Predicted mutation
evidence seq id position mutation freq annotation gene description
RA USA300TCH1516_ALE 1,343,622 G→T 12.1% intergenic (+35/‑95) USA300HOU_RS06640 → / → USA300TCH1516_01248 hypothetical protein/hypothetical protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE1,343,6220GT12.1% 644.6 / 66.9 199intergenic (+35/‑95)USA300HOU_RS06640/USA300TCH1516_01248hypothetical protein/hypothetical protein
Reads supporting (aligned to +/- strand):  ref base G (71/104);  new base T (15/9);  total (86/113)
Fisher's exact test for biased strand distribution p-value = 4.94e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.73e-01

Only 100 of 205 total aligned reads displayed.

ACATAAATACTAGTAAAGGGCTATTTCCTGAATCTGAACTCGTAGCATGGGGATAAAGAAAGTTTACTTTAAAAATTTTAACCTTCAAATGTGAAGGTTATTTTTTATTGCCCAAAACGTGCTGATGACATTTTAAAAGCAAGTATGGAATATCAGTCGACAGACTATAAACGGAGGTA  >  USA300TCH1516_ALE/1343532‑1343710
                                                                                          |                                                                                        
aCATAAATACTAGTAAAGGGCTATTTCCTGAATCTGAACTCGTAGCATGGGGATAAAGAAAGTTTACTTTAAAAATTTTAACCTTCAAAtg                                                                                          >  1:870107/1‑91 (MQ=255)
  aTAAATACTAGTAAAGGGCTATTTCCTGAATCTGAACTCGTAGCATGGGGATAAAGAAAGTTTACTTTAAAAATTTTAACCTTCAAAtgtg                                                                                        >  1:2848747/1‑91 (MQ=255)
  aTAAATACTAGTAAAGGGCTATTTCCTGAATCTGAACTCGTAGCATGGGGATAAAGAAAGTTTACTTTAAAAATTTTAACCTTCAAAtgtg                                                                                        >  1:546764/1‑91 (MQ=255)
   tAAATACTAGTAAAGGGCTATTTCCTGAATCTGAACTCGTAGCATGGGGATAAAGAAAGTTTACTTTAAAAATTTTAACCTTCAAATGTGa                                                                                       <  1:2303823/91‑1 (MQ=255)
    aaaTACTAGTAAAGGGCTATTTCCTGAATCTGAACTCGTAGCATGGGGATAAAGAAAGTTTACTTTAAAAATTTTAACCTTCACATTTGaa                                                                                      <  1:3583648/91‑1 (MQ=255)
     aaTACTAGTAAAGGGCTATTTCCTGAATCTGAACTCGTAGCATGGGGATAAAGAAAGTTTACTTTAAAAATTTTAACCTTCACATTTGAAg                                                                                     <  1:1152608/91‑1 (MQ=255)
       tACTAGTAAAGGGCTATTTCCTGAATCTGAACTCGTAGCATGGGGATAAAGAAAGTTTACTTTAAAAATTTTAACCTTCACATTTGAAGGt                                                                                   <  1:2542884/91‑1 (MQ=255)
       tACTAGTAAAGGGCTATTTCCTGAATCTGAACTCGTAGCATGGGGATAAAGAAAGTTTACTTTAAAAATTTTAACCTTCAAATGTGAAGGt                                                                                   <  1:4024584/91‑1 (MQ=255)
       tACTAGTAAAGGGCTATTTCCTGAATCTGAACTCGTAGCATGGGGATAAAGAAAGTTTACTTTAAAAATTTTAACCTTCAAATGTGAAGGt                                                                                   <  1:1505265/91‑1 (MQ=255)
       tACTAGTAAAGGGCTATTTCCTGAATCTGAACTCGTAGCATGGGGATAAAGAAAGTTTACTTTAAAAATTTTAACCTTCAAATGTGAAGGt                                                                                   <  1:172862/91‑1 (MQ=255)
          tAGTAAAGGGCTATTTCCTGAATCTGAACTCGTAGCATGGGGATAAAGAAAGTTTACTTTAAAAATTTTAACCTTCACATTTGAAGGTTaa                                                                                <  1:3261088/91‑2 (MQ=255)
          tAGTAAAGGGCTATTTCCTGAATCTGAACTCGTAGCATGGGGATAAAGAAAGTTTACTTTAAAAATTTTAACCTTCAAATGTGAAGGTTAt                                                                                <  1:2743970/91‑1 (MQ=255)
           aGTAAAGGGCTATTTCCTGAATCTGAACTCGTAGCATGGGGATAAAGAAAGTTTACTTTAAAAATTTTAACCTTCAAATGTGAAGGTTAtt                                                                               >  1:1665016/1‑91 (MQ=255)
           aGTAAAGGGCTATTTCCTGAATCTGAACTCGTAGCATGGGGATAAAGAAAGTTTACTTTAAAAATTTTAACCTTCAAATGTGAAGGTTAtt                                                                               >  1:1467215/1‑91 (MQ=255)
              aaaGGGCTATTTCCTGAATCTGAACTCGTAGCATGGGGATAAAGAAAGTTTACTTTAAAAATTTTAACCTTCAAATGTGAAGGTTAttttt                                                                            <  1:1828896/91‑1 (MQ=255)
              aaaGGGCTATTTCCTGAATCTGAACTCGTAGCATGGGGATAAAGAAAGTTTACTTTAAAAATTTTAACCTTCAAATGTGAAGGTTAttttt                                                                            <  1:3086200/91‑1 (MQ=255)
                 gggCTATTTCCTGAATCTGAACTCGTAGCATGGGGATAAAGAAAGTTTACTTTAAAAATTTTAACCTTCAAATGTGAAGGTTATTTTTTAt                                                                         >  1:3060331/1‑91 (MQ=255)
                  ggCTATTTCCTGAATCTGAACTCGTAGCATGGGGATAAAGAAAGTTTACTTTAAAAATTTTAACCTTCAAATGTGAAGGTTATTTTTTAtt                                                                        <  1:1683616/91‑1 (MQ=255)
                   gCTATTTCCTGAATCTGAACTCGTAGCATGGGGATAAAGAAAGTTTACTTTAAAAATTTTAACCTTCAAATGTGAAGGTTATTTTTTATTg                                                                       >  1:205254/1‑91 (MQ=255)
                   gCTATTTCCTGAATCTGAACTCGTAGCATGGGGATAAAGAAAGTTTACTTTAAAAATTTTAACCTTCAAATGTGAAGGTTATTTTTTATTg                                                                       >  1:3842798/1‑91 (MQ=255)
                    cTATTTCCTGAATCTGAACTCGTAGCATGGGGATAAAGAAAGTTTACTTTAAAAATTTTAACCTTCAAATGTGAAGGTTATTTTTTATTGc                                                                      >  1:1495721/1‑91 (MQ=255)
                     tATTTCCTGAATCTGAACTCGTAGCATGGGGATAAAGAAATTTTACTTTAAAAATTTTAACCTTCAAATGTGAAGGTTATTTTTTATTGcc                                                                     <  1:3707181/91‑1 (MQ=255)
                     tATTTCCTGAATCTGAACTCGTAGCATGGGGATAAAGAAAGTTTACTTTAAAAATTTTAACCTTCAAATGTGAAGGTTATTTTTTATTGcc                                                                     <  1:1530218/91‑1 (MQ=255)
                     tATTTCCTGAATCTGAACTCGTAGCATGGGGATAAAGAAAGTTTACTTTAAAAATTTTAACCTTCAAATGTGAAGGTTATTTTTTATTGcc                                                                     <  1:3526896/91‑1 (MQ=255)
                     tATTTCCTGAATCTGAACTCGTAGCATGGGGATAAAGAAAGTTTACTTTAAAAATTTTAACCTTCAAATGTGAAGGTTATTTTTTATTGcc                                                                     >  1:2685040/1‑91 (MQ=255)
                      aTTTCCTGAATCTGAACTCGTAGCATGGGGATAAAGAAAGTTTACTTTAAAAATTTTAACCTTCAAATGTGAAGGTTATTTTTTATTGccc                                                                    >  1:159987/1‑91 (MQ=255)
                        ttCCTGAATCTGAACTCGTAGCATGGGGATAAAGAAAGTTTACTTTAAAAATTTTAACCTTCAAATGTGAAGGTTATTTTTTATTGCCCaa                                                                  <  1:1955065/91‑1 (MQ=255)
                         tCCTGAATCTGAACTCGTAGCATGGGGATAAAGAAAGTTTACTTTAAAAATTTTAACCTTCAAATGTGAAGGTTATTTTTTATTGCCCaaa                                                                 >  1:3029656/1‑91 (MQ=255)
                         tCCTGAATCTGAACTCGTAGCATGGGGATAAAGAAAGTTTACTTTAAAAATTTTAACCTTCAAATGTGAAGGTTATTTTTTATTGCCCaaa                                                                 <  1:4066737/91‑1 (MQ=255)
                         tCCTGAATCTGAACTCGTAGCATGGGGATAAAGAAAGTTTACTTTAAAAATTTTAACCTTCAAATGTGAAGGTTATTTTTTATTGCCCaaa                                                                 >  1:876946/1‑91 (MQ=255)
                            tGAATCTGAACTCGTAGCATGGGGATAAAGAAAGTTTACTTTAAAAATTTTAACCTTCAAATGTGAAGGTTATTTTTTATTGCCCAAAACg                                                              <  1:41702/91‑1 (MQ=255)
                            tGAATCTGAACTCGTAGCATGGGGATAAAGAAAGTTTACTTTAAAAATTTTAACCTTCAAATGTGAAGGTTATTTTTTATTGCCCAAAACg                                                              <  1:943323/91‑1 (MQ=255)
                             gAATCTGAACTCGTAGCATGGGGATAAAGTAAGTTTACTTTAAAAATTTTAACCTTCAAATGTGAAGGTTATTTTTTATTGCCCAAAACGt                                                             >  1:418512/1‑91 (MQ=255)
                                  tGAACTCGTAGCATGGGGATAAAGAAAGTTTACTTTAAAAATTTTAACCTTCAAATGTGAAGGTTATTTTTTATTGCCCAAAACGTGCtga                                                        <  1:3016351/91‑1 (MQ=255)
                                  tGAACTCGTAGCATGGGGATAAAGAAAGTTTACTTTAAAAATTTTAACCTTCAAATGTGAAGGTTATTTTTTATTGCCCAAAACGTGCtga                                                        <  1:1039898/91‑1 (MQ=255)
                                    aaCTCGTAGCATGGGGATAAAGAAAGTTTACTTTAAAAATTTTAACCTTCAAATGTGAAGGTTATTTTTTATTGCCCAAAACGTGCtgatg                                                      <  1:286801/91‑1 (MQ=255)
                                     aCTCGTAGCATGGGGATAAAGAAAGTTTACTTTAAAAATTTTAACCTTCAAATGTGAAGGTTATTTTTTATTGCCCAAAACGTGCtgatga                                                     >  1:2719534/1‑91 (MQ=255)
                                       tCGTAGCATGGGGATAAAGAAAGTTTACTTTAAAAATTTTAACCTTCAAATGTGAAGGTTATTTTTTATTGCCCAAAACGTGCTGATGACa                                                   <  1:413622/91‑1 (MQ=255)
                                          tAGCATGGGGATAAAGAAAGTTTACTTTAAAAATTTTAACCTTCAAATGTGAAGGTTATTTTTTATTGCCCAAAACGTGCTGATGACAttt                                                <  1:2050263/91‑1 (MQ=255)
                                          tAGCATGGGGATAAAGAAAGTTTACTTTAAAAATTTTAACCTTCAAATGTGAAGGTTATTTTTTATTGCCCAAAACGTGCTGATGACAttt                                                <  1:622357/91‑1 (MQ=255)
                                            gCATGGGGATAAAGAAAGTTTACTTTAAAAATTTTAACCTTCAAATGTGAAGGTTATTTTTTATTGCCCAAAACGTGCTGATGACATTTTa                                              >  1:1939612/1‑91 (MQ=255)
                                             cATGGGGATAAAGAAAGTTTACTTTAAAAATTTTAACCTTCAAATGTGAAGGTTATTTTTTATTGCCCAAAACGTGCTGATGACATTTTaa                                             <  1:2678093/91‑1 (MQ=255)
                                               tGGGGATAAAGAAAGTTTACTTTAAAAATTTTAACCTTCAAATGTGAAGGTTATTTTTTATTGCCCAAAACGTGCTGATGACATTTTaaaa                                           >  1:71141/1‑91 (MQ=255)
                                                ggggATAAAGAAAGTTTACTTTAAAAATTTTAACCTTCAAATGTGAAGGTTATTTTTTATTGCCCAAAACGTGCTGATGACATTTTAAAAg                                          <  1:902334/91‑1 (MQ=255)
                                                acggATAAAGAAAGTTTACTTTAAAAATTTTAACCTTCAAATGTGAAGGTTATTTTTTATTGCCCAAAACGTGCTGATGACATTTTAAAAg                                          <  1:3335967/89‑1 (MQ=255)
                                                 gggATAAAGAAAGTTTACTTTAAAAATTTTAACCTTCAAATGTGAAGGTTATTTTTTATTGCCCAAAACGTGCTGATGACATTTTAAAAGc                                         <  1:1243531/91‑1 (MQ=255)
                                                 gggATAAAGAAAGTTTACTTTAAAAATTTTAACCTTCAAATGTGAAGGTTATTTTTTATTGCCCAAAACGTGCTGATGACATTTTAAAAGc                                         <  1:1166209/91‑1 (MQ=255)
                                                 gggATAAAGAAAGTTTACTTTAAAAATTTTAACCTTCAAATGTGAAGGTTATTTTTTATTGCCCAAAACGTGCTGATGACATTTTAAAAGc                                         <  1:3220133/91‑1 (MQ=255)
                                                  ggATAAAGAAAGTTTACTTTAAAAATTTTAACCTTCAAATGTGAAGGTTATTTTTTATTGCCCAAAACGTGCTGATGACATTTTAAAAGCa                                        <  1:1298341/91‑1 (MQ=255)
                                                  ggATAAAGAAAGTTTACTTTAAAAATTTTAACCTTCAAATGTGAAGGTTATTTTTTATTGCCCAAAACGTGCTGATGACATTTTAAAAGCa                                        <  1:1549936/91‑1 (MQ=255)
                                                  ggATAAAGAAAGTTTACTTTAAAAATTTTAACCTTCAAATGTGAAGGTTATTTTTTATTGCCCAAAACGTGCTGATGACATTTTAAAAGCa                                        >  1:2751410/1‑91 (MQ=255)
                                                  ggATAAAGAAAGTTTACTTTAAAAATTTTAACCTTCAAATGTGAAGGTTATTTTTTATTGCCCAAAACGTGCTGATGACATTTTAAAAGCa                                        >  1:1910414/1‑91 (MQ=255)
                                                   gATAAAGAAAGTTTACTTTAAAAATTTTAACCTTCAAATGTGAAGGTTATTTTTTATTGCCCAAAACGTGCTGATGACATTTTAAAAGCaa                                       >  1:2548171/1‑91 (MQ=255)
                                                   gATAAAGAAAGTTTACTTTAAAAATTTTAACCTTCAAATGTGAAGGTTATTTTTTATTGCCCAAAACGTGCTGATGACATTTTAAAAGCaa                                       >  1:1908622/1‑91 (MQ=255)
                                                    aTAAAGAAAGTTTACTTTAAAAATTTTAACCTTCAAATGTGAAGGTTATTTTTTATTGCCCAAAACGTGCTGATGACATTTTAAAAGCAAg                                      <  1:739088/91‑1 (MQ=255)
                                                     tAAAGAAAGTTTACTTTAAAAATTTTAACCTTCAAATGTGAAGGTTATTTTTTATTGCCCAAAACGTGCTGATGACATTTTAAAAGCAAGt                                     <  1:112619/91‑1 (MQ=255)
                                                       aagaaagTTTACTTTAAAAATTTTAACCTTCAAATGTGAAGGTTATTTTTTATTGCCCAAAACGTGCTGATGACATTTTAAAAGCAAGTAt                                   <  1:2432784/91‑1 (MQ=255)
                                                        agaaagTTTACTTTAAAAATTTTAACCTTCAAATGTGAAGGTTATTTTTTATTGCCCAAAACGTGCTGATGACATTTTAAAAGCAAGTATg                                  >  1:2910334/1‑91 (MQ=255)
                                                        agaaagTTTACTTTAAAAATTTTAACCTTCAAATGTGAAAGTTATTTTTTATTGCCCAAAACGTGCTGATGACATTTTAAAAGCAAGTATg                                  >  1:832023/1‑91 (MQ=255)
                                                         gaaagTTTACTTTAAAAATTTTAACCTTCAAATGTGAAGGTTATTTTTTATTGCCCAAAACGTGCTGATGACATTTTAAAAGCAAGTATgg                                 >  1:1740610/1‑91 (MQ=255)
                                                          aaagTTTACTTTAAAAATTTTAACCTTCAAATGTGAAGGTTATTTTTTATTGCCCAAAACGTGCTGATGACATTTTAAAAGCAAGTATGGa                                <  1:862834/91‑1 (MQ=255)
                                                           aagTTTACTTTAAAAATTTTAACCTTCAAATGTGAAGGTTATTTTTTATTGCCCAAAACGTGCTGATGACATTTTAAAAGCAAGTATGGaa                               >  1:218528/1‑91 (MQ=255)
                                                              tttACTTTAAAAATTTTAACCTTCAAATGTGAAGGTTATTTTTTATTGCCCAAAACGTGCTGATGACATTTTAAAAGCAAGTATGGAatat                            <  1:919344/91‑1 (MQ=255)
                                                                tACTTTAAAAATTTTAACCTTCAAATGTGAAGGTTATTTTTTATTGCCCAAAACGTGCTGATGACATTTTAAAAGCAAGTATGGAATATCa                          <  1:2762114/91‑1 (MQ=255)
                                                                tACTTTAAAAATTTTAACCTTCAAATGTGAAGGTTATTTTTTATTGCCCAAAACGTGCTGATGACATTTTAAAAGCAAGTATGGAATATCa                          <  1:1544140/91‑1 (MQ=255)
                                                                tACTTTAAAAATTTTAACCTTCAAATGTGAAGGTTATTTTTTATTGCCCAAAACGTGCTGATGACATTTTAAAAGCAAGTATGGAATATCa                          <  1:1094049/91‑1 (MQ=255)
                                                                tACTTTAAAAATTTTAACCTTCAAATGTGAAGGTTATTTTTTATTGCCCAAAACGTGCTGATGACATTTTAAAAGCAAGTATGGAATATCa                          >  1:1285000/1‑91 (MQ=255)
                                                                tACTTTAAAAATTTTAACCTTCAAATGTGAAGGTTATTTTTTATTGCCCAAAACGTGCTGATGACATTTTAAAAGCAAGTATGGAATATCa                          >  1:1285104/1‑91 (MQ=255)
                                                                tACTTTAAAAATTTTAACCTTCAAATGTGAAGGTTATTTTTTATTGCCCAAAACGTGCTGATGACATTTTAAAAGCAAGTATGGAATATCa                          <  1:364034/91‑1 (MQ=255)
                                                                 aCTTTAAAAATTTTAACCTTCAAATGTGAAGGTTATTTTTTATTGCCCAAAACGTGCTGATGACATTTTAAAAGCAAGTATGGAATATCAg                         <  1:729988/91‑1 (MQ=255)
                                                                 aCTTTAAAAATTTTAACCTTCAAATGTGAAGGTTATTTTTTATTGCCCAAAACGTGCTGATGACATTTTAAAAGCAAGTATGGAATATCAg                         <  1:237869/91‑1 (MQ=255)
                                                                   tttAAAAATTTTAACCTTCAAATGTGAAGGTTATTTTTTATTGCCCAAAACGTGCTGATGACATTTTAAAAGCAAGTATGGAATATCAGTc                       >  1:1005583/1‑91 (MQ=255)
                                                                     tAAAAATTTTAACCTTCAAATGTGAAGGTTATTTTTTATTGCCCAAAACGTGCTGATGACATTTTAAAAGCAAGTATGGAATATCAGTCGa                     <  1:3165844/91‑1 (MQ=255)
                                                                       aaaaTTTTAACCTTCAAATGTGAAGGTTATTTTTTATTGCCCAAAACGTGCTGATGACATTTTAAAAGCAAGTATGGAATATCAGTCGACa                   >  1:3667136/1‑91 (MQ=255)
                                                                       aaaaTTTTAACCTTCAAATGTGAAGGTTATTTTTTATTGCCCAAAACGTGCTGATGACATTTTAAAAGCAAGTATGGAATATCAGTCGACa                   >  1:1918351/1‑91 (MQ=255)
                                                                       aaaaTTTTAACCTTCAAATGTGAAGGTTATTTTTTATTGCCCAAAACGTGCTGATGACATTTTAAAAGCAAGTATGGAATATCAGTCGACa                   >  1:736614/1‑91 (MQ=255)
                                                                       aaaaTTTTAACCTTCAAATGTGAAGGTTATTTTTTATTGCCCAAAACGTGCTGATGACATTTTAAAAGCAAGTATGGAATATCAGTCGACa                   >  1:72763/1‑91 (MQ=255)
                                                                       aaaaTTTTAACCTTCAAATGTGAAGGTTATTTTTTATTGCCCAAAACGTGCTGATGACATTTTAAAAGCAAGTATGGAATATCAGTCGACa                   >  1:1462410/1‑91 (MQ=255)
                                                                          aTTTTAACCTTCAAATGTGAAGGTTATTTTTTATTGCCCAAAACGTGCTGATGACATTTTAAAAGCAAGTATGGAATATCTGTCGACAGAc                <  1:497572/91‑1 (MQ=255)
                                                                          aTTTTAACCTTCAAATGTGAAGGTTATTTTTTATTGCCCAAAACGTGCTGATGACATTTTAAAAGCAAGTATGGAATATCAGTCGACAGAc                <  1:355682/91‑1 (MQ=255)
                                                                           ttttAACCTTCAAATGTGAAGGTTATTTTTTATTGCCCAAAACGTGCTGATGACATTTTAAAAGCAAGTATGGAATATCAGTCGACAGACt               <  1:1410918/91‑1 (MQ=255)
                                                                           ttttAACCTTCAAATGTGAAGGTTATTTTTTATTGCCCAAAACGTGCTGATGACATTTTAAAAGCAAGTATGGAATATCAGTCGACAGACt               <  1:818547/91‑1 (MQ=255)
                                                                            tttAACCTTCAAATGTGAAGGTTATTTTTTATTGCCCAAAACGTGCTGATGACATTTTAAAAGCAAGTATGGAATATCAGTCGACAGACta              <  1:2652633/91‑1 (MQ=255)
                                                                            tttAACCTTCAAATGTGAAGGTTATTTTTTATTGCCCAAAACGTGCTGATGACATTTTAAAAGCAAGTATGGAATATCAGTCGACAGACta              >  1:3830077/1‑91 (MQ=255)
                                                                            aatAACCTTCACATTTGAAGGTTATTTTTTATTGCCCAAAACGTGCTGATGACATTTTAAAAGCAAGTATGGAATATCAGTCGACAGACta              >  1:3144248/3‑91 (MQ=39)
                                                                            aatAACCTTCACATTTGAAGGTTATTTTTTATTGCCCAAAACGTGCTGATGACATTTTAAAAGCAAGTATGGAATATCAGTCGACAGACta              >  1:314090/3‑91 (MQ=39)
                                                                            aatAACCTTCACATTTGAAGGTTATTTTTTATTGCCCAAAACGTGCTGATGACATTTTAAAAGCAAGTATGGAATATCAGTCGACAGACta              >  1:3047803/3‑91 (MQ=39)
                                                                             atAACCTTCACATTTGAAGGTTATTTTTTATTGCCCAAAACGTGCTGATGACATTTTAAAAGCAAGTATGGAATATCAGTCGACAGACtat             >  1:1587252/2‑91 (MQ=255)
                                                                              tAACCTTCAAATGTGAAGGTTATTTTTTATTGCCCAAAACGTGCTGATGACATTTTAAAAGCAAGTATGGAATATCAGTCGACAGACtata            >  1:1787209/1‑91 (MQ=255)
                                                                               aaCCTTCAAATGTGAAGGTTATTTTTTATTGCCCAAAACGTGCTGATGACATTTTAAAAGCAAGTATGGAATATCAGTCGACAGACTATaa           >  1:452472/1‑91 (MQ=255)
                                                                                aCCTTCACATTTGAAGGTTATTTTTTATTGCCCAAAACGTGCTGATGACATTTTAAAAGCAAGTATGGAATATCAGTCGACAGACTATaaa          >  1:1202072/1‑91 (MQ=255)
                                                                                aCCTTCAAATGTGAAGGTTATTTTTTATTGCCCAAAACGTGCTGATGACATTTTAAAAGCAAGTATGGAATATCAGTCGACAGACTATaaa          >  1:1634317/1‑91 (MQ=255)
                                                                                 ccTTCAAATGTGAAGGTTATTTTTTATTGCCCAAAACGTGCTGATGACATTTTAAAAGCAAGTATGGAATATCAGTCGACAGACTATAAAc         >  1:1121979/1‑91 (MQ=255)
                                                                                 ccTTCAAATGTGAAGGTTATTTTTTATTGCCCAAAACGTGCTGATGACATTTTAAAAGCAAGTATGGAATATCAGTCGACAGACTATAAAc         <  1:160692/91‑1 (MQ=255)
                                                                                 ccTTCAAATGTGAAGGTTATTTTTTATTGCCCAAAACGTGCTGATGACATTTTAAAAGCAAGTATGGAATATCAGTCGACAGACTATAAAc         >  1:2555395/1‑91 (MQ=255)
                                                                                  cTTCACATTTGAAGGTTATTTTTTATTGCCCAAAACGTGCTGATGACATTTTAAAAGCAAGTATGGAATATCAGTCGACAGACTATAAACg        >  1:3606698/1‑91 (MQ=255)
                                                                                  cTTCACATTTGAAGGTTATTTTTTATTGCCCAAAACGTGCTGATGACATTTTAAAAGCAAGTATGGAATATCAGTCGACAGACTATAAACg        >  1:1695309/1‑91 (MQ=255)
                                                                                   ttCACATTTGAAGGTTATTTTTTATTGCCCAAAACGTGCTGATGACATTTTAAAAGCAAGTATGGAATATCAGTCGACAGACTATAAACgg       >  1:3883852/1‑91 (MQ=255)
                                                                                    tCAAATGTGAAGGTTATTTTTTATTGCCCAAAACGTGCTGATGACATTTTAAAAGCAAGTATGGAATATCAGTCGACAGACTATAAACGGa      >  1:342949/1‑91 (MQ=255)
                                                                                        aTGTGAAGGTTATTTTTTATTGCCCAAAACGTGCTGATGACATTTTAAAAGCAAGTATGGAATATCAGTCGACAGACTATAAACGGAGGta  <  1:3496010/91‑1 (MQ=255)
                                                                                          |                                                                                        
ACATAAATACTAGTAAAGGGCTATTTCCTGAATCTGAACTCGTAGCATGGGGATAAAGAAAGTTTACTTTAAAAATTTTAACCTTCAAATGTGAAGGTTATTTTTTATTGCCCAAAACGTGCTGATGACATTTTAAAAGCAAGTATGGAATATCAGTCGACAGACTATAAACGGAGGTA  >  USA300TCH1516_ALE/1343532‑1343710

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: ‑