New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	2085296 =	29 (0.820)	21 (0.660)	16/232	NT	42.9%	coding (173/201 nt)	hlb_1	Phospholipase C
	?	USA300TCH1516_ALE	= 2128343	30 (0.950)					coding (1/825 nt)	hlb_2	Phospholipase C

ACATCCGTGTATTCTCATTTGTTAGAAGAAAAATTTAATGAAGAGGACAAAAAAACAACTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCGGACAATCTTCTTATATTAAAAATAATGATGTCGTAATATTCAATGAAGCATTTGATAATGGTGCATCAGACAAATTATTAAGTAATGTGAAAAAAGAA  >  USA300TCH1516_ALE/2128206‑2128483                                                                                                                                          |                                                                                                                                             aCATCCGTGTATTCTCATTTGTTAGAAGAAAAATTTAATGAAGAGGACAAAAAAACAACTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTATAtgt                                                                                                                                           <  1:382594‑M2/141‑4 (MQ=255)    tCCGTGTATTCTCATTTGTTAGAAGAAAAATTTAATGAAGAGGACAAAAAAACAACTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTAtgtatc                                                                                                                                        <  1:362745‑M2/141‑7 (MQ=255)       gtgtATTCTCATTTGTTAGAAGAAAAATTTAATGAAGAGGACAAAAAAACAACTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTAtgtatccaa                                                                                                                                     >  1:2981‑M2/1‑132 (MQ=255)        tgtATTCTCATTTGTTAGAAGAAAAATTTAATGAAGAGGACAAAAAAACAACTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTAtgtatccaaa                                                                                                                                    <  1:292172‑M2/141‑11 (MQ=255)        ctcactctcatttgTTAGAAGAAAAATTTAAAGATAAGGACAAAAAAACAACTAAAATTTTAGAAAGTATGTAATTTAGGGACCCAGTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTAtgtatccaaa                                                                                                                                    >  1:180809‑M2/6‑131 (MQ=255)         gtATTCTCATTTGTTAGAAGAAAAATTTAATGAAGAGGACAAAAAAACAACTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTAtgtatccaaac                                                                                                                                   >  1:13463‑M2/1‑130 (MQ=255)         gtATTCTCATTTGTTAGAAGAAAAATTTAATGAAGAGGACAAAAAAACAACTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTAtgtatccaaac                                                                                                                                   >  1:378870‑M2/1‑130 (MQ=255)           aTTCTCATTTGTTAGAAGAAAAATTTAATGAAGAGGACAAAAAAACAACTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCCAACCCAATAAATACTGTTGTTACAAGGTTTCTAtgtatccaaactg                                                                                                                                 <  1:96758‑M2/141‑14 (MQ=255)           aTTCTCATTTGTTAGAAGAAAAATTTAATGAAGAGGACAAAAAAACAACTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTAtgtatccaaactg                                                                                                                                 <  1:813930‑M2/141‑14 (MQ=255)           aTTCTCATTTGTTAGAAGAAAAATTTAATGAAGAGGACAAAAAAACAACTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTAtgtatccaaactg                                                                                                                                 <  1:134425‑M2/141‑14 (MQ=255)           aTTCTCATTTGTTAGAAGAAAAATTTAATGAAGAGGACAAAAAAACAACTAAAATTATAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTGGTGACAAGGTTTCTAtgtatccaaacgg                                                                                                                                 <  1:649568‑M2/141‑14 (MQ=255)                     gTCAGAAGAAAAATTTAATGAAGAGGACAAAAAAACAACTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTAtgtatccaaactggagactttta                                                                                                                       >  1:507116‑M2/1‑118 (MQ=255)                        agaagaAAAATTTAATGAAGAGGACAAAAAAACCACGAAGATGCCACAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTAtgtatccaaactggagacttttaaca                                                                                                                    >  1:628041‑M2/1‑115 (MQ=255)                        agaagaAAAATTTAATGAAGAGGACAAAAAAACAACTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTCtgtatccaaactggagacttttaaca                                                                                                                    >  1:600101‑M2/1‑115 (MQ=255)                            gaaAAATTTAATGAAGAGGACAAAAAAACAACTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTAtgtatccaaactggagacttttaacataaa                                                                                                                <  1:730269‑M2/141‑31 (MQ=255)                                  tttAATGAAGAGGACAAAAAAACAACTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGAtt                                                                                                          >  1:432039/1‑141 (MQ=255)                                  tttAATGAAGAGGACAAAAAAACAACTAAAATTTTAGAAAGTATGAAATTTAGGGACCCATTAGTGACTCCAAACCCAATAAATTCAGAATCCACATGTTCGATATGCATCCCAACTATGTGAAATATAAACGCCCTGAtt                                                                                                          >  1:385720/1‑141 (MQ=255)                                         aaGAGGACAAAAAAACAACTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTAtgtatccaaactggagacttttaacataaaattacttatcatt                                                                                                   >  1:156514‑M2/1‑98 (MQ=255)                                         aaGAGGACAAAAAAACAACTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCgg                                                                                                   >  1:306198/1‑141 (MQ=255)                                            gggACAAAAAAACAACTTATCTTCAAGAAGGTGTGCAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCGGACa                                                                                                <  1:321164/140‑1 (MQ=255)                                            agaaCAAAAAAACAACTAAAATTGTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCGGACa                                                                                                <  1:660717/138‑1 (MQ=255)                                            agGAAAAAAAAACAACTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCGGACa                                                                                                <  1:679345/141‑1 (MQ=255)                                                cAAAAAAACAACTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCGGCCAAtct                                                                                            >  1:178180/1‑141 (MQ=255)                                                          acTAAAATTTTAGAAAGTATCTAATTTAGGGACCCATTAGGGACTCCAAACCTAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGCTTTAATCGGACAATCTTCTTATATTa                                                                                  >  1:496921/1‑141 (MQ=255)                                                              aaaTTTTAGAAGGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTAtgtatccaaactggagacttttaacataaaattacttatcattcaaaaagtaaaacagcataat                                                                              >  1:149680‑M2/1‑77 (MQ=255)                                                               aaTTTTAGAAAGTATGTAATGTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCGGACAATCTTCTTATATTAAAaat                                                                             <  1:94018/141‑1 (MQ=255)                                                                   ttAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCATACTTGGGTCAATATAAACGCGCTGATTTAATCGGACAATCTTCTTATATTAAAAATAatg                                                                         <  1:556094/141‑1 (MQ=255)                                                                   ttAGAAAGTATGGAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAACCTATATACAATATAAACGCGCTGATTTAATCGGACAATCTTCTTATATTAAAAATAatg                                                                         <  1:556049/141‑1 (MQ=255)                                                                          gTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCGGACAATCTTCTTATATTAAAAATAATGATGTCga                                                                  >  1:284468/1‑140 (MQ=255)                                                                          gTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCGGACAATCTTCTTATATTAAAAATAATGATGTCGt                                                                  >  1:124462/1‑141 (MQ=255)                                                                          gTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCGGACAATCTTCTTATATTAAAAATAATGATGTCGt                                                                  >  1:284611/1‑141 (MQ=255)                                                                            aggTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTTTTACAAGTGTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCGGACAATCTTCTTATATTAAAAATAATGATGTCGTaa                                                                <  1:554840/139‑1 (MQ=255)                                                                                       ggACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCGGACAATCTTCTTATATTAAAAATAATGATGTCGTAATATTCAATGaa                                                     >  1:735518/1‑141 (MQ=255)                                                                                        gACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCGGACAATCTTCTTATATTAAAAATAATGATGTCGTAATATTCAATGAAg                                                    >  1:100911/1‑141 (MQ=255)                                                                                         ccccctTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTAtgtatccaaactggagacttttaacataaaattacttatcattcaaaaagtaaaacagcataatatcaaggtttataactttatcattatc                                                   >  1:422105‑M2/2‑50 (MQ=255)                                                                                         aCCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTAtgtatccaaactggagacttttaacataaaattacttatcattcaaaaagtaaaacagcataatatcaaggtttataactttatcattatc                                                   >  1:663146‑M2/1‑50 (MQ=255)                                                                                         aCCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTAtgtatccaaactggagacttttaacataaaattacttatcatgcaaaaagtaaaacagcataatatcaaggtttataactttatcattatc                                                   >  1:403226‑M2/1‑50 (MQ=255)                                                                                          cccATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCGGACAATCTTCTTATATTAAAAATAATGATGTCGTAATATTCAATGAAGCa                                                  <  1:318270/141‑1 (MQ=255)                                                                                          cccATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCGGACAATCTTCTTATATTAAAAATAATGATGTCGTAATATTCAATGAAGCa                                                  <  1:318032/141‑1 (MQ=255)                                                                                             aTTAGGGACTTGAAATCCAATNANTACNGTTGTTACAAGGTTTCTGTGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCGGACAATCTTCTTATATTAAAAATAATGATGTCGTAATATTCAATGAAGCAttt                                               <  1:441509/141‑1 (MQ=255)                                                                                              ttAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTAtgtatccaaactggagacttttaacataaaattacttatcattcaaaaagtaaaacagcataatatcaaggtttataactttatcattatcaataa                                              <  1:716478‑M2/141‑97 (MQ=255)                                                                                               tAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTAtgtatccaaactggaggcttttaacataaaattacttatcattcaaaaagtaaaacagcataatatcaaggtttctaactttatcattatcaataat                                             <  1:70712‑M2/141‑98 (MQ=255)                                                                                               tAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCGGACTATCTTCTTATATTAAAAATAATGATGTCGTAATATTCAATGAAAAATTTGa                                             >  1:205732/1‑141 (MQ=255)                                                                                               tAGGCACTCCAAACCCAATAAATACTGTTGTTACAATGTTACTAtgtatccaaactggagacttttaacataaaattacttatcattcataaagtaaaacagcataatatcaaggtttataactttatcattatcaataat                                             >  1:504401‑M2/1‑44 (MQ=255)                                                                                                aGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTAtgtatccaaactggagacttttaacataaaattacttatcattcaaaaagtaaaacagcataatatcaaggtttataactttatcattatcaataata                                            >  1:6541‑M2/1‑43 (MQ=255)                                                                                                        cAAACCCAATAAATACTGGTGTTACAAGGTTTCTAtgtatccaaactggagacttttaacataaaattacttatcattcaaaaagtaaaacagcataatatcaaggtttataactttatcattatcaataatacctcatat                                    >  1:541444‑M2/1‑35 (MQ=255)                                                                                                          accccAATAAATCCTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCGGACAATCTTCTTATATTAAAAATAATGATGTCGTAATATTCAATGAAGCATTTGATAATGGTGCAt                                  <  1:426712/139‑1 (MQ=255)                                                                                                           aCCCAATAAATACTGTTGTTACAAGGTTTCTAtgtatccaaactggagacttttaacataaaattacttatcattcaaaaagtaaaacagcataatatcaaggtttataactttatcattatcaataatacctcatataaa                                 <  1:532803‑M2/141‑110 (MQ=255)                                                                                                           aCCCAATAAATACTATTGTTACAAGGTTTCTAtgtatccaaactggagacttttaacataaaattacttatcattcaaaaagtaaaacagcataatatcaaggtttataactttatcattatcaataatacctcatataaa                                 <  1:533008‑M2/141‑110 (MQ=255)                                                                                                            cccAACAAACACTGTTGTTACAAGGTTTCTATTTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCGGACAATCTTCTTATATTAAAAATAATGATGTCGTAATATTCAATGAAGCATTTGATAATGGTGCATCa                                <  1:36043/141‑1 (MQ=255)                                                                                                              cAATAAATTCTTTCGTTACAAGGTTTCTATGTATCCAAACTGGGGTAAATATAAACGCGCTGATTTAATCGGACAATCTTCTTATATTAAAAATAATGATGTCGTAATATTCAATGAAGCATTTGATAATGGTGCATCAGa                              <  1:626120/141‑1 (MQ=255)                                                                                                                 taaataCTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCGGACAATCTTCTTATATTAAAAATAATGATGTCGTAATATTCAATGAAGCATTTGATAATGGTGCATCAGACaa                           >  1:246925/1‑141 (MQ=255)                                                                                                                 taaataCTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCGGACAATCTTCTTATATTAAAAATAATAATGTTGTAATATTCAATGAAGCATTTGATGATGGGGCATAAGACaa                           >  1:151172/1‑141 (MQ=255)                                                                                                                      aCTGTTGTTACAAGGTTTCTAtgtatccaaactggagacttttaacataaaattacttatcattcaaaaagtaaaacagcataatatcaaggtttagaactttatcattatcaataatacctcatataaaatacaattttt                      <  1:506047‑M2/141‑121 (MQ=255)                                                                                                                      aCTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCGGACAATCTTCTTATATTAAAAATAATGATGTCGTAATATTCAATGAAGCATTTGATAATGGTGCATCAGACAAattat                      <  1:455344/141‑1 (MQ=255)                                                                                                                       cTGTTGTTACAAGGTTTCTAtgtatccaaactggagacttttaacataaaattacttatcattcaaaaagtaaaacagcataatatcaaggtttataactttatcattatcaataatacctcatataaaataaaattttag                     >  1:210375‑M2/1‑20 (MQ=255)                                                                                                                             ttACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCGGACAATCTTCTTATATTAAAAATAATGATGTCGTAATATTCAATGAAGCATTTGATAATGGTGCATCAGACAAATTATTAAGTaa               <  1:268660/141‑1 (MQ=255)                                                                                                                              tACAAGGTTTCTACGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCGGACAATCTTCTTATATTAAAAATAATGATGTCGTAATATTCAATGAAGCATTTGATAATGGTGCATCAGACAAATTATTAAGTAAt              <  1:56678/141‑1 (MQ=255)                                                                                                                                cAAGGTTTCTAtgtatccaaactggagacttttaacataaaattacttatcattcaaaaagtaaaacagcataatatcaaggtttataactttatcattatcaataatacctcatataaaataaaattttagggacttttt            <  1:361047‑M2/141‑131 (MQ=255)                                                                                                                                  aGGTTTCTAtgtatccaaactggagacttttaacataaaattacttatcattcaaaaagtaaaacagcataatatcaaggtttataactttatcattatcaataatacctcatataaaataaaattttagggactttttag          <  1:602735‑M2/141‑133 (MQ=255)                                                                                                                                  aGGTTTCTAtgtatccaaactggagacttttaacataaaattacttatcattcaaaaagtaaaacagcataacatcaaggtttataaattaatcattatcaataatacctcatataaaataaaatattggtgactttttag          <  1:108392‑M2/141‑133 (MQ=255)                                                                                                                                    gTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCGGACAATCTTCTTATATTAAAAATAATGATGTCGTAATATTCAATGAAGCATTTGATAATGGTGCATCAGACAAATTCTTAAGTAATGTGaaa        <  1:605160/141‑1 (MQ=255)                                                                                                                                      ttCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCGGACAATCTTCTTATATTAAAAATAATGATGTCGTAATATTCAATGAAGCATTTGATAATGGTGCATCAGACAAATTATTAAGTAATGTGaaaaa      >  1:160/1‑141 (MQ=255)                                                                                                                                         tAtgtatccaaactggagacttttaacataaaattacttatcattcaaaaagtaaaacagcataatatcaaggtttataactttatcattatcaataatacctcatataaaataaaattttagggactttttagggacttt   <  1:56054‑M2/141‑140 (MQ=255)                                                                                                                                          aTGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCGGACAATCTTCGTATATTAAAAATAATGATGTCGTAATATTTAATTAAGCATTTGCTAATGGTGCACCAGAAAAATTATTAGGTAATGTGTAAAAAGaa  >  1:653579/1‑141 (MQ=255)                                                                                                                                          |                                                                                                                                             ACATCCGTGTATTCTCATTTGTTAGAAGAAAAATTTAATGAAGAGGACAAAAAAACAACTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCGGACAATCTTCTTATATTAAAAATAATGATGTCGTAATATTCAATGAAGCATTTGATAATGGTGCATCAGACAAATTATTAAGTAATGTGAAAAAAGAA  >  USA300TCH1516_ALE/2128206‑2128483

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