Predicted mutation
evidence seq id position mutation freq annotation gene description
RA USA300TCH1516_ALE 2,413,260 A→T 5.2% S494T (TCT→ACT)  nphR ← Transcriptional activator NphR

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE2,413,2600AT 5.2% 493.0 / 11.8 156S494T (TCT→ACT) nphRTranscriptional activator NphR
Reads supporting (aligned to +/- strand):  ref base A (71/76);  new base T (4/4);  total (75/81)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.78e-01

Only 100 of 158 total aligned reads displayed.

CCTCGTAATTGATTAAGTATATTTATGATAAAAATGAATATTGATAATCTAGTTAAATTTATTTCTTTGCTCGATTCACTTATAATTGACATGTGCATAATAAGTCCTCGAAATTTTGTATAATTTGTCAAAAGTTCAGAAACCTTATTAATATCAGACATTGTGATTTTTTCTTTTAAGTCATTATTCTCATTAATCAAATCTACATCACATATAATTTTAGAACGTGCAATAGACACCTGTTCTATTTGTCTTAGCGGTAAGATAAAATAGTCTATTA  >  USA300TCH1516_ALE/2413121‑2413400
                                                                                                                                           |                                                                                                                                            
ccTCGTAATTGATTAAGTATATTTATGATAAAAATGAATATTGATAATCTAGTTAAATTTATTTCTTTGCTCGATTCACTTATAATTGACATGTGCATAATAAGTCCTCGAAATTTTGTATAATTTGTCAAAAGTTCAGaa                                                                                                                                             >  2:215191/1‑141 (MQ=255)
   cGTAATTGATTAAGTATATTTATGATAAAAATGAATATTGATAATCTAGTTAAATTTATTTCTTTGCTCGATTCACTTATAATTGACATGTGCATAATAAGTCCTCGAAATTTTGTATAATTTGTCAAAAGTTCAGAAAcc                                                                                                                                          <  4:231850/141‑1 (MQ=255)
     tAATTGATTAAGTATATTTATGATAAAAATGAATATTGATAATCTAGTTAAATTTATTTCTTTGCTCGATTCACTTATAATTGACATGTGCATAATAAGTCCTCGAAATTTTGTATAATTTGTCAAAAGTTCAGAAACCtt                                                                                                                                        <  1:560215/141‑1 (MQ=255)
      aaTTGATTAAGTATATTTATGATAAAAATGAATATTGATAATCTAGTTAAATTTATTTCTTTGCTCGATTCACTTATAATTGACATGTGCATAATAAGTCCTCGAAATTTTGTATAATTTGTCAAAAGTTCAGAAACCtta                                                                                                                                       <  1:223276/141‑1 (MQ=255)
          gATTAAGTATATTTATGATAAAAATGAATATTGATAATCTAGTTAAATTTATTTCTTTGCTCGATTCACTTATAATTGACATGTGCATAATAAGTCCTCGAAATTTTGTATAATTTGTCAAAAGTTCAGAAACCTTATTaa                                                                                                                                   <  2:892932/141‑1 (MQ=255)
           aTTAAGTATATTTATGATAAAAATGAATATTGATAATCTAGTTAAATTTATTTCTTTGCTCGATTCACTTATAATTGACATGTGCATAATAAGTCCTCGAAATTTTGTATAATTTGTCAAAAGTTCAGAAACCTTATTAat                                                                                                                                  >  1:229116/1‑141 (MQ=255)
               aGTATATTTATGATAAAAATGAATATTGATAATCTAGTTAAATTTATTTCTTTGCTTGATTCACTTATAATTGACATGTGCATAATAAGTCTTCGAAATTTTGTATAATTTGTCAAAAGTTCAGAAACCTTATTAATATCa                                                                                                                              >  2:777759/1‑141 (MQ=255)
                gTATATTTATGATAAAAATGAATATTGATAATCTAGTTAAATTTATTTCTTTGCTCGATTCACTTATAATTGACATGTGCATAATAAGTCCTCGAAATTTTGTATAATTTGTCAAAAGTTCAGAAACCTTATTAATATCAg                                                                                                                             <  2:506773/141‑1 (MQ=255)
                   tatTTATGATAAAAATGAATATTGATAATCTAGTTAAATTTATTTCTTTGCTCGATTCACTTATAATTGACATGTGCATAATAAGTCCTCGAAATTTTGTATAATTTGTCAAAAGTTCAGAAACCTTATTAATATCAGACa                                                                                                                          <  2:109276/141‑1 (MQ=255)
                    atTTATGATAAAAATGAATATTGATAATCTAGTTAAATTTATTTCTTTGCTCGATTCACTTATAATTGACATGTGCATAATAAGTCCTCGAAATTTTGTATAATTTGTCAAAAGTTCAGAAACCTTATTAATATCAGACAt                                                                                                                         >  1:280138/1‑141 (MQ=255)
                    atTTATGATAAAAATGAATATTGATAATCTAGTTAAATTTATTTCTTTGCTCGATTCACTTATAATTGACATGTGCATAATAAGTCCTCGAAATTTTGTATAATTTGTCAAAAGTTCAGAAACCTTATTAATATCAGACAt                                                                                                                         <  4:172882/141‑1 (MQ=255)
                     tttATGATAAAAATGAATATTGATAATCTAGTTAAATTTATTTCTTTGCTCGATTCACTTATAATTGACATGTGCATAATAAGTCCTCGAAATTTTGTATAATTTGTCAAAAGTTCAGAAACCTTATTAATATCAGACAtt                                                                                                                        <  2:810670/141‑1 (MQ=255)
                         tGATAAAAATGAATATTGATAATCTAGTTAAATTTATTTCTTTGCTCGATTCACTTATAATTGACATGTGCATAATAAGTCCTCGAAATTTTGTATAATTTGTCAAAAGTTCAGAAACCTTATTAATATCAGACATTGTGa                                                                                                                    <  1:469920/141‑1 (MQ=255)
                         tGATAAAAATGAATATTGATAATCTAGTTAAATTTATTTCTTTGCTCGATTCACTTATAATTGACATGTGCATAATAAGTCCTCGAAATTTTGTATAATTTGTCAAAAGTTCAGAAACCTTATTAATATCAGACATTGTGa                                                                                                                    >  2:507193/1‑141 (MQ=255)
                           aTAAAAATGAATATTGATAATCTAGTTAAATTTATTTCTTTGCTCGATTCACTTATAATTGACATGTGCATAATAAGTCCTCGAAATTTTGTATAATTTGTCAAAAGTTCAGAAACCTTATTAATATCAGACATTGTGAtt                                                                                                                  <  1:518994/141‑1 (MQ=255)
                           aTAAAAATGAATATTGATAATCTAGTCAAATTTATTTCTTTGCTAGCTTCACTTATAATTGACATGTGCATAATAAGTCCTCGAAATTTTGTATAATTTGTCAAAAGTTCAGTAACCTTATTAAAATCAGACATTGTGAtt                                                                                                                  <  2:113631/141‑1 (MQ=255)
                            tAAAAATGAATATTGATAATCTAGTCAAATTTATTTCTTTGCTAGCTTCACTTATAATTGACATGTGCATAATAAGTCCTCGAAATTTTGTATAATTTGTCAAAAGTTCAGTAACCTTATTAAAATCAGACATTGTGAttt                                                                                                                 <  1:60961/141‑1 (MQ=255)
                             aaaaaTGAATATTGATAATCTAGTTAAATTTATTTCTTTGCTCGATTCACTTATAATTGACATGTGCATAATAAGTCCTCGAAATTTTGTATAATTTGTCAAAAGTTCAGAAACCTTATTAATATCAGACATTGTGAtttt                                                                                                                <  1:1018868/141‑1 (MQ=255)
                               aaaTGAATATTGATAATCTAGTTAAATTTATTTCTTTGCTCGATTCACTTATAATTGACATGTGCATAATAAGTCCTCGAAATTTTGTATAATTTGTCAAAAGTTCAGAAACCTTATTAATATCAGACATTGTGAtttttt                                                                                                              >  2:880609/1‑141 (MQ=255)
                                   gAATATTGATAATCTAGTTAAATTTATTTCTTTGCTCGATTCACTTATAATTGACATGTCCATAATAAGTCCTCGAAATTTTGTATAATTTGTCAAAAGTTCAGAAACCTTATTAATATCAGACATTGTGATTTTTTCttt                                                                                                          >  1:749537/1‑141 (MQ=255)
                                         tGATAATCTAGTTAAATTTATTTCTTTGCTCGATTCACTTATAATTGACATGTGCATAATAAGTCCTCGAAATTTTGTATAATTTGTCAAAAGTTCAGAAACCTTATTAATATCAGACATTGTGATTTTTTCTTTTAAGTc                                                                                                    <  1:991474/141‑1 (MQ=255)
                                         tGATAATCTAGTTAAATTTATTTCTTTGCTCGATTCACTTATAATTGACATGTGCATAATAAGTCCTCGAAATTTTGTATAATTTGTCAAAAGTTCAGAAACCTTATTAATATCAGACATTGTGATTTTTTCTTTTAAGTc                                                                                                    <  1:121048/141‑1 (MQ=255)
                                          gATAATCTAGTTAAATTTATTTCTTTGCTCGATTCACTTATAATTGACATGTGCATAATAAGTCCTCGAAATTTTGTATAATTTGTCAAAAGTTCAGAAACCTTATTAATATCAGACATTGTGATTTTTTCTTTTAAGTCa                                                                                                   <  2:715722/141‑1 (MQ=255)
                                          gATAATCTAGTTAAATTTATTTCTTTGCTCGATTCACTTATAATTGACATGTGCATAATAAGTCCTCGAAATTTTGTATAATTTGTCAAAAGTTCAGAAACCTTATTAATATCAGACATTGTGATTTTTTCTTTTAAGTCa                                                                                                   <  3:286105/141‑1 (MQ=255)
                                           aTAATCTAGTTAAATTTATTTCTTTGCTCGATTCACTTATAATTGACATGTGCATAATAAGTCCTCGAAATTTTGTATAATTTGTCAAAAGTTCAGAAACCTTATTAATATCAGACATTGTGATTTTTTCTTTTAAGTCat                                                                                                  <  2:453889/141‑1 (MQ=255)
                                                cTAGTTAAATTTATTTCTTTGCTCGATTCACTTATAATTGACATGTGCATAATAAGTCCTCGAAATTTTGTATAATTTGTCAAAAGTTCAGAAACCTTATTAATATCAGACATTGTGATTTTTTCTTTTAAGTCATTATtc                                                                                             <  3:272550/141‑1 (MQ=255)
                                                cTAGTTAAATTTATTTCTTTGCTCGATTCACTTATAATTGACATGTGCATAATAAGCCCTCGAAATTTTGTATAATTTGTCAAAAGTTCAGAAACCTTATTAATATCAGACATTGTGATTTTTTCTTTTAAGTCATTATtc                                                                                             <  4:413948/141‑1 (MQ=255)
                                                  agtcaaaTTTATTTCTTTGCTAGCTTCACTTATAATTGACATGTGCATAATAAGTCCTCGAAATTTTGTATAATTTGTCAAAAGTTCAGTAACCTTATTAAAATCAGACATTGTGATTTTTTCTTTTAAGTCATTATtctc                                                                                           >  2:97533/5‑141 (MQ=255)
                                                    ttAAATTTATTTCTTTGCTCTATTCACTTATAATTGACATGTGCATAATAATTCCTCCAAATTTTGTATAATTTGTCAAAAGTTCAGAAACCTTATTAATATCAGACATTGTCATTTTTTCTTTTAAGTCATTATTCTCAt                                                                                         <  4:45370/141‑1 (MQ=255)
                                                      aaaTTTATTTCTTTGCTCGATTCACTTATAATTNACATGTGCATAATAAGTCCTCGAAATTTTGTATAATTTGTCAAAAGTTCAGAAACCTTATTAATATCAGACATTGTGATTTTTTCTTTTAAGTCTTTATTCNCATTa                                                                                       >  1:133098/1‑141 (MQ=255)
                                                      aaaTTTATTTCTTTGCTCGATTCACTTATAATTGACATGTGCATAATAAGTCCTCGAAATTTTGTATAATTTGTCAAAAGTTCAGAAACCTTATTAATATCAGACATTGTGATTTTTTCTTTTAAGTCATTATTCTCATTa                                                                                       <  3:114646/141‑1 (MQ=255)
                                                       aaTTTATTTCTTTGCTCGATTCACTTATAATTGACATGTGCATAATAAGTCCTCGAAATTTTGTATAATTTGTCAAAAGTTCAGAAACCTTATTAATATCAGACATTGTGATTTTTTCTTTTAAGTCATTATTCTCATTaa                                                                                      <  2:910304/141‑1 (MQ=255)
                                                       aaTTTATTTCTTTGCTCGATTCACTTATAATTGACATGTGCATAATAAGTCCTCGAAATTTTGTATAATTTGTCAAAAGTTCAGAAACCTTATTAATATCAGACATTGTGATTTTTTCTTTTAAGTCATTATTCTCATTaa                                                                                      <  1:372798/141‑1 (MQ=255)
                                                        atttatttCTTTGCTCGATTCACTTATAATTGACATGTGCATAATAAGTCCTCGAAATTTTGTATAATTTGTCAAAAGTTCAGAAACCTTATTAATATCAGACATTGTGATTTTTTCTTTTAAGTCATTATTCTCATTAAt                                                                                     <  2:96332/141‑1 (MQ=255)
                                                             tttCTTTGCTCGATTCACTTATAATTGACATGTGCATAATAAGTCCTCGAAATTTTGTATAATTTGTCAAAAGTTCAGAAACCTTATTAATATCAGACATTGTGATTTTTTTTTTTTTTTCATTATTCTCATTAATCAAAt                                                                                >  2:825881/1‑141 (MQ=255)
                                                             tttCTTTGCTCGATTCACTTATAATTGACATGTGCATAATAAGTCCTCGAAATTTTGTATAATTTGTCAAAAGTTCAGAAACCTTATTAATATCAGACATTGTGATTTTTTCTTTTAAGTCATTATTCTCATTAATCAAAt                                                                                >  3:133512/1‑141 (MQ=255)
                                                             tttCTTTGCTCGATTCACTTATAATTGACATGTGCATAATAAGTCCTCGAAATTTTGTATAATTTGTCAAAAGTTCAGAAACCTTATTAATATCAGACATTGTGATTTTTTCTTTTAAGTCATTATTCTCATTAATCAAAt                                                                                >  3:320802/1‑141 (MQ=255)
                                                               tCTTTGCTCGATTCACTTATAATTGACATGTGCATAATAAGTCCTCGAAATTTTGTATAATTTGTCAAAAGTTCAGAAACCTTATTAATATCAGACATTGTGATTTTTTCTTTTAAGTCATTATTCTCATTAATCAAATCt                                                                              <  1:379933/141‑1 (MQ=255)
                                                                  ttGCTCGATTCACTTATAATTGACATGTGCATAATAAGTCCTCGAAATTTTGTATAATTTGTCAAAAGTTCAGAAACCTTATTAATATCAGACATTGTGATTTTTTTTTTTTTTTCATTATTCTCATTAATCAAATCTACa                                                                           >  2:414966/1‑141 (MQ=255)
                                                                   tGCTCGATTCACTTATAATTGACATGTGCATAATAAGTCCTCGAAATTTTGTATAATTTGTCAAAAGTTCAGAAACCTTATTAATATCAGACATTGTGATTTTTTCTTTTAAGTCATTATTCTCATTAATCAAATCTACAt                                                                          >  2:398932/1‑141 (MQ=255)
                                                                    gCTCGATTCACTTATAATTGACATGTGCATAATAAGTCCTCGAAATTTTGTATAATTTGTCAAAAGTTCAGAAACCTTATTAATATCAGACATTGTGATTTTTTCTTTTAAGTCATTATTCTCATTAATCAAATCTACATc                                                                         >  1:493855/1‑141 (MQ=255)
                                                                     cTCGATTCACTTATAATTGACATGTGCATAATAAGTCCTCGAAATTTTGTATAATTTGTCAAAAGTTCAGAAACCTTATTAATATCAGACATTGTGATTTTTTCTTTTAAGTCATTATTCTCATTAATCAAATCTACATca                                                                        >  1:530800/1‑141 (MQ=255)
                                                                       cGATTCACTTATAATTGACATGTGCATAATAAGTCCTCGAAATTTTGTATAATTTGTCAAAAGTTCAGAAACCTTATTAATATCAGACATTGTGATTTTTTCTTTTAAGTCATTATTCTCATTAATCAAATCTACATcaca                                                                      >  1:691303/1‑141 (MQ=255)
                                                                       cGATTCACTTATAATTGACATGTGCATAATAAGTCCTCGAAATTTTGTATAATTTGTCAAAAGTTCAGAAACCTTATTAATATCAGACATTGTGATTTTTTCTTTTAAGTCATTATTCTCATTAATCAAATCTACATcaca                                                                      <  2:339211/141‑1 (MQ=255)
                                                                        gATTCACTTATAATTGACATGTGCATAATAAGTCCTCGAAATTTTGTATAATTTGTCAAAAGTTCAGAAACCTTATTAATATCAGACATTGTGATTTTTTCTTTTAAGTCATTATTCTCATTAATCAAATCTACATCACat                                                                     <  1:544495/141‑1 (MQ=255)
                                                                             aCTTATAATTGACATGTGCATAATAAGTCCTCGAAATTTTGTATAATTTGTCAAAAGTTCAGAAACCTTATTAATATCAGACATTGTGATTTTTTCTTTTAAGTCATTATTCTCATTAATCAAATCTACATCACATATAAt                                                                <  2:473929/141‑1 (MQ=255)
                                                                              cTTATAATTGACATGTGCATAATAAGTCCTCGAAATTTTGTATAATTTGTCAAAAGTTCAGAAACCTTATTAATATCAGACATTGTGATTTTTTCTTTTAAGTCATTATTCTCATTAATCAAATCTACATCACATATAAtt                                                               >  1:959460/1‑141 (MQ=255)
                                                                              cTTATAATTGACATGTGCATAATAAGTCCTCGAAATTTTGTATAATTTGTCAAAAGTTCAGAAACCTTATTAATATCAGACATTGTGATTTTTTCTTTTAAGTCATTATTCTCATTAATCAAATCTACATCACATATAAtt                                                               <  4:335313/141‑1 (MQ=255)
                                                                               ttATAATTGACATGTGCATAATAAGTCCTCGAAATTTTGTATAATTTGTCAAAAGTTCAGAAACCTTATTAATATCAGACATTGTGATTTTTTCTTTTAAGTCATTATTCTCATTAATCAAATCTACATCACATATAAttt                                                              >  4:6503/1‑141 (MQ=255)
                                                                               ttATAATTGACATGTGCATAATAAGTCCTCGAAATTTTGTATAATTTGTCAAAAGTTCAGAAACCTTATTAATATCAGACATTGTGATTTTTTCTTTTAAGTCATTATTCTCATTAATCAAATCTACATCACATATAAttt                                                              <  3:407747/141‑1 (MQ=255)
                                                                               ttATAATTGACATGTGCATAATAAGTCCTCGAAATTTTGTATAATTTGTCAAAAGTTCAGAAACCTTATTAATATCAGACATTGTGATTTTTTCTTTTAAGTCATTATCCTCATTAATCAAATCTACATCTCATATAAttt                                                              >  4:408621/1‑141 (MQ=255)
                                                                                 ataATTGACATGTGCATAATAAGTCCTCGAAATTTTGTATAATTTGTCAAAAGTTCAGAAACCTTATTAATATCAGACATTGTGATTTTTTCTTTTAAGTCATTATTCTCATTAATCAAATCTACATCACATATAATTTTa                                                            <  1:808231/141‑1 (MQ=255)
                                                                                  taATTGACATGTGCATAATAAGTCCTCGAAATTTTGTATAATTTGTCAAAAGTTCAGTAACCTTATTAAAATCAGACATTGTGATTTTTTCTTTTAAGTCATTATTCTCATTAATCAAATCTACATCACATATAATTTTAg                                                           <  1:560116/141‑1 (MQ=255)
                                                                                    aTTGACATGTGCATAATAAGTCCTCGAAATTTTGTATAATTTGTCAAAAGTTCAGAAACCTTATTAATATCAGACATTGTGATTTTTTCTTTTAAGTCATTATTCTCATTAATCAAATCTACATCACATATAATTTTAGaa                                                         <  1:88325/141‑1 (MQ=255)
                                                                                    aTTGACATGTGCATAATAAGTCCTCGAAATTTTGTATAATTTGTCAAAAGTTCAGAAACCTTATTAATATCAGACATTGTGATTTTTTCTTTTAAGTCATTATTCTCATTAATCAAATCTACATCACATATAATTTTAGaa                                                         <  3:403588/141‑1 (MQ=255)
                                                                                       gACATGTGCATAATAAGTCCTCGAAATTTTGTATAATTTGTCAAAAGTTCAGAAACCTTATTAATATCAGACATTGTGATTTTTTTTTTTTTTTTTTTATTCTCATTAATCAAATCTACATCACTTATAATTTTAGAACGt                                                      >  2:1008967/1‑141 (MQ=255)
                                                                                       gACATGTGCATAATAAGTCCTCGAAATTTTGTATAATTTGTCAAAAGTTCAGAAACCTTATTAATATCAGACATTGTCATTTTTTCTTTTAAGTCATTATTCTCATTAATCAAATCTACATCACATATAATTTTAGAACGt                                                      <  3:386330/141‑1 (MQ=255)
                                                                                        aCATGTGCATAATAAGTCCTCGAAATTTTGTATAATTTGTCAAAAGTTCAGAAACCTTATTAATATCAGACATTGTGATTTTTTCTTTTAAGTCATTATTCTCATTAATCAAATCTACATCACATATAATTTTAGAACGTg                                                     <  2:341232/141‑1 (MQ=255)
                                                                                         cATGTGCATAATAAGTCCTCGAAATTTTGTATAATTTGTCAAAAGTTCAGAAACCTTATTAATATCAGACATTGTGATTTTTTCTTTTAAGTCATTATTCTCATTAATCAAATCTACATCACATATAATTTTAGAACGTGc                                                    >  2:15305/1‑141 (MQ=255)
                                                                                         cATGTGCATAATAAGTCCTCGAAATTTTGTATAATTTGTCAAAAGTTCAGAAACCTTATTAATATCAGACATTGTGATTTTTTCTTTTAAGTCATTATTCTCATTAATCAAATCTACATCACATATAATTTTAGAACGTGc                                                    >  3:56547/1‑141 (MQ=255)
                                                                                            gtgCATAATAAGTCCTCGAAATTTTGTATAATTTGTCAAAAGTTCAGAAACCTTATTAATATCAGACATTGTGATTTTTTCTTTTAAGTCATTATTCTCATTAATCAAATCTACATCACATATAATTTTAGAACGTGCAAt                                                 >  4:207907/1‑141 (MQ=255)
                                                                                              gCATAATAAGTCCTCGAAATTTTGTATAATTTGTCAAAAGTTCAGAAACCTTATTAATATCAGACATTGTGATTTTTTCTTTTAAGTCATTATTCTCATTAATCAAATCTACATCACATATAATTTTAGAACGTGCAATAg                                               >  1:179152/1‑141 (MQ=255)
                                                                                                 taataaGTCCTCGAAATTTTGTATAATTTGTCAAAAGTTCAGAAACCTTATTAATATCAGACATTGTGATTTTTTCTTTTAATTTATTATTCTCATTAATCAAATCTACATCACATATAATTTTAGAACGTACAATAGaca                                            >  4:164173/1‑141 (MQ=255)
                                                                                                 taataaGTCCTCGAAATTTTGTATAATTTGTCAAAAGTTCAGAAACCTTATTAATATCAGACATTGTGATTTTTTCTTTTAAGTCATTATTCTCATTAATCAAATCTACATCACATATAATTTTAGAACGTGCAATAGaca                                            >  2:640276/1‑141 (MQ=255)
                                                                                                  aataaGTCCTCGAAATTTTGTATAATTTGTCAAAAGTTCAGAAACCTTATTAATATCAGACATTGTGATTTTTTCTTTTAAGTCATTATTCTCATTCATCAAATCTACATCACATATAATTTTAGAACGTGCAATAGacac                                           <  4:201932/141‑1 (MQ=255)
                                                                                                    taaGTCCTCGAAATTTTGTATAATTTGTCAAAAGTTCAGAAACCTTATTAATATCAGACATTGTGATTTTTTCTTTTAAGTCATTATTCTCATTAATCAAATCTACATCACATATAATTTTAGAACGTGCAATAGACACCt                                         <  1:774871/141‑1 (MQ=255)
                                                                                                      aGTCCTCGAAATTTTGTATAATTTGTCAAAAGTTCAGAAACCTTATTAATATCAGACATTGTGATTTTTTCTTTTAAGTCATTATTCTCATTAATCAAATCTACATCACATATAATTTTAGAACGTGCAATAGACACCTGt                                       <  1:1048598/141‑1 (MQ=255)
                                                                                                       gTCCTCGAAATTTTGTATAATTTGTCAAAAGTTCAGAAACCTTATTAATATCAGACATTGTGATTTTTTCTTTTAAGTCATTATTCTCATTAATCAAATCTACATCACATATAATTTTAGAACGTGCAATAGACACCTGtt                                      >  1:507215/1‑141 (MQ=255)
                                                                                                        tCCTCGAAATTTTGTATAATTTGTCAAAAGTTCAGAAACCTTATTAATATCAGACATTGTGATTTTTTCTTTTAAGTCATTATTCTCATTAATCAAATCTACATCACATATAATTTTAGAACGTGCAATAGACACCTGTTc                                     >  1:1029842/1‑141 (MQ=255)
                                                                                                        tCCTCGAAATTTTGTATAATTTGTCAAAAGTTCAGAAACCTTATTAATATCAGACATTGTGATTTTTTCTTTTAAGTCATTATTCTCATTAATCAAATCTACATCACATATAATTTTAGAACGTGCAATAGACACCTGTTc                                     >  1:297251/1‑141 (MQ=255)
                                                                                                        tCCTCGAAATTTTGTATAATTTGTCAAAAGTTCAGAAACCTTATTAATATCAGACATTGTGATTTTTTCTTTTAAGTCATTATTCTCATTAATCAAATCTACATCACATATAATTTTAGAACGTGCAATAGACACCTGTTc                                     <  3:20927/141‑1 (MQ=255)
                                                                                                           tCGAAATTTTGTATAATTTGTCAAAAGTTCAGAAACCTTATTAATATCAGACATTGTGATTTTTTCTTTTAAGTCATTATTCTCATTAATCAAATCTACATCACATATAATTTTAGAACGTGCAATAGACACCTGTTCTAt                                  >  1:505276/1‑141 (MQ=255)
                                                                                                             gAAATTTTGTATAATTTGTCAAAAGTTCAGAAACCTTATTAATATCAGACATTGTGATTTTTTCTTTTAAGTCATTATTCTCATTAATCAAATCTACATCACATATAATTTTAGAACGTGCAATAGACACCTGTTCTAttt                                >  4:57801/1‑141 (MQ=255)
                                                                                                             gAAATTTTGTATAATCTGTCAAAAGTTCAGAAACCTTATTAATAACAGACATTGTCATTTCTTCCTTTAAGTCAATAATCTCATTAATCAAATCTACATCACATATAATTTTAGAACGTGCAATAGACACCTGTTCTAttt                                <  1:647244/141‑1 (MQ=255)
                                                                                                                 ttttGTATAATTTGTCAAAAGTTCAGAAACCTTATTAATATCAGACATTGCGATTTTTTCTTTTAAGTCATTATTCTCATTAATCAAATCTACATCACATATAATTTTAGAACGTGCAATAGACACCTGTTCTATTTGTCt                            <  2:288398/141‑1 (MQ=255)
                                                                                                                   ttGTATAATTTGTCAAAAGTTCAGAAACCTTATTAATATCAGACATTGTGATTTTTTCTTTTAAGTCATTATTCTCATTAATCAAATCTACATCACATATAATTTTAGAACGTGCAATAGACACCTGTTCTATTTGTCTTa                          >  2:349118/1‑141 (MQ=255)
                                                                                                                    tGTATAATTTGTCAAAAGTTCAGTAACCTTATTAAAATCAGACATTGTGATTTTTTCTTTTAAGTCATTATTCTCATTAATCAAATCTACATCACATATAATTTTAGAACATGCAATAGACACCTGTTCTATTTGTCTTat                         >  2:799713/1‑140 (MQ=255)
                                                                                                                    tGTATAATTTGTCAAAAGTTCAGAAACCTTATTAATATCAGACATTGTGATTTTTTTTTTTTTTTCATTATTCTCATTAATCAAATCTATATCACATATAATTTTAGAACGTGCAATAGACACCTGTTCTATTTGTCTTat                         >  2:616207/1‑140 (MQ=255)
                                                                                                                    tGTATAATTTGTCAAAAGTTCAGAAACCTTATTAATATCAGACATTGTGATTTTTTCTTTTAAGTCATTATTCTCATTAATCAAATCTACATCACATATAATTTTAGAACGTGCAATAGACACCTGTTCTATTTGTCTTAg                         <  1:812209/141‑1 (MQ=255)
                                                                                                                    tGTATAATTTGTCAAAAGTTCAGAAACCTTATTAATATCAGACATTGTGATTTTTTCTTTTAAGTCATTATTCTCATTAATCAAATCTACATCACATATAATTTTAGAACGTGCAATAGACACCTGTTCTATTTGTCTTAg                         >  1:136904/1‑141 (MQ=255)
                                                                                                                     gTATAATTTGTCAAAAGTTCAGAAACCTTATTAATATCAGACATTGTGATTTTTTCTTTTAAGTCATTATTCTCATTAATCAAATCTACATCACATATAATTTTAGAACGTGCAATAGACACCTGTTCTATTTGTCTTAGc                        <  1:5007/141‑1 (MQ=255)
                                                                                                                      tataATTTGTCAAAAGTTCAGAAACCTTATTAATATCAGACATTGTGATTTTTTCTTTTAAGTCATTATTCTCATTAATCAAATCTACATCACATATAATTTTAGAACGTGCAATAGACACCTGTTCTATTTGTCTTAGCg                       <  2:160975/141‑1 (MQ=255)
                                                                                                                      tataATTTGTCAAAAGTTCAGAAACCTTATTAATATCAGACATTGTGATTTTTTCTTTTAAGTCATTATTCTCATTAATCAAATCTACATCACATATAATTTTAGAACGTGCAATAGACACCTGTTCTATTTGTCTTAGCg                       >  3:349187/1‑141 (MQ=255)
                                                                                                                        taATTTGTCAAAAGTTCAGAAACCTTATTAATATCAGACATTGTGATTTTTTCTTTTAAGTCATTATTCTCATTAATCAAATCTACATCACATATAATTTTAGAACGTGCAATAGACACCTGTTCTATTTGTCTTAGCGGt                     <  2:556510/141‑1 (MQ=255)
                                                                                                                          aTTTGTCAAAAGTTCAGAAACCTTATTAATATCAGACATTGTGATTTTTTCTTTTAAGTCATTATTCTCATTAATCAAATCTACATCACATATAATTTTAGAACGTGCAATAGACACCTGTTCTATTTGTCTTAGCGGTaa                   <  2:1063113/141‑1 (MQ=255)
                                                                                                                             tGTCAAAAGTTCAGAAACCTTATTAATATCAGACATTGTGATTTTTTCTTTTAAGTCATTATTCTCATTAATCAAATCTACATCACATATAATTTTAGAACGTGCAATAGACACCTGTTCTATTTGTCTTAGCGGTAAGAt                <  1:608677/141‑1 (MQ=255)
                                                                                                                               tCAAAAGTTCAGAAACCTTATTAATATCAGACATTGTGATTTTTTCTTTTAAGTCATTATTCTCATTAATCAAATCTACATCACATATAATTTTAGAACGTGCAATAGACACCTGTTCTATTTGTCTTAGCGGTAAGATaa              >  3:244844/1‑141 (MQ=255)
                                                                                                                                 aaaaGTTCAGAAACCTTATTAATATCAGACATTGTGATTTTTTCTTTTAAGTCATTATTCTCATTAATCAAATCTACATCACATATAATTTTAGAACGTGCAATAGACACCTGTTCTATTTGTCTTAGCGGTAAGATaaaa            <  2:1034830/141‑1 (MQ=255)
                                                                                                                                    aGTTCAGAAACCTTATTAATATCAGACATTGTGATTTTTTCTTTTAAGTCATTATTCTCATTAATCAAATCTACATCACATATAATTTTAGAACGTGCAATAGACACCTGTTCTATTTGTCTTAGCGGTAAGATAAAATAg         <  3:454442/141‑1 (MQ=255)
                                                                                                                                    aGTTCAGAAACCTTATTAATATCAGACATTGTGATTTTTTCTTTTAAGTCATTATTCTCATTAATCAAATCTACATCACATATAATTTTAGAACGTGCAATAGACACCTGTTCTATTTGTCTTAGCGGTAAGATAAAATAg         <  1:900899/141‑1 (MQ=255)
                                                                                                                                     gTTCAGAAACCTTATTAATATCAGACATTGTGATTTTTTCTTTTAAGTCATTATTCTCATTAATCAAATCTACATCACATATAATTTTAGAACGTGCAATAGACACCTGTTCTATTTGTCTTAGCGGTAAGATAAAATAGt        <  4:107368/141‑1 (MQ=255)
                                                                                                                                     gTTCAGAAACCTTATTAATATCAGACATTGTGATTTTTTCTTTTAAGTCATTATTCTCATTAATCAAATCTACATCACATATAATTTTAGAACGTGCAATAGACACCTGTTCTATTTGTCTTAGCGGTAAGATAAAATAGt        <  3:44196/141‑1 (MQ=255)
                                                                                                                                      ttCAGAAACCTTATTAATATCAGACATTGTGATTTTTTCTTTTAAGTCATTATTCTCATTAATCAAATCTACATCACATATAATTTTAGAACGTGCAATAGACACCTGTTCTATTTGTCTTAGCGGTAAGATAAAATAGTc       >  3:214285/1‑141 (MQ=255)
                                                                                                                                        cAGAAACCTTATTAATATCAGACATTGTGATTTTTTCTTTTAAGTCATTATTCTCATTAATCAAATCTACATCACATATAATTTTAGAACGTGCAATAGACACCTGTTCTATTTGTCTTAGCGGTAAGATAAAATAGTCTa     >  1:629564/1‑141 (MQ=255)
                                                                                                                                         aGAAACCGTATTAATATCAGACATTGTGATTTTTTCTTTTAAGTCATTATTCTCATTAATCAAATCTACATCACATATAATTTTAGAACGTGCAATAGACACCTGTTCTATTTGTCTTAGCGGTAAGATAAAATAGTCTAt    >  1:859697/1‑141 (MQ=255)
                                                                                                                                          gAAACCTTATTAATATCAGACATTGTGATTTTTTCTTTTAAGTCATTATTCTCATTAATCAAATCTACATCACATATAATTTTAGAACGTGCAATAGACACCTGTTCTATTTGTCTTAGCGGTAAGATAAAATAGTCTAtt   >  4:18883/1‑141 (MQ=255)
                                                                                                                                          gAAACCTTATTAATATCAGACATTGTGATTTTTTCTTTTAAGTCATTATTCTCATTAATCAAATCTACATCACATATAATTTTAGAACGTGCAATAGACACCTGTTCTATTTGTCTTAGCGGTAAGATAAAATAGTCTAtt   >  2:706018/1‑141 (MQ=255)
                                                                                                                                          gAAACCTTATTAATATCAGACATTGTGATTTTTTCTTTTAAGTCATTATTCTCATTAATCAAATCTACATCACATATAATTTTAGAACGTGCAATAGACACCTGTTCTATTTGTCTTAGCGGTAAGATAAAATAGTCTAtt   >  2:305911/1‑141 (MQ=255)
                                                                                                                                          gAAACCTTATTAATATCAGACATTGTGATTTTTTCTTTTAAGTCATTATTCTCATTAATCAAATCTACATCACATATAATTTTAGAACGTGCAATAGACACCTGTTCTATTTGTCTTAGCGGTAAGATAAAACAGTCTAtt   >  2:747193/1‑141 (MQ=255)
                                                                                                                                           aaaCCTTATTAATATCAGACATTGTGATTTTTTCTTTTAAGTCATTATTCTCATTAATCAAATCTACATCACATATAATTTTAGAACGTGCAATAGACACCTGTTCTATTTGTCTTAGCGGTAAGATAAAATAGTCTATTa  >  3:374558/1‑141 (MQ=255)
                                                                                                                                           |                                                                                                                                            
CCTCGTAATTGATTAAGTATATTTATGATAAAAATGAATATTGATAATCTAGTTAAATTTATTTCTTTGCTCGATTCACTTATAATTGACATGTGCATAATAAGTCCTCGAAATTTTGTATAATTTGTCAAAAGTTCAGAAACCTTATTAATATCAGACATTGTGATTTTTTCTTTTAAGTCATTATTCTCATTAATCAAATCTACATCACATATAATTTTAGAACGTGCAATAGACACCTGTTCTATTTGTCTTAGCGGTAAGATAAAATAGTCTATTA  >  USA300TCH1516_ALE/2413121‑2413400

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: