New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_002947	= 5789214	55 (0.770)	4 (0.060)	4/254	NT	7.8%	coding (371/1278 nt)	ynfM	efflux transporter
	?	NC_002947	= 5789242	42 (0.620)					coding (399/1278 nt)	ynfM	efflux transporter

CACCGCCATGCTGGCGTTCGGCCTGCTGATCACCGGCCCCATTTCTGACCGCATCGGACGCAAGCCCGTGATGGTGTTCGCGCTGGTCTGCGCCGCCCTGTCCACCTTGGCCAGCGCAGTGATGCCCAGCTGGGAGCTGGTACTGGCCACCCGCGCATTGGTCGGCCTGTCGCTGAGCGGCCTGGCGGCAGTGGCGATGACTTACCTGAGCGAAGAGATCCACCCGCAACACA‑TTGGCCTGGCCATGGGCCTGTACATCGGCGGCAACGCGATTGGCGGCAT  >  NC_002947/5789101‑5789382                                                                                                                                              |                                                                                                                                              cACCGCCATGCTGGCGTTCGGCCTGCTGATCACCGGCCCCATTTCTGACCGCATCGGACGCAAGCCCGTGATGGTGTTCGCGCTGGTCTGCGCCGCCCTGTCCACCTTGGCCAGCGCAGTGATGCCCAGCTGGGAGCTGGTActggcca                                                                                                                                        <  4:22994‑M2/149‑8 (MQ=255) cACCGCCATGCTGGCGTTCGGCCTGCTGATCACCGGCCCCATTTCTGACCGCATCGGACGCAAGCCCGTGATGGTGTTCGCGCTGGTCTGCGCCGCCCTGTCCACCTTGGCCAGCGCAGTGATGCCCAGCTGGGAGCTGGTActggcca                                                                                                                                        <  6:396377‑M2/149‑8 (MQ=255)  aCCGCCATGCTGGCGTTCGGCCTGCTGATCACCGGCCCCATTTCTGACCGCATCGGACGCAAGCCCGTGATGGTGTTCGCGCTGGTCTGCGCCGCCCTGTCCACCTTGGCCAGCGCAGTGATGCCCAGCTGGGAGCTGGTACTGGCCAc                                                                                                                                       >  8:266903/1‑149 (MQ=255)                          ctgATCACCGGCCCCATTTCTGACCGCATCGGACGCAAGCCCGTGATGGTGTTCGCGCTGGTCTGCGCCGCCCTGTCCACCTTGGCCAGCGCAGTGATGCCCAGCTGGGAGCTGGTACTGGCCACCCGCGCATTGGTCGGCCTGTCGCt                                                                                                               <  2:288837/149‑1 (MQ=255)                              tCACCGGCCCCATTTCTGACCGCATCGGACGCAAGCCCGTGATGGTGTTCGCGCTGGTCTGCGCCGCCCTGTCCACCTTGGCCAGCGCAGTGATGCCCAGCTGGGAGCTGGTACTGGCCACCCGCGCATTGGTCGGCCTGTCGCTGAGc                                                                                                           <  4:84535/149‑1 (MQ=255)                              tCACCGGCCCCATTTCTGACCGCATCGGACGCAAGCCCGTGATGGTGTTCGCGCTGGTCTGCGCCGCCCTGTCCACCTTGGCCAGCGCAGTGATGCCCAGCTGGGAGCTGGTACTGGCCACCCGCGCATTGGTCGGCCTGTCGCTGAGc                                                                                                           <  8:296427/149‑1 (MQ=255)                                aCCGGCCCCATTTCTGACCGCATCGGACGCAAGCCCGTGATGGTGTTCGCGCTGGTCTGCGCCGCCCTGTCCACCTTGGCCAGCGCAGTGATGCCCAGCTGGGAGCTGGTACTGGCCACCCGCGCATTGGTCGGCCTGTCGCTGAGCgg                                                                                                         <  7:190320/149‑1 (MQ=255)                                   ggCCCCATTTCTGACCGCATCGGACGCAAGCCCGTGATGGTGTTCGCGCTGGTCTGCGCCGCCCTGTCCACCTTGGCCAGCGCAGTGATGCCCAGCTGGGAGCTGGTACTGGCCACCCGCGCATTGGTCGGCCTGTCGCTGAGCGGCCt                                                                                                      >  4:13142/1‑149 (MQ=255)                                       ccATTTCTGACCGCATCGGACGCAAGCCCGTGATGGTGTTCGCGCTGGTCTGCGCCGCCCTGTCCACCTTGGCCAGCGCAGTGATGCCCAGCTGGGAGCTGGTACTGGCCACCCGCGCATTGGTCGGCCTGTCGCTGAGCGGCCTggcg                                                                                                  >  3:27454/1‑149 (MQ=255)                                        cATTTCTGACCGCATCGGACGCAAGCCCGTGATGGTGTTCGCGCTGGTCTGCGCCGCCCTGTCCACCTTGGCCAGCGCAGTGATGCCCAGCTGGGAGCTGGTACTGGCCACCCGCGCATTGGTCGGCCTGTCGCTGAGCGGCCTggcgg                                                                                                 <  1:383216/149‑1 (MQ=255)                                                aCCGCATCGGACGCAAGCCCGTGATGGTGTTCGCGCTGGTCTGCGCCGCCCTGTCCACCTTGGCCAGCGCAGTGATGCCCAGCTGGGAGCTGGTACTGGCCACCCGCGCATTGGTCGGCCTGTCGCTGAGCGGCCTGGCGGCAGTg                                                                                            <  1:76358/146‑1 (MQ=255)                                                      tCGGACGCAAGCCCGTGATGGTGTTCGCGCTGGTCTGCGCCGCCCTGTCCACCTTGGCCAGCGCAGTGATGCCCAGCTGGGAGCTGGTACTGGCCACCCGCGCATTGGTCGGCCTGTCGCTGAGCGGCCTGGCGGCAGTGGCGATGACt                                                                                   >  1:390497/1‑149 (MQ=255)                                                        ggACGCAAGCCCGTGATGGTGTTCGCGCTGGTCTGCGCCGCCCTGTCCACCTTGGCCAGCGCAGTGATGCCCAGCTGGGAGCTGGTACTGGCCACCCGCGCATTGGTCGGCCTGTCGCTGAGCGGCCTGGCGGCAGTGGCGATGACTTa                                                                                 >  6:367609/1‑149 (MQ=255)                                                         gACGCAAGCCCGTGATGGTGTTCGCGCTGGTCTGCGCCGCCCTGTCCACCTTGGCCAGCGCAGTGATGCCCAGCTGGGAGCTGGTACTGGCCACCCGCGCATTGGTCGGCCTGTCGCTGAGCGGCCTGGCGGCAGTGGCGATGACTTAc                                                                                <  7:266903/149‑1 (MQ=255)                                                             cAAGCCCGTGATGGTGTTCGCGCTGGTCTGCGCCGCCCTGTCCACCTTGGCCAGCGCAGTGATGCCCAGCTGGGAGCTGGTACTGGCCACCCGCGCATTGGTCGGCCTGTCGCTGAGCGGCCTGGCGGCAGTGGCGATGACTTACCTGa                                                                            <  3:11257/149‑1 (MQ=255)                                                             cAAGCCCGTGATGGTGTTCGCGCTGGTCTGCGCCGCCCTGTCCACCTTGGCCAGCGCAGTGATGCCCAGCTGGGAGCTGGTACTGGCCACCCGCGCATTGGTCGGCCTGTCGCTGAGCGGCCTGGCGGCAGTGGCGATGACTTACCTGa                                                                            <  5:396377/149‑1 (MQ=255)                                                              aaGCCCGTGATGGTGTTCGCGCTGGTCTGCGCCGCCCTGTCCACCTTGGCCAGCGCAGTGATGCCCAGCTGGGAGCTGGTACTGGCCACCcg                                                                                                                                    >  4:324637/1‑92 (MQ=255)                                                              aaGCCCGTGATGGTGTTCGCGCTGGTCTGCGCCGCCCTGTCCACCTTGGCCAGCGCAGTGATGCCCAGCTGGGAGCTGGTACTGGCCACCcg                                                                                                                                    <  3:324637/92‑1 (MQ=255)                                                              aaGCCAGAGATGCTGTTCGCGCTCGACAGCGCCGCCCTGTCCACCTAGGCCAGCCCAGTCATGCCCAGCTGTGAGCTGGTACTGCCCACACGCGCATTTGTCGGCCTGTCGCTGAGCGGCCTGGCGGCAGTCGCGATGACTTACCTGAg                                                                           >  8:326213/1‑149 (MQ=255)                                                                gCCCGTGATGGTGTTCGCGCTGGTCTGCGCCGCCCTGTCCACCTTGGCCAGCGCAGTGATGCCCAGCTGGGAGCTGGTACTGGCCACCCGCGCATTGGTCGGCCTGTCGCTGAGCGGCCTGGCGGCAGTGGCGATGACTTACCTGAGCg                                                                         <  3:22994/149‑1 (MQ=255)                                                                 cccGTGATGGTGTTCGCGCTGGTCTGCGCCGCCCTGTCCACCTTGGCCAGCGCAGTGATGCCCAGCTGGGAACAGGTACTGGCCACCCGCGCATTGGTCGGCCTGTCGCTGAGCGGCCTGGCGGCAGTGGCGATGACTTACCTGAGCg                                                                         >  1:354790/1‑148 (MQ=255)                                                                  ccGTGATGGTGTTCGCGCTGGTCTGCGCCGCCCTGTCCACCTTGGCCAGCGCAGTGATGCCCAGCTGGGAGCTGGTACTGGCCACCCGCGCATTGGTCGGCCTGTCGCTGAGCGGCCTGGCGGCAGTGGCGATGACTTACCTGAGCg                                                                         >  4:388625/1‑147 (MQ=255)                                                                  ccGTGATGGTGTTCGCGCTGGTCTGCGCCGCCCTGTCCACCTTGGCCAGCGCAGTGATGCCCAGCTGGGAGCTGGTACTGGCCACCCGCGCATTGGTCGGCCTGTCGCTGAGCGGCCTGGCGGCAGTGGCGATGACTTACCTGAGCGaa                                                                       <  4:27454/149‑1 (MQ=255)                                                                  ccGTGATGGTGTTCGCGCTGGTCTGCGCCGCCCTGTCCACCTTGGCCAGCGCAGTGATGCCCAGCTGGGAGCTGGTACTGGCCACCCGCGCATTGGTCGGCCTGTCGCTGAGCGGCCTGGCGGCAGTGGCGATGACTTACCTGAGCGaa                                                                       <  2:390497/149‑1 (MQ=255)                                                                  ccGTGATGGTGTTCGCGCTGGTCTGCGCCGCCCTGTCCACCTTGGCCAGCGCAGTGATGCCCAGCTGGGAGCTGGTACTGGCCACCCGCGCATTGGTCGGCCTGTCGCTGAGCGGCCTGGCGGCAGTGGCGATGACTTACCTGAGCGaa                                                                       <  5:317986/149‑1 (MQ=255)                                                                   cGTGATGGTGTTCGCGCTGGTCTGCGCCGCCCTGTCCACCTTGGCCAGCGCAGTGATGCCCAGCTGGGAGCTGGTACTGGCCACCCGCGCATTGGTCGGCCTGTCGCTGAGCGGCCTGGCGGCAGTGGCGATGACTTACCTGAGCGAag                                                                      <  3:186536/149‑1 (MQ=255)                                                                      gATGGTGTTCGCGCTGGTCTGCGCCGCCCTGTCCACCTTGGCCAGCGCAGTGATGCCCAGCTGGGAGCTGGTACTGGCCACCCGCGCATTGGTCGGCCTGTCGCTGAGCGGCCTGGCGGCAGTgg                                                                                           <  1:415592/125‑1 (MQ=255)                                                                      gATGGTGTTCGCGCTGGTCTGCGCCGCCCTGTCCACCTTGGCCAGCGCAGTGATGCCCAGCTGGGAGCTGGTACTGGCCACCCGCGCATTGGTCGGCCTGTCGCTGAGCGGCCTGGCGGCAGTgg                                                                                           >  2:415592/1‑125 (MQ=255)                                                                          gtgtTCGCGCTGGTCTGCGCCGCCCTGTCCACCTTGGCCAGCGCAGTGATGCCCAGCTGGGAGCTGGTACTGGCCACCCGCGCATTGGTCGGCCTGTCGCTGAGCGGCCTGGCGGCAGTGGCGa                                                                                        >  6:358914/1‑124 (MQ=255)                                                                          gtgtTCGCGCTGGTCTGCGCCGCCCTGTCCACCTTGGCCAGCGCAGTGATGCCCAGCTGGGAGCTGGTACTGGCCACCCGCGCATTGGTCGGCCTGTCGCTGAGCGGCCTGGCGGCAGTGGCGa                                                                                        <  5:358914/124‑1 (MQ=255)                                                                          gtgtTCGCGCTGGTCTGCGCCGCCCTGTCCACCTTGGCCAGCGCAGTGATGCCCAGCTGGGAGCTGGTACTGGCCACCCGCGCATTGGTCGGCCTGTCGCTGAGCGGCCTGGCGGCAGTGGCGATGACTTACCTGAGCGAAGAGATCCa                                                               >  2:188439/1‑149 (MQ=255)                                                                            gtTCGCGCTGGTCTGCGCCGCCCTGTCCACCTTGGCCAGCGCAGTGATGCCCAGCTGGGAGCTGGTACTGGCCACCCGCGCATTGGTCGGCCTGTCGCTGAGCGGCCTGGCGGCAGTGGCGATGACTTACCTGAGCGAAGAGATCCAcc                                                             >  5:406001/1‑149 (MQ=255)                                                                                gcgcTGGTCTGCGCCGCCCTGTCCACCTTGGCCAGCGCAGTGATGCCCAGCTGGGAGCTGGTACTGGCCACCCGCGCATTGGTCGGCCTGTCGCTGAGCGGCCTGGCGGCAGTGGCGATGACTTACCTGAGCGAAGAGATCCACCCGc                                                          <  2:81183/148‑1 (MQ=255)                                                                                         tGCGCCGCCCTGTCCACCTTGGCCAGCGCAGTGATGCCCAGCTGGGAGCTGGTACTGGCCACCCGCGCATTGGTCGGCCTGTCGCTGAGCGGCCTGGCGGCAGTGGCGATGACTTACCTGAGCGAAGAGATCCACCCGCAACACA‑Ttgg                                               >  3:132111/1‑149 (MQ=255)                                                                                          gcgcCGCCCTGTCCACCTTGGCCAGCGCAGTGATGCCCAGCTGGGAGCTGGTACTGGCCACCCGCGCATTGGTCGGCCTGTCGCTGAGCGGCCTGGCGGCAGTGGCGATGACTTACCTGAGCGAAGAGATCCACCCGCAACACA‑Ttggc                                              >  1:116372/1‑149 (MQ=255)                                                                                           cgccgcCCTGTCCACCTTGGCCAGCGCAGTGATGCCCAGCTGGGAGCTGGTACTGGCCACCCGCGCATTGGTCGGCCTGTCGCTGAGCGGCCTGGCGGCAGTGGCGATGACTTACCTGAGCGAAGAGATCCACCCGCAACACA‑Ttggcc                                             >  2:394722/1‑149 (MQ=255)                                                                                             ccgccCTGTCCACCTTGGCCAGCGCAGTGATGCCCAGCTGGGAGCTGGTACTGGCCACCCGCGCATTGGTCGGCCTGTCGCTGAGCGGCCTGGCGGCAGTGGCGATGACTTACCTGAGCGAAGAGATCCACCCGCAACACA‑Ttggcctg                                           <  3:13142/149‑1 (MQ=255)                                                                                                cccTGTCCACCTTGGCCAGCGCAGTGATGCCCAGCTGGGAGCTGGTACTGGCCACCCGCGCATTGGTCGGCCTGTCGCTGAGCGGCCTGGCGGCAGTGGCGATGACTTACCTGAGCGAAGAGATCCACCCGCAACACA‑Ttggcctggc                                         >  6:270877/1‑148 (MQ=255)                                                                                                     tCCACCTTGGCCAGCGCAGTGATGCCCAGCTGGGAGCTGGTACTGGCCACCCGCGCATTGGTCGGCCTGTCGCTGAGCGGCCTGGCGGCAGTGGCGATGACTTACCTGAGCGAAGAGATCCACCCGCAACACA‑TTGGCCTGGCCATggg                                   <  8:68224/149‑1 (MQ=255)                                                                                                        aCCTTGGCCAGCGCAGTGATGCCCAGCTGGGAGCTGGTActggccaaggtggacagggcggcgcagaccagcgcgaacaccatcacgggcttgcgtccgatgcggtcagaaatggggccggtgatcagcaggccgaacgccagcatggc                                 <  5:380166‑M2/149‑111 (MQ=255)                                                                                                         ccTTGGCCAGCGCAGTGATGCCCAGCTGGGAGCTGGTActggccaaggtggacagggcggcgcagaccagcgcgaacaccatcacgggcttgcgtccgatgcggtcagaaatggggccggtgatcagcaggccgaacgccagcatggcg                                <  5:98912‑M2/149‑112 (MQ=255)                                                                                                          cTTGGCCAGCGCAGTGATGCCCAGCTGGGAGCTGGTActggccaaggtggacagggcggcgcagaccagcgcgaacaccatcacgggcttgcgtccgatgcggtcagaaatggggccggtgatcagcaggccgaacgccagcatggcgg                               <  6:110476‑M2/149‑113 (MQ=255)                                                                                                                      aGTGATGCCCAGCTGGGAGCTGGTACTGGCCACCCGCGCATTGGTCGGCCTGTCGCTGAGCGGCCTGGCGGCAGTGGCGATGACTTACCTGAGCGAAGAGATCCACCCGCAACACA‑TTGGCCTGGCCATGGGCCTGTACATCggcggc                   >  2:270840/1‑148 (MQ=255)                                                                                                                           tGCCCAGCTGGGAGCTGGTACTGGCCACCCGCGCATTGGGCGGCCTGTCGCTGAGCGGCCTGGCGGCAGTGGCGATGACTTACCTGAGCGAAGAGATCCACCCGCAACACA‑TTGGCCTGGCCATGGGCCTGTACATCGGCGGCAAcgcg             <  6:261842/149‑1 (MQ=255)                                                                                                                            gCCCAGCTGGGAGCTGGTACTGGCCACCCGCGCATTGGTCGGCCTGTCGCTGAGCGGCCTGGCGGCAGTGGCGATGACTTACCTGAGCGAAGAGATCCACCCGCAACACA‑TTGGCCTGGCCATGGGCCTGTACATCGGCGGCAACGCGa            >  7:238376/1‑149 (MQ=255)                                                                                                                              ccAGCTGGGAGCTGGTACTGGCCACCCGCGCATTGGTCGGCCTGTCGCTGAGCGGCCTGGCGGCAGTGGCGATGACTTACCTGAGCGAAGAGATCCACCCGCAACACA‑TTGGCCTGGCCATGGGCCTGTACATCGACGGCAACGCGAtt          <  6:154916/149‑1 (MQ=255)                                                                                                                                aGCTGGGAGCTGGTACTGGCCACCCGCGCATTGGTCGGCCTGTCGCTGAGCGGCCTGGCGGCAGTGGCGATGACTTACCTGAGCGAAGAGATCCACCCGCAACACA‑TTGGCCTGGCCATGGGCCTGTACATCGGCGGCAACGCGATTgg        <  1:270840/149‑1 (MQ=255)                                                                                                                                  cTGGGAGCTGGTACTGGCCACCCGCGCATTGGTCGGCCTGTCGCTGAGCGGCCTGGCGGCAGTGGCGATGACTTACCTGAGCGAAGAGATCCACCCGCAACACA‑TTGGCCTGGCCATGGGCCTGTACATCGGCGGCAACGCGATTggcg      <  5:367609/149‑1 (MQ=255)                                                                                                                                    gggAGCTGGTACTGGCCACCCGCGCATTGGTCGGCCTGTCGCTGAGCGGCCTGGCGGCAGTGGCGATGACTTACCTGAGCGAAGAGATCCACCCGCAACACA‑TTGGCCTGGCCATGGGCCTGTACATCGGCGGCAACGCGATTggcgg     >  5:178368/1‑148 (MQ=255)                                                                                                                                     ggAGCTGGTACTGGCCACCCGCGCATTGGTCGGCCTGTCGCTGAGCGGCCTGGCGGCAGTGGCGATGACTTACCTGAGCGAAGAGATCCACCCGCAACACATTTGGCCTGGCCATGGGCCTGTACATCGGCGGCAACGCGATTggcggc    <  1:188439/149‑1 (MQ=255)                                                                                                                                       aGCTGGTActggccaaggtggacagggcggcgcagaccagcgcgaacaccatcacgggcttgcgtccgatgcggtcagaaatggggccggtgatcagcaggccgaacgccagcatggcggtggacaccgacagcaccaggctgctctgt  >  6:98912‑M2/1‑8 (MQ=255)                                                                                                                                              |                                                                                                                                              CACCGCCATGCTGGCGTTCGGCCTGCTGATCACCGGCCCCATTTCTGACCGCATCGGACGCAAGCCCGTGATGGTGTTCGCGCTGGTCTGCGCCGCCCTGTCCACCTTGGCCAGCGCAGTGATGCCCAGCTGGGAGCTGGTACTGGCCACCCGCGCATTGGTCGGCCTGTCGCTGAGCGGCCTGGCGGCAGTGGCGATGACTTACCTGAGCGAAGAGATCCACCCGCAACACA‑TTGGCCTGGCCATGGGCCTGTACATCGGCGGCAACGCGATTGGCGGCAT  >  NC_002947/5789101‑5789382

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