Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C2415
  Reference Plasmid   1111525849768046_bin.37__k141_197385
  Reference Plasmid Size   5195
  Reference Plasmid GC Content   0.33
  Reference Plasmid Mobility Type   non-mobilizable





Mutation sites in the plasmid cluster


The table lists mutations identified in the plasmid cluster.
Note: Mutations identified in this plasmid cluster are listed below. Click on a mutation ID to view full details..

mutid gname pos count tissue frequnt biotype consequence impact nucchange aachange
M0123772 JODLKLMF_00001 47 3 Oral 0.30 protein_coding upstream_gene_variant MODIFIER -31C>T None
M0123773 JODLKLMF_00001 65 4 Oral 0.40 protein_coding upstream_gene_variant MODIFIER -13G>A None
M0123774 JODLKLMF_00001 68 3 Oral 0.30 protein_coding upstream_gene_variant MODIFIER -10C>A None
M0123775 JODLKLMF_00001 71 3 Oral 0.30 protein_coding upstream_gene_variant MODIFIER -7A>C None
M0123776 JODLKLMF_00001 416 5 Oral 0.50 protein_coding synonymous_variant LOW 339T>A Pro113Pro
M0123777 JODLKLMF_00001 470 4 Oral 0.40 protein_coding synonymous_variant LOW 393T>A Leu131Leu
M0123778 JODLKLMF_00001 473 4 Oral 0.40 protein_coding synonymous_variant LOW 396A>G Val132Val
M0123779 JODLKLMF_00001 548 5 Oral 0.50 protein_coding missense_variant MODERATE 471T>G Asp157Glu
M0123780 JODLKLMF_00001 671 4 Oral 0.40 protein_coding synonymous_variant LOW 594A>G Val198Val
M0123781 JODLKLMF_00001 701 6 Oral 0.60 protein_coding synonymous_variant LOW 624A>T Gly208Gly
M0123782 JODLKLMF_00001 890 6 Oral 0.60 protein_coding synonymous_variant LOW 813A>G Lys271Lys
M0123783 JODLKLMF_00001 980 5 Oral 0.50 protein_coding synonymous_variant LOW 903T>C Asp301Asp
M0123784 JODLKLMF_00001 1025 5 Oral 0.50 protein_coding synonymous_variant LOW 948T>A Pro316Pro
M0123785 JODLKLMF_00002 1509 5 Oral 0.50 protein_coding synonymous_variant LOW 300A>G Ser100Ser
M0123786 JODLKLMF_00002 1527 3 Oral 0.30 protein_coding synonymous_variant LOW 318A>G Lys106Lys
M0123787 JODLKLMF_00002 1536 3 Oral 0.30 protein_coding synonymous_variant LOW 327C>T Phe109Phe
M0123788 JODLKLMF_00002 1539 3 Oral 0.30 protein_coding synonymous_variant LOW 330C>T Pro110Pro
M0123789 JODLKLMF_00002 1560 3 Oral 0.30 protein_coding synonymous_variant LOW 351T>G Ala117Ala
M0123790 JODLKLMF_00002 1578 3 Oral 0.30 protein_coding synonymous_variant LOW 369T>A Leu123Leu
M0123791 JODLKLMF_00002 1653 5 Oral 0.50 protein_coding synonymous_variant LOW 444A>T Ile148Ile
M0123792 JODLKLMF_00002 1713 5 Oral 0.50 protein_coding synonymous_variant LOW 504C>T Phe168Phe
M0123793 JODLKLMF_00002 1725 5 Oral 0.50 protein_coding synonymous_variant LOW 516T>C His172His
M0123794 JODLKLMF_00002 1849 3 Oral 0.30 protein_coding missense_variant MODERATE 640G>T Ala214Ser
M0123795 JODLKLMF_00002 1857 3 Oral 0.30 protein_coding synonymous_variant LOW 648T>C Thr216Thr
M0123796 JODLKLMF_00002 1858 7 Oral 0.70 protein_coding synonymous_variant LOW 649C>T Leu217Leu
M0123797 JODLKLMF_00002 1860 3 Oral 0.30 protein_coding synonymous_variant LOW 651A>G Leu217Leu
M0123798 JODLKLMF_00002 1911 4 Oral 0.40 protein_coding synonymous_variant LOW 702A>T Gly234Gly
M0123799 JODLKLMF_00002 2034 3 Oral 0.30 protein_coding synonymous_variant LOW 825T>C Ile275Ile
M0123800 JODLKLMF_00002 2214 3 Oral 0.30 protein_coding synonymous_variant LOW 1005T>C Asp335Asp
M0123801 JODLKLMF_00002 2215 3 Oral 0.30 protein_coding synonymous_variant LOW 1006C>T Leu336Leu
M0123802 JODLKLMF_00002 2238 3 Oral 0.30 protein_coding synonymous_variant LOW 1029G>A Leu343Leu
M0123803 JODLKLMF_00002 2340 6 Oral 0.60 protein_coding synonymous_variant LOW 1131G>A Ala377Ala
M0123804 JODLKLMF_00002 2373 6 Oral 0.60 protein_coding synonymous_variant LOW 1164A>T Gly388Gly
M0123805 JODLKLMF_00002 2376 3 Oral 0.30 protein_coding synonymous_variant LOW 1167G>T Val389Val
M0123806 JODLKLMF_00003 2504 6 Oral 0.60 protein_coding synonymous_variant LOW 27C>T His9His
M0123807 JODLKLMF_00003 2540 3 Oral 0.30 protein_coding synonymous_variant LOW 63A>G Gly21Gly
M0123808 JODLKLMF_00003 2671 6 Oral 0.60 protein_coding missense_variant MODERATE 194A>G Asn65Ser
M0123809 JODLKLMF_00003 2693 4 Oral 0.40 protein_coding synonymous_variant LOW 216G>A Glu72Glu
M0123810 JODLKLMF_00003 2711 3 Oral 0.30 protein_coding synonymous_variant LOW 234T>C Val78Val
M0123811 JODLKLMF_00003 2913 3 Oral 0.30 protein_coding synonymous_variant LOW 436T>C Leu146Leu
M0123812 JODLKLMF_00003 2945 3 Oral 0.30 protein_coding synonymous_variant LOW 468T>G Thr156Thr
M0123813 JODLKLMF_00003 2985 3 Oral 0.30 protein_coding synonymous_variant LOW 508C>T Leu170Leu
M0123814 JODLKLMF_00003 3032 3 Oral 0.30 protein_coding synonymous_variant LOW 555G>A Gly185Gly
M0123815 JODLKLMF_00004 3039 3 Oral 0.30 protein_coding upstream_gene_variant MODIFIER -7T>A None
M0123816 JODLKLMF_00004 3262 4 Oral 0.40 protein_coding missense_variant MODERATE 217G>A Ala73Thr
M0123817 JODLKLMF_00004 3291 4 Oral 0.40 protein_coding synonymous_variant LOW 246A>T Ile82Ile
M0123818 JODLKLMF_00004 3345 4 Oral 0.40 protein_coding synonymous_variant LOW 300G>A Glu100Glu
M0123819 JODLKLMF_00004 3582 3 Oral 0.30 protein_coding synonymous_variant LOW 537A>G Leu179Leu
M0123820 JODLKLMF_00001 3794 3 Oral 0.30 protein_coding downstream_gene_variant MODIFIER *2733T>C None
M0123821 JODLKLMF_00005 3917 3 Oral 0.30 protein_coding synonymous_variant LOW 453C>T Asn151Asn
M0123822 JODLKLMF_00005 3971 3 Oral 0.30 protein_coding synonymous_variant LOW 399G>C Gly133Gly
M0123823 JODLKLMF_00005 4019 3 Oral 0.30 protein_coding missense_variant MODERATE 351G>T Glu117Asp
M0123824 JODLKLMF_00005 4082 3 Oral 0.30 protein_coding synonymous_variant LOW 288C>T Ile96Ile
M0123825 JODLKLMF_00005 4131 3 Oral 0.30 protein_coding missense_variant MODERATE 239C>T Ala80Val
M0123826 JODLKLMF_00005 4157 3 Oral 0.30 protein_coding synonymous_variant LOW 213A>G Leu71Leu
M0123827 JODLKLMF_00005 4208 3 Oral 0.30 protein_coding synonymous_variant LOW 162A>G Glu54Glu
M0123828 JODLKLMF_00005 4277 3 Oral 0.30 protein_coding synonymous_variant LOW 93C>T Ser31Ser
M0123829 JODLKLMF_00005 4332 3 Oral 0.30 protein_coding missense_variant MODERATE 38C>T Thr13Ile
M0123830 JODLKLMF_00005 4362 3 Oral 0.30 protein_coding missense_variant MODERATE 8T>C Ile3Thr
M0123831 JODLKLMF_00005 4386 3 Oral 0.30 protein_coding upstream_gene_variant MODIFIER -17A>C None
M0123832 JODLKLMF_00005 4405 4 Oral 0.40 protein_coding upstream_gene_variant MODIFIER -36G>A None
M0123833 JODLKLMF_00005 4443 4 Oral 0.40 protein_coding upstream_gene_variant MODIFIER -74C>T None
M0123834 JODLKLMF_00005 4444 4 Oral 0.40 protein_coding upstream_gene_variant MODIFIER -75A>C None
M0123835 JODLKLMF_00005 4445 4 Oral 0.40 protein_coding upstream_gene_variant MODIFIER -76G>A None
M0123836 JODLKLMF_00005 4451 4 Oral 0.40 protein_coding upstream_gene_variant MODIFIER -82G>C None
M0123837 JODLKLMF_00005 4460 4 Oral 0.40 protein_coding upstream_gene_variant MODIFIER -91A>T None
M0123838 JODLKLMF_00005 4478 4 Oral 0.40 protein_coding upstream_gene_variant MODIFIER -109G>A None
M0123839 JODLKLMF_00005 4567 4 Oral 0.40 protein_coding upstream_gene_variant MODIFIER -198A>G None
M0123840 JODLKLMF_00005 4840 5 Oral 0.50 protein_coding upstream_gene_variant MODIFIER -471A>G None
M0123841 JODLKLMF_00005 5140 5 Oral 0.50 protein_coding upstream_gene_variant MODIFIER -771T>A None
M0123842 JODLKLMF_00005 5149 3 Oral 0.30 protein_coding upstream_gene_variant MODIFIER -780C>T None
M0123843 JODLKLMF_00001 152 3 Oral 0.30 protein_coding synonymous_variant LOW 75G>T Ser25Ser
M0123844 JODLKLMF_00001 221 3 Oral 0.30 protein_coding synonymous_variant LOW 144A>T Gly48Gly
M0123845 JODLKLMF_00001 245 3 Oral 0.30 protein_coding synonymous_variant LOW 168T>C Ser56Ser
M0123846 JODLKLMF_00001 257 3 Oral 0.30 protein_coding synonymous_variant LOW 180T>C Ala60Ala
M0123847 JODLKLMF_00001 376 4 Oral 0.40 protein_coding missense_variant MODERATE 299C>G Ala100Gly
M0123848 JODLKLMF_00001 377 4 Oral 0.40 protein_coding synonymous_variant LOW 300A>C Ala100Ala
M0123849 JODLKLMF_00001 392 5 Oral 0.50 protein_coding synonymous_variant LOW 315C>A Ile105Ile
M0123850 JODLKLMF_00001 440 4 Oral 0.40 protein_coding synonymous_variant LOW 363G>A Val121Val
M0123851 JODLKLMF_00001 488 4 Oral 0.40 protein_coding synonymous_variant LOW 411A>G Lys137Lys
M0123852 JODLKLMF_00001 491 4 Oral 0.40 protein_coding synonymous_variant LOW 414C>T Ile138Ile
M0123853 JODLKLMF_00001 495 4 Oral 0.40 protein_coding missense_variant MODERATE 418C>A His140Asn
M0123854 JODLKLMF_00001 503 4 Oral 0.40 protein_coding synonymous_variant LOW 426A>T Leu142Leu
M0123855 JODLKLMF_00001 719 5 Oral 0.50 protein_coding synonymous_variant LOW 642T>C Asn214Asn
M0123856 JODLKLMF_00001 720 5 Oral 0.50 protein_coding missense_variant MODERATE 643G>A Asp215Asn
M0123857 JODLKLMF_00001 863 5 Oral 0.50 protein_coding synonymous_variant LOW 786G>T Pro262Pro
M0123858 JODLKLMF_00002 1380 4 Oral 0.40 protein_coding synonymous_variant LOW 171A>C Ile57Ile
M0123859 JODLKLMF_00002 1686 4 Oral 0.40 protein_coding synonymous_variant LOW 477C>T Thr159Thr
M0123860 JODLKLMF_00004 3076 3 Oral 0.30 protein_coding missense_variant MODERATE 31G>T Ala11Ser
M0123861 JODLKLMF_00004 3147 3 Oral 0.30 protein_coding synonymous_variant LOW 102T>A Pro34Pro
M0123862 JODLKLMF_00001 675 4 Oral 0.40 protein_coding synonymous_variant LOW 598C>A Arg200Arg
M0123863 JODLKLMF_00001 866 4 Oral 0.40 protein_coding synonymous_variant LOW 789C>T Phe263Phe
M0123864 JODLKLMF_00001 948 4 Oral 0.40 protein_coding synonymous_variant LOW 871C>T Leu291Leu
M0123865 JODLKLMF_00001 464 3 Oral 0.30 protein_coding synonymous_variant LOW 387T>G Gly129Gly
M0123866 JODLKLMF_00001 508 3 Oral 0.30 protein_coding missense_variant MODERATE 431T>C Val144Ala
M0123867 JODLKLMF_00001 602 3 Oral 0.30 protein_coding synonymous_variant LOW 525T>A Thr175Thr
M0123868 JODLKLMF_00001 620 3 Oral 0.30 protein_coding synonymous_variant LOW 543T>C Leu181Leu
M0123869 JODLKLMF_00001 989 3 Oral 0.30 protein_coding synonymous_variant LOW 912C>G Thr304Thr
M0123870 JODLKLMF_00001 995 3 Oral 0.30 protein_coding synonymous_variant LOW 918T>C Cys306Cys
M0123871 JODLKLMF_00001 1058 3 Oral 0.30 protein_coding synonymous_variant LOW 981G>A Ser327Ser
M0123872 JODLKLMF_00002 1080 3 Oral 0.30 protein_coding upstream_gene_variant MODIFIER -130A>T None
M0123873 JODLKLMF_00002 1674 3 Oral 0.30 protein_coding synonymous_variant LOW 465A>C Gly155Gly
M0123874 JODLKLMF_00002 1695 3 Oral 0.30 protein_coding synonymous_variant LOW 486T>A Val162Val
M0123875 JODLKLMF_00002 1698 3 Oral 0.30 protein_coding synonymous_variant LOW 489A>C Val163Val






Analysis of virulence factors contributing to bacterial pathogenicity


This table presents virulence factors identified within the plasmid cluster.
      Note: Virulence factor analysis was performed using VFDB. Genes in plasmid clusters showing strong homology (identity > 70%, coverage > 70%, E-value < 1e-5) to known virulence factors are listed.

Gene Name vf_gene_id vf_name identity evalue qstart qend query_coverage subject_coverage vf_category gene_description condition







        Analysis of biocide and heavy metal resistance genes to assess antimicrobial risk and environmental impact


This table presents biocides and heavy metals resistance genes identified within the plasmid cluster.
      Note: Analyzing biocide and heavy metal resistance genes based on BacMet to evaluate bacterial resistance risk and the potential impact of environmental heavy metal contamination. Genes in plasmid clusters showing strong homology (identity > 70%, subject coverage > 70%, E-value < 1e-5) to known biocide and heavy metal resistance genes are listed.

Gene Name compound identity evalue qstart qend query_coverage subject_coverage group






        Analyzing antimicrobial resistance genes to assess bacterial resistance to antibiotics and other antimicrobial agents


This table presents antimicrobial resistance genes identified within the plasmid cluster.
      Note: Antimicrobial resistance was performed using CARD. Genes in plasmid clusters showing strong homology (identity > 70%, coverage > 70%, E-value < 1e-5) to known antimicrobial resistance genes are listed.

Gene Name aro_accession identity evalue qstart qend query_coverage subject_coverage drug_class amr_gene_family resistance_mechanism






Analysis of pathogenicity genes to explore pathogen-host interactions


This table presents host pathogen-host interactions within the plasmid cluster.
      Note: Analyzing pathogenicity-related genes using PHI-base to understand pathogen virulence mechanisms and their impact on host interactions. Genes in plasmid clusters showing strong homology (identity > 70%, subject coverage > 70%, and E-value < 1e-5) to known pathogenicity-related genes are listed.

Gene Name phi_molconn_id host gene_name identity evalue qstart qend query_coverage subject_coverage host_descripton disease_name function phenotype_of_mutant






        Analyzing carbohydrate-active enzyme genes to uncover mechanisms of nutrient degradation


This table presents carbohydrate-active enzyme genes identified within the plasmid cluster.
      Note: Annotation of carbohydrate-active enzyme genes was performed using CAZy to explore mechanisms of nutrient breakdown and utilization. Genes in plasmid clusters showing strong homology (identity > 70%, subject coverage > 70%, and E-value < 1e−5) to known CAZyme genes are listed.

Gene Name cazy_id identity evalue qstart qend query_coverage subject_coverage





        Analyzing transport proteins to understand bacterial strategies for substrate uptake and detoxification


This table presents transport proteins within the plasmid cluster.
      Note: Investigation of transport proteins based on TCDB to uncover bacterial mechanisms of substrate transport and environmental detoxification. Genes in plasmid clusters showing strong homology (identity > 70%, subject coverage > 70%, and E-value < 1e−5) to known transport protein entries are listed.

Gene Name tcid identity evalue qstart qend query_coverage subject_coverage class_field class_term subclass subclass_term family family_term