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

TGGAGGGTGACCTGATGAGAACAGAGGTTGCCGGTATGTCTGTGACCGCGGGGGTATATGGTGCTGCTGGCCATTCTTCCGTTGATGTTAAGGATGATGACGGCTCCCGTGCCGGCACGGTCCGGGATGATGCCGGCAGCCTGGGCGGATACCTG‑AATCTGGTACACACGTCCTCCGGCCTGTGGGCTGACATTGTGGCACAGGGAACCCGCCACAGCATGAAAGCGTCATCGGACAATAACGACTTCCGCGCCCGGGGCTGGGGC  >  NC_000913/2073871‑2074136                                                                                                                                  |                                                                                                                                          tGGAGGGTGACCTGATGTGGTTGGGGGCTGCCAGAATGTCTGTGACCGCGGGGGGATATGGTGCTGCTGGCCATTCTTCCGTTGATGTTAAGGATGATGACGGCTCCCGTGCCGGCACGGTCCGGGATGATGCCGGCAGCCTg                                                                                                                              <  1:376521/143‑1 (MQ=255) tGGAGGATGACCTGATGAGAACAGAGGTTGCCGGTATGTCTGTGACCGCGGGGGTATATGGTGCTGCTGGCCATTCTTCCGTTGATGTTAAGGATGATGACGGCTCCCGTGCCGGCACGGTCCGGGATGATGCCGGCAGCCTg                                                                                                                              >  2:332851/1‑143 (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)                      cAGAGGTTGCCGGCATGTCTGTGACCGCGGGGGTATATGGTGCTGCTGGCCATTCTTCCGTTGATGTTAAGGATGATGACGGCTCCCGTGCCGGCACGGTCCGGGATGATGCCGGCAGCCTGGGCGGATACCTG‑AATCTGGTa                                                                                                        <  1:290441/143‑1 (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)                                                                                                                         tCCGGGATGAGGCCGGCAGCCTGGGCGGATACCTG‑AATCTGGTACACACGTCCTCCGGCCTGTGGGCTGACATTGTGGCACAGGGAACCCGTCACAGCATGAAAGCGTCATCGGACAATAACGACTTCCGCGCCCggggctgg     <  1:288924/143‑1 (MQ=255)                                                                                                                            gggATGATGCCGGCAGCCTGAGCGGATACCTG‑AATCTGGTACACACGTCCTCCGGCCTGTGGGCTGACATTGTGGCACAGGGAACGCGCCACAGCATGAAAGCGTCATCGGACAATAACGACTTCCGCGACCtgggctggggg  >  2:629370/1‑142 (MQ=255)                                                                                                                                  |                                                                                                                                          TGGAGGGTGACCTGATGAGAACAGAGGTTGCCGGTATGTCTGTGACCGCGGGGGTATATGGTGCTGCTGGCCATTCTTCCGTTGATGTTAAGGATGATGACGGCTCCCGTGCCGGCACGGTCCGGGATGATGCCGGCAGCCTGGGCGGATACCTG‑AATCTGGTACACACGTCCTCCGGCCTGTGGGCTGACATTGTGGCACAGGGAACCCGCCACAGCATGAAAGCGTCATCGGACAATAACGACTTCCGCGCCCGGGGCTGGGGC  >  NC_000913/2073871‑2074136

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ 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.