Predicted mutation
evidence seq id position mutation freq annotation gene description
RA USA300TCH1516_ALE 2,833,387 G→C 11.9% intergenic (‑723/+367) lipA_2 ← / ← hisI Lipase 1/Phosphoribosyl‑AMP cyclohydrolase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE2,833,3870GC11.9% 950.0 / 99.4 301intergenic (‑723/+367)lipA_2/hisILipase 1/Phosphoribosyl‑AMP cyclohydrolase
Reads supporting (aligned to +/- strand):  ref base G (115/150);  new base C (12/24);  total (127/174)
Fisher's exact test for biased strand distribution p-value = 2.84e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

Only 100 of 308 total aligned reads displayed.

TTTCGGGATGCATATCTTAGTTCTAATGGAGATTGTCTTTTAAATAGGCTATGACATTTCTATTTCAGGCTAGATATATTTGTATTTATAGTATAAATACAAAGAATGTAAAGACAACTATGATATTAATAGGTAGTAACGACAAACATAACTCTTTAGCTTTTTCGCCATTTTTTCCCTT  >  USA300TCH1516_ALE/2833297‑2833477
                                                                                          |                                                                                          
tttCGGGATGCATATCTTAGTTCTAATGGAGATTGTCTTTTAAATAGGCTATGACATTTCTATTTCAGGCTAGATATATTTGTATTTATAg                                                                                            <  1:1852447/91‑1 (MQ=255)
 ttCGGGATGCATATCTTAGTTCTAATGGAGATTGTCTTTTAAATAGGCTATGACATTTCTATTTCAGGCTAGATATATTTGTATTTATAGt                                                                                           <  2:3251875/91‑1 (MQ=255)
  tCGGGATGCATATCTTAGTTCTAATGGAGATTGTCTTTTAAATAGGCTATGACATTTCTATTTCGGGCTAGATATATTTGTATTTATAGta                                                                                          <  2:2241693/91‑1 (MQ=255)
  tCGGGATGCATATCTTAGTTCTAATGGAGATTGTCTTTTAAATAGGCTATGACATTTCTATTTCAGGCTAGATATATTTGTATTTATAGta                                                                                          >  2:3014609/1‑91 (MQ=255)
  tCGGGATGCATATCTTAGTTCTAATGGAGATTGTCTTTTAAATAGGCTATGACATTTCTATTTCAGGCTAGATATATTTGTATTTATAGta                                                                                          <  1:3818083/91‑1 (MQ=255)
     ggATGCATATCTTAGTTCTAATGGAGATTGTCTTTTGAATAGGCTATGACATTTCTATTTCAGGCTAGATATATTTGTATTTATAGTATaa                                                                                       <  2:3572247/91‑1 (MQ=255)
       aTGCATATCTTAGTTCTAATGGAGATTGTCTTTTAAATAGGCTATGACATTTCTATTTCAGGCTAGATATATTTGTATTTATAGTATAAAt                                                                                     >  2:2742006/1‑91 (MQ=255)
       aTGCATATCTTAGTTCTAATGGAGATTGTCTTTTAAATAGGCTATGACATTTCTATTTCAGGCTAGATATATTTGTATTTATAGTATAAAt                                                                                     >  1:2919257/1‑91 (MQ=255)
       aTGCATATCTTAGTTCTAATGGAGATTGTCTTTTAAATAGGCTATGACATTTCTATTTCAGGCTAGATATATTTGTATTTATAGTATAAAt                                                                                     <  1:1688177/91‑1 (MQ=255)
       aTGCATATCTTAGTTCTAATGGAGATTGTCTTTTAAATAGGCTATGACATTTCTATTTCAGGCTAGATATATTTGTATTTATACTATAAAt                                                                                     <  1:268257/91‑1 (MQ=255)
        tGCATATCTTAGTTCTAATGGAGATTGTCTTTTAAATAGGCTATGACATTTCTATTTCAGGCTAGATATATTTGTATTTATAGTATAAATa                                                                                    >  2:1269292/1‑91 (MQ=255)
        tGCATATCTTAGTGCTAATGGAGATTGTCTTTTAAATAGGCTAGGACATTTCTATTTCAGGCTAGATATATTTGTATTTATACTATAAATa                                                                                    <  1:3958304/91‑1 (MQ=255)
          cATATCTTCGTTCTACTGGAGATTGTCTTTTAAATAGGCTATGACATTTCTATTTCAGGCTAGATATATTTGTATTTATACTATAAATACa                                                                                  <  1:910330/91‑1 (MQ=255)
           gtatCTTAGTTCTATTGGAGATTGTCTGGTGAGTAGGCTATGGCAGTTCTACTTCAGGCTAGATATATTTGTCTTTAGACTATAAAGACaa                                                                                 <  2:419821/90‑1 (MQ=255)
           atatCTTAGTTCTAATGGAGATTGTCTTTTAAATAGGCTATGACATTTCTATTTCAGGCTAGATATATTTGTATTTATAGTATAAATACaa                                                                                 <  2:3184016/91‑1 (MQ=255)
           atatCTTAGTTCTAATGGAGATTGTCTTTTAAATAGGCTATGACATTTCTATTTCAGGCTAGATATATTTGTATTTATACTATAAATACaa                                                                                 <  1:2601914/91‑1 (MQ=255)
           atatCTTAGTGCTAATGGAGATTGTCTTTTAAATAGGCTATGACATTTCTATTTCAGGCTAGATATATTTGTATTTATACTATAAATACaa                                                                                 <  2:1697688/91‑1 (MQ=255)
               cTTAGTTCTAATGGAGATTGTCTTTTAAATAGGCTATGACATTTCTATTTCAGGCTAGATATATTTGTATTTATAGTATAAATACAAAGaa                                                                             <  1:2236784/91‑1 (MQ=255)
                 tAGTTCTAATGGAGATTGTCTTTTAAATAGGCTATGACATTTCTATTTCAGGCTAGATATATTTGTATTTATAGTATAAATACAAAGAATg                                                                           <  2:1336877/91‑1 (MQ=255)
                  aGTTCTAATGGAGATTGTCTTTTAAATAGGCTATGACATTTCTATTTCAGGCTAGATATATTTGTATTTATAGTATAAATACAAAGAATGt                                                                          >  1:766194/1‑91 (MQ=255)
                  aGTTCTAATGGAGATTGTCTTTTAAATAGGCTATGACATTGCTATTTCAGGCTAGATATATTTGTAATTATAGTATAAATACAAAGAATGt                                                                          >  2:3663822/1‑91 (MQ=255)
                   gTTCTAATGGAGATTGTCTTTTAAATAGGCTATGACATTTCTATTTCAGGCTAGATATATTTGTATTTATAGTATAAATACAAAGAATGTa                                                                         >  2:66169/1‑91 (MQ=255)
                    ttCTAATGGAGATTGTCTTTTAAATAGGCTATGACATTTCTATTTCAGGCTAGATATATTTGTATTTATAGTATAAATACAAAGAATGTaa                                                                        <  1:1953249/91‑1 (MQ=255)
                    ttCTAATGGAGATTGTCTTTTAAATAGGCTATGACATTTCTATTTCAGGCTAGATATATTTGTATTTATAGTATAAATACAAAGAATGTaa                                                                        >  2:2746559/1‑91 (MQ=255)
                    ttCTAATGGAGATTGTCTTTTAAATAGGCTATGACATTTCTATTTCAGGCTAGATATATTTGTATTTATAGTATAAATACAAAGAATGTaa                                                                        >  1:1383531/1‑91 (MQ=255)
                     tCTAATGGAGATTGTCTTTTAAATAGGCTATGACATTTCTATTTCAGGCTAGATATATTTGTATTTATAGTATAAATACAAAGAATGTaaa                                                                       <  2:372158/91‑1 (MQ=255)
                     tCTAATGGAGATTGTCTTTTAAATAGGCTATGACATTTCTATTTCAGGCTAGATATATTTGTATTTATAGTATAAATACAAAGAATGTaaa                                                                       <  1:353176/91‑1 (MQ=255)
                       tAATGGAGATTGTCTTTTAAATAGGCTATGACATTTCTATTTCAGGCTAGATATATTTGTATTTATAGTATAAATACAAAGAATGTAAAGa                                                                     <  1:2422085/91‑1 (MQ=255)
                        aaTGGAGATTGTCTTTTAAATAGGCTATGACATTTCTATTTCAGGCTAGATATATTTGTATTTATAGTATAAATACAAAGAATGTAAAGAc                                                                    >  2:3793956/1‑91 (MQ=255)
                        aaTGGAGATTGTCTTTTAAATAGGCTATGACATTTCTATTTCAGGCTAGATATATTTGTATTTATAGTATAAATACAAAGAATGTAAAGAc                                                                    <  2:3902746/91‑1 (MQ=255)
                        aaTGGAGATTGTCTTTTAAATAGGCTATGACATTTCTATTTCAGGCTAGATATATTTGTATTTATAGTATAAATACAAAGAATGTAAAGAc                                                                    >  2:2827183/1‑91 (MQ=255)
                          tGGAGATTGTCTTTTAAATAGGCTATGACATTGCTATTTCAGGCTAGATATATTTGTATTTATAGTATAAATACAGAGAATGTAAAGACaa                                                                  <  1:3372662/91‑1 (MQ=255)
                           ggAGATTGTCTTTTAAATAGGCTATGACATTTCTATTTCAGGCTAGATATATTTGTATTTATAGTATAAATACAAAGAATGTAAAGACAAc                                                                 <  1:2321511/91‑1 (MQ=255)
                             agaTTGTCTTTTAAATGGGCGATGACATTTCTATTTCAGGCTAGATATATTTGTATTTATAGTATAAATACAAAGAATGTAACGACAACTa                                                               <  2:486562/91‑1 (MQ=255)
                              gaTTGTCTTTTAAATAGGCTATGACATTTCTATTTCAGGCTAGATATATTTGTATTTATAGTATAAATACAAAGGATGTAAAGACAACTAt                                                              <  2:3108156/91‑1 (MQ=255)
                              gaTTGTCTTTTAAATAGGCTATGACATTTCTATTTCAGGCTAGATATATTTGTATTTATAGTATAAATACAAAGAATGTAAAGACAACTAt                                                              >  2:1766447/1‑91 (MQ=255)
                              gaTTGTCTTTTAAATAGGCTATGACATTTCTATTTCAGGCTAGATATATTTGTATTTATAGTATAAATACAAAGAATGTAAAGACAACTAt                                                              <  1:1301255/91‑1 (MQ=255)
                               aTTGTCTTTTAAATAGGCTATGACATTTCTATTTCAGGCTAGATATATTTGTATTTATAGTATAAATACAAAGAATGTAAAGACAACTATg                                                             >  1:515576/1‑91 (MQ=255)
                                ttGTCTTTTAAATAGGCTATGACATTTCTATTTCAGGCTAGATATATTTGTATTTATAGTATAAATACAAAGAATGTAAAGACAACTATGa                                                            >  1:3714873/1‑91 (MQ=255)
                                ttGTCTTTTAAATAGGCTATGACATTTCTATTTCAGGCTAGATATATTTGTATTTATAGTATAAATACAAAGAATGTAAAGACAACTATGa                                                            <  1:3866309/91‑1 (MQ=255)
                                 tGTCTTTTAAATAGGCTATGACATTTCTATTTCAGGCTAGATATATTTGTATTTATAGTATAAATACAAAGAATGTAAAGACAACTATGat                                                           <  2:2997682/91‑1 (MQ=255)
                                 tGTCTTTTAAATAGGCTATGACATTTCTATTTCAGGCTAGATATATTTGTATTTATAGTATAAATACAAAGAATGTAAAGACAACTATGat                                                           >  2:3860581/1‑91 (MQ=255)
                                  gTCTTTTAAATAGGCTATGACATTTCTATTTCAGGCTAGATATATTTGTATTTATAGTATAAATACAAAGAATGTAAAGACAACTATGata                                                          >  1:2047984/1‑91 (MQ=255)
                                    cTTTTAAATAGGCTATGACATTTCTCTTTCAGGCTAGATATATTTGTCTTTATAGTATAAATACAAAGAATCTCAAGACCACCATGATAtt                                                        >  2:814458/1‑91 (MQ=255)
                                    cTTTTAAATAGGCTATGACATTTCTATTTCAGGCTAGATATATTTGTATTTATAGTATAAATACAAAGAATGTAAAGACAACTATGATAtt                                                        >  2:3477201/1‑91 (MQ=255)
                                    cTTTTAAATAGGCTATGACATTTCTATTTCAGGCTAGATATATTTGTATTTATAGTATAAATACAAAGAATGTAAAGACAACTATGATAtt                                                        <  2:2954139/91‑1 (MQ=255)
                                      tttAAATAGGCTATGACATTTCTATTTCAGGCTAGATATATTTGTATTTATAGTATAAATACAAAGAATGTAAAGACAACTATGATATTaa                                                      <  1:3464890/91‑1 (MQ=255)
                                      tttAAATAGGCTATGACATTTCTATTTCAGGCTAGATATATTTGTATTTATAGTATAAATACAAAGAATGTAAAGACAACTATGATATTaa                                                      >  2:1513102/1‑91 (MQ=255)
                                       ttAAATAGGCTATGACATTTCTATTTCAGGCTAGATATATTTGTATTTATAGTATAAATACAAAGAATGTAAAGACAACTATGATATTAAt                                                     <  2:1856202/91‑1 (MQ=255)
                                        tAAATAGGCTATGACATATCTATTTCAGGCTAAATATATTTGTATTTATAGTATAAATACAAAGAATGTAAAGACAACTATGATATTAATa                                                    <  2:794251/91‑1 (MQ=255)
                                          aaTAGGCTATGACATTTCTATTTCAGGCTAGATATATTTGTATTTATAGTATAAATACAAAGAATGTAAAGACAACTATGATACTAATAgg                                                  >  2:3510811/1‑91 (MQ=255)
                                            tAGGCTATGACATTTCTATTTCAGGCTAGATATATTTGTATTTATAGTATAAATACAAAGAATGTAAAGACAACTATGATATTAATAGgta                                                <  2:1748246/91‑1 (MQ=255)
                                             aGGCTATGACATTTCTATTTCAGGCTAGATATATTTGTATTTATAGTATAAATACAAAGAATGTAAAGACAACTATGATATTAATAGgtag                                               >  2:2394431/1‑91 (MQ=255)
                                             aGGCTATGACATTTCTATTTCAGGCTAGATATATTTGTATTTATAGTATAAATACAAAGAATGTAAAGACAACTATGATATTAATAGgtag                                               <  2:3841306/91‑1 (MQ=255)
                                             aGGCTATGACATTTCTATTTCAGGCTAGATATATTTGTATTTATAGTATAAATACAAAGAATGTAAAGACAACTATGATATTAATAGgtag                                               <  1:2701865/91‑1 (MQ=255)
                                             aGGCTATGACATTTCTATTTCAGGCTAGATATATTTGTATTTACAGTATAAATACAAAGAATGTAAAGACAACTATGATATTAATAGgtag                                               <  1:3946188/91‑1 (MQ=255)
                                              ggCTATGACATTTCTATTTCAGGCTAGATATATTTGTATTTATAGTATAAATACAAAGAATGTAAAGACAACTATGATATTAATAGgtagt                                              >  2:3361026/1‑91 (MQ=255)
                                              ggCTATGACATTTCTATTTCAGGCTAGATATATTTGTATTTATAGTATAAATACAAAGAATGTAAAGACAACTATGATATTAATAGgtagt                                              <  1:2110153/91‑1 (MQ=255)
                                              ggCTATGACATTTCTATTTCAGGCTAGATATATTTGTATTTATAGTATAAATACAAAGAATGTAAAGACAACTATGATATTAATAGgtagt                                              >  2:2049046/1‑91 (MQ=255)
                                              ggCTATCACATTTCTATTTCAGGCTAGATATATTTGTATTTATAGTATAAATACAAAGAATGTAAAGACAACTATGATATTAATAGgaagt                                              >  1:3070196/1‑91 (MQ=255)
                                               gCTCTGACATTTCTATTTCAGGCTAGATATATTTGTATTTATAGTATAAATACAAAGAATGTAAAGACAACTATGATATTAATAGgtagta                                             <  1:3110649/91‑1 (MQ=255)
                                               gCTATGACATTTCTATTTCAGGCTAGATATATTTGTATTTATAGTATAAATACAAAGAATGTAAAGACAACTATGATATTAATAGgtagta                                             >  1:2784313/1‑91 (MQ=255)
                                                 tATGACATTTCTATTTCAGGCTAGATATATTTGTATTTATAGTATAAATACAAAGAATGTAAAGACAACTATGATATTAATAGGTAGTAAc                                           >  1:3418002/1‑91 (MQ=255)
                                                  aTGACATTTCTATTTCAGGCTAGATATATTTGTATTTATAGTATAAATACAAAGAATGTAAAGACAACTATGATATTAATAGGTAGTAACg                                          <  2:583680/91‑1 (MQ=255)
                                                    gACATTTCTATTTCAGGCTAGATATATTTGTATTTATAGTATAAATACAAAGAATGTAAAGACAACTATGATATTAATAGGTAGTAACGAc                                        >  2:2908217/1‑91 (MQ=255)
                                                     aCATTTCTATTTCAGGCTAGATATATTTGTATTTATAGTATCAATACAAAGAATGTAAAGACAACTATGATATTAACAGGTAGTAACGACa                                       >  2:251790/1‑91 (MQ=255)
                                                      cATTTCTATTTCAGGCTAGATATATTTGTATTTATAGTATAAATACAAAGAATGTAAAGACAACTATGATATTAATAGGTAGTAACGACaa                                      >  2:2334000/1‑91 (MQ=255)
                                                         ttCTATTTCAGGCTAGATATATTTGTATTTATAGTATAAATACAAAGAATGTAAAGACAACTATGATATTAATAGGTAGTAACGACAAACa                                   <  1:813071/91‑1 (MQ=255)
                                                          tCTATATCAGGCTAGATATATTTGTATTTATAGTATAAATACAAAGAATGTAAAGACAACTATGATATTAATAGGTAGTAACGACAAACAt                                  <  2:2461279/91‑1 (MQ=255)
                                                               ttCAGGCTAGATATATTTGTATTTATAGTATAAATACAAAGAATGTAAAGACAACTATGATATTAATAGGTAGTAACGACAAACATAActc                             <  1:448849/91‑1 (MQ=255)
                                                               ttCAGGCTAGATATATTTGTATTTATAGTATAAATACAAAGAATGTAAAGACAACTATGATATTAATAGGTAGTAACGACAAACATAActc                             <  1:2286246/91‑1 (MQ=255)
                                                                tCAGGCTAGATATATTTGTATTTATAGTATAAATACAAAGAATGTAAAGACAACTATGATATTAATAGGTAGTAACGACAAACATAActct                            >  2:1927096/1‑91 (MQ=255)
                                                                 cAGGCTAGATATATTTGTATTTATAGTATAAATACACAGAATGTAAAGACAACTATGATATTAATAGGTAGTAACGACAAACATAACTCtt                           >  2:2173738/1‑91 (MQ=255)
                                                                  aGGCTAGATATATTTGTATTTATAGTATAAATACAAAGAATGTAAAGACAACTATGATATTAATAGGTAGTAACGACAAACATAACTCttt                          >  2:706152/1‑91 (MQ=255)
                                                                  aGGCTAGATATATTTGTATTTATAGTATAAATACAAAGAATGTAAAGACAACTATGATATTAATAGGTAGTAACGACAAACATAACTCttt                          >  1:1670863/1‑91 (MQ=255)
                                                                         atatatTTGTATTTATAGTATAAATACAAAGAATGTAAAGACAACTATGATATTAATAGGTAGTAACGACAAACATAACTCTTTAGCtttt                   >  2:2590754/1‑91 (MQ=255)
                                                                           atatTTGTATTTATAGTATAAATACAAAGAATGTAAAGACAACTATGATATTAATAGGTAGTAACGACAAACATAACTCTTTAGCTTTTTc                 <  2:1867711/91‑1 (MQ=255)
                                                                            tatTTGTATTTATAGTATAAATACAAATAATGTAAAGACAACTATGATATTAATAGGTAGTAACGACAAACATAACTCTTTAGCTTTTTCg                <  2:1068426/91‑1 (MQ=255)
                                                                            tatTTGTATTTATAGTATAAATACAAAGAATGTAAAGACAACTATGATATTAATAGGTAGTAACGACAAACATAACTCTTTAGCTTTTTCg                <  1:3659455/91‑1 (MQ=255)
                                                                            tatTTGTATTTATAGTATAAATACAAAGAATGTAAAGACAACTATGATATTAATAGGTAGTAACGACAAACATAACTCTTTAGCTTTTTCg                <  1:2364015/91‑1 (MQ=255)
                                                                            tatTTGTATTTATAGTATAAATACAAAGAATGTAAAGACAACTATGATATTAATAGGTAGTAACGACAAACATAACTCTTTAGCTTTTTCg                <  1:266831/91‑1 (MQ=255)
                                                                               ttGTATTTATAGTATAAATACAAAGAATGTAAAGACAACTATGATATTAATAGGTAGTAACGACAAACATAACTCTTTAGCTTTTTCGCCa             <  1:301882/91‑1 (MQ=255)
                                                                               ttGTATTTATAGTATAAATACAAAGAATGTAAAGACAACTATGATATTAATAGGTAGTAACGACAAACATAACTCTTTAGCTTTTTCGCCa             <  1:3574813/91‑1 (MQ=255)
                                                                               ttGTATTTATACTATAAATACAAATAATGTAAAGACAACTATGATATTAATAGGTAGTAACGACAAACATAACTCTTTAGCTTTTTCGCCa             >  1:3291371/1‑91 (MQ=255)
                                                                                  tATTTATAGTATAGATACAAAGAATGTAAAGACAACTATGATATTAATAGGTAGTAACGACAAACATAACTCTTTAGCTTTTTCGCCAttt          <  2:813568/91‑1 (MQ=255)
                                                                                  tATTTATAGTATAAATACAAAGAATGTAAAGACAACTATGATATTAATAGGTAGTAACGACAAACATAACTCTTTAGCTTTTTCGCCAttt          >  2:2083155/1‑91 (MQ=255)
                                                                                  tATTTATACTATAAATACAAAGAATGTAAAGACAACTATGATATTAATAGGTAGTAACGACAAACATAACTCTTTAGCTTTTTCGCCAttt          >  1:1222583/1‑91 (MQ=255)
                                                                                   aTTTATAGTATAAATACAAAGAATGTAAAGACAACTATGATATTAATAGGTAGTAACGACAAACATAACTCTTTAGCTTTTTCGCCAtttt         >  1:1913316/1‑91 (MQ=255)
                                                                                   aTTTATAGTATAAATACAAAGAATGTAAAGACAACTATGATATTAATAGGTAGTAACGACAAACATAACTCTTTAGCTTTTTCGCCAtttt         <  1:1535831/91‑1 (MQ=255)
                                                                                   aTTTATACTATAAATACAAAGAATGTAAAGACACCTAAGATATTAAAAGGTAGTAACGACAGACATAACTCTTTAGCTTTTTCGCCAtttt         >  1:3162920/1‑91 (MQ=255)
                                                                                   aTTTATACTATAAATACAAAGAATGTAAAGACAACTATGATATTAATAGGTAGTAACGACAAACATAACTCTTTAGCTTTTTCGCCAtttt         >  1:1630466/1‑91 (MQ=255)
                                                                                   aTTTATACTATAAATACAAAGAATGTAAAGACAACTATGATATTAATAGGTAGTAACGACAAACATAACTCTTTAGCTTTTTCGCCAtttt         >  1:146323/1‑91 (MQ=255)
                                                                                    tttATAGTATAAATACAAAGAATGTAAAGACAACTATGATATTAATAGGTAGTAACGACAAACATAACTCTTTAGCTTTTTCGCCAttttt        <  1:2191740/91‑1 (MQ=255)
                                                                                    tttATAGTATAAATACAAAGAATGTAAAGACAACTATGATATTAATAGGTAGTAACGACAAACATAACTCTTTAGCTTTTTCGCCAttttt        <  1:1017563/91‑1 (MQ=255)
                                                                                       ataGTATAAATACAAAGAATGTAAAGACAACTATGATATTAATAGGTAGTAACGACAAACATAACTCTTTAGCTTTTTCGCCATTTTTTcc     >  2:2617797/1‑91 (MQ=255)
                                                                                        taGTATAAATACAAAGAATGTAAAGACAACTATGATATTAATAGGTAGTAACGACAAACATAACTCTTTAGCTTTTTCGCCATTTTTTccc    >  2:1291162/1‑91 (MQ=255)
                                                                                        taGTATAAATACAAAGAATGTAAAGACAACTATGATATTAATAGGTAGTAACGACAAACATAACTCTTTAGCTTTTTCGCCATTTTTTccc    <  2:2356283/91‑1 (MQ=255)
                                                                                         aGTATAAATACAAAGAATGTAAAGACAACTATGATATTAATAGGTAGTAACGACAAACATAACTCTTTAGCTTTTTCGCCATTTTTTCCCt   <  1:1880760/91‑1 (MQ=255)
                                                                                          gTATAAATACAAAGAATGTAAAGACAACTATGATATTAATAGGTAGTAACGACAAACATAACTCTTTAGCTTTTTCGCCATTTTTTCCCtt  >  1:948539/1‑91 (MQ=255)
                                                                                          gTATAAATACAAAGAATGTAAAGACAACTATGATATTAATAGGTAGTAACGACAAACATAACTCTTTAGCTTTTTCGCCATTTTTTCCCtt  <  2:1590994/91‑1 (MQ=255)
                                                                                          |                                                                                          
TTTCGGGATGCATATCTTAGTTCTAATGGAGATTGTCTTTTAAATAGGCTATGACATTTCTATTTCAGGCTAGATATATTTGTATTTATAGTATAAATACAAAGAATGTAAAGACAACTATGATATTAATAGGTAGTAACGACAAACATAACTCTTTAGCTTTTTCGCCATTTTTTCCCTT  >  USA300TCH1516_ALE/2833297‑2833477

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap:     Deleted base: