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_ALE2,352,8150GA99.0% 339.5 / ‑4.0 95A92V (GCA→GTA) rpsI30S ribosomal protein S9
Reads supporting (aligned to +/- strand):  ref base G (1/0);  new base A (47/47);  total (48/47)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.97e-01

TTAAGACCTGGTTTTTTACGTTCTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTGCTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAACCACCACCATGAACGTTAACTAAAACATCAT  >  USA300TCH1516_ALE/2352728‑2352902
                                                                                       |                                                                                       
ttAAGACCTGGTTTTTTACGTTCTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACtt                                                                                      >  1:2114309/1‑91 (MQ=255)
   aGACCTGGTTTTTTACGTTCTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCta                                                                                   >  1:15994/1‑91 (MQ=255)
     aCCTGGTTTTTTACGTTCTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCtaat                                                                                 <  1:1068253/91‑1 (MQ=255)
      ccTGGTTTTTTACGTTCTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCtaata                                                                                >  1:3249491/1‑91 (MQ=255)
       cTGGTTTTTTACGTTCTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTACAGAACCTCTGTATTCAGGATCTACTTCtaataa                                                                               >  1:3283040/1‑91 (MQ=255)
       cTGGTTTTTTACGTTCTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCtaataa                                                                               >  1:3103607/1‑91 (MQ=255)
       cTGGTTTTTTACGTTCTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCtaataa                                                                               >  1:3104346/1‑91 (MQ=255)
       cTGGTTTTTTACGTTCTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCtaataa                                                                               <  1:130592/91‑1 (MQ=255)
        tGGTTTTTTACGTTCTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTaataat                                                                              >  1:2437598/1‑91 (MQ=255)
        tGGTTTTTTACGTTCTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTaataat                                                                              >  1:3685501/1‑91 (MQ=255)
         ggTTTTTTACGTTCTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATg                                                                             >  1:3023961/1‑91 (MQ=255)
         ggTTTTTTACGTTCTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATg                                                                             >  1:3023995/1‑91 (MQ=255)
           ttttttACGTTCCTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCa                                                                           >  1:2859106/1‑91 (MQ=255)
            tttttACGTTCTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCAc                                                                          >  1:1203809/1‑91 (MQ=255)
             ttttACGTTCTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACg                                                                         <  1:846681/91‑1 (MQ=255)
             ttttACGTTCTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACg                                                                         <  1:2632846/91‑1 (MQ=255)
              tttACGTTCTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGa                                                                        <  1:2292536/91‑1 (MQ=255)
              tttACGTTCTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGa                                                                        >  1:1850200/1‑91 (MQ=255)
               ttACGTTCTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAg                                                                       >  1:1609187/1‑91 (MQ=255)
                tACGTTCTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGc                                                                      >  1:432901/1‑91 (MQ=255)
                 aCGTTCTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCg                                                                     >  1:2298734/1‑91 (MQ=255)
                 aCGTTCTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCg                                                                     <  1:2028063/91‑1 (MQ=255)
                 aCGTTCTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCg                                                                     >  1:3283016/1‑91 (MQ=255)
                  cGTTCTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGa                                                                    >  1:3671359/1‑91 (MQ=255)
                  cGTTCTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGa                                                                    <  1:221512/91‑1 (MQ=255)
                       tttCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCg                                                               <  1:90053/91‑1 (MQ=255)
                       tttCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCg                                                               <  1:3333502/91‑1 (MQ=255)
                       tttCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCg                                                               >  1:761734/1‑91 (MQ=255)
                        ttCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGt                                                              <  1:323790/91‑1 (MQ=255)
                         tCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTg                                                             <  1:3285047/91‑1 (MQ=255)
                         tCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTg                                                             <  1:3284807/91‑1 (MQ=255)
                         tCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTg                                                             <  1:3285711/91‑1 (MQ=255)
                         tCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTg                                                             <  1:3286239/91‑1 (MQ=255)
                          cATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGa                                                            >  1:2794661/1‑91 (MQ=255)
                          cATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGa                                                            >  1:2479479/1‑91 (MQ=255)
                           aTACGTGGGTCACGAGTAAGTAATCCATCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGAc                                                           >  1:1000585/1‑91 (MQ=255)
                           aTACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGAc                                                           >  1:2735778/1‑91 (MQ=255)
                           aTACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGAc                                                           >  1:2735754/1‑91 (MQ=255)
                            tACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACg                                                          >  1:2499466/1‑91 (MQ=255)
                            tACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACg                                                          <  1:3581342/91‑1 (MQ=255)
                            tACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACg                                                          <  1:608176/91‑1 (MQ=255)
                             aCGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACgg                                                         <  1:193478/91‑1 (MQ=255)
                             aCGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACgg                                                         <  1:193477/91‑1 (MQ=255)
                              cGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGa                                                        <  1:1155734/91‑1 (MQ=255)
                              cGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGa                                                        <  1:56587/91‑1 (MQ=255)
                              cGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGa                                                        >  1:1841131/1‑91 (MQ=255)
                               gTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGAt                                                       <  1:444459/91‑1 (MQ=255)
                                    tCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATagctt                                                  <  1:2579303/91‑1 (MQ=255)
                                    tCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATagctt                                                  >  1:457994/1‑91 (MQ=255)
                                    tCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATagctt                                                  <  1:2579333/91‑1 (MQ=255)
                                    tCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGCGACGGATagctt                                                  <  1:2840535/91‑1 (MQ=255)
                                      aCGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATagcttga                                                >  1:2991975/1‑91 (MQ=255)
                                      aCGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATagcttga                                                >  1:244654/1‑91 (MQ=255)
                                       cGAGTAAGTAATCCTGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATagcttgag                                               <  1:159661/91‑1 (MQ=255)
                                       cGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATagcttgag                                               <  1:1119376/91‑1 (MQ=255)
                                       cGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATagcttgag                                               <  1:159705/91‑1 (MQ=255)
                                       cGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATagcttgag                                               <  1:3137077/91‑1 (MQ=255)
                                       cGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATagcttgag                                               <  1:3149685/91‑1 (MQ=255)
                                        gAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTGCTTCTAATAATGCACGAGCGATTCCGTGACGGATagcttgagc                                              >  1:1945979/1‑91 (MQ=255)
                                          gtaagtaaTCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATagcttgagctt                                            >  1:2539346/1‑91 (MQ=255)
                                          gtaagtaaTCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATagcttgagctt                                            >  1:2539511/1‑91 (MQ=255)
                                          gtaagtaaTCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATagcttgagctt                                            >  1:1305861/1‑91 (MQ=255)
                                          gtaagtaaTCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATagcttgagctt                                            >  1:1303717/1‑91 (MQ=255)
                                             agtaaTCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTc                                         <  1:2042935/91‑1 (MQ=255)
                                             agtaaTCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTc                                         >  1:662249/1‑91 (MQ=255)
                                                aaTCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAg                                      >  1:1076367/1‑91 (MQ=255)
                                                aaTCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAg                                      >  1:1077178/1‑91 (MQ=255)
                                                  tCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTg                                    >  1:686479/1‑91 (MQ=255)
                                                  tCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTg                                    >  1:2518665/1‑91 (MQ=255)
                                                      gcgcGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAac                                >  1:1810733/1‑91 (MQ=255)
                                                      gcgcGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAac                                >  1:3503997/1‑91 (MQ=255)
                                                       cgcgTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAacc                               >  1:668353/1‑91 (MQ=255)
                                                         cgTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAaccac                             <  1:3546416/91‑1 (MQ=255)
                                                         cgTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAaccac                             <  1:2492833/91‑1 (MQ=255)
                                                          gTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAaccacc                            <  1:3002800/91‑1 (MQ=255)
                                                             ttAAAGAACCTCTGTATTCAGGATCTACTCCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAaccaccacc                         >  1:1234887/1‑91 (MQ=255)
                                                                aaGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAACCACCACCATg                      <  1:3030358/91‑1 (MQ=255)
                                                                aaGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAACCACCACCATg                      <  1:2004776/91‑1 (MQ=255)
                                                                aaGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAACCACCACCATg                      <  1:1143632/91‑1 (MQ=255)
                                                                  gAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAACCACCGCCATGaa                    >  1:3221307/1‑91 (MQ=255)
                                                                   aaCCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAACCACCACCATGAAc                   <  1:1756809/91‑1 (MQ=255)
                                                                        ctGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAACCACCACCATGAACGTTaa              >  1:2070146/1‑91 (MQ=255)
                                                                         tGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAACCACCACCATGAACGTTAAc             >  1:812138/1‑91 (MQ=255)
                                                                         tGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAACCACCACCATGAACGTTAAc             <  1:2624777/91‑1 (MQ=255)
                                                                         tGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAACCACCACCATGAACGTTAAc             <  1:1599727/91‑1 (MQ=255)
                                                                          gTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAACCACCACCATGAACGTTAACt            <  1:3139145/91‑1 (MQ=255)
                                                                          gTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAACCACCACCATGAACGTTAACt            <  1:441321/91‑1 (MQ=255)
                                                                          gTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAACCACCACCATGAACGTTAACt            <  1:3536166/91‑1 (MQ=255)
                                                                           tATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAACCACCACCATGAACGTTAACTa           >  1:251549/1‑91 (MQ=255)
                                                                            aTTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAACCACCACCATGAACGTTAACTaa          <  1:922591/91‑1 (MQ=255)
                                                                            aTTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAACCACCACCATGAACGTTAACTaa          <  1:3458368/91‑1 (MQ=255)
                                                                            aTTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAACCACCACCATGAACGTTAACTaa          <  1:3433379/91‑1 (MQ=255)
                                                                             ttCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAACCACCACCATGAACGTTAACTaaa         >  1:2343594/1‑91 (MQ=255)
                                                                                    tCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAACCACCACCATGAACGTTAACTAAAAcatcat  <  1:2720885/91‑1 (MQ=255)
                                                                                    tCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAACCACCACCATGAACGTTAACTAAAAcatcat  <  1:1403018/91‑1 (MQ=255)
                                                                                       |                                                                                       
TTAAGACCTGGTTTTTTACGTTCTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTGCTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAACCACCACCATGAACGTTAACTAAAACATCAT  >  USA300TCH1516_ALE/2352728‑2352902

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