTCCCATGATGAGCACCTTTAAAGTAGTGCTCTGCGGCGCAGTGCTGGCGCGGGTGGATGCCGGTGACGAACAGCTGGAGCGAAAGATCCACTATCGCCAGCAGGATCTGGTGGACTACTCGCCGGTCAGCGAAAAACACCTTGCCGACGGCATGACGGTCGGCGAACTCTGCGCCGCCGCCATTACCATGAGCGATAACAGCGCCGCCAATCTGCTGCTGGCCACCGTCGGCGGCCCCGCAGGATTGACTGCCTTT"}, {"Name": "contig_36_polypolish:9587-10024", "Contig id": "contig_36_polypolish", "Start": "9587", "Stop": "10024", "Strand": "+", "Gene symbol": "blaSHV", "Sequence name": "SHV family class A beta-lactamase", "Length": 438, "Sequence": "CCCCGCAGGATTGACTGCCTTTTGCGCCAGATCGGCGACAACGTCACCCGCCTTGACCGCTGGGAAACGGAACTGAATGAGGCGCTTCCCGGCGACGCCCGCGACACCACTACCCCGGCCAGCATGGCCGCGACCCTGCGCAAGCTGCTGACCAGCCAGCGTCTGAGCGCCCGTTCGCAACGGCAGCTGCTGCAGTGGATGGTGGACGATCGGGTCGCCGGACCGTTGATCCGCTCCGTGCTGCCGGCGGGCTGGTTTATCGCCGATAAGACCGGAGCTAGCAAGCGGGGTGCGCGCGGGATTGTCGCCCTGCTTGGCCCGAATAACAAAGCAGAGCGCATTGTGGTGATTTATCTGCGGGATACGCCGGCGAGCATGGCCGAGCGAAATCAGCAAATCGCCGGGATCGGCGCGGCGCTGATCGAGCACTGGCAACGC"}, {"Name": "contig_37_polypolish:18-569", "Contig id": "contig_37_polypolish", "Start": "18", "Stop": "569", "Strand": "+", "Gene symbol": "aac(6')-Ib3", "Sequence name": "aminoglycoside N-acetyltransferase AAC(6')-Ib3", "Length": 552, "Sequence": "GTGACCAACAGCAACGATTCCGTCACACTGCGCCTCATGACTGAGCATGACCTTGCGATGCTCTATGAGTGGCTAAATCGATCTCATATCGTCGAGTGGTGGGGCGGAGAAGAAGCACGCCCGACACTTGCTGACGTACAGGAACAGTACTTGCCAAGCGTTTTAGCGCAAGAGTCCGTCACTCCATACATTGCAATGCTGAATGGAGAGCCGATTGGGTATGCCCAGTCGTACGTTGCTCTTGGAAGCGGGGACGGATGGTGGGAAGAAGAAACCGATCCAGGAGTACGCGGAATAGACCAGTTACTGGCGAATGCATCACAACTGGGCAAAGGCTTGGGAACCAAGCTGGTTCGAGCTCTGGTTGAGTTGCTGTTCAATGATCCCGAGGTCACCAAGATCCAAACGGACCCGTCGCCGAGCAACTTGCGAGCGATCCGATGCTACGAGAAAGCGGGGTTTGAGAGGCAAGGTACCGTAACCACCCCAGATGGTCCAGCCGTGTACATGGTTCAAACACGCCAGGCATTCGAGCGAACACGCAGTGATGCC"}, {"Name": "contig_37_polypolish:3006-3863", "Contig id": "contig_37_polypolish", "Start": "3006", "Stop": "3863", "Strand": "+", "Gene symbol": "blaTEM-1", "Sequence name": "broad-spectrum class A beta-lactamase TEM-1", "Length": 858, "Sequence": "ATGAGTATTCAACATTTTCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGTGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCTGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGG"}, {"Name": "contig_37_polypolish:642-1424", "Contig id": "contig_37_polypolish", "Start": "642", "Stop": "1424", "Strand": "+", "Gene symbol": "aadA1", "Sequence name": "ANT(3'')-Ia family aminoglycoside nucleotidyltransferase AadA1", "Length": 783, "Sequence": "ATGAGGGAAGCGGTGATCGCCGAAGTATCGACTCAACTATCAGAGGTAGTTGGCGTCATCGAGCGCCATCTCGAACCGACGTTGCTGGCCGTACATTTGTACGGCTCCGCAGTGGATGGCGGCCTGAAGCCACACAGTGATATTGATTTGCTGGTTACGGTGACCGTAAGGCTTGATGAAACAACGCGGCGAGCTTTGATCAACGACCTTTGGAAACTTCGGCTTCCCGGAGAGAGCGAGATTCTCCGCGCTGTAGAAGTCACCATTGTTGTGCACGACGACATCATTCCGTGGCGTTATCCAGCTAAGCGCGAACTGCAATTTGGAGAATGGCAGCGCAATGACATTCTTGCAGGTATCTTCGAGCCAGCCACGATCGACATTGATCTGGCTATCTTGCTGACAAAAGCAAGAGAACATAGCGTTGCCTTGGTAGGTCCAGCGGCGGAGGAACTCTTTGATCCGGTTCCTGAACAGGATCTATTTGAGGCGCTAAATGAAACCTTAACGCTATGGAACTCGCCGCCCGACTGGGCTGGCGATGAGCGAAATGTAGTGCTTACGTTGTCCCGCATTTGGTACAGCGCAGTAACCGGCAAAATCGCGCCGAAGGATGTCGCTGCCGACTGGGCAATGGAGCGCCTGCCGGCCCAGTATCAGCCCGTCATACTTGAAGCTAGGCAGGCTTATCTTGGACAAGAAGATCGCTTGGCCTCGCGCGCAGATCAGTTGGAAGAATTTGTTCACTACGTGAAAGGCGAGATCACCAAGGTAGTCGGCAAA"}, {"Name": "contig_37_polypolish:8924-9133", "Contig id": "contig_37_polypolish", "Start": "8924", "Stop": "9133", "Strand": "-", "Gene symbol": "merC", "Sequence name": "organomercurial transporter MerC", "Length": 210, "Sequence": "CTTGAGCCAGTACGAGGACTGTTCATCAGCCGCCTGCTGCCGCTGTTTGCCGCGCTGGCCTTCTCGGCGAACGCGCTGGGTTGGTTCAGTCATCGGCAATGGCTGCGCAGTCTGCTCGGCATGATCGGCCCGGCCATCGTGTTTGCGGCCACGGTCTGGCTGCTCGGCAACTGGTGGACGGCGAACCTGATGTACGTCGGCACCGGCCTT"}, {"Name": "contig_39_polypolish:3496-3825", "Contig id": "contig_39_polypolish", "Start": "3496", "Stop": "3825", "Strand": "-", "Gene symbol": "qacE", "Sequence name": "quaternary ammonium compound efflux SMR transporter QacE", "Length": 330, "Sequence": "ATGAAAGGCTGGCTTTTTCTTGTTATCGCAATAGTTGGCGAAGTAATCGCAACATCCGCATTAAAATCTAGCGAGGGCTTTACTAAGCTTGCCCCTTCCGCCGTTGTCATAATCGGTTATGGCATCGCATTTTATTTTCTTTCTCTGGTTCTGAAATCCATCCCTGTCGGTGTTGCTTATGCAGTCTGGTCGGGACTCGGCGTCGTCATAATTACAGCCATTGCCTGGTTGCTTCATGGGCAAAAGCTTGATGCGTGGGGCTTTGTAGGTATGGGGCTCATAGTTAGTGGTGTAGTAGTTTTAAACTTGCTTTCCAAAGCAAGTGCCCAC"}, {"Name": "contig_39_polypolish:4010-4327", "Contig id": "contig_39_polypolish", "Start": "4010", "Stop": "4327", "Strand": "-", "Gene symbol": "dfrA30", "Sequence name": "trimethoprim-resistant dihydrofolate reductase DfrA30", "Length": 318, "Sequence": "GGGGCGCTCCCCAATAGGAAATACGCGGTCGTTACTCGCTCAGCTCGGACGGCCAATAATGACAACGTAGTAGTATTCCCGTCGATCGAAGAGGCCATGGGCGGTCTAGCTAAACTCACCGGTCACGTTATAGTGTCTGGTGGCGGGGAGATTTACAGAGAAACGTTGCCCATGGCCTCTACGCTCCATGTATCGACGATCGACATTGAGCCAGAAGGGGATGTTTTCTTCCCGAATATTCCCAACTTCTTCGAAGTTGTTTTTGAGCAACATTTTAGTTCAAACATTAACTATTGCTATCAAATTTGGAAAAAGGGT"}, {"Name": "contig_40_polypolish:2574-3359", "Contig id": "contig_40_polypolish", "Start": "2574", "Stop": "3359", "Strand": "+", "Gene symbol": "aph(3'')-Ib", "Sequence name": "aminoglycoside O-phosphotransferase APH(3'')-Ib", "Length": 786, "Sequence": "ATATTTTTTGGTGAATCGCATTCTGACTGGTTGCCTGTCAGAGGCGGAGAATCTGGTGATTTTGTTTTTCGACGTGGTGACGGGCATGCCTTCGCGAAAATCGCACCTGCTTCCCGCCGCGGTGAGCTCGCTGGAGAGCGTGACCGCCTCATTTGGCTCAAAGGTCGAGGTGTGGCTTGCCCCGAGGTGATCAACTGGCAGGAGGAACAGGAGGGTGCATGCTTGGTGATAACGGCAATTCCGGGAGTACCGGCGGCTGATCTGTCTGGAGCGGATTTGCTCAAAGCGTGGCCGTCAATGGGGCAGCAACTTGGCGCTGTTCACAGCCTATCGGTTGATCAATGTCCGTTTGAGCGCAGGCTGTCGCGAATGTTCGGACGCGCCGTTGATGTGGTGTCCCGCAATGCCGTCAATCCCGACTTCTTACCGGACGAGGACAAGAGTACGCCGCAGCTCGATCTTTTGGCTCGTGTCGAACGAGAGCTACCGGTGCGGCTCGACCAAGAGCGCACCGATATGGTTGTTTGCCATGGTGATCCCTGCATGCCGAACTTCATGGTGGACCCTAAAACTCTTCAATGCACGGGTCTGATCGACCTTGGGCGGCTCGGAACAGCAGATCGCTATGCCGATTTGGCACTCATGATTGCTAACGCCGAAGAGAACTGGGCAGCGCCAGATGAAGCAGAGCGCGCCTTCGCTGTCCTATTCAATGTATTGGGGATCGAAGCCCCCGACCGCGAACGCCTTGCCTTCTATCTGCGATTGGACCCTCTGACTTGGGGT"}, {"Name": "contig_40_polypolish:3555-4103", "Contig id": "contig_40_polypolish", "Start": "3555", "Stop": "4103", "Strand": "+", "Gene symbol": "aph(6)-Id", "Sequence name": "aminoglycoside O-phosphotransferase APH(6)-Id", "Length": 549, "Sequence": "GGAGCAGTCCGGTTGCTCGGTCGTGAGAACAATCTGATGTTGCTCGAATATGCCGGGGAGCGAATGCTCTCTCACATCGTTGCCGAGCACGGCGACTACCGAGCGACCGAAATTGCAGCGGAACTAATGGCGAAGCTGTATGCCGCATCTGAGGAACCCCTGCCTTCTGCCCTTCTCCCGATCCGGGATCGCTTTGCAGCTTTGTTTCAGCGGGCGCGCGATGATCAAAACGCAGGTTGTCAAACTGACTACGTCCACGCGGCGATTATAGCCGATCAAATGATGAGCAATGCCTCGGAACTGCGTGGGCTACATGGCGATCTGCATCATGAAAACATCATGTTCTCCAGTCGCGGCTGGCTGGTGATAGATCCCGTCGGTCTGGTCGGTGAAGTGGGCTTTGGCGCCGCCAATATGTTCTACGATCCGGCTGACAGAGACGACCTTTGTCTCGATCCTAGACGCATTGCACAGATGGCGGACGCATTCTCTCGTGCGCTGGACGTCGATCCGCGTCGCCTGCTCGACCGTGCGTACGCTTATGGGTGC"}, {"Name": "contig_40_polypolish:632-1258", "Contig id": "contig_40_polypolish", "Start": "632", "Stop": "1258", "Strand": "+", "Gene symbol": "aph(3')-Ia", "Sequence name": "aminoglycoside O-phosphotransferase APH(3')-Ia", "Length": 627, "Sequence": "ATGAGCCATATTCAACGGGAAACGTCTTGCTCGAGGCCGCGATTAAATTCCAACATGGATGCTGATTTATATGGGTATAAATGGGCTCGCGATAATGTCGGGCAATCAGGTGCGACAATCTATCGATTGTATGGGAAGCCCGATGCGCCAGAGTTGTTTCTGAAACATGGCAAAGGTAGCGTTGCCAATGATGTTACAGATGAGATGGTCAGACTAAACTGGCTGACGGAATTTATGCCTCTTCCGACCATCAAGCATTTTATCCGTACTCCTGATGATGCATGGTTACTCACCACTGCGATCCCCGGGAAAACAGCATTCCGGGTATTAGAAGAATATCCTGATTCAGGTGAAAATATTGTTGATGCGCTGGCAGTGTTCCTGCGCCGGTTGCATTCGATTCCTGTTTGTAATTGTCCTTTTAACAACGATCGCGTATTTCGTCTCGCTCAGGCGCAATCACGAATGAATAACGGTTTGGTTGATGCGAGTGATTTTGATGACGAGCGTAATGGCTGGCCTGTTGAACAAGTCTGGAAAGAAATGCATAAGCTTTTGCCATTCTCACCGGATTCAGTCGTCACTCATGGTGATTTCTCACTTGATAACCTTATTTTTGACGAGGGA"}, {"Name": "contig_41_polypolish:100023-100541", "Contig id": "contig_41_polypolish", "Start": "100023", "Stop": "100541", "Strand": "-", "Gene symbol": "terD", "Sequence name": "tellurium resistance membrane protein TerD", "Length": 519, "Sequence": "ATGAGCGTTTCACTATCTAAAGGCGGCAACGTTTCCCTGAGCAAAACCGCGCCAAGCATGAAAAACGTGCTGGTTGGCCTTGGCTGGGATGCACGTTCTACGGACGGTCAGGACTTTGACCTCGATGCTTCCGCATTTCTGCTGGCAGCCAATGGCAAGGTTCGTGGCGATGCAGATTTCATTTTCTATAACAACCTGAAATCTGCTGATGGTTCCGTTACTCATACCGGTGATAACCGTACCGGTGAAGGTGATGGCGACGATGAATCCCTCAAAATCAAACTGGACGCGGTACACGGGGATGTCGACAAAATTATTTTCGTTGTCACTATCCATGATGCTCAGGCTCGTCGCCAGAGCTTCGGTCAGGTTTCCGGCGCATTTATCCGTCTGGTGAATGATGACAATCAGACTGAAGTTGCTCGCTACGATCTGACAGAAGACGCTTCTACTGAAACTGCCATGCTGTTTGGGGAGCTGTATCGTCACAACGGAGAATGGAAATTCCGTGCGGTTGGC"}]}], "tool_has_database": true}]
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