New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_002947	= 5816927	34 (0.950)	11 (0.350)	9/236	2.2	25.7%	intergenic (+57/+72)	PP_5092/pilT	NLP/P60 protein/twitching motility protein
	?	NC_002947	= 5816954	34 (1.090)					intergenic (+84/+45)	PP_5092/pilT	NLP/P60 protein/twitching motility protein

AGCACTACGTGGTGGCCAAGCGGGTGCTGCCGAAAGAGCAGCAGCTGAGTCTGGCCAAGCGTTAAGCTGATCGGCGCTATCCGGTACCGGCCCCTTCGCGGGCACGCCCGCTCCCACAGGTAGCGCGTCGCTCTCGCGCGCAGCTCACATACCTGTGGGAGCGGGCGCGCCCGCGAAAGGGCCTTTGCAGGTACTACAAGCCTTTGATCAACCCTCGCTCCCTCAGCCTCCGCA‑ACGCCCCCTCCATCGTCAGCATCCCCTCCGCCGCCCCGCCCTGCATCACTGAAGACAACTGC  >  NC_002947/5816806‑5817101                                                                                                                                                     |                                                                                                                                                     aGCACTACGTGGTGGCCAAGCGGGTGCTGCCGAAAGAGCAGCAGCTGAGTCTGGCCAAGCGTTAAGCTGATCGGCGCTATCCGGTACCGGCCCCTTCGCGGGCACGCCCGCTCCCACAGGTAGCGCGTCGCTCTCGCGCGCAGCTCACAt                                                                                                                                                     <  1:556859‑M2/150‑2 (MQ=255)  gCACTACGTGGTGGCCAAGCGGGTGCTGCCGAAAGAGCAGCAGCTGAGTCTGGCCAAGCGTTAAGCTGATCGGCGCTATCCGGTACCGGCCCCTTCGCGGGCACGCCCGCTCCCACAGGTAGCGCGTCGCTCTCGCGCGCAGCTCACAta                                                                                                                                                    <  2:729142‑M2/150‑3 (MQ=255)         gtggtgGCCAAGCGGGTGCTGCCGAAAGAGCAGCAGCTGAGTCTGGCCAAGCGTTAAGCTGATCGGCGCTATCCGGTACCGGCCCCTTCGCGGGCACGCCCGCTCCCACAGGTAGCGCGTCGCTCTCGCGCGCAGCTCACAtacctgtgg                                                                                                                                             >  1:817141‑M2/1‑141 (MQ=255)         gtggtgGCCAAGCGGGTGCTGCCGAAAGAGCAGCAGCTGAGTCTGGCCAAGCGTTAAGCTGATCGGCGCTATCCGGTACCGGCCCCTTCGCGGGCACGCCCGCTCCCACAGGTAGCGCGTCGCTCTCGCGCGCAGCTCACAtacctgtgg                                                                                                                                             >  2:823007‑M2/1‑141 (MQ=255)         gtggtgGCCAAGCGGGTGCTGCCGAAAGAGCAGCAGCTGAGTCTGGCCAAGCGTTAAGCTGATCGGCGCTATCCGGTACCGGCCCCTTCGCGGGCACGCCCGCTCCCACAGGTAGCGCGTCGCTCTCGCGCGCAGCTCACAtacctgtgg                                                                                                                                             >  2:175687‑M2/1‑141 (MQ=255)                  aaGCGGGTGCTGCCGAAAGAGCAGCAGCTGCGTCTGGCCAAGCGTTAAGCTGATCGGCGCTATCCGGTACCGGCCCCGTCGCGGGCACGCCCGCTCCCACAGGTAACGCCCCGCTCTCGCCCGCCGCTCACAtccctgtgggagctcgcg                                                                                                                                    <  2:71684‑M2/150‑19 (MQ=255)                                gAAAGAGCAGCAGCTGAGTCTGGCCAAGCGTTAAGCTGATCGGCGCTATCCGGTACCGGCCCCTTCGCGGGCACGCCCGCTCCCACAGGTAGCGCGTCGCTCTCGCGCGCAGCTCACAtacctgtgg                                                                                                                                             >  2:779580‑M2/1‑118 (MQ=255)                                gAAAGAGCAGCAGCTGAGTCTGGCCAAGCGTTAAGCTGATCGGCGCTATCCGGTACCGGCCCCTTCGCGGGCACGCCCGCTCCCACAGGTAGCGCGTCGCTCTCGCGCGCAGCTCACAtacctgtgg                                                                                                                                             <  1:779580‑M2/127‑10 (MQ=255)                                 aaaGAGCAGCAGCTGAGTCTGGCCAAGCGTTAAGCTAATCGGCGCTATCCGGTACCGGCCCCTTCGCGGGCACGCCCGCTCCCACAGGTAGCGCGTCGCTCTCGCGCGCAGCTCACATACCTGTGGGAGCGGGCGCGCCCGCGAAAGGGc                                                                                                                     >  2:511537/1‑150 (MQ=255)                                          cagcTGAGTCTGGCCAAGCGTTAAGCTGATCGGCGCTATCCGGTACCGGCCCCTTCGCGGGCACGCCCGCTCCCACAGGTAGCGCGTCGCTCTCGCGCGCAGCTCACATACCTGTGGGAGCGGGCGCGCCCGCGAAAGGGCCTTTGCAgg                                                                                                            <  1:558482/150‑1 (MQ=255)                                              tGAGTCTGGCCAAGCGTTAAGCTGATCGGCGCTATCCGGTACCGGCCCCTTCGCGGGCACGCCCGCTCCCACAGGTAGCGCGTCGCTCTCGCGCGCAGCTCACATACCTGTGGGAGCGGGCGCGCCCGCGAAAGGGCCTTTGCAGGta                                                                                                          <  2:666413/148‑1 (MQ=255)                                              tGAGTCTGGCCAAGCGTTAAGCTGATCGGCGCTATCCGGTACCGGCCCCTTCGCGGGCACGCCCGCTCCCACAGGTAGCGCGTCGCTCTCGCGCGCAGCTCACATACCTGTGGGAGCGGGCGCGCCCGCGAAAGGGCCTTTGCAGGta                                                                                                          >  1:666413/1‑148 (MQ=255)                                               gAGTCTGGCCAAGCGTTAAGCTGATCGGCGCTATCCGGTACCGGCCCCTTCGCGGGCACGCCCGCTCCCACAGGTAGCGCGTCGCTCTCCAGCCGGGCGCACATACCTGTGGGCGCGGGCGCGCCCGCGAAAGGGCCTTTGCAGGtactc                                                                                                       >  1:230096/1‑149 (MQ=38)                                                  tCTGGCCAAGCGTTAAGCTGATCGGCGCTATCCGGTACCGGCGCCTTCGCGGACACGCCGGCTCCCACAGGTAGCGCGTCGCTCTCGCGAGCAGCTCACATACCTGTGGGATGGGGCGGGGCCGCGAAAGGGGCTTTGGCGGGACTACaa                                                                                                    >  1:254361/1‑150 (MQ=255)                                                  tCTGGCCAAGCGTTAAGCTGATCGGCGCTATCCGGTACCGGCCCCTTCGCGGGCACGCCCGCTCCCACAGGTAGCGCGTCGCTCTCGCGCGCAGCTCACATACCTGTGGGAGCGGGCGCGCCCGCGAAAGGGCCTTTGCAGGTACTACaa                                                                                                    >  2:783764/1‑150 (MQ=255)                                                      gCCAAGCGTTAAGCTGATCGGCGCTATCCGGTACCGGCCCCTTCGCGGGCACGCCCGCTCCCCCAGGTAGCGCGTCGCTCTCGCGCGCAGCTCACATACCTGTGGGAGCGGGCGCGCCCGCGAAAGGGCCTTTGCAGGTACTACAAGCCt                                                                                                >  1:855272/1‑150 (MQ=255)                                                       ccAAGCGTTAAGCTGATCGGCGCTATCCGGTACCGGCCCCTTCGCGGGCACGCCCGCTCCCACAGGTAGCGCGTCGCTCTCGCGCGCAGCTCACATACCTGTGGGAGCGGGCGCGCCCGCGAAAGGGCCTTTGCAGGTACTACAAGCCtt                                                                                               <  2:681973/150‑1 (MQ=255)                                                              ttAAGCTGATCGGCGCTATCCGGTACCGGCCCGATCGAGGGTGCGCCCGGTGCCACAGGGAGCGCGTCGCGCTCGCGCGCAGCTCACATACCTGTGGGAGCGGGAGCGCCCGCGAAAGAGCCTTTGCAGGTCCTACAAGCCTGTGATCaa                                                                                        <  2:53822/150‑1 (MQ=255)                                                                aaGCTGATCGGCGCTATCCGGTACCGGCCCCTTCGCGGGCACGCCCGCTCCCACAGGTAGCGCGTCGCTCTCGCGCGCAGCTCACATACCTGCGGGGGCGGGCGCGCCCGCGCAAGGGCCTTTGCAGGGCCTAGAAGCCGTTGAGCAAcc                                                                                      >  1:338742/1‑150 (MQ=37)                                                                  gCTGATCGGCGCTATCCGGTACCGGCCCCTTCGCGGGCACGCCCGCTCCCACAGGTAGCGCGTCGCTCTCGCGCGCAGCTCACATACCGGTGGGAGCGGGCGCGCCCGCGAAAGGGCCTTTGCAGGTACTACAAGCCTTTGCTCAACCCt                                                                                    >  1:312712/1‑150 (MQ=255)                                                                        cGGCGCTATCCGGTACCGGCCCCTTCGCGGGCACGCACGCTCCCACAGGTAGCGCGTCGCTCCCGCGCGCAGCTCACATACCTGTGGGAGCGAGCGCGCCCGCGAACGGGCCTTTGCAGGTAGTACAAGCCTTTGATCAACCCTCGCTcc                                                                              >  1:870146/1‑150 (MQ=255)                                                                            gcTATCCGGTACCGGCCCCTTCGCGGGCACGCCCGCTCCCACAGGTAGCGCGTCGCTCTCGCGCGCAGCTCACATAGCTGTGGGAGCGGGCGCGCCCGCGAAAGGGCCTTTGCAGGTACTACAAGCCTTTGATCAACCCTCGCTCCCTCa                                                                          <  2:726548/150‑1 (MQ=255)                                                                             cTATCCGGTACCGGCCCCTTCGCGGGCACGCCCGCTCCCACAGGTAGCGCGTCGCTCTCGCGCGCAGCTCACATACCTGTGGGAGCGGGCGCGCCCGCGAAAGGGCCTTTGCAGGTACTACAAGCCTTTGATCAACCCTCGCTCCCTCAg                                                                         <  1:729142/150‑1 (MQ=255)                                                                              tATCCGGTACCGGCCCCTTCGCGGGCACGCCCGCTCCCACAGGTAGCGCGTCGCTCTCGCGCGCAGCTCACATACCTGTGGGAGCGGGCGCGCCCGCGAAAGGGCCTTTGCAGGTACTACAAGCCTTTGATCAACCCTCGCTCCCTCAGc                                                                        <  2:556859/150‑1 (MQ=255)                                                                                tCCGGTACCGGCCCCTTCGCGGGCACGCCCGCTCCCACAGGTAGCGCGTCGCTCTCCCGCGCAGCTCACATACCTGTGGGAGCTGGCGCGCCCGCGAAAGGGCCTTTGCAGGTACTACAAGCCTTTGATCAACCCTCGCTCCCTCAGCCt                                                                      >  1:320361/1‑150 (MQ=255)                                                                                accGGTACCGGCCCCTTCGCGGGCACGCCCGCTCCCACAGGTAGCGCGTCGCTCTCGCGCGCAGCTCACATACCTGTGGGAGCGGGCGCGCCCGCGAAAGGGCCTTTGCAg                                                                                                             <  2:818205/110‑1 (MQ=255)                                                                                accGGTACCGGCCCCTTCGCGGGCACGCCCGCTCCCACAGGTAGCGCGTCGCTCTCGCGCGCAGCTCACATACCTGTGGGAGCGGGCGCGCCCGCGAAAGGGCCTTTGCAg                                                                                                             >  1:818205/2‑111 (MQ=255)                                                                                        cGGCCCCTTCGCGGGCACGCCCGCTCCCACAGGTAGCGCGTCGCTCTCGCGCGCAGCTCACATACCTGTGGGAGCGGGCGCGCCCGCGAAAGGGCCTTTGCAGGTACTACAGCGGTTTGATCAACCCTCGCTCCCTCAGCCTCCGCA‑ACg                                                             >  1:701747/1‑150 (MQ=255)                                                                                             ccTTCGCGGGCACGCCCGCTCCCACAGGTAGCGCGTCGCTCTCGCGCGCAGCTCACATACCTGTGGGAGCGGGCGCGCCCGCGAAAGGGCCTTTGCAGGTACTACAAGCCTTTGATCAACCCTCGCTCCCTCAGCCTCCGCA‑ACGccccc                                                        >  1:685186/1‑150 (MQ=255)                                                                                              cTTCGCGGGCACGCCCGCTCCCACAGGTAGCGCGTCGCTCTCGCGCGCAGCTCACATACCTGTGGGAGCGGGCGCGCCCGCGAAAGGGCCTTTGCAGGTACTACAAGCCTTTGATCAACCCTCGCTCCCTCAGCCTCCGCA‑ACGc                                                            <  1:554440/145‑1 (MQ=255)                                                                                              cTTCGCGGGCACGCCCGCTCCCACAGGTAGCGCGTCGCTCTCGCGCGCAGCTCACATACCTGTGGGAGCGGGCGCGCCCGCGAAAGGGCCTTTGCAGGTACTACAAGCCTTTGATCAACCCTCGCTCCCTCAGCCTCCGCA‑ACGc                                                            >  2:554440/1‑145 (MQ=255)                                                                                                      gCACGCCCGCTCCCACAGGTAGCGCGTCGCTCTCGCGCGCAGCTCACATACCTGTGGGAGCGGGCGCGCCCGCGAAAGGGCCTTTGCAGGTACTACAAGCCTTTGATCAACCCTCGCTCCCTCAGCCTCCGCA‑ACGCCCCCTCCATCGTc                                               >  1:5631/1‑150 (MQ=255)                                                                                                            ccGCTCCCACAGGTAGCGCGTCGCTCTCGCGCGCAGCTCACAtacctgtgggagcgggcgcgcccgcgaagggg                                                                                                                      >  1:24376‑M2/1‑42 (MQ=255)                                                                                                            ccGCTCCCACAGGTAGCGCGTCGCTCTCGCGCGCAGCTCACAtacctgtgggagcgggcgcgcccgcgaagggg                                                                                                                      <  2:24376‑M2/74‑33 (MQ=255)                                                                                                            ccGCTCCCACAGGTAGCGCGTCGCTCTCGCGCGCAGCTCACATACCTGTGGGAGCGGGCGCGCCCGCGAAAGGGCCTTTGCAGGTACTACAAGCCTTTGATCAACCCTCGCTCCCTCAGCCTCCGCA‑ACGCCCCCTCCATCGTCAGCATc                                         >  1:579227/1‑150 (MQ=255)                                                                                                            ccGCTCCCACAGGTAGCGCGTCGCTCTCGCGCGCAGCTCACATACCTGTGGGAGCGGGCGCGCCCGCGAAAGGGCCTTTGCAGGTACTACAAGCCTTTGATCAACCCTCGCTCCCTCAGCCTCCGCA‑ACGCCCCCTCCATCGTCAGCATc                                         >  2:613020/1‑150 (MQ=255)                                                                                                              gCTCCCACAGGTAGCGCGTCGCTCTCGCGCGCAGCTCACAtacctgtgggagcgggcgtgcccg                                                                                                                              <  2:456537‑M2/64‑25 (MQ=255)                                                                                                              gCTCCCACAGGTAGCGCGTCGCTCTCGCGCGCAGCTCACAtacctgtgggagcgggcgtgcccg                                                                                                                              >  1:456537‑M2/1‑40 (MQ=255)                                                                                                                  ccACAGGTAGCGCGTCGCTCTCGCGCGCAGCTCACAtacctgtgggagcgggcgtgcccgcgaaggggccggtaccggatagcgccgatcagcttaacgcttggccagactcagctgctgc                                                                 >  1:65034‑M2/1‑36 (MQ=255)                                                                                                                  ccACAGGTAGCGCGTCGCTCTCGCGCGCAGCTCACAtacctgtgggagcgggcgtgcccgcgaaggggccggtaccggatagcgccgatcagcttaacgcttggccagactcagctgctgc                                                                 <  2:65034‑M2/121‑86 (MQ=255)                                                                                                                  ccACAGGTAGCGCGTCGCTCTCGCGCGCAGCTCACATACCTGTGGGAGCGGGCGCGCCCGCGAAAGGGCCTTTGCAGGTACTACAAGCCTTTGATCAACCCTCGCTCCCTCAGCCTCCGCA‑ACGCCCCCTCCATCGTCAGCATCCCCTcc                                   >  1:110753/1‑150 (MQ=255)                                                                                                                   cacaGGTAGCGCGTCGCTCTCGCGCGCAGCTCACAtacctgtgggagcgggcgtgcccgcgaaggggccggtaccggat                                                                                                          >  1:133944‑M2/1‑35 (MQ=255)                                                                                                                   cacaGGTAGCGCGTCGCTCTCGCGCGCAGCTCACAtacctgtgggagcgggcgtgcccgcgaaggggccggtaccggat                                                                                                          <  2:133944‑M2/79‑45 (MQ=255)                                                                                                                    acaGGTAGCGCGTCGCTCTCGCGCGCAGCTCACAtacctgtgggaacgggcgtgcccgcgaaggggccggtaccggatagcgccgatcagcttaacgcttggccagactcagctgctgctctttcggcagcacccgcttggccaccacgt                                  <  2:161861‑M2/150‑117 (MQ=255)                                                                                                                      aGGTAGCGCGTCGCTCTCGCGCGCAGCTCACATACCTGTGGGAGCGGGCGCGCCCGCGAAAGGGCCTTTGCAGGTACTACAAGCCTTTGATCAACACTCGCTCCCTCAGCCTCCGCA‑ACGCCCCCTCCATCGTCAGCATCCCCtcctccc                               >  1:149367/1‑149 (MQ=255)                                                                                                                        gTAGCGCGTCGCTCTCGCGCGCAGCTCACAtacctgtgggagcgggcgtgcccgcgaaggggccggtaccggatagcgccgatcagcttaacgcttggccagactcagctgctgctctttcggcagcacccgcttggccaccacgtagtg                              <  1:316952‑M2/150‑121 (MQ=255)                                                                                                                           gcgcGTCGCTCTCGCGCGCAGCTCACAtacctgtgggagcgggcgtgcccgcgaaggggccggtaccggatagcgccgatcagcttaacgcttggccagactcagctgctgctctttcggcagcacccgcttggccaccacgtagtgctt                           >  2:316952‑M2/1‑27 (MQ=255)                                                                                                                             gcgTCGCTCTCGCGCGCAGCTCACATACCTGTGGGAGCGGGCGCGCCCGCGAAAGGGCCTTTGCAGGTACTACAAGCCTTTGATCAACCCTCGCTCCCTCAGCCTCCGCA‑ACGCCCCCTCCATCGTCAGCATCCCCTCCGccgccccgcc                        <  1:613020/150‑1 (MQ=255)                                                                                                                                 cGCTCTCGCGCGCAGCTCACATACCTGTGGGAGCGGGCGCGCCCGCGAAAGGGCCTTTGCAGGTACTACAAGCCTTTGATCAACCCTCGCTCCCTCAGCCTCCGCA‑ACGCCCCCTCCATCGTCAGCATCCCCTCCGCCGCCCCGCCCTGc                    <  1:783764/150‑1 (MQ=255)                                                                                                                                      tcGCGCGCAGCTCACATACCTGTGGGAGCGGGCGCGCCCGCGAAAGGGCCTTTGCAGGTACTACAAGCCTTTGATCAACCCTCGCTCCCTCAGCCTCCGGA‑ACGCCCCCTCCATCGTCAGCATCCCCTCCGCCGCCCCGCCCTGCATCAc               >  2:671986/1‑150 (MQ=255)                                                                                                                                       cgcgcgCAGCTCACATACCTGTGGGAGCGGGCGCGCCCGCGAAAGGGCCTTTGCAGGTACTACAAGCCTTTGATCAACCCTCGCTCCCTCAGCCTCCGCA‑ACGCCCCCTCCATCGTCAGCATCCCCTCCGCCGCCCCGCCCTGCATCACt              <  2:5631/150‑1 (MQ=255)                                                                                                                                          gcgcAGCTCACATACCTGTGGGAGCGGGCGCGCCCGCGAAAGGGCCTTTGCAGGTACTACAAGCCTTTGATCAACCCTCGCTCCCTCAGCCTCCGCG‑ACGCCCCCTCCATCGTCAGCATCCCCTCCGCCGCCCCGCCCTGCATCACTGaa           <  1:142294/150‑1 (MQ=255)                                                                                                                                                   acaTACCTGTGGGAGCGGGCGCGCCCGCGAAAGGGCCTTTGCAGGTACTACAAGCCTTTGATCAACCCTCGCTTCCTCAGCCTCAGCACCCACCCACTTC‑GCCTCGGGATCCCCTCCCCCGCCCCGCCCTGCATCACTGAAGACAACTgc  >  1:631234/1‑150 (MQ=255)                                                                                                                                                     |                                                                                                                                                     AGCACTACGTGGTGGCCAAGCGGGTGCTGCCGAAAGAGCAGCAGCTGAGTCTGGCCAAGCGTTAAGCTGATCGGCGCTATCCGGTACCGGCCCCTTCGCGGGCACGCCCGCTCCCACAGGTAGCGCGTCGCTCTCGCGCGCAGCTCACATACCTGTGGGAGCGGGCGCGCCCGCGAAAGGGCCTTTGCAGGTACTACAAGCCTTTGATCAACCCTCGCTCCCTCAGCCTCCGCA‑ACGCCCCCTCCATCGTCAGCATCCCCTCCGCCGCCCCGCCCTGCATCACTGAAGACAACTGC  >  NC_002947/5816806‑5817101

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑
Reads not counted as support for junction
read_name Not counted due to insufficient overlap past the breakpoint.
read_name Not counted due to not crossing MOB target site duplication.