New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	= 1373642	45 (0.970)	3 (0.070)	3/238	NT	7.0%	intergenic (+17/‑107)	USA300TCH1516_01283/sbcD	hypothetical protein/Nuclease SbcCD subunit D
	?	USA300TCH1516_ALE	= 1373669	39 (0.920)					intergenic (+44/‑80)	USA300TCH1516_01283/sbcD	hypothetical protein/Nuclease SbcCD subunit D

AATGAAATAGATCCTGGAGAATTAGGCGGCATGTTCTTTTTATTAGCATTCTGTATGATTGTTCCTTGGAGAGCAGCAATGCTATATAAATACAAAAAACTAAAGAAAACATTAATCAATTAATTACTTTTAAAACCACTTGTGATCGACTTCTAAATCAGTCAATGAGTGGTTTTAATTTTACTTGAAAAGGTGAAATGATTATATTAAAATAAAAGCGAACAAATGTTCTATATGGAGGCAGTAATGAAAATTATACATACAGCAGACTGGCACTTA  >  USA300TCH1516_ALE/1373503‑1373781                                                                                                                                            |                                                                                                                                            aaTGAAATAGATCCTGGAGAATTAGGCGGCATGTTCTTTTTATTAGCATTCTGTATGATTGTTCCTTGGAGAGCAGCAATGCTATATAAATACAAAAAACTAAAGAAAACATTAATCAATTAATTACTTTTAAAACCACtt                                                                                                                                            <  1:461170/141‑1 (MQ=255)   tGAAATAGATCCTGGAGAATTAGGCGGCATGTTCTTTTTATTAGCATTCTGTATGATTGTTCCTTGGAGAGCAGCAATGCTATATAAATACAAAAAACTAAAGAAAACATTAATCAATTAATTACTTTTAAAACCACTtgt                                                                                                                                          <  2:324532/141‑1 (MQ=255)    gAAATAGATCCTGGAGAATTAGGCGGCATGTTCTTTTTATTAGCATTCTGTATGATTGTTCCTTGGAGAGCAGCAATGCTATATAAATACAAAAAACTAAAGAAAACATTAATCAATTAATTACTTTTAAAACCACTtgtg                                                                                                                                         <  1:218403/141‑1 (MQ=255)     aaaTAGATCCTGGAGAATTAGGCGGCATGTTCTTTTTATTAGCATTCTGTATGATTGTTCCTTGGAGAGCAGCAATGCTATATAAATACAAAAAACTAAAGAAAACATTAATCAATTAATTACTTTTAAAACCACTTGTGa                                                                                                                                        >  1:89190/1‑141 (MQ=255)      aaTAGATCCTGGAGAATTAGGCGGCATGTTCTTTTTATTAGCATTCTGTATGATTGTTCCTTGGAGAGCAGCAATGCTATATAAATACAAAAAACTAAAGAAAACATTAATCAATTAATTACTTTTAAAACCACATGTGAt                                                                                                                                       >  1:611846/1‑141 (MQ=255)       aTAGATCCTGGAGAATTAGGCGGCATGTTCTTTTTATTAGCATTTTGTATGATTGTTCCTTGGAGAGCAGCAATGCTATATAAATACAAAAAACTAAAGAAAACATTAATCAATTAATTACTTTTAAAACCACTTGTGATc                                                                                                                                      <  2:254730/141‑1 (MQ=255)       aTAGATCCTGGAGAATTAGGCGGCATGTTCTTTTTATTAGCATTCTGTATGATTGTTCCTTGGAGAGCAGCAATGCTATATAAATACAAAAAACTAAAGAAAACATTAATCAATTAATTACTTTTAAAACCACTTGTGATc                                                                                                                                      <  1:20247/141‑1 (MQ=255)         aGATCCTGGAGAATTAGGCGGCATGTTCTTTTTATTAGCATTCGGTATGATTGTTCCTTGGAGAGCAGCAATGCTATATAAATACAAAAAACTAAAGAAAACATTAATCAATTAATTACTTTTAAAACCACTTGTGATCGa                                                                                                                                    <  1:618388/141‑1 (MQ=255)           aTCCTGGAGAATTAGGCGGCATGTTCTTTTTATTAGCATTCTGTATGATTGTTCCTTGGAGAGCAGCAATGCTATATAAATACAAAAAACTAAAGAAAACATTAATCAATTAATTACTTTTAAAACCACTTGTGATCGACt                                                                                                                                  <  1:135688/141‑1 (MQ=255)           aTCCTGGAGAATTAGGCGGCATGTTCTTTTTATTAGCATTCTGTATGATTGTTCCTTGGAGAGCAGCAATGCTATATAAATACAAAAAACTAAAGAAAACATTAATCAATTAATTACTTTTAAAACCACTTGTGATCGACt                                                                                                                                  <  2:242086/141‑1 (MQ=255)            tCCTGGAGAATTAGGCGGCATGTTCTTTTTATTAGCATTCTGTATGATTGTTCCTTGGAGAGCAGCAATGCTATATAAATACAAAAAACTAAAGAAAACATTAATCAATTAATTACTTTTAAAACCACTTGTGATCGACtt                                                                                                                                 >  1:625795/1‑141 (MQ=255)            tCCTGGAGAATTAGGCGGCATGTTCTTTTTATTAGCATTCTGTATGATTGTTCCTTGGAGAGCAGCAATGCTATATAAATACAAAAAACTAAAGAAAACATTAATCAATTAATTACTTTTAAAACCACTTGTGATCGACtt                                                                                                                                 >  2:335792/1‑141 (MQ=255)            tCCTGGAGAATTAGGCGGCATGTTCTTTTTATTAGCATTCTGTATGATTGTTCCTTGGAGAGCAGCAATGCTATATAAATACAAAAAACTAAAGAAAACATTAATCAATTAATTACTTTTAAAACCACTTGTGATCGACtt                                                                                                                                 >  1:625842/1‑141 (MQ=255)             ccTGGAGAATTAGGCGGCATGTTCTTTTTATTAGCATTCTGTATGATTGTTCCTTGGAGAGCAGCAATGCTATATAAATACAAAAAACTAAAGAAAACATTAATCAATTAATTACTTTTAAAACCACTTGTGATCGACTTc                                                                                                                                <  1:439109/141‑1 (MQ=255)                ggAGAATTAGGCGGCATGTTCTTTTTATTAGCATTCTGTATGATTGTTCCTTGGAGAGCAGCAATGCTATATAAATACAAAAAACTAAAGAAAACATTAATCAATTAATTACTTTTAAAACCACTTGTGATCGACTTCTaa                                                                                                                             <  1:331106/141‑1 (MQ=255)                   gaATTAGGCGGCATGTTCTTTTTATTAGCATTCTGTATGATTGTTCCTTGGAGAGCAGCAATGCTATATAAATACAAAAAACTAAAGAAAACATTAATCAATTAATTACTTTTAAAACCACTTGTGATCGACTTCTAAATc                                                                                                                          <  2:80602/141‑1 (MQ=255)                             taagtgccagtctgctgtatgtataattttcattactgcctccatatagaacatttgttcgcttttattttaatataatcatttcaccttttcaagtaaaaTTAAAACCACTTGTGATCGACTTCTAAATCAGTCAATGAg                                                                                                                >  1:85804‑M1/102‑141 (MQ=255)                               aTGTTCTTTTTATTAGCATTCTGTATGATTGTTCCTTGGAGAGCAGCAATGCTATATAAATACAAAAAACTAAAGAAAACATTAATCAATTAATTACTTTTAAAACCACTcattgactgatttagaagtcgatcacaagtg                                                                                                              <  2:188081‑M1/141‑32 (MQ=255)                                    cagtctgctgtatgtataattttcattactgcctccatatagaacatttgttcgcttttattttaatataatcatttcaccttttcaagtaaaaTTAAAACCACTTGTGATCGACTTCTAAATCAGTCAATGAGTGGtttt                                                                                                         >  1:488703‑M1/95‑141 (MQ=255)                                     agtctgctgtatgtataattttcattactgcctccatatagaacatttgttcgcttttattttaatataatcatttcaccttttcaagtaaaaTTAAAACCACTTGTGATCGACTTCTAAATCAGTCAATGAGTGGTTTTa                                                                                                        >  1:104834‑M1/94‑141 (MQ=255)                                        ttattaGCATTCTGTATGATTGTTCCTTGGAGAGCAGCAATGCTATATAAATACAAAAAACTAAAGAAAACATTAATCAATTAATTACTTTTAAAACCACTcattgactgatttagaagtcgatcacaagtggttttaaaa                                                                                                     <  2:38044‑M1/141‑41 (MQ=255)                                        ttattaGCATTCTGTATGATTGTTCCTTGGAGAGCAGCAATGCTATATAAATACAAAAAACTAAAGAAAACATTAATCAATTAATTACTTTTAAAACCACTTGTGATCGACTTCTAAATCAGTCAATGAGTGGTTTTAAtt                                                                                                     <  1:295776/141‑1 (MQ=255)                                             aGCATTCTGTATGATTGTTCCTTGGAGAGCAGCAATGCTATATAAATACAAAAAACTAAAGAAAACATTAATCAATTAATTACTTTTAAAACCACTTGTGATCGACTTCTAAATCAGTCAATGAGTGGTTTTAATTTTACt                                                                                                <  2:170130/141‑1 (MQ=255)                                              gCATTCTGTATGATTGTTCCTTGGAGAGCAGCAATGCTATATAAATACAAAAAACTAAAGAAAACATTAATCAATTAATTACTTTTAAAACCACTTGTGATCGACTTCTAAATCAGTCAATGAGTGGTTTTAATTTTACtt                                                                                               >  2:142594/1‑141 (MQ=255)                                                        tGATTGTTCCTTGGAGAGCAGCAATGCTATATAAATACAAAAAACTAAAGAAAACATTAATCAATTAATTACTTTTAAAACCACTcattgactgatttagaagtcgatcacaagtggttttaaaagtaattaattgattaa                                                                                     <  1:714401‑M1/141‑57 (MQ=255)                                                                    ggAGAGCAGCAATGCTATATAAATACAAAAAACTAAAGAAAACATTAATCAATTAATTACTTTTAAAACCACTTGTGATCGACTTCTAAATCAGTCCATGAGTGGTTTTAATTTTACTTGAAAAGGTGAAATGATTATAtt                                                                         <  2:74629/141‑1 (MQ=255)                                                                    ggAGAGCAGCAATGCTATATAAATACAAAAAACTAAAGAAAACATTAATCAATTAATTACTTTTAAAACCACTTGTGATCGACTTCTAAATCAGTCAATGAGTGGTTTTAATTTTACTTGAAAAGGTGAAATGATTATAtt                                                                         <  1:105366/141‑1 (MQ=255)                                                                      agagCAGCAATGCTATATAAATACAAAAAACTAAAGAAAACATTAATCAATTAATTACTTTTAAAACCACTTGTGATCGACTTCTAAATCAGTCAATGAGTGGTTTTAATTTTACTTGAAAAGGTGAAATGATTATATtaa                                                                       <  1:255733/141‑1 (MQ=255)                                                                      agagCAGCAATGCTATATAAATAAAAAAAACTAAAGAAAACATTAATCAATTAATTACTTTTAAAACCACTTGTGATCGACTTCTAAATCAGTCAATGAGTGGTTTTAATTTTACTTGAAAAGGTGAAATGATTATATtaa                                                                       <  1:169747/141‑1 (MQ=255)                                                                          cagcaATGCTATATAAATACAAAAAACTAAAGAAAACATTAATCAATTAATTACTTTTAAAACCACTTGTGATCGACTTCTAAATCAGTCAATGAGTGGTTTTAATTTTACTTGAAAAGGTGAAATGATTATATtaaaata                                                                   >  1:499005/1‑141 (MQ=255)                                                                            gcaATGCTATATAAATACAAAAAACTAAAGAAAACATTAATCAATTAATTACTTTTAAAACCACTTGTGATCGACTTCTAAATCAGTCAATGAGTGGTTTTAATTTTACTTGAAAAGGTGAAATGATTATATtaaaataaa                                                                 <  2:303585/141‑1 (MQ=255)                                                                              aaTGCTATATAAATACAAAAAACTAAAGAAAACATTAATCAATTAATTACTTTTAAAACCACTTGTGATCGACTTCTAAATCAGTCAATGAGTGGTTTTAATTTTACTTGAAAAGGTGAAATGATTATATTAAAATAAAAg                                                               <  1:553095/141‑1 (MQ=255)                                                                              aaTGCTATATAAATACAAAAAACTAAAGAAAACATTAATCAATTAATTACTTTTAAAACCACTTGTGATCGACTTCTAAATCAGTCAATGAGTGGTTTTAATTTTACTTGAAAAGGTGAAATGATTATATTAAAATAAAAg                                                               <  1:440102/141‑1 (MQ=255)                                                                                  cTATATAAATACAAAAAACTAAAGAAAACATTAATCAATTAATTACTTTTAAAACCACTTGTGATCGACTTCTAAATCAGTCAATGAGTGGTTTTAATTTTACTTGAAAAGGTGAAATGATTATATTAAAATAAAAGCGaa                                                           <  1:734546/141‑1 (MQ=255)                                                                                        aaaTACAAAAAACTAAAGAAAACATTAATCAATTAATTACTTTTAAAACCACTTGTGATCGACTTCTAAATCAGTCAATGAGTGGTTTTAATTTTACTTGAAAAGGTGAAATGATTATATTAAAATAAAAGCGAACAAATg                                                     >  2:50804/1‑141 (MQ=255)                                                                                          aTACAAAAAACTAAAGAAAACATTAATCAATTAATTACTTTTAAAACCACTTGTGATCGACTTCTAAATCAGTCAATGAGTGGTTTTAATTTTACTTGAAAAGGTGAAATGATTATATTAAAATAAAAGCGAACAAATGtt                                                   <  2:245607/141‑1 (MQ=255)                                                                                          aTACAAAAAACTAAAGAAAACATTAATCAATTAATCACTTTTAAAACCACTTGTGATCGACTTCTAAATCAGTCAATGAGTGGTTTTAATTTTACTTGAAAAGGTGAAATGATTATATTAAAATAAAAGCGAACAAATGtt                                                   >  1:688294/1‑141 (MQ=255)                                                                                                aaaaCTAAAGAAAACATTAATCAATTAATTACTTTTAAAACCACTTGTGATCGACTTCTAAATCAGTCAATGAGTGGTTTTAATTTTACTTGAAAAGGTGAAATGATTATATTAAAATAAAAGCGAACAAATGTTCTatat                                             <  2:31764/141‑1 (MQ=255)                                                                                                 aaaCTAAAGAAAACATTAATCAATTAATTACTTTTAAAACCACTTGTGATCTACTTCTAACTCAGTCAATGAGTGGTTTTAATTTTACTAGAAAAGGATAAATGATTATATTAAAATAAAAGCGAACAAATGTTCTAGATg                                            >  1:71006/1‑141 (MQ=255)                                                                                                   aCTAAAGAAAACATTAATCAATTAATTACTTTTAAAACCACTTGTGATCGACTTCTAAATCAGTCAATGAGTGGTTTTAATTTTACTTGAAAAGGTGAAATGATTATATTAAAATAAAAGCGAACAAATGTTCTATATGGa                                          <  1:109313/141‑1 (MQ=255)                                                                                                     tAAAGAAAACATTAATCAATTAATTACTTTTAAAACCACTTGTGATCGACTTCTAAATCAGTCAATGAGTGGTTTTAATTTTACTTGAAAAGGTGAAATGATTATATTAAAATAAAAGCGAACAAATGTTCTATATGGAgg                                        <  1:757218/141‑1 (MQ=255)                                                                                                      aaaGAAAACATTAATCAATTAATTACTTTTAAAACCACTTGTGATCGACTTCTAAATCAGTCAATGAGTGGTTTTAATTTTACTTGAAAAGGTGAAATGATTATATTAAAATAAAAGCGAACAAATGTTCTATATGGAGGc                                       <  1:492285/141‑1 (MQ=255)                                                                                                       aaGAAAACATTAATCAATTAATTACTTTTAAAACCACTTGTGATCGACTTCTAAATCAGTCAATGAGTGGTTTTAATTTTACTTGAAAAGGTGAAATGATTATATTAAAATAAAAGCGAACAAATGTTCTATATGGAGGCa                                      <  1:584536/141‑1 (MQ=255)                                                                                                       aaGAAAACATTAATCAATTAATTACTTTTAAAACCACTTGTGATCGACTTCTAAATCAGTCAATGAGTGGTTTTAATTTTACTTGAAAAGGTGAAATGATTATATTAAAATAAAAGCGAACAAATGTTCTATATGGAGGCa                                      >  1:187167/1‑141 (MQ=255)                                                                                                       aaGAAAACATTAATCAATTAATTACTTTTAAAACCACTTGTGATCGACTTCTAAATCAGTCAATGAGTGGTTTTAATTTTACTTGAAAAGGTGAAATGATTATATTAAAATAAAAGCGAACAAATGTTCTATATGGAGGCa                                      >  1:366562/1‑141 (MQ=255)                                                                                                       aaGAAAACATTAATCAATTAATTACTTTTAAAACCACTTGTGATCGACTTCTAAATCAGTCAATGAGTGGTTTTAATTTTACTTGAAAAGGTGAAATGATTATATTAAAATAAAAGCGAACAAATGTTCTATATGGAGGCa                                      >  1:348830/1‑141 (MQ=255)                                                                                                       aaGAAAACATTAATCAATTAATTACTTTTAAAACCACTTGTGATCGACTTCTAAATCAGTCAATGAGTGGTTTTAATTTTACTTGAAAAGGTGAAATGATTATATTAAAATAAAAGCGAACAAATGTTCTATATGGAGGCa                                      >  1:657435/1‑141 (MQ=255)                                                                                                          aaaaCATTAATCAATTAATTACTTTTAAAACCACTTGTGATCGACTTCTAAATCAGTCAATGAGTGGTTTTAATTTTACTTGAAAAGGTGAAATGATTATATTAAAATAAAAGCGAACAAATGTTCTATATGGAGGCAGTa                                   >  2:298424/1‑141 (MQ=255)                                                                                                             tcATTAATCAATTAATTACTTTTAAAACCACTTGTGATCGACTTCTAAATCAGTCAATGAGTGGTTTTAATTTTACTTGAAAAGGTGAAATGATTATATTAAAATAAAAGCGAACAAATGTTCTATATGGAGGCAGTAATg                                <  2:244630/140‑1 (MQ=255)                                                                                                             aCATTAATCAATTAATTACTTTTAAAACCACTTGTGATCGACTTCTAAATCAGTCAATGAGTGGTTTTAATTTTACTTGAAAAGGTGAAATGATTATATTAAAATAAAAGCGAACAAATGTTCTATATGGAGGCAGTAATg                                <  1:206450/141‑1 (MQ=255)                                                                                                              cATTAATCAATTAATTACTTTTAAAACCACTTGTGATCGACTTCTAAATCAGTCAATGAGTGGTTTTAATTTTACTTGAAAAGGTGAAAAGATTATATTAAAATAAAAGCGAACAAATGTTCTATATGGAGGCAGTAATGa                               <  2:257098/141‑1 (MQ=255)                                                                                                                ttAATCAATTAATTACTTTTAAAACCACTTGTGATCGACTTCTAAATCAGTCAATGagtggttttaaaagtaattaattgattaatgttttctttagttttttgtatttatatagcattgctgctctccaaggaacaatca                             <  1:714401‑M2/141‑86 (MQ=255)                                                                                                                     cAATTAATTACTTTTAAAACCACTTGTGATCGACTTCTAAATCAGTCAATGAGTGGTTTTAATTTTACTTGAAAAGGTGAAATGATTATATTAAAATAAAAGCGAACAAATGTTCTATATGGAGGCAGTAATGAAAATtat                        <  1:211015/141‑1 (MQ=255)                                                                                                                             taCTTTTAAAACCACTTGTGATCGACTTCTAAATCAGTCAATGAGTGGTTTTAATTTTACTTGAAAAGGTGAAATGATTATATTAAAATAAAAGCGAACAAATGTTCTATATGGAGGCAGTAATGAAAATTATACATAcag                <  1:404617/141‑1 (MQ=255)                                                                                                                               