New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	CP000731	= 12646	80 (0.230)	13 (0.040)	8/146	NT	15.1%	coding (140/675 nt)	USA300HOU_pUSA300HOUMR0016	IS257 transposase
	?	CP000731	= 12648	NA (NA)					coding (142/675 nt)	USA300HOU_pUSA300HOUMR0016	IS257 transposase

TGGTGTAAACGTTCATCATTCAACGGTCTACCGTTGGGTTCAAGAATATGCCCCAATTTTATATCAAATTTGGAAGAAAAAGCATAAAAAAGCTTATTACAAATGGCGTATTGATG  >  CP000731/12620‑12735                             |                                                                                        tggtgTAAACGTTCATCATTCAACGGTCTACCGTTGGGTTCAAGAATATGCCCCAATTTTATATCAAATTTGGAAGAAAAAGCATaaaaaa                           >  1:1008833/1‑91 (MQ=31) tggtgTAAACGTTCATCATTCAACGGTCTACCGTTGGGTTCAAGAATATGCCCCAATTTTATATCAAATTTGGAAGAAAAAGCATaaaaaa                           <  1:3101134/91‑1 (MQ=31) tggtgTAAACGTTCATCATTCAACGGTCTACCGTTGGGTTCAAGAATATGCCCCAATTTTATATCAAATTTGGAAGAAAAAGCATaaaaaa                           >  1:1988928/1‑91 (MQ=31) tggtgTAAACGTTCATCATTCAACGGTCTACCGTTGGGTTCAAGAATATGCCCCAATTTTATATCAAATTTGGAAGAAAAAGCATaaaaaa                           <  1:33640/91‑1 (MQ=31) tggtgTAAACGTTCATCATTCAACGGTCTACCGTTGGGTTCAAGAATATGCCCCAATTTTATATCAAATTTGGAAGAAAAAGCATaaaaaa                           >  1:1733358/1‑91 (MQ=31) tggtgTAAACGTTCATCATTCAACGGTCTACCGTTGGGTTCAAGAATATGCCCCAATTTTATATCAAATTTGGAAGAAAAAGCATaaaaaa                           >  1:1610455/1‑91 (MQ=31) tggtgTAAACGTTCATCATTCAACGGTCTACCGTTGGGTTCAAGAATATGCCCCAATTTTATATCAAATTTGGAAGAAAAAGCATaaaaaa                           >  1:1199460/1‑91 (MQ=31) tggtgTAAACGTTCATCATTCAACGGTCTACCGTTGGGTTCAAGAATATGCCCCAATTTTATATCAAATTTGGAAGAAAAAGCATaaaaaa                           >  1:613534/1‑91 (MQ=31) tggtgTAAACGTTCATCATTCAACGGTCTACCGTTGGGTTCAAGAATATGCCCCAATTTTATATCAAATTTGGAAGAAAAAGCATaaaaaa                           <  1:947578/91‑1 (MQ=31) tggtgTAAACGTTCATCATTCAACGGTCTACCGTTGGGTTCAAGAATATGCCCCAATTTTATATCAAATTTGGAAGAAAAAGCATaaaaaa                           <  1:910757/91‑1 (MQ=31)  ggtgTAAACGTTCATCATTCAACGGTCTACCGTTGGGTTCAAGAATATGCCCCAATTTTATATCAAATTTGGAAGAAAAAGCATAAAAAAg                          <  1:2458001/91‑1 (MQ=32)  ggtgTAAACGTTCATCATTCAACGGTCTACCGTTGGGTTCAAGAATATGCCCCAATTTTATATCAAATTTGGAAGAAAAAGCATAAAAAAg                          >  1:2470376/1‑91 (MQ=32)  ggtgTAAACGTTAATCATTCAACGGTCTACCGTTGGGTTCAAGAATATGCCCCAATTTTATATCAAATTTGGAAGAAAAAGCATAAAAAAg                          >  1:3171738/1‑91 (MQ=17)   