Predicted mutation
evidence seq id position mutation annotation gene description
RA USA300TCH1516_ALE 2,352,815 G→A A92V (GCA→GTA)  rpsI ← 30S ribosomal protein S9

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE2,352,8150GA98.8% 248.9 / NA 86A92V (GCA→GTA) rpsI30S ribosomal protein S9
Reads supporting (aligned to +/- strand):  ref base G (0/0);  major base A (47/38);  minor base C (0/1);  total (47/39)
Fisher's exact test for biased strand distribution p-value = 4.53e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

ATCGTCCGACAATTAACGTTTTGAGAATTGAGGTGAACGACGAGCTGCTTTAAGACCTGGTTTTTTACGTTCTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTGCTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAACCACCACCATGAACGTTAACTAAAACATCATAGTTACCTTTAGTTTCAGTTACATCAAATGGTTGGTTTAAGTCTAAAA  >  USA300TCH1516_ALE/2352679‑2352950
                                                                                                                                        |                                                                                                                                       
atCGTCCGACAATTAACGTTTTGAGAATTGAGGTGAACGACGGGCTGCTTTAAGACCTGGTTTTTTACGTTCTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACtt                                                                                                                                      <  2:625169/140‑1 (MQ=255)
      cGACAATTATCGTTTTGAGAATTGAGGTGTACGACGAGCTGCTTTAAGTCCTGGTTTTTTACGTTCTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCtaata                                                                                                                                <  2:778264/140‑1 (MQ=255)
      cGACAATTAACGTTTTGAGAATTGAGGTGAACGACGAGCTGCTTTAAGACCTGGTTTTTTACGTTCTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCtaata                                                                                                                                <  2:677134/140‑1 (MQ=255)
       gACAATTAACGTTTTGAGAATTGAGGTGAACGACGAGCTGCTTTAAGACCTGGTTTTTTACGTTCTTTCATACGTGGGTCACGAGTAAGTATTCCAGCGCGTTTTAAAGCCACTCTGTATTCGGGGTCCACTTTtagtaa                                                                                                                               >  2:96286/1‑140 (MQ=25)
        aCAATTAACGTTTTGAGAATTGAGGTGAACGACGAGCTGCTTTAAGACCTGGTTTTTTACGTTCTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTaataat                                                                                                                              >  2:643492/1‑140 (MQ=255)
         cAATTAACGTTTTGAGAATTGAGGTGAACGACGAGCTGCTTTAAGACCTGGTTTTTTACGTTCTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTaataatt                                                                                                                             >  2:821264/1‑139 (MQ=255)
         cAATTAACGTTTTGAGAATTGAGGTGAACGACGAGCTGCTTTAAGACCTGATTTTTTACGTTCTTTCATACGTGGGTCACGAGTAAGTAATCCAGGGCGTTTTAAAGAACCTCTTTATTCGGGATCTACTTCTTATAATg                                                                                                                             >  2:742421/1‑140 (MQ=37)
         cAATTAACGTTTTGAGAATTGAGGTGAACGACGAGCTGCTGTAAGACCTGGTTTTTTACGTTCTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTGTCATAATg                                                                                                                             >  2:502064/1‑140 (MQ=255)
          aaTTAACGTTTTGAGAATTGAGGTGAACGACGAGCTGCTTTAAGACCTGGTTTTTTACGTTCTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGc                                                                                                                            >  1:592852/1‑140 (MQ=255)
          aaTTAACGTTTTGAGAATTGAGGTGAACGACGAGCTGCTTTAAGACCTGGTTTTTTACGTTCTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGc                                                                                                                            <  1:464505/140‑1 (MQ=255)
          aaTTAACGTTTTGAGAATTGAGGTGAACGACGAGCTGCTTTAAGACCTGGTTTTTTACGTTCTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAAAACCTCTGTATTCAGGATCTACTTCTaataattc                                                                                                                            >  2:24520/1‑138 (MQ=255)
          aaTTAACGTTTTGAGAATTGAGGTGAACGACGAGCTGCTTTAAGACCTGGTTTTTTACGTTCTTTCATACGTGGGTCACCAGTAAGTGATCCAGCGCGGTTTAAAGAACCTCTGTATTCAGGGTCTACTTCTAATAATGc                                                                                                                            >  2:860285/1‑140 (MQ=38)
               aCGTTTTGAGAATTGAGGTGAACGACGAGCTGCTTTAAGACCTGGTTTTTTACGTTCTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAg                                                                                                                       >  1:391120/1‑140 (MQ=255)
               aCGTTTTGAGAATTGAGGTGAACGACGAGCTGCTTTAAGACCTGGTTTTTTACGTTCTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAg                                                                                                                       >  1:571841/1‑140 (MQ=255)
                cGTTTTGAGTATTGAGGTGAACGACGAGCTGCTTTAAGACCTGGTTTTTTACGTTCTTTCATACGTGGGTCACGACTGAGTAATCCAGCGCGTATTAAAGAACCACTGCATTCCGGATCTACCTCTAATAATGCACGAGc                                                                                                                      >  2:745035/1‑140 (MQ=38)
                cGTTTTGAGAATTGAGGTGAACGACGAGCTGCTTTAAGACCTGGTTTTTTACGTTCTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGAACTACTTCTAATAATGCACGAGc                                                                                                                      >  1:14283/1‑140 (MQ=255)
                   tttGAGAATTGAGGTGAACGACGAGCTGCTTTAAGACCTGGTTTTTTACGTTCTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGAt                                                                                                                   <  1:135527/140‑1 (MQ=255)
                   tttGAGAATTGAGGTGAACGACGAGCTGCTTTAAGACCTGGTTTTTTACGTTCTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGAt                                                                                                                   <  1:159797/140‑1 (MQ=255)
                      gagaATTGAGGTGAACGACGAGCTGCTTTAAGACCTGGTTTTTTACGTTCTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTcc                                                                                                                <  1:301751/140‑1 (MQ=255)
                        gaATTGAGGTGAACGACGAGCTGCTTTAAGACCTGGTTTTTTACGTTCATTCATACGTGGATCACGAGTAAGTAATCCAGCGCGTTGTCAAGAACCTCTGTATTAAGGATCTACTTCTAATAATGCACGAGCGCTTCCGt                                                                                                              >  2:262457/1‑140 (MQ=38)
                          aTTGAGGTGAACGACGAGCTGCTTTAAGACCTGGTTTTTTACGTTCTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGa                                                                                                            >  1:314760/1‑140 (MQ=255)
                            tGAGGTGAACGACGAGCTGCTTTAAGACCTGGTTTTTTACGTTCTTTCATAGGTGGGTCACGAGTAAGTATTCCAGCGGGGTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATACTGCACGAGGGATTCGGTGACg                                                                                                          >  2:807096/1‑140 (MQ=255)
                               ggTGAACGACGAGCTGCTTTAAGACCTGGTTTTTTACGTTCTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGAt                                                                                                       <  1:458891/140‑1 (MQ=255)
                               ggTGAACGACGAGCTGCTTTAAGACCTGGTTTTTTACGTTCTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGAt                                                                                                       <  1:965558/140‑1 (MQ=255)
                                       cagggctgctTTAAGACCTGGTTTTTTACGTTCTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATagcttgag                                                                                               <  2:774710/136‑1 (MQ=255)
                                        cgaGCTGCTTTAAGACCTGGTTTTTTACGTTCTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATagcttgagc                                                                                              <  1:643492/140‑1 (MQ=255)
                                            ttgctTTAAGACGTGGTTTTTTACGTTCTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGt                                                                                          <  1:766100/139‑1 (MQ=255)
                                               ctTTAAGACCTGGTTTTTTACGTTCTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCGTGTCCa                                                                                       >  1:420234/1‑140 (MQ=255)
                                                 ttAAGACCTGGTTTTTTACGTTCTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGt                                                                                     <  1:975451/140‑1 (MQ=255)
                                                    aggccTGGTTTTTTACGTTCTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTTACGGATAGCTTGAGCTTGTCCAGTGaa                                                                                  <  2:595368/137‑1 (MQ=255)
                                                      aCCTGGTTTTTTACGTTCTTTCATACGTTGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGCACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACAGATAGCTTTAGCTTGTCCAGTGCAac                                                                                >  2:478547/1‑140 (MQ=255)
                                                      aCCTGGTTTTTTACGTTCTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAac                                                                                >  1:671466/1‑140 (MQ=255)
                                                           gTTTTTTACGTTCTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAaccacca                                                                           <  1:678545/140‑1 (MQ=255)
                                                            ttttttACGTTCTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGGGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAacaaccac                                                                          >  1:312057/1‑140 (MQ=255)
                                                             tttttGCGGTCTTCTATCCGTTGGTCACGAGTATGTAATTCAGCGCGTTTTAAAGAACCTCTGTATTCAGGACCTATTTCTAATAATGCACGTGCCATTCCGTGACGGATAGTTTGAGCTTGTCAAGTGAAaccaccacc                                                                         <  2:40049/140‑1 (MQ=255)
                                                             tttttACGTTCTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAaccaccacc                                                                         <  2:809660/140‑1 (MQ=255)
                                                             tttttACGTTCTTTCATACGTGGGTAACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCGGTGACGGGTAGCTGGAGCTTGTCCAGTGAGaccacaccc                                                                         >  2:64650/1‑136 (MQ=255)
                                                             tttttACGGTTTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAaccaccacc                                                                         <  2:223817/140‑1 (MQ=255)
                                                             gggttACGGTATTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTGTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGACaccaccacc                                                                         >  2:487177/4‑140 (MQ=255)
                                                               tttACGTTCTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATATAGTACGCGCTTCTCCGTGTCGGATAGCTTGAGCTTGTCCAGTGAAACCCCCACCAt                                                                       >  1:27814/1‑140 (MQ=255)
                                                               tttACGTTCTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAACCACCACCAt                                                                       <  1:900005/140‑1 (MQ=255)
                                                               tttACGTTCTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAACAACCACCAt                                                                       >  1:5923/1‑140 (MQ=255)
                                                                ttACGTTCTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAACCACCACCATg                                                                      <  2:234467/140‑1 (MQ=255)
                                                                 tACGTTCTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAACCACCACCATGa                                                                     >  1:979427/1‑140 (MQ=255)
                                                                 tACGTTCTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAACCACCACCATGa                                                                     >  1:271390/1‑140 (MQ=255)
                                                                  aCGTTCTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAATGAAACAACCACCCTGaa                                                                    >  2:22674/1‑140 (MQ=255)
                                                                  aCGTTCTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACAGCTGTATTCAGGATCGACTTCTAATCATGCCAGAGCGATTACGTGACGGATAGCTTGACCTTGTCCAGTGAAACCACCACCATGag                                                                    >  2:160456/1‑139 (MQ=255)
                                                                   cGTTCTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAACCCCCACCATGAAc                                                                   >  1:787432/1‑140 (MQ=255)
                                                                         ttCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAACCACCACCATGAACGTTAAc                                                             >  1:570309/1‑140 (MQ=255)
                                                                         ttCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCGCTGTATTCAGGATCTACTTCTAATAATGCACGGGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAACCACCACCATGAACGTTAAc                                                             <  1:154655/140‑1 (MQ=255)
                                                                           cATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAACCACCACCCTGAACGTTAACTa                                                           >  1:185287/1‑140 (MQ=255)
                                                                           cATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAACCACCACCATGAACGTTAACTa                                                           >  1:906643/1‑140 (MQ=255)
                                                                           cATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAACCACCACCATGAACGTTAACTa                                                           >  1:909223/1‑140 (MQ=255)
                                                                           cATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAACCACCACCATGAACGTTAACTa                                                           <  2:324717/140‑1 (MQ=255)
                                                                           cATACGTGGGTCACGAGTAACTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGAGCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTCAAACCACCACCATGAACGTTAACTa                                                           >  1:607138/1‑140 (MQ=255)
                                                                            aTACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAACCACCACCATGAACGTTAACTaa                                                          <  2:571841/140‑1 (MQ=255)
                                                                            aTACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAACCACCACCATGAACGTTAACTaa                                                          <  2:391120/140‑1 (MQ=255)
                                                                              aagTGCGTCACGAGTAAGTAATCCAACGCGTTTCAAAGACAATCTGTATTCAGGATATAGTCCTTATAATGGTCGCGCGATTCAGTGATAGCTAGCCTGGCCTAGTCCACTGAAACCACCACGATGAACGTTAACTatag                                                        >  2:333226/3‑137 (MQ=255)
                                                                                gTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAACCACCACCATGAACGTTAACTAAAAca                                                      <  2:42766/140‑1 (MQ=255)
                                                                                       aCGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAACCACCACCATGAACGTTAACTAAAACCTCATAGt                                               >  2:821490/1‑140 (MQ=255)
                                                                                       aCGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAACCACCACCATGAACGTTAACTAAAACATCATAGt                                               >  2:926668/1‑140 (MQ=255)
                                                                                       aCGAGTAAGTAATCCAGCGCCTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAACCACCACCCTGAACGTTAACTAAAACATCATAGt                                               >  1:609088/1‑140 (MQ=255)
                                                                                        cGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGAACTACTTCTAATAATTCAGGAACGATTCCGTGACGGATAACGTGAGCTTGTCCGGTGCAACCTACACCATGAACGTTATGTAAAAGATCATAGta                                              >  2:532925/1‑139 (MQ=255)
                                                                                         gAGTAAGGAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACTGATAGCTTGAGCTTGTCCAGTGAAACCACCACCATGAACGTTAACTAAAACATCATAGTTa                                             <  2:573408/140‑1 (MQ=255)
                                                                                                 aaTCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAACCACCACCATGAACGTTAACTAAAACATCATAGTTACCTTTAGt                                     <  2:536115/140‑1 (MQ=255)
                                                                                                  aTCCAGCGCGTTTTAAAGAACCGCTGGATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAACCACCACCATTAACGTTAACTAAAACATCATAGTTACCTTTAGtt                                    <  2:359566/140‑1 (MQ=255)
                                                                                                  aTCCAGCGCCTCTTAAACAACCTCTGTATTCAGCATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAACCACCACCATGAACGTTAACTAAAACATCATAGTTACCTTTAGtt                                    <  2:298080/140‑1 (MQ=255)
                                                                                                    ccAGCGCGTTTTAAAGAACCTCTTTATTAAAGTGCAACGTCTAATAATGCTCGTGCGAGTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAACCACCACCACGAACGTTAACTAAAACATCATAGTTACCTTTAGTTTc                                  <  1:883783/140‑1 (MQ=255)
                                                                                                    ccAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAACCACCACCATGAACGTTAACTAAAACATCATAGTTACCTTTAGTTTc                                  <  1:670207/140‑1 (MQ=255)
                                                                                                            ttttAAAGAACCTCTGTATTCAGGATATACTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAACCACCACCATGAACGTTAACTAAAACATCATAGTTACCTTTAGTTTCAGTCACAt                          >  2:168768/1‑140 (MQ=255)
                                                                                                             tttAAAGAACCTATGTATTCAAGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAACCACCACCATGCACGTCACCTAAAACATCATAGTTACCTTTAGTTTCAGTTACATc                         >  1:520648/1‑140 (MQ=255)
                                                                                                                 aaGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAACCACCACCATGAACGTTAACTAAAACATCATAGTTACCTTTAGTTTCAGTTACATCACAt                     >  1:367529/1‑140 (MQ=255)
                                                                                                                   gagccTCTGTATTCAGGATCTCCTTCTAATAATGGACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAACCACCACCATGAACGTTAACTAAAACATCATAGTTACCTTTAGTTTCAGTTACATCAAAtgg                   <  1:324962/137‑1 (MQ=255)
                                                                                                                       ctctGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGGGGTTGTCCAGTGAAACCACCACCATGAAGGTTAATTTAAACATCATAGTTTCCTTTAGTTTCAGTTTCATCAAGcggttgg               >  2:139247/1‑140 (MQ=255)
                                                                                                                         ctGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAACCACCACCATGAACGTTAACTCAAACATCATAGTTACCTTTAGTTTCAGTTACATCAAATggttggtt             <  2:641385/140‑1 (MQ=255)
                                                                                                                          tGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAACCACCACCATGAACGTTAACTAAAACATCATAGTTACCTTTAGTTTCAGTAACATCAAAGggatggtta            >  1:161892/1‑139 (MQ=255)
                                                                                                                            tATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCGGTGAAACCACCCCCATGAACGTTAACTAAAACATCATAGTTACCTTTCGTTTCAGTTACATCAAAtggttcttttga          >  2:354440/1‑133 (MQ=255)
                                                                                                                            tATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAACCACCACCATGAACGTTAACTAAAACATCATAGTTACCTTTAGTTTCAGTTACATCAAATGGTTGGTTTaa          <  1:1005885/140‑1 (MQ=255)
                                                                                                                            tATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATAACTTGAGCTTGTCCAGTGAAACCACCACCATGAACGTTAACTAAAACATCATAGTTACCTTTAGTTTCAGTTCCATCAATAGGTTGttttca          >  2:100410/1‑138 (MQ=255)
                                                                                                                             aTTCAGGATCTACTTCTAATAATGCACGCGCCACTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAACCACCACCATGAACGTTAACTAAAACATCTTAGTTACCTTTAGTTTCAGTTACATCAAATGGTTGGTTTAAg         <  2:441899/140‑1 (MQ=255)
                                                                                                                              ttCAGGATCTACCTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCACTGAACCCACTACCATTAACGTTAACTAAAACATCATAGTTACCTTTAGTTTCAGTTACATCAAATGGTTGGTTTAAGt        <  2:605326/140‑1 (MQ=255)
                                                                                                                               tCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAACCACCACCATGAACGTTAACTAAAACATCATAGTTACCTTTAGTTTCAGTTACATCAAATGGTTGGTTTAAGTc       <  1:916925/140‑1 (MQ=255)
                                                                                                                               tCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAACCACCACCATGAACGTTAACTAAAACATCATAGTTACCTTTAGTTTCAGTTACATCAAATGGTTGGTTTAAGTc       <  2:924635/140‑1 (MQ=255)
                                                                                                                                 aGGATCTACTTCTAATAATACACCAGCGATTCCGTGACGGATAGCTTGAGCTTGTACAGTGAAACCACCACCATGAACGTTAACTAAAACATCATAGTTACCTTTAGTTTCGGTTCAGTCAAATGGATAGTTTAAGTcga     >  2:810687/1‑138 (MQ=255)
                                                                                                                                    aTCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAACCACCACCATGAACGTTAACTAAAACATCATAGTTACCTTTAGTTTCAGTTACATCAAATGGTTGGTTTAATGCTaaaa  >  1:99222/1‑140 (MQ=255)
                                                                                                                                    aTCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAACCACCACCATGAACGTTAACTAAAACATCATAGTTACCTTTAGTTTCAGTTACATCAAATGGTTGGTTTAAGTCTaaaa  <  2:787432/140‑1 (MQ=255)
                                                                                                                                        |                                                                                                                                       
ATCGTCCGACAATTAACGTTTTGAGAATTGAGGTGAACGACGAGCTGCTTTAAGACCTGGTTTTTTACGTTCTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTGCTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAACCACCACCATGAACGTTAACTAAAACATCATAGTTACCTTTAGTTTCAGTTACATCAAATGGTTGGTTTAAGTCTAAAA  >  USA300TCH1516_ALE/2352679‑2352950

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