Predicted mutation
evidence seq id position mutation freq annotation gene description
RA USA300TCH1516_ALE 1,158,427 G→A 9.0% intergenic (+11/‑313) uvrC → / → sdhC UvrABC system protein C/Succinate dehydrogenase cytochrome b558 subunit

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE1,158,4270GA 9.0% 617.4 / 33.8 204intergenic (+11/‑313)uvrC/sdhCUvrABC system protein C/Succinate dehydrogenase cytochrome b558 subunit
Reads supporting (aligned to +/- strand):  ref base G (87/98);  new base A (2/17);  total (89/115)
Fisher's exact test for biased strand distribution p-value = 2.64e-03
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

Only 100 of 205 total aligned reads displayed.

AAGCTACACTTGAAGATTTTAAAAATATAGGTATTCCTGAAAACGTCGCAAAGAACCTACATGAACAATTGCATAAATAAATTACTGGGCGTGAGAATCATTCTCATGCCCCAAAATATATGAAATAATGTTACAATATGGTTAACAAAGTTATTTTTTTGAATGTACGTGGAAGCGTTT  >  USA300TCH1516_ALE/1158337‑1158516
                                                                                          |                                                                                         
  gCTACACTTGAAGATTTTAAAAATATAGGTATTCCTGAAAACGTCGCAAAGAACCTACATGAATAATTGCATAAATAAATTACTGGGCGTg                                                                                         <  1:176056/91‑1 (MQ=255)
  gCTACACTTGAAGATTTTAAAAATATAGGTATTCCTGAAAACGTCGCAAAGAACCTACATGAACAATTGCATAAATAAATTACTGGGCGTg                                                                                         <  2:2665261/91‑1 (MQ=255)
   cTACACTTGAAGATTTTAAAAATATAGGTATTCCTGAAAACGTCGCAAAGAACCTACATGAACAATTGCATAAATAAATTACTGGGCGTga                                                                                        <  1:3795654/91‑1 (MQ=255)
   cTACACTTGAAGATTTTAAAAATATAGGTATTCCTGAAAACGTCGCAAAGAACCTACATGAACAATTGCATAAATAAATTACTGGGCGTga                                                                                        <  1:2456149/91‑1 (MQ=255)
    tACACTTGAAGATTTTAAAAATATAGGTATTCCTGAAAACGTCGCAAAGAACCTACATGAACAATTGCATAAATAAATTACTGGGCGTgag                                                                                       <  2:585644/91‑1 (MQ=255)
    tACACTTGAAGATTTTAAAAATATAGGTATTCCTGAAAACGTCGCAAAGAACCTACATGAACAATTGCATAAATAAATTACTGGGCGTgag                                                                                       >  1:1629395/1‑91 (MQ=255)
     acacTTGAAGATTTTAAAAATATAGGTATTCCTGAAAACGTCGCAAAGAACCTACATGAACAATTGCATAAATAAATTACTGGGCGTgaga                                                                                      <  2:3746388/91‑1 (MQ=255)
     acacTTGAAGATTTTAAAAATATAGGTATTCCTGAAAACGTCGCAAAGAACCTACATGAACAATTGCATAAATAAATTACTGGGCGTgaga                                                                                      <  2:2850088/91‑1 (MQ=255)
     acacTTGAAGATTTTAAAAATATAGGTATTCCTGAAAACGTCGCAAAGAACCTACATGAACAATTGCATAAATAAATTACTGGGCGTgaga                                                                                      <  1:261344/91‑1 (MQ=255)
      cacTTGAAGATTTTAAAAATATAGGTATTCCTGAAAACGTCGCAAAGAACCTACATGAACAATTGCATAAATAAATTACTGGGCGTGAGaa                                                                                     <  2:3010977/91‑1 (MQ=255)
