New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_002947	3947957 =	18 (0.190)	7 (0.100)	6/194	NT	26.9%	coding (136/1797 nt)	PP_3483	type II secretion system protein
	?	NC_002947	3948042 =	24 (0.330)					coding (51/1797 nt)	PP_3483	type II secretion system protein

AGGAGGTCGCGGGGGTAGGCGGAAATTTTTGCTGGGTTCTTCGCGGGCATGCCCGCTCCCACAGGTACATCACAGGTCTGTGGGCTGCATACATCCTGTGGGAGCGGGCATGCCCGCGAAGACGTCGGTGCAGGCTTTGCAGATTCCGGGGTTGCATCGAATGCTTCTGGCATGGCCTGCGACTCCGCTCAGGGGCGCGTCGCAGGCTGGCTCGGCCAGGGGTGCGGGCGCCGCTATTCCCCTGTGAGCAGTTGATCGTCGT  >  NC_002947/3947920‑3948181                                                                                                                           |                                                                                                                                            aggaggTCGCGGGGGTAGGCGGAAATTTTTGCTGGGTTCTTCGCGGGGATGCCCGCTCCCACAGGTACAGCACAGGTCTGTGGGCTGCATACATCCTGTGCGAGCGGGCATGCCCGCGAGGACGTCGTTGCAGGCTGTGCGGTGTCCggg                                                                                                                  >  2:1229074/1‑150 (MQ=38)                                         gaGCGGGCATGCCCGCTCCCACAGGTACATCACAGGTCTGTGGGCTGCATACATCCTGTGGGAACGGGCATGCCCGCGAAGACGTCGGTGCAGGCTTTGCAGATTCCGGGGTTGCATCGAATGCTTCTGGCATGGCCTGCGACTCCGCTc                                                                          <  2:1327122‑M1/148‑1 (MQ=255)                                             GGGCATGCCCGCTCCCACAGGTACATCACAGGTCTGTGGGCTGCATACATCCTGTGGGAGCGGGCATGCCCGAGCATACGTCGGTGCAGGCTTTGCAGATTCCGGGGTTGCATCGAATGCTTCTGGCATGGCCTGCGACTCCGCTCAggg                                                                      <  1:757565‑M1/150‑1 (MQ=255)                                                 ATGCCCGCTCCCACAGGTACATCACAGGTCTGTGGACTGCATACATCCTGTGGGAGCGGGCATGCCCGCGAAGACGTCGGTGCAGGCTTTGCAGATTCCGGGGTTGCATCGAATGCTTCTGGCATGGCCTGCGACTCCGCTCAGGGgcgc                                                                  <  2:1275468‑M1/150‑1 (MQ=255)                                                   gcccgctcccacaggatgtatgcagcccacagacctgtgatgtacctgtgggagcgggcatgcccgcgaagaCGTCGGTGCAGGCTTTGCAGATTCCGGGGTTGCATCGAATGCTTCTGGCATGGCCTGCGACTCCGCTCAGGGGCGCGt                                                                >  1:2399816‑M2/73‑150 (MQ=255)                                                    CCCGCTCCCACAGGTACATCACAGGTCTGTGGGCTGCATACATCCTGTGGGAGCGGGCATGCCCGCGAAGACGTCGGTGCAGGCTTTGCAGATTCCGGGGTTGCATCGAATGCTTCTGACATGGCCTGCGACTCCGCTCAGGGGCGCGTc                                                               <  2:697272‑M1/150‑1 (MQ=255)                                                     CCGCTCCCACAGGTACATCACAGGTCTGTGGGCTGCATACATCCTGTGGGAGCGGGCATGCCCGCGAAGACGTCGGTGCAGGCTTTGCAGATTCCGGGGTTGCATCTAATGCTTCTGGCATGGCCTGCGACTCCGCTCaggggcgcccgc                                                              <  2:2394354‑M1/150‑5 (MQ=255)                                                      cgctcccacaggatgtatgcagcccacagacctgtgatgtacctgtgggagcgggcatgcccgcgaagaCGTCGGTGCAGGCTTTGCAGATTCCGGGGTTGCATCGAATGCTTCTGGCATGGCCTGCGACTCCGCTCAGGGGCGCGTCGc                                                             >  2:1779382‑M2/70‑150 (MQ=255)                                                         tcccacaggatgtatgcagcccacagacctgtgatgtacctgtgggagcgggcatgcccgcgaagaCGTCGGTGCAGGCTTTGCAGATTCCGGGGTTGCATCGAATGCTTCTGGCATGGCCTACGACTCCGCTCAGGGGCGCGTCGCAgg                                                          >  2:1267944‑M2/67‑150 (MQ=255)                                                         TCCCACAGGTACATCACAGGTCTGTGGGCTGCATACATCCTGTGGGAGCGGGCATGCCCGCGAAGACGTCGGTGCAGGCTTTGCAGATTCCGGGGTTGCATCGAATGCTTCTGGCATGGCCTGCGACTCCGCTCAGGGGCGCGTCGCAgg                                                          <  1:1805768‑M1/150‑1 (MQ=255)                                                           ccacaggatgtatgcagcccacagacctgtgatgtacctgtgggagcgggcatgcccgcgaagaCGTCGGTGCAGGCTTTGCAGATTCCGGGGTTGCATCGAATGCTTCt                                                                                                <  1:1746445‑M2/46‑1 (MQ=255)                                                           ccacaggatgtatgcagcccacagacctgtgatgtacctgtgggagcgggcatgcccgcgaagaCGTCGGTGCAGGCTTTGCAGATTCCGGGGTTGCATCGAATGCTTCt                                                                                                >  2:1746445‑M2/65‑110 (MQ=255)                                                           ccacaggatgtatgcagcccacagacctgtgatgtacctgtgggagcgggcatgcccgcgaagaCGTCGGTGCAGGCTTTGCAGATTCCGGGGTTGCATCGAATGCTTCTGGCATGGCCTGCGACTCCGCTCAGGGGCGCGTCGCAggct                                                        >  2:1478937‑M2/65‑150 (MQ=255)                                                             acaggatgtatgcagcccacagacctgtgatgtacctgtgggagcgggcatgcccgcgaagaCGTCGGTGCAGGCTTTGCAGATTCCGGGGTTGCATCGAATGCTTCTGGCATGGCCTTCGACGCCGCTCAGGGGCGCGTCGCAggctgg                                                      >  2:2016155‑M2/63‑150 (MQ=255)                                                             ACAGGTACATCACAGGTCTGTGGGCTGCATACATCCTGTGGGAGCGGGCATGCCCGCGAAGACGTCGGTGCAGGCTTTGTAGATTCCGGGGTTGCATCGAATGCTTCTGGCATGGCCTGCGACTCCGCTCAGGGGCGCGTCGCAggctgg                                                      <  1:1099836‑M1/150‑1 (MQ=255)                                                             ACAGGTACATCACAGGTCTGTGGGCTGCATACATCCTGTGGGAGCGGGCATGCCCGCGAAGACGTCGGTGCAGGCTTTGCAGATTCCGGGGTTGCATCGAATACTTCTGGCATGGCCTGCGACTCCGCTCAGGGGCGcgtcgcacccctg                                                      <  1:521850‑M1/150‑7 (MQ=255)                                                              CAGGTACATCACAGGTCTGTGGGCTGCATACATCCTGTGGGAGCGGGCATGCCCGCGAAGACGTCGGTGCAGGCTTTGCAGATTCCGGGGTTGCATCGAATGCTTCTGGCATGGCCTGCGACTCCGCTCAGGGGCGCGTCGCAggctggc                                                     >  1:1327122‑M1/1‑150 (MQ=255)                                                                 GTACATCACAGGTCTGTGGGCTGCATACATCCTGTGGGAGCGGGCATGCCCGCGAAGACGTCGGTGCAGGCTTTGCAGATTCCGGGGTTGCATCGAAt                                                                                                      >  1:1166504‑M1/1‑98 (MQ=255)                                                                 GTACATCACAGGTCTGTGGGCTGCATACATCCTGTGGGAGCGGGCATGCCCGCGAAGACGTCGGTGCAGGCTTTGCAGATTCCGGGGTTGCATCGAAt                                                                                                      <  2:1166504‑M1/98‑1 (MQ=255)                                                                   aCATCACAGGTCTGTGGGCTGCATACATCCTGTGGGAGCGGGCATGCCCGCGAAGACGTCGGTGCAGGCTTTGCAGATTCCGGGGTTGCATCGAATGCTTCTGGCATGGCCTGCGACTCCGCTCAGGGGCGCGTCGCAGGCTGGCACGGc                                                >  1:1554033/1‑150 (MQ=255)                                                                     aTCACAGGTCTGTGGGCTGCATACATCCTGTGGGAGCGGGCATGCCCGCGAAGACGTCGGTGCAGGCTTTGCAGATTCCGGGGTTGCATCGAATGCTTCTGGCATGGCCTGCGACTcc                                                                              <  1:407597/118‑1 (MQ=255)                                                                     aTCACAGGTCTGTGGGCTGCATACATCCTGTGGGAGCGGGCATGCCCGCGAAGACGTCGGTGCAGGCTTTGCAGATTCCGGGGTTGCATCGAATGCTTCTGGCATGGCCTGCGACTcc                                                                              >  2:407597/1‑118 (MQ=255)                                                                      tCACAGGTCTGTGGGCTGCATACATCCTGTGGGAGCGGGCATGCCCGCGAAGACGTCGGTGCAGGCTTTGCAGATTCCGGGGTTGCATCGAATGCTTCTGGCATGGCCTGCGACTCCGCTCAggg                                                                      >  2:1477008/1‑125 (MQ=255)                                                                      tCACAGGTCTGTGGGCTGCATACATCCTGTGGGAGCGGGCATGCCCGCGAAGACGTCGGTGCAGGCTTTGCAGATTCCGGGGTTGCATCGAATGCTTCTGGCATGGCCTGCGACTCCGCTCAggg                                                                      <  1:1477008/125‑1 (MQ=255)                                                                      tCACAGGTCTGTGGGCTGCATACATCCTGTGGGAGCGGGCATGCCCGCGAAGACGTCGGTGCAGGCTTTGCAGATTCCGGGGTTGCATCGAATGCTTCTGGCATGGCCTGCGACTCCGCTCAGGGGCGCGTCGCAGGCTGGCTCGGCCAg                                             >  2:849127/1‑150 (MQ=255)                                                                      tCACAGGTCTGTGGGCTGCATACATCCTGTGGGAGCGGGCATGCCCGCGAAGACGTCGGTGCAGGCTTTGCAGATTCCGGGGTTGCATCGAATGCTTCTGGCATGGCCTGCGACTCCGCTCAGGGGCGCGTCGCAGGCTGGCTCGGCCAg                                             <  1:697272/150‑1 (MQ=255)                                                                      tCACAGGTCTGTGGGCTGCATACATCCTGTGGGAGCGGGCATGCCCGCGAAGACGTCGGTGCAGGCTTTGCAGATTCCGGGGTTGCATCGAATGCTTCTGGCATGGCCTGCAATTCCTCTCAGGGGCGCGTCGCAGGCTGGCTCGGCCAg                                             >  2:1145191/1‑150 (MQ=255)                                                                          aGGTCTGTGGGCTGCATACATCCTGTGGGAGCGGGCATGCCCGCGAAGACGTCGGTGCAGGCTTTGCAGATTCCGGGGTTGCATCGAATGCTTCTGGCATGGCCTGCGACTCCGCTCAGGGGCGCGTCGCAGGCTGGCTCGGCCAGGGGt                                         >  2:288951/1‑150 (MQ=255)                                                                               tgtgGGCTGCATACATCCTGTGGGAGCGGGCATGCCCGCGAAGACGTCGGTGCAGGCTTTGCAGATTCCGGGGTTGCATCGAATGCTTCTGGCATGGCCTGCGACTCCGCTCAGGGGCGCGTCGCAGGCTGGCTCGGCCAGGGGTGCggg                                    >  2:1589122/1‑150 (MQ=255)                                                                               tgtgGGCTGCATACATCCTGTGGGAGCGGGCATGCCCGCGAAGACGTCGGTGCAGGCTTTGCAGATTCCGGGGTTGCATCGAATGCTTCTGGCATGGCCTGCGACTCCGCTCAGGGGCGCGTCGCAGGCTGGCTCGGCCAGGGGTGCggg                                    >  2:1587973/1‑150 (MQ=255)                                                                                   ggCTGCATACATCCTGTGGGAGCGGGCATGCCCGCGAAGACGTCGGTGCAGGCTTTGCAGATTCCGGGGTTGCATCGAATGCTTCTGGCATGGCCTGCGa                                                                                  >  2:1991781/1‑100 (MQ=255)                                                                                   ggCTGCATACATCCTGTGGGAGCGGGCATGCCCGCGAAGACGTCGGTGCAGGCTTTGCAGATTCCGGGGTTGCATCGAATGCTTCTGGCATGGCCTGCGa                                                                                  <  1:1991781/100‑1 (MQ=255)                                                                                   ggCTGCATACATCCTGTGGGAGCGGGCATGCCCGCGAAGACGTCGGTGCAGGCTTTGCAGATTCCGGGGTTGCATCGAATGCTTCTGGCATGGCCTGCGACTCCGCTCAGGGGCGCGTCGCAGGCTGGCTCGGCCAGGGGTGCGGGcgcc                                >  2:1545296/1‑150 (MQ=255)                                                                                    gCTGCATACATCCTGTGGGAGCGGGCATGCCCGCGAAGACGTCGGTGCAGGCTTTTCAGATTCCGGGGTTGCATCGAATGCTTCTGGCATGGCCTGCGACTCCGCTCAg                                                                        <  1:1669422/109‑1 (MQ=255)                                                                                    gCTGCATACATCCTGTGGGAGCGGGCATGCCCGCGAAGACGTCGGTGCAGGCTTTTCAGATTCCGGGGTTGCATCGAATGCTTCTGGCATGGCCTGCGACTCCGCTCAg                                                                        >  2:1669422/1‑109 (MQ=255)                                                                                     cTGCATACATCCTGTGGGAGCGGGCATGCCCGCGAAGACGTCGGTGCAGGCTTTGCAGATTCCGGGGTTGCATCGAATGCTTCTGGCATGGCCTGCGACTCCGCTCAGGGGCGCGTCGCAGGCTGGCTCGGCCAGGGGCGCGGGcgccgc                              >  2:715300/1‑150 (MQ=255)                                                                                      tGCATACATCCTGTGGGAGCGGGCATGCCCGCGAAGACGTCGGTGCAGGCTTTGCAGATTCCGGGGTTGCATCGAATGCTTCTGGCATGGCCTGCGACTCCGCTCAGGGGCGCGTCGCAGGCTGGCTCGGCCAGGGGTGCGGGCGCCGCt                             >  2:748752/1‑150 (MQ=255)                                                                                       gCATACATCCTGTGGGAGCGGGCATGCCCGCGAAGACGTCGGTGCAGGCTTTGCAGATTCCGGGGTTGCATCGAATGCTTCTGGCATGGCCTGCGACTCCGCTCAGGGGCGCGTCGCAGGCTGGCTCGGCCAGGGGTGCGGGCGCCGCTa                            >  2:1217307/1‑150 (MQ=255)                                                                                         aTACATCCTGTGGGAGCGGGCATGCCCGCGAAGACGTCGGTGCAGGCTTTGCAGATTCCGGGGTTGCATCGAATGCTTCTGGCATGGCCTGCGACTCCGCTCAGGGGCGCGTCGCAGGCTGGCTCGGCCAGGGGTGCGGGCGCCGCTAtt                          >  1:890960/1‑150 (MQ=255)                                                                                         aTACATCCTGTGGGAGCGGGCATGCCCGCGAAGACGTCGGTGCAGGCTTTGCAGATTCCGGGGTTGCATCGAATGCTTCTGGCATGGCCTGCGACTCCGCTCAGGGGCGCGTCGCAGGCTGGCTCGGCCAGGGGTGCGGGCGCCGCTAtt                          >  1:316589/1‑150 (MQ=255)                                                                                         aTACATCCTGTGGGAGCGGGCATGCCCGCGAAGACGTCGGTGCAGGCTTTGCAGATTCCGGGGTTGCATCGAATGCTTCTGGCATGGCCTGCGACTCCGCTCAGGGGCGCGTCGCAGGCTGGCTCGGCCAGGGGTGCGGGCGCCGCTAtt                          >  1:602213/1‑150 (MQ=255)                                                                                         aTACATCCTGTGGGAGCGGGCATGCCCGCGAAGACGTCGGTGCAGGCTTTGCAGATTCCGAAGTTGCATCGTCCAGCTCTGGGATGGCCTGCGACTCCGCTCAGGGGCGCGTCGCAGGCTGGCTCGGCCAGGGGTGCGGGCGCCGCTAtt                          >  1:2123019/1‑150 (MQ=255)                                                                                              tCCTGTGGGAGCGGGCATGCCCGCGAAGACGTCGTTGCAGGCTTTGCAGATTCCGGGGTTGCATCGACTGCTTCTGGCATGGCCTGCGACTCCGCTCAGGGGCGCGTCGCAGGCTGGCTCGGCCAGGGGTGCGGGCGCCGCTATTCCCCt                     <  1:1229074/150‑1 (MQ=255)                                                                                              tCCTGTGGGAGCGGGCATGCCCGCGAAGACGTCGGTGCAGGCTTTGCAGATTCCGGGGTTGCATCGAATGCTTCTTGCATGGCCTGCGACTCCGCTCAGGGGCGCGTCGCAGCCTGTCTCGGCCAGGGGTGCTGGCGCCGCTATTCCCCt                     <  1:1145191/150‑1 (MQ=255)                                                                                              tCCTGTGGGAGCGGGCATGCCCGCGAAGACGTCGGTGCAGGCTTTGCAGATTCCGGGGTTGCATCGAATGCTTCTGGCATGGCCTGCGACTCCGCTCAGGGGCGCGTCGCAGGCTGGCTCGGCCAGGGGTGCGGGCGCCGCTATTCCCCt                     >  1:848898/1‑150 (MQ=255)                                                                                              tCCTGTGGGAGCGGGCATGCCCGCGAAGACGTCGGTGCAGGCTTTGCAGATTCCGGGGTTGCATCGAATGCTTCTGGCATGGCCTGCGACTCCGCTCAGGGGCGCGTCGCAGGCTGGCTCGGCCAGGGGTGCGGGCGCCGCTATTCCCCt                     <  1:288951/150‑1 (MQ=255)                                                                                                ctgtgggagcgggcatgcccgcgaagaCGTCGGTGCAGGCTTTGCAGATTCCGGGGTTGCATCGAATGCTTCTGGCATGGCCTGCGACTCCGCTCAGGGGCGCGTCGCAGGCTGGCTCGGCCAGGGGTGCGGGCGCCGCTATTCCCCtgt                   <  1:1545296‑M2/123‑1 (MQ=255)                                                                                                ctgtgggagcgggcatgcccgcgaagaCGTCGGTGCAGGCTTTGCAGATTCCGGGGTTGCATCGAATGCTTCTGGCATGGCCTGCGACTCCGCTCAGGGGCGCGTCGCAGGCTGGCTCGGCCAGGGGTGCGGGCGCCGCTATTCCCCtgt                   >  1:852043‑M2/28‑150 (MQ=255)                                                                                                   tcttcgcgggcatgcccgcgaagaCGTCGGTGCAGGCTTTGCAGATTCCGGGGTTGCATCGAATGCTTCTGGCATGGCCTGCGACTCCGCTCAGGGGCGCGTCGCAGGCTGGCTCGGCCAGGGGTGCGGGCGCCGCTATTCCCCTGTGAg                >  2:164509‑M2/25‑150 (MQ=255)                                                                                                     ttcgcgggcatgcccgcgaagaCGTCGGTGCAGGCTTTGCAGATTCCGGGGTTGCATCGAATGCTTCTGGCATGGCCTGCGACTCCGCTCAGGGGCGCGTCGCAGGCTGGCTCGGCCAGGGGTGCGGGGGCCGCTATTCCCCTGTGAGCa              >  2:606211‑M2/23‑150 (MQ=255)                                                                                                          gggcatgcccgcgaagaCGTCGGTGCAGGCTTTGCAGATTCCGGGGTTGCATCGAATGCTTCTGGCATGGCCTGCGACTCCGCTCAGGGGCGCGTCGCAGGCTGGCTCGGCCAGGGGTGCGGGCGCCGCTATTCCCCTGTGAGCAGTTGa         <  2:757565‑M2/133‑1 (MQ=255)                                                                                                           ggcatgcccgcgaagcCGTCGGTGCAGGCTTTGCAGATTCCGGGGTTGCATCGAATGCTTCTGGCATGGCCTGCGACTCCGCTCAGGGGCGCGTCGCAGGCTGGCTCGGCCAGGGGTGCGGGCGCCGCTATTCCCCTGTGAGCAGTTGAt        <  1:849127‑M2/134‑1 (MQ=255)                                                                                                               tgcccgcgaagaCGTCGGTGCAGGCTTTGCAGATTCCGGGGTTGCATCGAATGCTTCTGGCATGGCCTGCGACTCCGCTCAGGGGCGCGTCGCAGGCTGGCTCGGCCAGGGGTGCGGGCGCCGCTATTCCCCTGTGAGCAGTTGAtcgtc    <  1:1275468‑M2/138‑1 (MQ=255)                                                                                                                 cgcgcgaagaCTTCGGGGCAGGCTTTGCAGATTCCGGGGTTGCATCGAATGCTTCTGGCATGGCCTGCGACTCCGCTCAGGGGCGCGTCGCAGGCTGGCTCGGCCAGGGGTGCGGGCGCCGCTATTCCCCTGTGAGCAGTTGAtcgtcgt  >  2:1274663‑M2/11‑150 (MQ=255)                                                                                                                 cccgcgaagaCGTCGGTGCAGGCTTTGCAGATTCCGGGGTTGCATCGAATGCTTCTGGCATGGCCTGCGACTCCGCTCAGGGGCGCGTCGCAGGCTGGCTCGGCCAGGGGTGCGGGCGCCGCTATTCCCCTGTGAGCAGTTGAtcgtcgt  >  2:2113162‑M2/11‑150 (MQ=255)                                                                                                                         gaCGTCGGTGCAGGCTTTGCAGATTCCGGGGTTGCATCGAATGCTTCTGGCATGGCCTGCGACTCCGCTCAGGGGCGCGTCGCa                                                            <  2:659010‑M2/82‑1 (MQ=255)                                                                                                                         gaCGTCGGTGCAGGCTTTGCAGATTCCGGGGTTGCATCGAATGCTTCTGGCATGGCCTGCGACTCCGCTCAGGGGCGCGTCGCa                                                            >  1:659010‑M2/3‑84 (MQ=255)                                                                                                                           |                                                                                                                                            AGGAGGTCGCGGGGGTAGGCGGAAATTTTTGCTGGGTTCTTCGCGGGCATGCCCGCTCCCACAGGTACATCACAGGTCTGTGGGCTGCATACATCCTGTGGGAGCGGGCATGCCCGCGAAGACGTCGGTGCAGGCTTTGCAGATTCCGGGGTTGCATCGAATGCTTCTGGCATGGCCTGCGACTCCGCTCAGGGGCGCGTCGCAGGCTGGCTCGGCCAGGGGTGCGGGCGCCGCTATTCCCCTGTGAGCAGTTGATCGTCGT  >  NC_002947/3947920‑3948181

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 32 ≤ 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.