New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	= 1660030	40 (0.870)	5 (0.120)	4/238	NT	11.7%	coding (1279/1464 nt)	gluP	Rhomboid protease GluP
	?	USA300TCH1516_ALE	= 1660054	39 (0.920)					coding (1255/1464 nt)	gluP	Rhomboid protease GluP

CATTTAATGCTTTACGCACATATTTTAATGCTTTTTCATCATCATTTAATGAACGATTTGCTATCGCTAACTCAAAATTTAATAAACCTGATTTAGGAAACATTCTAAGTCCTCGCTCCCATTCTGTCATACCTTCGGACTTAGAATTGATAGTAGCCATAATCATACCACTTAAATAATATGTTTGATCATCGGCATAATTTTTATTTATTGTCTGCTTCACAATATTTTGAGCATTATCATAATTACCACTAGTCATATCATCTTTGATCAAT  >  USA300TCH1516_ALE/1659919‑1660193                                                                                                                                        |                                                                                                                                            cATTTACTGCTTTACGCACATATTTTAATGCTTTTTCATCATCATTTAATGAACGATTTTCTATCGCTAACTCAAAATTTAATAAACCTGATTTAGGAAACATTCTAAGTCCTCGCTCCCATTCTGTCATACCTTCggact                                                                                                                                        >  1:93967‑M2/1‑136 (MQ=255)               cGCACATATTTTAATGCTTTTTCATCATCATTTAATGAACGATTTGCTATCGCTAACTCAAAATTTAATAAACCTGATTTAGGAAACATTCTAAGTCCTCGCTCCCATTCTGTCATACCTTCGGACTTAGAATTGAtagta                                                                                                                          >  1:19889/1‑141 (MQ=255)               cGCACATATTTTAATGCTTTTTCATCATCATTTAATGAACGATTTGCTATCGCTAACTCAAAATTTAATAAACCTGATTTAGGAAACATTCTAAGTCCTCGCTCCCATTCTGTCATACCTTCGGACTTAGAATTGAtagta                                                                                                                          >  1:414559/1‑141 (MQ=255)                 cacaTATTTTAATGCTTTTTCATCATCATTTAATGAACGATTTGCTATCGCTAACTCAAAATTTAATAAACCTGATTTAGGAAACATTCTAAGTCCTCGCTCCCATTCTGTCATACCTTCGGACTTAGAATTGATAGTAGc                                                                                                                        <  2:233328/141‑1 (MQ=255)                  acaTATTTTAATGCTTTTTCATCATCATTTAATGAACGATTTGCTATCGCTAACTCAAAATTTAATAAACCTGATTTAGGAAACATTCTAAGTCCTCGCTCCCATTCTGTCATACCTTCGGACTTAGAATTGATAGTAGcc                                                                                                                       <  2:87544/141‑1 (MQ=255)                  acaTATTTTAATGCTTTTTCATCATCATTTAATGAACGATTTGCTATCGCTAACTCAAAATTTAATAAACCTGATTTAGGAAACATTCTAAGTCCTCGCTCCCATTCTGTCATACCTTCGGACTTAGAATTGATAGTAGcc                                                                                                                       <  1:407750/141‑1 (MQ=255)                             tGCTTTTTCATCATCATTTAATGAACGATTTGCTATCGCTAACTCAAAATTTAATAAACCTGATTTAGGAAACATTCTAAGTCCTCGCTCCCATTCTGTCATACCTTCGGACTTAGAATTGATAGTAGCCATAATCATAct                                                                                                            >  1:730889/1‑140 (MQ=255)                                   ttCATCATCATTTAATGAACGATTTGCTATCGCTAACTCAAAATTTAATAAACCTGATTTAGGAAACATTCTAAGTCCTCGCTCCCATTCTGTCATACCTTCGGACTTAGAATTGATAGTAGCCATAATCATACCACTTaa                                                                                                      <  2:9159/141‑1 (MQ=255)                                             tttAATGAACGATTTGCTATCGCTAACTCAAAATTTAATAAACCTGATTTAGGAAACATTCTAAGTCCTCGCTCCCATTCTGTCATACCTTCGGACTTAGAATTGATAGTAGCCATAATCATACCACTTAAATAATATGtt                                                                                            <  1:60659/141‑1 (MQ=255)                                              ttAATGAACGATTTGCTATCGCTAACTCAAAATTTAATAAACCTGATTTAGGAAACATTCTAAGTCCTCGCTCCCATTCTGTCATACCTTCGGACTTAGAATTGATAGTAGCCATAATCATACCACTTAAATAATATGttt                                                                                           >  2:138531/1‑141 (MQ=255)                                                   