Sample Resequencing Stats

Note: The mutation counts shown below represent unfiltered mutation sets.
ALE, Flask, Isolate Predicted Mutations Mean Coverage Total Reads Percent Mapped Mapped Reads Average Read Length
A5 F58 I0 R1 35 61.1 1410250 95.0% 1339737 139.9

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA USA300TCH1516_ALE 2,532,298 A→T 100% T15T (ACA→ACT)  femA_3 → Aminoacyltransferase FemA

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE2,532,2980AT100.0% 265.9 / NA 83T15T (ACA→ACT) femA_3Aminoacyltransferase FemA
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base T (31/52);  total (31/52)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

TGTGTATTTGTAATCAGTTTTTGATAAAATAAAAAAATAGCATTATTAATAAATTCAAAAATTATAGTTCAATTCAGAGAGGGATGG‑GATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACAACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGCATCTTGTAGGGGTTAAAGATGACAATGGTCAAGTGATTGCAGGATGCTTATTGACAGAAGCAC  >  USA300TCH1516_ALE/2532161‑2532434
                                                                                                                                          |                                                                                                                                        
tgtgTATTTGTAATCAGTTTTTGATAAAATAAAAAAATAGCATTATTAATAAATTCAAAAATTATAGTTCAATTCAGAGAGGGATGG‑GATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTtactac                                                                                                                                        >  1:51642/1‑140 (MQ=255)
   gtAGTTGTAATCAGTGTTTGATAAAATAAAAAAAGAGCATTAGTAATAAATTCAAAAATTATAGTTCAATTCAGAGAGGGATGG‑GATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACaaa                                                                                                                                     <  1:49004/140‑1 (MQ=255)
          tAATCAGTTTTTGATAAAATAAAAAAATAGCATTATTAATAAATTCAAAAATTATAGTTCAATTCAGAGAGGGATGG‑GATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCAtttt                                                                                                                              <  1:670908/140‑1 (MQ=255)
          aaaTCAGTTTTTGATAAAAGAAAAAAATAGCACTAGTAATAAATTCAAAAATTATAGTTCAATTCAGAGAGGGATGG‑GATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCAtttt                                                                                                                              <  1:594332/139‑1 (MQ=255)
              cAGTTTTTGATAAAATAAAAAAATAGCATTATTAATAAATTCAAAAATTATAGTTCAATTCAGAGAGGGATGG‑GATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTcac                                                                                                                          >  1:483283/1‑140 (MQ=255)
              cAGTTTTTGATAAAATAAAAAAATAGCATTATTAATAAATTCAAAAATTATAGTTCAATTCAGAGAGGGATGG‑GATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTcac                                                                                                                          <  1:374724/140‑1 (MQ=255)
              cAGTTGTTGAGAAAATAAATAAATAGCATTAGTAATAAAGTGAAAAATTATAGTTCAATTCAGAGAGGGATGG‑GATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTcac                                                                                                                          <  2:321454/140‑1 (MQ=255)
                gTTTTTGATAAAATAAAAAAATAGCATTCTTAATAAATTCAAAAATTATAGTTCAATTCAGAGAGGGATGG‑GATAAAATGAACTTTGTAACGTTGACTTCGGATGGGTTCAATGCGTTTACTACAAAGCATTTTTCACAt                                                                                                                        >  1:144793/1‑140 (MQ=255)
                gTTTTTGATAAAATAAAAAAATAGCATTATTAATAAATTCAAAAATTATAGTTCAATTCAGAGAGGGATGG‑GATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACAt                                                                                                                        >  1:59835/1‑140 (MQ=255)
                    ttGATAAAATAAAAAAATAGCATTATTAATAAATTCAAAAATTATAGTTCAATTCAGAGAGGGATGGATATTAAATTAA‑AATGGAACTTTGCATTCTAGTTCTGACAATGCGTTTACTACAAAGCATTTTTCACATTaca                                                                                                                    <  1:517976/140‑1 (MQ=255)
                      gATAAAATAAAAAAATAGCATTATTAATAAATTCAAAAATTATAGTTCAATTCAGAGAGGGCTGG‑GATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTacaca                                                                                                                  >  1:503113/1‑140 (MQ=255)
                      gATAAAATAAAAAAATAGCATTATTAATAAATTCAAAAATTATAGTTCAATTCAGAGAGGGATGG‑GATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAGGCATTTTTCACATTacaca                                                                                                                  >  1:81086/1‑140 (MQ=255)
                      gATAAAATAAAAAAATAGCATTATTAATAAATTCAAAAATTATAGTTCAATTCAGAGAGGGATGG‑GATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTacaca                                                                                                                  >  1:616523/1‑140 (MQ=255)
                      gATAAAATAAAAAAATAGCATTATTAATAAATTCAAAAATTATAGTTCAATTCAGAGAGGGATGG‑GATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTacaca                                                                                                                  <  2:142414/140‑1 (MQ=255)
                      gATAAAATAAAAAAATAGCATTATTAATAAATTCAAAAATTATAGTACAATTCAGAGAGGGATGG‑GATAAAATGAACTTTGTAACGTTGACTGCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCGCATTacaca                                                                                                                  >  1:418496/1‑140 (MQ=255)
                              aaaaaaaTAGCATTATTAATAAATTCAAAAATTATAGTTCAATTCAGAGAGGGATGG‑GATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGc                                                                                                          <  1:397538/140‑1 (MQ=255)
                              aaaaaaaTAGCATTATTAATAAATGCAAAAATTATAGTTCAATTCAGAGAGGGATGG‑GATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGc                                                                                                          <  1:329337/140‑1 (MQ=255)
                               aaaaaaTAGCATTATTAATAAATTCAAAAATTATAGTTCAATTCAGAGAGGGATGG‑GATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCt                                                                                                         <  2:634037/140‑1 (MQ=255)
                               aaaaaaTAGCATTATTAATAAATTCAAAAATTATAGTTCAATTCAGAGAGGGATGG‑GATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATT‑‑ACACAATCAGCTAt                                                                                                       >  2:190222/1‑140 (MQ=255)
                                aaaaaTAGCATTATTAATAAATTCAAAAATTATAGTTCAATTCAGAGAGGGATGG‑GATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTa                                                                                                        <  1:86395/140‑1 (MQ=255)
                                 aaaaTAGCATTATTAATAAATTCAAAAATTATAGTTCAATTCAGAGAGGGATGG‑GATAAAATGAACTTTGTAACGTTGACGTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCAGATTACAAGCAATCAGcatt                                                                                                       >  2:145423/1‑137 (MQ=255)
                                      aGCATTATTAATAAATTCAAAAATTATAGTTCAATTCAGAGAGGGATGG‑GATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCAta                                                                                                  >  1:203874/1‑139 (MQ=255)
                                      aGCATTATTAATAAATTCAAAAATTATAGTTCAATTCAGAGAGGGATGG‑GATAAAATGAACTTTGTAACGTGGAATTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACGATCAGCTCTTCGtt                                                                                                  >  1:25536/1‑140 (MQ=255)
                                      aGCAGTATTGATAAATTCAAAAATTATGGTTCAATTCATAGAGGGATGG‑GATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCAtt                                                                                                  <  2:64984/140‑1 (MQ=255)
                                        cATTATTAATAAATTCAAAAATTATAGTTCAATTCAGAGAGGGATGG‑GATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTAc                                                                                                <  2:350457/140‑1 (MQ=255)
                                         attattAATAAATTCAAAAATTATAGTTCAATTCAGAGAGGGATGG‑GATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACa                                                                                               >  1:20022/1‑140 (MQ=255)
                                              taataaATTCAAAAATTATATTGCAATTCAGAGAGGGATGG‑GATAAAATGAACTTTGTAACGTTGTCTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCAt                                                                                          <  2:40069/140‑1 (MQ=255)
                                              taataaATTCAAAAATTATAGTTCAATTCAGAGAGGGATGG‑GATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCAt                                                                                          <  2:221230/140‑1 (MQ=255)
                                               aataaATTCAAAAATTATAGTTCAATTCAGAGAGGGATGG‑GATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCATa                                                                                         <  1:3447/140‑1 (MQ=255)
                                                ataaATTCAAAAATTATAGTTCAATTCAGAGAGGGATGG‑GATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCATag                                                                                        <  1:509014/140‑1 (MQ=255)
                                                   aaTTCGAAAATTATAGTTCAATTCAGAGAGGGATGG‑GATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGt                                                                                     <  2:587943/140‑1 (MQ=255)
                                                   aaTTCAAAAATTATAGTTCAATTCAGAGAGGGATGG‑GATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTCCTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGt                                                                                     <  1:267559/140‑1 (MQ=255)
                                                   aaTTCAAAAATTATAGTTCAATTCAGAGAGGGATGG‑GATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGt                                                                                     <  2:501818/140‑1 (MQ=255)
                                                    aTTCAAAAATTATAGTTCAATTCAGAGAGGGATGG‑TATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGtt                                                                                    <  1:335846/140‑1 (MQ=255)
                                                     ttCAAAAATTATAGTTCAATTCAGAGAGGGATGG‑GATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGTTg                                                                                   <  1:530401/140‑1 (MQ=255)
                                                     ttCAAAAATTATAGTTCAATTCAGAGAGGGATGG‑GATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACAGTACACACAATCAGCTATTCATCACAATCATAGAGTTg                                                                                   >  1:608054/1‑140 (MQ=255)
                                                            aTTATAGTTCAATTCAGAGAGGGATGG‑GATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCCGCTATCCATTACAAGCATAGAGTTGATTTaaa                                                                            >  2:457193/1‑140 (MQ=255)
                                                                 aGTTCAATTCAGAGAGGGATGG‑GATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTTTTTTTTTACTCAATAAGCTATTCATTACAATCATATTTTTGATTTaatgggct                                                                       >  2:224399/1‑134 (MQ=255)
                                                                  gTTCAATTCAGAGAGGGATGG‑GATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCATGCAGTTGATTTAAAAGGcca                                                                      >  2:637981/1‑138 (MQ=255)
                                                                       atccAGCGAGGAATTG‑GAGAAAATACCCTTTGTAACGTTGACTTCGAATACCTTCACTATTTTTACTACAAAGCATTTTTCACATTACACACAATAAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGc                                                                 <  2:282069/137‑1 (MQ=255)
                                                                           agagagagATGG‑GATAAAATGAACTTTGTAACGTTGACGTCGGATGAGTTCAATGCGGTTACTACAAAGAATTTTTCACAATACAGACAATCCGCTATTCATTACAATCATAGAGTTGATGTAAAAGGCGATGTGCAtat                                                             >  2:661702/1‑138 (MQ=255)
                                                                           agagagGGATGG‑GATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGCATCt                                                             <  2:179466/140‑1 (MQ=255)
                                                                            gagagGGATGG‑GATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGCATCtt                                                            <  2:375438/140‑1 (MQ=255)
                                                                             agagGGATGG‑GATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGCATCTTg                                                           <  2:51642/140‑1 (MQ=255)
                                                                               agGGATGG‑GCTAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGCATCTTGTa                                                         <  2:602678/140‑1 (MQ=255)
                                                                                gggatgg‑gatAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCATACAGTTGATTTAAAAAGCGATGTGCATCTTGTAg                                                        >  2:66495/1‑140 (MQ=255)
                                                                                gggatgg‑gatAAAATGAACTTGGTAGCGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCGATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGCATCTTGTAg                                                        <  2:394351/140‑1 (MQ=255)
                                                                                 ggatgg‑gatAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGCATCTTGTAgg                                                       >  2:482817/1‑140 (MQ=255)
                                                                                 ggatgg‑gatAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTCCACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGCATCTTGTAgg                                                       >  2:569205/1‑140 (MQ=255)
                                                                                  gatgc‑gatAAAATGATCTTTGGAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTTAAAGGCGATGTGCATCTTGTAggg                                                      <  2:319141/140‑1 (MQ=255)
                                                                                        gatAAAATGTCGTTAGTAGCTTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGCATCTTGTAGGGGTTaa                                                 <  2:275674/140‑1 (MQ=255)
                                                                                         atAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGCATCTTGTAGGGGTTaaa                                                <  1:171651/140‑1 (MQ=255)
                                                                                         atAAAATGAACTTTGGAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGCATCTTGTAGGGGTTaaa                                                <  1:286245/140‑1 (MQ=255)
                                                                                          tAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACCTTACACACAATCAGCTATTCATTACAATCATAGAGTTGTTTTTTAAGGCTATGGGCATCTTGTAGGGGTTAAAg                                               <  2:348961/140‑1 (MQ=255)
                                                                                             aaTGGACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGCATCTTGTAGGGGTTAAAGATg                                            <  2:305456/140‑1 (MQ=255)
                                                                                             aaTGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGCATCTTGTAGGGGTTAgagaca                                            >  1:508497/1‑138 (MQ=255)
                                                                                             aaTGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGCATCTTGTAGGGGTTAAAGATg                                            <  1:482285/140‑1 (MQ=255)
                                                                                             aaTGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGCATCTTGTAGGGGTTAAAGATg                                            <  1:564745/140‑1 (MQ=255)
                                                                                             aaTGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGCATCTTGTAGGGGTTAAAGATg                                            <  1:229653/140‑1 (MQ=255)
                                                                                                   cTTTGTAACGTTGACTTCGGATGAGTCCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGCATCTTGTAGGGGTTAAAGATGACAATg                                      >  2:153750/1‑140 (MQ=255)
                                                                                                    tttGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGCATCTTGTAGGGGTTAAAGATGACAATgg                                     <  1:206177/140‑1 (MQ=255)
                                                                                                      tGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGACGTGCATCTTGTAGGGGTTAAAGATGACAATGGTc                                   <  1:106177/140‑1 (MQ=255)
                                                                                                       gTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGCATCTTGTAGGGGTTAAAGATGACAATGGTCa                                  <  1:606898/140‑1 (MQ=255)
                                                                                                       gTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTACATCTTGTAGGGGTTAAAGATGACAATGGTCa                                  <  1:95515/140‑1 (MQ=255)
                                                                                                       gTAACGATGACTTCGGATGAGTTTAATGCGAATACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGCAACTAGTAGGGGTGAAAGATGACAATGGTCa                                  >  2:468273/1‑140 (MQ=255)
                                                                                                        tAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGCGTTGATTTAAAAGGCGCTGTGCATCTTGTAGGGGTTAAAGATGACAATGGTCaa                                 >  1:482476/1‑140 (MQ=255)
                                                                                                          aCGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGCATCTTGTAGGGGTTAAAGATGACAATGGTCAAGt                               <  2:537672/140‑1 (MQ=255)
                                                                                                          aCGGTGACGTCGGATGAGTTCAAGGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGCATCTTGTAGGGGTTAAAGATGACAATGGTCAAGt                               <  1:340099/140‑1 (MQ=255)
                                                                                                           cGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGCATCTTGTAGGGGTTAAAGATGACAATGGTCAAGTg                              <  2:637468/140‑1 (MQ=255)
                                                                                                             ttGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGCATCTTGTAGGGGTTAAAGATGACAATGGTCAAGTGAt                            >  1:421785/1‑140 (MQ=255)
                                                                                                             ttGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGCATCTTGTAGGGGTTAAAGATGACAATGGTCAAGTGAt                            <  2:580542/140‑1 (MQ=255)
                                                                                                             tggattgcGGATCAGTTCCAGTCGTTTACTACAAAGCATTTTTCACGTTACACACCATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGCATCTTGTAGGGGTTAAAGATGACAATGGTCAAGTGAt                            <  2:172584/133‑1 (MQ=255)
                                                                                                                    cGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAACGGCGAGGTGCAACACGTAGGGGTTAAAGATGACAATGGTCAAGTGATTGCAGGa                     >  2:681873/1‑140 (MQ=255)
                                                                                                                    cGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGCATCTTGTAGGGGTTAAAGATGACAATGGTCAAGTGATTGCAGGa                     >  2:415878/1‑140 (MQ=255)
                                                                                                                      gATGAGTTGAATGCGTTTACTATAAGGCATTGTTCAGATTACACACAAGCAGCTATTCATTACAGTCATAGAGTTGATTTAAGAGGCGATGTGCATCTTGTAGGGGTTAAAGATGACAATGGTCAAGTGATTGCAGGATg                   <  2:118244/140‑1 (MQ=255)
                                                                                                                        tGAGTTGAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGCATCTTGTAGGGGTTAAAGATGACAATGGTCAAGTGATTGCAGGATGCt                 <  2:582502/140‑1 (MQ=255)
                                                                                                                           gTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGCATCTTGTAGGGGTTAAAGATGACAATGGTCAAGCGATTGCAGGATGATTAt              >  2:699492/1‑140 (MQ=255)
                                                                                                                               aaTGCGTTTACTACAAAGCATTTTTCACATTACACACACTCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGCATCTTGTAGGGGTTAAAGATGACAATGGTCAAGTGATTGCAGGATGCTTATTGag          >  2:368044/1‑139 (MQ=255)
                                                                                                                                    gTTTACTACAAAGCATTCTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGCATCTTGTAGGGGTTAAAGATGACAATGGTCAAGTGATTGCAGGATGCTAATTAACAGAAg     >  2:287362/1‑140 (MQ=255)
                                                                                                                                     tttACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGCATCTTGTAGGGGTTAAAGATGACAATGGTCAAGTGATTGCAGGATGCTCATTGACAGAAgc    >  1:699488/1‑140 (MQ=255)
                                                                                                                                      ttACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGCATCTTGTAGGGGTTAAAGATGACAATGGTCAAGTGATTGCAGGATGCTTATTGACAGAAgca   <  1:700019/140‑1 (MQ=255)
                                                                                                                                      ttACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGCATCTTGTAGGGGTTAAAGATGACAATGGTCAAGTGATTGCAGGATGCTTATTGACAGAAgca   <  1:332439/140‑1 (MQ=255)
                                                                                                                                      ttACTACAAAGCATTTTTCACATTACACACAAGCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGCATCTTGTAGGGGTTAAAGATGACAATGGTCAAGTGATTGCAGGATGCTTATTGACAGAAgca   <  1:365163/140‑1 (MQ=255)
                                                                                                                                      ttACTACAAAGCATTCTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGCATCTTGTAGGGGTTAAAGACGACAATGGTCAAGTGATTGCAGGATGCTTATTGACAGAAgca   <  1:94157/140‑1 (MQ=255)
                                                                                                                                       tactacAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGCATCTTGTAGGGGTTAAAGATGACAATGGTCAAGTGATTGCAGGATGCTTATTGACAGAAgcac  <  2:136411/140‑1 (MQ=255)
                                                                                                                                          |                                                                                                                                        
TGTGTATTTGTAATCAGTTTTTGATAAAATAAAAAAATAGCATTATTAATAAATTCAAAAATTATAGTTCAATTCAGAGAGGGATGG‑GATAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACAACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGCATCTTGTAGGGGTTAAAGATGACAATGGTCAAGTGATTGCAGGATGCTTATTGACAGAAGCAC  >  USA300TCH1516_ALE/2532161‑2532434

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: ‑

GATK/CNVnator alignment

N/A