New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_002947	= 343512	42 (1.420)	6 (0.210)	7/236	NT	12.7%	intergenic (‑65/‑175)	PP_5439/PP_5440	hypothetical protein/hypothetical protein
	?	NC_002947	= 343531	42 (1.480)					intergenic (‑84/‑156)	PP_5439/PP_5440	hypothetical protein/hypothetical protein

CTTGGCCGCTGCGTACCATGCGGTTCTGCTTGGCCTTGCTGGCGGCGCGCTTGGCGCGTTTCTGTTGCTTGGTAGGGGTGGCCATGGGGAAATCCTTGGGTGAGTCTGAAAGTGCGCGTATTGAAGCGCAATTGCCCGATAAACCCAAGCGGC‑GCGCCTGGGCGCTGCAGCTTGAGATGTCTGTGGGATACATATCCAGATTATTCGGACCGTGGGCCCTGCGTAGCTTCTCTCCTGCTGCCAGCCATGTTGGCTGGCAGCCTGTCACTGCGCCAATTCGGCGTCCGTGAGTGATGCG  >  NC_002947/343363‑343660                                                                                                                                                      |                                                                                                                                                      cTTGGCCGCTGCGTATCATGCGGTTCTGCTTGGCCTTGCTGGCGGCGCGCTTGGCGCGTTTCTGTTGCTTGGTAGGGGTGGCCATGGGGAAATCCTTGGGTGAGTCTGAAAGTGCGCGTATTGAAGCGCAATTGCCCGATAAACCCAAGC                                                                                                                                                       <  2:555810‑M1/150‑1 (MQ=255)      ccGCTGCGTACCATGCGGTTCTGCTTGGCCTTGCTGGCGGCGCGCTTGGCGCGTTTCTGTTGCTTGGTAGGGGTGGCCATGGGGAAATCCTTGGGTGAGTCTGAAAGTGCGCGTATTGAAGCGCAATTGCCCGATAAACCCAAGCGgc‑gc                                                                                                                                                 >  2:677063/1‑150 (MQ=255)             gTACCATGCGGTTCTGCTTGGCCTTGCTGGCGGCGCGCTTGGCGCGTTTCTGTTGCTTGGTAGGGGTGGCCATTGGGAAATCCTTGGGTGAGTCTGAAAGTGCGCGTATTGAAGCGCAATTGCCCGATAAACCCAAGCGGC‑GCGCCTggg                                                                                                                                          <  2:281092/150‑1 (MQ=255)                   tGCGGTTCTGCTTGGCCTTGCTGGCGGCGCGCTTGGCGCGTTTCTGTTGCTTGGTAGGGGTGGCCATGGGGAAATCCTTGGGTGAGTCTGAAAGTGCGCGTATTGAAGCGCAATTGCCCGATAAACCCAAGCGGC‑GCGCCTGGGCGCTGc                                                                                                                                    <  2:552463/150‑1 (MQ=255)                    gCGGTTCTGCTTGGCCTTGCTGGCGGCGCGCTTGGCGCGTTTCTGTTGCTTGGTAGGGGTGGCCATGGGGAAATCCTTGGGTGAGTCTGAAAGTGCGCGTATTGAAGCGCAATTGCCCGATAAACCCAAGCGGC‑GCGCCTGGGCGCTGCa                                                                                                                                   <  2:525893/150‑1 (MQ=255)                      ggTTCTGCTTGGCCTTGCTGGCGGCGCGCTTGGCGCGTTTCTGTTGCTTGGGAGGGGTGGCCATGGGGAAATCCTTGGGTGAGTCTGAAAGTGCGCGTATTGAAGCGCAATTGCCCGATAAACTCAAGCtgcagcgcccaggcgcgccgc                                                                                                                                  <  1:300506‑M1/150‑22 (MQ=255)                          cTGCTTGGCCTTGCTGGCGGCGCGCTTGGCGCGTTTCTGTTGCTTGGTAGGTGTGGCCATGGGGCAATCCTTGGGTGAGTCTGAAAGTGCGCGTACTGAAGCGCAATTGCCCGATAAACCCAAGCTGCAGCGCCCAGGCGC‑GCCgcttgg                                                                                                                             >  1:417744‑M2/1‑144 (MQ=255)                            gCTTGGCCTTGCTGGCGGCGCGCTTGGCGCGTTTCTGTTGCTTGGTAGGGGTGGCCATGGGGAAATCCTTGGGTGAGTCTGAAAGTGCGCGTATTGAAGCGCAATTGCCCGATAAACCCAAGCtgcagcgcccaggcgcgccgcttgggt                                                                                                                            <  1:680237‑M1/150‑28 (MQ=255)                            gCTTGGCCTTGCTGGCGGCGCGCTTGGCGCGTTTCTGTTGCTTGGTAGGGGTGGCCATGGGGAAATCCTTGGGTGAGTCTGAAAGTGCGCGTATTGAAGCGCAATTGCCCGATAAACCCAAGCGGC‑GCGCCTGGGCGCTGCAGCTTgaga                                                                                                                           >  2:621584/1‑150 (MQ=255)                                ggCCTTGCTGGCGGCGCGCTTGGCGCGTTTCTGTTGCTTGGTAGGGGTGGCCATGGGGAAATCCTTGGGTGAGTCTGAAAGTGCGCGTATTGAAGCGCAATTGCCCGATAAACCCAAGCTGCAGCGCCCAGGCGC‑GCCgcttgggtttat                                                                                                                       <  1:512307‑M2/150‑13 (MQ=255)                                   cTTGCTGGCGGCGCGCTTGGCGCGTTTCTGTTGCTTGGTAGGGGTGGCCATGGGGAAATCCTTGGGTGAGTCTGAAAGTGCGCGTATTGAAGCGCAATTGCCCGATAAACCCAAGCTGCAGCGCCCAGGCGC‑GCCgcttgggtttatcgg                                                                                                                    >  2:512307‑M2/1‑135 (MQ=255)                                     tGCTGGCGGCGCGCTTGGCGCGTTTCTGTTGCTTGGTAGGGGTGGCCATGGGGAAATCCTTGGGTGAGTCTGAAAGTGCGCGTATTGAAGCGCAATTGCCCGATAAACCCAAGCGGC‑GCGCCTGGGCGCTGCAGCTTGAGATGTCTGTgg                                                                                                                  <  2:760250/150‑1 (MQ=255)                                         ggcggcGCGCTTGGCGCGTTTCTGTTGCTTGGTAGGGGTGGCCATGGGGAAATCCTTGGGTGAGTCTGAAAGTGCGCGTATTGAAGCGCAATTGCCCGATAAACCCAAGCGGC‑GCGCCTGGGCGCTGCAGCTTGAGATGTCTGTGGGATa                                                                                                              >  1:500459/1‑150 (MQ=255)                                                 gcTTGGCGCGTTTCTGTTGCTTGGTAGGGGTGGCCATGGGGAAATCCTTGGGTGAGTCTGAAAGTGCGCGTATTGAAGCGCAATTGCCCGATAAACCCAAGCGGC‑GCGCCTGGGCGCTGCAGCTTGAGATGTCTGTGGGATa                                                                                                              <  2:42479/142‑1 (MQ=255)                                                 gcTTGGCGCGTTTCTGTTGCTTGGTAGGGGTGGCCATGGGGAAATCCTTGGGTGAGTCTGAAAGTGCGCGTATTGAAGCGCAATTGCCCGATAAACCCAAGCGGC‑GCGCCTGGGCGCTGCAGCTTGAGATGTCTGTGGGATa                                                                                                              >  1:42479/1‑142 (MQ=255)                                                      gcgcGTTTCTGTTGCTTGGTAGGGGTGGCCATGGGGAAATCCTTGGGTGAGTCTGAAAGTGCGCGTATTGAAGCGCAATTGCCCGATAAACCCAAGCGGC‑GCGCCTGGGCGCTGCAGATTGAGATGTCTGTGGGATACATATCCAGatta                                                                                                 >  1:3190/1‑150 (MQ=255)                                                                cgatcctGGTAGGGGTGGCCATGGGGAAATCCTTGGGTGAGTCTGAAAGTGCGCGTATTGAAGCGCAATTGCCCGATAAACCCAAGCGGC‑GCGCCTGGGCGCTGCAGCTTGAGATGTCTGTGGGATACATATCCAGATTATTCGGACCGt                                                                                       <  1:488650/144‑1 (MQ=255)                                                                 ttGCTTGGTAGGGGTGGCCATGGGGAAATCCTTGGGTGAGTCTGAAAGTGCGCGTATTGAAGCGCAATTGCCCGATAAACCCAAGCGGC‑GCGCCTGGGCGCTGCAGCTTGAGATGTCTGTGGGATACATATCCAGATTATTCGGACCGTg                                                                                      >  1:388994/1‑150 (MQ=255)                                                                    cTTGGTAGGGGTGGCCATGGGGAAATCCTTGGGTGAGTCTGAAAGTGCGCGTATTGAAGCGCAATTGCCCGATAAACCCAAGCtgcagcgcccaggcgcgccgcttg                                                                                                                               >  2:204053‑M1/1‑83 (MQ=255)                                                                    cTTGGTAGGGGTGGCCATGGGGAAATCCTTGGGTGAGTCTGAAAGTGCGCGTATTGAAGCGCAATTGCCCGATAAACCCAAGCtgcagcgcccaggcgcgccgcttg                                                                                                                               <  1:204053‑M1/107‑25 (MQ=255)                                                                      tGGTAGGGGTGGCCATGGGGAAATCCTTGGGTGAGTCTGAAAGTGCGCGTATTGAAGCGCAATTGCCCGATAAACCCAAGCGGC‑GCGCCTGGGCGCTGCAGCTTGAGATGTCTGTGGGATACATATCCAGATTATTCGGACCGTGGGccc                                                                                 <  2:136457/150‑1 (MQ=255)                                                                       ggTAGGGGTGGCCATGGGGAAATCCTTGGGTGCGTCTGCGAGTGCACGTATTGAACGGCCAATGCATGGTAAACCCAAACGCC‑ACGGCTGGGCGCTTCATCTTGATATGTCTGTGGGATACATATCCAGATTATTCGGACCGTgagatcg                                                                                >  2:488650/1‑144 (MQ=255)                                                                        gTAGGGGTGGCCATGGGGAAATCCTTGGGTGAGTCTGAAAGTGCGCGTATTGAAGCGCAATTGCCCGATAAACCCAAGCGGC‑GCGCCTGGGCGCTGCAGCTTGAGATGTCTGTGGGATACATATCCAGATTATTCGGACCGTGGGCCCTg                                                                               >  1:702376/1‑150 (MQ=255)                                                                            gggTGGCCATGGGGAAATCCTTGGGTGAGTCTGAAAGTGCGCGTATTGAAGCGCAATTGCCCGATAAACCCAAGCGGC‑GCGCCTGGGCGCTGCAGCTTGAGATGTCTGTGGGATACATATCCAGATTATTCGGACCGTGGGCCCTGCGTa                                                                           <  2:702376/150‑1 (MQ=255)                                                                                        ggAAATCCTTGGGTGAGTCTGAAAGTGCGCGTATTGAAGCGCAATTGCCCGATAAACCCAAGCGGC‑GCGCCTGGGCGCTGCAGCTTGAGATGTCTGTGGGATACATATCCAGATTATTCGGACCGTGGGCCCTGCGTAGCTTCTCTCctg                                                               >  1:723320/1‑150 (MQ=255)                                                                                               cTTGGGTGAGTCTGAAAGTGCGCGTATTGAAGCGCAATTGCCCGATAAACCCAAGCGGC‑GCGCCTGGGCGCTGCAGCTTGAGATGTCTGTGGGATACATATCCAGattatt                                                                                               <  2:263571/111‑1 (MQ=255)                                                                                               cTTGGGTGAGTCTGAAAGTGCGCGTATTGAAGCGCAATTGCCCGATAAACCCAAGCGGC‑GCGCCTGGGCGCTGCAGCTTGAGATGTCTGTGGGATACATATCCAGattatt                                                                                               >  1:263571/1‑111 (MQ=255)                                                                                                           tGAAAGTGCGCGTATTGAAGCGCAATTGCCCGATAAACCCAAGCGGC‑GCGCCTGGGCGCTGCAGCTTGAGATGTCTGTGGGATACATATCCAGCTTATTCGGACCGTGGGCCCTGCGTAGCTTCTCTCctgct                                                             >  1:777092/1‑133 (MQ=255)                                                                                                           tGAAAGTGCGCGTATTGAAGCGCAATTGCCCGATAAACCCAAGCGGC‑GCGCCTGGGCGCTGCAGCTTGAGATGTCTGTGGGATACATATCCAGATTATTCGGACCGTGGGCCCTGCGTAGCTTCTCTCctgct                                                             <  2:777092/133‑1 (MQ=255)                                                                                                            gAAAGTGCGCGTATTGAAGCGCAATTGCCCGATAAACCCAAGCGGC‑GCGCCTGGGCGCTGCAGCTTGAGATGTCTGTGGGATACATATCCAGATTATTCGGACCGTGGGCCCTGCGTAGCTTCTCTCCTGCTGCCAGCCATGTtggctgg                                           >  1:728627/1‑150 (MQ=255)                                                                                                             aaaGTGCGCGTATTGAAGCGCAATTGCCCGATAAACCCAAGCGGC‑GCGCCTGGGCGCTGCAGCTTGAGATGTCTGTGGGATa                                                                                                              <  2:568363/82‑1 (MQ=255)                                                                                                             aaaGTGCGCGTATTGAAGCGCAATTGCCCGATAAACCCAAGCGGC‑GCGCCTGGGCGCTGCAGCTTGAGATGTCTGTGGGATa                                                                                                              >  1:568363/1‑82 (MQ=255)                                                                                                             aaaGTGCGCGTATTGAAGCGCAATTGCCCGATAAACCCAAGCGGC‑GCGCCTGGGCGCTGCAGCTTGAGATGTCTGTGGGATACATATCCAGATTATTCGGACCGTGGGCCCTGCGTAGCTTCTCTCctgct                                                             >  1:309406/1‑131 (MQ=255)                                                                                                             aaaGTGCGCGTATTGAAGCGCAATTGCCCGATAAACCCAAGCGGC‑GCGCCTGGGCGCTGCAGCTTGAGATGTCTGTGGGATACATATCCAGATTATTCGGACCGTGGGCCCTGCGTAGCTTCTCTCctgct                                                             <  2:309406/131‑1 (MQ=255)                                                                                                                gTGCGCGTATTGAAGCGCAATTGCCCGATAAACCCAAGCGGC‑GCGCCTGGGCGCTGCAGCTTGAGATGTCTGTGGGATACATATCCAGATTATTCGGACCGTGGGCCCTGCGTAGCTTCTCTCCTGCTGCCAGCCATGTTGGCTGGCAGc                                       <  1:621584/150‑1 (MQ=255)                                                                                                                    gcgTATTGAAGCGCAATTGCCCGATAAACCCAAGCGGC‑GCGCCTGGGCGCTGCAGCTTGAGATGTCTGTGGGATACATATCCAGATTATTCGGACCg                                                                                        >  1:716147/1‑97 (MQ=255)                                                                                                                    gcgTATTGAAGCGCAATTGCCCGATAAACCCAAGCGGC‑GCGCCTGGGCGCTGCAGCTTGAGATGTCTGTGGGATACATATCCAGATTATTCGGACCg                                                                                        <  2:716147/97‑1 (MQ=255)                                                                                                                    gcgTATTGAAGCGCAATTGCCCGATAAACCCAAGCGGC‑GCGCCTGGGCGCTGCAGCTTGAGATGTCTGTGGGATACATATCCAGATTATTCGGACCGTGGGCCCTGCGTAGCTTCTCTCCTGCTGCCAGCCAACATGGCTGGCAGcagga                                   >  2:444544/1‑146 (MQ=255)                                                                                                                      gTATTGAAGCGCAATTGCCCGATAAACCCAAGCGGC‑GCGCCTGGGCGCTGCAGCTTGAGATGTCTGTGGGATACATATCCAGATTATTCGGACCGTGGGCCCTGCGTAGCTTCTCTCCTGCTGCCAGCCATGTTGGCTGGCAGCCTGTCa                                 <  2:716949/150‑1 (MQ=255)                                                                                                                              gcgcAATTGCCCGATAAACCCAAGCGGC‑GCGCCTGGGCGCTGCAGCTTGAGATGTCTGTGGGATACATATCCAGATTATTCGGACCGTGGGCCCTGCGTAGCTTCTCTCCTGCTGCCAGCCATGTTGGCTTGCAGCCTGTCACTGCGCCa                         >  1:33102/1‑150 (MQ=255)                                                                                                                                        ccGATAAACCCAAGCggcgcgcctgggcgctgcagcttgggtttatcgggcaattgcgcttcaatacgcgcactttcagactcacccaaggatttccccatggccacccctaccaagcaacagaaacgcgccaagcgcgccgccagcaag                >  2:512307‑M1/1‑15 (MQ=255)                                                                                                                                        ccGATAAACCCAAGCGGC‑GCGCCTGGGCGCTGCAGCTTGAGATGTCTGTGGGATACATATCCAGATTATTCGGACCGTGGGCCCTGCGTAGCTTCTCTCCTGCTGCCAGCCATGTTGGCTGGCAGCCTGTCACTGCGCCAATTCGGCGTc               >  2:499841/1‑150 (MQ=255)                                                                                                                                        ccGATAAACCCAAGCGGC‑GCGCCTGGGCGCTGCAGCTTGAGATGTCTGTGGGATACATATCCAGATTATTCGGACCGTGGGCCCTGCGTAGCTTCTCTCCTGCTGCCAGCCATGTTGGCTGGCAGCCTGTCACTGCGCCAATTCGGCGTc               <  2:723320/150‑1 (MQ=255)                                                                                                                                          gATAAACCCAAGCGGC‑GCGCCTGGGCGCTGCAGCTTGAGATGTCTGTGGGATACATATCCAGATTATTCGGACCGTGGGCCCTGCGTAGCTTCTCTCCTGCTGCCAGCCATGTTGGCTGGCAGCCTGTCACTGCGCCAATTCGGCGTCCg             >  2:347093/1‑150 (MQ=255)                                                                                                                                           aTAAACCCAAGCggcgcgcctgggcgctgcagcttgggtttatcgggcaattgcgcttcaatacgcgcactttcagactcacccaaggatttccccatggccacccctaccaagcaacagaaacgcgccaagcgcgccgccagcaaggcc             <  1:512307‑M1/150‑139 (MQ=255)                                                                                                                                               aCCCAAGCGGC‑GCGCCTGGGCGCTGCAgcttgggtttatcgggcaattgcgcttcaatacgcgcactttcagactcacccaaggatttccccatggccacccctaccaagcaacagaaacgcgccaagcgcgccgccagcaaggccaagc        <  1:680237‑M2/150‑124 (MQ=255)                                                                                                                                               aCCCAAGCGGC‑GCGCCTGGGCGCTGCAGCTTGAGATGTCTGTGGGATACATATCCAGATTATTCGGACCGTGGGCCCTGCGTAGCTTCTCTCCTGCTGCCAGCCATGTTGGCTGGCAGCCTGTCACTGCGCCAATTCg                    <  1:671483/138‑1 (MQ=255)                                                                                                                                               aCCCAAGCGGC‑GCGCCTGGGCGCTGCAGCTTGAGATGTCTGTGGGATACATATCCAGATTATTCGGACCGTGGGCCCTGCGTAGCTTCTCTCCTGCTGCCAGCCATGTTGGCTGGCAGCCTGTCACTGCGCCAATTCg                    >  2:671483/1‑138 (MQ=255)                                                                                                                                                cccAAGCGGC‑GCGCCTGGGCGCTGCAGCTTGAGATGTCTGTGGGATACATATCCAGATTATTCGGACCGTGGGCCCTGCGTAGCTTCTCTCCTGCTGCCAGCCATGTTGGCTGGCAGCCTGTCACTGCGCCAATTCGGCGTCCgtgagtg       >  1:467217/1‑150 (MQ=255)                                                                                                                                                 ccAAGCggcgcgcctgggcgctgcagcttgggtttatcgggcaattgcgcttcagtacgcgcactttcagactcacccaaggattgccccatggccacacctaccaagcaacagaaacgcgccaagcgcgccgccagcaaggccaagcag       >  1:417744‑M1/1‑6 (MQ=255)                                                                                                                                                 ccAAGCGGC‑GCGCCTGGGCGCTGCAGCTTGAGATGTCTGTGGGATACATATCCAGATTATTCGGACCGTGGGCCCTGCGTAGCTTCTCTCCTGCTGCCAGCCATGTTGGCTGGCAGCCTGt                                   >  2:567603/1‑121 (MQ=255)                                                                                                                                                 ccAAGCGGC‑GCGCCTGGGCGCTGCAGCTTGAGATGTCTGTGGGATACATATCCAGATTATTCGGACCGTGGGCCCTGCGTAGCTTCTCTCCTGCTGCCAGCCATGTTGGCTGGCAGCCTGt                                   <  1:567603/121‑1 (MQ=255)                                                                                                                                                 ccAAGCGGC‑GCGCCTGGGCGCTGCAGCTTGAGATGTCTGTGGGATACATATCCAGATTATTCGGACCGTGGGCCCTGCGTAGCTTCTCTCCTGCTGCCAGCCATGTTGGCTGGCAGCCTGTCACTGCGCCAATTCGGCGTCCgtgagtga      >  2:588518/1‑150 (MQ=255)                                                                                                                                                 ccAAGCGGC‑GCGCCTGGGCGCTGCAGCTTGAGATGTCTGTGGGATACATATCCAGATTATTCGGACCGTGGGCCCTGCGTAGCTTCTCTCCTGCTGCCAGCCATGTTGGCTGGCAGCCTGTCACTGCGCCAATTCGGCGTCCgtgagtg       >  1:415445/1‑149 (MQ=255)                                                                                                                                                 ccAAGCGGC‑GCGCCTGGGCGCTGCAGCTTGAGATGTCTGTGGGATACATATCCAGATTATTCGGACCGTGGGCCCTGCGTAGCTTCTCTCCTGCTGCCAGCCATGTTGGCTGGCAGCCTGTCACTGCGCCAATTCGGCGTCCgtgagtg       <  2:415445/149‑1 (MQ=255)                                                                                                                                                  cAAGCGGC‑GCGCCTGGGCGCTGCAgcttgggtttatcgggcaattgcgcttcaatacgcgcactttcagactcacccaaggatttccccatggccacccctaccaag                                                >  2:204053‑M2/1‑24 (MQ=255)                                                                                                                                                  cAAGCGGC‑GCGCCTGGGCGCTGCAgcttgggtttatcgggcaattgcgcttcaatacgcgcactttcagactcacccaaggatttccccatggccacccctaccaag                                                <  1:204053‑M2/107‑84 (MQ=255)                                                                                                                                                   aaGCGGC‑GCGCCTGGGCGCTGCAGCTTGAGAGGTCTGTGGGATACATATCCAGATTATTCGGACCGTGGGCCCTGCGTAGCTTCTCTCCTGCTGCCAGCCATGTTGGCTGGCAGCCTGTCACTGCGCCAATTCGGCGTCCGTGAGTGATg    <  1:347093/150‑1 (MQ=255)                                                                                                                                                     gcggc‑gCGCCTGGGCGCTGCAgcttgagtttatcgggcaattgcgcttcaatacgcgcactttcagactcacccaaggatttccccatggccacccctcccaagcaacagaaacgcgccaagcgcgccgccagcaaggccaagcagaacc  <  1:300506‑M2/150‑130 (MQ=255)                                                                                                                                                      |                                                                                                                                                      CTTGGCCGCTGCGTACCATGCGGTTCTGCTTGGCCTTGCTGGCGGCGCGCTTGGCGCGTTTCTGTTGCTTGGTAGGGGTGGCCATGGGGAAATCCTTGGGTGAGTCTGAAAGTGCGCGTATTGAAGCGCAATTGCCCGATAAACCCAAGCGGC‑GCGCCTGGGCGCTGCAGCTTGAGATGTCTGTGGGATACATATCCAGATTATTCGGACCGTGGGCCCTGCGTAGCTTCTCTCCTGCTGCCAGCCATGTTGGCTGGCAGCCTGTCACTGCGCCAATTCGGCGTCCGTGAGTGATGCG  >  NC_002947/343363‑343660

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 32 ≤ 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.