cTTTTAAAACCACTTGTGATCGACTTCTAAATCAGTCAATGAGTGGTTTTAATTTTACTTGAAAAGGTGAAATGATTATATTAAAATAAAAGCGAACAAATGTTCTATATGGAGGCAGTAATGAAAATTATACATAcagca              <  1:746194/141‑1 (MQ=255)                                                                                                                                ttttAAAACCACTTGTGATCGACTTCTAAATCAGTCAATGagtggttttaaaagtaattaattgattaatgttttctttagttttttgtatttatatagcattgctgctctccaaggaacaatcatacagaatgctaataa             <  2:38044‑M2/141‑102 (MQ=255)                                                                                                                                ttttAAAACCACTTGTGATCGACTTCTAAATCAGTCAATGAGTGGTTTTAATTTTAATTGAAAAGGTGAAATGATTATATTAAAATAAAAGCGAACAAATGTTCTATATGGAGGCAGTAATGAAAATTATACATAcagcag             >  1:214745/1‑141 (MQ=255)                                                                                                                                   TAAAACCACTTGTGATCGACTTCTAAATCAGTCAATGAGTGGTTTTAATTTTACTTGAAAAGGTGAAATGATTATATTAAAATAAAAGCGAACAAATGTTCTATATGGAGGCAGTAATGAAAATTATACATACAGCAGACt          >  1:25045‑M1/1‑141 (MQ=255)                                                                                                                                   TAAAACCACTTGTGATCGACTTCTAAATCAGTCAATGAGTGGTTTTAATTTTACTTGAAAAGGTGAAATGATTATATTAAAATAAAAGCGAACAAATGTTCTATATGGAGGCAGTAATGAAAATTATACATACAGCAGACt          >  2:293929‑M1/1‑141 (MQ=255)                                                                                                                                    AAAACCACTTGTGATCGACTTCTAAATCAGTCAATGAGTGGTTTTAATTTTACTTGAAAAGGTGAAATGATTATATTAAAATAAAAGCGGACAAATGTTCTATATGGAGGCAGTAATGAAAATTATACATACAGCAGACTg         <  1:743078‑M1/141‑1 (MQ=255)                                                                                                                                         cACTTGTGATCGACTTCTAAATCAGTCAATGagtggttttaaaagtaattaattgattaatgttttctttagttttttgtatttatatagcattgctgctctccaaggaacaatcatacagaatgctaataaaaagaacat    <  2:188081‑M2/141‑111 (MQ=255)                                                                                                                                           CTTGTGTTCGACGGCGAAATCAGTCAAGGAGTATTTGTGGTGTGATTTGAAAAGGTGAGATGATTATATTAAAATAAAAGCGAACAAATGTTCTATATGGAGGCAGTAATGAAAATTATACATACAGCAGACTGGCACTTa  >  1:748985‑M1/1‑141 (MQ=255)                                                                                                                                           CTTGTGATCGACTTCTAAATCAGTCAATGAGTGGTTTTAATTTTACTTGAAAAGGTGAAATGATTATATTAAAATAAAAGCGAACAAATGTTCTATATGGAGGCAGTAATGAAAATTATACATACAGCAGACTGGCACTTa  <  2:47684‑M1/141‑1 (MQ=255)                                                                                                                                           CTTGTGATCGACTTCTAAATCAGTCAATGAGTGGTTTTAATTTTACTTGAAAAGGTGAAATGATTATATTAAAATAAAAGCGAACAAATGTTCTATATGGAGGCAGTAATGAAAATTATACATACAGCAGACTGGCACTTa  <  1:457768‑M1/141‑1 (MQ=255)                                                                                                                                            |                                                                                                                                            AATGAAATAGATCCTGGAGAATTAGGCGGCATGTTCTTTTTATTAGCATTCTGTATGATTGTTCCTTGGAGAGCAGCAATGCTATATAAATACAAAAAACTAAAGAAAACATTAATCAATTAATTACTTTTAAAACCACTTGTGATCGACTTCTAAATCAGTCAATGAGTGGTTTTAATTTTACTTGAAAAGGTGAAATGATTATATTAAAATAAAAGCGAACAAATGTTCTATATGGAGGCAGTAATGAAAATTATACATACAGCAGACTGGCACTTA  >  USA300TCH1516_ALE/1373503‑1373781

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