Predicted mutation
evidence seq id position mutation freq annotation gene description
RA USA300TCH1516_ALE 1,984,315 A→T 5.4% E213D (GAA→GAT)  rluD_3 → Ribosomal large subunit pseudouridine synthase D

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE1,984,3150AT 5.4% 318.2 / 7.8 93E213D (GAA→GAT) rluD_3Ribosomal large subunit pseudouridine synthase D
Reads supporting (aligned to +/- strand):  ref base A (43/45);  new base T (3/2);  total (46/47)
Fisher's exact test for biased strand distribution p-value = 6.77e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.85e-01

AATAAACGACGTGTGTCTCCTACTGGACAGCGTGCAATTACACACATTTTAACTTCAAAAATGATAAAAGAAGCTGTGTGCCAACTTGAAATCAAGTTGGATACTGGACGTACTCATCAAATTCGTGTGCATTTAGCTGAAATTGGTCACCCTGTTATCGGTGATCCTTTATATGGTGAT  >  USA300TCH1516_ALE/1984226‑1984405
                                                                                         |                                                                                          
aaTAAACGACGTGTGTCTCCTACTGGACAGCGTGCAATTACACACATTTTAACTTCAAAAATGATAAAAGAAGCTGTGTGCCAACTTGaaa                                                                                           <  1:1408181/91‑1 (MQ=255)
  tAAACGACGTGTGTCTCCTACTGGACAGCGTGCAATTACACACATTTTAACTTCAAAAATGATAAAAGAAGCTGTGTGCCAACTTGAAATc                                                                                         >  1:4025408/1‑91 (MQ=255)
    aaCGACGTGTGTCTCCTACTGGACAGCGTGCAATTACACACATTTTAACGTCAAAAATGATAAAAGAAGCTGTGTGCCAACTTGAAATCaa                                                                                       <  1:3593544/91‑1 (MQ=255)
      cgacgTGTGTCTCCTACTGGACAGCGTGCAATTACACACATTTTAACTTCAAAAATGATAAAAGAAGCTGTGTGCCAACTTGAAATCAAGt                                                                                     <  1:3992815/91‑1 (MQ=255)
      cgacgTGTGTCTCCTACTGGACAGCGTGCAATTACACACATTTTAACTTCAAAAATGATAAAAGAAGCTGTGTGCCAACTTGAAATCAAGt                                                                                     >  1:3895340/1‑91 (MQ=255)
      cgacgTGTGTCTCCTACTGGACAGCGTGCAATTACACACATTTTAACTTCAAAAATGATAAAAGAAGCTGTGTGCCAACTTGAAATCAAGt                                                                                     <  1:2539942/91‑1 (MQ=255)
        acgTGTGTCTCCTACTGGACAGCGTGCAATTACACACATTTTAACTTCAAAAATGATAAAAGAAGCTGTGTGCCAACTTGAAATCAAGTTg                                                                                   >  1:650914/1‑91 (MQ=255)
         cgTGTGTCTCCTACTGGACAGCGTGCAATTACACACATTTTAACTTCAAAAATGATAAAAGAAGCTGTGTGCCAACTTGATTTCAAGTTgg                                                                                  <  1:191572/91‑1 (MQ=255)
         cgTGTGTCTCCTACTGGACAGCGTGCAATTACACACATTTTAACTTCAAAAATGATAAAAGAAGCTGTGTGCCAACTTGATTTCAAGTTgg                                                                                  <  1:191695/91‑1 (MQ=255)
         cgTGTGTCTCCTACTGGACAGCGTGCAATTACACACATTTTAACTTCAAAAATGATAAAAGAAGCTGTGTGCCAACTTGAAATCAAGTTgg                                                                                  >  1:688709/1‑91 (MQ=255)
         cgTGTGTCTCCTACTGGACAGCGTGCAATTACACACATTTTAACTTCAAAAATGATAAAAGAAGCTGTGTGCCAACTTGAAATCAAGTTgg                                                                                  >  1:688721/1‑91 (MQ=255)
         cgTGTGTCTCCTACTGGACAGCGTGCAATTACACACATTTTAACTTCAAAAATGATAAAAGAAGCTGTGTGCCAACTTGAAATCAAGTTgg                                                                                  >  1:1504237/1‑91 (MQ=255)
          gtgtgtCTCCTACTGGACAGCGTGCAATTACACACATTTTAACTTCAAAAATGATAAAAGAAGCTGTGTGCCAACTTGAAATCAAGTTGGa                                                                                 <  1:668982/91‑1 (MQ=255)
          gtgtgtCTCCTACTGGACAGCGTGCAATTACACACATTTTAACTTCAAAAATGATAAAAGAAGCTGTGTGCCAACTTGAAATCAAGCTGGa                                                                                 >  1:3456703/1‑91 (MQ=255)
           tgtgtCTCCTACTGGACAGCGTGCAATTACACACATTTTAACTTCAAAAATGATAAAAGAAGCTGTGTGCCAACTTGAAATCAAGTTGGAt                                                                                <  1:2906251/91‑1 (MQ=255)
            gtgtCTCCTACTGGACAGCGTGCAATTACACACATTTTAACTTCAAAAATGATAAAAGAAGCTGTGTGCCAACTTGAAATCAAGTTGGATa                                                                               <  1:551684/91‑1 (MQ=255)
            gtgtCTCCTACTGGACAGCGTGCAATTACACACATTTTAACTTCAAAAATGATAAAAGAAGCTGTGTGCCAACTTGAAATCAAGTTGGATa                                                                               >  1:1863573/1‑91 (MQ=255)
              gtCTCCTACTGGACAGCGTGCAATTACACACATTTTAACTTCAAAAATGATAAAAGAAGCTGTGTGCCAACTTGAAATCAAGTTGGATACt                                                                             >  1:371172/1‑91 (MQ=255)
              gtCTCCTACTGGACAGCGTGCAATTACACACATTTTAACTTCAAAAATGATAAAAGAAGCTGTGTGCCAACTTGAAATCAAGTTGGATACt                                                                             >  1:242679/1‑91 (MQ=255)
                ctcCTACTGGACAGCGTGCAATTACACACATTTTAACTTCAAAAATGATAAAAGAAGCTGTGTGCCAACTTGAAATCAAGTTGGATACTgg                                                                           >  1:1152316/1‑91 (MQ=255)
                 tcCTACTGGACAGCGTGCAATTACACACATTTTAACTTCAAAAATGATAAAAGAAGCTGTGTGCCAACTTGAAATCAAGTTGGATACTGGa                                                                          <  1:151520/91‑1 (MQ=255)
                 tcCTACTGGACAGCGTGCAATTACACACATTTTAACTTCAAAAATGATAAAAGAAGCTGTGTGCCAACTTGAAATCAAGTTGGATACTGGa                                                                          <  1:151519/91‑1 (MQ=255)
                  ccTACTGGACAGCGTGCAATTACACACATTTTCACTTCAAAAATGATAAAAGAAGCTGTGTGACAACTTGAAATCAAGTTGGATACTGGAc                                                                         >  1:1974803/1‑91 (MQ=255)
                  ccTACTGGACAGCGTGCAATTACACACATTTTAACTTCAAAAATGATAAAAGAAGCTGTGTGCCAACTTGAAATCAAGTTGGATACTGGAc                                                                         >  1:3274461/1‑91 (MQ=255)
                   cTACTGGACAGCGTGCAATTACACACATTTTAACTTCAAAAATGATAAAAGAAGCTGTGTGCCAACTTGAAATCAAGTTGGATACTGGACg                                                                        <  1:1638449/91‑1 (MQ=255)
                     aCTGGACAGCGTGCAATTACACACATTTTAACTTCAAAAATGATAAAAGAAGCTGTGTGCCAACTTGAAATCAAGTTGGATACTGGACGTa                                                                      <  1:1277087/91‑1 (MQ=255)
                        ggACAGCGTGCAATTACACACATTTTAACTTCAAAAATGATAAAAGAAGCTGTGTGCCAACTTGAAATCAAGTTGGATACTGGACGTACtc                                                                   >  1:3879491/1‑91 (MQ=255)
                        ggACAGCGTGCAATTACACACATTTTAACTTCAAAAATGATAAAAGAAGCTGTGTGCCAACTTGAAATCAAGTTGGATACTGGACGTACtc                                                                   <  1:3806360/91‑1 (MQ=255)
                        ggACAGCGTGCAATTACACACATTTTAACTTCAAAAATGATAAAAGAAGCTGTGTGCCAACTTGAAATCAAGTTGGATACTGGACGTACtc                                                                   <  1:438125/91‑1 (MQ=255)
                         gACAGCGTGCAATTACACACATTTTAACTTCACAAATGACAAAAGAAGCTGTGTGCCAACTTGAAATCAAGCTGGATACTGGACGTACtcc                                                                  >  1:2616726/1‑90 (MQ=255)
                         gACAGCGTGCAATTACACACATTTTAACTTCAAAAATGATAAAAGAAGCTGTGTGCCAACTTGAAATCAAGTTGGATACTGGACGTACtca                                                                  >  1:2616773/1‑91 (MQ=255)
                          aCAGCGTGCAGTTACACACATTTTAACTTCAAAAATGATAAAAGAAGCTGTGTGCCAACTTGAAATCAAGTTGGATACTGGACGTACtcat                                                                 <  1:1998934/91‑1 (MQ=255)
                          aCAGCGTGCAATTACGCACATTTTAACTTCAAAAATGATAAAAGAAGCTGTGTGCCAACTTGAAATCAAGTTGGATACTGGACGTACtcat                                                                 <  1:879915/91‑1 (MQ=255)
                          aCAGCGTGCAATTACACACATTTTAACTTCAAAAATGATAAAAGAAGCTGTGTGCCAACTTGAAATCAAGTTGGATACTGGACGTACtcat                                                                 <  1:1998571/91‑1 (MQ=255)
                            aGCGTGCAATTACACACATTTTAACTTCAAAAATGATAAAAGAAGCTGTGTGCCAACTTGAAATCAAGTTGGATACTGGACGTACtcatca                                                               <  1:519216/91‑1 (MQ=255)
                                  cAATTACACACATTTTAACTTCAAAAATGATAAAAGAAGCTGTGTGCCAACTTGAAATCAAGTTGGATACTGGACGTACTCATCAAATTCg                                                         >  1:3928181/1‑91 (MQ=255)
                                    aTTACACACATTTTAACTTCAAAAATGATAAAAGAAGCTGTGTGCCAACTTGAAATCAAGTTGGATACTGGACGTACTCATCAAATTCgtg                                                       <  1:776101/91‑1 (MQ=255)
                                    aTTACACACATTTTAACTTCAAAAATGATAAAAGAAGCTGTGTGCCAACTTGAAATCAAGTTGGATACTGGACGTACTCATCAAATTCgtg                                                       <  1:776223/91‑1 (MQ=255)
                                    aTTACACACATTTTAACTTCAAAAATGATAAAAGAAGCTGTGTGCCAACTTGAAATCAAGTTGGATACTGGACGTACTCATCAAATTCgtg                                                       <  1:572751/91‑1 (MQ=255)
                                      tACACACATTTTAACTTCAAAAATGATAAAAGAAGCTGTGTGCCAACTTGAAATCAAGTTGGATACTGGACGTACTCATCAAATTCGtgtg                                                     <  1:2829665/91‑1 (MQ=255)
                                      tACACACATTTTAACTTCAAAAATGATAAAAGAAGCTGTGTGCCAACTTGAAATCAAGTTGGATACTGGACGTACTCATCAAATTCGtgtg                                                     <  1:2829445/91‑1 (MQ=255)
                                          cacaTTTTAACTTCAAAAATGATAAAAGAAGCTGTGTGCCAACTTGAAATCAAGTTGGATACTGGACGTACTCATCAAATTCGTGTGCAtt                                                 >  1:155966/1‑91 (MQ=255)
                                          cacaTTTTAACTTCAAAAATGATAAAAGAAGCTGTGTGCCAACTTGAAATCAAGTTGGATACTGGACGTACTCATCAAATTCGTGTGCAtt                                                 <  1:2662253/91‑1 (MQ=255)
                                           acaTTTTAACTTCAAAAATGATAAAAGAAGCTGTGTGCCAACTTGAAATCAAGTTGGATACTGGACGTACTCATCAAATTCGTGTGCAttt                                                <  1:792786/91‑1 (MQ=255)
                                           acaTTTTAACTTCAAAAATGATAAAAGAAGCTGTGTGCCAACTTGAAATCAAGTTGGATACTGGACGTACTCATCAAATTCGTGTGCAttt                                                <  1:3773321/91‑1 (MQ=255)
                                           acaTTTTAACTTCAAAAATGATAAAAGAAGCTGTGTGCCAACTTGAAATCAAGTTGGATACTGGACGTACTCATCAAATTCGTGTGCAttt                                                <  1:3750916/91‑1 (MQ=255)
                                             aTTTTAACTTCAAAAATGATAAAAGAAGCTGTGTGCCAACTTGAAATCAAGTTGGATACTGGACGTACTCATCAAATTCGTGTGCATTTAg                                              <  1:840130/91‑1 (MQ=255)
                                              ttttAACTTCAAAAATGATAAAAGAAGCTGTGTGCCAACTTGAAATCAAGTTGGATACTGGACGTACTCATCAAATTCGTGTGCATTTAGc                                             <  1:2238856/91‑1 (MQ=255)
                                               tttAACTTCAAAAATGATAAAAGAAGCTGTGTGCCAACTTGAAATCAAGTTGGATACTGGACGTACTCATCAAATTCGTGTGCATTTAGCt                                            <  1:3234426/91‑1 (MQ=255)
                                                ttAACTTCAAAAATGATAAAAGAAGCTGTGTGCCAACTTGAAATCAAGTTGGATACTGGACGTACTCATCAAATTCGTGTGCATTTAGCTg                                           <  1:3035232/91‑1 (MQ=255)
                                                    cTTCAAAAATGATAAAAGAAGCTGTGTGCCAACTTGAAATCAAGTTGGATACTGGACGTACTCATCAAATTCGTGTGCATTTAGCTGAAAt                                       >  1:3629015/1‑91 (MQ=255)
                                                    cTTCAAAAATGATAAAAGAAGCTGTGTGCCAACTTGAAATCAAGTTGGATACTGGACGTACTCATCAAATTCGTGTGCATTTAGCTGAAAt                                       >  1:2429317/1‑91 (MQ=255)
                                                      tCAAAAATGATAAAAGAAGCTGTGTGCCAACTTGAAATCAAGTTGGATACTGGACGTACTCATCAAATTCGTGTGCATTTAGCTGAAATTg                                     <  1:233207/91‑1 (MQ=255)
                                                         aaaaTGATAAAAGAAGCTGTGTGCCAACTTGAAATCAAGTTGGATACTGGACGTACTCATCAAATTCGTGTGCATTTAGCTGAAATTGGTc                                  >  1:1776536/1‑91 (MQ=255)
                                                          aaaTGATAAAAGAAGCTGTGTGCCAACTTGAAATCAAGTTGGATACTGGACGTACTCATCAAATTCGTGTGCATTTAGCTGAAATTGGTCa                                 <  1:3576303/91‑1 (MQ=255)
                                                           agtGATAAAAGAAGCTGTGGGCCAACTTGAAATCAAGTTGGATACTGGACGTACTCATCAAATTCGTGTGCATTTAGCTGAAATTGGTCAc                                <  1:4089290/89‑1 (MQ=255)
                                                           aaTGATAAAAGAAGCTGTGTGCCAACTTGAAATCAAGTTGGATACTGGACGTACTCATCAAATTCGTGTGCATTTAGCTGAAATTGGTCAc                                <  1:3580048/91‑1 (MQ=255)
                                                             tGATAAAAGAAGCTGTGTGCCAACTTGAAATCAAGTTGGATACTGGACGTACTCATCAAATTCGTGTGCATTTAGCTGAAATTGGTCAccc                              <  1:519898/91‑1 (MQ=255)
                                                              gATAAAAGAAGCTGTGTGCCAACTTGAAATCAAGTTGGATACTGGACGTACTCATCAAATTCGTGTGCATTTAGCTGAAATTGGTCACCCt                             >  1:2464999/1‑91 (MQ=255)
                                                                 aaaaGAAGCTGTGTGCCAACTTGAAATCAAGTTGGATACTGGACGTACTCATCAAATTCGTGTGCATTTAGCTGAAATTGGTCACCCTGtt                          >  1:1380103/1‑91 (MQ=255)
                                                                 aaaaGAAGCTGTGTGCCAACTTGAAATCAAGTTGGATACTGGACGTACTCATCAAATTCGTGTGCATTTAGCTGAAATTGGTCACCCTGtt                          >  1:1380579/1‑91 (MQ=255)
                                                                  aaaGAAGCTGTGTGCCAACTTGAAATCAAGTTGGATACTGGACGTACTCATCAAATTCGTGTGCATTTAGCTGAAATTGGTCACCCTGTTa                         >  1:2636266/1‑91 (MQ=255)
                                                                  aaaGAAGCTGTGTGCCAACTTGAAATCAAGTTGGATACTGGACGTACTCATCAAATTCGTGTGCATTTAGCTGAAATTGGTCACCCTGTTa                         >  1:2636292/1‑91 (MQ=255)
                                                                    agaagCTGTGTGCCAACTTGAAATCAAGTTGGATACTGGACGTACTCATCAAATTCGTGTGCATTTAGCTGAAATTGGTCACCCTGTTATc                       <  1:787957/91‑1 (MQ=255)
                                                                     gaagCTGTGTGCCAACTTGAAATCAAGTTGGATACTGGACGTACTCATCAAATTCGTGTGCATTTAGCTGAAATTGGTCACCCTGTTATCg                      <  1:985984/91‑1 (MQ=255)
                                                                      aagCTGTGTGCCAACTTGAAATCAAGTTGGATACTGGACGTACTCATCAAATTCGTGTGCATTTAGCTGAAATTGGTCACCCTGTTAttgg                     <  1:2418951/91‑4 (MQ=255)
                                                                      aagCTGTGTGCCAACTTGAAATCAAGTTGGATACTGGACGTACTCATCAAATTCGTGTGCATTTAGCTGAAATTGGTCACCCTGTTATCgg                     <  1:2833234/91‑1 (MQ=255)
                                                                       agCTGTGTGCCAACTTGAAATCAAGTTGGATACTGGACGTACTCATCAAATTCGTGTGCATTTAGCTGAAATTGGTCACCCTGTTATCGGt                    >  1:3564679/1‑91 (MQ=255)
                                                                       agCTGTGTGCCAACTTGAAATCAAGTTGGATACTGGACGTACTCATCAAATTCGTGTGCATTTAGCTGAAATTGGTCACCCTGTTATCGGt                    <  1:792933/91‑1 (MQ=255)
                                                                       agCTGTGTGCCAACTTGAAATCAAGTTGGATACTGGACGTACTCATCAAATTCGTGTGCATTTAGCTGAAATTGGTCACCCTGTTATCGGt                    >  1:3566017/1‑91 (MQ=255)
                                                                          tgtgtgCCAACTTGAAATCAAGTTGGATACTGGACGTACTCATCAAATTCGTGTGCATTTAGCTGTAATTGGTCACCCTGTTATCGGTGAt                 >  1:3866652/1‑91 (MQ=255)
                                                                          tgtgtgCCAACTTGAAATCAAGTTGGATACTGGACGTACTCATCAAATTCGTGTGCATTTAGCTGAAATTGGTCACCCTGTTATCGGTGAt                 >  1:3795191/1‑91 (MQ=255)
                                                                           gtgtgCCAACTTGAAATCAAGTTGGATACTGGACGTACTCATCAAATTCGTGTGCATTTAGCTGAAATTGGTCACCCTGTTATCGGTGATc                >  1:4066241/1‑91 (MQ=255)
                                                                           gtgtgCCAACTTGAAATCAAGTTGGATACTGGACGTACTCATCAAATTCGTGTGCATTTAGCTGAAATTGGTCACCCTGTTATCGGTGATc                >  1:4066344/1‑91 (MQ=255)
                                                                           gtgtgCCAACTTGAAATCAAGTTGGATACTGGACGTACTCATCAAATTCGTGTGCATTTAGCTGAAATTGGTCACCCTGTTATCGGTGATc                >  1:608955/1‑91 (MQ=255)
                                                                            tgtgCCAACTTGAAATCAAGTTGGATACTGGACGTACTCATCAAATTCGTGTGCATTTAGCTGAAATTGGTCACCCTGTTATCGGTGATcc               <  1:3242394/91‑1 (MQ=255)
                                                                             gtgCCAACTTGAAATCAAGTTGGATACTGGACGTACTCATCAAATTCGTGTGCATTTAGCTGAAATTGGTCACCCTGTTATCGGTGATCCt              <  1:3468479/91‑1 (MQ=255)
                                                                              tgCCAACTTGAAATCAAGTTGGATACTGGACGTACTCATCAAATTCGTGTGCATTTAGCTGAAATTGGTCACCCTGTTATCGGTGATCCtt             >  1:3665766/1‑91 (MQ=255)
                                                                              tgCCAACTTGAAATCAAGTTGGATACTGGACGTACTCATCAAATTCGTGTGCATTTAGCTGAAATTGGTCACCCTGTTATCGGTGATCCtt             <  1:3590219/91‑1 (MQ=255)
                                                                              tgCCAACTTGAAATCAAGTTGGATACTGGACGTACTCATCAAATTCGTGTGCATTTAGCTGAAATTGGTCACCCTGTTATCGGTGATCCtt             <  1:3590218/91‑1 (MQ=255)
                                                                               gCCAACTTGAAATCAAGTTGGATACTGGACGTACTCATCAAATTCGTGTGCATTTAGCTGAAATTGGTCACCCTGTTATCGGTGATCCttt            >  1:46082/1‑91 (MQ=255)
                                                                               gCCAACTTGAAATCAAGTTGGATACTGGACGTACTCATCAAATTCGTGTGCATTTAGCTGAAATTGGTCACCCTGTTATCGGTGATCCttt            >  1:46281/1‑91 (MQ=255)
                                                                                ccAACTTGATTTCAAGTTGGATACTGGACGTACTCATCAAATTCGTGTGCATTTAGCTGAAATTGGTCACCCTGTTATCGGTGATCCTTta           >  1:1168523/1‑91 (MQ=255)
                                                                                  aaCTTGATTTCAAGTTGGATACTGGACGTACTCATCAAATTCGTGTGCATTTAGCTGAAATTGGTCACCCTGTTATCGGTGATCCTTtata         >  1:4101500/1‑91 (MQ=255)
                                                                                  aaCTTGAAATCAAGTTGGATACTGGACGTACTCATCAAATTCGTGTGCATTTAGCTGATATTGGTCACCCTGTTATCGGTGATCCTTtata         >  1:3545539/1‑91 (MQ=255)
                                                                                   aCTTGATTTCAAGTTGGATACTGGACGTACTCATCAAATTCGTGTGCATTTAGCTGAAATTGGTCACCCTGTTATCGGTGATCCTTTatat        >  1:435666/1‑91 (MQ=255)
                                                                                   aCTTGAAATCAAGTTGGATACTGGACGTACTCATCAAATTCGTGTGCATTTAGCTGAAATTGGTCACCCTGTTATCGGTGATCCTTTatat        >  1:2859298/1‑91 (MQ=255)
                                                                                   aCTTGAAATCAAGTTGGATACTGGACGTACTCATCAAATTCGTGTGCATTTAGCTGAAATTGGTCACCCTGTTATCGGTGATCCTTTatat        >  1:2193267/1‑91 (MQ=255)
                                                                                    cTTGAAATCAAGTTGGATACTGGACGTACTCATCAAATTCGTGTGCATTTAGCTGAAATTGGTCACCCTGTTATCGGTGATCCTTTATATg       <  1:4126059/91‑1 (MQ=255)
                                                                                    cTTGAAATCAAGTTGGATACTGGACGTACTCATCAAATTCGTGTGCATTTAGCTGAAATTGGTCACCCTGTTATCGGTGATCCTTTATATg       >  1:1341313/1‑91 (MQ=255)
                                                                                     ttGAAATCAAGTTGGATACTGGACGTACTCATCAAATTCGTGTGCATTTAGCTGAAATTGGTCACCCTGTTATCGGTGATCCTTTATATgg      <  1:1225959/91‑1 (MQ=255)
                                                                                       gAAATCAAGTTGGATACTGGACGTACTCATCAAATTCTTGTGCATTTAGCTGAAATTGGTCACCCTGTTATCGGTGATCCTTTATATGGTg    >  1:3503989/1‑91 (MQ=255)
                                                                                       gAAATCAAGTTGGATACTGGACGTACTCATCAAATTCGTGTGCATTTAGCTGAAATTGGTCACCCTGTTATCGGTGATCCTTTATATGGTg    >  1:1174405/1‑91 (MQ=255)
                                                                                       gAAATCAAGTTGGATACTGGACGTACTCATCAAATTCGTGTGCATTAAGCTGAAATTGGTCACCCTGTTATCGGTGATCCTTTATATGGTg    >  1:3288805/1‑91 (MQ=255)
                                                                                         aaTCAAGTTGGATACTGGACGTACTCATCAAATTCGTGTGCATTTAGCTGAAATTGGTCACCCTGTTATCGGTGATCCTTTATATGGTGAt  <  1:3154191/91‑1 (MQ=255)
                                                                                         aaTCAAGTTGGATACTGGACGTACTCATCAAATTCGTGTGCATTTAGCTGAAATTGGTCACCCTGTTATCGGTGATCCTTTATATGGTGAt  <  1:2001761/91‑1 (MQ=255)
                                                                                         |                                                                                          
AATAAACGACGTGTGTCTCCTACTGGACAGCGTGCAATTACACACATTTTAACTTCAAAAATGATAAAAGAAGCTGTGTGCCAACTTGAAATCAAGTTGGATACTGGACGTACTCATCAAATTCGTGTGCATTTAGCTGAAATTGGTCACCCTGTTATCGGTGATCCTTTATATGGTGAT  >  USA300TCH1516_ALE/1984226‑1984405

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: ‑