gtgtAAACGTTCATCATTCAACGGTCTACCGTTGGGTTCAAGAATATGCCCCAATTTTATATCAAATTTGGAAGAAAAAGCATAAAAAAGc                         >  1:480532/1‑91 (MQ=33)   gtgtAAACGTTCATCATTCAACGGTCTACCGTTGGGTTCAAGAATATGCCCCAATTTTATATCAAATTTGGAAGAAAAAGCATAAAAAAGc                         >  1:3249790/1‑91 (MQ=33)    tgtAAACGTTCATCATTCAACGGTCTACCGTTGGGTTCAAGAATATGCCCCAATTTTATATCAAATTTGGAAGAAAAAGCATAAAAAAGCt                        <  1:2901218/91‑1 (MQ=34)    tgtAAACGTTCATCATTCAACGGTCTACCGTTGGGTTCAAGAATATGCCCCAATTTTATATCAAATTTGGAAGAAAAAGCATAAAAAAGCt                        >  1:3479738/1‑91 (MQ=34)    tgtAAACGTTCATCATTCAACGGTCTACCGTTGGGTTCAAGAATATGCCCCAATTTTATATCAAATTTGGAAGAAAAAGCATAAAAAAGCt                        >  1:4084351/1‑91 (MQ=34)    tgtAAACGTTCATCATTCAACGGTCTACCGTTGGGTTCAAGAATATGCCCCAATTTTATATCAAATTTGGAAGAAAAAGCATAAAAAAGCt                        <  1:4129845/91‑1 (MQ=34)     gtAAACGTTCATCATTCAACGGTCTACCGTTGGGTTCAAGAATAGGCCCCAATTTTATATCAAATTTGGAAGAAAAAGCATAAAAAAGCtt                       <  1:3292925/91‑1 (MQ=21)      tAAACGTTCATCATTCAACGGTCTACCGTTGGGTTCAAGAATATGCCCCAATTTTATCTCAAATTTGGAAGAAAAAGCATAAAAAAGCtta                      >  1:463912/1‑91 (MQ=21)      tAAACGTTCATCATTCAACGGTCTACCGTTGGGTTCAAGAATATGCCCCAATTTTATATCAAATTTGGAAGAAAAAGCATAAAAAAGCtta                      >  1:463691/1‑91 (MQ=34)      tAAACGTTCATCATTCAACGGTCTACCGTTGGGTTCAAGAATATGCCCCAATTTTATATCAAATTTGGAAGAAAAAGCATAAAAAAGCtta                      >  1:1702584/1‑91 (MQ=34)      tAAACGTTCATCATTCAACGGTCTACCGTTGGGTTCAAGAATATGCCCCAATTTTATATCAAATTTGGAAGAAAAAGCATAAAAAAGCtta                      >  1:464232/1‑91 (MQ=34)      tAAACGTTCATCATTCAACGGTCTACCGTTGGGTTCAAGAATATGCCCCAATTTTATATCAAATTTGGAAGAAAAAGCATAAAAAAGCtta                      >  1:736779/1‑91 (MQ=34)      tAAACGTTCATCATTCAACGGTCTACCGTTGGGTTCAAGAATATGCCCCAATTTTATATCAAATTTGGAAGAAAAAGCATAAAAAAGCtta                      >  1:948945/1‑91 (MQ=34)       aaaCGTTCATCATTCAACGGTCTACCGTTGGGTTCAAGAATATGCCCCAATTTTATATCAAATTTGGAAGAAAAAGCATAAAAAAGCttat                     >  1:3133006/1‑91 (MQ=34)       aaaCGTTCATCATTCAACGGTCTACCGTTGGGTTCAAGAATATGCCCCAATTTTATATCAAATTTGGAAGAAAAAGCATAAAAAAGCttat                     <  1:113411/91‑1 (MQ=34)        aaCGTTCATCATTCAACGGTCTACCGTTGGGTTCAAGAATATGCCCCAATTTTATATCAAATTTGGAAGAAAAAGCATAAAAAAGCttatt                    <  1:3962725/91‑1 (MQ=34)        aaCGTTCATCATTCAACGGTCTACCGTTGGGTTCAAGAATATGCCCCAATTTTATATCAAATTTGGAAGAAAAAGCATAAAAAAGCttatt                    <  1:2326005/91‑1 (MQ=34)        aaCGTTCATCATTCAACGGTCTACCGTTGGGTTCAAGAATATGCCCCAATTTTATATCAAATTTGGAAGAAAAAGCATAAAAAAGCttatt                    <  1:881015/91‑1 (MQ=33)        aaCGTTCATCATTCAACGGTCTACCGTTGGGTTCAAGAATATGCCCCAATTTTATATCAAATTTGGAAGAAAAAGCATAAAAAAGCttatt                    <  1:1495839/91‑1 (MQ=34)        aaCGTTCATCATTCAACGGTCTACCGTTGGGTTCAAGAATATGCCCCAATTTTATATCAAATTTGGAAGAAAAAGCATAAAAAAGCttatt                    <  1:274159/91‑1 (MQ=34)         aCGTTCATCATTCAACGGTCTACCGTTGGGTTCAAGAATATGCCCCAATTTTATATCAAATTTGGAAGAAAAAGCATAAAAAAGCttatta                   <  1:1568199/91‑1 (MQ=34)         aCGTTCATCATTCAACGGTCTACCGTTGGGTTCAAGAATATGCCCCAATTTTATATCAAATTTGGAAGAAAAAGCATAAAAAAGCttatta                   <  1:3039913/91‑1 (MQ=34)         aCGTTCATCATTCAACGGTCTACCGTTGGGTTCAAGAATATGCCCCAATTTTATATCAAATTTGGAAGAAAAAGCATAAAAAAGCttatta                   >  1:619443/1‑91 (MQ=34)           gTTCATCATTCAACGGTCTACCGTTGGGTTCAAGAATATGCCCCAATTTTATATCAAATTTGGAAGAAAAAGCATAAAAAAGCTTATTACa                 >  1:4037780/1‑91 (MQ=34)           gTTCATCATTCAACGGTCTACCGTTGGGTTCAAGAATATGCCCCAATTTTATATCAAATTTGGAAGAAAAAGCATAAAAAAGCTTATTACa                 <  1:970568/91‑1 (MQ=34)           gTTCATCATTCAACGGTCTACCGTTGGGTTCAAGAATATGCCCCAATTTTATATCAAATTTGGAAGAAAAAGCATAAAAAAGCTTATTACa                 >  1:3097855/1‑91 (MQ=34)           gTTCATCATTCAACGGTCTACCGTTGGGTTCAAGAATATGCCCCAATTTTATATCAAATTTGGAAGAAAAAGCATAAAAAAGCTTATTACa                 <  1:406767/91‑1 (MQ=34)           gTTCATCATTCAACGGTCTACCGTTGGGTTCAAGAATATGCCCCAATTTTATATCAAATTTGGAAGAAAAAGCATAAAAAAGCTTATTACa                 <  1:1024328/91‑1 (MQ=33)           gTTCATCATTCAACGGTCTACCGTTGGGTTCAAGAATATGCCCCAATTTTATATCAAATTTGGAAGAAAAAGCATAAAAAAGCTTATTACa                 >  1:1137800/1‑91 (MQ=34)            ttCATCATTCAACGGTCTACCGTTGGGTTCAAGAATATGCCCCAATTTTATATCAAATTTGGAAGAAAAAGCATAAAAAAGCTTATTACaa                >  1:2706405/1‑91 (MQ=34)            ttCATCATTCAACGGTCTACCGTTGGGTTCAAGAATATGCCCCAATTTTATATCAAATTTGGAAGAAAAAGCATAAAAAAGCTTATTACaa                >  1:685840/1‑91 (MQ=34)            ttCATCATTCAACGGTCTACCGTTGGGTTCAAGAATATGCCCCAATTTTATATCAAATTTGGAAGAAAAAGCATAAAAAAGCTTATTACaa                >  1:685290/1‑91 (MQ=34)            ttCATCATTCAACGGTCTACCGTTGGGTTCAAGAATATGCCCCAATTTTATATCAAATTTGGAAGAAAAAGCATAAAAAAGCTTATTACaa                >  1:2375239/1‑91 (MQ=34)            ttCATCATTCAACGGTCTACCGTTGGGTTCAAGAATATGCCCCAATTTTATATCAAATTTGGAAGAAAAAGCATAAAAAAGCTTATTACaa                >  1:2706914/1‑91 (MQ=34)             tcatcaTTCAACGGTCTACCGTTGGGTTCAAGAATATGCCCCAATTTTATATCAAATTTGGAAGAAAAAGCATAAAAAAGCTTATTACaaa               >  1:2536333/1‑91 (MQ=33)             tcatcaTTCAACGGTCTACCGTTGGGTTCAAGAATATGCCCCAATTTTATATCAAATTTGGAAGAAAAAGCATAAAAAAGCTTATTACaaa               <  1:742204/91‑1 (MQ=34)              catcatTCAACGGTCTACCGTTGGGTTCAAGAATATGCCCCAATTTTATATCAAATTTGGAAGAAAAAGCATAAAAAAGCTTATTACAAAt              <  1:104358/91‑1 (MQ=34)              catcatTCAACGGTCTACCGTTGGGTTCAAGAATATGCCCCAATTTTATATCAAATTTGGAAGAAAAAGCATAAAAAAGCTTATTACAAAt              >  1:2572164/1‑91 (MQ=33)              catcatTCAACGGTCTACCGTTGGGTTCAAGAATATGCCCCAATTTTATATCAAATTTGGAAGAAAAAGCATAAAAAAGCTTATTACAAAt              >  1:2984452/1‑91 (MQ=34)              catcatTCAACGGTCTACCGTTGGGTTCAAGAATATGCCCCAATTTTATATCAAATTTGGAAGAAAAAGCATAAAAAAGCTTATTACAAAt              >  1:3510964/1‑91 (MQ=34)              catcatTCAACGGTCTACCGTTGGGTTCAAGAATATGCCCCAATTTTATATCAAATTTGGAAGAAAAAGCATAAAAAAGCTTATTACAAAt              >  1:3511179/1‑91 (MQ=34)               atcatTCAACGGTCTACCGTTGGGTTCAAGAATATGCCCCAATTTTATATCAAATTTGGAAGAAAAAGCATAAAAAAGCTTATTACAAATg             >  1:1066065/1‑91 (MQ=33)               atcatTCAACGGTCTACCGTTGGGTTCAAGAATATGCCCCAATTTTATATCAAATTTGGAAGAAAAAGCATAAAAAAGCTTATTACAAATg             >  1:3812096/1‑91 (MQ=34)                tcatTCAACGGTCTACCGTTGGGTTCAAGAATATGCCCCAATTTTATATCAAATTTGGAAGAAAAAGCATAAAAAAGCTTATTACAAATgg            <  1:1140063/91‑1 (MQ=34)                tcatTCAACGGTCTACCGTTGGGTTCAAGAATATGCCCCAATTTTATATCAAATTTGGAAGAAAAAGCATAAAAAAGCTTATTACAAATgg            <  1:1439323/91‑1 (MQ=34)                tcatTCAACGGTCTACCGTTGGGTTCAAGAATATGCCCCAATTTTATATCAAATTTGGAAGAAAAAGCATAAAAAAGCTTATTACAAATgg            <  1:823539/91‑1 (MQ=34)                tcatTCAACGGTCTACCGTTGGGTTCAAGAATATGCCCCAATTTTATATCAAATTTGGAAGAAAAAGCATAAAAAAGCTTATTACAAATgg            <  1:487482/91‑1 (MQ=34)                tcatTCAACGGTCTACCGTTGGGTTCAAGAATATGCCCCAATTTTATATCAAATTTGGAAGAAAAAGCATAAAAAAGCTTATTACAAATgg            <  1:595510/91‑1 (MQ=34)                tcatTCAACGGTCTACCGTTGGGTTCAAGAATATGCCCCAATTTTATATCAAATTTGGAAGAAAAAGCATAAAAAAGCTTATTACAAATgg            <  1:2687504/91‑1 (MQ=34)                tcatTCAACGGTCTACCGTTGGGTTCAAGAATATGCCCCAATTTTATATCAAATTTGGAAGAAAAAGCATAAAAAAGCTTATTACAAATgg            <  1:2593109/91‑1 (MQ=34)                tcatTCAACGGTCTACCGTTGGGTTCAAGAATATGCCCCAATTTTATATCAAATTTGGAAGAAAAAGCATAAAAAAGCTTATTACAAATgg            <  1:1134107/91‑1 (MQ=33)                tcatTCAACGGTCTACCGTTGGGTTCAAGAATATGCCCCAATTTTATATCAAATTTGGAAGAAAAAGCATAAAAAAGCTTATTACAAATgg            <  1:1049338/91‑1 (MQ=34)                tcatTCAACGGTCTACCGTTGGGTTCAAGAATATGCCCCAATTTTATATCAAATTTGGAAGAAAAAGCATAAAAAAGCTTATTACAAATgg            <  1:1112438/91‑1 (MQ=34)                 catTCAACGGTCTACCGTTGGGTTCAAGAATATGCCCCAATTTTATATCAAATTTGGAAGAAAAAGCATAAAAAAGCTTATTACAAATGGc           >  1:1280615/1‑91 (MQ=33)                  atTCAACGGTCTACCGTTGGGTTCAAGAATATGCCCCAATTTTATATCAAATTTGGAAGAAAAAGCATAAAAAAGCTTATTACAAATGGCg          <  1:2329658/91‑1 (MQ=33)                  atTCAACGGTCTACCGTTGGGTTCAAGAATATGCCCCAATTTTATATCAAATTTGGAAGAAAAAGCATAAAAAAGCTTATTACAAATGGCg          <  1:1729826/91‑1 (MQ=34)                  atTCAACGGTCTACCGTTGGGTTCAAGAATATGCCCCAATTTTATATCAAATTTGGAAGAAAAAGCATAAAAAAGCTTATTACAAATGGCg          <  1:1285444/91‑1 (MQ=34)                   ttCAACGGTCTACCGTTGGGTTCAAGAATATGCCCCAATTTTATATCAAATTTGGAAGAAAAAGCATAAAAAAGCTTATTACAAATGGCGt         <  1:3638023/91‑1 (MQ=34)                   cccAACGGTAGACCGTTGGGTTCAAGAATATGCCCCAATTTTATATCAAATTTGGAAGAAAAAGCATAAAAAAGCTTATTACAAATGGCGt         >  1:134062/3‑91 (MQ=11)                    tCAACGGTCTACCGTTGGGTTCAAGAATATGCCCCAATTTTATATCAAATTTGGAAGAAAAAGCATAAAAATGCTTATTACAAATGGCGTa        <  1:1869922/91‑1 (MQ=18)                    tCAACGGTCTACCGTTGGGTTCAAGAATATGCCCCAATTTTATATCAAATTTGGAAGAAAAAGCATAAAAAAGCTTATTACAAATGGCGTa        >  1:406300/1‑91 (MQ=34)                    tCAACGGTCTACCGTTGGGTTCAAGAATATGCCCCAATTTTATATCAAATTTGGAAGAAAAAGCATAAAAAAGCTTATTACAAATGGCGTa        >  1:406542/1‑91 (MQ=34)                     cAACGGTCTACCGTTGGGTTCAAGAATATGCCCCAATTTTATATCAAATTTGGAAGAAAAAGCATAAAAAAGCTTATTACAAATGGCGTAt       >  1:2335615/1‑91 (MQ=34)                      aaCGGTCTACCGTTGGGTTCAAGAATATGCCCCAATTTTATATCAAATTTGGAAGAAAAAGCATAAAAAAGCTTATTACAAATGGCGTAtt      <  1:1380615/91‑1 (MQ=34)                      aaCGGTCTACCGTTGGGTTCAAGAATATGCCCCAATTTTATATCAAATTTGGAAGAAAAAGCATAAAAAAGCTTATTACAAATGGCGTAtt      <  1:3714617/91‑1 (MQ=34)                      aaCGGTCTACCGTTGGGTTCAAGAATATGCCCCAATTTTATATCAAATTTGGAAGAAAAAGCATAAAAAAGCTTATTACAAATGGCGTAtt      <  1:1381082/91‑1 (MQ=34)                      aaCGGTCTACCGTTGGGTTCAAGAATATGCCCCAATTTTATATCAAATTTGGAAGAAAAAGCATAAAAAAGCTTATTACAAATGGCGTAtt      <  1:2022069/91‑1 (MQ=34)                       aCGGTCTACCGTTGGGTTCAAGAATATGCCCCTATTTTATATCAAATTTGGAAGAAAAAGCATAAAAAAGCTTATTACAAATGGCGTATtg     <  1:3543397/91‑1 (MQ=21)                       aCGGTCTACCGTTGGGTTCAAGAATATGCCCCAATTTTATATCAAATTTGGAAGAAAAAGCATAAAAAAGCTTATTACAAATGGCGTATtg     >  1:656166/1‑91 (MQ=33)                       aCGGTCTACCGTTGGGTTCAAGAATATGCCCCAATTTTATATCAAATTTGGAAGAAAAAGCATAAAAAAGCTTATTACAAATGGCGTATtg     >  1:873715/1‑91 (MQ=34)                        cGGTCTACCGTTGGGTTCAAGAATATGCCCCAATTTTATATCAAATTTGGAAGAAAAAGCATAAAAAAGCTTATTACAAATGGCGTATtga    <  1:798533/91‑1 (MQ=33)                        cGGTCTACCGTTGGGTTCAAGAATATGCCCCAATTTTATATCAAATTTGGAAGAAAAAGCATAAAAAAGCTTATTACAAATGGCGTATtga    <  1:798559/91‑1 (MQ=33)                        cGGTCTACCGTTGGGTTCAAGAATATGCCCCAATTTTATATCAAATTTGGAAGAAAAAGCATAAAAAAGCTTATTACAAATGGCGTATtga    <  1:152769/91‑1 (MQ=33)                         ggTCTACCGTTGGGTTCAAGAATATGCCCCAATTTTATATCAAATTTGGAAGAAAAAGCATAAAAAAGCTTATTACAAATGGCGTATtgat   <  1:821634/91‑1 (MQ=32)                         ggTCTACCGTTGGGTTCAAGAATATGCCCCAATTTTATATCAAATTTGGAAGAAAAAGCATAAAAAAGCTTATTACAAATGGCGTATtgat   <  1:425203/91‑1 (MQ=32)                         ggTCTACCGTTGGGTTCAAGAATATGCCCCAATTTTATATCAAATTTGGAAGAAAAAGCATAAAAAAGCTTATTACAAATGGCGTATtgat   <  1:425147/91‑1 (MQ=32)                         ggTCTACCGTTGGGTTCAAGAATATGCCCCAATTTTATATCAAATTTGGAAGAAAAAGCATAAAAAAGCTTATTACAAATGGCGTATtgat   <  1:1640794/91‑1 (MQ=32)                         ggTCTACCGTTGGGTTCAAGAATATGCCCCAATTTTATATCAAATTTGGAAGAAAAAGCATAAAAAAGCTTATTACAAATGGCGTATtgat   <  1:1644240/91‑1 (MQ=32)                         ggTCTACCGTTGGGTTCAAGAATATGCCCCAATTTTATATCAAATTTGGAAGAAAAAGCATAAAAAAGCTTATTACAAATGGCGTATtgat   <  1:2362214/91‑1 (MQ=32)                         ggTCTACCGTTGGGTTCAAGAATATGCCCCAATTTTATATCAAATTTGGAAGAAAAAGCATAAAAAAGCTTATTACAAATGGCGTATtgat   <  1:2366507/91‑1 (MQ=32)                         ggTCTACCGTTGGGTTCAAGAATATGCCCCAATTTTATATCAAATTTGGAAGAAAAAGCATAAAAAAGCTTATTACAAATGGCGTATtgat   >  1:3010503/1‑91 (MQ=32)                          gTCTACCGTTGGGTTCAAGAATATGCCCCAATTTTATATCAAATTTGGAAGAAAAAGCATAAAAAAGCTTATTACAAATGGCGTATtgatg  >  1:626552/1‑91 (MQ=31)                          gTCTACCGTTGGGTTCAAGAATATGCCCCAATTTTATATCAAATTTGGAAGAAAAAGCATAAAAAAGCTTATTACAAATGGCGTATtgatg  <  1:2911669/91‑1 (MQ=31)                             |                                                                                        TGGTGTAAACGTTCATCATTCAACGGTCTACCGTTGGGTTCAAGAATATGCCCCAATTTTATATCAAATTTGGAAGAAAAAGCATAAAAAAGCTTATTACAAATGGCGTATTGATG  >  CP000731/12620‑12735

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 37 ≤ 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.