Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C2165
  Reference Plasmid   1111525849743756_bin.3__k141_140800
  Reference Plasmid Size   7850
  Reference Plasmid GC Content   0.67
  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
M0028823 IJONIMAH_00003 1702 3 Skin 0.50 protein_coding upstream_gene_variant MODIFIER -114A>C None
M0028824 IJONIMAH_00003 1800 3 Skin 0.50 protein_coding upstream_gene_variant MODIFIER -16C>A None
M0028825 IJONIMAH_00003 1813 3 Skin 0.50 protein_coding upstream_gene_variant MODIFIER -3C>A None
M0028826 IJONIMAH_00003 1837 3 Skin 0.50 protein_coding missense_variant MODERATE 22A>G Arg8Gly
M0028827 IJONIMAH_00003 1887 3 Skin 0.50 protein_coding synonymous_variant LOW 72G>A Glu24Glu
M0028828 IJONIMAH_00003 1900 3 Skin 0.50 protein_coding missense_variant MODERATE 85T>C Phe29Leu
M0028829 IJONIMAH_00003 1930 3 Skin 0.50 protein_coding missense_variant MODERATE 115A>G Ile39Val
M0028830 IJONIMAH_00003 1935 3 Skin 0.50 protein_coding synonymous_variant LOW 120G>C Val40Val
M0028831 IJONIMAH_00003 1971 3 Skin 0.50 protein_coding synonymous_variant LOW 156T>C Asn52Asn
M0028832 IJONIMAH_00003 1983 3 Skin 0.50 protein_coding synonymous_variant LOW 168T>G Leu56Leu
M0028833 IJONIMAH_00003 2013 3 Skin 0.50 protein_coding synonymous_variant LOW 198C>T Thr66Thr
M0028834 IJONIMAH_00003 2070 3 Skin 0.50 protein_coding synonymous_variant LOW 255C>G Arg85Arg
M0028835 IJONIMAH_00003 2110 3 Skin 0.50 protein_coding stop_lost&splice_region_variant HIGH 295T>C Ter99Glnext*?
M0028836 IJONIMAH_00004 2133 3 Skin 0.50 protein_coding synonymous_variant LOW 9T>C Ile3Ile
M0028837 IJONIMAH_00004 2136 3 Skin 0.50 protein_coding synonymous_variant LOW 12G>A Ala4Ala
M0028838 IJONIMAH_00004 2157 3 Skin 0.50 protein_coding synonymous_variant LOW 33G>A Lys11Lys
M0028839 IJONIMAH_00004 2167 3 Skin 0.50 protein_coding synonymous_variant LOW 43C>T Leu15Leu
M0028840 IJONIMAH_00006 2958 4 Skin 0.67 protein_coding missense_variant MODERATE 164C>G Ala55Gly
M0028841 IJONIMAH_00001 3681 4 Skin 0.67 protein_coding downstream_gene_variant MODIFIER *3132C>T None
M0028842 IJONIMAH_00007 3766 4 Skin 0.67 protein_coding missense_variant MODERATE 923G>T Trp308Leu
M0028843 IJONIMAH_00007 3767 4 Skin 0.67 protein_coding missense_variant MODERATE 922T>A Trp308Arg
M0028844 IJONIMAH_00007 3775 4 Skin 0.67 protein_coding missense_variant MODERATE 914G>C Trp305Ser
M0028845 IJONIMAH_00007 3804 4 Skin 0.67 protein_coding missense_variant MODERATE 885G>T Met295Ile
M0028846 IJONIMAH_00007 3840 3 Skin 0.50 protein_coding synonymous_variant LOW 849G>C Val283Val
M0028847 IJONIMAH_00007 3969 4 Skin 0.67 protein_coding synonymous_variant LOW 720G>C Thr240Thr
M0028848 IJONIMAH_00007 4027 4 Skin 0.67 protein_coding missense_variant MODERATE 662G>C Gly221Ala
M0028849 IJONIMAH_00007 4043 3 Skin 0.50 protein_coding missense_variant MODERATE 646G>T Ala216Ser
M0028850 IJONIMAH_00007 4122 4 Skin 0.67 protein_coding synonymous_variant LOW 567T>C Val189Val
M0028851 IJONIMAH_00006 3192 4 Skin 0.67 protein_coding missense_variant MODERATE 398G>C Arg133Pro
M0028852 IJONIMAH_00001 3276 3 Skin 0.50 protein_coding downstream_gene_variant MODIFIER *2727T>G None
M0028853 IJONIMAH_00001 3409 4 Skin 0.67 protein_coding downstream_gene_variant MODIFIER *2860T>C None
M0028854 IJONIMAH_00001 3341 3 Skin 0.50 protein_coding downstream_gene_variant MODIFIER *2792G>A None
M0028855 IJONIMAH_00001 3380 3 Skin 0.50 protein_coding downstream_gene_variant MODIFIER *2831A>C None
M0028856 IJONIMAH_00001 3505 3 Skin 0.50 protein_coding downstream_gene_variant MODIFIER *2956T>C None
M0028857 IJONIMAH_00001 3565 3 Skin 0.50 protein_coding downstream_gene_variant MODIFIER *3016A>T None
M0028858 IJONIMAH_00001 3566 3 Skin 0.50 protein_coding downstream_gene_variant MODIFIER *3017T>G None
M0028859 IJONIMAH_00001 3577 3 Skin 0.50 protein_coding downstream_gene_variant MODIFIER *3028C>G None
M0028860 IJONIMAH_00007 3752 3 Skin 0.50 protein_coding missense_variant MODERATE 937C>T Arg313Trp
M0028861 IJONIMAH_00007 3771 3 Skin 0.50 protein_coding synonymous_variant LOW 918C>G Arg306Arg
M0028862 IJONIMAH_00007 4677 3 Skin 0.50 protein_coding synonymous_variant LOW 12C>T Pro4Pro
M0028863 IJONIMAH_00007 4688 3 Skin 0.50 protein_coding start_lost HIGH 1T>G Leu1?
M0028864 IJONIMAH_00008 4845 3 Skin 0.50 protein_coding missense_variant MODERATE 1298G>A Arg433Lys
M0028865 IJONIMAH_00008 5042 3 Skin 0.50 protein_coding synonymous_variant LOW 1101T>C Asp367Asp
M0028866 IJONIMAH_00008 5648 3 Skin 0.50 protein_coding synonymous_variant LOW 495G>C Arg165Arg
M0028867 IJONIMAH_00008 5711 3 Skin 0.50 protein_coding synonymous_variant LOW 432G>A Gly144Gly
M0028868 IJONIMAH_00008 5765 3 Skin 0.50 protein_coding synonymous_variant LOW 378A>G Thr126Thr
M0028869 IJONIMAH_00008 5773 3 Skin 0.50 protein_coding missense_variant MODERATE 370T>C Ser124Pro
M0028870 IJONIMAH_00008 5794 3 Skin 0.50 protein_coding missense_variant MODERATE 349T>G Ser117Ala
M0028871 IJONIMAH_00008 5867 3 Skin 0.50 protein_coding synonymous_variant LOW 276C>A Val92Val
M0028872 IJONIMAH_00008 5894 3 Skin 0.50 protein_coding synonymous_variant LOW 249C>T His83His
M0028873 IJONIMAH_00008 6053 3 Skin 0.50 protein_coding synonymous_variant LOW 90C>T Pro30Pro
M0028874 IJONIMAH_00008 6055 3 Skin 0.50 protein_coding missense_variant MODERATE 88C>G Pro30Ala
M0028875 IJONIMAH_00008 6056 3 Skin 0.50 protein_coding synonymous_variant LOW 87T>C Arg29Arg
M0028876 IJONIMAH_00008 6090 3 Skin 0.50 protein_coding missense_variant MODERATE 53A>C His18Pro
M0028877 IJONIMAH_00008 6115 3 Skin 0.50 protein_coding synonymous_variant LOW 28C>T Leu10Leu
M0028878 IJONIMAH_00009 6635 3 Skin 0.50 protein_coding missense_variant MODERATE 764A>C Asp255Ala
M0028879 IJONIMAH_00009 6685 3 Skin 0.50 protein_coding synonymous_variant LOW 714C>G Gly238Gly
M0028880 IJONIMAH_00009 6715 3 Skin 0.50 protein_coding synonymous_variant LOW 684G>T Leu228Leu
M0028881 IJONIMAH_00009 7009 3 Skin 0.50 protein_coding synonymous_variant LOW 390T>C Ile130Ile
M0028882 IJONIMAH_00009 7083 3 Skin 0.50 protein_coding missense_variant MODERATE 316G>C Gly106Arg
M0028883 IJONIMAH_00009 7185 3 Skin 0.50 protein_coding synonymous_variant LOW 214T>C Leu72Leu
M0028884 IJONIMAH_00009 7186 3 Skin 0.50 protein_coding missense_variant MODERATE 213G>T Gln71His
M0028885 IJONIMAH_00009 7246 3 Skin 0.50 protein_coding synonymous_variant LOW 153C>T Tyr51Tyr
M0028886 IJONIMAH_00009 7281 3 Skin 0.50 protein_coding synonymous_variant LOW 118C>A Arg40Arg
M0028887 IJONIMAH_00009 7285 3 Skin 0.50 protein_coding synonymous_variant LOW 114C>G Ala38Ala
M0028888 IJONIMAH_00009 7297 3 Skin 0.50 protein_coding synonymous_variant LOW 102C>G Gly34Gly






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