New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	= 2073987	41 (0.900)	4 (0.090)	4/248	NT	9.1%	coding (2449/3120 nt)	flu	CP4‑44 prophage; self recognizing antigen 43 (Ag43) autotransporter
	?	NC_000913	= 2074000	41 (0.950)					coding (2462/3120 nt)	flu	CP4‑44 prophage; self recognizing antigen 43 (Ag43) autotransporter

CAGCGGCAGCTATGGATTCGTCCGTCTGGAGGGTGACCTGATGAGAACAGAGGTTGCCGGTATGTCTGTGACCGCGGGGGTATATGGTGCTGCTGGCCATTCTTCCGTTGATGTTAAGGATGATGACGGCTCCCGTGCCGGCACGGTCCGGGATGATGCCGGCAGCCTGGGCGGATACCTG‑AATCTGGTACACACGTCCTCCGGCCTGTGGGCTGACATTGTGGCACAGGGAACCCGCCACAGCATGAAAGCGTCATCGGACAATAACGACTTCCGCGCCCGGGG  >  NC_000913/2073845‑2074129                                                                                                                                               |                                                                                                                                                cagcGGCAGCTATGGATTCGTCCGTCTGGAGGGTGACCTGATGAGAACAGAGGTTGCCGGTATGTCTGTGACCGCGGGGGTATATGGTGCTGCTGGCCATTCTTCAGTTGATGTGAAGGATGATGACGGCTCCCGTGCCGGCA                                                                                                                                                 >  2:623311‑M1/1‑143 (MQ=255)   gcGGCAGCTATGAGTTCGTCCGTCTGGAGGGTGACCTGATGAGAACAGAGGTTGCCGGTATGTCTGTGACCGCGGGGGTATATGGTGCTGCTGGCCATTCTTCCGTTGATGTTAAGGATGATGACGGCTCCCGTGCCGGCACg                                                                                                                                               <  2:832505/143‑1 (MQ=255)    cGGCAGCTATGGATTCGTCCGTCTGGAGGGTGACCTGATGAGAACAGAGGTTGCCGGTATGTCTGTGACCGCGGGGGTATATGGTGCTGCTGGCCATTCTTCCGTTGATGTTAAGGATGATGACGGCTCCCGTGCCGGCACgg                                                                                                                                              >  2:303386/1‑143 (MQ=255)            aTGGATTCGTCCGTCTGGAGGGTGACCTGATGAGAACAGAGGTTGCCGGTATGTCTGTGACCGCGGGGGTATATGGTGCTGCTGGCGATTCTTCCGGAGATGTGAAGGATGATGACGGCTCCCGTGCCGGGACGGTCCGGgaa                                                                                                                                      >  2:79680/1‑142 (MQ=255)                           tGGAGGGTGACCTGATGTGGTTGGGGGCTGCCAGAATGTCTGTGACCGCGGGGGGATATGGTGCTGCTGGCCATTCTTCCGTTGATGTTAAGGATGATGACGGCTCCCGTGCCGGCACGGTCCGGGATGATGCCGGCAGCCTg                                                                                                                       <  1:376521/143‑1 (MQ=255)                           tGGAGGATGACCTGATGAGAACAGAGGTTGCCGGTATGTCTGTGACCGCGGGGGTATATGGTGCTGCTGGCCATTCTTCCGTTGATGTTAAGGATGATGACGGCTCCCGTGCCGGCACGGTCCGGGATGATGCCGGCAGCCTg                                                                                                                       >  2:332851/1‑143 (MQ=255)                                   gACCTGATGAGAACAGAGGTTGCCGGTATGTCTGTGACCGCGGGGGTATATGGTGCTGCTGGCCATTCTTCCGTTGATGTTAAGGATGATGACGGCTCCCGTGCCGGCAtcatcccggaccgtgccggcacgggagccgtcat                                                                                                               <  2:216414‑M1/143‑35 (MQ=255)                                   gACCTGATGAGAACAGAGGTTGCCGGTATGTCTGTGACCGCGGGGGTATATGGTGCTGCTGGCCATTCTTCCGTTGATGTTAAGGATGATGACGGCTCCCGTGCCGGCACGGTCCGGGATGCTGCCGGCAGCCTGGGCGGATa                                                                                                               >  1:723692/1‑143 (MQ=255)                                      cTGATGAGAACAGAGGTTGCCGGTATGTCTGTGACCGCGGGGGTATATGGTGCTGCTGGCCATTCTTCCGTTGATGTTAAGGATGATGACGGCTCCCGTGCCGGCACGGGCCGGGATGATGCCGGCAGCCTGGGCGGATACCt                                                                                                            >  1:593847/1‑143 (MQ=255)                                        gatgaCAACGGAGGTGGCCGGGATGGCTTTCACCGCGGGGGTATAGGGTGCTGATGGCCATTCTTCCGTTGATGTTAAGGATGATGACGGCTCCCGTGCCGGCACGGTCCGGGATGATGCCGGCAGCCTGGGCGGATACCTG‑a                                                                                                         <  2:31844/143‑1 (MQ=255)                                              aaCAGAGTTTGCCGGTATGTCCGCGGCCGCGGGAGTATATGGTGCGGCTGGCCATTCTTCCGTTGATGTTAAGGATGATGACGGCTCCCGTGCCGGCACGGTCCGGGATGATGCCGGCAGCCTGGGCGGATACCTG‑AATCTgg                                                                                                   <  1:567865/143‑1 (MQ=255)                                              aaCAGAGGTTGCCGGTATGTCTGTGACCGCGGGGGTATATGGTGCTGCTGGCCATTCTTCCGTTGATGTTAAGGATGATGACGGCTCCCGTGCCGGCACGGTCCGGGATGATGCCGGCAGCCTGGGCGGATACCTG‑AATCTgg                                                                                                   <  1:303386/143‑1 (MQ=255)                                               aCAGAGGTTGCCGGTATGTCTGTGACCGCGGGGGTATATGGTGCTGCTGGCCATTCTTCCGTTGATGTTAAGGATGATGACGGCTCCCGTGCCGGCAtcatcccggaccgtgccggcacggga                                                                                                                       <  2:288970‑M1/123‑27 (MQ=255)                                               aCAGAGGTTGCCGGTATGTCTGTGACCGCGGGGGTATATGGTGCTGCTGGCCATTCTTCCGTTGATGTTAAGGATGATGACGGCTCCCGTGCCGGCAtcatcccggaccgtgccggcacggga                                                                                                                       >  1:288970‑M1/1‑97 (MQ=255)                                                cAGAGGTTGCCGGCATGTCTGTGACCGCGGGGGTATATGGTGCTGCTGGCCATTCTTCCGTTGATGTTAAGGATGATGACGGCTCCCGTGCCGGCACGGTCCGGGATGATGCCGGCAGCCTGGGCGGATACCTG‑AATCTGGTa                                                                                                 <  1:290441/143‑1 (MQ=255)                                                            tgatgTCTGTGACCGCTGGGGTATAGGGCGCCGCTGGCCATTCTTCCGTTGATGTTAAGGATGATGACGTCTCCCGGGCCGGCAtcatcctggaccgtgccggcactggagccgtcatcatccttaacatcaacggaagaatg                                                                                      <  1:275011‑M1/141‑60 (MQ=255)                                                                 tCTGTGACCGCGGGGGTATATGGTGCTGCTGGCCATTCTTCCGTTGATGTTAAGGATGATGACGGCTCCCGTGCCGGCACGGTCCGGGATGATGCCGGCCGCCTGGGCGGATACCTG‑AATCCGGTACACACGTCCTCCGGCCt                                                                                >  2:147809/1‑143 (MQ=255)                                                                   tgtgACCGCGGGGGTATATGGTGCTGCTGGCCATTCTTCCGTTGATGTTAAGGATGATGACGGCTCCCGTGCCGGCACGGTCCGGGATGATGCCGGCAGCCTGGGCGGCTACCTG‑AATCTGGTACACACGTCCTCCGGCCtgt                                                                              >  1:823809/1‑143 (MQ=255)                                                                    gtgACCGCGGGGGTATATGGTGCTGCTGGCCATTCTTCCGTTGATGTTAAGGATGATGACGGCTCCCGTGCCGGCACGGTCCGGGATGATGCCGGCAGCCTGGGCGGATACCTG‑AATCTGGTACACACGTCCTCCGGCCtctg                                                                             >  1:501108/1‑143 (MQ=255)                                                                    gtgACCGCGGGGGTATATGGTGCTGCTGGCCATTCTTCCGTTGATGTTAAGGATGATGACGGCTCCCGTGCCGGCACGGTCCGGGATGATGCCGGCAGCCTGGGCGGATACCTG‑AATCTGGTACACACGACCTCCGGCCggtg                                                                             >  2:676686/1‑143 (MQ=255)                                                                     cgACCGCGGGGGTATATGGTGGTGCTGGCCATTCTTCCGTTGATGTTAAGGATGATGACGGCTCCCGTGCCGGCACGGTCCGGGATGATGCCGGCAGCCTGGGCGGATACCTG‑AATCTGGTACACACGTCCTCCGGCCTGTgg                                                                            <  1:655745/142‑1 (MQ=255)                                                                      ggccGCGGGGGTATATGGTGCTGCTGGCCATTCTTCCGTTGATGTTAAGGATGATGACGGCTCCCGTGCCGGCACGGTCCGGGATGATGCCGGCAGCCTGGGCGGATACCTG‑AATCTGGTACACACGTCCTCCGGCCTGTggg                                                                           <  1:845358/141‑1 (MQ=255)                                                                      gACCGCGGGGGTATATGGTGCTGCTGGCCATTCTTCCGTTGATGTTAAGGATGATGACGGCTCCCGTGCCGGCACGGTCCGGGATGATGCCGGCAGCCTGGGCGGCTACCTG‑GATCTGGTCCACCCGTCCTCCGGCCCGTggg                                                                           >  2:519169/1‑143 (MQ=255)                                                                                 tataTGGTGCTGCTGGCCATTCTGCCGTTGATGTTAAGGATGATGACGGCTCCCGTGCCGGCACGGTCCGGGATGATGCCGGCAGCCTGGGCGGATACCTG‑AATCTGGTACACACGTCCTCCGGCCTGTGGGCTGACATtgtg                                                                <  2:697555/143‑1 (MQ=255)                                                                                  gttcggTGCTGCTGGCCATTCTTCCGTTGCTGTCAAGGATGATGTCGGCTCCCGTGGCGCCACGGTCCGGGATGATGCCGGCAGCCTGGGCGGATACCTG‑AATCTGGTACACACGTCCTCCGGCCTGTGGGCTGACATTGTgg                                                               <  2:172329/139‑1 (MQ=255)                                                                                       gTGCTGCTGGCCATTCTTCCGTTGATGTTAAGGATGATGACGGCTCCCGTGCCGGCACGGTCCGGGATGATGCGGGCAGCGTGGGCGGATACGCG‑AAGCTGGTGCACACGTCCTCCGGCCTGTGGGCTGACATTGTGGGACAg                                                          >  2:417452/1‑143 (MQ=255)                                                                                       gTGCTGCTGGCCATTCTTCCGTTGATGTTAAGGATGATGACGGCTCCCGTGCCGGCACGGTCCGGGATGATGCCGGCAGCCTGGGCGGATACCTG‑AATCTGGTACACACGTCCTCCGGCCTGTGGGCTGACATTGTGGCACAg                                                          >  2:665568/1‑143 (MQ=255)                                                                                        tgcttcTGGCCATTCTTCCGTTGATGTTAAGGATGGTGACGGCTCTCGTGCCGGCATGGTCTTTGATGATGTGGGCAGGATGGGCGGATACCTG‑AATCGGGTGCACACGGCCTCCGGCCTGTGGGCTGACATTGTGGCACAgg                                                         <  1:398573/143‑1 (MQ=255)                                                                                        tgctgcCGGCCATTCTTCTGTTGATGGTAAGGAGGATGACGGCTCCCGTGCCGGCACGGTCCGGGATGATGCCGGCAGCCTGGGCGGATACCTG‑AATCTGGTACACACGTCCTCCGGCCTGTGGGCTGACATTGTGGCACAgg                                                         <  1:634617/143‑1 (MQ=255)                                                                                         gctgctGGCCATTCTTCCGTTGATGTTAAGGATGATGACGGCTCCCGTGCCGGCACGGTCCGGGATGATGCCGGCAGCCTGGGCGGATACCTG‑AATCTGGTACACACGTCCTCCGGCCTGTGGGCCGACATTGCGGCGCAggg                                                        >  2:123016/1‑143 (MQ=255)                                                                                                gCCATTCTTCCGTTGATGTTAAGGATGATGACGGCTCCCGTGCCGGCACGGTCCGGGATGATGCCGGCAGCCGGGGCGGATACCTG‑AATGTGGTGCAGACGTCCTCCGGCGTGTGGGCTGACATTGCGGAACAGGGAACCAGc                                                 >  2:322340/1‑143 (MQ=255)                                                                                                gCCATTCTTCCGGTGATGTTAAGGATGGTGACGGCTCCCGTGCCGGCACGGTCCGGGATGATGCCGGCAGCCTGGGCGGATACCTG‑AATCTGGTACACACGTCCTCCGGCCTGTGGGCTGACATTGTGGCACAGGGAACCCGc                                                 <  2:563141/143‑1 (MQ=255)                                                                                                  cATTCTTCCGTTGATGTTAAGGATGATGACGGCTCCAGTGCCGGCACGGTCCAGGATGAtgccggcccgggagacgtcatcatccttaacatcaacggaagaatggccagcggcgccctataccccagcggtcacagacatca                                                <  1:275011‑M2/143‑85 (MQ=255)                                                                                                    ttcgtcCGTTGATGTTAAGGATGATGACGGCTCCCGTGCCGGCACGGTCCGGGATGATGCCGGCAGCCTGGGCGGATACCTG‑AATCTGGTACACACGTCCTCCGGCCTGTGGGCTGACATTGTGGCACAGGGAACCCGCcact                                             <  1:258313/143‑2 (MQ=255)                                                                                                                  ttAAGGATGATGACGGCTCCCGTGCCGGCACGGTCCGGGGTGATGGAGGGGGTCGGACCGGACACTTGCCAACT‑ACACACACGTCCTCCGGCCTGTGGGCTGACATTGTGGCACCGGGAACCCGCCACAGCATGCAAGCGTCa                               >  1:422174/1‑143 (MQ=255)                                                                                                                    cagtatgctgCCGGCTCCCCGGCCGGCACGTGTCGGGGGGATGCGGGCAGCCTGGGCGGATACCTG‑AATCTGGTACACACGTCCTCCGGCCTGTGGGCTGACATTGTGGCACAGGTAACCCGCCACAGCATGAAAGCGTCATc                             <  2:593847/139‑1 (MQ=255)                                                                                                                     aGGTTGAGGCCGGCTCCCGTGCCGGCACGGTCCGGGATGATGCCGGCAGCCTGGGCGGATACCTG‑AATCTGCTACACACGTCCTCCGGCCTGTGGGCTGACATTGTGGCACAGGGAACCCGCCACAGCATGAAAGCGTCATCg                            <  2:414905/143‑1 (MQ=255)                                                                                                                     aGGATGATGACGGCTCCCGTGCCGGCACGGTCCGGGATGATGCCGGCAGCCTGGGCGGATACCTG‑AATCTGGTACACACGTCCTCCGGCCTGTGGGCTGACCTTGTGGCCCAGCGAACCCGCCACAGCATGAAACCGTCATCg                            >  2:290962/1‑143 (MQ=255)                                                                                                                      ggATGATGACGGCTCCCGTGCCGGCACGGTCCGGGATGATGCCGGCAGCCTGGGCGGATACCTG‑AATCTGGTCCCCACGTCCTCCGGCCTGTGGGCTGACATTGTTGCACACGGACCCCGCCCCAGCATGAAAGCGTCCTCgg                           >  1:862870/1‑143 (MQ=255)                                                                                                                           atgaCGGCTCCCGTGCCGGCACGGTCCGGGATGAtgccggcacgggagccgtcatcatccttaacatcaacggaagaatggccagcagcaccatatacccccgcggtcacagacataccggcaacctctgttctcatcaggtc                       <  2:216414‑M2/143‑110 (MQ=255)                                                                                                                           atgaCGGCTCCCGTGCCGGCACGGTCCGGGATGATGCCGGCAGCCTGGGCGGATACCTG‑AATCTGGTACACACGTCCTCCGGCCCGTGGGCTGACATTGTGGCACAGGGGACCCGCCACAGCGTGAAAGCGCCATCGGGCact                      >  2:531506/1‑141 (MQ=255)                                                                                                                              ccgccTCCCGTGCCCGTCCCCTCCTGGATCATGCCGGCAGCCTGGTCCGATCCCTA‑AATCTGGTACACACGTCCTCCGGCCTGTGGGCTGACATTGTGGCACAGGGAACCCGCCACAGCATGAAAGCGTCATCGGACAATAAc                   <  1:858729/139‑1 (MQ=255)                                                                                                                              aCGGCTCCCGTGCCGGCACGGTCCGGGATGATGCCGGCAGCCTGGGCGGATACCTG‑AATCTGGTACACACGTCCTCCGGCCTGTGGGCTGACATTGTGGCACAGGGAACCCGCCACAGCATGACAGCGGCACCGGACacaaac                   >  2:633737/1‑138 (MQ=255)                                                                                                                               cGGCGCGCGGGCCGGTACGCTCCGGGGTGATGCCGGCGGCCTGGGTGGATACCTG‑AATCTGGTACACACGCGCGCCGGCTTGGGGTCTGACATAGTGGCACAGGGAACCCGCCACAGCATGAAAGCGTCATCGGACAATAACg                  <  2:362343/143‑1 (MQ=255)                                                                                                                               cGGCCCCCGTGCCGGCACGGTCCGGGATGATGCCGGCAGCCTGGGCGGATACCCG‑AAGCTGGTACACACGTCCTCCGGCCTGTGGGCTGACATTGTGGCACAGGGAACCCGCCACAGCATGAAAGCGTCATCGGACAATAACg                  <  1:762439/143‑1 (MQ=255)                                                                                                                                ggCTCCCGTGCCGGCACGGTCCGGGATGATGCCGGCAGCCTGGGCGGATACCTG‑AATCTGGTACACACGTCCTCCGGCCTGTGGGCTGACATTGTGGCCCAGGGAACCCGCCCCAGCATGAAAGCGTCATCGGACAATCACGa                 >  1:771080/1‑143 (MQ=255)                                                                                                                                ggCTCCCGTGCCGGCACGGTCCGGGATGATGCCGGCAGCCTGGGCGGATACCTG‑AATCTGGTACACACGTCCTCCGGCCTGTGGGCTGACATTGTGGCACAGGGAACCCGCCACAGCATGAAAGCGTCATCGGACAATAACGa                 <  1:441507/143‑1 (MQ=255)                                                                                                                                ggCTCCCGTGCCGGCACGGTCCGGGATGATGCCGGCAGCCTGGGCGGATACCTG‑AATCCGGTACACACGTCCTCCGGCCTGTGGGCTGACATTGTGGCACAGGGAACCCGCCACAGCATGAAAGCTGCATCTGACACTAACGa                 >  1:2653/1‑143 (MQ=255)                                                                                                                                   tCCCGTGCCGGCACGGTCCGGGATGAtgccggcacgggagccgtcatcatccttaacatcaacggaagaatggccagcagcaccatatacccccgcggtcacagacataccggcaacctctgt                                   >  1:288970‑M2/1‑26 (MQ=255)                                                                                                                                   tCCCGTGCCGGCACGGTCCGGGATGAtgccggcacgggagccgtcatcatccttaacatcaacggaagaatggccagcagcaccatatacccccgcggtcacagacataccggcaacctctgt                                   <  2:288970‑M2/123‑98 (MQ=255)                                                                                                                                   tCCCGTGCCGGCACCGCCCGGGATGATGCCGGCAGCCCGGGCGGATACCTG‑AATCTGGTACACACGTCCTCCGGCCTGTGGGCTGACATTGTGGCACAGGGAACCCGCCACAGCATGAAAGCGTCATCGGACAATAACGACtt              <  2:3124/143‑1 (MQ=255)                                                                                                                                          ccGGCACGGTCCGGGATGATGCCGGCAGCCTGGGCGGATACCTG‑AATCTGGTACACACGTCCTCCGGCCTGTGGGCTGACATTGTGGCACAGGGAACCCGCCACAGCATGAAAGCGTCATCGGACAATAACGACTTCCGCGcc       >  1:593461/1‑143 (MQ=255)                                                                                                                                               aCGGTCCGGGATGATGCCGGCAGCCTGGGCGGATACCTG‑AATCTGGTACACACGTCCTCCGGCCTGTGGGCTGACATTGTGGCACAGGGAACCCGCCACAGCATGAAAGCGTCATCGGACAATCACGACTTCCGCGCCCgggg  >  1:249776/1‑143 (MQ=255)                                                                                                                                               |                                                                                                                                                CAGCGGCAGCTATGGATTCGTCCGTCTGGAGGGTGACCTGATGAGAACAGAGGTTGCCGGTATGTCTGTGACCGCGGGGGTATATGGTGCTGCTGGCCATTCTTCCGTTGATGTTAAGGATGATGACGGCTCCCGTGCCGGCACGGTCCGGGATGATGCCGGCAGCCTGGGCGGATACCTG‑AATCTGGTACACACGTCCTCCGGCCTGTGGGCTGACATTGTGGCACAGGGAACCCGCCACAGCATGAAAGCGTCATCGGACAATAACGACTTCCGCGCCCGGGG  >  NC_000913/2073845‑2074129

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ 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.