New junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? USA300TCH1516_ALE 2681949 =181 (0.990)5 (0.030) 5/244 NT 2.8% coding (873/1278 nt) mvaA 3‑hydroxy‑3‑methylglutaryl‑coenzyme A reductase
?USA300TCH1516_ALE 2681984 = 170 (0.970)coding (838/1278 nt) mvaA 3‑hydroxy‑3‑methylglutaryl‑coenzyme A reductase
Rejected: Frequency below/above cutoff threshold.

Only 100 of 216 total aligned reads displayed.

CCAACGATTGCCAATGTCATAGGCACTTCAATTGTACCAATCAATCGTTGACGATCTTGATCGTAACGCCATGTAGCAATACCACGATACTGTCCGTCACGACTCGCGTATGCATGCGCACTTGCTTCTGCACCACGCGTATCATTTCCTGTTGCTAAAACAACAGCATGTATGCCATTCATAACACCTTTATTATGTGTTGCTGCACGATGAATATCTACTTGGGCCAATACAGAAGCACGTTCCATTCGTTTGGCAACCTCTTCTCCAGTTCTCTCGC  >  USA300TCH1516_ALE/2681845‑2682124
                                                                                                                                           |                                                                                                                                            
ccAACGATTGCCAATGTCATAGGCACTTCAATTGTACCAATCAATCGTTGATGATCTTGATCGTAACGCCATGTAGCAATACCACGATACTGTCCGTCACGACTCGCGTATGCATGCGCACTTGCTTCTGCACCACGCGTa                                                                                                                                             <  1:1166607/141‑1 (MQ=255)
ccAACGATTGCCAATGTCATAGGCACTTCAATTGTACCAATCAATCGTTGACGATCTTGATCGTAACGCCATGTAGCAATACCACGATACTGTCCGTCACGACTCGCGTATGCATGCGCACTTGCTTCTGCACCACGCGTa                                                                                                                                             <  1:757781/141‑1 (MQ=255)
  aaCGATTGCCAATGTCATAGGCACTTCAATTGTACCAATCAATCGTTGACGATCTTGATCGTAACGCCATGTAGCAATACCACGATACTGTCCGTCACTACTCGCGTATGCATGCGCACTTGCTTCTGCACCACGCGTATc                                                                                                                                           <  1:1425518/141‑1 (MQ=255)
  aaCGATTGCCAATGTCATAGGCACTTCAATTGTACCAATCAATCGTTGACGATCTTGATCGTAACGCCATGTAGCAATACCACGATACTGTCCGTCACGACTCGCGTATGCATGCGCACTTGCTTCTGCACCACGCGTATc                                                                                                                                           >  4:152366/1‑141 (MQ=255)
  aaCGATTGCCAATGTCATAGGCACTTCAATTGTACCAATCAATCGTTGACGATCTTGATCGTAACGCCATGTAGCAATACCACGATACTGTCCGTCACGACTCGCGTATGCATGCGCACTTGCTTCTGCACCACGCGTATc                                                                                                                                           <  2:973963/141‑1 (MQ=255)
  aaCGATTGCCAATGTCATAGGCACTTCAATTGTACCAATCAATCGTTGACGATCTTGATCGTAACGCCATGTAGCAATACCACGATACTGTCCGTCACGACTCGCGTATGCATGCGCACTTGCTTCTGCACCACGCGTATc                                                                                                                                           <  2:1071042/141‑1 (MQ=255)
   aCGATTGCCAATGTCATAGGCACTTCAATTGTACCAATCAATCGTTGACGATCTTGATCGTAACGCCATGTAGCAATACCACGATACTGTCCGTCACGACTCGCGTATGCATGCGCACTTGCTTCTGCACCACGCGTATCa                                                                                                                                          <  2:1515981/141‑1 (MQ=255)
    cGATTGCCAATGTCATAGGCACTTCAATTGTACCAATCAATCGTTGACGATCTTGATCGTAACGCCATGTAGCAATACCACGATACTGTCCGTCACGACTCGCGTATGCATGCGCACTTGCTTCTGCACCGCGCGTATCAt                                                                                                                                         <  2:1463296/141‑1 (MQ=255)
    cGATTGCCAATGTCATAGGCACTTCAATTGTACCAATCAATCGTTGACGATCTTGATCGTAACGCCATGTAGCAATACCACGATACTGTCCGTCACGACTCGCGTATGCATGCGCACTTGCTTCTGCACCACGCGTATCAt                                                                                                                                         >  1:202450/1‑141 (MQ=255)
     gATTGCCAATGTCATAGGCACTTCAATTGTACCAATCAATCGTTGACGATCTTGATCGTAACGCCATGTAGCAATACCACGATACTGTCCGTCACGACTCGCGTATGCATGCGCACTTGCTTCTGCACCACGCGTATCAtt                                                                                                                                        <  1:35992/141‑1 (MQ=255)
     gATTGCCAATGTCATAGGCACTTCAATTGTACCAATCAATCGTTGACGATCTTGATCGTAACGCCATGTAGCAATACCACGATACTGTCCGTCACGACTCGCGTATGCATGCGCACTTGCTTCTGCACCACGCGTATCAtt                                                                                                                                        >  3:445758/1‑141 (MQ=255)
         gCCAATGTCATAGGCACTTCAATTGTACCAATCAATCGTTGAGGATCTTGATCGTAACGCCATGTAGCAATACCACGATACTGTCCGTCACGACTCGCGTATGCATGCGCACTTGCTTCTGCACCACGCGTATCATTTCCt                                                                                                                                    <  2:1580847/141‑1 (MQ=255)
         gCCAATGTCATAGGCACTTCAATTGTACCAATCAATCGTTGACGATCTTGATCGTAACGCCATGTAGCAATACCACGATACTGTCCGTCACGACTCGCGTATGCATGCGCACTTGCTTCTGCACCACGCGTATCATTTCCt                                                                                                                                    >  2:125348/1‑141 (MQ=255)
           cAATGTCATAGGCACTTCAATTGTACCAATCAATCGTTGACGATCTTGATCGTAACGCCATGTAGCAATACCACGATACTGTCCGTCACGACTCGCGTATGCATGCGCACTTGCTTCTGCACCACGCGTATCATTTCCTGt                                                                                                                                  <  1:1530136/141‑1 (MQ=255)
           cAATGTCATAGGCACTTCAATTGTACCAATCAATCGTTGACGATCTTGATCGTAACGCCATGTAGCAATACCACGATACTGTCCGTCACGACTCGCGTATGCATGCGCACTTGCTTCTGCACCACGCGTATCATTTCCTGt                                                                                                                                  <  1:1277562/141‑1 (MQ=255)
             aTGTCATAGGCACTTCAATTGTACCAATCAATCGTTGACGATCTTGATCGTAACGCCATGTAGCAATACCACGATACTGTCCGTCACGACTCGCGTATGCATGCGCACTTGCTTCTGCACCACGCGTATCATTTCCTGTTg                                                                                                                                <  3:414956/141‑1 (MQ=255)
              tGTCATAGGCACTTCAATTGTACCAATCAATCGTTGACGATCTTGATCGTAACGCCATGTAGCAATACCACGATACTGTCCGTCACGACTCGCGTATGCATGCGCACTTGCTTCTGCACCACGCGTATCATTTCCTGTTGc                                                                                                                               >  3:537983/1‑141 (MQ=255)
                   tAGGCACTTCAATTGTACCAATCAATCGTTGACGATCTTGATCGTAACGCCATGTAGCAATACCACGATACTGTCCGTCACGACTCGCGTATGCATGCGCACTTGCTTCTGCACCACGCGTATCATTTCCTGTTGCTaaaa                                                                                                                          <  3:67048/141‑1 (MQ=255)
                   tAGGCACTTCAATTGTACCAATCAATCGTTGACGATCTTGATCGTAACGCCATGTAGCAATACCACGATACTGTCCGTCACGACTCGCGTATGCATGCGCACTTGCTTCTGCACCACGCGTATCATTTCCTGTTGCTaaaa                                                                                                                          <  1:776512/141‑1 (MQ=255)
                   tAGGCACTTCAATTGTACCAATCAATCGTTGACGATCTTGATCGTAACGCCATGTAGCAATACCACGATACTGTCCGTCACGACTCGCGTATGCATGCGCACTTGCTTCTGCACCACGCGTATCATTTCCTGTTGCTaaaa                                                                                                                          <  1:775302/141‑1 (MQ=255)
                   tAGGCACTTCAATTGTACCAATCAATCGTTGACGATCTTGATCGTAACGCCATGTAGCAATACCACGATACTGTCCGTCACGACTCGCGTATGCATGCGCACTTGCTTCTGCACCACGCGTATCATTTCCTGTTGCTaaaa                                                                                                                          >  2:251273/1‑141 (MQ=255)
                      gCACTTCAATTGTACCAATCAATCGTTGACGATCTTGATCGTAACGCCATGTAGCAATACCACGATACTGTCCGTCACGACTCGCGTATGCATGCGCACTTGCTTCTGCACCACGCGTATCATTTCCTGTTGCTAAaacaa                                                                                                                       <  1:46961/141‑1 (MQ=255)
                       cACTTCAATTGTACCAATCAATCGTTGACGATCTTGATCGTAACGCCATGTAGCAATACCACGATACTGTCCGTCACGACTCGCGTATGCATGCGCACTTGCTTCTGCACCACGCGTATCATTTCCTGTTGCTAAaacaac                                                                                                                      <  1:392412/141‑1 (MQ=255)
