Predicted mutation
evidence seq id position mutation freq annotation gene description
RA USA300TCH1516_ALE 2,358,670 T→C 6.7% K83R (AAA→AGA)  rpoA_1 ← DNA‑directed RNA polymerase subunit alpha

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE2,358,6700TC 6.7% 1413.2 / 52.0 475K83R (AAA→AGA) rpoA_1DNA‑directed RNA polymerase subunit alpha
Reads supporting (aligned to +/- strand):  ref base T (188/252);  new base C (16/17);  total (204/271)
Fisher's exact test for biased strand distribution p-value = 5.86e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

Only 100 of 486 total aligned reads displayed.

CTGTTGCAATTTTAAGCTCTGGGTTTAAAATTTCAACATCACTATCATGTGTAATGTCGCTTGCTGTTACTTCGCCTTCATCACGTACATCAATTTCTAAAGTTTTATCTTCTTCAGAGTAAATTTTCAATGCTAATTGTTTAATGTTCATAATAATTGTAGAAACATCTTCAACTACATTGTCTACTGCTGAGAATTCATGTAAAACTCCCTCAATTTCAATATACTTAACGGCTGCACCTGGTAATGAAGATAGTAGGATACGACGTAAGGAGTTTCC  >  USA300TCH1516_ALE/2358530‑2358809
                                                                                                                                            |                                                                                                                                           
  gTTGCAATTTTAAGCTCTGGGTTTAAAATTTCAACATCACTATCATGTGTAATGTCGCTTGCTGTTACTTCGCCTTCATCACGTACATCAATTTCTAAAGTTTTATCTTCTTCAGAGTAAATTTTCAATGCTAATTGTTTa                                                                                                                                           <  2:1922869/141‑1 (MQ=255)
   ttGCAATTGTAGGGTCTGGTGTTAGAATTTCAACGGCACTATCATGTGTAATGTCGCTTGCTGTGACTTCGTCTTCATCACGTACATCAATGTCTAAAGTGTTATCTTCTTCAGAGTAAATTTTCAATGCTAATTGTTTaa                                                                                                                                          <  2:3463684/141‑1 (MQ=255)
     gCAATTTTAAGCTCTGGGTTTAAAATTTCAACATCACTATCATGTGTAATGTCGCTTGCTGTTACTTCGCCTTCATCACGTACATCAATTTCTCAAGTTTTATCTTCTTCAGAATAAATTTTAATTGCTACTTTTCTAATg                                                                                                                                        >  2:2442241/1‑141 (MQ=255)
        aTTTTATGCGTTGTGTTTAACATTTGAACATATCTATCGTGTGTAATGCAGCTTCTTGGTATTTGTCCTTCATCACGTACATCAATTTCTCAATTTTTATCTTTTTCAGAGTAAATTTTCAATGCTAATTGTTTAATGTTc                                                                                                                                     <  2:725169/141‑1 (MQ=255)
        aTTTTAAGCTCTGGGTTTAAAATTTCAACATCACTATCATGTGTAATGTCGCTTGCTGTTACTTCGCCTTCATCACGTACATCAATTTCTAAAGTTTTATCTTCTTCAGAGTAAATTTTCAATGCTAATTGTTTAATGTTc                                                                                                                                     <  1:687163/141‑1 (MQ=255)
         ttttAAGCTCTGGGTTTAAAATTTCAACATCACTATCATGTGTAATGTCGCTTGCTGTTACTTCGCCTTCATCACGTACATCAATTTCTAAATTTTTATCTTCTTCAGAGTAAATTTTCAATGCTAATTGTTTAAtcctca                                                                                                                                    >  2:2070427/1‑136 (MQ=255)
            tAAGCTCTGGGTTTAAAATTTCAACATCACTATCATGTGTAATGTCGCTTGCTGTTACTTCGCCTTCATCACGTACATCAATTTCTAAAGTTTTATCTTCTTCAGAGTAAATTTTCAATGCTAATTGTTTAATGTTCataa                                                                                                                                 >  2:1830608/1‑141 (MQ=255)
             aaGCTCTGGGTTTAAAATTTCAACATCACTATCATGTGTAATGTCGCTTGCTGTTACTTCGCCTTCATCACGTACATCAATTTCTAAAGTTTTATCTTCTTCAGAGTAAATTTTCAATGCTAATTGTTTAATGTTCataat                                                                                                                                <  1:4243038/141‑1 (MQ=255)
              aGCTCTGGGTTTAAAATTTCAACATCACTATCATGTGTAATGTCGCTTGCTGTTACTTCGCCTTCATCACGTACATCAATTTCTAAAGTTTTATCTTCTTCAGAGTAAATTTTCAATGCTAATTGTTTAATGTTCataata                                                                                                                               >  2:3381241/1‑141 (MQ=255)
                 tctGGGTTTAAAATTTCAACATCACTATCATGTGTAATGTCGCTTGCTGTTACTTCGCCTTCATCACGTACATCAATTTCTAAAGTTTTATCTTCTTCAGAGTAAATTTTCAATGCTAATTGTTTAATGTTCATAATAAtt                                                                                                                            >  1:2270329/1‑141 (MQ=255)
                  ctGGGTTTAAAATTTCAACATCACTATCATGTGTAATGTCGCTTGCTGTTACTTCGCCTTCATCACGTACATCAATTTCTAAAGTTTTATCTTCTTCAGAGTAAATTTTCAATGCTAATTGTTTAATGTTCATAATAAttt                                                                                                                           >  1:3515832/1‑140 (MQ=255)
                      gTTTAAAATTTCAACATCACTATCATGTGTAATGTCGCTTGCTGTTACTTCGCCTTCATCACGTACATCAATTTCTAAAGTTTTATCTTCTTCAGAGTAAATTTTCAATGCTAATTGTTTAATGTTCATAATAATTGTAGa                                                                                                                       <  1:2897361/141‑1 (MQ=255)
                       tttAAAATTTCAACATCACTATCATGTGTAATGTCGCTTGCTGTTACTTCGCCTTCATCACGTACATCAATTTCTAAAGTTTTATCTTCTTCAGAGTAAATTTTCAATGCTAATTGTTTAATGTTCCTAATAATTGTAGaa                                                                                                                      >  1:3119174/1‑141 (MQ=255)
                        ttAAAATTTCAACATCACTATCATGTGTAATGTCGCTTGCTGTTACCTCGCCTTCATCACGTACATCAATTTCTAAAGTTTTATCTTCTTCAGAGTAAATTTTCAATGCTAATTGTTTAATGTTCATAATAATTGTAGaaa                                                                                                                     <  1:1142805/141‑1 (MQ=255)
                         aaaagTTTCACATCACTATCATGTGTAATGGCGCTTGCTTGTACTTCGCCTTCATCACGTACATCAATTTCTAAAGTTTTATGTTCTTCAGCGTAAATTTTCAATGCTAATTGTTTAATGTTCATAATAATTGTAGAAACa                                                                                                                   <  1:1280730/140‑1 (MQ=255)
                          aaaaTTTCAACATCACTATCATGTGTAATGTCGCTTGCTGTTACTTCGCCTTCATCACGTACATCAATTTCTAAAGTTTTATCTTCTTCAGAGTAAATTTTCAATGCTAATTGTTTAATGTTCATAATAATTGTAGAAACa                                                                                                                   <  1:2598009/141‑1 (MQ=255)
                             agttCAATATCACTATCATGTGTAATGTCGCTTGCTGTTACTTCGCCTTCATCACGTACATCAATTTCTAAAGTTTTATCTTCTTCAGAGTAAATTTTCAATGCTAATTGTTTAATGTTCATAATAATTGTAGAAACATCt                                                                                                                <  2:3893138/139‑1 (MQ=255)
                             aTTTCAACATCACTATCATGTGTAATGTCGCTTGCTGTTACTTCGCCTTCATCACGTACATCAATTTCTAAAGTTTTATCTTCTTCAGAGTAAATTTTCAATGCTAATTGTTTAATGTTCATAATAATTGTAGAAACATCt                                                                                                                <  2:2152919/141‑1 (MQ=255)
                              tttCAACATCACTATCATGTGTAATGTCGCTTGCTGTTACTTCGCCTTCATCACGTACATCAATTTCTAAAGTTTTATCTTCTTCAGAGTAAATTTTCAATGCTAATTGTTTAATGTTCATAATAATTGTAGAAACATCtt                                                                                                               >  1:1847417/1‑141 (MQ=255)
                               ttCAAAATCACGATCATGTGTAATGTCGCTTGCTGTTACTTCGCCTTCATCACGTACATCAATTTCTAAAGTTTTATCTTCTTCAGAGTAAATTTTCAATGCTAATTGTTTAATGTTCATAATAATTGTAGAAACATCTTc                                                                                                              <  2:818574/141‑1 (MQ=255)
                                tCAACATCACTATCATGTGTAATGTCGCTTGCTGTTACTTCGACTTCATCACGTACATCAATTTCTAAAGTTTTATCTTCTTCAGAGTAAATTTTCAATGCTAATTGTTTAATGTACATAATAAGTGTAGAAACATCTTCa                                                                                                             >  2:3541860/1‑141 (MQ=255)
                                  aaCATCACTATCATGTGTAATGTCGCTTGCTGTTACTTCGCCTTCATCACGTACATCAATTTCTAAAGTTTTATCTTCTTCAGAGTAAATTTTCAATGCTAATTGTTTAATGTTCATAATAATTGTAGAAACATCTTCAAc                                                                                                           <  1:469096/141‑1 (MQ=255)
                                    cATCACTATCATGTGTAATGTCGCTTGCTGTTACTTCGCCTTCATCACGTAAGTAAATTTCAAAAGTTTTATCTTCTTCAGAGTAAATTTTCAATGCTAATTGTTTAATGTTCATAATAATTGTAGAAACATCTTCAACTa                                                                                                         >  1:635328/1‑141 (MQ=255)
                                     aTCGCTATGATGTGTAATGTCGGTTGCTGATACTTCGCCTTCATCACGTACATCAATTTCTAAAGTTTTATCTTCTTCAGAGTAAATTTTCAATGCTAATTGTTTAATGTTCATAATAATTGTAGAAACATCTTCAACTAc                                                                                                        <  2:3704380/141‑1 (MQ=255)
                                       cACTATCATGTGTAATGTCGCTTGCTGTTACTTCGCCTTCATCACGTACATCAATTTCTAAAGTTTTATCTTCTTCAGAGTAAATTTTCAATGCTAATTGTTTAATGTTCATAATAATTGTAGAAACATCTTCAACTACAt                                                                                                      <  2:2593791/141‑1 (MQ=255)
                                       cACTATCATGTGTAATGTCGCTTGCTGTTACTTCGCCTTCATCACGTACATCAATTTCTAAAGTTTTATCTTCTTCAGAGTAAATTTTCAATGCTAATTGTTTAATGTTCATAATAATTGTAGAAACATCTTCAACTACAt                                                                                                      <  1:3066240/141‑1 (MQ=255)
                                           aTCATGTGTAATGTCGCTTGCTGTTACTTCGCCTTCATCACGTACATCAATTTCTAAAGTTTTATCTTCTTCAGAGTAAATTTTCAATGCTAATTGTTTAATGTTCATAATAATTGTAGAAACATCTTCAACTACATTGTc                                                                                                  <  1:2471301/141‑1 (MQ=255)
                                           aTCATGTGTAATATCGCTTGCTGTTACTTCGCCTTCATCACGTCCGTTAATTTCGAAGCCCTTACCTTTGGCGGAGTAAATTTTCAATGCTAATTGTTTAATGTTCATAATAATTGTAGAAACATCTTCAACTACATTGTc                                                                                                  >  2:4294997/1‑141 (MQ=255)
                                              aTGTGTAATGTCGCTTGCTGTTACTTCGCCTTCATCACGTACATCAATTTCTAAAGTTTTATCTTCTTCAGAGTAAATTTTCAATGCTAATTGTTTAATGTTCATAATAATTGTAGAAACATCTTCAACTACATTGTCTAc                                                                                               <  1:2221412/141‑1 (MQ=255)
                                                 tgtaggttCGCGTGCTGTTACTTCGCCGTCATCACGTATATCAATTTCTAAAGTTTTATCTTCTTCAGAGTAAATTTTCAATGCTAATTGTTTAATGTTCATAATAATTGTAGAAACATCTTCAACTACATTGTCTActgc                                                                                            <  2:4007024/134‑1 (MQ=255)
                                                 tgtAATGTCGCTTGCTGTTACTTCGCCTTCATCACGTACATCAATTTCTAAAGTTTTATCTTCTTCAGAGTAAATTTTCAATGCTAATTGTTTAATGTTCATAATAATTGTAGAAACATCTTCAACTACATTGTCTActgc                                                                                            <  1:2192388/141‑1 (MQ=255)
                                                     agttCGCTTGCTGTTACTGCGCCTTCATCACGTACATCAATTTCTAAAGTTTTATCTTCTTCAGAGTAAATTTTCAATGCTAATTGTTTAAGGTTCATAATAATTGTAGAAACATCTTCAACTACATTGTCTACTGCTgag                                                                                        <  1:1428936/138‑1 (MQ=255)
                                                     aTGTCGCTTGCTGTTACTTCGCCTTCATCACGTACATCAATTTCTAAAGTTTTATCTTCTTCAGAGTAAATTTTCAATGCTAATTGTTTAATGTTCATAATAATTGTAGAAACATCTTCAACTACATTTTCTActgcttca                                                                                        >  2:2410988/1‑138 (MQ=255)
                                                       gTCGCTTGCTGTTACTTCGCCTTCATCACGTACATCAATTTCTAAAGTTTTATCTTCTTCAGAGTAAATTTTCAATGCTAATTGTTTAATGTTCATAATAATTGTAGAAACATCTTCAACTACATTGTCTACTGCTGAGaa                                                                                      <  1:2822394/141‑1 (MQ=255)
                                                        tCGCTTGCTGTTACTTCGCCTTCATCACGTACATCAATTTCTAAAGTTTTATCTTCTTCAGAGTAAATTTTCAATGCTAATTGTTTAATGTTCATAATAATTGTAGAAACATCTTCAACTACATTGTCTACTGCTGAGAAt                                                                                     >  1:3758264/1‑141 (MQ=255)
                                                         cGCTTGCTGTTACTTCGCCTTCATCACGTACATCAATTTCTAAAGTTTTATCTTCTTCAGAGTAAATTTTCAATGCTAATTGTTTAATGTTCATAATAATTGTAGAAACATCTTAAACTACATTGTCTACTGCTGCGAAtt                                                                                    >  2:251368/1‑141 (MQ=255)
                                                              gCTGTTACTTCGCCTTCATCACGTACATCAATTTCTAAAGTTTTATCTTCTTCAGAGTAAATTTTCAATGCTAATTGTTTAATGTTCATAATAATTGTAGAAACATCTTCAACTACATTGTCTACTGCTGAGAATTCATGt                                                                               >  2:3776393/1‑141 (MQ=255)
                                                                tGTTACTTCGCCTTCATCACGTACATCAATTTCTAAAGTTTTATCTTCTTCAGAGTAAATTTTCCATGCTAATTGTCTAATGTTCATAATAATTGTAGAAACATCTTCAACTACATTGTCTACTGCTGAGAATTCATTTaa                                                                             >  2:2715914/1‑141 (MQ=255)
                                                                tGTTACTTCGCCTTCATCACGTACATCAATTTCTAAAGTTTTATCTTCTTCAGAGTAAATTTTCAATGCTAATTGTTTAATGTTCATAATAATTGTAGAAACATCTTCAACTACATTGTCTACTGCTGAGAATTCATGTaa                                                                             >  1:1104383/1‑141 (MQ=255)
                                                                      ttCGCCTTCATCACGTACATCAATTTCTAAAGTTTTATCTTCTTCAGAGTAAATTTTCAATGCTAATTGTTTAATGTTCATAATAATTGTAGAAACATCTTCAACTACATTGTCTACTGCTGAGAATTCATGTAAAACTcc                                                                       <  1:3554112/141‑1 (MQ=255)
                                                                       tCGCCTTCATCACGTACATCAATTTCTAAAGTTTTATCTTCTTCAGAGTAAAGTTTCAATGCTAATTGTTTAATGTTCATAATAATTGTAGAAACATCTTCACCTACATTGTCTACTGCTGAGAATTCATGTAAAACTccc                                                                      >  2:2930083/1‑141 (MQ=255)
                                                                        cgtcTTCATCACGTACATCAATTTCTAAAGTTTTATCTTCTTCAGAGTAAATTTTCAATGCTAATTGTTTAATGTTCATAATAATTGTAGAAACATCTTCAACTACATTGTCTACTGCTGAGAATTCATGTAAAACTCCCt                                                                     <  2:4371481/138‑1 (MQ=255)
                                                                        cctcTTCATCACGTACATCAATTTCTTAAGTTTTATCTTCTTCAGAGTAAATTTTCAATGCTAATTGTTTAATGTTCATAATAATTGTAGCAACATCTTCAACTACATTGTTTACTGCTGAGAATTCATGTAAAACTCCCt                                                                     <  2:3632367/138‑1 (MQ=255)
                                                                          ccTTCATCACGTATATCAATTTCTAAAGTTTTATCTTCTTCAGAGTAAATTTTCAATGCTAATTGTTTAATGTTCATAATAATTGTAGAAACATCTTCAACTACATTGTCTACTGCTGAGAATTCATGTAAAACTCCCTCa                                                                   <  2:1541496/141‑1 (MQ=255)
                                                                          ccTTCATCACGTACATCAATTTCTAAAGTTTTATCTTCTTCAGAGTAAATTTTCACTGCTAATCGTTTACTGTTATTAATCATTGTAGAAACATCTTTACCTACATTGTCTACTGCTCATAATTCATCTAAAACttcaccc                                                                   >  2:1804588/1‑135 (MQ=255)
                                                                             tcatcaCGTACATCAATTTCTAAAGTTTTATCTTCTTCAGCGTAAATTTTCACTGCTAATTGTTTCTTGTTCATACTCATTGTAGAAACATCTTCAACTAAATAGTCTACTGCTGAGAATTCATGTAAAACTCCCACAAtt                                                                >  1:1603331/1‑141 (MQ=255)
                                                                             tcatcaCGTACATCAATTTCTAAAGTTTTATCTTCTTCAGAGTAAATTTTCAATGCTAATTGTTTAATGTTCATAATAATTGTAGAAACATCTTCAACTACATTGTCTACTCCTGAGAATTCATGTACAACTCCCTAAAtt                                                                >  2:139379/1‑141 (MQ=255)
                                                                              catcaCGTACATCAATTTCTAAAGTTTTATCTTCTTCAGAGTAAATTTTCAATGCTAATTGTTTAATGTTCATAATAATTGTAGAAACATCTTCAACTACATTGTCTACTGCTGAGAATTCATGTAAAACTCCCTCAAttt                                                               >  2:3060984/1‑141 (MQ=255)
                                                                              catcaCGTACATCAATTTCTAAAGTTTTATCTTCTTAAGAGTAAATTTTCAATGCTAATTGTTTAATGTTCATAATAATTGTAGAAACATCTTCAACTACATTGTCTACTGCTGAGAATTCATGTAAAACTCCCTCAAttt                                                               <  2:2806745/141‑1 (MQ=255)
                                                                              catcaCGTACATCAATTTATACAGTTTTATCTTCTTCAGAGTAAATTTTCAATGCTAATTGTTTAATGTTCATAATAATTGTAGAAACATCTTCAACTACATTGTCTACTGCTGAGAATTCATGTAAAACTCCCTCAAttt                                                               <  2:3291403/141‑1 (MQ=255)
                                                                               atcaCGTACATCAATTTCTAAAGTTTTATCTTCTTCAGAGTAAATTTTCAATGCTAATTGTTTAATGTTCATAATAATTGTAGAAACATCTTCAACTACATTATCTACTGCTAAGAATTCATGTAAAACTCCCTCAATTTc                                                              >  2:50069/1‑141 (MQ=255)
                                                                                   cGTACATCAATTTCTAAAGTTTTATCTTCTTCAGAGTAAATTTTCAATGCTAATTGTTTAATGTTCATAATAATTGTAGAAACATCTTCAACTACATTGTCTACTGCTGAGAATTCATGTAAAACTCCCTCAATTTCAata                                                          >  1:3677885/1‑141 (MQ=255)
                                                                                     tACATCAATTTCTAAAGTTTTATCTTCTTCAGAGTAAATTTTCAATGCTAATTGTTTAATGTTCATAATAATTGTAGAAACATCTTCAACTACATTGTCTACTGCTGAGAATTCATGTAAAACTCCCTCAATTTCAAtata                                                        <  1:1464418/141‑1 (MQ=255)
                                                                                        aTCAATTACTAAAGTTTTATCTTCTTCAGAGTAAATTTTCAATGCTAATTGTTTAATGTTCATAATAATTGTAGAAACATCTTCAACTACATTGTCTACTGCTGAGAATTCATGTAAAAAACCATCAATTTCAATATACtt                                                     >  2:2244660/1‑141 (MQ=255)
                                                                                         tCAATTTCTAAAGTTTTATCTTCTTCAGAGTAAATTTTCAATGCTAATTGTTTAATGTTCATAATAATTGTAGAAACATGTTCAACTACATTGTCTACTGCTGAGAATTCATGTAAAAATCTCTCAATTTAAATATACTTa                                                    >  1:134507/1‑141 (MQ=255)
                                                                                          cAATTTCTAAAGTTTTATCTTCTTCAGAGTAAATTTTCAATGCTAATTGTTTAATGTTCATAATAATTGTAGAAACATCTTCAACTACATTGTCTACTGCTGAGAATTCATGTAAAACTCCCTCAATTTCAATATACTTaa                                                   <  1:1809935/141‑1 (MQ=255)
                                                                                           aaTTTCTAATGTTTTATCTTCTTCAGAGTAAATTTTCAATGCTGATTGTTTAATGTTCATAATAATTGTAGAAACAGCTTCAACTACATTTTCTACTGCTGAGAATTCATGTAAAACTCCCTCAATTTCAATATACTTAAc                                                  <  1:2745734/141‑1 (MQ=255)
                                                                                             tttCTAAAGTTTTATCTTCTTCAGAGTAAATTTTCAATGCTAATTGTTTAATGTTCATAATAATTGTAGAAACATCTTCAACTACATTGTCTACTGCTGAGAATTCATGTAAAACTCCCTCAATTTCAATATACTTAACgg                                                <  1:1531781/141‑1 (MQ=255)
                                                                                             tttCTAAAGTTTTATCTTCTTCAGAGTAAATTTTCAATGCTAATTGTTTAATGTTCATAATAATTGTAGAAAACCGGGCGCCGACAGGTTCTACTGCTGAGATTTCATGTAAAACTCCCTCAATTTCAATATACTTAACga                                                >  1:3227485/1‑140 (MQ=255)
                                                                                              ttCTCAAGTTTTATCTTCTTCAGAGTAAATTTTCAATGCTAATTGTTTAATGTTCATAATAATTGTAGAAACATCTTCAACTACATTGTCTACTGCTGAGAATTCATGTAAAACTCCCTCAATTTCAATATACTTAACGGc                                               <  2:1142719/141‑1 (MQ=255)
                                                                                              ttCTAAAGTTTTATCTTCTTCAGAGTAAATTTTCAATGCTAATTGTTTAATGTTCATAATAATTGTAGAAACATCTTCAACTACATTGTCTACTGCTGAGAATTCATGTAAAACTCCCTCAATTTCAATATACTTAACGGc                                               <  2:1236959/141‑1 (MQ=255)
                                                                                              ttCTAAAGTTTTATCTTCTTCAGAGTAAATTTTCAATGCTAATTGTTTAATGTTCATAATAATTGTAGAAACATCTTCAACTACATTGTCTACTGCTGAGAATTCATGTAAAACTCCCTCAATTTCAATATACTTAACGGc                                               >  1:567636/1‑141 (MQ=255)
                                                                                               tCTACAGATTTATCTTCTTCAGAGTAAATTTTCAATGCTAATTGTTTAATGTTCATAATAATTGTAGAAACATCTTCAACTACATTGTCTACTGCTGAGAATTCATGTAAAACTCCCTTAATTTCAATATACTTAACGGCt                                              <  1:3845780/141‑1 (MQ=255)
                                                                                               tCTAAAGTTTTATCTTCTTCAGAGTAAATTTTCAATGCTAATTGTTTAATGTTCATAATAATTGTAGAAACATCTTCAACTACATTGTCTACTGCTGAGAATTCATGTAAAACTCCCTCAATTTCAATATACTTAACGGCt                                              <  1:3618881/141‑1 (MQ=255)
                                                                                               tCTAAAGTTTTATCTTCTTCAGAGTAAATTTTCAATGCTAATTGTTTAATGTTCATAATAATTGTAGAAACATCTTCAACTACATTGTCTACTGCTGAGAATTCATGTAAAACTCCCTCAATTTCAATATACTTAACGGCt                                              <  2:3728896/141‑1 (MQ=255)
                                                                                               tCTAAAGTTTTATCTTCTTCAGAGTAAATTTTCAATGCTAATTGTTTAATGTTCATAATAATTGTAGAAACATCTTCAACTACATTGTCTACTGCTGAGAATTCATGTAAAACTCCCTCAATTTCAATATACTTAACGGCt                                              <  2:4150237/141‑1 (MQ=255)
                                                                                               tCTAAAGTTTTATCTTCTTCAGAGTAAAGTTTCAATGCTAATTGTTTAATGTTCATAATAATTGTAGAAACATCTTCAACTACATTGTCTACTGCTGAGAATTCATGTAAAACTCCCTCAATTTCAATATACTTAACGGCt                                              <  2:3215011/141‑1 (MQ=255)
                                                                                               ccTAAAGTTTTATCTTCTTCAGAGTAAATTTTCAATGCTAATTGTTTAATGTTCATAATAATTGTAGAAACATCTTCTACTACATTGTCTACTGCTGAGAATTCATGTAAAACTCCCTCAATTTCAATATACTTAACGGCt                                              <  1:242548/140‑1 (MQ=255)
                                                                                                 tAAAGTTTTATCTTCTTCAGAGTAAATTTTCAATGCTAATTGTTTAATGTTCATAATAATTGTAGAAACATCTTCAACTACATTGTCTACTGCTGAGAATTCATGTAAAACTCCCTCAATTTCAATATACTTAACGGCTGc                                            <  1:167244/141‑1 (MQ=255)
                                                                                                 tAAAGTTTTATCTTCTTCAGAGTAAATTTTCAATGCTAATTGTTTAATGTTCATAATAATTGTAGAAACATCTTCAACTACATTGTCTACTGCTGAGAATTCATGTAAAACTCCCTCAATTTCAATATACTTAACGGCTGc                                            >  1:3403713/1‑141 (MQ=255)
                                                                                                  aaaGTTTTATCTTCTTCAGAGTAAATTTTCAATGCTAATTGTTTAATGTTCATAATAATTGTAGAAACATCTTCAACTACATTGTCTACTGCTGAGAGTTCATGTAAAACTCCCTCAATTTCAATATACTTAACGGCTGcc                                           >  1:768035/1‑140 (MQ=255)
                                                                                                    aGTTTTATCTTCTTCAGAGTAAATTTTCAATGCTAATTGTTTAATGTTCATAATAATTGTAGAAACATCTTCAACTACATTGTCTACTGCTGATAATTCATGTAAAACTCCCTCAATTTCAATATACTTAACGGCTGCAcc                                         <  2:2270329/141‑1 (MQ=255)
                                                                                                     gTTTTATCTTCTTCAGAGTAAATTTTCAATGCTAATTGTTTAATGTTCATAATAATTGTAGAAACATCTTCAACTACATTGTCTACTGCTGAGAATTCATGTAAAACTCCCTCAATTTCAATATACTTAACGGCTGCACCt                                        <  2:1443119/141‑1 (MQ=255)
                                                                                                     gTTTTATCTTCTTCAGAGTAAATTTTCAATGCTAATTGTTTAATGTTCATAATAATTGTAGAAACATCTTCAACTACATTGTCTACTGATGAGAATTCAAGTAACACTCCCTCACTTTAAATATACTTAACGGCTGCACCt                                        >  2:53911/1‑141 (MQ=255)
                                                                                                     gTTTTATCTTCTTCAGAGTAAAGTTTTAATGCTAATTGTTTAATGTTCATAATAATTGTAGAAACATCTTCAACTACATTGTCTACTGCTGAGAATTCATGTAAAACTCCCTCAATTTCAATATACTTAACGGCTGCACCt                                        <  2:1274591/141‑1 (MQ=255)
                                                                                                      ttttttCTTCTTCAGAGTAAATTTTCAATGCTAATTGTTTAATGTTCATAATAATTGTAGAAACATCTTCAACTACATTGTCTACTGCTGAGAATTCATGTAAAACTCCCTCAATTTCAATATACTTAACGGCTGCACCTg                                       <  2:2841722/141‑1 (MQ=255)
                                                                                                       tttATCTTCTTCAGAGTAAATTTTCAATGCTAATTGTTTAATGTTCATAATAATTGTAGAAACATCTTCAACTACATTGTCTACTGCTGAGAATTCATGTAAAACTCCCTCAATTTCAATATACTTAACGGCTGCACCTgg                                      <  1:2145450/141‑1 (MQ=255)
                                                                                                         tATCTTCTTCAGAGTAAATTTTCAATGCTAATTGTTTAATGTTCATAATAATTGTAGACACATCTTCAACTACATTGTCTACTGTTGCGTGCCCATTGAAAAATCACTCTATTACAATATACTTAACGCCTGCACCTGGTa                                    >  1:1008455/1‑141 (MQ=255)
                                                                                                         tATCTTCTTCAGAGTAAATTTTCAATGCTAATTGTTTAATGTTCATAATAATTGTAGAAACATCTTCAACTACATTGTCTACTGCTGAGAATTCATGTAAAACTCCCTCAATTTCAATATACTTAACGGCTGCACCTGGTa                                    >  2:2288311/1‑141 (MQ=255)
                                                                                                            cttcttCAGAGTAAATTTTCCATGCTAATTGTTTAATGTTCATAATAATTGTAGAAACATCTTTAACTACATTGTCTACTGCTGAGAATACATGTAAAAGTCCCTCAATGTCAAGATCATTAACGGCTGCATCTGGTaggt                                 >  2:10640/1‑138 (MQ=255)
                                                                                                            cttcttCAGAGTAAATTTTCAATGCTAATTGTTTAATGTTCATAATAATTGTAGAAACATCTTCTACTACATTGTCTACTGCTGAGAATTCATGTAAAACTCCAACAATTTCAATATACTTAACGGCCGCACATGATAAta                                 >  2:62619/1‑140 (MQ=255)
                                                                                                            cttcttCAGAGTAAATTTTCAATGCTAATTGTTTAATGTTCATAATAATTGTAGAAACATCTTCAACTACATTGTCTACTGCTGAGAATTCATGTAAAACTCCCTCAATTTCAATATACTTAACGGCTGCACCTGGTAATg                                 <  1:1985173/141‑1 (MQ=255)
                                                                                                              tcttcAGAGTAAATTTTCAATGCTAATTGTTTAATGTTCATAATAATTGTAGAAACATCTTCAACTACATTGTCTACTGCTGAGAATTCATGTAAAACTCCCTCAATTTCAATATACTTAACGGCTGCACCTGGTAATGaa                               >  1:3362096/1‑141 (MQ=255)
                                                                                                              tcttcAGAGTAAATTTTCAAAGCTAATTGTCTAATGTTCATAATAATTGTAGAAACATCTTCAACTACATTGTCTACTGCTGAGAATTCATGTAAAACTCCCTCAATTTCAATATACTTAACGGCTGCACCTGGTAATGaa                               <  2:1499821/141‑1 (MQ=255)
                                                                                                                ttcAGAGTAAATTTTCAATGCTAATTGTTTAATGTTCATAATAATTGTAGAAACATCTTCAACTACATTGTCTACTGCTGAGAATTCATGTAAAACTCCCTCAATTTCAATATACTTAACGGCTGCACCTGGTAATGAAGa                             <  1:4016638/141‑1 (MQ=255)
                                                                                                                   agagTAAATTTTCAATGCTAATTGTTTAATGTTCATAATAATTGTAGAAACATCTTCAACTACATTGTCTACTGCTGAGAATTCATGTAAAACTCCCTCAATTTCAATATACTTAACGGCTGCACCTGGTAATGAGGAtgg                          >  1:1050130/1‑139 (MQ=255)
                                                                                                                    gagTAAATTTTCAATGCTAATTGTTTAATGTTCATAATAATTGTAGAAACATCTTCAACTACATTGTCTACTGTTGAGAATTCATGTAAAACTCCCTCAATTTCAATATACTTAACGGCTGCACATGGTATTGAAGAtatt                         >  2:2754716/1‑139 (MQ=255)
                                                                                                                     agTAAAGTTTCAATGCTAAGTGTTTAATGTTCATAATTCAAGTATAGATATCTTCAACTACATTGTCTACTGCTGAGAATTCATGTAAAACTCCCTCAATTTCAATATACTTAACGGCTGCACCTGGTAATGAAGAtagta                        <  2:3119174/141‑1 (MQ=255)
                                                                                                                      gTAAATTTTCAATGCTAATTGTTTAATGTTCATAATAATTGTAGAAACATCTTCAACTACATTGTCTACTGCTGAGAATTCATGTAAAACTCCCTCAATTTCAATATACTTAACGGCTGCACCTGGTAATGAAGAtagtag                       >  2:4191173/1‑141 (MQ=255)
                                                                                                                        aaaTTTTCAATGCTAATTGTTTAATGTTCATAATAATTGTAGAAACATCTTCAACTACATTGTCTACTGCTGAGAATTCATGTACACCACCATCAAGTCCAATATCATTAATGGCTGCACCTGGTCATGAAGAtagtagca                     >  2:1990969/1‑139 (MQ=255)
                                                                                                                        aaaTTTTCAATGCTAATTGTTTAATGTTCATAATAATTGTAGAAACATCTTAAACTACATTGTCTACTGCTGAGAATTCATGTAAAACTCCCTCAATTTCAATATACTTAACGGCTGCACCTGGTAATGAAGATAGTAGGa                     >  1:2946513/1‑141 (MQ=255)
                                                                                                                         acttttCAATGCTAATTGTTTAATGTTTCGCAGAATTCGAGTCTTATTATCAACGACAATGTCTACTGCTGAGAATTCATGTAAAACTCCCTCAATTTCAATATACTTAACGGCTGCACCTGGTAATGAAGATAGTAGGAt                    <  1:4355183/139‑1 (MQ=255)
                                                                                                                         aaTTTTCAATGCTAATTGTTTAATGTTCATAATAATTGAAGAAACATCTTCAACTACATTGTCTACTGCTGAGAATTCATGTAAAACTCCCTCAATTTCAATATACTTAACGGCTGCACCTGGTAATGAAGATAGTAGGAt                    <  1:880921/141‑1 (MQ=255)
                                                                                                                             ttCAATGCTAATTGTTTAATGTTCATAATAATTGTAGAAACATCTTCAACTACATTGTCTACTGCTGAGAATTCATGTAAAACTCCCTCAATTTCAATATACTTAACGGCTGCACCTGGTAATGAAGATAGTAGGATacga                >  1:4199777/1‑141 (MQ=255)
                                                                                                                             ttCAATGCTAATTGTTTAATGTTCATAATAATTGTAGAAACATCTTCAACTACATTGTCTACTGCTGAGAATTCATGTAAAACTCCCTCAATTTCAATATACTTAACGGCTGCACCTGGTAATGAAGATAGTAGGATacga                >  2:166258/1‑141 (MQ=255)
                                                                                                                              tCAATGCTAATTGTTTAATGTTCATAATAATTGTAGAAACATCTTCAACTACATTGTCTACTGCTGAGAATTCATGTAAAACTCCCTCAATTTCAATATACTTAACGGCTGCACCTGGTAATGAAGATCGTAGGGTtcgac               >  1:2045688/1‑141 (MQ=255)
                                                                                                                              tCAATGCTAATTGTTTAATGTTCATAATAATTGTAGAAACATCTTCAACTACATTGTCTACTGCTGAGAATTCATGTAAAACTCCCTCAATTTCAATATACTTAACGGCTGCACCTGGTAATGAAGATAGTAGGATacgac               >  2:1181199/1‑141 (MQ=255)
                                                                                                                                       aTTGTTTAATGTTCATAATAATTGTAGAAACATCTTCAACTACATTGTCTACTGCTGAGAATTCATGTAAAACTCCCTCAATTTCAATATACTTAACGGCTGCACCTGGTAATGAAGATAGTAGGATACGACGTAAGGAGt      <  1:4116459/141‑1 (MQ=255)
                                                                                                                                       aTTGTTTAATGTTCATAATAATTGTAGAAACATCTTCAACTACATTGTCTACTGCTGAGAATTCATGTAAAACTCCCTCAATTTCAATATACTTAACGGCTGCACCTGGTAATGAAGATAGTAGGATACGACGTAAGGAGt      <  1:1889481/141‑1 (MQ=255)
                                                                                                                                       aTTGTTTAATGTTCATAATAATTGTAGAAACATCTCCAACTTCATTGTCTACTGCTGAGAATTCATGTAAAACTCCCTCAATTTCAATATACTTAACGGCTGCACCTGGTAATGAAGATAGTAGGATACGACGTAAGGAGt      <  1:1211132/141‑1 (MQ=255)
                                                                                                                                            |                                                                                                                                           
CTGTTGCAATTTTAAGCTCTGGGTTTAAAATTTCAACATCACTATCATGTGTAATGTCGCTTGCTGTTACTTCGCCTTCATCACGTACATCAATTTCTAAAGTTTTATCTTCTTCAGAGTAAATTTTCAATGCTAATTGTTTAATGTTCATAATAATTGTAGAAACATCTTCAACTACATTGTCTACTGCTGAGAATTCATGTAAAACTCCCTCAATTTCAATATACTTAACGGCTGCACCTGGTAATGAAGATAGTAGGATACGACGTAAGGAGTTTCC  >  USA300TCH1516_ALE/2358530‑2358809

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap:     Deleted base: