New junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? CP000730 = 45071625 (0.380)33 (0.580) 27/226 NT 63.0% intergenic (+83/‑266) set19/set20 staphylococcal exotoxin/staphylococcal exotoxin
?CP000730 451778 = 17 (0.300)intergenic (+77/‑369) set20/set21 staphylococcal exotoxin/staphylococcal exotoxin

AATCGCATGAGTGACGTCATTGACGGTAGAAATATTGAAAAAATAGAAGCCAACATTAGATAATTCAATGAAATATGGATAATAGTAAAATATGGATAGTATAGAGGAGTTAGGCAACATAAGTTGCTTAGCTTCTTTTTTGTGTTGGAGAGATGAAAATGAAGCGTATCGATGAATAATAAAAACACCAATAAAACTTGTGGAAATAGTTGATACTTATAGTCGCGCGTTGTCCTTTTCGTGACATGAAACAATGTGGAAAACATAGTTAAATTGA  >  CP000730/451639‑451915
                                                                                                                                           |                                                                                                                                         
tggcagatgtcatagatggcactaatattgatcacattgaagtgaatataaaataatcatgacaatctctaaatagaagctgtcatcggaaaaacaagaagttaagtgaaaacggcctacatgttccatagcttcattttt                                                                                                                                          >  2:118344‑M2/140‑141 (MQ=255)
aagcGCATGAGTGACGTCATTGACGGTAGAAATATTGAAAAAATAGAAGCCAACATTAGATAATTCAATGAAATATGGATAATAGTAAAATATGGATAGTATAGAGGAGTTAGGCAACATAAGTTGCTTAGCTTCtttttt                                                                                                                                          <  1:550532/138‑1 (MQ=255)
   cagatgtcatagatggcactaatattgataacattgaagtgaatataaaagaatcatgacattctctaaatagaagctgtcatcgtagaaacaagaagttaagtgactacggcctacatgttgcttagcttcttttTtgtg                                                                                                                                       >  2:433908‑M2/137‑141 (MQ=255)
   cGCATGAGTGACGTCATTGACGGTAGAAATATTGAAAAAATAGAAGCCAACATTAGATAATTCAATGAAATATGGATAATAGTAAAATATGGATAGTATAGAGGAGTTAGGCAACATAAGTTGCTTAGCTTCTTTTTtggg                                                                                                                                       >  1:52585/1‑139 (MQ=255)
    agatgtcatagatggcactaatattgataacattgaagtgaatataaaataatcatgacattctctaaatagaagctgtcatcggaaaaacaagaagttaagtgacaacggcctacatgttgcttagcttcttttTTgtgt                                                                                                                                      >  1:73576‑M2/136‑141 (MQ=255)
             agatggcactaatattgataacattgaagtgaatataaaataatcatgacattctctaactataagctgtcatcggaaaaaacagaaattaagtgacaacggcctcaatgtttcttagcttcttttTTGTGTtggaaagct                                                                                                                             >  2:147145‑M2/127‑139 (MQ=255)
                tggcactaatattgataacattgaagtgaatataaaataatcatgacattctctaaatagaagctgtcatcggaaaaacaagaagttaagtgacaacggcctacatgttgcttagcttcttttTTGTGTTGGAGAGATGaa                                                                                                                          >  1:747543‑M2/124‑141 (MQ=255)
                tggcactaatattgataacattgaagtgaatataaaataatcatgacattctctaaatagaagctgtcatcggaaaaacaagaagttaagtgacaacggcctacatgttgcttagcttcctttTGGTGTTGGAGAGATGaa                                                                                                                          <  1:405512‑M2/18‑1 (MQ=255)
                tCATTGACGGTAGAAATATTGAAAAAATAGAAGCCAACATTAGATAATTCAATGAAATATGGATAATAGTAAAATATGGATAGTATAGAGGAGTTAGGCAACATAAGTTGCTTAGCTTCTTTTTTGTGTTGGAGAGATGaa                                                                                                                          >  1:639665/1‑141 (MQ=255)
                 cATTGACGGTAGAAATATTGAAAAAATAGAAGCCAACATTAGATAATTCAATGAAATATGGATAATAGTAAAATATGGATAGTATAGAGGAGTTAGGCAACATAAGTTGCTTAGCTTCTTTTTTGTGTTGGAGAGATGaaa                                                                                                                         >  2:296556/1‑141 (MQ=255)
                  gcactaatattgataacattgaagtgaatataaaataatcatgacattctctaaatagaagctgtcatcggaaaaacaagaagttaagtgacaacggcctacatgttgcttagcttcttttTTGTGTTGGAGAGATGaaaa                                                                                                                        <  1:498725‑M2/20‑1 (MQ=255)
                       aatattgataacattgaagtgaatataaaataatcatgacattctctaaatagaagctgtcatcggaaaaacaagaagttaagtgacaacggcctacatgttgcttagcttcttttTTGTGTTGGAGAGATGAAAATGAAg                                                                                                                   <  1:519579‑M2/25‑1 (MQ=255)
                        atattgataacattgaagtgaatataaaataatcatgacattctctaaatagaagctgtcatcggaaaaacaagaagttaagtgacaacggcctacatgttgcttagcttcttttTTGTGTTGGAGAGATGAAAATGAAGc                                                                                                                  <  1:371094‑M2/26‑1 (MQ=255)
                        aaattgataatattgaagtgaatataaaataatcatgacattccttaaatagaagcggtcatcggaaaaacaagaagttaagtgacaacggcctacatgttgcttagcttcttttTTGTGTTGGAGAGATGAAAATGAAGc                                                                                                                  <  2:774311‑M2/26‑1 (MQ=255)
                         gTAGAAATATTGAAAAAATAGAAGCCAACATTAGATAATTCAATGAAATATGGATAATAGTAAAATATGGATAGTATAGAGGAGTTAGGCAACATAAGTTGCTTAGCTTCTTTTTTGTGTTGGAGAGATGAAAATGAAGCg                                                                                                                 <  1:17687/141‑1 (MQ=255)
                           ttgataacattgaagtgaatataaaataatcatgacattctctacatagaatctgtcatcggaaaaacaagaagttaagtgacaacggcctacatgttgcttagcttcttttTTGTGTTGGAGAGATGAAAATGAAGCGTa                                                                                                               >  1:416087‑M2/113‑141 (MQ=255)
                             gataacattgaagtgaatataaaataatcatgacattctctaaatagaagctgtcatcggaaaaacaagaagttaagtgacaacggcctacatgttgcttagcttcttttTTGTGTTGGAGAGATGAAAATGAAGCGTATc                                                                                                             >  1:83441‑M2/111‑141 (MQ=255)
                             gataacattgaagtgaatataaaataatcatgacattctctaaatagaagctgtcataggaaaaacaagaagttaagtgacaacggcctacaagttgcttagcttcttttTTGTGTTGGAGAGATGAAAATGAAGCGTata                                                                                                             >  2:143705‑M2/111‑140 (MQ=255)
                                 atTGAAAAAATAGAAGCCAACATTAGATAATTCAATGAAATATGGATAATAGTAAAATATGGATAGTATAGAGGAGTTAGGCAACATAAGTTGCTTAGCTTCTTTTTTGTGTTGGAGAGATGAAAATGAAGCGTATCGATg                                                                                                         >  2:243822/1‑141 (MQ=255)
                                   attgaagtgaatatagaatcatcatgacattctctaaatagaagctgtaatcggaaaaacacgaagtgaagtgagaacggcctacatgttacttagcttcttttTTGTGTTGGAGAGATGAAAATGAAGCATATCGATGaa                                                                                                       >  1:589322‑M2/105‑141 (MQ=255)
                                   attgaagtgaatataaaataatcatgacattctctaaatagaagctgtcatcggaaaaacaagaagttaagtgacaacggcctacatgttgcttagcttcttttTTGTGTTGGAGAGATGAAAATGAAGCGTATCGATGaa                                                                                                       >  2:664033‑M2/105‑141 (MQ=255)
                                      gaagtgaatataaaataatcatgacattctctaaatagaagctgtcatcggaaaaacaagaagttaagtgacaatggcctacatgttgcttagcttctttgTTGTGTTGGAGTGATGAAAATGAATCGTATCGATGaataa                                                                                                    >  2:717450‑M2/102‑141 (MQ=255)
                                      gaagtgaatataaaataatcatgacattctctaaatagaagctgtcatcggaaaaacaagaagttaagtgacaacggcctacatgttgcttagcttcttttTTGTGTTGGAGAGATGAAAATGAAGCTTATCGATGaataa                                                                                                    >  2:269383‑M2/102‑141 (MQ=255)
                                      gaagtgaatataaaataatcatgacattctctaaatagaagctgtcatcggaaaaacaagaagttaagtgacaacggcctacatgttgcttagcttcttttTTGTGTTGGAGAGATGAAAATGAAGCGTATCGATGaataa                                                                                                    <  1:428021‑M2/40‑1 (MQ=255)
                                       aaaaTAGAAGCCAACATTAGATAATTCAATGAAATATGGATAATAGTAAAATATGGATAGTATAGAGGAGTTAGGCAACATAAGTTGCTTAGCTTCTTTTTTGTGTTGGAGAGATGAAAATGAAGCGTATCGATGaataat                                                                                                   <  1:675577/141‑1 (MQ=255)
                                       aaaaTAGAAGCCAACATTAGATAATTCAATGAAATATGGATAATAGTAAAATATGGATAGTATAGAGGAGTTAGGCAACATAAGTTGCTTAGCTTCTTTTTTGTGTTGGAGAGATGAAAATGAAGCGTATCGATGaataat                                                                                                   <  1:608040/141‑1 (MQ=255)
                                              tataaaataatcatgacattctctaaatagaagctgtcatcggaaaaacaagaagttaagtgacaacggccgacatgttgcttagcttcttctTTGTGTTGGAGAGATGAAAATGAAGCGTATCGATGAATAATAAAAaca                                                                                            <  1:418145‑M2/48‑1 (MQ=255)
                                              aaGCCAACATTAGATAATTCAATGAAATATGGATAATAGTAAAATATGGATAGTATAGAGGAGTTAGGCAACATAAGTTGCTTAGCTTCTTTTTTGTGTTGGAGAGATGAAAATGAAGCGTATCGATGAATAATAAAAaca                                                                                            <  1:591490/141‑1 (MQ=255)
                                              aaGCCAAAATTAGATAATTCAATGAAATATGGATAATAGTAAAATATGGATAGTATAGAGGAGTTAGGCAACATAAGTTGCTTAGCTTCTTTTTTGTGTTGGAGAGATGTAAATGTAGCGTATCGATGAATAATAAAAaca                                                                                            <  2:219997/141‑1 (MQ=255)
                                                  aaataatcatgacattctctaaatagaagctgtcatcggaaaaacaagaagttaagtgacaacggcctacatgttgcttagcttcttttTTGTGTTGGCGAGATGAAAATGAAGCGTCTCGATGAATAATAAAAACACCaa                                                                                        >  2:618916‑M2/90‑141 (MQ=255)
                                                        tcatgacattctctaaatagaagctgtcatcggaaaaacaagaagttaagtgacaacggcctacatgttgcttagcttcttttTTGTGTTGGAGAGATGAAAATGAAGCGTATCGATGAATAATAAAAACACCAATAAAAc                                                                                  <  1:779656‑M2/58‑1 (MQ=255)
                                                        tAGATAATTCAATGAAATATGGATAATAGTAAAATATGGATAGTATAGAGGAGTTAGGCAACATAAGTTGCTTAGCTTCTTTTTTGTGTTGGAGAGATGAAAATGAAGCGTATCGATGAATAATAAAAACACCAATAAAAc                                                                                  >  2:46822/1‑141 (MQ=255)
                                                               attctctaaatagaagctgtcatcggaaaaacaagaagttaagtgacaacggcctacatgttgcttagcttcttttTTGTGTTGGAGAGATGAAAATGAAGCGTATCGATGAATAATAAAAACACCAATAAAACTTGTGGa                                                                           >  1:234296‑M2/77‑141 (MQ=255)
                                                                ttctctaaatagaagctgtcatcggaaaaacaagaagttaagtgacaacggcctacatgttgcttagcttcttttTTGTGTTGGAGAGATGAAAATGAAGCGTATCGATGAATAATAAAAACACCAATAAAACTTGTGGaa                                                                          >  2:327955‑M2/76‑141 (MQ=255)
                                                                 tctctaaatagaagctgtcatcggaaaaacaagaagttaagtgacaacggcctacatgttgcttagcttcttttTTGTGTTGGAGAGATGAAAATGAAGCGTATCGATGAATAATAAAAACACCAATAAAACTTGTGGaaa                                                                         <  2:778074‑M2/67‑1 (MQ=255)
                                                                        atagaagctgtcatcggaaaaacaagaagttaagtgacaacggcctacatgttgcttagcttcttttTTTTTTTTTTTTGATGAAAATGAAGCGTATCGATGATTAATAAAAATACCGATAAAACTTGTGGAAATAGTTGa                                                                  >  2:53523‑M2/68‑141 (MQ=255)
                                                                            aagctgtcatcggaaaaacaagaagttaagtgacaacggcctacatggtgcttagcttcttttTTGTGTTGGAGAGATGAAAATGAAGCGTATCGATGAATAATAAAAACACCAATAAAACTTGTGGAAATAGTTGATACt                                                              <  2:255177‑M2/78‑1 (MQ=255)
                                                                              ataataGTAAAATATGGATAGTATGGAGCAGTTAGGCAACATAAGTTGCTTAGCTTCTTTTTTGTGTTGGAGAGATGAAAATGAAGCGTATCGATGAATAATAAAAACACCAAGAAAACTTGTGGAAATAGTTGATACTta                                                            >  1:501451/1‑141 (MQ=255)
                                                                               taataGTAAAATATGGATAGTATAGAGGAGTTAGGCAACATAAGTTGCTTAGCTTCTTTTTTGTGTTGGAGAGATGAAAATGAAGCGTATCGATGAATAATAAAAACACCAATAAAACTTGTGGAAATAGTTGATACTtat                                                           <  2:208367/141‑1 (MQ=255)
                                                                                 ataGTAAAATATGGATAGTATAGAGGAGTTAGGCAACATAAGTTGCTTAGCTTCTTTTTTGTGTTGGAGAGATGAAAATGAAGCGTATCGATGAATAATAAAAACACCAGTAAAACTTGTGGAAATAGTTGATACTTATAg                                                         >  1:143708/1‑141 (MQ=255)
                                                                                   catcggaaaaacaagaagttaagtgacaacggcctacatgttgctgtgcttctcttCTGTTTAGGAGAGATGAAAATGAAGCATATCGCTGAAGCATAAAAACACCAATAAAACTTGTGGGAATAGTTGAtacttatcatc                                                       >  2:48817‑M2/57‑137 (MQ=255)
                                                                                      cggaaaaacaagaagttaagtgacaacggcctacatgttgcttagcttcttttTTGTGTTGGAGAGATGAAAATGAAGCGTATCGATGAATAATAAAAACACCAATAAAACTTGTGGAAATAGTTGATACTTATAGTcgcg                                                    >  2:687022‑M2/54‑141 (MQ=255)
                                                                                         atatGGATAGTATAGAGGAGTTAGGCAACATAAGTTGCTTAGCTTCTTTTTTGTGTTGGAGAGATGAAAATGAAGCGTATCGATGAATAATAAAAACACCAATAAAACTTGTGGAAATAGTTGATACTTATAGTCGCGCGt                                                 >  1:287749/1‑141 (MQ=255)
                                                                                               aagaagttaagtgacaacggcctacatgttgcttagcttcttttTTGTGTTGGAGAGATGAAAATGAAGCGTATCGATGAATAATAAAAACACCAATAAAACTTGTGGAAATAGTTGATACTTATAGTCGCGCGTTGTCCt                                           <  2:648011‑M2/97‑1 (MQ=255)
                                                                                                agaagttaagtgacaacggcctacatgttgcttagcttcttttTTGTGTTGTAGAGATGAAAATGAAGCGTATCGATGAATAATAAAAACACCAATAAAGCTTGTGGAAATAGTTGATACTTATAGTCGCGCGTTGTCCtt                                          >  1:541829‑M2/44‑141 (MQ=255)
                                                                                                agaagttaagtgacaacggcctacatgttgcttagcttcttttTTGTGTTGGAGAGATGAAAATGAAGCGTATCGATGAATAATAAAAACACCAATAAAACTTGTGGAAATAGTTGATACTTATAGTCGCGCGTTGTCCtt                                          >  1:247036‑M2/44‑141 (MQ=255)
                                                                                                agaagttaagtgacaacggcctacatgttgcttagcttcttttTTGTGTTGGAGAGATGAAAATGAAGCGTATCGATGAATAATAAAAACACCAATAAAACTTGTGGAAATAGTTGATACTTATAGTCGCGCGTTGTCCtt                                          >  1:246997‑M2/44‑141 (MQ=255)
                                                                                                  gTATAGGGGAGTTAGGCAACATAAGTTGCTTAGCTTCTTTTTTGTGTTGGAGAGATGAAAATGAAGCGTATCGATGAATAATAAAAACACCAATAAAACTTGTGGAAATAGTTGATACTTATAGTCGCGCGTTGTCCtctt                                        <  2:8290/141‑1 (MQ=255)
                                                                                                      agagGAGTTAGGCAACATAAGTTGCTTAGCTTCTTTTTTGTGTTGGAGAGATGAAAATGAAGCGTATCGATGAATAATAAAAACACCAATAAAACTTGTGGAAATAGTTGATACTTATAGTCGCGCGTTGTGCTGTTCGTg                                    >  1:100088/1‑141 (MQ=255)
                                                                                                           gacaacggcctacatgttgcttagcttcttttTTGTGTTGGAGAGATGAAAATGAAGCGTATCGATGAATAATAAAAACACCAATAAACCTTGTGGAAATAGTTGATACTTATAGTCGCGCGTTGTCCTTTTCGTGACATg                               <  2:311499‑M2/109‑1 (MQ=255)
                                                                                                            acaacggcctacatgttgcttagcttcttttTTGTGTTGGAGAGATGAAAATGAAGCGTATCGATGAATAATAAAAACACCAATAAAACTTGTGGAAATAGTTGATACTTATAGTCGCGCGTTGTCCTTTTCGTGACATGa                              <  2:644769‑M2/110‑1 (MQ=255)
                                                                                                              tAGGCAACATAAGTTGCTTAGCTTCTTTTTTTTTTTTTTTTCATGAAAATGAAGCGTATCGATGAATAATAAAGACACCAATAAAACTTGTGGAGATAGTTCATACTTATAAGGGCGCGTGGTCCTTTTCGTGACTTGaaa                            >  2:192392/1‑141 (MQ=255)
                                                                                                                ggCAACATAAGTTGCTTAGCTTCTTTTTTGTGTTGGAGAGATGAAAATGAAGCGTATCGATGAATAATAAAAACACCAATAAAACTTGTGGAAATAGTTGATACTTATAGTCGCGCGTTGTCCTTTTCGTGACATGAAACa                          >  1:13096/1‑141 (MQ=255)
                                                                                                                   cctacatgttgcttagcttcttttTTGTGTTGGAGAGATGAAAATGAAGCGTATCGATGAATAATAAAAACACCAATAAAACTTGTGGCAATAGTTGATACTTATAGTCGCGCGTTGTCCTTTTCGTGAACTGAAACAAtg                       >  2:313435‑M2/25‑141 (MQ=255)
                                                                                                                         aGTTGCTTAGCTTCTTTTTTTTTTTTTTTTGATGAAAATGAAGCGTATCGATGAATAATAAAAACACCAATAAAACTTGTGGAAATAGTTGATACTTATAGTCGCGCGTTGTCCTTTTCGTGACATGAAACAATGTGGaaa                 >  2:227830/1‑141 (MQ=37)
                                                                                                                                tagcttcttttTTGTGTTGGAGAGATGAAAATGAAGCGTATCGATGAATAATAAAAACACCAATAAAACTTGTGGAAATAGTTGATACTTATAGTCGCGCGTTGTCCTTTTCGTGACATGAAACAATGTGGAAAACATAGt          <  1:327955‑M2/130‑1 (MQ=255)
                                                                                                                                tagcgtcttttTTGTGTTGGAGAGATGAAAATGAAGCGTATCGAGGAATAATAAAAACACCAATAAAACTTGTGGAAATAGTTGATACTTATAGTCGCGCGTTGTCCTTTTCGTGACATGAAACAATGTGGAAAACATAGt          <  1:209024‑M2/130‑1 (MQ=255)
                                                                                                                                  gcttcttttTTGTGTTGGAGAGATGAAAATGAAGCGTATCGATGAATAATAAAAACACCAATAAAACTTGTGGAAATAGTTGATACTTATAGTCGCGCGTTGTCCTTTTCGTGACATGAAACAATGTGGAAAACATAGTTa        >  1:435586‑M2/10‑141 (MQ=255)
                                                                                                                                   cttcttttTTGAGTTGGAGAGATGAAAATGAAGCGTATCGATGAATAATAAAAACACCAATAAAACTTGTGGAAATAGTTGATAATTATAGTCGCGCGTTGTCCTTTTCGTGACATGAAACAATGTGGAAAACATAGTTaa       >  2:625156‑M2/9‑141 (MQ=255)
                                                                                                                                    ttcttttTTGTGTTGGAGAGATGAAAATGAAGCGTATCGATGAATAATAAAAACACCAATAAAACTTGTGGAAATAGTTGATACTTATAGTCGCGCGTTGTCCTTTTCGTGACATGAAACAATGTGGAAAACATAGTTaaa      >  1:345314‑M2/8‑141 (MQ=255)
                                                                                                                                       ttttTTGTGTTGGAGAGATGAAAATGAAGCGTATCGATGAATAATAAAAACACCAATAAAACTTGTGGAAATAGTTGATACTTATAGTCGCGCGTTGTCCTTTTCGTGACATGAAACAATGTGGAAAACATAGTTAAATTg   >  1:286334‑M2/5‑141 (MQ=255)
                                                                                                                                       ttttTTGTGTTGGAGAGATGAAAATGAAGCGTATCGATGAATAATAAAAACACCAATAAAACTTGTGGAAATAGTTGATACTTATAGTCGCGCGTTGTCCTTTTCGTGACATGAAACAATGTGGAAAACATAGTTAAATTg   >  1:362347‑M2/5‑141 (MQ=255)
                                                                                                                                       ttttTTGTGTTGGAGAGATGAAAATGAAGCGTATCGATGAATAATAAAAACACCAATAAAACTTGTGGAAATAGTTGATACTTATAGTCGCGCGTTGTCCTTTTCGTGACATGAAACAATGTGGAAAACATAGTTAAATTg   >  1:286322‑M2/5‑141 (MQ=255)
                                                                                                                                       ttttGTGTGTTGGAGAGATGAAAATGAAGCGTATCGATGAATAATAAAAACACCAATAAAACTTGTGGAAATAGTTGATACTTATAGTCGCGCGTTGTCCTTTTCGTGACATGAAACAATGTGGAAAACATAGTTAAATTg   <  1:487584‑M2/137‑1 (MQ=255)
                                                                                                                                        tttTTGTGTTGGAGAGATGAAAATGAAGCGTATCGATGAATAATAAAAACACCAATAAAACTTGTGGAAATAGTTGATACTTATAGTCGCGCGTTGTCCTTTTCGTGACATGAAACACTGTGGGAAACATAGTTAAATTGa  >  2:396471‑M2/4‑141 (MQ=255)
                                                                                                                                           |                                                                                                                                         
AATCGCATGAGTGACGTCATTGACGGTAGAAATATTGAAAAAATAGAAGCCAACATTAGATAATTCAATGAAATATGGATAATAGTAAAATATGGATAGTATAGAGGAGTTAGGCAACATAAGTTGCTTAGCTTCTTTTTTGTGTTGGAGAGATGAAAATGAAGCGTATCGATGAATAATAAAAACACCAATAAAACTTGTGGAAATAGTTGATACTTATAGTCGCGCGTTGTCCTTTTCGTGACATGAAACAATGTGGAAAACATAGTTAAATTGA  >  CP000730/451639‑451915

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 32 ≤ 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.