New junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? USA300TCH1516_ALE 2679952 =109 (0.970)4 (0.040) 4/240 16.3 3.9% intergenic (+4/+756) ssaA2_4/USA300HOU_RS13810 Staphylococcal secretory antigen ssaA2/hypothetical protein
?USA300TCH1516_ALE 2680007 = 99 (0.990)intergenic (+59/+701) ssaA2_4/USA300HOU_RS13810 Staphylococcal secretory antigen ssaA2/hypothetical protein
Rejected: Coverage evenness skew score above cutoff.
Rejected: Frequency below/above cutoff threshold.

Only 100 of 109 total aligned reads displayed.

GACATGTCGCAGTTGTTGAACAAGTATATAAAAACGGTAGTATTAAAGTTTCAGAATACAACTTTTATCGCCCATTAAAATACAATACACGTGTACTAAGCAAAAAGGCAGCACGTAACTTTAACTATATTTACTAATCAAAAAACTTCTATCACGAACGCTTCAATTTCCTGTATGCGTGTGATAGAAGTTTTTATTTTATGAAATTATATTATTACTTCTACAAATTTCAAATTGCCGTAATTGAACGTATATTTCTTCTTCAACTATTATTTCATCT  >  USA300TCH1516_ALE/2679812‑2680091
                                                                                                                                            |                                                                                                                                           
gACATGTCGCAGTTGTTGAACAAGTATATAAAAACGGTAGTATTAAAGTTTCAGAATACAACTTTTATCGCCCATTAAAATACAATACACGTGTACTAAGCAAAAAGGCAGCACGTAACTTTAACTATATTTACTAATCaa                                                                                                                                             >  1:340605/1‑141 (MQ=255)
  cATGTCGCAGTTGTTGAACAAGTATATAAAAACGGTAGTATTAAAGTTTCAGAATACAACTTTTATCGCCCATTAAAATACAATACACGTGTACTAAGCAAAAAGGCAGCACGTAACTTTAACTATATTTACTAATCaaaa                                                                                                                                           >  3:188594/1‑141 (MQ=255)
        gCAGTTGTTGAACAAGTATATAAAAACGGTAGTATTAAAGTTTCAGAATACAACTTTTATCGCCCATTAAAATACAATACACGTGTACTAAGCAAAAAGGCAGCACGTAACTTTAACTATATTTACTAATCAAAAAACTTc                                                                                                                                     >  1:419502/1‑141 (MQ=255)
            ttgttgAACAAGTATATAAAAACGGTAGTATTAAAGTTTCAGAATACAACTTTTATCGCCCATTAAAATACAATACACGTGTACTAAGCAAAAAGGCAGCACGTAACTTTAACTATATTTACTAATCAAAAAACTTCTATc                                                                                                                                 <  2:528221/141‑1 (MQ=255)
            ttgttgAACAAGTATATAAAAACGGTAGTATTAAAGTTTCAGAATACAACTTTTATCGCCCATTAAAATACAATACACGTGTACTAAGCAAAAAGGCAGCACGTAACTTTAACTATATTTACTAATCAAAAAACTTCTATc                                                                                                                                 >  1:305219/1‑141 (MQ=255)
            ttgttgAACAAGTATATAAAAACGGTAGTATTAAAGTTTCAGAATACAACTTTTATCGCCCATTAAAATACAATACACGTGTACTAAGCAAAAAGGCAGCACGTAACTTTAACTATATTTACTAATCAAAAAACTTCTATc                                                                                                                                 >  1:305154/1‑141 (MQ=255)
              gttgAACAAGTATATAAAAACGGTAGTATTAAAGTTTCAGAATACAACTTTTATCGCCCATTAAAATACAATACACGTGTACTAAGCAAAAAGGCAGCACGTAACTTTAACTATATTTACTAATCAAAAAACTTCTATCAc                                                                                                                               <  1:561772/141‑1 (MQ=255)
               ttgAACAAGTATATAAAAACGGTAGTATTAAAGTTTCAGAATACAACTTTTATCGCCCATTAAAATACAATACACGTGTACTAAGCAAAAAGGCAGCACGTAACTTTAACTATATTTACTAATCAAAAAACTTCTATCACg                                                                                                                              >  1:829493/1‑141 (MQ=255)
                 gAACAAGTATATAAAAACGGTAGTATTAAAGTTTCAGAATACAACTTTTATCGCCCATTAAAATACAATACACGTGTACTAAGCAAAAAGGCAGCACGTAACTTTAACTATATTTACTAATCAAAAAACTTCTATCACGaa                                                                                                                            >  2:737297/1‑141 (MQ=255)
                  aaCAAGTATATAAAAACGGTAGTATTAAAGTTTCAGAATACAACTTTTATCGCCCATTAAAATACAATACACGTGTACTAAGCAAAAAGGCAGCACGTAACTTTAACTATATTTACTAATCAAAAAACTTCTATCACGAAc                                                                                                                           >  2:615545/1‑141 (MQ=255)
                     aaGTATATAAAAACGGTAGTATTAAAGTTTCAGAATACAACTTTTATCGCCCATTAAAATACAATACACGTGTACTAAGCAAAAAGGCAGCACGTAACTTTAACTATATTTACTAATCAAAAAACTTCTATCACGAACGCt                                                                                                                        <  1:627904/141‑1 (MQ=255)
                        tatataAAAACGGTAGTATTAAAGTTTCAGAATACAACTTTTATCGCCCATTAAAATACAATACACGTGTACTAAGCAAAAAGGCAGCACGTAACTTTAACTATATTTACTAATCAAAAAACTTCTATCACGAACGCTTCa                                                                                                                     >  2:676183/1‑141 (MQ=255)
                        tatataAAAACGGTAGTATTAAAGTTTCAGAATACAACTTTTATCGCCCATTAAAATACAATACACGTGTACTAAGCAAAAAGGCAGCACGTAACTTTAACTATATTTACTAATCAAAAAACTTCTATCACGAACGCTTCa                                                                                                                     <  1:334766/141‑1 (MQ=255)
                          tataAAAACGGTAGTATTAAAGTTTCAGAATACAACTTTTATCGCCCATTAAAATACAATACACGTGTACTAAGCAAAAAGGCAGCACGTAACTTTAACTATATTTACTAATCAAAAAACTTCTATCACGAACGCTTCAAt                                                                                                                   <  1:56555/141‑1 (MQ=255)
                          tataAAAACGGTAGTATTAAAGTTTCAGAATACAACTTTTATCGCCCATTAAAATACAATACACGTGTACTAAGCAAAAAGGCAGCACGTAACTTTAACTATATTTACTAATCAAAAAACTTCTATCACGAACGCTTCAAt                                                                                                                   <  1:541008/141‑1 (MQ=255)
                          tataAAAACGGTAGTATTAAAGTTTCAGAATACAACTTTTATCGCCCATTAAAATACAATACACGTGTACTAAGCAAAAAGGCAGCACGTAACTTTAACTATATTTACTAATCAAAAAACTTCTATCACGAACGCTTCAAt                                                                                                                   >  1:347305/1‑141 (MQ=255)
                           ataAAAACGGTAGTATTAAAGTTTCAGAATACAACTTTTATCGCCCATTAAAATACAATACACGTGTACTAAGCAAAAAGGCAGCACGTAACTTTAACTATATTTACTAATCAAAAAACTTCTATCACGAACGCTTCAAtt                                                                                                                  >  1:203068/1‑141 (MQ=255)
                            taAAAACGGTAGTATTAAAGTTTCAGAATACAACTTTTATCGCCCATTAAAATACAATACACGTGTACTAAGCAAAAAGGCAGCACGTAACTTTAACTATAAAAAAAAAAAAAAAAACTTCTATCACGAACGCTTCAAttt                                                                                                                 <  4:48087/141‑1 (MQ=255)
                              aaaaCGGTAGTATTAAAGTTTCAGAATACAACTTTTATCGCCCATTAAAATACAATACACGTGTACTAAGCAAAAAGGCAGCACGTAACTTTAACTATATTTACTAATCAAAAAACTTCTATCACGAACGCTTCAATTTcc                                                                                                               >  2:900138/1‑141 (MQ=255)
                              aaaaCGGTAGTATTAAAGTTTCAGAATACAACTTTTATCGCCCATTAAAATAAAATACACGTGTACTAAGCAAAAAGGCAGCACGTAACTTTAACTATATTTACTAATCAAAAAACTTCTATCACGAACGCTTCAATTTcc                                                                                                               >  1:897722/1‑141 (MQ=255)
                                aaCGGTAGTATTAAAGTTTCAGAATACAACTTTTATCGCCCATTAAAATACAATACACGTGTACTAAGCAAAAAGGCAGCACGTAACTTTAACTATATTTACTAATCAAAAAACTTCTATCACGAACGCTTCAATTTCCTg                                                                                                             >  2:100618/1‑141 (MQ=255)
                                aaCGGTAGTATTAAAGTTTCAGAATACAACTTTTATCGCCCATTAAAATACAATACACGTGTACTAAGCAAAAAGGCAGCACGTAACTTTAACTATATTTACTAATCAAAAAACTTCTATCACGAACGCTTCAATTTCCTg                                                                                                             >  1:249846/1‑141 (MQ=255)
                                 aCGGTAGTATTAAAGTTTCCGAATACAACCTTTATCGCCGACAAAAATACAATACACGTTTACTAAGCAAAAAGGCAGCACGTAACTTTAACTACATTTACTAATCAAAAAACTTCTATCACGAACCCTTCCAATTCCTGt                                                                                                            >  4:195080/1‑141 (MQ=37)
                                  cGGTAGTATTAAAGTTTCAGAATACAACTTTTATCGCCCATTAAAATACAATACACGTGTACTAAGCAAAAAGGCAGCACGTAACTTTAACTATATTTACTAATCAAAAAACTTCTATCACGAACGCTTCAATTTCCTGTa                                                                                                           <  2:873005/141‑1 (MQ=255)
                                    gtagtaTTAAAGTTTCAGAATACAACTTTTATCGCCCATTAAAATACAATACACGTGTACTAAGCAAAAAGGCAGCACGTAACTTTAACTATATTTACTAATCAAAAAACTTCTATCACGAACGCTTCAATTTCCTGTATg                                                                                                         <  1:86060/141‑1 (MQ=255)
                                     tagtaTTAAAGTTTCAGAATACAACTTTTATCGCCCATTAAAATACAATACACGTGTACTAAGCAAAAAGGCAGCACGTAACTTTAACTATAATTACTAATCAAAAAACTTCTATCACGAACGCTTCAATTTCCTGTATGc                                                                                                        <  2:914470/141‑1 (MQ=255)
                                       gtaTTAAAGTTTCAGAATACAACTTTTATCGCCCATTAAAATACAATACACGTGTACTAAGCAAAAAGGCAGCACGTAACTTTAACTATATTTACTAATCAAAAAACTTCTATCACGAACGCTTCAATTTCCTGTATGCgt                                                                                                      >  4:180778/1‑141 (MQ=255)
                                       gtaTTAAAGTTTCAGAATACAACTTTTAACGCCCATTAAAATAAAATACACGTGTAATCAGCAAAAAGGCAGCACGTAACTTTAACTATATTTACTAATCAAAAAACTTCTATAACGAACATTTCAATTTCCTGTATGCgt                                                                                                      >  4:391373/1‑141 (MQ=38)
                                            aaaGTTTCAGAAAACAAGTTATATCGCCCATTAAAATACAATACACGTGTACTAAGCAAAAAGGCAGCACGTAACTTTAACTATATTTAATAATCAAAAAACTTCTATCACGAACGCTTAAATTTCCTGTATGCGTGTGAt                                                                                                 <  4:335587/141‑1 (MQ=38)
                                             aaGTTTCAGAATACAACTTTTATCGCCCATTAAAATACAATACACGTGTACTAAGCAAAAAGGCAGCACGTAACTTTAACTATATTTACTAATCAAAAAACTTCTATCACGAACGCTTCAATTTCCTGTATGCGTGTGATa                                                                                                <  2:18038/141‑1 (MQ=255)
                                              aGTTTCAGAATACAACTTTTATCGCCCATTAAAATACAATACACGTGTACTAAGCAAAAAGGCAGCACGTAACTTTAACTATATTTACTAATCAAAAAACTTCTATCACGAACGCTTCAATTTCCTGTATGCGTGTGATAg                                                                                               <  1:893966/141‑1 (MQ=255)
                                              aGTATCAGAATACAACTTTTATCGCACACTAAAATACAATACACAAAAAAAAAACAAAAAGGCAGCACGTAACTTTAACTATATTTACTAATCAAAAAACTTCTATCACGAACGCTTCAATTTCCTGTATGCGTGTGATAg                                                                                               <  2:129912/141‑1 (MQ=21)
                                                 ttCAGAATACAACTTTTATCGCCCATTAAAATACAATACACGTGTACTAAGCAAAAAGGCAGCACGTAACTTTAACTATATTTACTAATCAAAAAACTTCTATCACGAACGCTTCAATTTCCTGTATGCGTGTGATAGAAg                                                                                            >  3:11359/1‑141 (MQ=255)
                                                  tCAGAATACAACTTTTATCGCCCATTAAAATACAATACACGTGTACTAAGCAAAAAGGCAGCACGTAACTTTAACTATATTTACTAATCAAAAAACTTCTATCACGAACGCTTCAATTTCCTGTATGCGTGTGATAGAAGt                                                                                           <  2:435305/141‑1 (MQ=255)
                                                   cAGAATACAACTTATATAGCCCATTAAAATACAATACAAAAAAAAAAAAAAAAAAGGCAGCACGTAACTTTAACTATATTTACTAATCAAAAAACTTCTATCACGAACGCTTCAATTTCCTGTATGCGTGTGATAGAAGtt                                                                                          <  2:381464/141‑1 (MQ=21)
                                                    aGAATACAACTTTTATCGCCCATTAAAATACAATACACGTGTACTAAGCAAAAAGGCAGCACGTAACTTTAACTATATTTACTAATCAAAAAACTTCTATCACGAACGCTTCAATTTCCTGTATGCGTGTGATAGAAGttt                                                                                         >  3:280816/1‑141 (MQ=255)
                                                          cAACTTTTATCGCCCATTAAAATACAATACACGTGTACTAAGCAAAAAGGCAGCACGTAACTTTAACTATATTTACTAATCAAAAAAc                                                                                                                                        >  2:757990/1‑88 (MQ=255)
                                                          cAACTTTTATCGCCCATTAAAATACAATACACGTGTACTAAGCAAAAAGGCAGCACGTAACTTTAACTATATTTACTAATCAAAAAAc                                                                                                                                        <  1:757990/88‑1 (MQ=255)
                                                           aaCTTTTATCGCCCATTAAAATACAATACACGTGTACTAAGCAAAAAGGCAGCACGTAACTTTAACTATATTTACTAATCAAAAAACTTCTATCACGAACGCTTCAATTTCCTGTATGCGTGTGATAGAAGTttttatttt                                                                                  >  3:18321/1‑141 (MQ=255)
                                                            aCTTTTATCGCCCATTAAAATACAATACACGTGTACTAAGCAAAAAGGCAGCACGTAACTTTAACTATATTTACTAATCAAAAAACTTCTATCACGAACGCTTCAATTTCCTGTATGCGTGTGATAGAAGTttttatttta                                                                                 >  1:309303/1‑141 (MQ=255)
                                                            aCTTTTATCGCCCATTAAAATACAATACACGTGTACTAAGCAAAAAGGCAGCACGTAACTTTAACTATATTTACTAATCAAAAAACTTCTATCACGAACGCTTCAATTTCCTGTATGCGTGTGATAGAAGTttttatttta                                                                                 >  1:505232/1‑141 (MQ=255)
                                                             cTTTTATCGCCCATTAAAATACAATACACGTGTACTAAGCAAAAAGGCAGCACGTAACTTTAACTATATTTACTAATCAAAAAACTTCTATCACGAACGCTTCAATTTCCTGTATGCGTGTGATAGAAGTTtttattttat                                                                                <  3:216445/141‑1 (MQ=255)
                                                                ttATCGCCCATTAAAATACAATACACGTGTACTAAGCAAAAAGGCAGCACGTAACTTTAACTATATTTACTAATCACCAACGCCGTATCACGAACGCTTCAATTTCCTGTATGCGTGTGATAGAAGTTTTTATTTTATGaa                                                                             >  1:16675/1‑141 (MQ=37)
                                                                  aTCACCCATTAAAATACAATACACGTATACTAAGCAAAAAGGCAGCACGTAACTTTAACTATATTTACTAATCAAAAAACTTCTATCACGAACGCTTCAATTTCCTGTATGCGTGTGATAGAAGTTTTTATTTTATGAAat                                                                           <  2:583990/141‑1 (MQ=255)
                                                                   tCGCCCATTAAAATACAATACACGTGTACTAAGCAAAAAGGCAGCACGTAACTTTAACTATATTTACTAATCAAAAAACTTCTATCACGAACGCTTCAATTTCCTGTATGCGTGTGATAGAAGTTTTTATTTTATGAAatt                                                                          <  1:61015/141‑1 (MQ=255)
                                                                    cGCCCATTAAAATACAATACACGTGTACTAAGCAAAAAGGCAGCACGTAACTTTAACTATATTTACTAATCAAAAAACTTCTATCACGAACGCTTCAATTTCCTGTATGCGTGTGATAGAAGTTTTTATTTTATGAAatta                                                                         >  1:889108/1‑141 (MQ=255)
                                                                    cGCCCATTAAAATACAATACACGTGTACTAAGCAAAAAGGCAGCACGTAACTTTAACTATATTTACTAATCAAAAAACTTCTATCACGAACGCTTCAATTTCCTGTATGCGTGTGATAGAAGTTTTTATTTTATGAAatta                                                                         >  1:188232/1‑141 (MQ=255)
                                                                      cccATTAAAATACAATACACGTGTACTAAGCAAAAAGGCAGCACGTAACTTTAACTATATTTACTAATCAAAAAACTTCTATCACGAACGCTTCAATTTCCTGTATGCGTGTGATAGAAGTTTTTATTTTATGAAattata                                                                       >  2:701999/1‑141 (MQ=255)
                                                                      cccATTAAAATACAATACACGTGTACTAAGCAAAAAGGCAGCACGTAACTTTAACTATATTTACTAATCAAAAAACTTCTATCACGAACGCTTCAATTTCCTGTATGCGTGTGATAGAAGTTTTTATTTTATGAAattata                                                                       >  4:137575/1‑141 (MQ=255)
                                                                       ccATTAAAATACAATACACGTGTACTAAGCAAAAAGGCAGCACGTAACTTTAACTATATTTACTAATCAAAAAACTTCTATCACGAACGCTTCAATTTCCTGTATGCGTGTGATAGAAGTTTTTATTTTATGAAattatat                                                                      <  1:292503/141‑1 (MQ=255)
                                                                       ccATTAAAATACAATACACGTGTACTAAGCAAAAAGGCAGCACGTAACTTTAACTATATTTACTAATCAAAAAACTTCTATCACGAACGCTTCAATTTCCTGTATGCGTGTGATAGAAGTTTTTATTTTATGAAattatat                                                                      >  2:496974/1‑141 (MQ=255)
                                                                          ttAAAATACAATACACGTGTACTAAGCAAAAAGGCAGCACGTAACTTTAACTATATTTACTAATCAAAAAACTTCTATCACGAACGCTTCAATTTCCTGTATGCGTGTGATAGAAGTTTTTATTTTATGAAattatattat                                                                   <  1:52443/141‑1 (MQ=255)
                                                                            aaaaTACAATACACGTGTACTAAGCAAAAAGGCAGCACGTAACTTTAACTATATTTACTAATCAAAAAACTTCTATCACGAACGCTTCAATTTCCTGTATGCGTGTGATAGAAGTTTTTATTTTATGAAATTATAttatta                                                                 >  1:524583/1‑141 (MQ=255)
                                                                            aaaaTACAATACACGTGTACTAAGCAAAAAGGCAGCACGTAACTTTAACTATATTTACTAATCAAAAAACGTCTAGCACTAACGCTGCAATTTCCTGTATGCGTGTGATAGAAGTTTTTATTTTATGAAATTATAttatta                                                                 >  1:181832/1‑141 (MQ=255)
                                                                              aatacaatacACGTGTACTAAGCAAAAAGGCAGCACGTAACTTTAACTATATTTACTAATCAAAAAACTTCTATCACGAACGCTTCAATTTCCTGTATGCGTGTGATAGAAGTTTTTATTTTATGAAATTATATTATTACt                                                               <  1:737297/141‑1 (MQ=255)
                                                                               atacaatacaCGTGTACTAAGCAAAAAGGCAGCACGTAACTTTAACTATATTTACTAATCAAAAAACTTCTATCACGAACGCTTCAATTTCCTGTATGCGTGTGATAGAAGTTTTTATTTTATGAAATTATATTATTACtt                                                              >  2:263353/1‑141 (MQ=255)
                                                                                tacaatacaCGTGTACTAAGCAAAAAGGCAGCACGTAACTTTAACTATATTTACTAATCAAAAAACTTCTATCACGAACGCTTCAATTTCCTGTATGCGTGTGATAGAAGTTTTTATTTTATGAAATTATATTATTACTTc                                                             >  4:182479/1‑141 (MQ=255)
                                                                                tacaatacaCGTGTACTAAGCAAAAAGGCAGCACGTAACTTTAACTATATTTACTAATCAAAAAACTTCTATCACGAACGCTTCAATTTCCTGTATGCGTGTGATAGAAGTTTTAATTTTATGAAATTATATTATTACTTc                                                             >  2:728228/1‑141 (MQ=255)
                                                                                   aatacaCGTGTACTAAGCAAAAAGGCAGCACGTAACTTTAACTATATTTACTAATCAAAAAACTTCTATCACGAACGCTTCAATTTCCTGTATGCGTGTGATAGAAGTTTTTATTTTATGAAATTATATTATTACTTCTAc                                                          >  1:2725/1‑141 (MQ=255)
                                                                                   aatacaCGTGTACTAAGCAAAAAGGCAGCACGTAACTTTAACTATATTTACTAATCAAAAAACTTCTATCACGAACGCTTCAATTTCCTGTATGCGTGTGATAGAAGTTTTTATTTTATGAAATTATATTATTACTTCTAc                                                          >  1:720957/1‑141 (MQ=255)
                                                                                    atacaCGTGTACTAAGCAAAAAGGCAGCACGTAACTTTAACTATATTTACTAATCAAAAAACTTCTATCACGAACGCTTCAATTTCCTGTATGCGTGTGATAGAAGTTTTTATTTTATGAAATTATATTATTACTTCTACa                                                         <  1:100618/141‑1 (MQ=255)
                                                                                       cacGTGTACTAAGCAAAAAGGCAGCACGTAACTTTAACTATATTTACTAATCAAAAAACTTCTATCACGAACGCTTCAATTTCCTGTATGCGTGTGATAGAAGTTTTTATTTTATGAAATTATATTATTACTTCTACAAAt                                                      >  1:743108/1‑141 (MQ=255)
                                                                                       cacGTGTACTAAGCAAAAAGGCAGCACGTAACTTTAACTATATTTACTAATCAAAAAACTTCTATCACGAACGCTTCAATTTCCTGTATGCGTGTGATAGAAGTTTTTATTTTATGAAATTATATTATTACTTCTACAAAt                                                      <  4:388458/141‑1 (MQ=255)
                                                                                       cacGTGTACTAAGCAAAAAGGCAGCACGTAACTTTAACTATATTTACTAATCAAAAAACTTCTATCACGAACGCTTCAATTTCCTGTATGCGTGTGATAGAAGTTTTTATTTTATGAAATTATATTATTACTTCTACAAAt                                                      <  2:188232/141‑1 (MQ=255)
                                                                                         cGTGTACTAAGCAAAAAGGCAGCACGTAACTTTAACTATATTTACTAATCAAAAAACTTCTATCACGAACGCTTCAATTTCCTGTATGCGTGTGATAGAAGTTTTTATTTTATGAAATTATATTATTACTTCTACAAAttt                                                    <  2:255223/141‑1 (MQ=255)
                                                                                           tgtACTAAGCAAAAAGGCAGCACGTAACTTTAACTATATTTACTAATCAAAAAACTTCTATCACGAACGCTTCAATTTCCTGTATGCGTGTGATAGAAGTTTTTATTTTATGAAATTATATTATTACTTCTACAAATTTCa                                                  >  1:530443/1‑141 (MQ=255)
                                                                                             tACTAAGCAAAAAGGCAGCACGTAACTTTAACTATATTTACTAATCAAAAAACTTCTATCACGAACGCTTCAATTTCCTGTATGCGTGTGATAGAAGTTTTTATTTTATGAAATTATATTATTACTTCTACAAATTTCaaa                                                <  1:144634/141‑1 (MQ=255)
                                                                                              aCTAAGCAAAAAGGCAGCACGTAACTTTAACTATATTTACTAATCAAAAAACTTCTATCACGAACGCTTCAATTTCCTGTATGCGTGTGATAGAAGTTTTTATTTTATGAAATTATATTATTACTTCTACAAATTTCAAAt                                               >  1:393217/1‑141 (MQ=255)
                                                                                              aCTAAGCAAAAAGGCAGCACGTAACTTTAACTATATTTACTAATCAAAAAACTTCTATCACGAACGCTTCAATTTCCTGTATGCGTGTGATAGAAGTTTTTATTTTATGAAATTATATTATTACTTCTACAAATTTCAAAt                                               >  1:106061/1‑141 (MQ=255)
                                                                                                 aaGCAAAAAGGCAGCACGTAACTTTAACTATATTTACTAATCAAAAAACTTCTATCACGAACGCTTCAATTTCCTGTATGCGTGTGATAGAAGTTTTTATTTTATGAAATTATATTATTACTTCTACAAATTTCAAATTGc                                            >  3:38505/1‑141 (MQ=255)
                                                                                                 aaGCAAAAAGGCAGCACGTAACTTTAACTATATTTACTAATCAAAAAACTTCTATCACGAACGCTTCAATTTCCTGTATGCGTGTGATAGAAGTTTTTATTTTATGAAATTATATTATTACTTCTACAAATTTCAAATTGc                                            >  1:758408/1‑141 (MQ=255)
                                                                                                  aGCAAAAAGGCAGCACGTAACTTTAACTATATTTACTAATCAAAAAACTTCTATCACGAACGCTTCAATTTCCTGTATGCGTGTGATAGAAGTTTTTATTTTATGAAATTATATTATTACTTCTACAAATTTCAAATTGcc                                           <  4:250126/141‑1 (MQ=255)
                                                                                                   gCAAAAAGGCAGCACGTAACTTTAACTATATTTACTAATCAAAAAACTTCTATCACGAACGCTTCAATTTCCTGTATGCGTGTGATAGAAGTTTTTATTTTATGAAATTATATTATTACTTCTACAAATTTCAAATTGCCg                                          <  3:341416/141‑1 (MQ=255)
                                                                                                    cAAAAAGGCAGCACGTAACTTTAACTATATTTACTAATCAAAAAACTTCTATCACGAACGCTTCAATTTCCTGTATGCGTGTGATAGAAGTTTTTATTTTATGAAATTATATTATTACTTCTACAAATTTCAAATTGCCGt                                         >  2:841678/1‑141 (MQ=255)
                                                                                                    cAAAAAGGCAGCACGTAACTTTAACTATATTTACTAATCAAAAAACTTCTATCACGAACGCTTCAATTTCCTGTATGCGTGTGATAGAAGTTTTTATTTTATGAAATTATATTATTACTTCTACAAATTTCAAATTGCCGt                                         >  1:552340/1‑141 (MQ=255)
                                                                                                     aaaaaGGCAGCACGTAACTTTAACTATATTTACTAATCAAAAAACTTCTATCACGAACGCTTCAATTTCCTGTATGCGTGTGATAGAAGTTTTTATTTTATGAAATTATATTATTACTTCTACAAATTTCAAATTGCCGTa                                        <  2:133135/141‑1 (MQ=255)
                                                                                                     aaaaaGGCAGCACGTAACTTTAACTATATTTACTAATCAAAAAACTTCTATCACGAACGCTTCAATTTCCTGTATGCGTGTGATAGAAGTTTTTATTTTATGAAATTATATTATTACTTCTACAAATTTCAAATTGCCGTa                                        >  3:279660/1‑141 (MQ=255)
                                                                                                       aaaGGCAGCACGTAACTTTAACTATATTTACTAATCAAAAAACTTCTATCACGAACGCTTCAATTTCCTGTATGCGTGTGATAGAAGTTTTTATTTTATGAAATTATATTATTACTTCTACAAATTTCAAATTGCCGTAAt                                      <  4:18321/141‑1 (MQ=255)
                                                                                                           gcagcaCGTAACTTTAACTATATTTACTAATCAAAAAACTTCTATCACGAACGCTTCAATTTCCTGTATGCGTGTGATAGAAGTTTTTATTTTATGAAATTATATTATTACTTCTACAAATTTCAAATTGCCGTAATTGaa                                  >  3:370257/1‑141 (MQ=255)
                                                                                                             agcaCGTAACTTTAACTATATTTACTAATCAAAAAACTTCTATCACGAACGCTTCAATTTCCTGTATGCGTGTGATAGAAGTTTTTATTTTATGAAATTATATTATTACTTCTACAAATTTCAAATTGCCGTAATTGAACg                                >  1:222002/1‑141 (MQ=255)
                                                                                                             agcaCGTAACTTTAACTATATTTACTAATCAAAAAACTTCTATCACGAACGCTTCAATTTCCTGTATGCGTGTGATAGAAGTTTTTATTTTATGAAATTATATTATTACTTCTACAAATTTCAAATTGCCGTAATTGAACg                                <  3:10101/141‑1 (MQ=255)
                                                                                                              gcaCGTAACTTTAACTATATTTACTAATCAAAAAACTTCTATCACGAACGCTTCAATTTCCTGTATGCGTGTGATAGAAGTTTTTATTTTATGAAATTATATTATTACTTCTACAAATTTCAAATTGCCGTAATTGAACGt                               >  2:277057/1‑141 (MQ=255)
                                                                                                              gcaCGTAACTTTAACTATATTTACTAATCAAAAAACTTCTATCACGAACGCTTCAATTTCCTGTATGCGTGTGATAGAAGTTTTTATTTTATGAAATTATATTATTACTTCTACAAATTTCAAATTGCCGTAATTGAACGt                               >  1:41214/1‑141 (MQ=255)
                                                                                                                 cGTAACTTTAACTATATTTACTAATCAAAAAACTTCTATCACGAACGCTTCAATTTCCTGTATGCGTGTGATAGAAGTTTTTATTTTATGAAATTATATTATTACTTCTACAAATTTCAAATTGCCGTAATTGAACGtata                            <  1:900138/141‑1 (MQ=255)
                                                                                                                  gTAACTTTAACTATATTTACTAATCAAAAAACTTCTATCACGAACGCTTCAATTTCCTGTATGCGTGTGATAGAAGTTTTTATTTTATGAAATTATATTATTACTTCTACAAATTTCAAATTGCCGTAATTGAACGTatat                           <  2:133096/141‑1 (MQ=255)
                                                                                                                  gTAACTTTAACTATATTTACTAATCAAAAAACTTCTATCACGAACGCTTCAATTTCCTGTATGCGTGTGATAGAAGTTTTTATTTTATGAAATTATATTATTACTTCTACAAATTTCAAATTGCCGTAATTGAACGTatat                           <  2:743108/141‑1 (MQ=255)
                                                                                                                     aCTTTAACTATATTTACTAATCAAAAAACTTCTATCACGAACGCTTCAATTTCCTGTATGCGTGTGATAGAAGTTTTTATTTTATGAAATTATATTATTACTTCTACAAATTTCAAATTGCCGTAATTGAACGTATATttc                        <  3:309248/141‑1 (MQ=255)
                                                                                                                      cTTTAACTATATTTACTAATCAAAAAACTTCTATCACGAACGCTTCAATTTCCTGTATGCGTGTGATAGAAGTTTTTATTTTATGAAATTATATTATTACTTCTACAAATTTCAAATTGCCGTAATTGAACGTATATttct                       >  2:306934/1‑141 (MQ=255)
                                                                                                                       tttAACTATATTTACTAATCAAAAAACTTCTATCACGAACGCTTCAATTTCCTGTATGCGTGTGATAGAAGTTTTTATTTTATGAAATTATATTATTACTTCTACAAATTTCAAATTGCCGTAATTGAACGTATATttctt                      <  1:579539/141‑1 (MQ=255)
                                                                                                                        ttAACTATATTTACTAATCAAAAAACTTCTATCACGAACGCTTCAATTTCCTGTATGCGTGTGATAGAAGTTTTTATTTTATGAAATTATATTATTACTTCTACAAATTTCAAATTGCCGTAATTGAACGTATATttcttc                     <  1:171519/141‑1 (MQ=255)
                                                                                                                         tAACTATATTTACTAATCAAAAAACTTCTATCACGAACGCTTCAATTTCCTGTATGCGTGTGATAGAAGTTTTTATTTTATGAAatta                                                                         >  3:280966/1‑88 (MQ=255)
                                                                                                                         tAACTATATTTACTAATCAAAAAACTTCTATCACGAACGCTTCAATTTCCTGTATGCGTGTGATAGAAGTTTTTATTTTATGAAatta                                                                         <  4:280966/88‑1 (MQ=255)
                                                                                                                             tataTTTACTAATCAAAAAACTTCTATCACGAACGCTTCAATTTCCTGTATGCGTGTGATAGAAGTTTTTATTTTATGAAATTATATTATTACTTCTACAAATTTCAAATTGCCGTAATTGAACGTATATTTCTTCTTCaa                <  2:837440/141‑1 (MQ=255)
                                                                                                                               tatTTACTAATCAAAAAACTTCTATCACGAACGCTTCAATTTCCTGTATGCGTGTGATAGAAGTTTTTATTTTATGAAATTATATTATTACTTCTACAAATTTCAAATTGCCGTAATTGAACGTATATTTCTTCTTCAACt              >  3:143379/1‑141 (MQ=255)
                                                                                                                                atTTACTAATCAAAAAACTTCTATCACGAACGCTTCAATTTCCTGTATGCGTGTGATAGAAGTTTTTATTTTATGAAATTATATTATTACTTCTACAAATTTCAAATTGCCGTAATTGAACGTATATTTCTTCTTCAACta             <  2:330567/141‑1 (MQ=255)
                                                                                                                                     cTAATCAAAAAACTTCTATCACGAACGCTTCAATTTCCTGTATGCGTGTGATAGAAGTTTTTATTTTATGAAATTATATTATTACTTCTACAAATTTCAAATTGCCGTAATTGAACGTATATTTCTTCTTCAACTattatt        >  1:298996/1‑141 (MQ=255)
                                                                                                                                     cTAATCAAAAAACTTCTATCACGAACGCTTCAATTTCCTGTATGCGTGTGATAGAAGTTTTTATTTTATGAAATTATATTATTACTTCTACAAATTTCAAATTGCCGTAATTGAACGTATATTTCTTCTTCAACTattatt        <  1:911148/141‑1 (MQ=255)
                                                                                                                                      tAATCAAAAAACTTCTATCACGAACGCTTCAATTTCCTGTATGCGTGTGATAGAAGTTTTTATTTTATGAAATTATATTATTACTTCTACAAATTTCAAATTGCCGTAATTGAACGTATATTTCTTCTTCAACTATTAttt       >  2:393882/1‑141 (MQ=255)
                                                                                                                                         tCAAAAAACTTCTATCACGAACGCTTCAATTTCCTGTATGCGTGTGATAGAAGTTTTTATTTTATGAAATTATATTATTACTTCTACAAATTTCAAATTGCCGTAATTGAACGTATATTTCTTCTTCAACTATTATTTCAt    <  1:212737/141‑1 (MQ=255)
                                                                                                                                           aaaaaaCTTCTATCACGAACGCTTCAATTTCCTGTATGCGTGTGATAGAAGTTTTTATTTTATGAACTTATATTATTACTTCTACAAATTTCAAATTGCCGTAATTGAACGTATATTTCTTCTTCAACTATTATTTCATCt  >  2:462857/1‑141 (MQ=255)
                                                                                                                                            |                                                                                                                                           
GACATGTCGCAGTTGTTGAACAAGTATATAAAAACGGTAGTATTAAAGTTTCAGAATACAACTTTTATCGCCCATTAAAATACAATACACGTGTACTAAGCAAAAAGGCAGCACGTAACTTTAACTATATTTACTAATCAAAAAACTTCTATCACGAACGCTTCAATTTCCTGTATGCGTGTGATAGAAGTTTTTATTTTATGAAATTATATTATTACTTCTACAAATTTCAAATTGCCGTAATTGAACGTATATTTCTTCTTCAACTATTATTTCATCT  >  USA300TCH1516_ALE/2679812‑2680091

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