New junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? USA300TCH1516_ALE 2679952 =329 (0.900)6 (0.020) 5/230 NT 2.2% intergenic (+4/+756) ssaA2_4/USA300HOU_RS13810 Staphylococcal secretory antigen ssaA2/hypothetical protein
?USA300TCH1516_ALE 2680007 = 245 (0.760)intergenic (+59/+701) ssaA2_4/USA300HOU_RS13810 Staphylococcal secretory antigen ssaA2/hypothetical protein
Rejected: Frequency below/above cutoff threshold.

Only 100 of 396 total aligned reads displayed.

GACATGTCGCAGTTGTTGAACAAGTATATAAAAACGGTAGTATTAAAGTTTCAGAATACAACTTTTATCGCCCATTAAAATACAATACACGTGTACTAAGCAAAAAGGCAGCACGTAACTTTAACTATATTTACTAATCAAAAAACTTCTATCACGAACGCTTCAATTTCCTGTATGCGTGTGATAGAAGTTTTTATTTTATGAAATTATATTATTACTTCTACAAATTTCAAATTGCCGTAATTGAACGTATATTTCTTCTTCAACTATTATTTCATCTT  >  USA300TCH1516_ALE/2679812‑2680092
                                                                                                                                            |                                                                                                                                            
gagaTGTCGCAGTTGTTGAACAAGTATATAAAAACGGTAGTATTAAAGTTTCACAATACAACTTTTATCGCCCATTAAAATACAATACACGTGTACTAAGCAAAAAGGCAGCACGTAACTTTAACTATATTTACTAATCaa                                                                                                                                              <  1:2151432/138‑1 (MQ=255)
gACATGTCGCAGTTGTTGAACAAGTATATAAAAACGGTAGTATTAAAGTTTCAGAATACAACTTTTATGGCCCATTAAAATACAATACACGTGTACTAAGCAAAAAGGCAGCACGTAACTTTAACTATATTTACTAATCaa                                                                                                                                              >  1:3155216/1‑141 (MQ=255)
gACATGTCGCAGTTGTTGAACAAGTATATAAAAACGGTAGTATTAAAGTTTCAGAATACAACTTTTATCGCCCATTAAAATACAATACACGTGTACTAAGCAAAAAGGCAGCACGTAACTTTAACTATATTTACTAATCaa                                                                                                                                              >  2:3723136/1‑141 (MQ=255)
  cATGTCGCAGTTGTTGAACAAGTATATAAAAACGGTAGTATTAAAGTTTCAGAATACAACTTTTATCGCCCATTAAAATACAATACACGTGTACTAAGCAAAAATGCAGCACGTAACTTTAACTATATTTACCAATCaaaa                                                                                                                                            >  2:631182/1‑141 (MQ=255)
    tagcgaattatttaaataatagcataaaattttatatatagattatgctaaagatgaaataataattgaaaaaaaaatatacgttcaattacggcaatttgaaatttgtagaagtaataatataatttcataaaataaaaa                                                                                                                                          <  2:3828780‑M1/5‑1 (MQ=255)
     atcgaattatttaaatactagcataaaattttatatatagattatgctaaagatgaaataatatttgaagaagaaatatacgttcaattatggcaatttgaaatttttagaagtaataatatattctcataatatAAAAAc                                                                                                                                         <  2:3352550‑M1/6‑1 (MQ=255)
       cgaattatttaaataatagcataaaattttatatatagattatgctaaagatgaaataatagttgaagaagaaatatacgttcaattacggcaatttgaaatttgtagaagtaataatataatttcataaaatAAAAACtt                                                                                                                                       <  2:1840725‑M1/8‑1 (MQ=255)
        gaattatttaaataatagcataaaattttatatatagattatgctaaagatgaaataatagttgaagaagaaatatacgttcaattacggcaatttgaaatttgtagaagtaataatataatgacaaaaaagaaaacatac                                                                                                                                      <  2:4009705‑M1/9‑6 (MQ=255)
         aattatttaaataatagcataaaattttatatatagattatgctaaagatgaaataatagttgaagaagaaatatacgttcaattacggcaatttgaaatttgtagaagtaataatataatttcataaaatAAAAACTTCt                                                                                                                                     <  2:2875745‑M1/10‑1 (MQ=255)
          attatttaaataatagcataaaattttatatatagattatgctaaagatgaaataatagttgaagaagaaatatacgttcaattacggcaatttgaaatttgtaggagtaataatataatttcataaaatAAAAACTTCTa                                                                                                                                    <  2:4114678‑M1/11‑1 (MQ=255)
          aGTTGTTGAACAAGTATATAAAAACGGTAGTATTAAAGTTTCAGAATACAACTTTTATCGCCCATTAAAATACAATACACGTGTACTAAGCAAAAAGGCAGCACGTAACTTTAACTATATTTACTAATCAAAAAACTTCTa                                                                                                                                    >  1:3464835/1‑141 (MQ=255)
            ttgttgAACAAGTATATAAAAACGGTAGTATTAAAGTTTCAGAATACAACTTTTATCGCCCATTAAAATACAATACACGTGTACTAAGCAAAAAGGCAGCACGTAACTTTAACTATATTTACTAATCAAAAAACTTCTATc                                                                                                                                  <  1:1425525/141‑1 (MQ=255)
             tgttgAACAAGTATATAAAAACGGTAGTATTAAAGTTTCAGAATACAACTTTTATCGCCCATTAAAATACAATACACGTGTACTAAGCAAAAAGGCAGCACGTAACTTTAACTATATTTACTAATCAAAAAACTTCTATCa                                                                                                                                 <  2:3569687/141‑1 (MQ=255)
              tttaaataatagcataaaattttatatatagattatgctaaagatgaaataatagttgaagaagaaatatacgttcaattacggcaatttgaaatttgtagaagtaataatataatttcataaaatAAAAACTTCTATcaa                                                                                                                                <  2:3233018‑M1/15‑2 (MQ=255)
                tgAACAAGTATATAAAAACGGTAGTATTAAAGTTTCAGAATACAACTTTTATCGCCCATTAAAATACAATACACGTGTACTAAGCAAAAAGGCGGCACGTAACTTTAACTATATTTACTAATCAAAAAACTTCTATCACGa                                                                                                                              >  1:3198671/1‑141 (MQ=255)
                  aaCAAGTATATAAAAACGGTAGTATTAAAGTTTCAGAATACAACTTTTATCGCCCATTAAAATACAATACACGTGTACTAAGCAAAAAGGCAGCACGTAACTTTAACTATATTTACTAATCAAAAAACTTCTATCACGaaa                                                                                                                            >  2:2224546/1‑140 (MQ=255)
                    cAAGTATATAAAAACGGTAGTATTAAAGTTTCAGAATCCAACGTCGATCGCCCATTAAAATACAATACACGTGTACTAAGCAAAAAGGCAGCACGTAACTTTAACTATATTTACTAATCAAAAAACTTCTATCACGAACGc                                                                                                                          <  1:823126/141‑1 (MQ=255)
                     caGTATATAAAAACGGTAGTATTAAAGTTTCAGAATATTGGTTTTAACACCCATTAAAATACAATACACGTGTACTAAGCAAAAAGGCAGCACGTAACTTTAACTATATTTACTAATCAAAAAACTTCTATCACGAACGCt                                                                                                                         <  2:929573/140‑1 (MQ=39)
                      gcgatataAAAACGGTAGTATTAAAATTTCAGAATACAACTTTTATCGCCCATTAAAATACAATACAAGTGTACTAAGCAAAAAGGCAGCACGTAACTTTAACTATATTTACTAATCAAAAAACTTCTATCACGAACGCtt                                                                                                                        <  2:464188/138‑1 (MQ=255)
                      aGTATATAAAAACGGTAGTATTAAAGTTTCAGAATACAACTTTTATCGCCCATTAAAATACAATACACGTGTACTAAGCAAAAAGGCAGCACGTAACTTTAACTATATTTACTAATCAAAAAACTTCTATCACGAACGCtt                                                                                                                        <  1:893728/141‑1 (MQ=255)
                      aGTATATAAAAACGGTAGTATTAAAGTTTCAGAATACAACTTTTATCGCCCATTAAAATACAATACACGTGTACTAAGCAAAAAGGCAGCACGTAACTTTAACTATATTTACTAATCAAAAAACTTCTATCACGAACGCtt                                                                                                                        <  1:2349542/141‑1 (MQ=255)
                       gTATATAAAAACGGTAGTATTAAAGTTTCAGAATACAACTTTTATCGCCCATTAAAATACAATACACGTGTACTAAGCAAAAAGGCAGCACGTAACTTTAACTATATTTACTAATCAAAAAACTTc                                                                                                                                      <  1:2284231/126‑1 (MQ=255)
                       gTATATAAAAACGGTAGTATTAAAGTTTCAGAATACAACTTTTATCGCCCATTAAAATACAATACACGTGTACTAAGCAAAAAGGCAGCACGTAACTTTAACTATATTTACTAATCAAAAAACTTc                                                                                                                                      >  2:2284231/1‑126 (MQ=255)
                       gTATATAAAAACGGTAGTATTAAAGTTTCAGAATACAACTTTTATCGACACTTAAGGAACAATACATGCGTACTAAGCAAAAAGGCAGCACGTAACTTTAACTATATTTACTAATCAAAAAACTTCTATCACGAACGCTTc                                                                                                                       <  1:1229394/141‑1 (MQ=38)
                       gTATAGAAAAACGGTAGTATTAAAGTTACAGAATGCAACATATATCGACCATTAAAATACAATACACGAGAAAAAAGCAAAAAGGCAGCACGTAACTTTAACTATATTTACTAATCAAAAAACTTCTATCACGAACGCTTc                                                                                                                       <  2:1105081/141‑1 (MQ=38)
                          tataAAAACGGTAGTATTAAAGTTTCAGAATACAACTTTTATCGCCCACTAAAATACAATACACGTGTACTAAGCAAAAAGGCAGCACGTAACTTTAACTATATTTACTAATCAAAAAACTTCTATCACGAACGCTTCAAt                                                                                                                    <  1:4362842/141‑1 (MQ=255)
                            taAAAACGGTAGTATTAAAGTTTCAGAATACAACTTTTATCGCCCATTAAAATACAATACACGTGTACTAAGCAAAAAGGCAGCACGTAACTTTAACTATATTTACTAATCAAAAAACTTCTATCACGAACGCTTCAAttt                                                                                                                  >  1:4114678/1‑141 (MQ=255)
                            aaaaaaCGGTAGTATTAAAGTTTCAGAATACAACTTTTATCGCCCATTAAAATACATTTGTCGTCCACTAAGCAAAAAGGCAGCACGTAACTTTAACTATATTTACTAATCAAAAAACTTCTATCACGAACGCTTCAAttt                                                                                                                  <  1:1026979/140‑1 (MQ=38)
                             aaaaaCGGTAGTATTAAAGTTTAAGAATACAACTTTTATCGCCCATTAAAATACAATACACGTGTACTAAGCAAAAAGGCAGCACGTAACTTTAACTATATTTACTAATCAAAAAACTTCTATCACGAACGCTTCAATTTc                                                                                                                 <  2:1639165/141‑1 (MQ=255)
                              aaaaCGGTAGTATTACAGTTTCAGCATACAACTTTTATCGCCCATTAAAATACAATACACGTGTACTAAGCAAAAAGGCAGCACGTAACTCTAACTATACTTACTAATCAACAAACTACTATCACGAACCCTTCAATCTcc                                                                                                                >  2:51953/1‑141 (MQ=255)
                              aaaaCGGTAGTATTAAAGTTTCAGAATACAACTTTTATCGCCCATTAAAATACAATACACGTGTACTAAGCAAAAAGGCAGCACGTAACTTTAACTATATTTACTAATCAAAAAACTTCTATCACGAACGCTTCAATTTcc                                                                                                                >  1:3703313/1‑141 (MQ=255)
                              aaaaCGGTAGTATTAAAGTTTCAGAATACAACTTTTATCGCCCATTAAAATACAATACACGTGTACTAAGCAAAAAGGCAGCACGTAACTTTAACTATATTTACTAATCAAAAAACTTCTATCACGAACGCTTCAATTTcc                                                                                                                <  2:2535709/141‑1 (MQ=255)
                              aaaaCGGTAGGATGAAATTTTCAGAATACAACTTTTAATGCCCATTAAAATACAATACACTTGTACTAAGCAAAAAGGCAGCACGTAACTTTAACTATAGTTACGAATCAAAAAACTTCTATCACGAACGCTTCAATTTcc                                                                                                                <  1:4401417/141‑1 (MQ=38)
                              aaaaAGTTAGTATTAAAGTTTCAGAATACAACTTTTATCGCCCATTAAAATACAATACACGTGTACTAAGCAAAAAGGCAGCACGTAACTTTAACTATATTTACTAATCAAAAAACTTCTATCACGAACGCTTCAATTTcc                                                                                                                <  2:300874/141‑1 (MQ=255)
                                 aCGGTAGTATTAAAGTTTCAGAATACAACTTTTATCGCCCATTAAAATACAATACACGTGTACTAAGCAAAAAGGCAGCACGTAACTTTAACTATATTTACTAATCAAAAAACTTCTATCACGAACGCTTCAATTTCCTGt                                                                                                             <  1:531305/141‑1 (MQ=255)
                                  cGGTAGTATTAAAGTTTCAGAATACAACTTTTATCGCCCATTAAAATACAATACACGTGTACTAAGCAAAAAGGCAGCACGTAACTTTAACTATATTTACTAATCAAAAAACTTCTATCACGAACGCTTCAATTTCCTGTa                                                                                                            >  1:4183839/1‑141 (MQ=255)
                                       gtaTTAAAGTTTCAGAATACAACTTTTATCGCCCATTAAAATACAATACACGTGTACTAAGCAAAAAGGCAGCACGTAACTTTAACTATATTTACTAATCAAAAAACTTCTATCACGAACGCTTCAATTTCCTGTATGCgt                                                                                                       <  2:306383/141‑1 (MQ=255)
                                       gtaTTAAAGTTTCAGAATACAACTTTTATCGCCCATTAAAATACAATACACGTGTACTAAGCAAAAAGGCAGCACGTAACTTTAACTATATTTACTAATCAAAAAACTTCTATCACGAACGCTTCAATTTCCTGTATGCgt                                                                                                       <  2:2933498/141‑1 (MQ=255)
                                         aTTAAAGTTTCAGAATACAACTTTTATCGCCCATTAAAATACAATACACGTGTACTAAGCAAAAAGGCAGCACGTAACTTTAACTATATTTACTAATCAAAAAACTTCTATCACGAACGCTTCAATTTCCTGTATGCgtgt                                                                                                     <  1:2569338/141‑1 (MQ=255)
                                            aaaGTTTCAGAATACAACTTTTATCGCCCATTAAAATACAATACACGTGTACTAAGCAAAAAGGCAGCACGTAACTTTAACTATATTTACTAATCAAAAAACTTCTATCACAAACGCTTCAATTACCTGTATGCGTGTCAt                                                                                                  >  2:8269/1‑141 (MQ=255)
                                              aGTTTCAGAATACAACTTTTATCGCCCATTAAAATACAATACACGTGTACTAAGCAAAAAGGCAGCACGTAACTTTAACTATATTTACTAATCAAAAAACTTCTATCACGAACGCTTCAATTTCCTGTATGCGTGTGATAg                                                                                                <  1:3094231/141‑1 (MQ=255)
                                              aGTTTCAGAATACAACTTTTATCGCCCATTAAAATACAATACACGTGTACTAAGCAAAAAGGCAGCACGTAACTTTAACTATACTTACTAATCAAAAAACTTCTATCACGAACGCTTCAATTTCCTGTATGCGTGTGATAg                                                                                                <  1:495291/141‑1 (MQ=255)
                                                 ttCAGAATACAACTTTTATCGCCCATTAAAATACAATACACGTGTACTAAGCAAAAAGGCAGCACGTAACTTTAACTATATTTACTAATCAAAAAACTTCTATCACGCACGCTTCAATATCCTGTATCCGTGAGATAGaaa                                                                                             >  2:1059412/1‑140 (MQ=255)
                                                  tCAGAATACAACTTTTATCGCCCATTAAAATAAAATACACGTGTACTAAGCAAAAAGGCAGCACGTAACTTTAACTATATTTACTAATCAAAAAACTTCTATCACGAACGCTTCAATTTCCTGTATGCGTGTGATAGAAGt                                                                                            <  1:3819490/141‑1 (MQ=255)
                                                   cAGAATACAACTTTTATCGCCCATTAAAATACAATACACGTGTACTAAGCAAAAAGGCAGCACGTAACTTTAACTATATTTACTAATCAAAAAACTTCTATCACGAACGCTTCAATTTCCTGTATGCGTGTGATAGAAGtt                                                                                           >  1:637986/1‑141 (MQ=255)
                                                   aaGAATACAACTTTTATCGCCCATTAAAATAAAATACACGTGTACTAAGCAAAAAGGCAGCACGTAACTTTAACTATATTTACTAATCAAAAAACTTCTATCACGAACGCTTCAATTTCCTGTATGCGTGTGATAGAAGtt                                                                                           <  2:134807/140‑1 (MQ=255)
                                                      aaTACAACTTTTATCGCCCATTAAAATACAATACACGTGTACTAAGCAAAAAGGCAGCACGTAACTTTAACTATATTTACTAATCAAAAAACTTCTATCACGAACGCTTCAATTTCCTGTATGCGTGTGATAGAAGttttt                                                                                        <  2:3444497/141‑1 (MQ=255)
                                                       aTACAACTTTTATCGCCCATTAAAATACAATACACGTGTACTAAGCAAAAAGGCAGCACGTAACTTTAACTATATTTACTAATCAAAAAACTTCTATCACGAACGCTTCAATTTCCTGTATACGAGTGATAGAAGTtttta                                                                                       >  2:4177202/1‑141 (MQ=255)
                                                         aCAACTTTTATCGCCCATTAAAATACAATACACGTGTACTAAGCAAAAAGGCAGCACGTAACTTTAACTATATTTACTAATCAAAAAACTTCTATCACGAACGCTTCAATTTCCTGTATGCGTGTGATAGAAGTttttatt                                                                                     >  1:3267845/1‑141 (MQ=255)
                                                             cTTTTATCGCCCATTAAAATACAATACACGTGTACTAAGCAAAAAGGCAGCACGTAACTTTAACTATATTTACTAATCAAAAAACTTCTATCACGAACGCTTCAATTTCCTGTATGCGTGTGATAGAAGTTtttattttat                                                                                 <  1:2958845/141‑1 (MQ=255)
                                                             cTTTTATCGCCCATTAAAATACAATACACGTGTACTAAGCAAAAAGGCAGCACGTAACTTTAACTATATTTACTAATCAAAAAACTTCTATCACGAACGCTTCAATTTCCTGTATGCGTGTGATAGAAGTTtttattttat                                                                                 >  2:2106958/1‑141 (MQ=255)
                                                              tgttATCGCCCATTAAAATACAATACACGTGTACTAAGCAAAAAGGCAGCAGTTAACTTTAACTATATTTACTAATCAAAAAACTTCTAACACGAACGCTTCAATTTCCTGTATGCGTGTGATAGAAGTTTTTATTTTATg                                                                                <  2:3087357/139‑1 (MQ=255)
                                                               tttATCGCCCATTAAAATACAATACACGTGTACTAAGCAAAAAGGCAGCACGTAACTTTAACTATATTTACTAATCAAAAAACTTCTATCACGAACGCTTCAATTTCCTGTATGCGTGTGATAGAAGTTTTTATTTTATGa                                                                               <  1:2011582/141‑1 (MQ=255)
                                                               ttaaTCGCCAATTAAAATACAATACACGTTTAATAAGCAAAAAGGCAGCACGTAACTTTAACTATATTTACTAATCAAAAAACTTCTATCACGAACGCTTCAATTTCCTGTATGCGTGTGATAGAAGTTTTTATTTTATGa                                                                               <  2:1720222/138‑1 (MQ=255)
                                                                  aTCGCCCATTAAAATACAATACACGGGTACTAAGCAAAAAGGCAGCACGTAACTTTAACTATATTTACTAATCAAAAAACTTCTATCACGAACGCTTCAATTTGCTGGATGCGTGTGATAGAAGTTTTTATTTTATGAAat                                                                            <  1:1150166/141‑1 (MQ=255)
                                                                   tCGCCCATTAAAATACAATACACGTGTACTAAGCAAAAAGGCAGCACGTAACTTTAACTATATTTACTAATCAAAAAACTTCTATCACGAACGCTTCAATTTCCTGTATGCGTGTGATAGAAGTTTTTATTTTATGAAatt                                                                           >  1:712020/1‑141 (MQ=255)
                                                                    cGCCCATTAAAATACAATACACGTGTACTAAGCAAAAAGGCAGCACGTAACTTTAACTATATTTACTAATCAAAAAACTTCTATCACGAACGCTTCAATTTCCTGTATGCGTGTGATAGAAGTTTTTATTTTATGAAatta                                                                          <  1:940927/141‑1 (MQ=255)
                                                                       ccATTAAAATACAATACACGTGTACTAAGCAAAAAGGCAGCACGTAACTTTAACTATATTTACTAATCAAAAAACTTCTATCACGATCGCTTCAATTTCCTGTATGCGTGTGATAGAAGTTTTTATTTTATGAAattatat                                                                       <  2:2334260/141‑1 (MQ=255)
                                                                        cATTAAAATACAATACACGTGTACTAAGCAAAAAGGCAGCACGTAACTTTAACTATATTTCCTCGCTGGCTTGCTTCTATCACGAACGCTTCAATTTCCTGTATGCGTGTGATAGAAGTTTTTATTTTATGAAattatatt                                                                      <  1:2086225/141‑1 (MQ=21)
                                                                               atacaatacaCGTGTACTAAGCAAAAAGGCAGCACGTAACTTTAACTATATTTACTAATCAAAAAACTTCTATCACGAACGCTTCAATTTCCTGTATGCGTGTGATAGAAGTTTTTATTTTATGAAATTATATTATTACtt                                                               >  1:2609661/1‑141 (MQ=255)
                                                                                 acaatacaCGTGTACTAAGCAAAAAGGCAGCACGTAACTTTAACTATATTTACTAATCAAAAAACTTCTATCACGAACGCTTCAATTTCATGTATGCGTGTGATAGAAGTTTTTATTTTATGAAATTATATTATTtcttct                                                             >  2:1215038/1‑141 (MQ=255)
                                                                                 acaatacaCGTGTACTAAGCAAAAAGGCAGCACGTAACTTTAACTATATCTACTAATCAAAAAACTTCTATCACGAACGCTTCAATTTCCTGTATGCGTGTGATAGAAGTTTTTATTTTATGAAATTATATTATTACTTCt                                                             <  1:392505/141‑1 (MQ=255)
                                                                                         cGTGTACTAAGCAAAAAGGCAGCACGTAACTTTAACTATATTTACTAATCAAAAAACTTCTCTCACGAACGCTTCAATTTCCTGTATGCGTGTGATAGAAGTTTTTATTTTATGAAATTCTATTATTGCTTCTACAAAttt                                                     >  2:102237/1‑141 (MQ=255)
                                                                                         cGTGTACTAAGCAAAAAGGCAGCACGTAACTTTAACTATATTTACTAATCAAAAAACTTCTATCACGAACGCTTCAATTTCCTGTATGCGTGTGATAGAAGTTTTTATTTTATGAAATTATATTATTACTTCTACAAAttt                                                     <  1:2492284/141‑1 (MQ=255)
                                                                                         cGTGTACTAAGCAAAAAGGCAGCACGTAACTTTAACTATATTTACTAATCAAAAAACTTCTATCACGAACGCTTCAATTTCCTGTATGCGTGTGATAGAAGTTTTTATTTTATGAAATTATATTATTACTTCTACAAAttt                                                     >  1:2745835/1‑141 (MQ=255)
                                                                                          gtgtACTAAGCAAAAAGGCAGCACGTAACTTTAACTATATTTACTAATCAAAAAACTTCTATCACGATCGCTTCAATTTCCTGTATGCGTGTGATAGAAGTTTTTATTTTATGAAATTATATTATTACTTCTACAAATTTc                                                    <  2:2055736/141‑1 (MQ=255)
                                                                                              aCTAATCAAAAAGGCAGCACGTAACTTTAACTATATTTACTAATCAAAAAACTTCTATCACGAACGCTTCAATTTCCTGTATGCGTGTGATAGAAGTTTTTATTTTATGAAATTATATTATTACTTCTACAAATTTCAAAt                                                <  2:3155216/141‑1 (MQ=255)
                                                                                                 aaGCAAAAAGGCAGCACGTAACTTTAACTATATTTACTAATCAACAAACTTCTATCCCGAACGCTTCAATTTCCTGGATGCGCGTGACAGCAGTATTGCGTTTATGAAATGATATTCTTACTTTTACAGATTTCCAGTTGc                                             >  1:163191/1‑141 (MQ=21)
                                                                                                   gCAAAAAGGCAGCACGTAACTTTAACTATATTTACTAATCAAAAAACTTCTATCACGAACGCTTCAATTTCCTGTATGCGTGTGATAGAAGTTTTTATTTTATGAAATTATATTATTACTTATACAAATTTCACATTGcct                                           >  2:2751924/1‑140 (MQ=255)
                                                                                                    cAAAAAGGCAGCACGTAACTTTAACTATATTTACTAATCAAAAAACTTCTATCACGAACGCTTCAATTTCCTGTATGCGTGTGATAGAAGTTTTTATTTTATGAAATTATATTATTACTTCTACAAATTTCAAATTGCCGt                                          <  2:3505043/141‑1 (MQ=255)
                                                                                                      aaaaGGCAGCACGTAACTTTAACTATATTTACTAATCAAAAAACTTCTATCACGAACGCTTCAATTTCCTGTATGCGTGTGATAGAAGTTTTTATTTTATGAAATTATATTATTACTTCTACAAATTTCAAATTGCCGTaa                                        <  2:1998029/141‑1 (MQ=255)
                                                                                                        aaGGCAGCACGTAACTTTAACTATATTTACTAATCAAAAAACTTCTATCACGAACGCTTCAATTTCCTGTATGCGTGTGATAGAAGTTTTTATTTTATGAAATTATATTATTACTTCTACAAATTTCAAATTGCCGTAAtt                                      >  2:1458438/1‑141 (MQ=255)
                                                                                                        aaGGCAGCACGTAACTTTAACTATATTTACTAATCAAAAAACTTCTATCACGAACGCTTCAATTTCCTGTATGCGTGTGATAGAAGTTTTTATTTTATGAAATTATATTATTACTTCTACAAATTTCAAATTGCCGTAAtt                                      >  1:2854437/1‑141 (MQ=255)
                                                                                                         aGGCAGCACGTAACTTTAACTATATTTACTAATCAAAAAACTTCTATCACGAACGCTTCAATTTCCTGTATGCGTGTGATAGAAGTTTTTATTTTATGAAATTATATTATTACTTCTACAAATTTCAAATTGCCGTAATTg                                     >  1:1990139/1‑141 (MQ=255)
                                                                                                            cagcaCGTAACTTTAACTAAATTTACTAATCAAAAAACTTCTATCACGAACGCTTCAATTTCCTGTATGCGTGTGATAGAAGTTTTTATTTTATGAAATTATATTCTTACTTCTACAACTTTCAAATTGCCGTAATTGAAc                                  <  1:2461267/141‑1 (MQ=255)
                                                                                                              gcaCGTAACTTTAACTATATTTACTAATCAAAAAACTTCTATCACGAACGCTTCAATTTCCTGTATGCGTGTGATAGAAGTTTTTATTTTATGAAATTATATTATTACTTCTACAAATTTCAAATTGACGTAATTGAACGt                                >  1:2683600/1‑141 (MQ=255)
                                                                                                               caCGTAACTTTAACTATATTTACTAATCAAAAAACTTCTATCACGAACGCTTCAATTTCCTGTATGCGTGTGATAGAAGTTTTTATTTTATGAAATTATATTATTACTTCTCCTTATTTCAAATTGCCGTAATTGAACGta                               <  1:3051262/141‑1 (MQ=255)
                                                                                                               caCGTAACTTTAACTATATTTACTAATCAAAAAACTTCTATCACGAACGCTTCAATTTCCTGTATGCGTGTGATAGAAGTTTTTATTTTATGAAATTATATTATTACTTCTACAAATTTCAAATTGCCGTAATTGAACGta                               <  1:1086751/141‑1 (MQ=255)
                                                                                                               caCGTAACTTTAACTATATTTACTAATCAAAAAACTTCTATCACGAACGCTTCAATTTCCTGTATGCGTGTGATAGAAGTTTTTATTTTATGAAATTATATTATTACTTCTACAAATTTCAAATTGCCGTAATTGAACGta                               <  1:2829020/141‑1 (MQ=255)
                                                                                                                    aaCTTTAACTATATTTACTAATCAAAAAACTTCTATCACGAACGCTTCAATTTCCTGTATGCGTGTGATAGAAGTTTTTATTTTATGAAATTATATTATTACTTCTACAAATTTCAATTTGCCGTAATTGAACGTATAttt                          >  2:2665082/1‑141 (MQ=255)
                                                                                                                    aaCTTTAACTATATTTACTAATCAAAAAACTTCTATCACGAACGCTTCAATTTCCTGTATGCGTGTGATAGAAGTTTTTATTTTATGAAATTATATTATTACTTCTACAAATTTCAAATTGCCGTAATTGAACGTATAttt                          >  1:1864527/1‑141 (MQ=255)
                                                                                                                     aCTTTAACTATATTTACTAATCAAAAAACTTCTATCACGAACGCTTCAATTTCCTGTATGCGTGTGATAGAAGTTTTTATTTTATGAAATTATATTATTACTTCTACAAATTTCAAATTGCCGTAATTGAACGTATATttc                         <  1:3616260/141‑1 (MQ=255)
                                                                                                                      cTTTAACTATATTTACTAATCAAAAAACTTCTATCACGAACGCTTCAATTTCCTGTATGCGTGTGATAGAAGTTTTTATTTTATGAAATTATATTATTACTTCTACAAATTTCAAATTGCCGTAATTGAACGTATATttct                        >  2:1280070/1‑141 (MQ=255)
                                                                                                                      cTTTAACTATATTTACTAATCAAAAAACTTCTATCACGAACGCTTCAATTTCCTGTATGCGTGTGATAGAAGTTTTTATTTTATGAAATTATATTATTACTTCTACAAATTTCAAATTGCCGTAATTGAACGTATATttct                        >  1:1514892/1‑141 (MQ=255)
                                                                                                                         tAACTATATTTACTAATCAAAAAACTTCTATCACGAACGCTTCAATTTCCTGTATGCGTGTGATAGAAGTTTTTATTTTATGAAATTATATTATTACTTCTACAAATTTCAAATTGCCGTAATTGAACGTATATttcttct                     <  1:2217821/141‑1 (MQ=255)
                                                                                                                                    aCTAATCAAAAAACTTCTATCACGAACGCTTCAATTTCCTGTATGCGTGTGATAGAAGTTTTTATTTTGTGAAATTATATTATTACTTCTACAAATTTCAAATTGCCATAATTGAACGTATATTTCTTCTTCAACtattat          >  2:588751/1‑141 (MQ=255)
                                                                                                                                     cTAATCAAAAAACTTCTATCACGCACGCTTCAATTTCCTGTATGCGTGTGATAGAAGTTTTTATTTTATGAAATTATATTATTACTTCTACAAATTTCAAATTGCCGTAATTGAACGTATATTTCTTCTTCAACTattatt         <  1:131263/141‑1 (MQ=255)
                                                                                                                                     cTAATCAAAAAACTTCTATCACGAACGCTTCAGTTTCCTGTATGCGTGTGATAGAAGTTTTTATTTTATGAAATTATATTATTACTTCTACAAATTTCAAATTGCCGTAATTGAACGTATATTTCTTCTTCAACTattatt         >  2:3924239/1‑141 (MQ=255)
                                                                                                                                     cTAATCAAAAAACTTCTATCACGAACGCTTCAATTTCCTGTATGCGTGTGATAGAAGTTTTTATTTTATGAAATTATATTATTACTTCTACAAATTTCAAATTGCCGTAATTGAACGTATATTTCTTCTTCAACTattatt         >  2:4281602/1‑141 (MQ=255)
                                                                                                                                     cTAATCAAAAAACTTCTATCACGAACGCTTCAATTTCCTGTATGCGTGTGATAGAAGTTTTTATTTTATGAAATTATATTATTACTTCTACAAATTTCAAATTGCCGTAATTGAACGTATATTTCTTCTTCAACTattatt         >  2:2817723/1‑141 (MQ=255)
                                                                                                                                     cTAATCAAAAAACTTCTATCACGAACGCTTCAATTTCCTGTATGCGTGTGATAGAAGTTTTTATTTTATGAAATTATATTATTACTTCTACAAATTTCAAATTGCCGTAATTGAACGTATATTTCTTCTTCAACTattatt         <  1:4054447/141‑1 (MQ=255)
                                                                                                                                     cTAATCAAAAAACTTCTATCACGAACGCTTCAATTTCCTGTATGCGTGTGATAGAAGTTTTTATTTTATGAAATTATATTATTACTTCTACAAATTTCAAATTGCCGTAATTGAACGTATATTTCTTCTTCAACTattatt         <  1:577103/141‑1 (MQ=255)
                                                                                                                                     cTAATCAAAAAACTTCTATCACGAACGCTTCAATTTCCTGTATGCGTGTGATAGAAGTTTTTATTTTATGAAATTATATTATTACTTCTACAAATTTCAAATTGCCGTAATTGAACGTATATTTCTTCTTCAACTattatt         >  1:1904951/1‑141 (MQ=255)
                                                                                                                                     cTAATCAAAAAACTTCTATCACGAACGCTTCAATTTCCTGTATGCGTGTGATAGAAGTTTTTATTTTATGAAATTATATTATTACTTCTACAAATTTCAAATTGCCGTAATTGAACGTATATTTCTTCTTCAACTattatt         <  1:1680804/141‑1 (MQ=255)
                                                                                                                                      tAATCAAAAAACTTCTATCACGAACGCTTCAATTTCCTGTATGCGTGTGATAGAAGTTTTTATTTTATGAAATTATATTATTACTTCTACAAATTTCACATTGCCGTAATTGAACGTATATTTCTTCTTCAACtattatct        <  2:4335971/141‑3 (MQ=255)
                                                                                                                                       aaTCAAAAGACTTCTATCACGAACGCTTCAATTTCCTGTATGCGTGTGATAGAAGTTTTTATTTTATGAAATTATATTATTACTTCTACAAATTTCAAATTGCCGTAATTGAACGTATATTTCTTCTTCAACTATTATTTc       <  1:4296531/141‑1 (MQ=255)
                                                                                                                                        aTCAAAAAACTTCTATCACGAACGCTTCAATTTCCTGTATGCGTGTGATAGAAGTTTTTATTTTATGAAATTATATTATTACTTCTACAAATTTCAAATTGCCGTAATTGAACGTATATTTCTTCTTCAACTATTATTTCa      <  1:1800952/141‑1 (MQ=255)
                                                                                                                                            AAAAACTTCTATCACGGACGCTTCAATTTCCTGAGTGCGTGTCACCCAACTTTTTATTTTATGTAATGCTATTATTACTTCTACAAATTTCAAATTGCCGTAATTGAAAGTATATTTCTTCTTCAACTATTATTTCATCtt  <  2:2435506‑M1/141‑1 (MQ=255)
                                                                                                                                            AAAAACTTCTATCACGAACGCTTCAATTTCCTGTATGCGTGTGATAGAAGTTTTTATTTTATGAAATTATATTATTACTTCTACAAATTTCAAATTGCCGTCATTGAACGTATATTTCTTCTTGAACTATTATTTAATCtt  <  2:2385166‑M1/141‑1 (MQ=255)
                                                                                                                                            AAAAACTTCTATCACGAACGCTTCAATTTCCTGTATGCGTGTGATAGAAGTTTTTATTTTATGAAATTATATTATTACTTCTACAAATTTCAAATTGCCGTAATTGAACGTATATTTCTTCTTCAACTATTATTTCATCtt  >  2:712020‑M1/1‑141 (MQ=255)
                                                                                                                                            |                                                                                                                                            
GACATGTCGCAGTTGTTGAACAAGTATATAAAAACGGTAGTATTAAAGTTTCAGAATACAACTTTTATCGCCCATTAAAATACAATACACGTGTACTAAGCAAAAAGGCAGCACGTAACTTTAACTATATTTACTAATCAAAAAACTTCTATCACGAACGCTTCAATTTCCTGTATGCGTGTGATAGAAGTTTTTATTTTATGAAATTATATTATTACTTCTACAAATTTCAAATTGCCGTAATTGAACGTATATTTCTTCTTCAACTATTATTTCATCTT  >  USA300TCH1516_ALE/2679812‑2680092

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