gAACGATTTGCTATCGCTAACTCAAAATTTAATAAACCTGATTTAGGAAACATTCTAAGTCCTCGCTCCCATTCTGTCATACCTTCGGACTTAGAAATGATAGTAGCCATAATCATACCACTTAAATAATATGTTTGatca                                                                                      >  1:632487/1‑141 (MQ=255)                                                       gATTTGCTATCGCTAACTCAAAATTTAATAAACCTGATTTAGGAAACATTCTAAGTCCTCGCTCCCATTCTGTCATACTTTCGGACTTAGAATTGATAGTAGCCATAATCATACCACTTAAATAATATGTTTGATCATCgg                                                                                  <  1:462345/141‑1 (MQ=255)                                                        aTTTGCTATCGCTAACTCAAAATTTAATAAACCTGATTTAGGAAACATTCTAAGTCCTCGCTCCCATTCTGTCATACCTTCGGACTTAGAATTGATAGTAGCCATAATCATACCACTTAAATAATATGTTTGATCATCGGc                                                                                 <  1:307529/141‑1 (MQ=255)                                                            gCTATCGCTAACTCAAAATTTAATAAACCTGATTTAGGAAACATTCTAAGTCCTCGCTCCCATTCTGTCATACCTTCGGACTTAGAATTGATAGTAGCCATAATCATACCACTTAAATAATATGTTTGATCATCGGCAtca                                                                             >  1:364286/1‑139 (MQ=255)                                                             cTATCGCTAACTCAAAATTTAATAAACCTGATTTAGGAAACATTCTAAGTCCTCGCTCCCATTCTGTCATACCTTCGGACTTAGAATTGATAGTAGCCATAATCATACCACTTAAATAATATGTTTGATCATCGGCATAAt                                                                            <  1:97578/141‑1 (MQ=255)                                                             cTATCGCTAACTCAAAATTTAATAAACCTGATTTAGGAAACATTCTAAGTCCTCGCTCCCATTCTGTCATACCTTCGGACTTAGAATTGATAGTAGCCATAATCATACCACTTAAATAATATGTTTGATCATCGGCATAAt                                                                            >  1:471975/1‑141 (MQ=255)                                                               aTCGCTAACTCAAAATTTAATAAACCTGATTTAGGAAACATTCTAAGTCCTCGCTCCCATTCTGTCATACCTTCGGACTTAGAATTGATAGTAGCCATAATCATACCACTTAAATAATATGTTTGATCATCGGCATAAttt                                                                          <  2:107559/141‑1 (MQ=255)                                                                tCGCTAACTCAAAATTTAATAAACCTGATTTAGGAAACATTCTAAGTCCTCGCTCCCATTCTGTCATACCTTCGGACTTAGAATTGATAGTAGCCATAATCATACCACTTAAATAATATGTTTGATCATCGGCATAAtttt                                                                         >  2:65555/1‑141 (MQ=255)                                                                   cTAACTCAAAATTTAATAAACCTGATTTAGGAAACATTCTAAGTCCTCGCTCCCATTCTGTCATACCTTCGGACTTAGAATTGATAGTAGCCATAATCATACCACTTAAATAATATGTTTGATCATCGGCATAATTtttat                                                                      <  1:428590/141‑1 (MQ=255)                                                                       cTCAAAATTTAATAAACCTGATTTAGGAAACATTCTAAGTCCTCGCTCCCATTCTGTCATACCTTCGGACTTAGAATTGATAGTAGCCATAATCATACCACTTAAATAATATGTTTGATCATCGGCATAATTTttatttat                                                                  <  1:214459/141‑1 (MQ=255)                                                                       cTCAAAATTTAATAAACCTGATTTAGGAAACATTCTAAGTCCTCGCTCCCATTCTGTCATACCTTCGGACTTAGAATTGATAGGAGTCATAATCATACCACTTAAATAATATGTTTGATCATCGGCATAATTTttatttat                                                                  <  1:214634/141‑1 (MQ=255)                                                                           aaaTTTAATAAACCTGATTTAGGAAACATTCTAAGTCCTCGCTCCCATTCTGTCATACCTTCGGACTTAGAATTGATAGTAGCCATAATCATACCACTTAAATAATATGTTTGATCATCGGCATAATTTTTATTTATTGTc                                                              <  1:473124/141‑1 (MQ=255)                                                                           aaaTTTAATAAACCTGATTTAGGAAACATTCTAAGTCCTCGCTCCCATTCTGTCATACCTTCGGACTTAGAATTGATAGTAGCCATAATCATACCACTTAAATAATATGTTTGATCATCGGCATAATTTTTATTTATTGTc                                                              >  1:285404/1‑141 (MQ=255)                                                                                 aataaACCTGATTTAGGAAACATTCTAAGTCCTCGCTCCCATTCTGTCATACCTTCGGACTTAGAATTGATAGTAGCCATAATCATACCACTTAAATAATATGTTTGATCATCGGCATAATTTTTATTTATTGTCTGCTTc                                                        >  1:375388/1‑141 (MQ=255)                                                                                  ataaACCTGATTTAGGAAACATTCTAAGTCCTCGCTCCCATTCTGTCATACCTTCGGACTTAGAATTGATAGTAGCCATAATCATACCACTTAAATAATATGTTTGATCATCGGCATAATTTTTATTTATTGTCTGCTTca                                                       >  1:291474/1‑141 (MQ=255)                                                                                   taaACCTGATTTAGGAAACATTCTAAGTCCTCGCTCCCATTCTGTCATACCTTCGGACTTAGAATTGATAGTAGCCATAATCATACCACTTAAATAATATGTTTGATCATCGGCATAATTTTTATTTATTGTCTGCTTcac                                                      >  2:288558/1‑141 (MQ=255)                                                                                   taaACCTGATTTAGGAAACATTCTAAGTCCTCGCTCCCATTCTGTCATACCTTCGGACTTAGAATTGATAGTAGCCATAATCATACCACTTAAATAATATGTTTGATCATCGGCATAATTTTTATTTATTGTCTGCTTcac                                                      >  2:281821/1‑141 (MQ=255)                                                                                    aaaCCTGATTTAGGAAACATTCTAAGTCCTCGCTCCCATTCTGTCATACCTTCGGACTTAGAATTGATAGTAGCCATAATCATACCACTTAAATAATATGTTTGATCATCGGCATAATTTTTATTTATTGTCTGCTTcaca                                                     >  1:519568/1‑141 (MQ=255)                                                                                              tAGGAAACATTCTAAGTCCTCGCTCCCATTCTGTCATACCTTCGGACTTAGAATTGATAGTAGCCATAATCATACCACTTAAATAATATGTTTGATCATCGGCATAATTTTTATTTATTGTCTGCTTCACAATATTTTGAg                                           >  1:586937/1‑141 (MQ=255)                                                                                                 gAAACATTCTAAGTCCTCGCTCCCATTCTGTCATACCTTCGGACTTAGAATTGATAGTAGCCATAATCATACCACTTAAATAATATGTTTGATCATCGGCATAATTTTTATTTATTGTCTGCTTCACAATATTTTGAGCAt                                        >  1:575060/1‑141 (MQ=255)                                                                                                    aCATTCTAAGTCCTCGCTCCCATTCTGTCATACCTTCGGACTTAGAATTGATAGTAGCCATAATCATACCACTTAAATAATATGTTTGATCATCGGCATAATTTTTATTTATTGTCTGCTTCACAATATTTTGAGCATTAt                                     <  1:93834/141‑1 (MQ=255)                                                                                                      aTTCTAAGTCCTCGCTCCCATTCTGTCATACCTTCggacttagaatgtttcctaaatcaggtttattaaattttgagttagcgatagcaaatcgttcattaaatgatgatgaaaaagcattaaaatatgtgcgtaaagcat                                   <  1:117606‑M2/141‑107 (MQ=255)                                                                                                      aTTCTAAGTCCTCGCTCCCATTCTGTCATACCTTCGGACTTAGAATTGATAGTAGCCATAATCATACCACTTAAATAATATGTTTGATCATCGGCATAATTTTTATTTATTGTCTGCTTCACAATATTTTGAGCATTATCa                                   <  2:225933/141‑1 (MQ=255)                                                                                                      aTTCTAAGTCCTCGCTCCCATGCTGTCATACCTTCGGACTTAGAATTGATAGTAGCCATAATCATACCACTTAAATAATATGTTTGATCATCGGCATAATTTTTATTTATTGTCTGCTTCACAATATTTTGAGCATTATCa                                   <  2:225918/141‑1 (MQ=255)                                                                                                          tAAGTCCTCGCTCCCATTCTGTCATACCTTCggacttagaatgtttcctaaatcaggtttattaaattttgagttccagatcgcacgtagttcattacatgatgatgaaaaagcattaaaatctgtgcgtaaagcattaaa                               <  1:783594‑M2/141‑111 (MQ=255)                                                                                                           aaGTCCTCGCTCCCATTCTGTCATACCTTCggacttagaatgtttcctaaatcaggtttattaaattttgagttagcgatagcaaatcgttcattaaatgatgatgaaaaagcattaaaatatgtgcgtaaagcattaaat                              <  1:361556‑M2/141‑112 (MQ=255)                                                                                                           