Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C3413
  Reference Plasmid   SRR1950746_bin.1__k91_19624
  Reference Plasmid Size   10994
  Reference Plasmid GC Content   0.64
  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
M0116980 PHACEGNJ_00003 898 16 Skin 0.22 protein_coding missense_variant MODERATE 191C>G Thr64Ser
M0116981 PHACEGNJ_00004 2299 19 Skin 0.26 protein_coding synonymous_variant LOW 684C>G Leu228Leu
M0116982 PHACEGNJ_00004 3037 20 Skin 0.28 protein_coding synonymous_variant LOW 1422G>T Ser474Ser
M0116983 PHACEGNJ_00005 4353 22 Skin 0.31 protein_coding missense_variant MODERATE 784T>C Cys262Arg
M0116984 PHACEGNJ_00005 3632 12 Skin 0.17 protein_coding synonymous_variant LOW 63C>T Thr21Thr
M0116985 PHACEGNJ_00005 3647 12 Skin 0.17 protein_coding synonymous_variant LOW 78A>G Glu26Glu
M0116986 PHACEGNJ_00005 5214 5 Skin 0.07 protein_coding missense_variant MODERATE 1645G>A Ala549Thr
M0116987 PHACEGNJ_00005 6673 4 Skin 0.06 protein_coding missense_variant MODERATE 3104A>G His1035Arg
M0116988 PHACEGNJ_00004 8351 11 Skin 0.15 protein_coding downstream_gene_variant MODIFIER *4768T>C None
M0116989 PHACEGNJ_00006 8530 10 Skin 0.14 protein_coding missense_variant MODERATE 319A>G Ser107Gly
M0116990 PHACEGNJ_00007 9097 10 Skin 0.14 protein_coding synonymous_variant LOW 534A>G Ala178Ala
M0116991 PHACEGNJ_00001 646 6 Skin 0.08 protein_coding upstream_gene_variant MODIFIER -379G>C None
M0116992 PHACEGNJ_00002 388 4 Skin 0.06 protein_coding missense_variant MODERATE 26A>G Gln9Arg
M0116993 PHACEGNJ_00003 1461 7 Skin 0.10 protein_coding missense_variant MODERATE 754G>A Ala252Thr
M0116994 PHACEGNJ_00004 2729 3 Skin 0.04 protein_coding missense_variant MODERATE 1114C>T Pro372Ser
M0116995 PHACEGNJ_00005 4070 6 Skin 0.08 protein_coding synonymous_variant LOW 501C>T Phe167Phe
M0116996 PHACEGNJ_00005 5410 7 Skin 0.10 protein_coding missense_variant MODERATE 1841G>A Gly614Glu
M0116997 PHACEGNJ_00003 938 9 Skin 0.13 protein_coding synonymous_variant LOW 231A>G Arg77Arg
M0116998 PHACEGNJ_00003 1112 7 Skin 0.10 protein_coding synonymous_variant LOW 405A>G Leu135Leu
M0116999 PHACEGNJ_00003 1570 7 Skin 0.10 protein_coding missense_variant MODERATE 863G>C Gly288Ala
M0117000 PHACEGNJ_00004 1744 8 Skin 0.11 protein_coding synonymous_variant LOW 129G>A Leu43Leu
M0117001 PHACEGNJ_00004 2075 10 Skin 0.14 protein_coding missense_variant MODERATE 460T>C Cys154Arg
M0117002 PHACEGNJ_00004 2119 10 Skin 0.14 protein_coding synonymous_variant LOW 504G>A Glu168Glu
M0117003 PHACEGNJ_00004 3504 11 Skin 0.15 protein_coding missense_variant MODERATE 1889A>G Lys630Arg
M0117004 PHACEGNJ_00005 3671 10 Skin 0.14 protein_coding synonymous_variant LOW 102C>T Asp34Asp
M0117005 PHACEGNJ_00005 3722 9 Skin 0.13 protein_coding synonymous_variant LOW 153T>C Phe51Phe
M0117006 PHACEGNJ_00004 3567 10 Skin 0.14 protein_coding missense_variant MODERATE 1952C>A Ala651Asp
M0117007 PHACEGNJ_00001 211 3 Skin 0.04 protein_coding stop_gained HIGH 57G>A Trp19*
M0117008 PHACEGNJ_00002 386 4 Skin 0.06 protein_coding missense_variant MODERATE 24G>A Met8Ile
M0117009 PHACEGNJ_00002 578 4 Skin 0.06 protein_coding synonymous_variant LOW 216C>T Tyr72Tyr
M0117010 PHACEGNJ_00003 746 5 Skin 0.07 protein_coding synonymous_variant LOW 39A>G Val13Val
M0117011 PHACEGNJ_00004 1999 7 Skin 0.10 protein_coding synonymous_variant LOW 384T>C Arg128Arg
M0117012 PHACEGNJ_00004 2788 7 Skin 0.10 protein_coding synonymous_variant LOW 1173T>C Gly391Gly
M0117013 PHACEGNJ_00004 2851 6 Skin 0.08 protein_coding synonymous_variant LOW 1236G>A Gln412Gln
M0117014 PHACEGNJ_00004 3034 3 Skin 0.04 protein_coding synonymous_variant LOW 1419G>A Leu473Leu
M0117015 PHACEGNJ_00004 3128 3 Skin 0.04 protein_coding missense_variant MODERATE 1513G>A Ala505Thr






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