New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_002947	250227 =	47 (0.960)	3 (0.070)	3/242	NT	6.6%	coding (976/1347 nt)	nfeD	membrane bound peptidase NefD
	?	NC_002947	250271 =	42 (0.930)					coding (932/1347 nt)	nfeD	membrane bound peptidase NefD

CCGAGAGCAGCGCCAAGGTGCCGATCAAGGCCAGGGGGATGCCGAAACCGGGAGCGTCGGTGTCGATCAGGATCAATGCGCCGACCACAAAGGCAACGATGCCGCCGAAGCCGACCAC‑‑GCCGAAACTGGGCAAGAAGGCTTCGGCGATCATGAAGGTGATGCCAAGCAGGATCAGCGCCACCCCGGCAAAACTCACCGGCAACAGCTGCAGCGCATACAGCGCCAGCAGCAGGCAGATACCACCGACCACACCGCCCACCGCAGAACCTGGGTTCATGAATTCGAACAACAGGCC  >  NC_002947/250125‑250419                                                                                                                                                     |                                                                                                                                                     ccGAGAGCAGCTCCAAGGTGCCGATCTAGGCCAGGGGGATGCCGAAACCGGGAGCGTCGGTGTCGATCAGGATCAATGCGCCGACCACAAAGGAAACGATGCCGCCGAAGCCGACCAC‑‑GCCGAAACTGGGCAAGAAGGCTTCGGCGAt                                                                                                                                                     <  4:8976/148‑1 (MQ=255) ccGAGAGCAGCGCCAAGGTGCCGATCAAGGCCAGGGGGATGCCGAAACCGGGAGCGTCGGTGTCGATCAGGATCAATGCGCCGACCACAAAGGCAACGATGCCGCCGAAGCCGACCAC‑‑GCCGAAACTGGGCAAGAAGGCTTCGGCGAt                                                                                                                                                     >  2:233770/1‑148 (MQ=255) ccGAGAGCAGCGCCAAGGTGCCGATCAAGGCCAGGGGGATGCCGAAACCGGGAGCGTCGGTGTCGATCAGGATCAATGCGCCGACCACAAAGGCAACGATGCCGCCGAAGCCGACCAC‑‑GCCGAAACTGGGCAAGAAGGCTTCGGCGAt                                                                                                                                                     >  2:229835/1‑148 (MQ=255) ccGAGAGCAGCGCCAAGGTGCCGATCAAGGCCAGGGGGATGCCGAAAACGGGAGCGTCGGTGTCGATCAGGATCAATGCGCCGACCACAAAGGCAACGATGCCTCCGAAGCCGACCAC‑‑GCCGAAACTGGGCAAGAAGGCTGCGGCGAt                                                                                                                                                     >  3:8976/1‑148 (MQ=255)     gagCAGCGCCAAGGTGCCGATCAAGGCCAGGGGGATGCCGAAACCGGGAGCGTCGGTGTCGATCAGGATCAATGCGCCGACCACAAAGGCAACGATGCCGCCGAAGCCGACCAC‑‑GCCGAAACTGGGCAAGAAGGCTTCGGCGATCATGa                                                                                                                                                <  3:247657/149‑1 (MQ=255)        cagcGCCAAGGTGCCGATCAAGGCCAGGGGGATGCCGAAACCGGGAGCGTCGGTGTCGATCAGGATCAATGCGCCGACCACAAAGGCAACGATGCCGCCGAAGCCGACCAC‑‑GCCGAAACTGGGCAAGAAGGCTTCGGCGATCATGAAgg                                                                                                                                             <  7:276015/149‑1 (MQ=255)            gcCAAGGTGCCGATCAAGGCCAGGGGGATGCCGAAACCGGGAGCGTCGGTGTCGATCAGGATCAATGCGCCGACCACAAAGGCAACGATGCCGCCGAAGCCGACCAC‑‑GCCGAAACTGGGCAAGAAGGCTTCGGCGATCATGAAGGTGAt                                                                                                                                         <  1:229835/149‑1 (MQ=255)            gcCAAGGTGCCGATCAAGGCCAGGGGGATGCCGAAACCGGGAGCGTCGGTGTCGATCAGGATCAATGCGCCGACCACAAAGGCAACGATGCCGCCGAAGCCGACCAC‑‑GCCGAAACTGGGCAAGAAGGCTTCGGCGATCATGAAGGTGAt                                                                                                                                         <  1:233770/149‑1 (MQ=255)              cAAGGTGCCGATCAAGGCCAGGGGGATGCCGAAACCGGGAGCGTCGGTGTCGATCAGGATCAATGCGCCGCCCACAAAGGCAACGATGCCGCCGAAGCCGACCAC‑‑GCCGAAACTGGGCAAGAAGGCTTCGGCGATCATGAAGGTGATGc                                                                                                                                       >  2:94963/1‑149 (MQ=255)                aGGTGCCGATCAAGGCCAGGGGGATGCCGAAACCGGGAGCGTCGGTGTCGATCAGGATCAATGCGCCGACCACAAAGGCAACGATGCCGCCGAAGCCGACCAC‑‑GCCGAAACTGGGCAAGAAGGCTTCGGCGATCATGAAGGTGATGcc                                                                                                                                      >  4:11606/1‑148 (MQ=255)                 tgTGCCCATCAAGGCCATGGGGATGCCGAAACCGGGAGACTCGTTGTCGATCATGATCAATGCGCCGACCACAAAGGAAACTATGCCGCCGAACCCGACCAC‑‑GCCGAAACTGGGCAAGAAGGCTTCGGCGATCATGAAGTTGATGCCa                                                                                                                                     <  6:76707/147‑1 (MQ=255)                 ggTGCCGATCAAGGCCAGGGGGATGCCGAAACCGGGAGCGTCGGTGTCGATGAGGATCAATGCGCCGACGACTAAGGCAACGATGCCGCCGATGCCGACCAC‑‑GCCGAAACTGGGCAAGAAGGGTTCGGCGATCATGAAGGTGATGCGaa                                                                                                                                    >  5:76707/1‑149 (MQ=255)                   tGCCGATCAAGGCCAGGGGGATGCCGAAACCGGGAGCGTCGGTGTCGATCAGGATCAATGCGCCGACCACAAAGGCAACGATGCCGCCGAAGCCGACCAC‑‑GCCGAAACTGGGCAAGAAGGCTTCGGCGATCATGAAGGTGATGCCAAGc                                                                                                                                  <  4:178883/149‑1 (MQ=255)                   tGCCGATCAAGGCCAGGGGGATGCCGAAACCGGGAGCGTCGGTGTCGATCAGGATCAATGCGCCGACCACAAAGGCAACGATGCCGCCGAAGCCGACCAC‑‑GCCGAAACTGGGCAAGAAGGCTTCGGCGATCATGAAGGTGATGCCAAGc                                                                                                                                  <  5:98972/149‑1 (MQ=255)                            aGGCCAGGGGGATGCCGAAACCGGGAGCGTCGGTGTCGATCAGGATCAATGCGCCGACCACAAAGGCAACGATGCCGCCGAAGCCGACCAC‑‑GCCGAAACTGGGCAAGAAGGCTTCGGCGATCATGAAGGTGATGCCAAGCAGGATCAgc                                                                                                                         >  4:37727/1‑149 (MQ=255)                                       aTGCCGAAACCGGGAGCGTCGGTGTCGATCAGGATCAATGCGCCGACCACAAAGGCAACGATGCCGCCGAAGCCGACCAC‑‑GCCGAAACTGGGCAAGAAGGCTTCGGCGATCATGAAGGTGATGCCAAGCAGGATCAGCGCCACCCCgg                                                                                                               >  7:59221/1‑148 (MQ=255)                                         gCCGAAACCGGGAGCGTCGGTGTCGATCAGTAGCAATGCGCCGACCACAAAGGCAACTATGCCGCCGAATCCGCCCACCTCCCGAAACTGGGCAAGAAGGCTTCGGCGATCATGAAGGTGATGCCAAGCAGGATCAGCGCCACCCCgg                                                                                                               <  1:94963/148‑1 (MQ=255)                                           cGAAACCGGGAGCGTCGGTGTCGATCAGGATCAATGCGCCGACCACAAAGGCAACGATGCCGCCGAAGCCGACCAC‑‑GCCGAAACTGGGCAAGAAGGCTTCGGCGATCATGAAGGTGATGCCAAGCAGGATCAGCGCCACCCCGGCaaaa                                                                                                          >  1:200956/1‑149 (MQ=255)                                             aaaCCGGGAGCGTCGGTGTCGATCAGGATCAATGCGCCGACCACAAAGGCAACGATGCCGCCGAAGCCGACCAC‑‑GCCGAAACTGGGCAAGAAGGCTTCGGCGATCATGAAGGTGATGCCAAGCAGGATCAGCGCCACCCCGGCAAAACt                                                                                                        >  8:74710/1‑149 (MQ=255)                                                ccGGGAGCGTCGGTGTCGATCAGGATCAATGCGCCGACCACAAAGGCAACGATGCCGCCGAAGCCGACCAC‑‑GCCGAAACTGGGCAAGAAGGCTTCGGCGATCATGAAGGTGATGCCAAGCAGGATCAGCGCCACCCCGGCAAAACTCAc                                                                                                     <  8:59221/149‑1 (MQ=255)                                                 cGGGAGCGTCGGTGTCGATCAGGATCAATGCGCCGACCACAAAGGCAACGATGCCGCCGACGCCGACCAC‑‑GCCGAAACTGGGCAAGAAGGCTTCGGCGATCATGAAGGTGATGCCAAGCAGGATCAGCGCCACCCCg                                                                                                                >  4:247152/1‑137 (MQ=255)                                                  gggAGCGTCGGTGTCGATCAGGATCAATGCGCCGACCACAAAGGCAACGATGCCGCCGAAGCCGACCAC‑‑GCCGAAACTGGGCAAGAAGGCTTCGGCGATCATGAAGGTGATGCCAAGCAGGATCAGCGCCACCCCGGCAAAACTCACCg                                                                                                   <  2:200956/149‑1 (MQ=255)                                                      gCGTCGGTGTCGATCAGGATCAATGCGCCGACCACAAAGGCAACGATGCCGCCGAAGCCGACCAC‑‑GCCGAAACTGGGCAAGAAGGCTTCGGCGATCATGAAGGTGATGCCAAGCAGGATCAGCGCCACCCCGGCAAAACTCACCGGCaa                                                                                               <  3:11606/149‑1 (MQ=255)                                                                   tCAGGATCAATGCGCCGACCACAAAGGCAACGATGCCGCCGAAGCCGACCAC‑‑GCCGAAACTGGGCAAGAAGGCTTCGGCGATCATGAAGGTGATGCCAAGCAGGATCAGCGCCACCCCGGCAAAACTCACCGGCAACAGCTGCAGCGCa                                                                                  <  7:228888/149‑1 (MQ=255)                                                                     aGGATCAATGCGCCGACCACAAAGGCAACGATGCCGCCGAAGCCGACCAC‑‑GCCGAAACTGGGCAAGAAGGCTTCGGCGATCATGAAGGTGATGCCAAGCAGGATCAGCGCCACCCCGGCAAAACTCACCGGCAACAGCTGCAGCGCATa                                                                                <  6:195830/149‑1 (MQ=255)                                                                       gATCAATGCGCCGACCACAAAGGCAACGATGCCGCCGAAGCCGACCAC‑‑GCCGAAACTGGGCAAGAAGGCTTCGGCGATCATGAAGGTGATGCCAAGCAGGATCAGCGCCACCCCGGCAAAACTCACCGGCAACAGCTGCAGCGCATa                                                                                >  6:239584/1‑147 (MQ=255)                                                                            atccgcCGACCACAAAGGCAACGATGCCGCCGAAGCCGCCCAC‑‑GCCGAAACTGGGCAAGAAGGCTTCGGACAACAAGAAGGTGATGCCAAGCAGGATCAGCGCCACCCCGGCAAGACGCACCGGCAACAGCAGCAGCGCATACAgcgc                                                                          >  4:64453/4‑148 (MQ=255)                                                                                        caAAGGCAACGATGACGCAGAAAACCAACAC‑‑CCCGAAACAGGGCAAGAAGGCATAGGCCATCATGAAGGTGATGCCAAGCATGATAACCCCCAACCCGGCAAAACTCACCGGAAACAGCTGCAGCGCAAACAACCCcacccgcaac                                                                >  4:119326/1‑144 (MQ=255)                                                                                         aaaGGCAACGATGCCGCCGAAGCCGACCAC‑‑GCCGAAACTGGGCAAGAAGGCTTCGGCGATCATGAAGGTGATGCCAAGCAGGATCAGCGCCACCCCGGCAAAACTCACCGGCAACAGCTGCAGCGCATACAGCGCCAGCAgcagg                                                                >  3:232111/1‑145 (MQ=255)                                                                                            ggCAACGATGCCGCCGAAGCCGACCAC‑‑GCCGAAACTGGGCAAGAAGGCTTCGGCGATCATGAAGGTGATGCCAAGCAGGATCAGCGCCACCCCGGCAAAACTCACCGGCAACAGCTGCAGCGCATACAGCGCCAGCAGCAGGCAGATac                                                         <  7:74710/149‑1 (MQ=255)                                                                                                aCGATGCCGCCGAAGCCGACCAC‑‑GCCGAAACTGGGCAAGAAGGCTTCGGCGATCATGAAGGTGATGCCAAGCAGGATCAGCGCCACCCCGGCAAAACTCACCGGCAACAGCTGCAGCGCATACAGCGCCAGCAGCAGGCAGATaccacc                                                     <  3:37727/149‑1 (MQ=255)                                                                                                 cGATGCCGCCGAAGCCGACCAC‑‑GCCGAAACTGGGCAAGAAGGCTTCGGCGATCATGAAGGTGATGCCAAGCAGGATCAGCGCCACCCCGGCAAAACTCACCGGCAACAGCTGCAGCGCATACAGCGCCAGCAGCAGGCAGATACCACCg                                                    >  7:152394/1‑149 (MQ=255)                                                                                                   aTGCCGCCGAAGCCGACCAC‑‑GCCGAAACTGGGCAAGAAGGCTTCGGCGATCATGAAGGTGATGCCAAGCAGGATCAGCGCCACCCCGGCAAAACTCACCGGCAACAGCTGCAGCGCATACAGCGCCAGCAGCAGGCAGATACCACCGAc                                                  <  4:172581/149‑1 (MQ=255)                                                                                                     gccgccGAAGCCGACCAC‑‑GCCGAAACTGGGCAAGAAGGCTTCGGCGATCATGAAGGTGATGCCAAGCAGGATCAGCGCCACCCCGGCAAAACTCACCGGCAACAGCTGCAGCGCATACAGCGCCAGCAGCAGGCAGATACCACCGACca                                                >  3:253397/1‑149 (MQ=255)                                                                                                         cgccgaagccttcttgcccagtttcggcgtggtcggcttcggcgATCATGAAGGTGATGCCAAGCAGGATCAGCGCCACCCCGGCAAAACTCACCGGCAACAGCTGCAGCGCATACAGCGCCAGCAGCAGGCAGATACCACCGACcaca                                              >  6:132118‑M2/45‑149 (MQ=255)                                                                                                           ccgaagccttcttgcccagtttcggcgtggtcggcttcggcgATCATGAAGGTGATGCCAAGCAGGATCAGCGCCa                                                                                                                     <  8:146538‑M2/34‑1 (MQ=255)                                                                                                           ccgaagccttcttgcccagtttcggcgtggtcggcttcggcgATCATGAAGGTGATGCCAAGCAGGATCAGCGCCa                                                                                                                     >  7:146538‑M2/43‑76 (MQ=255)                                                                                                            AAGCCGACCAC‑‑GCCGAAACTGGGCAAGAAGGCTTCGGCGATCATGAAGGTGATGCCAAGCAGGATCAGCGCCACCCCGGCAAAACTCACCGGCAACAGCTGCAGCGCATACAGCGCCAGCAgcaggc                                                               <  1:300099‑M1/127‑1 (MQ=255)                                                                                                            AAGCCGACCAC‑‑GCCGAAACTGGGCAAGAAGGCTTCGGCGATCATGAAGGTGATGCCAAGCAGGATCAGCGCCACCCCGGCAAAACTCACCGGCAACAGCTGCAGCGCATACAGCGCCAGCAgcaggc                                                               >  2:300099‑M1/1‑127 (MQ=255)                                                                                                                    cAC‑‑GCCGAAACTGGGCAAGAAGGCTTCGGCGATCATGAAGGTGATGCCAAGCAGGATCAGCGCCACCCCGGCAAAACTCACCGGCAACAGCTGCAGCGCATACAGCGCCAGCAGCAGGCAGATACCACCGACCACACCGCCCACCg                                    >  7:25432/1‑146 (MQ=255)                                                                                                                      c‑‑GCCGAAACTGGGCAAGAAGGCTTCGGCGATCATGAAGGTGATGCCAAGCAGGATCAGCGCCACCCCGGCAAAACTCACCGGCAACAGCTGCAGCGCATACAGAGCCAGCAGCAGGCAGATACCACCGACCACACCGCCCACCGCAGaa                               >  6:15870/1‑149 (MQ=255)                                                                                                                         gCCGAAACTGGGCAAGAAGGCTTCGGCGATCATGAAGGTGATGCCAAGCAGGATCAGCGCCACCCCGGCAAAACTCACCGGCAACAGCTGCAGCGCATACAGCGCCAGCAGCAGGCAGATACCACCGACCACACCGCCCACCGCAGAAc                              >  1:83469/1‑149 (MQ=255)                                                                                                                         gCCGAAACTGGGCAAGAAGGCTTCGGCGATCATGAAGGTGATGCCAAGCAGGATAAGCGCCACCCCGGCAAAACTCACAGGCAACAGATGAAGCGCATACAGCGCCAGATGCAGGCAGATACCACCGCCCACACCGCCCACCGCAGAAc                              >  4:209088/1‑149 (MQ=255)                                                                                                                            gAAACTGGGCAAGAAGGCTTCGGCGATCATGAAGGTGATGCCAAGCAGGATCAGCGCCACCCCGGCAAAACTCACCGGCAACAGCTGCAGCGCATACAGCGCCAGCAGCAGGCAGATACCACCGACCACACCGCCCACCGCAGAACCTg                           >  3:268821/1‑149 (MQ=255)                                                                                                                              aaCTGGGCAAGAAGGCTTCGGCGATCATGAAGGTGATGCCAAGCAGGATCAGCGCCACCCCGGCAAAACTCACCGGCAACAGCTGCAGCGCATACAGCGCCAGCAGCAGGCAGATACCACCGACCACACCGCCCACCGCAGAACCTggg                         >  3:156032/1‑149 (MQ=255)                                                                                                                              aaCTGGGCAAGAAGGCTTCGGCGATCATGAAGGTGATGCCAAGCAGGATCAGCGCCACCCCGGCAAAACTCACCGGCAACAGCTGCAGCGCATACAGCGCCAGCAGCAGGCAGATACCACCGACCACACCGCCCACCGCAGAACCTggg                         >  1:264532/1‑149 (MQ=255)                                                                                                                              aaCTGGGCAAGAAGGCTTCGGCGATCATGAAGGTGATGCCAAGCAGGATCAGCGCCACCCCGGCAAAACTCACCGGCAACAGCTGCAGCGCATACAGCGCCAGCAGCAGGCAGATACCACCGACCACACCGCCCACCGCAGAACCTggg                         >  7:219182/1‑149 (MQ=255)                                                                                                                                  gggCAAGAAGGCTTCGGCGATCATGAAGGTGATGCCAAGCAGGATCAGCGCCACCCCGGCAAAACTCACCGGCAACAGCTGCAGCGCATACAGCGCCAGCAGCAGGCAGATACCACCGACCACACCGcc                                         <  1:167327/129‑1 (MQ=255)                                                                                                                                  gggCAAGAAGGCTTCGGCGATCATGAAGGTGATGCCAAGCAGGATCAGCGCCACCCCGGCAAAACTCACCGGCAACAGCTGCAGCGCATACAGCGCCAGCAGCAGGCAGATACCACCGACCACACCGcc                                         >  2:167327/1‑129 (MQ=255)                                                                                                                                   ggCAAGAAGGCTTCGGCGATCATGAAGGTGATGCCAAGCAGGATCAGCGCCACCCCGGCAAAACTCACCGGCAACAGCTGCAGCGCATACAGCGCCAGCAGCAGGCAGATACCACCGACCACACCGCCCACCGCAGAACCTGGGTTCAt                    <  2:83469/149‑1 (MQ=255)                                                                                                                                   ggCAAGAAGGCTTCGGCGATCATGAAGGTGATGCCAAGCAGGATCAGCGCCACCCCGGCAAAACTCACCGGCAACAGCTGCAGCGCATACAGCGCCAGCAGCAGGCAGATACCACCGACCACACCGCCCACCGCAGAACCTGGGTTCAt                    <  4:268821/149‑1 (MQ=255)                                                                                                                                        gaagGCTTCGGCGATCATGAAGGTGATGCCAAGCAGGATCAGCGCCACCCCGGCAAAACTCACCGGCAACAGCTGCAGCGCATACAGCGCCAGCAGCAGGCAGATACCACCGACCACACCGCCCACCGCAGAACCTGGGTTCATGAAtt               >  3:216800/1‑149 (MQ=255)                                                                                                                                           ggcttcggcgATCATGAAGGTGATGCCAAGCAGGATCAGCGCCACCCCGGCAAAACTCACCGGCAACAGCTGCAGCGCATACAGCGCCAGCAGCAGGCAGATACCACCGACCACACCGCCCACCGCAGAACCTGGGTTCATGAATTCg             >  3:925‑M2/11‑148 (MQ=255)                                                                                                                                           ggcttaggcgATCATGAAGGTGATGCCAAGCAGGATCAGCGCCACCCAGGCAAAACTCACCGGCAACAGCTGCAGCGCATACAGCGCCAGCTGCAGGCAGATACCACCGACCACACCGCCCACCTCAGAACCTGTGTTCATGAATTCGa            <  3:209088‑M2/139‑1 (MQ=255)                                                                                                                                             cttcggcgATCATGAAGGTGATGCCAAGCAGGATCAGCGCCACCCCGGCAAAACTCACCGGCAACAGCTGCAGCGCATACAGCGCCAGCAGCAGGCAGATACCACCGACCACACCGCCCACCGCAGAACCTGGGTTCATGAATTCGaac          <  8:152394‑M2/141‑1 (MQ=255)                                                                                                                                                     aTCATGAAGGTGATGCCAAGCAGGATCAGCGCCACCCCGGCAAAACTCACCGGCAACAGCTGCAGCGCATACAGCGCCAGCAGCAGGCAGATACCACCGACCACACCGCCCACCGCAGAACCTGGGTTCATGAATTCGAACAACAGGcc  >  1:190795/1‑149 (MQ=255)                                                                                                                                                     |                                                                                                                                                     CCGAGAGCAGCGCCAAGGTGCCGATCAAGGCCAGGGGGATGCCGAAACCGGGAGCGTCGGTGTCGATCAGGATCAATGCGCCGACCACAAAGGCAACGATGCCGCCGAAGCCGACCAC‑‑GCCGAAACTGGGCAAGAAGGCTTCGGCGATCATGAAGGTGATGCCAAGCAGGATCAGCGCCACCCCGGCAAAACTCACCGGCAACAGCTGCAGCGCATACAGCGCCAGCAGCAGGCAGATACCACCGACCACACCGCCCACCGCAGAACCTGGGTTCATGAATTCGAACAACAGGCC  >  NC_002947/250125‑250419

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 21 ≤ 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.