Predicted mutation
evidence seq id position mutation freq annotation gene description
RA USA300TCH1516_ALE 265,618 A→G 6.1% intergenic (+18/+146) ugpQ_2 → / ← scn_1 Glycerophosphodiester phosphodiesterase, cytoplasmic/Staphylococcal complement inhibitor

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE265,6180AG 6.1% 632.4 / 19.3 196intergenic (+18/+146)ugpQ_2/scn_1Glycerophosphodiester phosphodiesterase, cytoplasmic/Staphylococcal complement inhibitor
Reads supporting (aligned to +/- strand):  ref base A (83/101);  new base G (9/3);  total (92/104)
Fisher's exact test for biased strand distribution p-value = 7.02e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.97e-01

Only 100 of 206 total aligned reads displayed.

GCTGATCAGATTAAAGAAGAAAAGAAAGACGAAACATACTTCGATCGTTCTATAAGAATTTTGTTTGAATAATATAAACAAAGACCTCTAAAGTTATCAAGATGATACCTTCAGAGGTCTTTTTAATGTTGCCATCTATGGGATAGGCAATCGTTTCATTCGTTTATATTCATATGACAA  >  USA300TCH1516_ALE/265529‑265708
                                                                                         |                                                                                          
gCTGATCAGATTAAAGAAGAAAAGAAAGACGAAACATACTTCGATCGTTCTATAAGAATTTTGTTTGAATAATATAAACAATGACCTCTaa                                                                                           >  1:3484825/1‑91 (MQ=255)
gCTGATCAGATTAAAGAAGAAAAGAAAGACGAAACATACTTCGATCGTTCTATAAGAATTTTGTTTGAATAATATAAACAAAGACCTCTaa                                                                                           <  1:3705811/91‑1 (MQ=255)
 cTGATCAGATTAAAGAAGAAAAGAAAGACGAAACATACTTCGATCGTTCTATAAGAATTTTGTTTGAATAATATAAACAAAGACCTCTaaa                                                                                          <  1:793225/91‑1 (MQ=255)
  tGATCAGATTAAAGAAGAAAAGAAAGACGAAACATACTTCGATCGTTCTATAAGAATTTTGTTTGAATAATATAAACAAAGACCTCTAAAg                                                                                         >  1:3377681/1‑91 (MQ=255)
   ggtCAGATTAAAGAAGAAAAGAAAGACGAAACATACTTCGATCGTTCTATAAGAATTTTGTTTGAATAATATAAACAAAGACCTCTAAAGt                                                                                        >  1:354729/3‑91 (MQ=255)
   gATCAGATTAAAGAAGAAAAGAAAGACGAAACATACTTCGATCGTTCTATAAGAATTTTGTTTGAATAATATAAACAAAGACCTCTAAAGt                                                                                        <  2:3319334/91‑1 (MQ=255)
   gATCAGATTAAAGAAGAAAAGAAAGACGAAACATACTTCGATCGTTCTATAAGAATTTTGTTTGAATAATATAAACAAAGACCTCTAAAGt                                                                                        <  2:2328502/91‑1 (MQ=255)
    aTCAGATTAAAGAAGAAAAGAAAGACGAAACATACTTCGATCGTTCTATAAGAATTTTGTTTGAATAATATAAACAAAGACCTCTAAAGtt                                                                                       >  2:2530737/1‑91 (MQ=255)
         aTTAAAGAAGAAAAGAAAGACGAAACATACTTCGATCGTTCTATAAGAATTTTGTTTGAATAATATAAACAAAGACCTCTAAAGTTATCaa                                                                                  <  1:2530054/91‑1 (MQ=255)
             aagaagAAAAGAAAGACGAAACATACTTCGATCGTTCTATAAGAATTTTGTTTGAATAATATAAACAAAGACCTCTAAAGTTATCAAgatg                                                                              >  2:2641975/1‑91 (MQ=255)