        cTTGAAGATTTTAAAAATATAGGTATTCCTGAAAACGTCGCAAAGTACCTGCATGAACAATTGCATAAATAAATTACTGGGCATGAGAAtg                                                                                   <  2:3692190/91‑2 (MQ=255)
        cTTGAAGATTTTAAAAATATAGGTATTCCTGAAAACGTCGCAAAGAACCTACATGAACAATTGCATAAATAAATTACTGGGCGTGAGAATc                                                                                   >  1:709110/1‑91 (MQ=255)
         ttGAAGATTTTAAAAATATAGGTATTCCTGAAAACGTCGCAAAGAACCTACATGAACAATTGCATAAATAAATTACTGGGCGTGAGAATCa                                                                                  <  2:823957/91‑1 (MQ=255)
         ttGAAGATTTTAAAAATATAGGTATTCCTGAAAACGTCGCAAAGAACCTACATGAACAATTGCATAAATAAATTACTGGGCATGAGAAtga                                                                                  <  1:1004988/91‑3 (MQ=255)
          tGAAGATTTTAAAAATATAGGTATTCCTGAAAACGTCGCAAAGAACCTACATGAACAATTGCATAAATAAATTACTGGGCGTGAGAATCAt                                                                                 >  1:3537619/1‑91 (MQ=255)
           gAAGATTTTAAAAATATAGGTATTCCTGAAAACGTCGCAAAGAACCTACATGAACAATTGCATAAATAAATTACTGGGCATGAGAATGAtt                                                                                <  1:3204972/91‑1 (MQ=255)
           gAAGATTTTAAAAATATAGGTATTCCTGAAAACGTCGCAAAGAACCTACATGAACAATTGCATAAATAAATTACTGGGCATGAGAATGAtt                                                                                <  1:2867156/91‑1 (MQ=255)
            aaGATTTTAAAAATATAGGTATTCCTGAAAACGTCGCAAAGAACCTACATGAACAATTGCATAAATAAATTACTGGGCGTGAGAATCATtc                                                                               >  1:1000842/1‑91 (MQ=255)
            aaGATTTTAAAAATATAGGTATTCCTGAAAACGTCGCAAAGAACCTACATGAACAATTGCATAAATAAATTACTGGGCGTGAGAATCATtc                                                                               >  1:119676/1‑91 (MQ=255)
            aaGATTTTAAAAATATAGGTATTCCTGAAAACGTCGCAAAGAACCTACATGAACAATTGCATAAATAAATTACTGGGCGTGAGAATCATtc                                                                               <  2:3534441/91‑1 (MQ=255)
              gATTTTAAAAATATAGGTATTCCTGAAAACGTCGCAAAGAACCTACATGAACAATTGCATAAATAAATTACTGGGCATGAGAATGATtctc                                                                             <  1:1837163/91‑1 (MQ=255)
                ttttAAAAATATAGGTATTCCTGAAAACGTCGCAAAGAACCTACATGAACAATTGCATAAATAAATTACTGGGCGTGAGAATCATTCTCAt                                                                           >  1:1857122/1‑91 (MQ=255)
                ttttAAAAATATAGGTATTCCTGAAAACGTCGCAAAGAACCTACATGAACAATTGCATAAATAAATTACTGGGCGTGAGAATCATTCTCAt                                                                           >  1:1359320/1‑91 (MQ=255)
                 tttAAAAATATAGGTATTCCTGAAAACGTCGCAAAGAACCTACATGAACAATTGCATAAATAAATTACTGGGCGTGAGAATCATTCTCATg                                                                          <  1:530318/91‑1 (MQ=255)
                 tttAAAAATATAGGTATTCCTGAAAACGTCGCAAAGAACCTACATGAACAATTGCATAAATAAATTACTGGGCGTGAGAATCATTCTCATg                                                                          <  1:1095162/91‑1 (MQ=255)
