New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_002947	5118958 =	49 (1.160)	3 (0.070)	3/252	NT	5.4%	coding (732/1341 nt)	PP_4505	sensor histidine kinase
	?	NC_002947	5119003 =	57 (1.380)					coding (777/1341 nt)	PP_4505	sensor histidine kinase

CTGGCACGGCTGGCAGCGCGGCGCGACGAGTTTGGCGTGCTGGCCAAGGACTTCAACAAGATGGGCGCACGCCTGCAAAGCACCATTGGCAGCCAGCGCCAGCTGCTACGCGACGTGTCCCACGAACTGCGCTC‑‑GCCACTGGCCCGGCTGCGCATCGCCCTGGCCCTGGCCGAACGCGCCGAGCCTGAGCAGCGGCAAGCGCTGTGGCCGCGCCTGACCCGCGAATGCGACCGCCTGGAAGACCTGATCAGCGAAATCCTCGCCCTGGCCCGGGTGGATGC  >  NC_002947/5118818‑5119098                                                                                                                                               |                                                                                                                                             cTGGCACGGCTGGCAGCGCGGCGCGACGAGTTTGGCGTGCTGGCCAAGGACTTCAACAAGATGGGCGCACGCCTGCAAAGCACCATTGGCAGCCAGCGCCAGCTGCTACGCGACGTGTCCCACGAACTGCGCTC‑‑GCCACTGGCCCGGCt                                                                                                                                      >  1:260688/1‑149 (MQ=255) cTGGCACGGCTGGCAGCGCGGCGCGACGAGTTTGGCGTGCTGGCCAAGGACTTCAACAAGATGGGCGCACGCCTGCAAAGCACCATTGGCAGCCAGCGCCAGCTGCTACGCGACGTGTCCCACGAACTGCGCTC‑‑GCCACTGGCCCGGCt                                                                                                                                      >  6:130010/1‑149 (MQ=255)           tGGCAGCGCGGCGCGACGAGTTTGGCGTGCTGGCCAAGGACTTCAACAAGATGGGCGCACGCCTGCAAAGCACCATTGGCAGCCAGCGCCAGCTGCTACGCGACGTGTCCCACGAACTGCGCTC‑‑GCCACTGGCCCGGCTGCGCATCgcc                                                                                                                            <  2:260688/149‑1 (MQ=255)              cAGCGCGGCGCGACGAGTTTGGCGTGCTGGCCAAGGACTTCAACAAGATGGGCGCACGCCTGCAAAGCACCATTGGCAGCCAGCGCCAGCTGCTACGCGACGTGTCCCACGAACTGCGCTC‑‑GCCACTGGCCCGGCTGCGCATCgccctg                                                                                                                         <  2:109064/149‑1 (MQ=255)                    ggcgcgACGAGTTTGGCGTGCTGGCCAAGGACTTCAACAAGATGGGCGCACGCCTGCAAAGCACCATTGGCAGCCAGCGCCAGCTGCTACGCGACGTGTCCCACGAACTGCGCTC‑‑GCCACTGGCCCGGCTGCGCATCgccctggccctg                                                                                                                   <  7:26339/149‑1 (MQ=255)                     gcgcgACGAGTTTGGCGTGCTGGCCAAGGACTTCAACAAGATGGGCGCACGCCTGCAAAGCACCATTGGCAGCCAGCGCCAGCTGCTACGCGACGTGTCCCACGAACTGCGCTC‑‑GCCACTGGCCCGGCTGCGCATCGccctggccctgg                                                                                                                  <  5:177067/149‑1 (MQ=255)                      cgcgACGAGTTTGGCGTGCTGGCCAAGGACTTCAACAAGATGGGCGCACGCCTGCAAAGCACCATTGGCAGCCAGCGCCAGCTGCTACGCGACGTGTCCCACGAACTGCGCTC‑‑GCCACTGGCCCGGCTGCGCATCGCcctggccctggc                                                                                                                 <  1:164332/149‑1 (MQ=255)                         gacgaGTTTGGCGTGCTGGCCAAGGACTTCAACAAGATGGGCGCACGCCTGCAAAGCACCATTGGCAGCCAGCGCCAGCTGCTACGCGACGTGTCCCACGAACTGCGCTC‑‑GCCACTGGCCCGGCTGCGCATCGCCCTGGCCCTGGCCGa                                                                                                              <  7:77676/149‑1 (MQ=255)                               tttGGCGTGCTGGCCAAGGACTTCAACAAGATGGGCGCACGCCTGCAAAGCACCATTGGCAGCCAGCGCCAGCTGCTACGCGACGTGTCCCACGAACTGCGCTC‑‑GCCACTGGCCCGGCTGCGCATCGCCCTGGCCCTGGCCGAACgcgc                                                                                                        >  6:211946/1‑149 (MQ=255)                                 tGGCGTGCTGGCCAAGGACTTCAACAAGATGGGCGCACGCCTGCAAAGCACCATTGGCAGCCAGCGCCAGCTGCTACGCGACGTGTCCCACGAACTGCGCTC‑‑GCCACTGGCCCGGCTGCGCATCGCCCTGGCCCTGGCCGAACGCGcc                                                                                                       >  8:119802/1‑148 (MQ=255)                                     ggcttgttcggcatccacccgggccagggcgaggatttcgctgatcaggtcttccaggcggtcgcattcgcgggtcaggcgcggccacagcgcttgccgctgctcaGGCCCGGCTGCGCATCGCCCTGGCCCTGGCCGAACGCGCCGa                                                                                                     >  3:90084‑M1/107‑148 (MQ=255)                                      tGCTGGCCAAGGACTTCAACAAGATGGGCGCACGCCTGCAAAGCACCATTGGCAGCCAGCGCCAGCTGCTACGCGACGTGTCCCACGAACTGCGCTC‑‑GCCACTGGCCCGGCTGCGCATCGCCCTGGCCCTGGCCGAACGCGCCGAGCCt                                                                                                 >  2:33346/1‑149 (MQ=255)                                         tGGCCAAGGACTTCAACAAGATGGGCGCACGCCTGCAAAGCACAATTGGCAGCCAGCGCCAGCTGCTACGCGACGTGTCCCACCAACTGCGCTC‑‑GCCACTGGCCCGGCTGCGCATCGCCCTGGCCCTGGCCGAACGCGCCGCGCCt                                                                                                 >  4:60933/1‑146 (MQ=255)                                           ttcggcatccacccgggccagggcgaggatttcgctgatcaggtcttccaggcggtcgcattcgcgggtcaggcgcggccacagcgcttgccgctgctcaGGCCCGGCTGCGCATCGCCCTGGCCCTGGCCGAACGCGCCGAGCCt                                                                                                 <  4:220042‑M1/46‑1 (MQ=255)                                           ttcggcatccacccgggccagggcgaggatttcgctgatcaggtcttccaggcggtcgcattcgcgggtcaggcgcggccacagcgcttgccgctgctcaGGCCCGGCTGCGCATCGCCCTGGCCCTGGCCGAACGCGCCGAGCCTGa                                                                                               >  3:220042‑M1/101‑148 (MQ=255)                                            ccAAGGACTTCAACAAGATGGGCGCACGCCTGCAAAGCACCATTGGCAGCCAGCGCCAGCTGCTACGCGACGTGTCCCACGAACTGCGCTC‑‑GCCACTGGCCCGGCTgcg                                                                                                                                   >  7:13032/1‑109 (MQ=255)                                            ccAAGGACTTCAACAAGATGGGCGCACGCCTGCAAAGCACCATTGGCAGCCAGCGCCAGCTGCTACGCGACGTGTCCCACGAACTGCGCTC‑‑GCCACTGGCCCGGCTgcg                                                                                                                                   <  8:13032/109‑1 (MQ=255)                                              aaGGACTTCAACAAGATGGGCGCACGCCTGCAAAGCACCATTGGCAGCCAGCGCCAGCTGCTACGCGACGTGTCCCACGAACTGCGCTC‑‑GCCACTGGCCCGGCTGCGCATCGCCCTGGCCCTGGCCGAACGCGCCGAGCCTGAGCAGCg                                                                                         >  1:10726/1‑149 (MQ=255)                                                      caacaaGATGGGCGCACGCCTGCAAAGCACCATTGGCAGCCAGCGCCAGCTGCTACGCGACGTGTCCCACGAACTGCGCTC‑‑GCCACTGGCCCGGCTGCGCATCGCCCTGGCCCTGGCCGAACGCGCCGAGCCTGAGCAGCGGCAAgcgc                                                                                 >  7:191055/1‑149 (MQ=255)                                                       aacaaGATGGGCGCACGCCTGCAAAGCACCATTGGCAGCCAGCGCCAGCTGCTACGCGACGTGTCCCACGAACTGCGCTC‑‑GCCACTGGCCCGGCTGCGCATCGCCCTGGCCCTGGCCGAACGCGCCGAGc                                                                                                   <  6:1257/130‑1 (MQ=255)                                                       aacaaGATGGGCGCACGCCTGCAAAGCACCATTGGCAGCCAGCGCCAGCTGCTACGCGACGTGTCCCACGAACTGCGCTC‑‑GCCACTGGCCCGGCTGCGCATCGCCCTGGCCCTGGCCGAACGCGCCGAGc                                                                                                   >  5:1257/1‑130 (MQ=255)                                                       aacaaGATGGGCGCACGCCTGCAAAGCACCATTGGCAGCCAGCGCCAGCTGCTACGCGACGTGTCCCACGAACTGCGCTC‑‑GCCACTGGCCCGGCTCCGCATCGCCCTGGCCCTGGCCGAACGCGCCGAGCCTGAGCAGCGGCAAGCGCt                                                                                <  8:40920/149‑1 (MQ=255)                                                       aacaaGATGGGCGCACGCCTGCAAAGCACCATTGGCAGCCAGCGCAAGCTGCTACGCGACGTGTCCCACGAACTGCGCTC‑‑GCCACTGGcc                                                                                                                                           <  7:680/90‑1 (MQ=255)                                                         caaGATGGGCGCACGCCTGCAAAGCACCATTGGCAGCCAGCGCCAGCTGCTACGCGACGTGTCCCACGAACTGCGCTC‑‑GCCACTGGCCCGGCTGCGCATCGCCCTGGCCCTGGCCGAACGCGCCGAGCCTGAGCAGCGGCAAGCGCtgt                                                                              >  8:99664/1‑149 (MQ=255)                                                            gATGGGCGCACGCCTGCAAAGCACCATTGGCAGCCAGCGCCAGCTGCTACGCGACGTGTCCCACGAACTGCGCTC‑‑GCCACTGGCCCGGCTGCGCATCGCCCTGGCCCTGGCCGAACGCGCCGAGCCTGAGCAGCGGCAAGCGCTGTGGc                                                                           <  3:105854/149‑1 (MQ=255)                                                                ggCGCACGCCTGCAAAGCACCATTGGCAGCCAGCGCCAGCTGCTACGCGACGTGTCCCACGAACTGCGCTC‑‑GCCACTGGCCCGGCTGCGCATCGCCCTGGCCCTGGCCGAACGCGCCGAGCCTGAGCAGCGGCAAGCGCTGTGGCcgcg                                                                       <  3:161631/149‑1 (MQ=255)                                                                 gcgcACGCCTGCAAAGCACCATTGGCAGCCAGCGCCAGCTGCTACGCGACGTGTCCCACGAACTGCGCTC‑‑GCCACTGGCCCGGCTGCGCATCGCCCTGGCCCTGGCCGAACGCGCCGAGCCTGAGCAGCGGCACGCGCTGTGGCCgcgc                                                                      >  2:265887/1‑149 (MQ=255)                                                                  cgcACGCCTGCAAAGCACCATTGGCAGCCAGCGCCAGCTGCTACGCGACGTGTCCCACGAACTGCGCTC‑‑GCCACTGGCCCGGCTGCGCATCGCCCTGGCCCTGGCCGAACGCGCCGAGCCTGAGCAGCGGCAAGCGCTGTGGCCGCGcc                                                                     >  3:158652/1‑149 (MQ=255)                                                                  cgcACGCCTGCAAAGCACCATTGGCAGCCAGCGCCAGCTGCTACGCGACGTGTCCCACGAACTGCGCTC‑‑GCCACTGGCCCGGCTGCGCATCGCCCTGGCCCTGGCCGAACGCGCCGAGCCTGAGCAGCGGCAAGCGCTGTGGCCGCGcc                                                                     <  8:191055/149‑1 (MQ=255)                                                                       gCCTGCAAAGCACCATTGGCAGCCAGCGCCAGCTGCTACGCGACGTGTCCCACGAACTGCGCTCCGGGCACTGGCCCGGCTCCGAATCGCACTGGCACTGCCCGAACCCGCCGAGCCTGAGCAGCGTCAAGCGCTGTGGCCGCGCCTGa                                                                  >  1:80802/1‑149 (MQ=255)                                                                        ccTGCAAAGCACCATTGGCAGCCAGCGCCAGCTGCTACGCGACGTGTCCCACGAACTGCGCTC‑‑GCCACTGGCCCGGCTGCGCATCGCCCTGGCCCTGGCCGAACGCGCCGAGCCTGAGCAGCGGCAAGCGCtgt                                                                              <  1:204893/134‑1 (MQ=255)                                                                        ccTGCAAAGCACCATTGGCAGCCAGCGCCAGCTGCTACGCGACGTGTCCCACGAACTGCGCTC‑‑GCCACTGGCCCGGCTGCGCATCGCCCTGGCCCTGGCCGAACGCGCCGAGCCTGAGCAGCGGCAAGCGCtgt                                                                              <  1:201536/134‑1 (MQ=255)                                                                        ccTGCAAAGCACCATTGGCAGCCAGCGCCAGCTGCTACGCGACGTGTCCCACGAACTGCGCTC‑‑GCCACTGGCCCGGCTGCGCATCGCCCTGGCCCTGGCCGAACGCGCCGAGCCTGAGCAGCGGCAAGCGCtgt                                                                              >  2:201536/1‑134 (MQ=255)                                                                        ccTGCAAAGCACCATTGGCAGCCAGCGCCAGCTGCTACGCGACGTGTCCCACGAACTGCGCTC‑‑GCCACTGGCCCGGCTGCGCATCGCCCTGGCCCTGGCCGAACGCGCCGAGCCTGAGCAGCGGCAAGCGCtgt                                                                              >  2:204893/1‑134 (MQ=255)                                                                        ccTGCAAAGCACCATTGGCAGCCAGCGCCAGCTGCTACGCGACGTGTCCCACGAACTGCGCTC‑‑GCCACTGGCCCGGCTGCGCATCGCCCTGGCCCTGGCCGAACGCGCCGAGCCTGAGCAGCGGCAAGCGCTGTGGCCGCGCCTGAccc                                                               <  7:119802/149‑1 (MQ=255)                                                                                          cagccagcGCCAGCTGCTACGCGACGTGTCCCACGAACTGCGCTC‑‑GCCACTGGCCCGGCTGCGCATCGCCCTGGCCCTGGCCGAACGCGCCGAGCCTGAGCAGCGGCAAGCGCTGTGGCCGCGCCTGACCCGCGAATGCGACCGCCTg                                              >  4:49460/1‑148 (MQ=255)                                                                                           agccagcGCCAGCTGCTACGCGACGTGTCCCACGAACTGCGCTC‑‑GCCACTGGCCCGGCTGCGCATCGCCCTGGCCCTGGCCGAACGCGCCGAGCCTGAGCAGCGGCAAGCGCTGTGGCCGCGCCTGACCCGCGAATGCGACCGCCTgg                                             >  8:41744/1‑148 (MQ=255)                                                                                               agcgccagcTGCTACGCGACGTGTCCCACGAACTGCGCTC‑‑GCCACTGGCCCGGCTGCGCATCGCCCTGGCCCTGGCCGAACGCGCCGAGCCTGAGCAGCGGCAAGCGCTGTGGCCGCGCCTGACCCGCGAATGCGACCGCCTGGAAGAc                                        <  7:41744/149‑1 (MQ=255)                                                                                                              gcgACGTGTCCCACGAACTGCGCTC‑‑GCCACTGGCCCGGCTGCGCATCGCCCTGGCCCTGGCCGAACGCGCCGAGCCTGAGCAGCGGCAAGCGCTGTGGCCGCGCCTGACCCGCGAATGCGACCGCCTGGAAGACCTGATCAGCGAAATc                         <  5:211946/149‑1 (MQ=255)                                                                                                              gcgACGTGTCCCACGAACTGCGCTC‑‑GCCACTGGCCCGGCTGCGCATCGCCCTGGCCCTGGCCGAACGCGCCGAGCCTGAGCAGCGGCAAGCGCTGTGGCCGCGCCTGACCCGCGAATGCGACCGCCTGGAAGACCTGATCAGCGAAATc                         >  5:43739/1‑149 (MQ=255)                                                                                                                      tCCCACGAACTGCGCTC‑‑GCCACTGGCCCGGCTGCGCATCGCCCTGGCCCTGGCCGAACGCGCCGAGCCTGAGCAGCGGCAAGCGCTGTGGCCGCGCCTGACCCGCGAATGCGACCGCCTGGAAGACCTGATCAGCGAAATCCTCGccc                  <  2:10726/148‑1 (MQ=255)                                                                                                                      tCCCACGAACTGCGCTC‑‑GCCACTGGCCCGGCTGCGCATCGCCCTGGCCCTGGCCGAACGCGCCGAGCCTGAGCAGCGGCAAGCGCTGTGGCCGCGCCTGACCCGCGAATGCGACCGCCTGGAACACCTGATCAGCGAAATCCTCGCCCt                 >  4:256299/1‑149 (MQ=255)                                                                                                                        ccACGAACTGCGCTC‑‑GCCACTGGCCCGGCTGCGCATCGCCCTGGCCCTGGCCGAACGCGCCGAGCCTGAGCAGCGGCAAGCGCTGTGGCcgctc                                                                      <  5:163376/94‑3 (MQ=255)                                                                                                                        ccACGAACTGCGCTC‑‑GCCACTGGCCCGGCTGCGCATCGCCCTGGCCCTGGCCGAACGCGCCGAGCCTGAGCAGCGGCAAGCGCTGTGGCCgcgc                                                                      >  6:163376/1‑94 (MQ=255)                                                                                                                        ccACGAACTGCGCTC‑‑GCCACTGGCCCGGCTGCGCATCGCCCTGGCCCTGGCCGAACGCGCCGAGCCTGAGCAGCGGCAAGCGCTGTGGCCGCGCCTGACCCGCGAATGCGACCGCCTGGAAGACCt                                      >  7:1513/1‑126 (MQ=255)                                                                                                                        ccACGAACTGCGCTC‑‑GCCACTGGCCCGGCTGCGCATCGCCCTGGCCCTGGCCGAACGCGCCGAGCCTGAGCAGCGGCAAGCGCTGTGGCCGCGCCTGACCCGCGAATGCGACCGCCTGGAAGACCt                                      <  8:1513/126‑1 (MQ=255)                                                                                                                         cACGAACTGCGCTC‑‑GCCACTGGCCCGGCTGCGCATCGCCCTGGCCCTGGCCGAACGCGCCGAGCCTGAGCAGCGGCAAGCGCTGTGGCCGCGCCTGACCCGCGAATGCGACCGCCTGGAAGCCCTGATCAGCGCAATCCTCGCCCTGGc              >  5:208789/1‑149 (MQ=255)                                                                                                                         cACGAACTGCGCTC‑‑GCCACTGGCCCGGCTGCGCATCGCCCTGGCCCTGGCCGAACGCGCCGAGCCTGAGCAGCGGCAAGCGCTGTGGCCGCGCCTGACCCGCGAATGCGACCGCCTGGAAGACCTGATCAGCGAAATCCTCGCCCTGGc              >  2:182014/1‑149 (MQ=255)                                                                                                                            gAACTGCGCTC‑‑GCCACTGGCCCGGCTGCGCATCGCCCTGGCCCTGGCCGAACGCGCCGAGCCTGAGCAGCGGCAAGCGCTGTGGCCGCGCCTGACCCGCGAATGCGACCGCCTGGAAGACCTGATCAGCGAAATCCTCGCCCTGGCCCg           <  6:155888/149‑1 (MQ=255)                                                                                                                            gAACTGCGCTC‑‑GCCACTGGCCCGGCTGCGCATCGCCCTGGCCCTGGCCGAACGCGCCGAGCCTGAGCAGCGGCAAGCGCTGTGGCCGCGCCTGACCCGCGAATGCGACCGCCTGGAAGACCTGATCAGCGAAATCCTCGCCCTGGCCCg           <  4:158652/149‑1 (MQ=255)                                                                                                                               cTGCGCTC‑‑GCCACTGGCCCGGCTGCGCATCGCCCTGGCCCTGGCCGAACGCGCCGAGCCTGAGCAGCGGCAAGCGCTGTGGCCGCGCCTGACCCGAGAATGCGACCTCCTGGATGACCTGATCAGCGAAATCCTCGCCCTGGCCCGGGt        <  2:80802/149‑1 (MQ=255)                                                                                                                                  cgcTC‑‑GCCACTGGCCCGGCTGCGCATCGCCCTGGCCCTGGCCGAACGCGCCGAGCCTGAGCAGCGGCAAGCGCTGTGGCCGCGCCTGACCCGCGAATGCGACCGCCTGGAAGACCTGATCAGCGAAATCCTCGCCCTGGCCCGGGTg       <  7:99664/147‑1 (MQ=255)                                                                                                                                         gCCACTGGCCCGGCTGCGCATCGCCCTGGCCCTGGCCGAACGCGCCGAGCCTGAGCAGCGGCAAGCGCTGTGGCCGCGCCTGACCCGCGAATGCGACCGCCTGGAAGACCTGATCAGCGAAATCCTCGCCCTGGCCCGGGTGGATGc  <  4:132860/147‑1 (MQ=255)                                                                                                                                           cACTGGCCCGGCTGCGCATCGCCCTGGCCCTGGCCGAACGCGCCGAGCCTGAGCAGCGGCAAGCGCTGTGGCCGCGCCTGACCCGCGAATGCGACCGCCTGGAAGACCTGAt                                   <  7:107367/112‑1 (MQ=255)                                                                                                                                           cACTGGCCCGGCTGCGCATCGCCCTGGCCCTGGCCGAACGCGCCGAGCCTGAGCAGCGGCAAGCGCTGTGGCCGCGCCTGACCCGCGAATGCGACCGCCTGGAAGACCTGAt                                   >  8:107367/1‑112 (MQ=255)                                                                                                                                               |                                                                                                                                             CTGGCACGGCTGGCAGCGCGGCGCGACGAGTTTGGCGTGCTGGCCAAGGACTTCAACAAGATGGGCGCACGCCTGCAAAGCACCATTGGCAGCCAGCGCCAGCTGCTACGCGACGTGTCCCACGAACTGCGCTC‑‑GCCACTGGCCCGGCTGCGCATCGCCCTGGCCCTGGCCGAACGCGCCGAGCCTGAGCAGCGGCAAGCGCTGTGGCCGCGCCTGACCCGCGAATGCGACCGCCTGGAAGACCTGATCAGCGAAATCCTCGCCCTGGCCCGGGTGGATGC  >  NC_002947/5118818‑5119098

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ 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.