              agaagaAAAGAAAGACGAAACATACTTCGATCGTTCTATAAGAATTTTGTTTGAATAATATAAACAAAGACCTCTAAAGTTATCAAgatga                                                                             <  2:1341022/91‑1 (MQ=255)
                aagaaaagaaAGACGAAACATACTTCGATCGTTCTATAAGAATTTTGTTTGAATAATATAAACAAAGACCTCTAAAGTTATCAAGATGATa                                                                           <  2:1628735/91‑1 (MQ=255)
                aagaaaagaaAGACGAAACATACTTCGATCGTTCTATAAGAATTTTGTTTGAATAATATAAACAAAGACCTCTAAAGTTATCAAGATGATa                                                                           <  1:2628750/91‑1 (MQ=255)
                 agaaaagaaaGACGAAACATACTTCGATCGTTCTATAAGAATTTTGTTTGAATAATATAAACAAAGACCTCTAAAGTTATCAAGATGATAc                                                                          <  1:2691/91‑1 (MQ=255)
                  gaaaagaaaGACGAAACATACTTCGATCGTTCTATAAGAATTTTGTTTGAATAATATAAACAAAGACCTCTAAAGTTATCAAGATGATAcc                                                                         >  1:1385700/1‑91 (MQ=255)
                  gaaaagaaaGACGAAACATACTTCGATCGTTCTATAAGAATTTTGTTTGAATAATATAAACAAAGACCTCTAAAGTTATCAAGATGATAcc                                                                         >  1:1681178/1‑91 (MQ=255)
                   aaaagaaaGACGAAACATACTTCGATCGTTCTATAAGAATTTTGTTTGAATAATATAAACAAAGACCTCTAAAGTTATCAAGATGATACCt                                                                        >  2:3425475/1‑91 (MQ=255)
                    aaagaaagACGAAACATACTTCGATCGTTCTATAAGAATTTTGTTTGAATAATATAAACAAAGACCTCTAAAGTTATCAAGATGATACCtt                                                                       >  2:546589/1‑91 (MQ=255)
                    aaagaaagACGAAACATACTTCGATCGTTCTATAAGAATTTTGTTTGAATAATATAAACAAAGACCTCTAAAGTTATCAAGATGATACCtt                                                                       >  2:1709454/1‑91 (MQ=255)
                       gaaagaCGAAACATACTTCGATCGTTCTATAAGAATTTTGTTTGAATAATATAAACAAAGACCTCTAAAGTTATCAAGATGATACCTTCag                                                                    <  1:567828/91‑1 (MQ=255)
                       gaaagaCGAAACATACTTCGATCGTTCTATAAGAATTTTGTTTGAATAATATAAACAAAGACCTCTAAAGTTATCAAGATGATACCTTCag                                                                    <  2:758424/91‑1 (MQ=255)
                        aaagaCGAAACATACTTCGATCGTTCTATAAGAATTTTGTTTGAATAATATAAACAAAGACCTCTAAAGTTATCAAGATGATACCTTCaga                                                                   >  1:432866/1‑91 (MQ=255)
                        aaagaCGAAACATACTTCGATCGTTCTATAAGAATTTTGTTTGAATAATATAAACAAAGACCTCTAAAGTTATCAAGATGATACCTTCaga                                                                   <  2:2086911/91‑1 (MQ=255)
                         aagaCGAAACATACTTCGATCGTTCTATAAGAATTTTGTTTGAATAATATAAACAAAGACCTCTAAAGTTATCAAGATGATACCTTCagag                                                                  >  1:1496177/1‑91 (MQ=255)
                         aagaCGAAACATACTTCGATCGTTCTATAAGAATTTTGTTTGAATAATATAAACAAAGACCTCTAAAGTTATCAAGATGATACCTTCagag                                                                  <  1:1995411/91‑1 (MQ=255)
                          agaCGAAACATACTTCGATCGTTCTATAAGAATTTTGTTTGAATAATATAAACAAAGACCTCTAAAGTTATCAAGATGATACCTTCAGAgg                                                                 <  1:3703566/91‑1 (MQ=255)
                          agaCGAAACATACTTCGATCGTTCTATAAGAATTTTGTTTGAATAATATAAACAAAGACCTCTAAAGTTATCAAGATGATACCTTCAGAgg                                                                 <  1:1571186/91‑1 (MQ=255)
                          agaCGAAACATACTTCGATCGTTCTATAAGAATTTTGTTTGAATAATATAAACAAAGACCTCTAAAGTTATCAAGATGATACCTTCAGAgg                                                                 <  1:2333650/91‑1 (MQ=255)
                           gaCGAAACATACGTCGATCGTTCTATAAGATTTTTGTTTGAATAATATAAACAAAGACCTCTGAAGGTATCATCTTGATAACTTTAGAGGt                                                                <  2:1766055/91‑1 (MQ=18)
                            aCGAAACATACTTCGATCGTTCTATAAGAATTTTGTTTGAATAATATAAACAAAGACCTCTAAAGTTATCAAGATGATACCTTCAGAGGTc                                                               >  2:1938856/1‑91 (MQ=255)
                              gAAACATACTTCGATCGTTCTATAAGAATTTTGTTTGAATAATATAAACAAAGACCTCTAAAGTTATCAAGATGATACCTTCAGAGGTCtt                                                             <  1:3558522/91‑1 (MQ=255)
                                  cATACTTCGATCGTTCTATAAGAATTTTGTTTGAATAATATAAACAAAGACCTCTAAAGATCTCAAGATGATACCTTCAGAGGTCTTTTTa                                                         >  1:3104184/1‑91 (MQ=255)
                                   aTACTTCGATCGTTCTATAAGAATTTTGTTTGAATAATATAAACAAAGACCTCTGAAGGTATCATCTTGATAACTTTAGAGGTCtttgttt                                                        <  2:2473489/91‑5 (MQ=14)
                                   aTACTTCGATCGTTCTATAAGAATTTTGTTTGAATAATATAAACAAAGACCTCTGAAGGTATCATCTTGATAACTTTAGAGGTCtttgttt                                                        <  2:3868254/91‑5 (MQ=17)
                                   aTACTTCGATCGTTCTATAAGAATTTTGTTTGAATAATATAAACAAAGACCTCTAAAGTTATCAAGATGATACCTTCAGAGGTCTTTTTaa                                                        <  2:1477615/91‑1 (MQ=255)
                                   aTACTTCGATCGTTCTATAAGAATTTTGTTTGAATAATATAAACAAAGACCTCTAAAGTTATCAAGATGATACCTTCAGAGGTCTTTTTaa                                                        <  1:65441/91‑1 (MQ=255)
                                     aCTTCGATCGTTCTATAAGAATTTTGTTTGAATAATATAAACAAAGACCTCTAAAGTTATCAAGATGATACCTTCAGAGGTCTTTTTAATg                                                      >  1:1382630/1‑91 (MQ=255)
                                     aCTTCGATCGTTCTATAAGAATTTTGTTTGAATAATATAAACAAAGACCTCTAAAGTTATCAAGATGATACCTTCAGAGGTCTTTTTAATg                                                      >  2:931112/1‑91 (MQ=255)
                                        tCGATCGTTCTATAAGAATTTTGTTTGAATAATATAAACAAAGACCTCTAAAGTTATCAAGATGATACCTTCAGAGGTCTTTTTAATGTTg                                                   <  2:3763880/91‑1 (MQ=255)
                                        tCGATCGTTCTATAAGAATTTTGTTTGAATAATATAAACAAAGACCTCTAAAGTTATCAAGATGATACCTTCAGAGGTCTTTTTAATGTTg                                                   <  2:93503/91‑1 (MQ=255)
                                         cGATCGTTCTATAAGAATTTTGTTTGAATAATATAAACAAAGACCTCTAAAGTTATCAAGATGATACCTTCAGAGGTCTTTTTAATGttac                                                  <  2:453932/91‑3 (MQ=255)
                                         cGATCGTTCTATAAGAATTTTGTTTGAATAATATAAACAAAGACCTCTAAAGTTATCAAGATGATACCTTCAGAGGTCTTTTTAATGTTGc                                                  <  2:2908771/91‑1 (MQ=255)
                                         cGATCGTTCTATAAGAATTTTGTTTGAATAATATAAACAAAGACCTCTAAAGTTATCAAGATGATACCTTCAGAGGTCTTTTTAATGTTGc                                                  <  2:337256/91‑1 (MQ=255)
                                         cGATCGTTCTATAAGAATTTTGTTTGAATAATATAAACAAAGACCTCTAAAGTTATCAAGATGATACCTTCAGAGGTCTTTTTAATGTTGc                                                  >  1:1608086/1‑91 (MQ=255)
                                          gATCGTTCTATAAGAATTTTGTTTGAATAATATAAACAAACACCTCTAAAGTTATCAAGATGATACCTTCAGAGGTCTTTTTAATGTTGcc                                                 >  2:3193163/1‑91 (MQ=255)
                                             cGTTCTATAAGAATTTTGTTTGAATAATATAAACAAAGACCTCTAAAGTTATCAAGATGATACCTTCAGAGGTCTTTTTAATGTTGCCATc                                              <  1:183919/91‑1 (MQ=255)
                                              gTTCTATAAGAATTTTGTTTGAATAATATAAACAAAGACCTCTAAAGTTATCAAGATGATACCTTCAGAGGTCTTTTTAATGTTGcctatc                                             <  1:1073024/91‑5 (MQ=255)
                                              gTTCTATAAGAATTTTGTTTGAATAATATAAACAAAGACCTCTAAAGTTATCAAGATGATACCTTCAGAGGTCTTTTTAATGTTGCCATCt                                             <  2:3729964/91‑1 (MQ=255)
                                              gTTCTATAAGAATTTTGTTTGAATAATATAAACAAAGACCTCTAAAGTTATCAAGATGATACCTTCAGAGGTCTTTTTAATGTTGCCATCt                                             >  2:1837544/1‑91 (MQ=255)
                                               ttCTATAAGAATTTTGTTTGAATAATATAAACAAAGGCCTCTAAAGTTATCAAGATGATACCTTCAGAGGTCTTTTTAATGTTGCCATCTa                                            <  2:3058870/91‑1 (MQ=255)
                                               ttCTATAAGAATTTTGTTTGAATAATATAAACAAAGACCTCTAAAGTTATCAAGATGATACCTTCAGAGGTCTTTTTAATGTTGCCATCTa                                            <  1:1405227/91‑1 (MQ=255)
                                                tCTATAAGAATTTTGTTTGAATAATATAAACAAAGACCTCTAAAGTTATCAAGATGATACCTTCAGAGGTCTTTTTAATGTTGCCATCTAt                                           >  1:1449476/1‑91 (MQ=255)
                                                  tataAGAATTTTGTTTGAATAATATAAACAAAGACCTGTAAAGTTATCAAGATGATACCTTCAGAGGTCTTTTTAATGTTGCCATCTATgg                                         >  1:3262659/1‑91 (MQ=255)
                                                  tataAGAATTTTGTTTGAATAATATAAACAAAGACCTCTAAAGTTATCAAGATGATACCTTCAGAGGTCTTTTTAATGTTGCCATCTATgg                                         >  2:3686307/1‑91 (MQ=255)
                                                       gAATTTTGTTTGAATAATATAAACAAAGACCTCTAAAGTTATCAAGATGATACCTTCAGAGGTCTTTTTAATGTTGCCATCTATGGGATAg                                    <  2:2782108/91‑1 (MQ=255)
                                                        gaTTTTGTTTGAATAATATAAACAAAGTCCTCTAAAGTTATCAAGATGATACCTTCAGAGGTCTTTTTAATGTTGCCATCTATGGGATAgg                                   <  1:2258785/90‑1 (MQ=255)
                                                        aaTTTTGTTTGAATAATATAAACAAAGACCTCTAAAGTTATCACGATGATACCTTCAGAGGTCTTTTTAATGTTGCCATCTATGGGATAgg                                   <  1:3868024/91‑1 (MQ=255)
                                                        aaTTTTGTTTGAATAATATAAACAAAGACCTCTAAAGTTATCAAGATGATACCTTCAGAGGTCTTTTTAATGTTGCCATCTATGGGATAgg                                   <  1:2235735/91‑1 (MQ=255)
                                                        aaTTTTGTTTGAATAATATAAACAAAGACCTCTAAAGTTATCAAGATGATACCTTCAGAGGTCTTTTTAATGTTGCCATCTATGGGATAgg                                   >  2:2422668/1‑91 (MQ=255)
                                                        aaTTTTGTTTGAATAATATAAACAAAGACCTCTAAAGTTATCAAGATGATACCTTCAGAGGTCTTTTTAATGTTGCCATCTATGGGATAgg                                   >  1:714187/1‑91 (MQ=255)
                                                        aaTTTTGTTTGAATAATATAAACAAAGACCTCTAAAGTTATCAAGATGATACCTTCAGAGGTCTTTTTAATGTTGCCATCTATGGGATAgg                                   <  2:1919181/91‑1 (MQ=255)
                                                        aaTTTTGTTTGAATAATATAAACAAAGACCTCTAAAGTTATCAAGATGATACCTTCAGAGGTCTTTTTAATGTTGCCATCTATGGGATAgg                                   <  2:1375816/91‑1 (MQ=255)
                                                        aaTTTTGTTTGAATAATATAAACAAAGACCTCTAAAGTTATCAAGATGATACCTTCAGAGGTCTTTTTAATGTTGCCATCTATGGGATAgg                                   <  1:1031212/91‑1 (MQ=255)
                                                         aTTTTGTTTGAATAATATAAACAAAGACCTCTAAAGTTATCAAGATGATACCTTCAGAGGTCTTTTTAATGTTGCCATCTATGGGATAGGc                                  <  1:3310268/91‑1 (MQ=255)
                                                          ttttGTTTGAATAATATAAACAAAGACCTCTAAAGTTATCAAGATGATACCTTCAGAGGTCTTTTTAATGTTGCCATCTATGGGATAGGCa                                 >  2:734445/1‑91 (MQ=255)
                                                            ttgtttgAATAATATAAACAAAGACCTCTAAAGTTATCAAGATGATACCTTCAGAGGTCTTTTTAATGTTGCCATCTATGGGATAGGCAAt                               <  1:916474/91‑1 (MQ=255)
                                                              gtttgAATAATATAAACAAAGACCTCTAAAGTTATCAAGATGATACCTTCAGAGGTCTTTTTAATGTTGCCATCTATGGGATAGGCAATCg                             >  1:2374599/1‑91 (MQ=255)
                                                              gtttgAATAATATAAACAAAGACCTCTAAAGTTATCAAGATGATACCTTCAGAGGTCTTTTTAATGTTGCCATCTATGGGATAGGCAATCg                             >  2:1227119/1‑91 (MQ=255)
                                                               tttgAATAATATAAACAAAGACCTCTAAAGTTATCAAGATGATACCTTCAGAGGTCTTTTTAATGTTGCCATCTATGGGATAGGCAATCGt                            <  2:112684/91‑1 (MQ=255)
                                                               tttgAATAATATAAACAAAGACCTCTAAAGTTATCAAGATGATACCTTCAGAGGTCTTTTTAATGTTGCCATCTATGGGATAGGCAATCGt                            >  2:2005971/1‑91 (MQ=255)
                                                               tttgAATAATATAAACAAAGACCTCTAAAGTTATCAAGATGATACCTTCAGAGGTCTTTTTAATGTTGCCATCTATGGGATAGGCAATCGt                            >  2:1778335/1‑91 (MQ=255)
                                                                ttgAATAATATAAACAAAGACCTCTAAAGTTATCAAGATGATACCTTCAGAGGTCTTTTTAATGTTGCCATCTATGGGATAGGCAATCGtt                           >  1:1213376/1‑91 (MQ=255)
                                                                ttgAATAATATAAACAAAGACCTCTAAAGTTATCAAGATGATACCTTCAGAGGTCTTTTTAATGTTGCCATCTATGGGATAGGCAATCGtt                           <  2:798063/91‑1 (MQ=255)
                                                                ttgAATAATATAAACAAAGACCTCTAAAGTTATCAAGATGATACCTTCAGAGGACTTTTTAATGTTGCCATCTATGGGATAGGCAATCGtt                           <  1:3259736/91‑1 (MQ=255)
                                                                ttgAATAATATAAACAAAGACCTCTAAAGTGATCAAGATGATACCTTCAGAGGTCTTTTTAATGTTGCCATCTATGGGATAGGCAATCGtt                           <  2:2175437/91‑1 (MQ=255)
                                                                     taataTAAACAAAGACCTCTAAAGTTATCAAGATGATACCTTCAGAGGTCTTTTTAATGTTGCCATCTATGGGATAGGCAATCGTTTCAtt                      <  1:2816926/91‑1 (MQ=255)
                                                                     taataTAAACAAAGACCTCTAAAGTTATCAAGATGACACCTTCAGAGGTCTTTTTAATGTTGCCATCTATGGGATAGGCAATCGTTTCAtt                      <  1:2085695/91‑1 (MQ=255)
                                                                        tataAACAAAGACCTCTAAAGTTATCAAGATGATACCTTCAGAGGTCTTTTTAATGTTGCCATCTATGGGATAGGCAATCGTTTCATTCGt                   >  1:1087140/1‑91 (MQ=255)
                                                                        tataAACAAAGACCTCTAAAGTTATCAAGATGATACCTTCAGAGGTCTTTTTAATGTTGCCATCTATGGGATAGGCAATCGTTTCATTCGt                   >  1:639002/1‑91 (MQ=255)
                                                                         ataAACAAAGACCTCTAAAGTTATCAAGATGATACCTTCAGAGGTCTTTTTAATGTTGCCATCTATGGGATAGGCAATCGTTTCATTCGtt                  <  2:432866/91‑1 (MQ=255)
                                                                         ataAACAAAGACCTCTAAAGTTATCAAGATGATACCTTCAGAGGTCTTTTTAATGTTGCCATCTATGGGATAGGCAATCGTTTCATTCGtt                  <  1:266536/91‑1 (MQ=255)
                                                                         ataAACAAAGACCTCTAAAGTTATCAAGATGATACCTTCAGAGGTCTTTTTAATGTTGCCATCTATGGGATAGGCAATCGTTTCATTCGtt                  >  2:2817582/1‑91 (MQ=255)
                                                                           aaaCAAAGACCTCTAAAGTTATCAAGATGATACCTTCAGAGGTCTTTTTAATGTTGCCATCTATGGGATAGGCAATCGTTTCATTCGTTta                <  2:1177834/91‑1 (MQ=255)
                                                                            aaCAAAGACCTCTAAAGTTATCAAGATGATACCTTCAGAGGTCTTTTTAATGTTGCCATCTATGGGATAGGCAATCGTTTCATTCGTTtat               >  2:1405647/1‑91 (MQ=255)
                                                                             aCAAAGACCTCTAAAGTTATCAAGATGATACCTTCAGAGGTCTTTTTAATGTTGCCATCTATGGGATAGGCAATCGTTTCATTCGTTtata              >  1:2240729/1‑91 (MQ=255)
                                                                             aCAAAGACCTCTAAAGTTATCAAGATGATACCTTCAGAGGTCTTTTTAATGTTGCCATCTATGGGATAGGCAATCGTTTCATTCGTTtata              <  1:81132/91‑1 (MQ=255)
                                                                              cAAAGACCTCTAAAGTTATCAAGATGATACCTTCAGAGGTCTTTTTAATGTTGCCATCTATGGGATAGGCAATCGTTTCATTCGTTTatat             <  2:3023634/91‑1 (MQ=255)
                                                                               aaaGACCTCTGAAGGTATCATCTTGATAACTTTAGAGGTCTTTTTAATGTTGCCATCTATGGGATAGGCAATCGTTTCATTCGTTTATAtt            >  2:914308/1‑91 (MQ=17)
                                                                                aaGACCTCTGAAGGTATCATCTTGATAACTTTAGAGGTCTTTTTAATGTTGCCATCTATGGGATAGGCAATCGTTTCATTCGTTTATATTc           >  1:2597628/1‑91 (MQ=18)
                                                                                 aGACCTCTAAAGTTATCAAGATGATACCTTCAGAGGTCTTTTTAATGTTGCCATCTATGGGATAGGCAATCGTTTCATTCGTTTATATTCa          <  1:1930585/91‑1 (MQ=255)
                                                                                  gACCTCTGAAGGTATCATCTTGATAACTTTAGAGGTCTTTTTAATGTTGCCATCTATGGGATAGGCAATCGTTTCATTCGTTTATATTCat         >  2:488524/1‑91 (MQ=21)
                                                                                   aCCTCTGAAGGTATCATCTTGATAACTTTAGAGGTCTTTTTAATGTTGCCATATATGGGATAGGCAATCGTTTCATTAGTTTATATTAata        >  1:3832413/1‑91 (MQ=18)
                                                                                   aCCTCTGAAGGTATCATCTTGATAACTTTAGAGGACTTTTTAATGTTGCCATCTATGGGATAGGCAATCGTTTCATTCGTTTATATTCata        >  2:358108/1‑91 (MQ=21)
                                                                                   aCCTCTAAAGTTATCAAGATGATACCTTCAGAGGTCTTTTTAATGTTGCCATCTATGGGATAGGCAATCGTTTCATTCGTTTATATTCata        >  2:2147749/1‑91 (MQ=255)
                                                                                    ccTCTAAAGTTATCAAGATGATACCTTCAGAGGTCTTTTTAATGTTGCCATCTATGGGATAGGCAATCGTTTCATTCGTTTATATTCatat       <  1:182047/91‑1 (MQ=255)
                                                                                    ccTCTAAAGTTATCAAGATGATACCTTCAGAGGTCTTTTTAATGTTGCCATCTATGGGATAGGCAATCGTTTCATTCGTTTATATTCatat       <  1:182556/91‑1 (MQ=255)
                                                                                    ccTCTAAAGTTATCAAGATGATACCTTCAGAGGTCTTTTTAATGTTGCCATCTATGGGATAGGCAATCGTTTCATTCGTTTATATTCatat       <  2:1824615/91‑1 (MQ=255)
                                                                                     ctctAAAGTTATCAAGATGATACCTTCAGAGGTCTTTTTAATGTTGCCATCTATGGGATAGGCAATCGTTTCATTCGTTTATATTCATATg      <  1:3425475/91‑1 (MQ=255)
                                                                                      tctAAAGTTATCAAGATGATACCTTCAGAGGTCTTTTTAATGTTGCCATCTATGGGATAGGCAATCGTTTCATTCGTTTATATTCATATGa     >  2:3462420/1‑91 (MQ=255)
                                                                                      tctAAAGTTATCAAGATGATACCTTCAGAGGTCTTTTTAATGTTGCCATCTATGGGATAGGCAATCGTTTCATTCGTTTATATTCATATGa     >  1:1910755/1‑91 (MQ=255)
                                                                                         |                                                                                          
GCTGATCAGATTAAAGAAGAAAAGAAAGACGAAACATACTTCGATCGTTCTATAAGAATTTTGTTTGAATAATATAAACAAAGACCTCTAAAGTTATCAAGATGATACCTTCAGAGGTCTTTTTAATGTTGCCATCTATGGGATAGGCAATCGTTTCATTCGTTTATATTCATATGACAA  >  USA300TCH1516_ALE/265529‑265708

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: ‑