                  ttAAAAATATAGGTATTCCTGAAAACGTCGCAAAGAACCTACATGAACAATTGCATAAATAAATTACTGGGCGTGAGAATCATTCTCATGc                                                                         >  1:1339053/1‑91 (MQ=255)
                   tAAAAATATAGGTATTCCTGAAAACGTCGCAAAGAACCTACATGAACAATTGCATAAATAAATTACTGGGCGTGAGAATCATTCTCATGcc                                                                        <  1:965853/91‑1 (MQ=255)
                   tAAAAATATAGGTATTCCTGAAAACGTCGCAAAGAACCTACATGAACAATTGCATAAATAAATTACTGGGCGTGAGAATCATTCTCATGcc                                                                        <  1:2834513/91‑1 (MQ=255)
                    aaaaaTATAGGTATTCCTGAAAACGTCGCAAAGAACCTACATGAACAATTGCATAAATAAATTACTGGGCGTGAGAATCATTCTCATGccc                                                                       <  1:1536080/91‑1 (MQ=255)
                     aaaaTATAGGTATTCCTGAAAACGTCGCAAAGAACCTACATGAACAATTGCATAAATAAATTACTGGGCGTGAGAATCATTCTCATGcccc                                                                      >  1:1733102/1‑91 (MQ=255)
                     aaaaTATAGGTATTCCTGAAAACGTCGCAAAGAACCTACATGAACAATTGCATAAATAAATTACTGGGCGTGAGAATCATTCTCATGcccc                                                                      <  2:3326059/91‑1 (MQ=255)
                      aaaTATAGGTATTCCTGAAAACGTCGCAAAGAACCTACATGAACAATTGCATAAATAAATTACTGGGCGTGAGAATCATTCTCATGCCCCa                                                                     <  1:1315970/91‑1 (MQ=255)
                       aaTATAGGTATTCCTGAAAACGTCGCAAAGAACCTACATGAACAATTGCATAAATAAATTACTGGGCGTGAGAATCATTCTCATGCCCCaa                                                                    <  1:2862449/91‑1 (MQ=255)
                       aaTATAGGTATTCCTGAAAACGTCGCAAAGAACCTACATGAACAATTGCATAAATAAATTACTGGGCATGAGAATGATTCTCACGcccagt                                                                    <  1:3010929/91‑4 (MQ=38)
                        atatAGGTATTCCTGAAAACGTCGCAAAGAACCTACATGAACAATTGCATAAATAAATTACTGGGCATGAGAATGATTCTCACGcccagta                                                                   <  2:1030040/91‑5 (MQ=37)
                         tataGGTATTCCTGAAAACGTCGCAAAGAACCTACATGAACAATTGCATAAATAAATTACTGGGCGTGAGAATCATTCTCATGCCCCaaaa                                                                  <  1:948518/91‑1 (MQ=255)
                         tataGGTATTCCTGAAAACGTCGCAAAGAACCTACATGAACAATTGCATAAATAAATTACTGGGCGTGAGAATCATTCTCATGCCCCaaaa                                                                  <  2:653136/91‑1 (MQ=255)
                             ggTATTCCTGAAAACGTCGCAAAGAACCTACATGAACAATTGCATAAATAAATTACTGGGCGTGAGAATCATTCTCATGCCCCAAAatata                                                              >  2:25749/1‑91 (MQ=255)
                                 ttCCTGAAAACGTCGCAAAGAACCTACATGAACAATTGCATAAATAAATTACTGGGCGTGAGAATCATTCTCATGCCCCAAAATATATGaa                                                          <  2:3256855/91‑1 (MQ=255)
                                 ttCCTGAAAACGTCGCAAAGAACCTACATGAACAATTGCATAAATAAATTACTGGGCGTGAGAATCATTCTCATGCCCCAAAATATATGaa                                                          <  2:1283263/91‑1 (MQ=255)
                                 ttCCTGAAAACGTCGCAAAGAACCTACATGAACAATTGCATAAATAAATTACTGGGCGTGAGAATCATTCTCATGCCCCAAAATATATGaa                                                          <  1:2152889/91‑1 (MQ=255)
                                   ccTGAAAACGTCGCAAAGAACCTACATGAACAATTGCATAAATAAATTACTGGGCGTGAGAATCATTCTCATGCCCCAAAATATATGAaat                                                        <  1:2875638/91‑1 (MQ=255)
                                        aaaCGTCGCAAAGAACCTACATGAACAATTGCATAAATAAATTACTGGGCGTGAGAATCATTCTCATGCCCCAAAATATATGAAATAATGt                                                   >  1:3793176/1‑91 (MQ=255)
                                         aaCGTCGCAAAGAACCTACATGAACAATTGCATAAATAAATTACTGGGCGTGAGAATCATTCTCATGCCCCAAAATATATGAAATAATGtt                                                  <  2:1460015/91‑1 (MQ=255)
                                         aaCGTCGCAAAGAACCTACATGAACAATTGCATAAATAAATTACTGGGCGTGAGAATCATTCTCATGCCCCAAAATATATGAAATAATGtt                                                  >  1:476452/1‑91 (MQ=255)
                                          aCGTCGCAAAGAACCTACATGAACAATTGCATAAATAAATTACTGGGCGTGAGAATCATTCTCATGCCCCAAAATATATGAAATAATGTTa                                                 >  1:77019/1‑91 (MQ=255)
                                           cGTCGCAAAGAACCTACATGAACAATTGCATAAATAAATTACTGGGCGTGAGAATCATTCTCATGCCCCAAAATATATGAAATAATGTTAc                                                <  1:2193257/91‑1 (MQ=255)
                                            gTCGCAAAGAACCTACATGAACAATTGCATAAATAAATTACTGGGTGTGAGAATCATTCTCATGCCCCGAAATATATGAAATAATGTTACa                                               >  2:3131108/1‑91 (MQ=255)
                                             tCGCAAAGAACGTACATGAACAATTGCATAAATAAATTACTGGGCGTGAGAATCATTCTCATGCCCCAAAATATATGAAATAATGTTACaa                                              <  1:3514575/91‑1 (MQ=255)
                                             tCGCAAAGAACCTACATGAACAATTGCATAAATAAATTACTGGGCGTGAGAATCATTCTCATGCCCCAAAATATATGAAATAATGTTACaa                                              >  2:1146087/1‑91 (MQ=255)
                                              cGCAAAGAACCTACATGAACAATTGCATAAATAAATTACTGGGCGTGAGAATCATTCTCATGCCCCAAAATATATGAAATAATGTTACAat                                             >  2:2391804/1‑91 (MQ=255)
                                              cGCAAAGAACCTACATGAACAATTGCATAAATAAATTACTGGGCGTGAGAATCATTCTCATGCCCCAAAATATATGAAATAATGTTACAat                                             <  1:2667382/91‑1 (MQ=255)
                                              cGCAAAGAACCTACATGAACAATTGCATAAATAAATTACTGGGCGTGAGAATCATTCTAATGCCCCAAAATATCTGAAATAATGTTACAat                                             >  1:3325771/1‑91 (MQ=255)
                                               gCAAAGAACCTACATGAACAATTGCATAAATAAATTACTGGGCGTGAGAATCATTCTCATGCCCCAAAATATATGAAATAATGTTACAata                                            >  2:2068677/1‑91 (MQ=255)
                                                cAAAGAACCTACATGAACAATTGCATAAATAAATTACTGGGCGTGAGAATCATTCTCATGCCCCAAAATATATGAAATAATGTTACAatat                                           <  1:2707833/91‑1 (MQ=255)
                                                 aaaGAACCTACATGAACAATTGCATAAATAAATTACTGGGCGTGAGAATCATTCTCATGCCCCAAAATATATGAAATAATGTTACAATATg                                          <  1:3057730/91‑1 (MQ=255)
                                                         tACATGAACAATTGCATAAATAAATTACTGGGCGTGAGAATCATTCTCATGCCCCAAAATATATGAAATAATGTTACAATATGGTTAACaa                                  >  2:3210225/1‑91 (MQ=255)
                                                         tACATGAACAATTGCATAAATAAATTACTGGGCGTGAGAATCATTCTCATGCCCCAAAATATATGAAATAATGTTACAATATGGTTAACaa                                  >  2:2458768/1‑91 (MQ=255)
                                                          aCATGAACAATTGCATAAATAAATTACTGGGCGTGAGAATCATTCTCATGCCCCAAAATATATGAAATAATGTTACAATATGGTTAACaaa                                 <  1:1433234/91‑1 (MQ=255)
                                                          aCATGAACAATTGCATAAATAAATTACTGGGCGTGAGAATCATTCTCATGCCCCAAAATATATGAAATAATGTTACAATATGGTTAACaaa                                 <  2:1480550/91‑1 (MQ=255)
                                                          aCATGAACAATTGCATAAATAAATTACTGGGCGTGAGAATCATTCTCATGCCCCAAAATATATGAAATAATGTTACAATATGGTTAACaaa                                 <  2:240672/91‑1 (MQ=255)
                                                           cATGAACAATTGCATAAATAAATTACTGGGCGTGAGAATCATTCTCATGCCCCAAAATATATGAAATAATGTTACAATATGGTTAACAAAg                                >  2:1533570/1‑91 (MQ=255)
                                                           cATGAACAATTGCATAAATAAATTACTGGGCGTGAGAATCATTCTCATGCCCCAAAATATATGAAATAATGTTACAATATGGTTAACAAAg                                <  1:3085049/91‑1 (MQ=255)
                                                            ctGAACAATTGCATAAATAAATTACTGGGCGTGAGACTCATTCTCATGCCCCAAAATATATGAAATAATGTTACAATATGGTTAACAAAGt                               <  2:3840250/90‑1 (MQ=255)
                                                            ctGAACAATTGCATAAATAAATTACTGGGCGTGAGAATCATTCTCATGCCCCAAAATATATGAAATAATGTTACAATATGGTTAACAAAGt                               <  2:1557293/90‑1 (MQ=255)
                                                            aTGAACAATTGCATAAATAAATTACTGGGCGTGAGAATCATTCTCATGCCCCAAAATATATGAAATAATGTTACAATATGGTTAACAAAGt                               <  2:2153556/91‑1 (MQ=255)
                                                            aTGAACAATTGCATAAATAAATTACTGGGCGTGAGAATCATTCTCATGCCCCAAAATATATGAAATAATGTTACAATATGGTTAACAAAGt                               <  2:2830480/91‑1 (MQ=255)
                                                            aTGAACAATTGCATAAATAAATTACTGGGCGTGAGAATCATTCTCATGCCCCAAAATATATGAAATAATGTTACAATATGGTTAACAAAGt                               >  1:890763/1‑91 (MQ=255)
                                                             tGAACAATTGCATAAATAAATTACTGGGCGTGAGAATCATTCTCATGCCCCAAAATATATGAAATAATGTTACAATATGGTTAACAAAGtt                              >  1:1906479/1‑91 (MQ=255)
                                                              gAACAATTGCATAAATAAATTACTGGGCGTGAGAATCATTCTCATGCCCCAAAATATATGAAATAATGTTACAATATGGTTAACAAAGTTa                             <  2:3537619/91‑1 (MQ=255)
                                                                aCAATTGCATAAATAAATTACTGGGCGTGAGAATCATTCTCATGCCCCAAAATATATGAAATAATGTTACAATATGGTTAACAAAGTTAtt                           >  1:3104401/1‑91 (MQ=255)
