New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	CP009273	993895 =	64 (1.190)	3 (0.060)	3/272	7.9	4.8%	intergenic (+32/‑51)	elfA/elfD	laminin‑binding fimbrin subunit/putative periplasmic pilin chaperone
	?	CP009273	993917 =	59 (1.170)					intergenic (+54/‑29)	elfA/elfD	laminin‑binding fimbrin subunit/putative periplasmic pilin chaperone
Rejected: Coverage evenness skew score above cutoff.
Rejected: Frequency below/above cutoff threshold.

TGACTTTTAAAGTTGATTATATCGCTACGGGGAAAGCGACTTCAGGTAATGTGAATGCGGTAACAAATTTCCATATTAACTATTATTAATAGAACTCATTAATTGTTTTATTAATTAGTACCCCTCCAGTGTTCTGGAGGGGATATTCATATTTTTTAAGAGTGACTATTTATGAAAACTTGCATAACAAAGGGAATTGTGACCGTAAGTTTAACGGCAATATTACTCAGCTGCTCATCCGCATGGGCGGCAGGTAAAGGCGGGATTGGACTTGCAGCAACACG  >  CP009273/993775‑994058                                                                                                                                               |                                                                                                                                              tGACTTTTAAAGTTGATTATATCGCTACGGGGAAAGCGACTTCAGGTAATGTGAATGCGGTAAGAAATTTCCATATTAACTATTATTAATAGAACTCATTAATTGTTTTATTAATTAGTACCCCTCCAGTGTTCTGGAGGGGATATTCa                                                                                                                                         >  1:611913/1‑149 (MQ=255)    cTTTTAAAGTTGATTATAGCGCTACGGGGAAAGCGACTTCAGGTAATGTGAATGCGGTAACAAATTTCCATATTAACTATTATTAATAGAACTCATTAATTGTTTTATTAATTAGTACCCCTCCAGTGTTCTGGAGGGGatat                                                                                                                                            <  2:264446/143‑1 (MQ=255)       ttAAAGTTGATTATATCGCTACGGGGAAAGCGACTTCAGGTAATGTGAATGCGGTAACAAATTTCCATATTAACTATTATTAATAGAACTCATTAATTGTTTTATTAATTAGTACCCCTCCAGTGTTCTGGAGGGGATATTCATAtttt                                                                                                                                   <  1:689651/149‑1 (MQ=255)           aGTTGATTATATCGCTACGGGGAAAGCGACTTCAGGTAATGTGAATGCGGTAACAAATTTCCATATTAACTATTATTAATAGAACTCATTAATTGTTTTATTAATTAGTACCCCTCCAGTGTTCTGGAGGGGATATTCATATTTTTTaa                                                                                                                               <  1:28755/149‑1 (MQ=255)             ttGATTATATCGCTACGGGGAAAGCGACTTCAGGTAATGTGAATGCGGTAACAAATTTCCATATTAACTATTATTAATAGAACTCATTAATTGTTTTATTAATTAGTACCCCTCCAGTGTTCTGGAGGGGATATTCATATTTTTTAaga                                                                                                                             >  1:367127/1‑149 (MQ=255)                 ttATATCGCTACGGGGAAAGCGACTTCAGGTAATGTGAATGCGGTAACAAATTTCCATATTAACTATTATTAATAGAACTCATTAATTGTTTTATTAATTAGTACCCCTCCAGTGTTCTGGAGGGGATATTCATATTTTTTAAGAGTGa                                                                                                                         <  1:414035/149‑1 (MQ=255)                  tataTCGCTACGGGGAAAGCGACTTCAGGTAATGTGAATGCGGTAACAAATTTCCATATTAACTATTATTAATAGAACTCATTAATTGTTTTCTTAATTAGTACCCCTCCAGTGTTCTGGCGGGGATATTCATATTTTTTAag                                                                                                                              >  2:487110/1‑143 (MQ=255)                       cGCTACGGGGAAAACGACTTCAGGTAATGTGAATGCGGTAACAAATTTCCATATTAACTATTATTAATAGAACTCATTAATTGTTTTATTAATTAGTACCCCTCCAGTGTTCTGGAGGGGATATTCATATTTTTTAAGAGTGACTAttt                                                                                                                   >  1:624855/1‑149 (MQ=255)                            cGGGGAAAGCGACTTCAGGTAATGTGAATGCGGTAACAAATTTCCATATTAACTATTATTAATAGAACTCATTAATTGTTTTATTAATTAGTACCCCTCCAGTGTTCTGGAGGGGATATTCATATTTTTTAAGAGTGACTAtt                                                                                                                    >  2:291009/1‑143 (MQ=255)                                 aaaGCGACGTCAGGTAATGTGAATGCGGTAACAAATTTCCATATTAACTATTATTAATAGAACTCATTAATTGTTTTATTAATTAGTACCCCTCCAGTGTTCTGGAGGGGATATTCATATTTTTTAAGAGTGACTATTTATGAAAACtt                                                                                                         <  1:223596/149‑1 (MQ=255)                                         ttCAGGTAATGTGAATGCGGTAACAAATTTCCATATTAACTATTATTAATAGAACTCATTAATTGTTTTATTAATTATTACCCCTCCAGTGTTCTGGAGGGGATATTCATATTTTTTAAGAGTGACTATTTATGAAAACTTGc                                                                                                       <  2:494447/143‑1 (MQ=255)                                             ggTAATGTGAATGCGGTAACAAATTTCCATATTAACTATTATTAATAGAACTCATTAATTGTTTTATTAATTAGTACCCCGCCAGTGTTCTGGAGGGGATATTCATATTTTTTAAGAGTGACTATTTATGAAAACTTGCATAACAAAgg                                                                                             <  1:550750/149‑1 (MQ=255)                                              gTAATGTGAATGCGGTAACAAATTTCCATATTAACTATTATTAATAGAACTCATTAATTGTTTTATTAATTAGTACCCCTCCAGTGTTCTGGAGGGGATATTCATATTTTTTAAGAGTGACTATTTATGAAAACTTGCATAAc                                                                                                  >  2:640819/1‑143 (MQ=255)                                               tAATGTGAATGCGGTAACAAATTTCCATATTAACTATTATTAATAGAACTCATTAATTGTTTTATTAATTATTACCCCTCCAGTGTTCTGGAGGGGATATTCATATTTTTTAAGAGTGACTATTTATGAAAACTTGCATAACa                                                                                                 >  2:211898/1‑143 (MQ=255)                                                 aTGTGAATGCGGTAACAAATTTCCATATTAACTATTATTAATAGAACTCATTAATTGTTTTATTAATTAGTACCCCTCCAGTGTTCTGGAGGGGCTATTCATATTTTTTAAGAGTGACTATTTATGAAAACTTGCATAACaaa                                                                                               >  2:553304/1‑143 (MQ=255)                                                   gtgAATGCGGTAACAAATTTCCATATTAACTATTATTAATAGAACTCATTAATTGTTTTATTAATTAGTACCCCTCCAGTGTTCTGGAGGGGATATTCATATTTTTTAAGAGTGACTATTTATGAAAACTTGCATAACAAAgg                                                                                             <  2:611745/143‑1 (MQ=255)                                                   gtgAATGCGGTAACAAATTTCCATATTAACTATTATTAATAGAACTCATTAATTGTTTTATTAATTAGTACCCCTCCAGTGTTCTGGAGGGGATATTCATATTTTTTAAGAGTGACTATTTATGAAAACTTGCATAACAAAgg                                                                                             <  2:656213/143‑1 (MQ=255)                                                       aTGCGGTAACAAATTTCCATATTAAATATTATTAATAGAACTCATTAATTGTTTTATTAATTAGTACCCCTCCAGTGTTCTGGAGGGGATATTCATATTTTTTAAGAGTGACTATTTATGAAAACTTGCATAACAAAGGGAAt                                                                                         <  2:398310/143‑1 (MQ=255)                                                         gCGGTAACAAATTTCCATATTAACTATTATTAATAGAACTAATTAATTATTTAGTGAATTAGTAACCCTCCAGTGTTCTGGAGGGGATATTCATATTTTTTAAGAGTGACTATTTATGAAAACTTGCATAACAAAGGAAATtg                                                                                       >  2:483848/1‑143 (MQ=255)                                                            gTACCAAAGTTCCATATTAACTATTATTAATAGCACTCAATAATTGTTTTATTAATTAGTACCCCTCCAGTGTTCTGTAGGGGATATTCATATTTTTTAAGAGTGACTATTTATGAAAACTTGCATAACAAAGGGAATTGTGACCGTaa                                                                              <  1:438263/149‑1 (MQ=255)                                                             tAACAAATTTCCATATTAACTATTATTAATAGAACTCATTAATTGTTTTATTAATTAGTACCCCTCCAGTGTTCTGGAGGGGATATTCATATTTTTTAAGAGTGACTATTTATGAAAACTTGCATAACAAAGGGAATTGTGAc                                                                                   <  2:760558/143‑1 (MQ=255)                                                              aaCAAATTTCCATATTAACTATTACTAATAGAACTCATTCCTCGTCAGAGTAATTAGTACCCCTCCAGTGTTCTGGAGGGGATATTCATATTTTTTAAGAGTGACTATTTATGAAAACTTGCATAACAAAGGGAATTGTGACCGTAAGt                                                                            <  1:71233/149‑1 (MQ=255)                                                                  aaTTTCCATATTAACTATTATTACTAGAAATCATTAATTGTTTTATTAATTAGTACCCCTCCAGTGTTCTGGAGGGGATATTAATATTTTTTAAGCGTGACTATTTATGAAAACTTGCATAACAAAGGGAATTGTGACCGTAAGTTTaa                                                                        <  1:385336/149‑1 (MQ=255)                                                                  aaTTTCCATATTAACTATTATTAATAGAACTCATTAATTGTTTTATTAATTAGTACCCCTCCAGTGTTCTGGAGGGGATATTCATATTTTTTAAGAGTGACTATTTATGAAAACTTGCATAACAAAGGGAATTGTGACCGTaa                                                                              >  2:675873/1‑143 (MQ=255)                                                                      tCCATATTAACTATTATTAATAGAACTCATTAATTGTTTTATTAATTAGTACCCCTCCAGTGTTCTGGAGGGGATATTCATATTTTTTAAGAGTGACTATTTATGAAAACTTGCATAACAAAGGGAATTGTGACCGTAAGttt                                                                          >  2:317025/1‑143 (MQ=255)                                                                        cATATTAACTATTATTACTATAACTCATTAATTGTTTTATTTATTAGTACCTCTCCAGTGTTCTGGAGGGGATATTCATATTTTTTAAGAGTGACTATTTATGAAAACTTGCATAACAAAGGGAATTGTGACCGTAAGTTTaa                                                                        <  2:120/143‑1 (MQ=255)                                                                           atTAACTATTATTAATAGAGCTCATTAATTGTTTTATTAATTAGTACCCCTCCAGTGTTCTGGAGGGGATATTCATATTTTTTAAGAGTGACTATTTATGAAAACTTGCATAACAAAGGGAATTGTGACCGTAGGTTTAACgg                                                                     >  2:563234/1‑143 (MQ=255)                                                                              aaCTATTATTAATAGAACTCATTAATTGTTTTATTAATTAGTACCCCTCCAGTGTTCTGGAGGGGATATTCATATTTTTTAAGAGTGACTATTTATGAAAACTTGCATAACAAAGGGAATTGTGACCGTAAGTTTAACGGCaa                                                                  <  2:821431/143‑1 (MQ=255)                                                                              aaCTATTATTAAAAGAACTCATTAATTGTCTTATTAATTACGACCCCTCCAGTGTTCTGGAGGGGATATTCATATTTTTGAAGAGTGACTATTTATGAACACTCGCATAACAAAGGGAATTGTGACCGTAAGTTTAACGGCaa                                                                  <  2:542084/143‑1 (MQ=255)                                                                               accattattAATAGAACTCATTAATTGTTTTATTAATTAGTACCCCTCCAGTGTTCTGGAGGGGATATTCATATTTTTTAAGAGTGACTATTTATGAAAACTTGCATAACAAAGGGAATTGTGACCGTAAGTTTAACGGCAATATTACt                                                           <  1:472687/146‑1 (MQ=255)                                                                                cTATTCTTAATAGCACCCATTAATTGTTTTATTAATTAGTACCCCTCCAGTGTTCTGGAGGGGATATTCATATTTTTTAAGAGTGACTATTTATGAAAACTTGCATAACAAAGGGAATTGTGACCGTAAGTTTAACGGCAATATTACTc                                                          <  1:328820/149‑1 (MQ=255)                                                                                 tattatTAATAGAACTCATTAATTGTTTTATTAATTCGTACCCCTCCAGTGTTCGGGGGGGGATATTCATATTTTTTAAGAGGGACTATTTATGAAAACTTACATAACAAAGGGAATTGTGACCGTAAGTTTAACGCCAatat                                                               >  2:237544/1‑143 (MQ=255)                                                                                 tattatTAATAGAACTCATTAATTGTTTTATTAATTAGTACCCCTCCAGTGTTCTGGAGGGGATATTCATATTTTTTAAGAGTGACTATTTATGAAAACTTGCATAACAAAGGGAATTGTGACCGTAAGTTTAACGGCAATATTACTCa                                                         >  1:639321/1‑149 (MQ=255)                                                                                    tattaATAGAACTCATTAATTGTTTTATTAATTAGTACCCCTCCAGTGTTCTGGAGGGGATATTCATATTTTTTAAGAGTGACTATTTATGAAAACTTGCATAACAAAGGGAATTGTGACCGTAAGTTTAACGGCAATATTACTCAgct                                                      >  1:132635/1‑149 (MQ=255)                                                                                     attaATAGAACTCATTAATTGTTTTATTAATTAGTACCCCTCCAGTGTTCTGGAGGGGATATTCATATTTTTTAAGAGTGACTATTTATGAAAACTTGCATAACAAAGGGAATTGTGACCGTAAGTTTAACGGCAATATTACTCAgctg                                                     >  1:908923/1‑149 (MQ=255)                                                                                       taATAGAACTCATTAATTGTTTTATTAATTAGTACCCCTCCAGTGTTCTGGAGGGGATATTCATATTTTTTAAGAGTGACTATTTATGAAAACTTGCATAACAAAGGGAATTGTGAGCGTCAGTTTAACGGCAATATTACTCAgctgct                                                   >  1:750148/1‑149 (MQ=255)                                                                                          tAGAACTCATTAATTGTTTTATTAATTAGTACCCCTCCAGTGTTCTGGAGGGGATATTCATATTTTTTAAGAGTGACTATTTATGAAAACTTGCATAACAAAGGGAATTGTGACCGTAAGTTTAACGGCAATATTACTCAgct                                                      <  2:82501/143‑1 (MQ=255)                                                                                             aaCTCATTAATTGTTTTATTAATTAGTACCCCTCCAGTGTTCTGGAGGGGATATTCATATTTTTTAAGAGTGACTATTTATGAAAACTTGCATAACAAAGGGAATTGTGACCGTAAGTTTAACGGCAATATTACTCAGCTGCTCATCCg                                             >  1:229949/1‑149 (MQ=255)                                                                                                tCATTAATTGTTTTATTAATTAGTACCCCCCCAGTGTTCTGGAGGGGATATTCATATTTTTTAAGAGTGACTATTTATGAAAACTTGCATAACAAAGGGACTTGTGACCGTAAGTTTAACGGCAATATTACTCAGCTGCTCATCCGCAt                                          <  1:34966/149‑1 (MQ=255)                                                                                                 cATTAATTGTTTTATTAATTAGTACCCCTCCAGTGTTCTGGAGGGGATATTCATATTTTTTAAGAGTGACTATTTATGAAAACTTGCATAACAAAGGGAATTGTGACCGTAAGTTTAAAGGCAATATTACTCAGCTGCTCATc                                               >  2:687829/1‑143 (MQ=255)                                                                                                   ttAATTGTTTTATTAATTAGTACCCCTTCAGTGTTCTGGAGGGGATTTTCATATTCTTTAATATTGACTATTTATGAAAACTTGCATAACAAAGGGAATTGTGACCGTAAGTTTAACGGCAATATTACTCAGCTGCTCATCCGCATggg                                       <  1:757639/149‑1 (MQ=255)                                                                                                      aTTGTTTTATTAATTAGTACCCCTCCAGTGTTCTGGAGGGGATATTCATATTTTTTAAGAGTGACTATTTATGAAAACTTGCATAACAAAGGGAATTGTGACCGTAAGTTTAACGGCAATATTACTCAGCTGCTCATCCGCATGggcgg                                    <  1:777816/149‑1 (MQ=255)                                                                                                      aTTGTTTTATTAATTAGTACCCCTCCAGTGTTCTGGAGGGGATATTCATATTTTTTAAGAGTGACTATTTATGAAAACTTGCATAACAAAGGGAATTGTGACCGTAAGTTTAACGGCAATATTACTCAGCTGCTCATCCGCATGggcgg                                    <  1:263513/149‑1 (MQ=255)                                                                                                        tGTTTTATTAATTAGTACCCCTCCAGTGTTCTGGAGGGGATATTCATATTTTTTAAGAGTGACTATTTATGAAAACTTGCATAACAAAGGGAATTGTGACCGTAAGTTTAACGGCAATATTACTCAGCTGCTCATCCGCATGGGCGGCa                                  <  1:688710/149‑1 (MQ=255)                                                                                                         gTTTTATTAATTAGTACCCCTCCAGTGTTCTGGAGGGGATATTCATATTTTTTAAGAGTGACTATTTATGAAAACTTGCATAACAAAGGGAATTGTGACCGTAAGTTTAACGGCAATATTACTCAGCTGCTCATCCGCATGGGCGGCAg                                 <  1:455400/149‑1 (MQ=255)                                                                                                          ttttATTAATTAGTACCCCTCCAGTGTTCTGGAGGGGATATTCATATTTTTTAAGAGTGACTATTTATGAAAACTTGCATAACAAAGGGAATTGTGACCGTAAGTTTAACGGCAATATTGCTCAGCTGCTCATCCGCATGggc                                      <  2:811235/143‑1 (MQ=255)                                                                                                           tttATTAATTAGTACCCCTCCAGTGTTCTGGAGGGGATATTCATATTTTTTAAGAGTGACTATTTATGAAAACTTGCATAACAAATGGAATTGTGACCGTAAGTTTAACGGCAATATTATTCAGCTGCTCATCCGCATGGGCGGCAGGt                               <  1:597171/149‑1 (MQ=255)                                                                                                             tattaATTAGTACCCCTCCAGTGTTCTGGAGGGGATATTCATATTTTTTAAGAGTGACTATTTATGAAAACTTGCATAACAAAGGGAATTGTGACCGTAAGTTTAACGGCAATATTACTCAGCTGCTCATCCGCATGGGCGGCAGGTaa                             >  1:168637/1‑149 (MQ=255)                                                                                                                  attaGTACCCCTTCAGTGTTCTGGAGGCGATATTCATATTTTTTAAGAGTGACTATTTATGAAAACTTGCATAACAAAGGGAATTGTGACCGTAAGTTTAACGGCAATATTACTCAGCTGCTCATCCGCATGGGCGGCAGGTa                              <  2:237820/143‑1 (MQ=255)                                                                                                                  attaGTACCCCTCCAGTGTTCTGGAGGGGATATTCATATTTTTTAAGAGTGACTATTTATGAAAACTTGCATAACAAAGGGAATTGTGACCGTAAGTTTAACGGCAATATTAGTCAGCTGCTGATCTGCCTGGGGGGCTGGTagggggg                        >  1:49064/1‑143 (MQ=255)                                                                                                                  atgaGTACCCCTCCAGTGTTCTGGAGGGGATATTCATATTTTTTAAGAGTGACTATTTATGAAAACCTGCATAACAAAGGGAATTGTGACCGTAAGTTTAACGGCAATATTACTCAGCTGCTCATCCGCATGGGCGGCAGGTa                              <  2:289619/140‑1 (MQ=255)                                                                                                                     aGTACCCCTCCAGTGTTCTGGAGGGGATATTCATATTTTTTAAGAGTGACTATTTATGAAAACTTGCATAACAAAGGGAATTGTGACCGTAAGTTTAACGGCAATATTACTCAGCTGCTCATCCGCATGGGCGGCAGGTAAAGGCGGGa                     >  1:145726/1‑149 (MQ=255)                                                                                                                      gTACCCCTCCAGTGTTCTGGAGGGGATATTCATATTTTTTAAGAGTGACTATTTATGAAAACTTGCATAACAAAGGGAATTGTGACCGTAAGTTTAACGGCAATATTACTCAGCTGCTCATCCGCATGGGCGGCAGGTAAAgg                          >  2:546699/1‑143 (MQ=255)                                                                                                                        gccccTCCAGTGTTCTGGAGGGGATATTCATATTTTTTAAGAGTGACTATTTATGAAAACTTGCATAACAAAGGGAATTGTGACCGTAAGTTTAACGGCAATATTACTCAGCTGCCCATCCGCATGGGCGGCAGGTAAAGGCGGGATTg                  <  1:611870/148‑1 (MQ=255)                                                                                                                          cccTCAAGTGGTTTGGAGGGGATATTCATATTTTTTAAGAGTGACTATTTTTGAAAATTTGCTTAACAAAGGGAATTGTGACCGTAAGTTTAACGGCAATATGACTCAGCTGCTCATCCGCATGGGCGGCAGGTAAAGGCGGGATTGGa                <  1:81225/149‑1 (MQ=255)                                                                                                                            cTCCAGTGTTCTGGAGGGGATATTCATATTTTTTAAGAGTGACTATTTATGAAAACTTGCATAACAAAGGGAATTTTGACCGTAAGTTTAACGGCAATATTACTCAGCTGCTCATCCGCATGGGCGGCAGGTAAAGGCGGGATTGGACt              <  1:36665/149‑1 (MQ=255)                                                                                                                             tCCAGTGTTCTGGAGGGGATATTCATATTTTTTAAGAGTGACTATTTATGAAAACTTGCATAACAAAGGGAATTGTGACCGTAAGTTTAACGGCAATATTACTCAGCTGCTCATCCGCATGGGCGGCAGGTAAAGGCGGGAtt                   >  2:735778/1‑143 (MQ=255)                                                                                                                             tCCAGTGTTCTGGAGGGGATATTCAGATTTTTTAAGAGCGACTATTTATGAAAACTTGCATAACAAAGGGAATTGTGACCGTAAGTTTAACGGCAATATTACTCAGCTGCTCAGCCGCATGGGCGGCAGGTAAAGGCGGGAtt                   <  2:149557/143‑1 (MQ=255)                                                                                                                                  tggtCTGGAGGGGATATTCATATTTCTTAAGGGTGACTATTTATGAAAACTTGCATAACAAAGGGAATTTTGACCGTAAGTTTAACGGCAATATTACTCAGCTGCTCATCCGCATGGGCGGCAGGTAAAGGCGGGATTGGACt              <  2:518681/140‑1 (MQ=255)                                                                                                                                       tGGAGGGGATATTCATATTTTTTAAGAGTGACTATTTATGAAAACTTGCATAACAAAGGGAATTGTGACCGTAAGTTTAACGGCAATATTACTCAGCTGCTCATCCGCATGGGCGGCAGGTAAAGGCGGGATTGGACTTGCAGCGacac   >  1:34998/1‑149 (MQ=255)                                                                                                                                              gATATTCATATTTTTTAAGAGTGACTATTTATGAAAACTTGCATAACAAAAGGAATTGTGACCGTAAGTTTAACGGCAATATTACTCAGCTGCTCATCCGCATGGACGGCAGGTAAAGGCGGGATTGGACTTGCACCAACACg  >  2:786450/1‑143 (MQ=255)                                                                                                                                               |                                                                                                                                              TGACTTTTAAAGTTGATTATATCGCTACGGGGAAAGCGACTTCAGGTAATGTGAATGCGGTAACAAATTTCCATATTAACTATTATTAATAGAACTCATTAATTGTTTTATTAATTAGTACCCCTCCAGTGTTCTGGAGGGGATATTCATATTTTTTAAGAGTGACTATTTATGAAAACTTGCATAACAAAGGGAATTGTGACCGTAAGTTTAACGGCAATATTACTCAGCTGCTCATCCGCATGGGCGGCAGGTAAAGGCGGGATTGGACTTGCAGCAACACG  >  CP009273/993775‑994058

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ 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.