New junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? USA300TCH1516_ALE 512620 =96 (1.140)52 (0.890)
+TTATCTTGTCCATTTTATTTTTTAACCAAAATTTGATTAA
31/180 NT 44.0% intergenic (+688/‑6075) recR/speA_2 Recombination protein RecR/Arginine decarboxylase
?USA300TCH1516_ALE 1998278 = NA (NA)intergenic (‑6/+3329) USA300TCH1516_01882/USA300TCH1516_01883 tRNA‑Val/tRNA‑Ala

GATTACAAGTCAGTTGCTCTACCAATTGAGCTAGGCCGGCAATATGTAAGAATAAATGGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGGTGTGACCTCCTTGCTATAGTCACCAGACATATGAATGTAATTTATAC  >  USA300TCH1516_ALE/1998141‑1998418
                                                                                                                                         |                                                                                                                                             
gATTACAAGTCAGTTTCTCTACCAATTGAGCTAGGACGGTAATATGTAAGAATAAATGGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTaaac                                                                                                                                           <  2:182402/141‑2 (MQ=255)
gATTACAAGTCAGTTGCTCTACCTATTGAGCTAGGCCGGCAATATGTAAGTATAAAGGGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTaaac                                                                                                                                           <  1:907613/141‑2 (MQ=255)
gATTACAAGTCAGTTGCGCTACCAATTGAGCTAGGTCGGCAATATGTAAGAATAAATTGTGGATAATGACGGGTTCGAACCGCCGGCCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTaaaa                                                                                                                                           <  1:2835/141‑1 (MQ=11)
      aaGTCAGTGGCTATACCAATTGAGCTAGGCCGGGAATATGTACGAATAAATGGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCt                                                                                                                                     <  2:62932/141‑1 (MQ=255)
       aGTCAGTTGCTCTACCAATTGAGCTAGGCCGTCAATATGTAAGAATAAATGGTGGAGAATGACGGGGTCGAACGGCCAACCCTCGGCTGGTAAGGAAGATGCTCTCCCAGCTGAGCGAATTCTCCGATATAAAACTGcccg                                                                                                                                    >  2:401031/1‑139 (MQ=14)
              tGCTCTACCAATTGAGCTATGGCGACAATACGGAAGAATAAATTGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGt                                                                                                                             <  2:672476/141‑1 (MQ=17)
                 tctACCAATTGAGCTAGGCCGGCAATATGTAAGAATAAATGGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCt                                                                                                                          <  1:491628/141‑1 (MQ=255)
                 tctACCAATTGAGCTAGGCCGGCAATATGTAAGAATAAATGGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCt                                                                                                                          >  1:995163/1‑141 (MQ=255)
                 cctACCAATTGAGCTAGGCCGGCAATATGTAAGAATAAATGGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCt                                                                                                                          <  1:121732/140‑1 (MQ=255)
                   tcccAATCGAGCTAGGCCCGCAATAAGTAAGAATAAATGGTGGAGAATGACGGGTGCGAACCGCCGCCCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTAc                                                                                                                        <  1:426455/139‑1 (MQ=17)
                    gccAATTTAGCGAGGCCGGAAATATGTAAGAATAGATGGTGGAGAATGACGGGTTCGAACCGCCGACCCTCGGCTGGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTAct                                                                                                                       <  2:818986/140‑1 (MQ=17)
                     ctaaTTGAGCTAGGACGGCAATATGTAAGAATAAATGGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTActc                                                                                                                      <  1:440377/139‑1 (MQ=255)
                     ccAATTGAGCTAGGCCGGCAATATGTAAGAATAAATGGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCATGGCAACGTTCTActc                                                                                                                      >  1:780673/1‑141 (MQ=255)
                            aGCTAGGCCGGCAATATGTAAGAATAAATGGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGa                                                                                                               >  1:457123/1‑141 (MQ=255)
                            aGCTAGGCCGGCAATATGTAAGAATAAATGGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGa                                                                                                               >  1:53107/1‑141 (MQ=255)
                              cTAGGCCGGCAATATGTAAGAATAAATGGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAAc                                                                                                             >  1:693687/1‑141 (MQ=255)
                               tAGGCCGTCGAGATGTAAGGAGAAAGGGTGGAGAATGACGGGTTCGAACCGCCGACCCTGTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACg                                                                                                            <  2:207401/141‑1 (MQ=17)
                               tAGGCCGGCAATATGTAAGAATAAATGGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACg                                                                                                            <  1:596779/141‑1 (MQ=255)
                                 ggCCGGCAATATGTAAGAATAAATGGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTa                                                                                                          >  1:1007876/1‑141 (MQ=255)
                                 ggCCGGCAATATGTAAGAATAAATGGTGGAGAATGACGGGTTCGAACCGCCGACACTCTACATATAAAGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCAGGCAACGGTCTACTCTAGCGAAACGTa                                                                                                          >  1:30374/1‑141 (MQ=17)
                                           atGTAAGAATAAATGGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTa                                                                                                >  1:10152/1‑141 (MQ=255)
                                            tgtgAGAATAAATGGTGGGGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTAc                                                                                               <  2:538133/141‑1 (MQ=255)
                                               aaGTATATATGTCGGAGAAGGACGGGTTCGAACCGCCGATCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCAt                                                                                            <  2:963410/141‑1 (MQ=17)
                                                aGAATAAATGGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATc                                                                                           <  2:237291/141‑1 (MQ=255)
                                                      aagagtggAGAATTACGGGTTCGAGCCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCt                                                                                     <  2:827637/137‑1 (MQ=255)
                                                      aaTGGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCt                                                                                     >  1:571377/1‑141 (MQ=255)
                                                           tggCGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGa                                                                                <  2:187626/141‑1 (MQ=255)
                                                            ggAGAAGGACGGGTTCTACCCGCCGACTCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTTTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAg                                                                               <  2:644372/141‑1 (MQ=14)
                                                             gggaATGACGGGTTCGAACCGCCGACCCTCTTCTTGTAAGGCACATGCTCTCCCGGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGc                                                                              <  1:389168/139‑1 (MQ=255)
                                                             gagaATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCAGCCACAGGTGCCCCCGGGCAACGTTCTACTCTGGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAg                                                                               >  1:1019599/1‑141 (MQ=1)
                                                               gaATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGCCGCTAAGGAGCtt                                                                            >  1:559480/1‑141 (MQ=255)
                                                                   gACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGTCGGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACt                                                                        <  1:197416/141‑1 (MQ=255)
                                                                    aCGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCCGATGCCGGCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACtt                                                                       <  1:702411/141‑1 (MQ=255)
                                                                      gggTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCt                                                                     >  1:833113/1‑141 (MQ=255)
                                                                      gggTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCt                                                                     >  1:76343/1‑141 (MQ=255)
                                                                        gTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCtgt                                                                   <  1:457760/141‑1 (MQ=255)
                                                                         ttggAACCGCCGACCGTCTGCTTGTAAGGCAGATGCTCTCCGAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCtgtg                                                                  <  2:805457/138‑1 (MQ=255)
                                                                          tCGATCCGCCGATCCTGTGCTTGTAAGGCAGATTCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTgtgt                                                                 <  2:440764/141‑1 (MQ=255)
                                                                          tCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTgtgt                                                                 <  1:564975/141‑1 (MQ=255)
                                                                                   cgACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTTGCGAGACTTAAGTTCGACTACCATCGACGCTAAGGAGCTTAGCTTCTGTGTTCGGCATgg                                                        <  1:654297/141‑1 (MQ=14)
                                                                                    gACCCTTTTCTTGTAAGGCAGATGCTCTGCCAGCTTAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACGCTAGCTGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATggg                                                       <  2:775567/141‑1 (MQ=14)
                                                                                    gACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATggg                                                       <  1:591182/141‑1 (MQ=255)
                                                                                        ttctGCTTGTAAGGTAGATGTTGTCCCAGTTGAGCTAATTCTCCGATTTAAAACTGCCTGGAAACGTTCTACTTTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACa                                                   <  2:624538/140‑1 (MQ=14)
                                                                                           ttcTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGgt                                                <  1:149116/139‑1 (MQ=255)
                                                                                           tGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGgt                                                >  1:155458/1‑141 (MQ=255)
                                                                                             gttGTAAGGGAGATGCTGTCCCAGCTGAGCTAATTCTCCGATTTGAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGgtgt                                              <  2:58849/140‑1 (MQ=255)
                                                                                             cgtGTACGGTAGAGGCTCTCCGAGCTGAGCTCATTCTCCGATTTAAAAATGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTGCGACGACCAGCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGgtgt                                              <  2:322977/139‑1 (MQ=14)
                                                                                             cTTGTATGGCAGTAGCTTCGCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGgtgt                                              <  2:495092/141‑1 (MQ=14)
                                                                                             cTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACAATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGgtgt                                              >  2:958157/1‑141 (MQ=255)
                                                                                               tGTAAGGCAGATGCTCTCCCTGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGGTGTGa                                            <  2:88961/141‑1 (MQ=255)
                                                                                                  aaGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGGTGTGAcct                                         >  1:532780/1‑141 (MQ=255)
                                                                                                        gacgCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGGTGTGACCTCCTTGc                                   <  1:306529/138‑1 (MQ=255)
                                                                                                         aTGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGGTGTGACCTCCTTGCt                                  <  1:78626/141‑1 (MQ=255)
                                                                                                         aTGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGGCGTGACCTCCTTGCt                                  >  1:94608/1‑141 (MQ=255)
                                                                                                          tGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGTCTTCGTTTTTCTTTAGCGTTACGTAAGTTTGACTACCATCGACGCTGAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGGTGTGACCTCCTTGCta                                 <  1:520753/141‑1 (MQ=14)
                                                                                                             tcgcccGGCTGAGCTAATTCTGCGATGTAAAACTGGCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTGAGGAGCTTAACGTCTGTGTTCGGCATGGGAACAGGTGTGACCTCCTTGCTATAg                              <  2:198345/138‑1 (MQ=14)
                                                                                                             ccctccAGCTGAGCTAATCTTCCGATTTAAAACTGCCTGGCAACGGTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGGTGTGACCTCCTTGCTATAg                              <  2:803316/137‑1 (MQ=255)
                                                                                                              ctcCCGGCTAAGCTAATTCTCCGATTTAAAACTCCCTGGCAACGTTCTACTCTAGCGGAACGTACGTTCGACTACCATCTACTCTAAGGAGCTCAACTCCTGTTTTCGGCATGAGACCCGCTGTTCCCTCCTTGCTATAgc                             >  2:664437/1‑140 (MQ=17)
                                                                                                                  ccgCTGAGCTTATTCCGCGATTCAAAAATGCCTGGTGACGATCTTCTCGTGCGGAACGTAAGTTCGACTACCATCGACACTAAGGAGCTTAACTTTTGTGTTCCGCATGGGAACAGGTGTGACCTCCTTGCTATAGTCAcc                         <  2:1017682/139‑1 (MQ=11)
                                                                                                                  cAGCTGAGCTAATTCTACGATTTAAAACGGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGGTGTGACCTCCTTGCTATAGTCAcc                         <  2:149536/141‑1 (MQ=255)
                                                                                                                   cgCTGAGCCTATTCTCCGATTTAAAACTGCCTGGGAACGTTTTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAAAAGGTGTGACCTCCTTGCTATAGTCACCa                        <  2:78844/140‑1 (MQ=14)
                                                                                                                   aGCTGCCCTAATTCTCCGATTTAAAACTGCCTGGCAACGTCCTGCTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTACCTTCTGTGTTCGGCATGGGAACAGGTGTGACCTCCTTGCTATAGTCActa                        <  2:1010863/141‑3 (MQ=14)
                                                                                                                   aGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGGTGTGACCTCCTTGCTATAGTCACCa                        <  2:231822/141‑1 (MQ=255)
                                                                                                                    gCTGAGCTAACTCGCCGATTTAAAACTGCCTGGCAACGTTCGACTCTGGCGGAACGTAAGTTCGACTACCATCGGCGCCAAGGAGCTTATCTTCTTTGTTCGGCATGGGAACAGGTGTGACCTCCTTGCTATAGTCACCAg                       <  2:422629/141‑1 (MQ=14)
                                                                                                                     cttggCTAATTCGCCGATTTAAAACTGTCTGGCAACGTTCTTCTTTAGCTGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCGGTGTTCGGCATGGGAACAGGTGTGACCTCCTTGCTATAGTCACCAGa                      <  2:849252/137‑1 (MQ=14)
                                                                                                                     cTGTGCTAATTTTTCGATTTAAATATGTCTGGTAACGTTCTATTCTAGCGGAACTTAAGTTCGATTACCATCGATGCTAAGGAGCTTAACTTCTGTTTTCGGCATGGGAATAGGTGTGACCTCCTTGCTATAGTCACCAGa                      <  2:30861/141‑1 (MQ=11)
                                                                                                                     cTGAGATAAATCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGGTGTGACCTCCTTGCTATAGTCACCAGa                      <  1:639302/141‑1 (MQ=255)