                                                                aCAATTGCATAAATAAATTACTGGGCGTGAGAATCATTCTCATGCCCCAAAATATATGAAATAATGTTACAATATGGTTAACAAAGTTAtt                           >  2:11910/1‑91 (MQ=255)
                                                                   aTTGCATAAATAAATTACTGGGCGTGAGAATCATTCTCATGCCCCAAAATATATGAAATAATGTTACAATATGGTTAACAAAGTTAttttt                        >  2:1920337/1‑91 (MQ=255)
                                                                   aTTGCATAAATAAATTACTGGGCGTGAGAATCATTCTCATGCCCCAAAATATATGAAATAATGTTACAATATGGTTAACAAAGTTAttttt                        >  2:521816/1‑91 (MQ=255)
                                                                     tGCATAAATAAATTACTGGGCGTGAGAATCATTCTCATGCCCCAAAATATATGAAATAATGTTACAATATGGTTAACAAAGTTAttttttt                      >  2:2033690/1‑91 (MQ=255)
                                                                     tGCATAAATAAATTACTGGGCGTGAGAATCATTCTCATGCCCCAAAATATATGAAATAATGTTACAATATGGTTAACAAAGTTAttttttt                      >  2:3769391/1‑91 (MQ=255)
                                                                     tGCATAAATAAATTACTGGGCGTGAGAATCATTCTCATGCCCCAAAATATATGAAATAATGTTACAATATGGTTAACAAAGTTAttttttt                      >  1:321204/1‑91 (MQ=255)
                                                                      gCATAAATAAATTACTGGGCGTGAGAATCATTCTCATGCCCCAAAATATATGAAATAATGTTACAATATGGTTAACAAAGTTATTTTTTTg                     >  1:831080/1‑91 (MQ=255)
                                                                       cATAAATAAATTACTGGGCGTGAGAATCATTCTCATGCCCCAAAATATATGAAATAATGTTACAATATGGTTAACAAAGTTATTTTTTTGa                    >  2:1442001/1‑91 (MQ=255)
                                                                       cATAAATAAATTACTGGGCGTGAGAATCATTCTCATGCCCCAAAATATATGAAATAATGTTACAATATGGTTAACAAAGTTATTTTTTTGa                    >  1:3555549/1‑91 (MQ=255)
                                                                        ataaataaATTACTGGGCGTGAGAATCATTCTCATGCCCCAAAATATATGAAATAATGTTACAATATGGTTAACAAAGTTATTTTTTTGaa                   <  2:763932/91‑1 (MQ=255)
                                                                         taaataaaTTACTGGGCGTGAGAATCATTCTCATGCCCCAAAATATATGAAATAATGTTACAATATGGTTAACAAAGTTATTTTTTTGAAt                  >  1:962807/1‑91 (MQ=255)
                                                                         taaataaaTTACTGGGCGTGAGAATCATTCTCATGCCACAAAATATATGAAATAATGTTACAATATGGTTAACAAAGTTATTTTTTTGAAt                  >  1:3269808/1‑91 (MQ=255)
                                                                          aaataaatTACTGGGCGTGAGAATCATTCTCATGCCCCAAAATATATGAAATAATGTTACAATATGGTTAACAAAGTTATTTTTTTGAATg                 <  2:1707569/91‑1 (MQ=255)
                                                                           aataaatTACTGGGCGTGAGAATCATTCTCATGCCCCAAAATATATGAAATAATGTTACAATATGGTTAACAAAGTTATTTTTTTGAATGt                <  2:1629395/91‑1 (MQ=255)
                                                                            ataaatTACTGGGCGTGAGAATCATTCTCATGCCCCAAAATATATGAAATAATGTTACAATATGGTTAACAAAGTTATTTTTTTGAATGTa               <  1:3496070/91‑1 (MQ=255)
                                                                             taaatTACTGGGCGTGAGAATCATTCTCATGCCCCAAAATATATGAAATAATGTTACAATATGGTTAACAAAGTTATTTTTTTGAATGTAc              <  1:3423602/91‑1 (MQ=255)
                                                                               aatTACTGGGCGTGAGAATCATTCTCATGCCCCAAAATATATGAAATAATGTTACAATATGGTTAACAAAGtt                              >  2:3479342/1‑73 (MQ=255)
                                                                                atTACTGGGCGTGAGAATCATTCTCATGCCCCAAAATATATGAAATAATGTTACAATATGGTTAACAAAGTTATTTTTTTGAATGTACGTg           >  2:697266/1‑91 (MQ=255)
                                                                                 ttACTGGGCGTGAGAATCATTCTCATGCCCCAAAATATATGAAATACTGTTACACTATGGTTAACACAGTTCTTTTTTTGAATGTACGTga          >  2:3880830/1‑90 (MQ=255)
                                                                                 ttACTGGGCGTGAGAATCATTCTCATGCCCCAAAATATATGAAATAATGTTACAATATGGTTAACAAAGTTATTTTTTTGAATGTACGTgg          >  1:463353/1‑91 (MQ=255)
                                                                                  tACTGGGCGTGAGAATCATTCTCATGCCCCAAAATATATGAAATAATGTTACAATATGGTTAACAAAGTTATTTTTTTGAATGTACGTGGa         <  1:2355918/91‑1 (MQ=255)
                                                                                   aCTGGGCGTGAGAATCATTCTCATGCCCCAAAATATATGAAATAATGTTACAATATGGTTAACAAAGTTATTTTTTTGTATGTTTGTGGaa        >  2:3310011/1‑91 (MQ=255)
                                                                                   aCTGGGCGTGAGAATCATTCTCATGCCCCAAAATATATGAAATAATGTTACAATATGGTTAACAAAGTTATTTTTTTGAATGTACGTGGaa        >  1:1669195/1‑91 (MQ=255)
                                                                                    cTGGGCGTGAGAATCATTCTCATGCCCCAAAATATATGAAATAATGTTACAATATGGTTAACAAAGTTATTTTTTTGAATGTACGTGGAAg       >  1:203483/1‑91 (MQ=255)
                                                                                     ggggCATGAGAATGATTCTCACGCCCCAAAATATATGAAATAATGTTACAATATGGTTAACAAAGTTATTTTTTTGAATGTACGTGGAAGc      >  1:3382116/2‑91 (MQ=39)
                                                                                       ggCGTGAGAATCATTCTCATGCCCCAAAATATATGAAATAATGTTACAATATGGTTAACAAAGTTATTTTTTTGAATGTACGTGGAAGCGt    <  1:2544830/91‑1 (MQ=255)
                                                                                       ggCGTGAGAATCATTCTCATGCCCCAAAATATATGAAATAATGTTACAATATGGTTAACAAAGTTATTTTTTTGAATGTACGTGGAAGCGt    <  1:192887/91‑1 (MQ=255)
                                                                                       ggCGTGAGAATCATTCTCATGCCCCAAAATATATGAAATAATGTTACAATATGGTTAACAAAGTTATTTTTTTGAATGTACGTGGAAGCGt    <  2:269485/91‑1 (MQ=255)
                                                                                        gCGTGAGAATCATTCTCATGCCCCAAAATATATGAAATAATGTTACAATATGGTTAACAAAGTTATTTTTTTGAATGTACGTGGAAGCGtt   >  2:1619928/1‑91 (MQ=255)
                                                                                          |                                                                                         
AAGCTACACTTGAAGATTTTAAAAATATAGGTATTCCTGAAAACGTCGCAAAGAACCTACATGAACAATTGCATAAATAAATTACTGGGCGTGAGAATCATTCTCATGCCCCAAAATATATGAAATAATGTTACAATATGGTTAACAAAGTTATTTTTTTGAATGTACGTGGAAGCGTTT  >  USA300TCH1516_ALE/1158337‑1158516

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: