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

TAATATAATCTGTATTTTTAGGGTCTGCATTTAATGCTTTACGCACATATTTTAATGCTTTTTCATCATCATTTAATGAACGATTTGCTATCGCTAACTCAAAATTTAATAAACCTGATTTAGGAAACATTCTAAGTCCTCGCTCCCATTCTGTCATACCTTCGGACTTAGAATTGATAGTAGCCATAATCATACCACTTAAATAATATGTTTGATCATCGGCATAATTTTTATTTATTGTCTGCTTCACAATATTTTGAGCATTATCATAATTA  >  USA300TCH1516_ALE/1659892‑1660166                                                                                                                                           |                                                                                                                                         tAATATAATCTGTATTTTTAGGGTCTGCATTTAATGCTTTACGCACATATTGTAATGCTTTTTCTGCATCATTTAATGAACGATTTGCTATCGCTAACTCAAAATTTAATAAACCTGATTTAGGAAACATTCTAAGTCCTc                                                                                                                                        <  2:30150/141‑1 (MQ=255)      taATCTGTATTTTTAGGGTCTGCATTTAATGCTTTACGCACATATTTTACTGCTTTTTCATCATCCTTTAATGAACGATTTGCTATCGCTAACTCAAAATTTAATAAACCTGATTTAGGAAACATTCTAAGTCCTCGCTcc                                                                                                                                   <  1:394546/141‑1 (MQ=255)            gTATTTTTAGGGTCTGCATTTAATGCTTTACGCACATATTTTAATGCTTTTTCATCATCATTTAATGAACGATTTGCTATCGCTAACTCAAAATTTAATAAACCTGATTTAGGAAACATTCTAAGTCCTCGCTCCCATTCt                                                                                                                             >  1:190465/1‑141 (MQ=255)            gTATTTTTAGGGTCTGCATTTAATGCTTTACGCACATATTTTAATGCTTTTTCATCATCATTTAATGAACGATTTGCTATCGCTAACTCAAAATTTAATAAACCTGATTTAGGAAACATTCTAAGTCCTCGCTCCCATTCt                                                                                                                             >  1:376999/1‑141 (MQ=255)             tATTTTTAGGGTCTGCATTTAATGCTTTACGCACATATTTTAATGCTTTTTCATCATCATTTAATGAACGATTTGCTATCGCTAACTCAAAATTTAATAAACCTGATTTAGGAAACATTCTAAGTCCTCGCTCCCATTCTg                                                                                                                            >  1:127482/1‑141 (MQ=255)                   tAGGGTCTGCATTTAATGCTTTACGCACATATTTTAATGCTTTTTCATCATCATTTAATGACCGATTTGCTATCGCTAACTCAAAATTTAATAAACCTGATTTAGGAAACATTCTAAGTCCgaaggtatgacagaatggga                                                                                                                      <  2:164961‑M1/141‑21 (MQ=255)                    aGGGTCTGCATTTAATGCTTTACGCACATATTTTAATGCTTTTTCATCATCATTTAATGAACGATTTGCTATCGCTAACTCAAAATTTAATAAACCTGATTTAGGAAACATTCTAAGTCCTCGCTCCCATTCTGTCATAcc                                                                                                                     <  1:610983/141‑1 (MQ=255)                     gggTCTGCATTTAATGCTTTACGCACATATTTTAATGCTTTTTCATCATCATTTAATGAACGATTTGCTATCGCTAACTCAAAATTTAATAAACCTGATTTAGGAAACATTCTAAGTCCTCGCTCCCATTCTGTCATACCt                                                                                                                    >  1:371705/1‑141 (MQ=255)                      ggTCTGCATTTAATGCTTTACGCACATATTTTAATGCTTTTTCATCATCATTTAATGAACGATTTGCTATCGCTAACTCAAAATTTAATAAACCTGATTTAGGAAACATTCTAAGTCCTCGCTCCCATTCTGTCATACCtt                                                                                                                   >  2:16853/1‑141 (MQ=255)                            cATTTACTGCTTTACGCACATATTTTAATGCTTTTTCATCATCATTTAATGAACGATTTTCTATCGCTAACTCAAAATTTAATAAACCTGATTTAGGAAACATTCTAAGTCCTCGCTCCCATTCTGTCATACCTTCggact                                                                                                             >  1:93967‑M2/1‑136 (MQ=255)                             aTTTAATGCTTTACGCACATATTTTAATGCTTTTTCATCATCATTTAATGAACGATTTGCTATCGCTAACTCAAAATTTAATAAACCTGATTTAGGAAACATTCTAAGTCCgaaggtatgacagaatgggagcgaggactt                                                                                                            <  1:356593‑M1/141‑31 (MQ=255)                             aTTTAATGCTTTACGCACATATTTTAATGCTTTTTCATCATCATTTAATGAACGATTTGCTATCGCTAACTCAAAATTTAATAAACCTGATTTAGGAAACATTCTAAGTCCgaaggtatgacagaatgggagcgaggactt                                                                                                            <  1:361556‑M1/141‑31 (MQ=255)                              tttAATGCTTTACGCACAGATTTTAATGCTTTTTCATCATCATGTAATGAACTACGTGCGATCTGGAACTCAAAATTTAATAAACCTGATTTAGGAAACATTCTAAGTCCgaaggtatgacagaatgggagcgaggactta                                                                                                           <  1:783594‑M1/141‑32 (MQ=255)                                  aTGCTTTACGCACATATTTTAATGCTTTTTCATCATCATTTAATGAACGATTTGCTATCGCTAACTCAAAATTTAATAAACCTGATTTAGGAAACATTCTAAGTCCgaaggtatgacagaatgggagcgaggacttagaat                                                                                                       <  1:117606‑M1/141‑36 (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                                                 >  1:471975/1‑141 (MQ=255)                                                                                        cTATCGCTAACTCAAAATTTAATAAACCTGATTTAGGAAACATTCTAAGTCCTCGCTCCCATTCTGTCATACCTTCGGACTTAGAATTGATAGTAGCCATAATCATACCACTTAAATAATATGTTTGATCATCGGCATAAt                                                 <  1:97578/141‑1 (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)                                                                                                                                       aGTCCgaaggtatgacagaatgggagcgaggacttagaatgtttcctaaatcaggtttattaaattttgagttagcgatagaaaatcgttcattaaatgatgatgaaaaagcattaaaatatgtgcgtaaagcagtaaatg  >  1:93967‑M1/1‑5 (MQ=255)                                                                                                                                           |                                                                                                                                         TAATATAATCTGTATTTTTAGGGTCTGCATTTAATGCTTTACGCACATATTTTAATGCTTTTTCATCATCATTTAATGAACGATTTGCTATCGCTAACTCAAAATTTAATAAACCTGATTTAGGAAACATTCTAAGTCCTCGCTCCCATTCTGTCATACCTTCGGACTTAGAATTGATAGTAGCCATAATCATACCACTTAAATAATATGTTTGATCATCGGCATAATTTTTATTTATTGTCTGCTTCACAATATTTTGAGCATTATCATAATTA  >  USA300TCH1516_ALE/1659892‑1660166

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.