                          ttCAATTGTACCAATCAATCGTTGACGATCTTGATCGTAACGCCATGTAGCAATACCACGATACTGTCCGTCACGACTCGCGTATGCATGCGCACTTGCTTCTGCACCACGCGTATCATTTCCTGTTGCTAAAACAACAGc                                                                                                                   >  1:481864/1‑141 (MQ=255)
                          ttCAATTGTACCAATCAATCGTTGACGATCTTGATCGTAACGCCATGTAGCAATACCACGATACTGTCCGTCACGACTCGCGTATGCATGCGCACTTGCTTCTGCACCACGCGTATCATTTCCTGTTGCTAAAACAACAGc                                                                                                                   >  2:184465/1‑141 (MQ=255)
                           tCAATTGTACCAATCAATCGTTGACGATCTTGATCGTAACGCCATGTAGCAATACCACGATACTGTCCGTCACGACTCGCGTATGCATGCGCACTTGCTTCTGCACCACGCGTATCATTTCCTGTTGCTAAAACAACAGCa                                                                                                                  >  2:1263828/1‑141 (MQ=255)
                              aTTGTACCAATCAATCGTTGACGATCTTGATCGTAACGCCATGTAGCAATACCACGATACTGTCCGTCACGACTCGCGTATGCATGCGCACTTGCTTCTGCACCACGCGTATCATTTCCTGTTGCTAAAACAACAGCATGt                                                                                                               <  1:1302581/141‑1 (MQ=255)
                                  tACCAATCAATCGTTGACGATCTTGATCGTAACGCCATGTAGCAATACCACGATACTGTCCGTCACGACTCGCGTATGCATGCGCACTTGCTTCTGCACCACGCGTATCATTTCCTGTTGCTAAAACAACAGCATGTATGc                                                                                                           <  1:1043924/141‑1 (MQ=255)
                                  cgtgcagcaacacataataaaggtgttatgaatggcatacatgctgttgttttagcaacaggaaatgatacgcgtggtgcagaagcaagtgcgcatgcatacgcgTATCATTTCCTGTTGCTAAAACAACAGCATGTATGc                                                                                                           <  3:386427‑M2/36‑1 (MQ=255)
                                   aCCAATCAATCGTTGACGATCTTGATCGTAACGCCATGTAGCAATACCACGATACTGTCCGTCACGACTCGCGTATGCATGCGCACTTGCTTCTGCACCACGCGTATCATTTCCTGTTGCTAAAACAACAGCATGTATGcc                                                                                                          >  2:682068/1‑141 (MQ=255)
                                   aCCAATCAATCGTTGACGATCTTGATCGTAACGCCATGTAGCAATACCACGATACTGTCCGTCACGACTCGCGTATGCATGCGCACTTGCTTCTGCACCACGCGTATCATTTCCTGTTGCTAAAACAACAGCATGTATGcc                                                                                                          >  2:745978/1‑141 (MQ=255)
                                     caatcaatCGTTGACGATCTTGATCGTAACGCCATGTAGCAATACCACGATACTGTCCGTCACGACTCGCGTATGCATGCGCACTTGCTTCTGCACCACGCGTATCATTTCCTGTTGCTAAAACAACAGCATGTATGCCAt                                                                                                        >  4:502885/1‑141 (MQ=255)
                                      catcaatcGTTGACGATCTTGATCGTAACGCCATGTAGCAATACCACGATACTGTCCGTCACGCCTCGCGTATGCATGCGCAATTGCTCCTGCCCCACGCCTATCATTTCCTGTTGCTAAAACAACAGCATGTATGCCAtt                                                                                                       <  4:420429/140‑1 (MQ=255)
                                          aatcGTTGACGATCTTGATCGTAACGCCATGTAGCAATACCACGATACTGTCCGTCACGACTCGCGTATGCATGCGCACTTGCTTCTGCACCACGCGTATCATTTCCTGTTGCTAAAACAACAGCATGTATGCCATTCATa                                                                                                   <  3:225998/141‑1 (MQ=255)
                                          aatcGTTGACGATCTTGATCGTAACGCCATGTAGCAATACCACGATACTGTCCGTCACGACTCGCGTATGCATGCGCACTTGCTTCTGCACCACGCGTATCATTTCCTGTTGCTAAAACAACAGCATGTATGCCATTCATa                                                                                                   <  3:551253/141‑1 (MQ=255)
                                          aatcGTTGACGATCTTGATCGTAACGCCATGTAGCAATACCACGATACTGTCCGTCACGACTCGCGTATGCATGCGCACTTGCTTCTGCACCACGCGTATCATTTCCTGTTGCTAAAACAACAGCATGTATGCCATTCATa                                                                                                   <  1:1007799/141‑1 (MQ=255)
                                           atcGTTGACGATCTTGATCGTAACGCCATGTAGCAATACCACGATACTGTCCGTCACGACTCGCGTATGCATGCGCACTTGCTTCTGCACCACGCGTATCATTTCCTGTTGCTAAAACAACAGCATGTATGCCATTCATaa                                                                                                  >  3:111345/1‑141 (MQ=255)
                                           atcGTTGACGATCTTGATCGTAACGCCATGTAGCAATACCACGATACTGTCCGTCACGACTCGCGTATGCATGCGCACTTGCTTCTGCACCACGCGTATCATTTCCTGTTGCTAAAACAACAGCATGTATGCCATTCATaa                                                                                                  >  3:638796/1‑141 (MQ=255)
                                           atcGTTGACGATCTTGATCGTAACGCCATGTAGCAATACCACGATACTGTCCGTCACGACTCGCGTATGCATGCGCACTTGCTTCTGCACCACGCGTATCATTTCCTGTTGCTAAAACAACAGCATGTATGCCATTCATaa                                                                                                  >  1:942448/1‑141 (MQ=255)
                                              gTTGACGATCTTGATCGTAACGCCATGTAGCAATACAACGATACTGTCCGTCACGACTCGCGTATGCATGCGCACTTGCTTCTGCACCACGCGTATCATTTCCTGTTGCTAAAACAACAGCATGTATGCCATTCATAacac                                                                                               >  3:372627/1‑141 (MQ=255)
                                               ttGACGATCTTGATCGTAACGCCATGTAGCAATACCACGATACTGTCCGTCACGACTCGCGTATGCATGCGCACTTGCTTCTGCACCACGCGTATCATTTCCTGTTGCTAAAACAACAGCATGTATGCCATTCATAACAcc                                                                                              >  4:563499/1‑141 (MQ=255)
                                                tGACGATCTTGATCGTAACGCCATGTAGCAATACCACGATACTGTCCGTCACGACTCGCGTATGCATGCGCACTTGCTTCTGCACCACGCGTATCATTTCCTGTTGCTAAAACAACAGCATGTATGCCATTCATAACACCt                                                                                             >  1:670152/1‑141 (MQ=255)
                                                    gATCTTGATCGTAACGCCCTGTAGCAATACCACGATACTGTCCGTCACGACTCGAGTATGCATGCGCACTTGCTTCTGCCCCCCGCGTATCATTTCCTGTTGCTAAATCAACAGCACGTATGCCATTTATAAAACCTttat                                                                                         >  2:819500/1‑141 (MQ=255)
                                                    gATCTTGATCGTAACGCCATGTAGCAATACCACGATACTGTCCGTCACGACTCGCGTATGCATGCGCACTTGCTTCTGCACCACGCGTATCATTTCCTGTTGCTAAAACAACAGCATGTATGCCATTCATAACACCTttat                                                                                         <  1:243948/141‑1 (MQ=255)
                                                     aTCTTGATCGTAACGCCATGTAGCAATACCACGATACTGTCCGTCACGACTCGCGTATGCATGCGCACTTGCTTCTGCACCACGCGTATCATTTCCTGTTGCTAAAACAACAGCATGTATGCCATTCATAACACCTttatt                                                                                        <  2:202450/141‑1 (MQ=255)
                                                         tGATCGTAACGCCATGTAGCAATACCACGATACTGTCCGTCACGACTCGCGTATGCATGCGCACTTGCTTCTGCACCACGCGTATCATTTCCTGTTGCTAAAACAACAGCATGTATGCCATTCATAACACCTTTATTAtgt                                                                                    <  2:385284/141‑1 (MQ=255)
                                                           aTCGTAACGCCATGTAGCAATACCACGAGACTGTCCGTCACGACTCTCGTATGCATGCGCACGTGCTTCTGCACCACTCGTATCATTTCCTGTTGCTAAAACAACAGCATGTATGCCATTCATAACACCTTTATTATgtgt                                                                                  <  1:493068/141‑1 (MQ=255)
                                                           aTCGTAACGCCAGGTAGCAATACCACGATACTGTCCGTCACGACGCGCGTATGCAGTCGCACTTGCTTCTGCACCACGCGTATCATTTCCTGTTGCTAAAACAACAGCATGGATGCCATTCATAACAACTTTATTATgtgt                                                                                  >  4:699293/1‑141 (MQ=255)
                                                             cGTAACGCCATGTAGCAATACCACGATACTGTCCGTCACGACTCGCGTATGCATGCGCACTTGCTTCTGCACCACGCGTATCATTTCCTGTTGCTAAAACAACAGCATGTATGCCATTCATAACACCTTTATTATGTGTtg                                                                                <  4:406499/141‑1 (MQ=255)
                                                             cGTAACGCCATGTAGCAATACCACGATACTGTCCGTCACGACTCGCGTATGCATGCGCACTTGCTTCTGCACCACGCGTATCATTTCCTGTTGCTAAAACAACAGCATGTATGCCATTCATAACACCTTTATTATGTGTtg                                                                                >  2:850632/1‑141 (MQ=255)
                                                              gTAACGCCATGTAGCAATACCACGATACTGTCCGTCACGACTCGCGTATGCATGCGCACTTGCTTCCGCACCACGCGTATCATTTCCTGTTGCTAAAACAACAGCATGTATGCCATTCATAACACCTTTATTATGTGTtgc                                                                               <  2:247655/141‑1 (MQ=255)
                                                                aaCGCCATGTAGCAATACCACGATACTGTCCGTCACGACTCGCGTATGCATGCGCACTTGCTTCTGCACCACGCGTATCATTTCCTGTTGCTAAAACAACAGCATGTATGCCATTCATAACACCTTTATTATGTGTtgctg                                                                             <  4:528155/141‑1 (MQ=255)
                                                                 aCGCCATGTAGCAATACCACGATACTGTCCGTGACGACTCGCGTATGCATGCGCACTTGCTTCTGCACCACGCGTATCATTTCCTGTTGCTAAAACAACAGCATGTATGCCATTCATAACCCCTTTATTATGTGTtgctgc                                                                            >  3:681674/1‑141 (MQ=255)
                                                                 aCGCCATGTAGCAATACCACGATACTGTCCGTCACGACTCGCGTATGCATGCGCCCTTGCTTCTTCACCACGCGTATCATTTCCTGTTGCTAAAACAACAGCATGTATGCCATTCATAACACCTTTATTATGTGTtgctgc                                                                            <  1:1090058/141‑1 (MQ=255)
                                                                   gCCATGTAGCAATACCACGATACTGTCCGTCACGACTCGCGTATGCATGCGCACTTGCTTCTGCACCACGCGTATCAtt                                                                                                                                        <  1:18564/79‑1 (MQ=255)
                                                                    ccATGTAGCAATACCACGATACTGTCCGTCACGACTCGCGTATGCATGCGCACTTGCTTCTGCACCACGCGTATCATTTCCTGTTGCTAAAACAACAGCATGTATGCCATTCATAACACCTTTATTATGTGTTGCTGCACg                                                                         >  1:1127664/1‑141 (MQ=255)
                                                                      aTGTAGCAATACCACGATACTGTCCGTCACGACTCGCGTATGCATGCGCACTTGCTTCTGCACCACGCGTATCATTTCCTGTTGCTAAAACAACAGCATGTATGCCATTCATAACACCTTTATTATGTGTTGCTGCACGAt                                                                       <  1:461259/141‑1 (MQ=255)
                                                                        gTAGCAATACCACGATACTGTCCGTCACGACTCGCGTATGCATGCGCACTTGCTTCTGCACCACGCGTATCATTTCCTGTTGCTAAAACAACAGCATGTATGCCATTCATAACACCTTTATTATGTGTTGCTGCACGATGa                                                                     >  2:491627/1‑141 (MQ=255)
                                                                            cAATAGCACGCTACTGTCTGGTACGACTCGCGTATGCAAGCGCACTTGCTTCTGCACAACGCGTAACATTTACTGTTGCTCAAACGGCAGCATGCATGCGATTCATAACACCTTGATTCGGTGTACCTGCACGATGaggat                                                                 >  4:107080/1‑137 (MQ=255)
                                                                                aCCACGATACTGTCCGTCACGACTCGCGTATGCATGCGCACTTGCTTCTGCACCACGCGTATCATTTCCTGTTGCTAAAACAACAGCATGTATGCCATTCATAACACCTTTATTATGTGTTGCTGCACGATGAATATCTAc                                                             >  1:1143378/1‑141 (MQ=255)
                                                                                 ccACGATACTGTCCGTCACGACTCGCGTATGCATGCGCACTTGCTTCTGCACCACGCGTATCAt                                                                                                                                         <  4:340844/64‑1 (MQ=255)
                                                                                 ccACGATACTGTCCGTCACGACTCGCGTATGCATGCGCACTTGCTTCTGCACCACGCGTATCAt                                                                                                                                         >  3:340844/1‑64 (MQ=255)
                                                                                      aTACTGTCCGTCACGACTCGCGTATGCATGCGCACTTGCTTCTGCACCACGCGTATCATTTCCTGTTGCTAAAACAACAGCATGTATGCCATTCATAACACCTTTATTATGTGTTGCTGCACGATGAATATCTACTTGGGc                                                       <  2:520974/141‑1 (MQ=255)
                                                                                       tACTGTCCGTCACGACTCGCGTATGCATGCGCACTTGCTTCTGCACCACGCGTATCATTTCCTGTTGCTAAAACAACAGCATGTATGCCATTCATAACACCTTTATTATGTGTTGCTGCACGATGAATATCTACTTGGGcc                                                      >  2:1634486/1‑141 (MQ=255)
                                                                                       tACTGTCCGTCACGACTCGCGTATGCATGCGCACTTGCTTCTGCACCACGCGTATCATTTCCTGTTGCTAAAACAACAGCATGTATGCCATTCATAACACCTTTATTATGTGTTGCTGCACGATGAATATCTACTTGGGcc                                                      <  2:70414/141‑1 (MQ=255)
                                                                                       tACTGTCCGTCACGACTCGCGTATGCATGCGCACTTGCTTCTGCACCACGCGTATCATTTCCTGTTGCTAAAACAACAGCATGTATGCCATTCATAACACCTTTATTATGTGTTGCTGCACGATGAATATCTACTTGGGcc                                                      <  2:964021/141‑1 (MQ=255)
                                                                                         cTGTCCGTCACGACTCGCGTATGCATGCGCACTTGCTTCTGCACCACGCGTATCATTTCCTGTTGCTAAAACAACAGCATGTATGCCATTCATAACACCTTTATTATGTGTTGCTGCACGATGAATATCTACTTGGGCCaa                                                    <  2:452966/141‑1 (MQ=255)
                                                                                           gTCCGTCACGACTCGCGTATGCATGCGCACTTGCTTCTGCACCACGCGTATCATTTCCTGTTGCTAAAACAACAGCATGTATGCCATTCATAACACCTTTATTATGTGTTGCTGCACGATGAATATCTACTTGGGCCAATa                                                  <  2:670152/141‑1 (MQ=255)
                                                                                           gTCCGTCACGACTCGCGCATGCATGCGCACTTGCTTCTGCACCACGCGTATCATTTCCTGTTGCTAAAACAACAGCATGTATGCCATTCATAACACCTTTATTATGTGTTGCTGCACGATGAATATCTACTTGGGCCAATa                                                  >  3:627586/1‑141 (MQ=255)
                                                                                             ccGTCACGACTCGCGTATGCATGCGCACTTGCTTCTGCACCACGCGTATCATTTCCTGTTGCTAAAACAACAGCATGTATGCCATTCATAACACCTTTATTATGTGTTGCTGCACGATGAATATCTACTTGGGCCAATACa                                                <  2:1227513/141‑1 (MQ=255)
                                                                                             ccGTCACGACACGCGTATGCATGCGCACTTGCTTCTGCACCACGCGTATCATTTCCTGTTGCTAAAACAACAGCATGTATGCCATTCATAACACCTTTATTATGTGTTGCTGCACGATGAATATCTACTTGGGCCAATACa                                                <  2:1431205/141‑1 (MQ=255)
                                                                                                       tCGCGTATGCATGCGCACTTGCTTCTGCACCACGCGTATCATTTCCTGTTGCTAAAACAACAGCATGTATGCCATTCATAACACCTTTATTATGTGTTGCTGCACGATGAATATCTACTTGGGCCAATACAGAAGCACGtt                                      <  1:1647094/141‑1 (MQ=255)
                                                                                                        cgcgtggtgcagaagcaagtgcgcatgcatacgcgTATCATTTCCTGTTGCTAAAACAACAGCATGTATGCCATTCATAACACCTTTATTATGTGTTGCTGCACGATGAATATATACTTGGGCCAATACAGAAGCACGTTc                                     >  4:132236‑M2/36‑141 (MQ=255)
                                                                                                        CGCGTATGCATGCGCACTTGCTTCTGCACCACGCGTATCATTTCCTGTTGCTAAAACAACAGCATGTATGCCATTCATAACACCTTTATTATGTGTTGCTGCACGATGAATATCTACTTGGGCCAATACAGAAGCACGTTc                                     >  2:1177951‑M1/1‑141 (MQ=255)
                                                                                                        CGCGTATGCATGCGCACTTGCTTCTGCACCACGCGTATCATTTCCTGTTGCTAAAACAACAGCATGTATGCCATTCATAACACCTTTATTATGTGTTGCTGCACGATGAATATCTACTTGGGCCAATACAGAAGCACGTTc                                     >  4:251035‑M1/1‑141 (MQ=255)
                                                                                                           GTATGCATGCGCACTTGCTTCTGCACCACGCGTATCATTTCCTGTTGCTAAAACAACAGCATGTATGCCATTCATAACACCTTTATTATGTGTTGCTGCACGATGAATATCTACTTGGGCCAATACAGAAGCACGTTCCAt                                  <  2:528950‑M1/141‑1 (MQ=255)
                                                                                                              tgcatgcGCACTTGCTTCTGCACCACGCGTATCATTTCCTGTTGCTAAAACAACAGCATGTATGCCATTCATAACACCTTTATTATGTGTTGCTGCACGATGAATATCTACTTGGGCCAATACAGAAGCACGTTCCATTCg                               >  2:88533/1‑141 (MQ=255)
                                                                                                              tgcatgcGCACTTGCTTCTGCACCACGCGTATCATTTCCTGTTGCTAAAACAACAGCATGTATGCCATTCATAACACCTTTATTATGTGTTGCTGCACGATGAATATCTACTTGGGCCAATACAGAAGCACGTTCCATTCg                               <  3:120204/141‑1 (MQ=255)
                                                                                                               gcatgcGCACTTGCTTCTGCACCACGCGTATCATTTCCTGTTGCTAAAACAACAGCATGTATGCCATTCATAACACCTTTATTATGTGTtgctgc                                                                            >  4:326561/1‑95 (MQ=255)
                                                                                                               gcatgcGCACTTGCTTCTACACCACGCGTATCATTTCCTGTTGCTAAAACAACAGCATGTATGCCATTCATAACACCTTTATTATGTGTTGCTGCACGATGAATATCTACTTGGGCCAATACAGAAGCACGTTCCATTCGt                              <  1:1199618/141‑1 (MQ=255)
                                                                                                                  tgcGCACTTGCTTCTGCACCACGCGTATCATTTCCTGTTGCTAAAACAACAGCATGTATGCCATTCATAACACCTTTATTATGTGTTGCTGCACGATGAATATCTACTTGGGCCAATACAGAAGCACGTTCCATTCGTTTg                           >  4:543802/1‑141 (MQ=255)
                                                                                                                     gcACTTGCTTCTGCACCACGCGTATCATTTCCTGTTGCTAAAACAACAGCATGTATGCCATTCATAACACCTTTATTATGTGTTGCTGCACGATGAATATCTACTTGGGCCAATACAGAAGCACGTTCCATTCGTTTGGCa                        <  2:638898/141‑1 (MQ=255)
                                                                                                                     gcACTTGCTTCTGCACCACGCGTATCATTTCCTGTTGCTAAAACAACAGCATGTATGCCATTCATAACACCTTTATTATGTGTTGCTGCACGATGAATATCTACTTGGGCCAATACAGAAGCACGTTCCATTCGTTTGGCa                        >  2:1552224/1‑141 (MQ=255)
                                                                                                                      cACTTGCTTCTGCACCACGCGTATCATTTCCTGTTGCTAAAACAACAGCATGTATGCCATTCATAACACCTTTATTATGTGTTGCTGCACGATGAATATCTACTTGGGCCAATACAGAAGCACGTTCCATTCGTTTGGCaa                       >  2:342578/1‑141 (MQ=255)
                                                                                                                      cACTTGCTTCTGCACCACGCGTATCATTTCCTGTTGCTAAAACAACAGCATGTATGCCATTCATAACACCTTTATTATGTGTTGCTGCACGATGAATATCTACTTGGGCCAATACAGAAGCACGTTCCATTCGTTTGGCaa                       <  1:817880/141‑1 (MQ=255)
                                                                                                                        cTTGCTTCTGCACCACGCGTATCATTTCCTGTTGCTAAAACAACAGCATGTATGCCATTCATAACACCTTTATTATGTGTTGCTGCACGATGAATATCTACTTGGGCCAATACAGAAGCACGTTCCATTCGTTTGGCAAcc                     <  3:321372/141‑1 (MQ=255)
                                                                                                                          tGCTTCTGCACCACGCGTATCATTTCCTGTTGCTAAAACAACAGCATGTATGCCATTCATAACACCTTTATTATGTGTTGCTGCACGATGAATATCTACt                                                            <  1:1222011/100‑1 (MQ=255)
                                                                                                                          tGCTTCTGCACCACGCGTATCATTTCCTGTTGCTAAAACAACAGCATGTATGCCATTCATAACACCTTTATTATGTGTTGCTGCACGATGAATATCTACt                                                            >  2:1222011/1‑100 (MQ=255)
                                                                                                                          tGCTTCTGCACCACGCGTATCATTTCCTGTTGCTAAAACAACAGCATGTATGCCATTCATAACACCTTTATTATGTGTTGCTGCACGATGAATATCTACTTggg                                                        <  1:1375128/104‑1 (MQ=255)
                                                                                                                          tGCTTCTGCACCACGCGTATCATTTCCTGTTGCTAAAACAACAGCATGTATGCCATTCATAACACCTTTATTATGTGTTGCTGCACGATGAATATCTACTTggg                                                        >  2:1375128/1‑104 (MQ=255)
                                                                                                                           gCTTCTGCACCACGCGTATCATTTCCTGTTGCTAAAACAACAGCATGTATGCCATTCATAACACCTTTATTATGTGTTGCTGCACGATGAATATCTACTTGGGCCAATACAGAAGCACGTTCCATTCGTTTGGCAACctct                  <  4:231733/141‑1 (MQ=255)
                                                                                                                              tCTGCACCACGCGTATCATTTCCTGTTGCTAAAACAACAGCATGTATGCCATTCATAACACCTTTATTATGTGTTGCTGCACGATGAATATCTACTTGGGCCAATACAGAAGCACGTTCCATTCGTTTGGCAACCtcttct               <  4:658950/141‑1 (MQ=255)
                                                                                                                                  caccacGCGTATCATTTCCTGTTGCTAAAACAACAGCATGTATGCCATTCATAACACCTTTATTATGTGTTGCTGCACGATGAATATCTACTTGGGCCAATACAGAAGCACGTTCCATTCGTTTGGCAACCTCTTCTCCAg           >  2:1476283/1‑141 (MQ=255)
                                                                                                                                  caccacGCGTATCATTTCCTGTTGCTAAAACAACAGCATGTATGCCATTCATAACACCTTTATTATGTGTTGCTGCACGATGAATATCTACTTGGGCCAATACAGAAGCACGTTCCATTCGTTTGGCAACCTCTTCTCCAg           >  3:268534/1‑141 (MQ=255)
                                                                                                                                    ccacGCGTATCATTTCCTGTTGCTAAAACAACAGCATGTATGCCATTCATAACACCTTTATTATGTGTTGCTGCACGATGAATATCTACTTGGGCCAATACAGAAGCACGTTCCATTCGTTTGGCAACCTCTTCTCCAGtt         >  1:275340/1‑141 (MQ=255)
                                                                                                                                     cacGCGTATCATTTCCTGTTGCTAAAACAACAGCATGTATGCCATTCATAACACCTTTATTATGTGTTGCTGCACGATGAATATTTACTTGGGCCAATACAGAAGCACGTTCCATTCATTTGGCAACCTCTTCTCCAGTtc        >  1:159000/1‑141 (MQ=255)
                                                                                                                                       cgcgTATCATTTCCTGTTGCTAAAACAACAGCATGTATGCCATTCATAACACCTTTATTATGTGTTGCTGCACGATGAATATCTACTTGGGCCAATACAGAAGCACGTTCCATTCGTTTGGCAACCTCTTCTCCAGTtctc      >  3:580977‑M2/5‑141 (MQ=255)
                                                                                                                                       cgcgTATCATTTCCTGTTGCTAAAACAACAGCATGTATGCCATTCATAACACCTTTATTATGTGTTGCTGCACGATGAATATCTACTTGGGCCAATACAGAAGCACGTTCCATTCGTTTGGCAACCTCTTCTCCAGTtctc      <  3:152366‑M2/137‑1 (MQ=255)
                                                                                                                                       cgcgTATCATTTCCTGTTGCTAAAACAACAGCATGTATGCCACTCATAACACCTTTATTATGTGTTGCTGCACGATGAATATCTACTTGGGCCAATACAGAAGCACGTTCCATTCGTTTGGCAACCTCTTCTCCAGTtctc      <  1:944585‑M2/137‑1 (MQ=255)
                                                                                                                                           tATCATTTCCTGTTGCTAAAACAACAGCATGTATGCCATTCATAACACCTTTATTATGTGTTGCTGCACGATGAATATCTACTTGGGCCAATACAGAAGCACGTTCCATTCGTTTGGCAACCTCTTCTCCAGTTCTCTCGc  >  4:278926/1‑141 (MQ=255)
                                                                                                                                           |                                                                                                                                            
CCAACGATTGCCAATGTCATAGGCACTTCAATTGTACCAATCAATCGTTGACGATCTTGATCGTAACGCCATGTAGCAATACCACGATACTGTCCGTCACGACTCGCGTATGCATGCGCACTTGCTTCTGCACCACGCGTATCATTTCCTGTTGCTAAAACAACAGCATGTATGCCATTCATAACACCTTTATTATGTGTTGCTGCACGATGAATATCTACTTGGGCCAATACAGAAGCACGTTCCATTCGTTTGGCAACCTCTTCTCCAGTTCTCTCGC  >  USA300TCH1516_ALE/2681845‑2682124

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.