New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_002947	5746405 =	51 (0.950)	3 (0.060)	3/258	NT	5.6%	coding (375/423 nt)	PP_5042	hypothetical protein
	?	NC_002947	5746469 =	52 (0.990)					intergenic (+16/+83)	PP_5042/PP_5043	hypothetical protein/PhoPQ‑activated pathogenicity‑like protein

CATCATCGAGCGCTTCAACCAGAAGTCCGGGATCTTCACCCTGACCCGGATGAGCAACGACGACTGCATGTACCTGGATCGTAAAAGCCGGCTGTGCACCATTTATGACAAGCGCCCGGATACCTGCCGCAACCACCCCAAGGTCGGGCCACGGCCGGGGTATTGCGCCTACAAGCCCAAGGTGGTTGGGCGTTGAGTCTTGCGCCGGGGCATAAATCGAGCGCCGCGCGGGCGGCGCTCGATTCTGTGGCGATGCCGAGCTGGGCATGAAGCACTGAACCCACCGCT  >  NC_002947/5746258‑5746545                                                                                                                                                    |                                                                                                                                             gacttatcctgagcatccaccagcggatcaggggggtgcttgccggagcttccccgctggctgaaatgggagcggtgggttcagtgcttcatgcccagctcggcatcgccacagaatcgagcgccgcccgcgcggcgctcgatttatGc                                                                                                                                             >  3:194645‑M1/148‑149 (MQ=255)  atcatcGAGCGCTTCAACCAGAAGTCCGGGATCTTCACCCTGACCCGGATGAGCAACGACGACTGCATGTACCTGGATCGTAAAAGCCGGCTGTGCACCATTTATGACAAGCGCCCGGATACCTGCCGCAACCACCCCAAGGTCGGGc                                                                                                                                             >  5:315337/1‑148 (MQ=255)    catcGAGCGCTTCAACCAGAAGTCCGGGATCTTCACCCTGACCCGGATGAGCAACGACGACTGCATGTACCTGGATCGTAAAAGCCGGCTGTGCACCATTTATGACAAGCGCCCGGATACCTGCCGCAACCACCCCAAGGTCGGGCCAc                                                                                                                                          >  6:59372/1‑149 (MQ=255)         aGCGCTTCAACCAGAAGTCCGGGATCTTCACCCTGACCCGGATGAGCAACGACGACTGCATGTACCTGGATCGTAAAAGCCGGCTGTGCACCATTTATGACAAGCGCCCGGATACCTGCCGCAACCACCCCAAGGTCGGGCCACGGCCg                                                                                                                                     <  2:241342/149‑1 (MQ=255)            gcTTCAACCAGAAGTCCGGGATCTTCACCCTGACCCGGATGAGCAACGACGACTGCATGTACCTGGATCGTAAAAGCCGGCTGTGCACCATTTATGACAAGCGCCCGGATACCTGCCGCAACCACCCCAAGGTCGGGCCACGGCCgggg                                                                                                                                  >  6:276052/1‑149 (MQ=255)              ttCAACCAGAAGTCCGGGATCTTCACCCTGACCCGGATGAGCAACGACGACTGCATGTACCTGGATCGTAAAAGCCGGCTGTGCACCATTTATGACAAGCGCCCGGATACCTGCCGCAACCACCCCAAGGTCGGGCCACGGCCGGGGTa                                                                                                                                >  7:189334/1‑149 (MQ=255)              ttCAACCAGAAGTCCGGGATCTTCACCCTGACCCGGATGAGCAACGACGACTGCATGTACCTGGATCGTAAAAGCCGGCTGTGCACCATTTATGACAAGCGCCCGGATACCTGCCGCAACCACCCCAAGGTCGGGCCACGGCCGGGGTa                                                                                                                                >  3:294150/1‑149 (MQ=255)                    cAGAAGTCCTGGATCTTCACCCTGACACGTATTAGAAACGAAGACTGCATGTACGTGGATCGTAAAAGCCGTCTGTGCACCATTTATGACAAGCGACCGGATACCTGCCGCAACCACCCCAAGGTCGGGCCACGGCCGGGGTATTgcgc                                                                                                                          <  8:237300/149‑1 (MQ=255)                      gAAGTCCGGGATCTTCACCCTGACCCGGATGAGCAACGACGACTGCATGTACCTGGATCGTAAAAGCCGGCTGTGCACCATTTATGACAAGCGCCCGGATACCTGCCGCAACCACCCCAAGGTCGGGCCACGGCCGGGGTATTGCGcc                                                                                                                         >  3:242776/1‑148 (MQ=255)                          tCCGGGATCTTCACCCTGACCCGGATGAGCAACGACGACTGCATGTACCTGGATCGTAAAAGCCGGCTGTGCACCATTTATGACAAGCGCCCGGATACCTGCCGCAACCACCCCAAGGTCGGGCCACGGCCGGGGTATTGCGCCTACaa                                                                                                                    >  1:173573/1‑149 (MQ=255)                            cGGTATCTTCACCCTTACCCGGATGAGCAACGACGACTGCATTTACCTGCATCGTAAAAGCCGGCTGTGCAACATTTATGACAAGCGACCGGATACCTGCCGCAACCTCCCCAAGGTCGGGCCACGGCCTGGGTATTGCGCCTACAAGc                                                                                                                  <  5:306346/149‑1 (MQ=255)                             gggATCTTCACCCTGACCCGGATGAGCAACGACGACTGCATGTACCTGGATCGTAAAAGCCGGCTGTGCACCATTTATGACAAGCGCCCGGATACCTGCCGCAACCACCCCAAGGTCGGGCCACGGCCGGGGTATTGCGCCTACAAGcc                                                                                                                 <  6:104107/149‑1 (MQ=255)                             gggATCTTCACCCTGACCCGGATGAGCAACGACGACTGCATGTACCTGGATCGTAAAAGCCGGCTGTGCACCATTTATGACAAGCGCCCGGATACCTGCCGCAACCACCCCAAGGTCGGGCCACGGCCGGGGTATTGCGCCTACAAGcc                                                                                                                 >  3:15446/1‑149 (MQ=255)                               gATCTTCACCCTGACCCGGATGAGCAACGACGACTGCATGTACCTGGATCGTAAAAGCCGGCTGTGCACCATTTATGACAAGCGCCCGGATACCTGCCGCAACCACCCCAAGGTCGGGCCACGGCCGGGGTATTGCGCCTACAAGCCCa                                                                                                               <  5:59372/149‑1 (MQ=255)                                    tCACCCTGACCCGGATGAGCAACGACGACTGCATGTACCTGGATCGTAAAAGCCGGCTGTGCACCATTTATGACAAGCGCCCGGATACCTGCCGCAACCACCCCAAGGTCGGGCCACGGCCGGGGTATTGCGCCTACAAGCCCAAggtg                                                                                                          >  7:155064/1‑149 (MQ=255)                                      aCCCTGACCCGGATGAGCAACGACGACTGCATGTACCTGGATCGTAAAAGCCGGCTGTGCACCATTTATGACAAGCGCCCGGATACCTGCCGCAACCACCCCAAGGTCGGGCCACGGCCGGGGTATTGCGCCTACAAGCCCAAggtgg                                                                                                         <  4:203846/148‑1 (MQ=255)                                        ttgccggagcttcaccgctggctgaaatgggagcggtgggttcagtgcttcatgcccagctcggcatcgccacagaatcgagcgccgcccgcgcggcgctcgatttatGCCACGGCCGGGGTATTGCGCCTACAAGCCCAAGGTGGTTg                                                                                                      <  1:224674‑M1/41‑1 (MQ=255)                                        ccTGACCCGGATGAGCAACGACGACTGCATGTACCTGGATCGTAAAAGCCGGCTGTGCACCATTTATGACAAGCGCCCGGATACCTGCCGCAACCACCCCAAGGTCGGGCCACGGCCGGGGTATTGCGCCTACAAGCCCAAGGTGGTTg                                                                                                      >  4:207160/1‑149 (MQ=255)                                        aagatcccGGATGAGCAACGACGACTGCATGTACCTGGATCGTAAAAGCCGGCTGTGCACCATTTATGACAAGCGCCCGGATACCTGCCGCAACCACCCCAAGGTCGGGCCACGGCCGGGGTATTGCGCCTACAAGCCCAAGGTGGtt                                                                                                       <  1:62356/143‑1 (MQ=255)                                         cTGACCCGGATGAGCAACGACGACTGCATGTACCTGGATCGTAAAAGCCGGCTGTGCACCATTTATGACAAGCGCCCGGATACCTGCCGCAACCACCCCAAGGTCGGGCCACGGCCGGGGTATTGCGCCTACAAGCCCAAGGTGGTTgg                                                                                                     <  2:114645/149‑1 (MQ=255)                                              ccGGATGAGCAACGACGACTGCATGTACCTGGATCGTAAAAGCCGGCTGTGCACCATTTATGACAAGCGCCCGGATACCTGCCGCAACCACCCCAAGGTCGGGCCACGGCCGGGGTATTgcgc                                                                                                                          >  2:306937/1‑123 (MQ=255)                                              ccGGATGAGCAACGACGACTGCATGTACCTGGATCGTAAAAGCCGGCTGTGCACCATTTATGACAAGCGCCCGGATACCTGCCGCAACCACCCCAAGGTCGGGCCACGGCCGGGGTATTgcgc                                                                                                                          <  1:306937/123‑1 (MQ=255)                                              ccGGATGAGCAACGACGACTGCATGTACCTGGATCGTAAAAGCCGGCTGTGCACCATTTATGACAAGCGCCCGGATACCTGCCGCAACCACCCCAAGGTCGGGCCACGGCCGGGGTATTGCGCCTACAAGCCCAAGGTGGTTGGGCGtt                                                                                                <  4:294150/149‑1 (MQ=255)                                                ggATGAGCAACGACGACTGCATGTACCTGGATCGTAAAAGCCGGCTGTGCACCATTTATGACAAGCGCCCTGATACCTGCCGCAACCACCCCAAGGTCGGGCCACGGCCGGGGTATTGCGCCTACAAGCCCAAGGTGGTTGGGCGTTGa                                                                                              <  3:124278/149‑1 (MQ=255)                                                 gATGAGCAACGACGACTGCATGTACCTGGATCGTAAAAGCCGGCTGTGCACCATTTATGACAAGCGCCCGGATACCTGCCGCAACCACCCCAAGGTCGGGCCACGGCCGGGGTATTGCGCCTACAAGCCCAAGGTGGTTGGGCGTTGAg                                                                                             <  2:144282/149‑1 (MQ=255)                                                 gATGAGCAACGACGACTGCATGTACCTGGATCGTAAAAGCCGGCTGTGCACCATTTATGACAAGCGCCCGGATACCTGCCGCAACCACCCCAAGGTCGGGCCACGGCCGGGGTATTGCGCCTACAAGCCCAAGGTGGTTGGGCGTTGAg                                                                                             <  1:25128/149‑1 (MQ=255)                                                     aGCAACGACGACTGCATGTACCTGGATCGTAAAAGCCGGCTGTGCACCATTTATGACAAGCGCCCGGATACCTGCCGCAACCACCCCAAGGTCGGGCCACGGCCGGGGTATTGCGCCTACAAGCCCAAGGTGGTTGGGCGTTGAGTCtt                                                                                         <  3:207160/149‑1 (MQ=255)                                                              gacTGCATGTACCTGGATCGTAAAAGCCGGCTGTGCACCATTTATGACAAGCGCCCGGATACCTGCCGCAACCACCCCAAGGTCGGGCCACGGCCGGGGTATTGCGCCTACAAGCCCAAGGTGGTTGGGCGTTGAGTCTTGCGCCgggg                                                                                >  4:27207/1‑149 (MQ=255)                                                              gacTGCATGTACCTGGATCGTAAAAGCCGGCTGTGCACCATTTATGACAAGCGCCCGGATACCTGCCGCAACCACCCCAAGGTCGGGCCACGGCCGGGGTATTGCGCCTACAAGCCCAAGGTGGTTGGGCGTTGAGTCTTGCGCCgggg                                                                                <  5:276052/149‑1 (MQ=255)                                                                   cATGTACCTGGATCGTAAAAGCCGGCTGTGCACCATTTATGACAAGCTCCCGGATACCTGCCGCAACCACCCCAAGGTCGGGCCACGGCCGGGGTATTGCGCCTACAAGCCCAAGGTGGTTGGGCGTTGAGTCTTGCGCCGGGGCAt                                                                             <  3:214831/147‑1 (MQ=255)                                                                     ggagcggtgggttcagtgcttcatgcccagctcggcatcgccacagaatcgagcgccgcccgcgcggcgctcgatttatGCCACGGCCGGGGTATTGCGCCTACAAGCCCAAGGTGGTTGGGCGTTGAGTCTTGCGCCGGGGCATaaa                                                                          >  2:296823‑M1/80‑148 (MQ=255)                                                                        gcggtgggttcagtgcttcatgcccagctcggcatcgccacagaatcgagcgccgcccgcgcggcgctcgatttatGCCACGGCCGGGGTATTGCGCCTACAAGCCCAAGGTGGTTGGGCGTTGAGTCTTGCGCCGGGGCATAAATCGa                                                                      >  2:224674‑M1/77‑149 (MQ=255)                                                                         ccTGGATCGTAAAAGCCGGCTGTGCACCATTTATGACAAGCGCCCGGATACCTGCCGCAACCACCCCAAGGTCGGGCCACGGCCGGGGTATTGCGCCTACAAGCCCAAGGTGGTTGGGCGTTGAGTCTTGCGCCGGGGCATAAATCGAg                                                                     <  8:189334/149‑1 (MQ=255)                                                                                  tAAAAGCCGGCTGTACAACATTTATGAAAATCTACCGGATACCTGCCGCAACCACACAAAGGTCGGGCCACGGCCGGGGTATTGCGCATACAAGCCCAAGGTGGTTGGGCGTTGAGTCTTGCGCCGGGGCATAAATCGAGCGCcgcgcg                                                            >  6:109394/1‑149 (MQ=255)                                                                                   aaaaGCCGGCTGTGCACCATTTATGACAAGCGCCCGGATACCTGCCGCAACCACCCCAAGGTCGGGCCACGGCCGGGGTATTGCGCCTACAAGCCCAAGGTGGTTGGGCGTTGAGTCTTGCGCCGGGGCATAAATCGAGCGCCGCgcgg                                                           >  7:162436/1‑149 (MQ=255)                                                                                    aaaGCCGGCTGTGCACCATTTATGACAAGCGCCCGGATACCTGCCGCAACCACCACAAGGTCGGGCCACGGCCGGGGTATTGCGCCTACAAGCCCAAGGTGGTTGGGCGTTGAGTCTTGCGCCGGGGCATAAATCGAGCGCCGCgcggg                                                          <  6:315337/149‑1 (MQ=255)                                                                                       gCCGGCTGTGCACCATTTATGACAAGCGCCCGGATACCTGCCGCAACCACCCCAAGGTCGGGCCACGGCCGGGGTATTGCGCCTACAAGCCCAAGGTGGTTGGGCGTTGAGTCTTGCGCCGGGGCATAAATCGAGCGCCGCgcgggcgg                                                       <  8:155064/149‑1 (MQ=255)                                                                                       gCCGGCGGTGCACCATTTATGACAAGCGCCCGGATACCTGCCGCAACCCCCCCAAGGTCGGGCCACGGCCGGGGTATTGCGCCTACAAGCCCAAGGTGGTTGGGCGTTGAGTCTTGCGCCGGGGCATAAATCGAGCGCCGCgcgggcgg                                                       <  5:209040/149‑1 (MQ=255)                                                                                           gCTGTGCACCATTTATGACAAGCGCCCGGATACCTGCCGCAACCACCCCAAGGTCGGGCCACGGCCGGGGTATTGCGCCTACAAGCCCAAGGTGGTTGGGCGTTGAGTCTTGCGCCGGGGCATAAATCGAGCGCCGCGCGGGCGGCGCt                                                   <  4:161273/149‑1 (MQ=255)                                                                                                            aCAAGCGCCCGGATACCTGCCGCAACCACCCCAAGGTCGGGCCACGGCCGGGGTATTGCGCCTACAAGCCCAAGGTGGTTGGGCGTTGAGTCTTGCGCCGGGGCATAAATCGAGCGCCGCGCGGGCGGCGCTCGATTCTGTGGCGATGc                                  >  3:81288/1‑149 (MQ=255)                                                                                                            aCAAGCGCCCGGATACCTGCCGCAACCACCCCAAGGTCGGGCCACGGCCGGGGTATTGCGCCTACAAGCCCAAGGTGGTTGGGCGTTGAGTCTTGCGCCGGGGCATAAATCGAGCGCCGCGCGGGCGGCGCTCGATTCTGTGGCGATGc                                  >  7:162730/1‑149 (MQ=255)                                                                                                             cAAGCGCCCGGATACCTGCCGCAACCACCCCAAGGTCGGGCCACGGCCGGGGTATTGCGCCTACAAGCCCAAGGTGGTTGGGCGTTGAGTCTTGCGCCGGGGCATAAATCGAGCGCCGCGCGGGCGGCGCTCGATTCTGTGGCGATGcc                                 <  4:81288/149‑1 (MQ=255)                                                                                                                      ggATACCTGCCGCAACCACCCCAAGGTCGGGCCACGGCCGGGGTATTGCGCCTACAAGCCCAAGGTGGTTGGGCGTTGAGTCTTGCGCCGGGGCATAAATCGAGCGCCGCGCGGGCGGCGCTCGATTCTGTGGCGATGCCGAGCTggg                         >  4:114100/1‑148 (MQ=255)                                                                                                                      ggATACCTGCCGCAACCACCCCAAGGTCGGGCCACGGCCGGGGTATTGCGCCTACAAGCCCAAGGTGGTTGGGCGTTGAGTCTTGCGCCGGGGCATAAATCGAGCGCCGCGCGGGCGGCGCTCGATTCTGTGGCGATGCCGAGCTGGGc                        <  3:114100/149‑1 (MQ=255)                                                                                                                            cTGCCGCAACCACCCCAAGGTCGGGCCACGGCCGGGGTATTGCGCCTACAAGCCCAAGGTGGTTGGGCGTTGAGTCTTGCGCCGGGGCATAAATCGAGCGCCGCGCGGGCGGCGGTCGATTCTGTGGCGATGCCGAGCTGGGCATGAAg                  >  3:153438/1‑149 (MQ=255)                                                                                                                            cTGCCGCAACCACCCCAAGGTCGGGCCACGGCCGGGGTATTGCGCCTACAAGCCCAAGGTGGTTGGGCGTTGAGTCTTGCGCCGGGGCATAAATCGAGCGCCGCGCGGGCGGCGCTCGAtt                                              >  5:5077/1‑121 (MQ=255)                                                                                                                            cTGCCGCAACCACCCCAAGGTCGGGCCACGGCCGGGGTATTGCGCCTACAAGCCCAAGGTGGTTGGGCGTTGAGTCTTGCGCCGGGGCATAAATCGAGCGCCGCGCGGGCGGCGCTCGAtt                                              <  6:5077/121‑1 (MQ=255)                                                                                                                            cTGCCGCAACCACCCCAAGGTCGGGCCACGGCCGGGGTATTGCGCCTACAAGCCCAAGGTGGTTGGGCGTTGAGTCTTGCGCCGGGGCATAAATCGAGCGCCGCGCGGGCGGCGCTCGATTCTGTGGCGATGCCGAGCTGGGCATGAAg                  >  2:116334/1‑149 (MQ=255)                                                                                                                            cTGCCGCAACCACCCCAAGGTCGGGCCACGGCCGGGGTATTGCGCCTACAAGCCCAAGGTGGTTGGGCGTTGAGTCTTGCGCCGGGGCATAAATCGAGCGCCGCGCGGGCGGCGCTCGATTCTGTGGCGATGCCGAGCTGGGCATGAAg                  >  7:158071/1‑149 (MQ=255)                                                                                                                            cTGCCGCAACCACCCCAAGGTCGGGCCACGGCCGGGGTATTGCGCCTACAAGCCCAAGGTGGTTGGGCGTTGAGTCTTGCGCCGGGGCATAAATCGACCGCCGCGCGGGCGGCGCTCGATTCTGTGGCGATGCCGAGCTGGGCATGAAg                  >  3:148405/1‑149 (MQ=255)                                                                                                                                     ccaccCCAAGGTCGGGCCACGGCCGGGGTATTGCGCCTACAAGCCCAAGGTGGTTGGGCGTTGAGTCTTGCGCCGGGGCATAAATCGAGCGCCGCGCGGGCGGCGCTCGATTCTGTGGCGATGCCGAGCTGGGc                        >  2:101427/1‑134 (MQ=255)                                                                                                                                     ccaccCCAAGGTCGGGCCACGGCCGGGGTATTGCGCCTACAAGCCCAAGGTGGTTGGGCGTTGAGTCTTGCGCCGGGGCATAAATCGAGCGCCGCGCGGGCGGCGCTCGATTCTGTGGCGATGCCGAGCTGGGc                        <  1:101427/134‑1 (MQ=255)                                                                                                                                         cccAAGGTCGGGCCACGGCCGGGGTATTGCGCCTACAAGCCCAAGGTGGTTGGGCGTTGAGTCTTGCGCCGGGGCATAAATCGAGCGCCGCGCGGGCGGCGCTCGATTCTGTGGCGATGCCGAGCTGGGCATGAAGCACTGAACCCAcc     >  7:113447/1‑149 (MQ=255)                                                                                                                                         cccAAGGTCGGGCCACGGCCGGGGTATTGCGCCTACAAGCCCAAGGTGGTTGGGCGTTGAGTCTTGCGCCGGGGCATAAATCGAGCGCCGCGCGGGCGGCGCTCGATTCTGTGGCGATGCCGAGCTGGGCATGAAGCACTGAACCCAcc     >  3:155452/1‑149 (MQ=255)                                                                                                                                           catgggggggCCTCGGCGGGGGTTTTGCGCTTACAAGCCCATGGTGGTGGGGGTTTGTGTTTTGGGCGGGGCCATAAATCTAGCGCCGGGGGGGGGGCGGTCGATTCTGTGGCGATGCCGAGCTGGGCATGAAGCACTGAACCCACCGc   <  4:155452/142‑1 (MQ=255)                                                                                                                                           cAAGGTCGGGCCACGGCCGGGGTATTGCGCCTACAAGCCCAAGGTGGTTGGGCGTTGAGTCTTGCGCCGGGGCATAAATCGAGCGCCGCGCGGGCGGCGCTCGATTCTGTGGCGATGCCGAGCTGGGCATGAAGCACTGAACCCACCGc   >  2:34387/1‑149 (MQ=255)                                                                                                                                            aaGGTCGGGCCACGGCCGGGGTATTGCGCCTACAAGCCCAAGGTGGTTGGGCGTTGAGTCTTGCGCCGGGGCATAAATCGAGCGCCGCGCGGGCGGCGCTCGATTCTGTGGCGATGCCGAGCTGGGCATGAAGCACTGAACCCACCGCt  >  5:245028/1‑149 (MQ=255)                                                                                                                                            aaGGTCGGGCCACGGCCGGGGTATTGCGCCTACAAGCCCAAGGTGGTTGGGCGTTGAGTCTTGCGCCGGGGCATAAATCGAGCGCCGCGCGGGCGGCGCTCGATTCTGTGGCGATGCCGAGCTGGGCATGAAGCACTGAACCCACCGCt  >  8:136235/1‑149 (MQ=255)                                                                                                                                                    |                                                                                                                                             CATCATCGAGCGCTTCAACCAGAAGTCCGGGATCTTCACCCTGACCCGGATGAGCAACGACGACTGCATGTACCTGGATCGTAAAAGCCGGCTGTGCACCATTTATGACAAGCGCCCGGATACCTGCCGCAACCACCCCAAGGTCGGGCCACGGCCGGGGTATTGCGCCTACAAGCCCAAGGTGGTTGGGCGTTGAGTCTTGCGCCGGGGCATAAATCGAGCGCCGCGCGGGCGGCGCTCGATTCTGTGGCGATGCCGAGCTGGGCATGAAGCACTGAACCCACCGCT  >  NC_002947/5746258‑5746545

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.