                                                                                                                      tGAGCTAATTCTCCGATTTAAAACAGCAAGGCAACGTCATAAGCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGGTGTGACCTCCTTGCTATAGTCACCAGAc                     >  1:489961/1‑141 (MQ=14)
                                                                                                                      tGAACTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGGTGTGACCTCCTTGCTATCGTCACCAGAc                     >  1:245962/1‑141 (MQ=255)
                                                                                                                       gAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGGTGTGACCTCCTTGCTATAGTCACCAGACa                    <  1:298452/141‑1 (MQ=255)
                                                                                                                       gAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGCCATGGGAACAGGTGTGACCTCCTTGCTATAGTCACCAGAcc                    >  2:366110/1‑140 (MQ=255)
                                                                                                                        aGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTGCGTCACCGTTCCATCGACCCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGGTCTGCCCTCCTCGCTATACTCAACAGACaa                   >  2:628813/1‑140 (MQ=14)
                                                                                                                        aGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGCAGCTTAACGTCTATGTTCGGCATGGCAACAGTTGTGACCTCCTTCCTATAGTCCCCAGACat                   >  2:762849/1‑141 (MQ=17)
                                                                                                                        aGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCCACCCTAAGGAGCTTAACTTCTGTGTTCGACATGGGAACAAGTGTGACCTCCTTGCTATAGTCACCAGACat                   >  2:424802/1‑141 (MQ=255)
                                                                                                                          cTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGGTGTGACCTCCTTGCTATAGTCACCAGACatat                 >  1:173001/1‑141 (MQ=255)
                                                                                                                          cTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGGTGTGACCTCCTTGCTATAGTCACCAGACatat                 >  1:961518/1‑141 (MQ=255)
                                                                                                                          cTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACACGTGTTACCTCCCTCCTATATTCACTAGACatat                 >  1:251148/1‑141 (MQ=14)
                                                                                                                           tgaTTCTCCGATTTAACACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGGTGTGACCTCCTTGCTATAGTCACCAGACATATg                <  2:352881/139‑1 (MQ=255)
                                                                                                                           taatgtgccGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGTTAATATGTGTGACCTCCTTGCTATAGTCACCAGACATATg                <  2:1003564/134‑1 (MQ=14)
                                                                                                                            aaTTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACAATCGACGCTAGGGAGCTTAACTTCTGTGTTCGGCATGGAAACAAGTGTGACCGCCTAGCGATAGTCACAAGAAATCTGa               >  2:149254/1‑141 (MQ=14)
                                                                                                                             agtctcCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGGTGTGACCTCCTTGCTATAGTCACCAGACATATGaa              <  1:382559/139‑1 (MQ=255)
                                                                                                                                ctcAGATTTAAAACTGGTTGACAACTCTCTACTCTGGCTGAATGTAAGTTCGAGGACCATCGACGTTAAGGAGCTTAACTTGTGTGTTCGGCATGGGAACAGGTTTGACCTTCTTGCTATAGTCACCAGACATATGAATGt           <  2:93032/141‑1 (MQ=11)
                                                                                                                                  ccGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGGTGTGACCTCCTTGCTATAGTCACCAGACATATGAATGTaa         >  2:450942/1‑141 (MQ=39)
                                                                                                                                       ttAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGGTGTGACCTCCTTGCTATAGTCACCAGACATATGAATGTAATTtat    >  1:317588/1‑141 (MQ=35)
                                                                                                                                       ttAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGGTGTGACCTCCTTGCTATAGTCACCAGACATATGAATGTAATTtat    >  1:131273/1‑141 (MQ=35)
                                                                                                                                       ttAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGGTGTAAAGTCGTGGGGATAGTCACCAGACATATGAATGTAATTtat    >  1:798527/1‑141 (MQ=11)
                                                                                                                                         aaaaCTGCCTGGCAACGTTGTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGGTGTGACCTCCTTGCTATAGTCACCAGACATATGAATGTAATTTATAc  <  1:348176/141‑1 (MQ=18)
                                                                                                                                         aaaaCTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGGTGTGACCTCCTTGCTATAGTCACCAGACATATGAATGTAATTTATAc  >  1:43870/1‑141 (MQ=33)
                                                                                                                                         |                                                                                                                                             
GATTACAAGTCAGTTGCTCTACCAATTGAGCTAGGCCGGCAATATGTAAGAATAAATGGTGGAGAATGACGGGTTCGAACCGCCGACCCTCTGCTTGTAAGGCAGATGCTCTCCCAGCTGAGCTAATTCTCCGATTTAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGGTGTGACCTCCTTGCTATAGTCACCAGACATATGAATGTAATTTATAC  >  USA300TCH1516_ALE/1998141‑1998418

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 27 ≤ 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.