aaGTCCTCGCTCCCATTCTGTCATACCTTCggacttagaatgtttcctaaatcaggtttattaaattttgagttagcgatagcaaatcgttcattaaatgatgatgaaaaagcattaaaatatgtgcgtaaagcattaaat                              <  1:356593‑M2/141‑112 (MQ=255)                                                                                                           aaGTCCTCGCTCCCATTCTGTCATACCTTCGGACTTAGAATTGATAGTAGCCATAATCATACCACTTAAATAATATGTTTGATCATCGGCATAATTTTTATTTATTGTCTGCTTCACAATATTTTGAGCATTATCATAAtt                              <  1:499617/141‑1 (MQ=255)                                                                                                                 tCGCTCCCATTCTGTCATACCTTCGGACTTAGAATTGATAGTAGCCATAATCATACCACTTAAATAATATGTTTGATCATCGGCATAATTTTTATTTATTGTCTGCTTCACAATATTTTGAGCATTATCATAATTACCACt                        <  1:608179/141‑1 (MQ=255)                                                                                                                     tCCCATTCTGTCATACCTTCggacttagaatgtttcctaaatcaggtttattaaattttgagttagcgatagcaaatcggtcattaaatgatgatgaaaaagcattaaaatatgtgcgtaaagcattaaatgcagacccta                    <  2:164961‑M2/141‑122 (MQ=255)                                                                                                                       ccATTCTGTCATACCTTCGGACTTAGAATTGATAGTAGCCATAATCATACCACTTAAATAATATGTTTGATCATCGGCATAATTTTTATTTATTGTCTGCTTCACAATATTTTGAGCATTATCATAATTACCACTAGTCat                  <  2:139576/141‑1 (MQ=255)                                                                                                                       ccATTCTGTCATACCTTCGGACTTAGAATTGATAGTAGCCATAATCATACCACTTAAATAATATGTTTGATCATCGGCATAATTTTTATTTATTGTCTGCTTCACAATATTTTGAGCATTATCATAATTACCACTAGTCat                  <  1:222171/141‑1 (MQ=255)                                                                                                                       ccATTCTGTCATACCTTCGGACTTAGAATTGATAGTAGCCATAATCATACCACTTAAATAATATGTTTGATCATCGGCATAATTTTTATTTATTGTCTGCTTCACAATATTTTGAGCATTATCATAATTACCACTAGTCat                  <  2:333042/141‑1 (MQ=255)                                                                                                                                cATACCTTCGGACTTAGAATTGATAGTAGCCATAATCATACCACTTAAATAATATGTTTGATCATCGGCATAATTTTTATTTATTGTCTGCTTCACAATATTTTGAGCATTATCATAATTACCACTAGTCATATCATCttt         >  2:272044/1‑141 (MQ=255)                                                                                                                                cATACCTTCGGACTTAGAATTGATAGTAGCCATAATCATACCACTTAAATAATATGTTTGATCATCGGCATAATTTTTATTTATTGTCTGCTTCACAATATTTTGAGCATTATCATAATTACCACTAGTCATATCATCttt         >  2:272056/1‑141 (MQ=255)                                                                                                                                      ttCGGACTTAGAATTGATAGTAGCCATAATCATACCACTTAAATAATATGTTTGATCATCGGCATAATTTTTATTTATTGTCTGCTTCACAATATTTTGAGCATTATCATAATTACCACTAGTCATATCATCTTTGATCaa   >  2:7917/1‑141 (MQ=255)                                                                                                                                       tCGGACTTAGAATTGATAGTAGCCATAATCATACCACTTAAATAATATGTTTGATCATCGGCATAATTTTTATTTATTGTCTGCTTCACAATATTTTGAGCATTATCATAATTACCACTAGTCATATCATCTTTGATCAAt  <  2:104166/141‑1 (MQ=255)                                                                                                                                        |                                                                                                                                            CATTTAATGCTTTACGCACATATTTTAATGCTTTTTCATCATCATTTAATGAACGATTTGCTATCGCTAACTCAAAATTTAATAAACCTGATTTAGGAAACATTCTAAGTCCTCGCTCCCATTCTGTCATACCTTCGGACTTAGAATTGATAGTAGCCATAATCATACCACTTAAATAATATGTTTGATCATCGGCATAATTTTTATTTATTGTCTGCTTCACAATATTTTGAGCATTATCATAATTACCACTAGTCATATCATCTTTGATCAAT  >  USA300TCH1516_ALE/1659919‑1660193

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.