Predicted mutation
evidence seq id position mutation freq annotation gene description
RA USA300TCH1516_ALE 1,440,085 G→T 22.1% intergenic (‑45/+126) cspA_2 ← / ← USA300TCH1516_01338 Cold shock protein CspA/hypothetical protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE1,440,0850GT22.1% 330.3 / 92.5 136intergenic (‑45/+126)cspA_2/USA300TCH1516_01338Cold shock protein CspA/hypothetical protein
Reads supporting (aligned to +/- strand):  ref base G (62/43);  new base T (18/12);  total (80/56)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.91e-01

Only 100 of 138 total aligned reads displayed.

CGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTA  >  USA300TCH1516_ALE/1439995‑1440174
                                                                                          |                                                                                         
cGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCg                                                                                           >  1:51538/1‑91 (MQ=255)
   aTCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCat                                                                                        <  1:2675189/91‑1 (MQ=255)
     ccTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCatat                                                                                      <  1:2450138/91‑1 (MQ=255)
     ccTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCatat                                                                                      <  1:2020685/91‑1 (MQ=255)
      cTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATAtt                                                                                     >  1:1124299/1‑91 (MQ=255)
      cTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATAtt                                                                                     <  1:195981/91‑1 (MQ=255)
      cTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATAtt                                                                                     >  1:51367/1‑91 (MQ=255)
       tttttCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTa                                                                                    >  1:2110477/1‑91 (MQ=255)
       tttttCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTa                                                                                    >  1:3398977/1‑91 (MQ=255)
        ttttCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTAc                                                                                   <  1:497383/91‑1 (MQ=255)
          ttCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACaa                                                                                 <  1:2223016/91‑1 (MQ=255)
           tCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATCTTACaaa                                                                                >  1:2082032/1‑91 (MQ=255)
             aGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACaaaaa                                                                              >  1:2527322/1‑91 (MQ=255)
             aGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACaaaaa                                                                              >  1:2524606/1‑91 (MQ=255)
                gTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTTCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACAAAAAATa                                                                           >  1:3776371/1‑91 (MQ=255)
                gTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACAAAAAATa                                                                           >  1:1986454/1‑91 (MQ=255)
                gTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACAAAAAATa                                                                           >  1:1207160/1‑91 (MQ=255)
                 ttAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACAAAAAATAc                                                                          >  1:1227235/1‑91 (MQ=255)
                  tAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACAAAAAATACa                                                                         <  1:1433871/91‑1 (MQ=255)
                  tAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACAAAAAATACa                                                                         <  1:1433859/91‑1 (MQ=255)
                  tAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGAATATTACAAAAAATACa                                                                         >  1:2022908/1‑91 (MQ=255)
                    aaCCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACAAAAAATACATg                                                                       <  1:3487128/91‑1 (MQ=255)
                    aaCCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACAAAAAATACATg                                                                       <  1:3487538/91‑1 (MQ=255)
                    aaCCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACAAAAAATACATg                                                                       <  1:1730727/91‑1 (MQ=255)
                     aCCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGc                                                                      <  1:632663/91‑1 (MQ=255)
                      ccATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCa                                                                     >  1:1795300/1‑91 (MQ=255)
                      ccATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCa                                                                     >  1:143274/1‑91 (MQ=255)
                       cATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACAAAAAATACATGCaa                                                                    >  1:676515/1‑91 (MQ=255)
                       cATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACAAAAAATACATGCaa                                                                    >  1:1702255/1‑91 (MQ=255)
                          ttAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACAAAAAATACATGCAAAtt                                                                 <  1:3059009/91‑1 (MQ=255)
                             aCTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACAAAAAATACATGCAAATTTCa                                                              >  1:3804944/1‑91 (MQ=255)
                                gTACATTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACAAAAAATACATGCAAATTTCACTc                                                           >  1:672561/1‑91 (MQ=255)
                                  aCCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACAAAAAATACATGCAAATTTCACTCaa                                                         >  1:1759933/1‑91 (MQ=255)
                                   ccTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCaaa                                                        <  1:3936079/91‑1 (MQ=255)
                                   ccTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACAAAAAATACATGCAAATTTCACTCaaa                                                        >  1:2833585/1‑91 (MQ=255)
                                   ccTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACAAAAAATACATGCAAATTTCACTCaaa                                                        <  1:3372579/91‑1 (MQ=255)
                                   ccTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACAAAAAATACATGCAAATTTCACTCaaa                                                        <  1:878413/91‑1 (MQ=255)
                                   ccTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACAAAAAATACATGCAAATTTCACTCaaa                                                        <  1:2350959/91‑1 (MQ=255)
                                    cTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAat                                                       >  1:191429/1‑91 (MQ=255)
                                     ttGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGTATATTACAAAAAATACATGCAAATTTCACTCAAata                                                      >  1:1272857/1‑91 (MQ=255)
                                     ttGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACAAAAAATACATGCAAATTTCACTCAGata                                                      >  1:3343482/1‑91 (MQ=255)
                                     ttGTTACATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACAAAAAATACATGCAAATTTCACTCAAata                                                      >  1:3815898/1‑91 (MQ=255)
                                       gTTTCATAATCTGAAACCTTCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACAAAAAATACATGCAAATTTCACTCAAATAtt                                                    <  1:150768/91‑1 (MQ=255)
                                       gTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATAtt                                                    >  1:1667266/1‑91 (MQ=255)
                                        tttCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACAAAAAATACATGCAAATTTCACTCAAATATTc                                                   >  1:2465170/1‑91 (MQ=255)
                                          tCATAATCTGAAAGCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCtt                                                 <  1:1078444/91‑1 (MQ=255)
                                          tCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCtt                                                 >  1:4130735/1‑91 (MQ=255)
                                          tCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCtt                                                 <  1:3236471/91‑1 (MQ=255)
                                           cATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCttt                                                <  1:2550107/91‑1 (MQ=255)
                                           cATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCttt                                                <  1:2549735/91‑1 (MQ=255)
                                           cATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCttt                                                >  1:2986147/1‑91 (MQ=255)
                                            aTAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTg                                               <  1:3992122/91‑1 (MQ=255)
                                            aTAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTg                                               >  1:3623005/1‑91 (MQ=255)
                                             tAATCTGAAACCTCCAAGACTAAAATTCATTCAATATTCTTATTCGCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGc                                              >  1:3491675/1‑91 (MQ=255)
                                             tAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGc                                              >  1:2654863/1‑91 (MQ=255)
                                             tAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGc                                              >  1:2655214/1‑91 (MQ=255)
                                             tAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGc                                              <  1:611893/91‑1 (MQ=255)
                                             tAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGc                                              >  1:690391/1‑91 (MQ=255)
                                             tAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGc                                              <  1:3922107/91‑1 (MQ=255)
                                             tAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGc                                              >  1:3802654/1‑91 (MQ=255)
                                             tAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACAAAAAATACATGCAAATCTCACTCAAATATTCATTGc                                              >  1:1009648/1‑91 (MQ=255)
                                                tCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTAATTCGCATATTACCAAAAATACATGCATATTTCACTCAAATATTCTTGGCAat                                           >  1:3864707/1‑91 (MQ=255)
                                                 cTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAata                                          >  1:3781917/1‑91 (MQ=255)
                                                 cTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAata                                          >  1:3781575/1‑91 (MQ=255)
                                                 cTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAata                                          <  1:2429264/91‑1 (MQ=255)
                                                  tGAACCCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAatat                                         <  1:2978728/91‑1 (MQ=255)
                                                  tGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAatat                                         >  1:3914824/1‑91 (MQ=255)
                                                      aCCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGaa                                     >  1:2996646/1‑91 (MQ=255)
                                                       ccTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGaat                                    <  1:3055273/91‑1 (MQ=255)
                                                         tCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGaataa                                  >  1:3485555/1‑91 (MQ=255)
                                                            aaGACTAAAATTCATTCAATATGCTTATTCGCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAatca                               >  1:4079502/1‑91 (MQ=255)
                                                             aGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAatcat                              >  1:3043606/1‑91 (MQ=255)
                                                             aGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAatcat                              >  1:3043914/1‑91 (MQ=255)
                                                             aGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATAAGGAATAatcat                              >  1:3754897/1‑91 (MQ=255)
                                                                cTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTg                           >  1:1972627/1‑91 (MQ=255)
                                                                  aaaaTTCATTCAATATGCTTATTCGCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCt                         >  1:4063960/1‑91 (MQ=255)
                                                                   aaaTTCATTCAATATGCTTATTCGCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCtt                        >  1:1386772/1‑91 (MQ=255)
                                                                   aaaTTCATTCAATATGCTTATTCGCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCtt                        >  1:1387678/1‑91 (MQ=255)
                                                                      ttcattcaATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAAc                     >  1:1220788/1‑91 (MQ=255)
                                                                      ttcattcaATATGCTTATTCGCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAAc                     <  1:3368156/91‑1 (MQ=255)
                                                                       tcattcaATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACt                    <  1:2194213/91‑1 (MQ=255)
                                                                       tcattcaATATGCTTATTCGCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACt                    <  1:2423738/91‑1 (MQ=255)
                                                                       tcattcaATATGCTTATTCGCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACt                    <  1:2961455/91‑1 (MQ=255)
                                                                        cattcaATATGCTTATTCGCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACtt                   >  1:1487333/1‑91 (MQ=255)
                                                                          ttcaATATGCTTGTTCGCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGt                 >  1:3176257/1‑91 (MQ=255)
                                                                          ttcaATATGCTTATTCGCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGt                 <  1:876451/91‑1 (MQ=255)
                                                                          ttcaATATGCTTATTCGCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGt                 <  1:1332887/91‑1 (MQ=255)
                                                                          ttcaATATGCTTATTCGCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGt                 <  1:1324266/91‑1 (MQ=255)
                                                                           tcaATATGCTTATTCGCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGta                <  1:2581211/91‑1 (MQ=255)
                                                                            caATATGCTTATTCGCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGtat               <  1:1891596/91‑1 (MQ=255)
                                                                             aaTATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGtatt              >  1:2941629/1‑91 (MQ=255)
                                                                              atatGCTTAATCGCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGtatta             >  1:2090903/1‑91 (MQ=255)
                                                                               tatGCTTATTCGCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGtattat            >  1:1529397/1‑91 (MQ=255)
                                                                               tatGCTTATTCGCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGtattat            <  1:2401878/91‑1 (MQ=255)
                                                                                 tGCTTATTCGCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAg          <  1:1069125/91‑1 (MQ=255)
                                                                                  gCTTATTCGCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGt         >  1:271992/1‑91 (MQ=255)
                                                                                   cTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTg        >  1:3748169/1‑91 (MQ=255)
                                                                                   cTTATTCGCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTg        <  1:1930556/91‑1 (MQ=255)
                                                                                    ttATTCGCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGc       >  1:1319459/1‑91 (MQ=255)
                                                                                         agCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGtta  >  1:2916081/2‑91 (MQ=255)
                                                                                          |                                                                                         
CGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTA  >  USA300TCH1516_ALE/1439995‑1440174

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap:     Deleted base: