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 F109 I0 R1 76 110.5 2404748 96.5% 2320581 141.0

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA USA300TCH1516_ALE 2,542,325 G→T 69.2% A29S (GCC→TCC)  hlgA → Gamma‑hemolysin component A

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE2,542,3250GT69.2% 97.7 / 71.5 101A29S (GCC→TCC) hlgAGamma‑hemolysin component A
Reads supporting (aligned to +/- strand):  ref base G (14/16);  new base T (34/31);  total (50/51)
Fisher's exact test for biased strand distribution p-value = 6.63e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.49e-01

Only 100 of 101 total aligned reads displayed.

TTAACTTTTAACGAACAGTTAATTCGAAAACGCTTACAAATGGATTATTATATATATGAACTTAAAATTAAATAGAAAGAAAGTGATTTCTATGATTAAAAATAAAA‑TATTAACAGCAACTTTAGCAGT‑TGGTTTAATAGCCCCTTTAGCCAATCCATTTATAGAAATTTCTAAAGCAGAAAATAAGATAGAAGATATCGGCCAAGGTGCAGAAATCATCAAAAGAACACAAGACATTACTAGCAAACGATTAGCTATAACTCAAAACATTCAAT  >  USA300TCH1516_ALE/2542186‑2542460
                                                                                                                                             |                                                                                                                                       
ttAACTTTTAACGAACAGTTAATTCGAAAACGCTTACAAATGGATTATTATATATATGAACTTAAAATTAAATAGAAAGAAAGTGATTTCTATGATTAAAAATAAAA‑TATTAACAGCAACTTTAGCAGT‑TGGTTTAATAGc                                                                                                                                        <  1:671091/141‑1 (MQ=255)
   aCTTTTAACGAACAGTTAATTCGCAAACGTTTACAACTTGCTTTTTCCAATTAGAAACTTAAAATTAAATAGAAAGAAAGTGATTTCTATGATTAAAAATAAAA‑TATTAACAGCAACTTTAGCAGT‑TGGTTTAATATcccc                                                                                                                                     <  1:562573/141‑1 (MQ=255)
      tttAACGAACAGTTAATTCGAAAACGCTTACAAATGGATTATTATATATATGAACTTAAAATTAAATAGAAAGAAAGTGATTTCTATGATTAAAAATAAAA‑TATTAACAGCAACTTTAGCAGT‑TGGTTTAATATCCCCttt                                                                                                                                  >  2:187032/1‑141 (MQ=255)
         aaCGAACAGTTAATTCGAAAACGCTTACAAATGGATTATTAGATATATGAACTTAAAATTAAGTAGAAAGAGAGTGATTTCTATGATTAACAATAAAA‑TATTAACAGCAACTTTAGCAGT‑TGGTTTAATAGCCCCTTTAGc                                                                                                                               <  2:361473/141‑1 (MQ=255)
             aaCAGTTAATTCGAAAACGCTTACAAATGGATTATTATATATATGAACTTAAAATTAAATAGAAAGAAAGTGATTTCTATGATTAAAAATAAAA‑TATTAACAGCAACTTTAGCAGT‑TGGTTTAATATCCCCTTTAGCCAAt                                                                                                                           >  1:828937/1‑141 (MQ=255)
              aCAGTTAATTCGAAAACGCTTACGAATGGATTATTATATATATGAACTTAAAATTAAATAGAAAGAAAGTGATTTCTATGATTAAAAATAAAA‑TATTAACAGCAACTTTAGCAGT‑TGGTTTAATATCCCCTTTAGCCAATc                                                                                                                          >  2:856929/1‑141 (MQ=255)
              aCAGTTAATTCGAAAACGCTTACAAATGGATTATTATATATATGAACTTAAAATTAAATAGAAAGAAAGTGATTTCTATGATTAAAAATAAAA‑TATTAACAGCAACTTTAGCAGT‑TGGTTTAATAACCCCTTTAGCCAATc                                                                                                                          >  2:1174285/1‑141 (MQ=255)
              aCAGTTAATTCGAAAACGCTTACAAATGGATTAATATATATATGAACTTAAAATTAAATAGAAAGAAAGTGATTTCTATGATGAAAAATGAAA‑TATTAACAGCAACTTTAGCAGT‑TGGTTTAATAGAACCTTTAAACAATc                                                                                                                          >  2:790407/1‑141 (MQ=255)
                 gTTAATTCGAAAACGCTTACAAATGGATTATTATATATATGAACTTAAAATTAAATAGAAAGAAAGTGATTTCTATGATTAAAAATAAAA‑TATTAACAGCAACTTTAGCAGT‑TGGTTTACTAGCCCCTTTAGCCAATCCAt                                                                                                                       >  1:516337/1‑141 (MQ=255)
                 gTTAATTCGAAAACGCTTACAAATGGATTATTATATATATGAACTTAAAATTAAATAGAAAGAAAGTGATTTCTATGATTAAAAATAAAA‑TATTAACAGCAACTTTAGCAGT‑TGGTTTAATATCCCCTTTAGCCAATCCAt                                                                                                                       <  2:410575/141‑1 (MQ=255)
                 gTTAATTCGAAAACGCTTACAAATGGATTATTATATATATGAACTTAAAATTAAATAGAAAGAAAGTGATTTCTATGATTAAAAATAAAA‑TATTAACAGCAACTTTAGCAAT‑TGGTTTAATAACCCCTTTAGCcaatcaat                                                                                                                       >  2:483075/1‑141 (MQ=255)
                   tAATTCGAAAACGCTTACAAATGGATTATTATATATATGGACTTAAAATTAAATAGAAAGAAGGTGATTTCTATGATTAAAAATAAAA‑TATTAACAGCAACTTTAGCAGG‑TGGTTTAATATCCCGTTTAGCCAATCCAttt                                                                                                                     >  2:599928/1‑141 (MQ=255)
                    aaTTCGAAAACGCTTACAAATGGATTATTATATATATGAACTTAAAATTAAATAGAAAGAAAGTGATTTCTATGATTAAAAATAAAA‑TATTAACAGCAACTTTAGCAGT‑TGGTTTAATATCCCCTTTAGCCAATCCATTta                                                                                                                    >  2:246204/1‑141 (MQ=255)
                     aTTCGAAAACGCTTACAAATGGATTATTATATATATGAACTTAAAATTAAATAGAAAGAAAGTGATTTCTATGATTAAAAATAAAA‑TATTAACAGCAACTTTAGCAGT‑TGGTTTAATATCCCCTTTAGCCAATCCATTtat                                                                                                                   <  2:547777/141‑1 (MQ=255)
                     aTTCGAAAACGCTTACAAATGGATTATTATATATATGAACTTAAAATTAAATAGAAAGAAAGTGATTTCTATGATTAAAAATAAAA‑TATTAACAGCAACTTTAGCAGT‑TGGTTTAATAGCCCCTTTAGCCAATCCATTtat                                                                                                                   >  1:480380/1‑141 (MQ=255)
                     aTTCGAAAACGCTTACAAATGGATTATTATATAAATGCACTTAAAATTAAATAGAAAGAAAGTGATTTCTATGATTAAAAACAAAA‑TATTAAAAGCAACTTTAGCAGT‑TGGTTTAATATCCCCTTTAGCCAATCCATTtaa                                                                                                                   >  2:491813/1‑140 (MQ=255)
                      ttCGAAAACGCTTACAAATGGATTATTATATATATGAACTTAAAATTAAATAGAAAGAAAGTGATTTCTATGATTAAAAATAAAA‑TATTAACAGCAACTTTAGCAGT‑TGGTTTAATAGCCCCTTTAGCCAATCCATTtata                                                                                                                  <  1:971439/141‑1 (MQ=255)
                       tCGCAAACGGTTACAAATGGATTAATATATGAAGGTACTTAAAATAAAATAGAAAGAAATGGATTTCTATGATTAAAAATAAAA‑TATTAACAGCAACTTTAGCAGT‑TGGTTTAATATCCCCTTTAGCCAATCCATTTATAg                                                                                                                 <  2:823061/141‑1 (MQ=255)
                         gAAAACGATTACAAATGGATTATTATATATATGAACTTAAAATTAAATAGAAAGAAAGTGATTTCTATGATTAAAAATAAAA‑TATTAACAGCAACTTTAGCAGT‑TGGTTTAATATCCCCTTTAGCCAATCCATTTATAGaa                                                                                                               <  2:203596/141‑1 (MQ=255)
                           aaaCGCTTACAAATGGATTATTATATATATGAACTTAAAATTAAATAGAAAGAAAGTGATTTCTATGATTAAAACTACTA‑TATTAACAGCAACTTTAGCAGT‑TGGTTTAATATCCCCTTTAGCAAATCCATTTATAGAAAt                                                                                                             >  1:276559/1‑141 (MQ=255)
                           aaaCGCTTACAAATGGATTATTATATATATGAACTTAAAATTAAATAGAAAGAAAGTGATTTCTATGATTAAAAATAAAA‑TATTAACAGTAACTTTAGCAGT‑TGGTTTACTACACCCGTTAGCCAATCCATTTATAGAAAt                                                                                                             <  2:849516/141‑1 (MQ=255)
                           aaaCGCTTACAAATGGATTATTATATATATGAACTTAAAATTAAATAGAAAGAAAGTGATTTCTATGATTAAAAATAAAA‑TATTAACAGCAACTTTAGCAGT‑TGGTTTAATATCCCCTTTAGCCAATCCATTTATAGAAAt                                                                                                             <  1:841941/141‑1 (MQ=255)
                           aaaCGCTTACAAATGGATTATTATATATATGAACTTAAAATTAAATAGAAAGAAAGTGATTTCTATGATTAAAAATAAAA‑TATTAACAGCAACTTTAGCAGT‑TGGTTTAATAGCCCCTTTAGCCAATCCATTTATAGAAAt                                                                                                             >  1:234636/1‑141 (MQ=255)
                             aCGCTTACAAATGGATTATTATATATATGAACTTAAAATTAAATAGAAAGAAAGTGATTTCTCTGATTAAAAATAAAA‑TATTAACAGCAACTTTAGCAGT‑TGGTTTAATATCCCCTTTAGCAAATCCATTTATAGAAAttt                                                                                                           >  1:1144564/1‑141 (MQ=255)
                             aCGCTTACAAATGGATTATTATATATATGAACTTAAAATTAAATAGAAAGAAAGTGATTTCTATGATTAAAAATAAAC‑TATTCACCGCACCTTTAGCAGT‑TGGATTAATATCCCCTTTAGCCAATCCATTTATAGAAAttt                                                                                                           <  2:962615/141‑1 (MQ=255)
                             aCGCTTACAAATGGATTATTATATATATGAACTTAAAATTAAATAGAAAGAAAGTGATTTCTATGATTAAAAATAAAA‑TATTAACAGCAACTTTAGCAGT‑TGGTTTAATATCCCCTTTAGCCAATCCATTTATAGAAAttt                                                                                                           >  1:1096808/1‑141 (MQ=255)
                              cGCTTTCAAGGGGATTATTTTATTTATGTACTTAAAATTAAATAGAAAGAAAGTGATTTCTATGATTACAAATAAAA‑TATTAACAGCAACTTTAGCAGT‑TGGTTTAATATCCCCTTTAACCAATTCATTTATTGAAAtttt                                                                                                          >  2:761106/1‑140 (MQ=255)
                                    aaaaTGGATTAGTATACATATGAACTTAAAATTAAATACAAAGAAAGTGATTTCTATGATTAAAAATAAAA‑TATTAACAGCAACTTTAGCAGT‑TGGTTTAATATCCCCTTTAGCCAATCCATTTATAGAAATTTCTAAAGc                                                                                                    <  1:428777/140‑1 (MQ=255)
                                      aaTGGATTATTATATATATGAACTTAAAATTAAATAGAAAGAAAGTGATTTCTATGATTAAAAATAAAA‑TATTAACAGCAACTTTAGCAGT‑TGGTTTAATATCCCCTTTAGCCAATCCATTTATAGAAATTTCTAAAGCAg                                                                                                  <  1:965095/141‑1 (MQ=255)
                                       aTGGATTATTATATATATGAACTTAAAATTAAATAGAAAGAAAGTGATTTCTATGATTAAAAATAAAA‑TATTAACAGCAACTTTAGCAGT‑TGGTTTAATAGCCCCTTTAGCCAATCCATTTATAGAAATTTCTGAAGCAGa                                                                                                 >  1:239413/1‑141 (MQ=255)
                                          gATTATTATATATATGAACTTAAAATTAAATAGAAAGAAAGTGATTTCTATGATTAAAAATAAAA‑TATTAACAGCAACTTTAGCAGT‑TGGTTTAATAGCCCCTTTAGCCAATCCATTTATAGAAATTTCTAAAGCAGaaaa                                                                                              >  2:422376/1‑141 (MQ=255)
                                          gATTATTATATATATGAACTGAAAATTAAATAGAAAGAAAGTGATTTCTATGATTAAAAATAAAA‑TATTAACAGCAACTTTAGCAGT‑TGGTTTAATATCCCCTTTAGCCAATCCATTTATAGAAATTTCTAAAGCAGaaaa                                                                                              <  2:945600/141‑1 (MQ=255)
                                           attattATATATATGAACTTAAAATTAAATAGAAAGAAAGTGATTTCTATGATTAAAAATAAAA‑TATTAACAGCAACTTTAGCAGT‑TGGTTTAATAGCCCCTTTAGCCAATCCATTTATAGAAATTTCTAAAGCAGAAAAt                                                                                             <  2:826784/141‑1 (MQ=255)
                                           attattATATATATGAACTTAAAATTAAATAGAAAGAAAGTGATTTCTATGATTAAAAATAAAA‑TATTAACAGCAACTTTAGCAGT‑TGGTTTAATAGCCCCTTTAGCCAATCCATTTATAGAAATTTCTAAAGCAGAAAAt                                                                                             <  1:849414/141‑1 (MQ=255)
                                           attattATATATATGAACTTAAAATTAAATAGAAAGAAAGAACCTAAAGTCATTAACAATAAAA‑TATTAACAGCAACTTTAGCAGT‑TGGTTTAATATCCCCTTTAGCCAATCCATTTATAGAAATTTCTAAAGCAGAAAAt                                                                                             <  1:388025/141‑1 (MQ=255)
                                            ttattaTATATATGAACTTAAAATTAAATAGAAAGAAAGTGATTTCTATGATTAAAAATAAAA‑TATTAACAGCAACTTTAGCAGT‑TGGTTTAATATCCCCTTTAGCCAATCAATTTATAGAAATTTCTAAAGCAGAAAATa                                                                                            >  2:467004/1‑141 (MQ=255)
                                            ttattaTATATATGAACTTAAAATTAAATAGAAAGAAAGTGATTTCTATGATTAAAAATAAAA‑TATTAACAGCAACTTTAGCAGT‑TGGTTTAATATACCCTTTAGCCAATCCATTTATAGAAATTTCTAAAGCAGACAATa                                                                                            >  2:291749/1‑141 (MQ=255)
                                             tattatATATATGAACTTAAAATTAAATAGAAAGAAAGTGATTTCTATGATTAAAAATAAAA‑TATTAACAGCAACTTTAGCAGT‑TGGTTTAATATCCCCTTTAGCCAATCCATTTATAGAAATTTCTAAAGCAGAAAATaa                                                                                           >  1:109491/1‑141 (MQ=255)
                                                   atatatGAACTTAAAATTAAATAGAAAGAAAGTGATTTCTATGATTAAAAATAAAA‑TATTAACAGCAACTTTAGCAGT‑TGGTTTAATATCCCCTTTAGCCAATCCATTTATAGAAATTTCTAAAGCAGAAAATAAGATaga                                                                                     <  1:467284/141‑1 (MQ=255)
                                                    tatatGAACTTAAAATTAAATAGAAAGAAAGTGATTTCTATGATTAAAAATAAAA‑TATTAACAGCAACTTTAGCAGT‑TGGTTTAATATCCCCTTTAGCCAATCCATTTATAGAAATTTCTAAAGCAGAAAATAAGATagaa                                                                                    <  1:48319/141‑1 (MQ=255)
                                                       atGAACTTAAAATTAAATAGAAAGAAAGTGATTTCTATGATTAAAAATAAAA‑TATTAACAGCAACTTTAGCAGT‑TGGTTTAATATCCCCTTTAGCCAATCCATTTATAGAAATTTCTAAAGCAGAAAATAAGATAGAAGat                                                                                 <  2:571912/141‑1 (MQ=255)
                                                       agtaaCCTAAAATTAAATATAAACAAAGTCCTTTCTATGATTAAAAATAAAA‑TATTAACAGCAACTTTAGCAGT‑TGGTTTAATAGCCTCTTTAGCCAATCCATTTATAGAAATTTCTAAAGCAGAAAATAAGATAGAAGat                                                                                 <  1:483075/138‑1 (MQ=255)
                                                        tGAACTTAAAATTAAATAGAAAGAAAGTGATTTCTATGATTAAAAATAAAA‑TATTAACAGCAACTTTAGCAGT‑TTGTTTAATAGCCCCTTTAGCCAATCCATTTATAGAAATTTCTAAAGCAGAAAATAAGATAGAAGata                                                                                <  2:358952/141‑1 (MQ=255)
                                                        tGAACTTAAAATTAAATAGAAAGAAAGTGATTTCTATGATTAAAAATAAAA‑TATTAACAGCAACTTTAGCAGT‑TGGTTTAATAGCCCCTTTAGCCAATCCATTTATAGAAATTTCTAAAGCAGAAAATAAGATAGAAGata                                                                                <  1:790407/141‑1 (MQ=255)
                                                             ttAAAATTAAATAGAAAGAAAGTTATTTCTATGATTAAAAATAAAA‑TATTAACAGCAACTTTAGCAGT‑TGGTTTAATATCCCCTTTAGCCAATCCATTTATAGAAATTTCTAAAGCAGAAAATAAGATAGAAGATATCGGc                                                                           <  2:594454/141‑1 (MQ=255)
                                                              tAAAATTAAATAGAAAGAAAGTGATTTCTATGATTAAAAATAAAA‑TATTAACAGCAACTTTAGCAGT‑TGGTTTAATATCCCCTTTAGCCAATCCATTTATAGAAATTTCTAAAGCAGAAAATAAGATAGAAGATATCGGcc                                                                          <  2:1028626/141‑1 (MQ=255)
                                                               aaaaTTAAATAGAAAGAAAGTGATTTCTATGATTAAAAATAAAA‑TATTAACAGCAACTTTAGCAGT‑TGGTTTAATATCCCCTTTAGCCAATCCATTTATAGAAATTTCTAAAGCAGAAAATAAGATAGAAGATATCGGCCa                                                                         >  1:47509/1‑141 (MQ=255)
                                                               aaaaTTAAATAGAAAGAAAGTGATTTCTATGATTAAAAATAAAA‑TATTAACAGCAACTTTAGCAGT‑TGGTTTAATAGCCCCTTTAGCCAATCCATTTATAGAAATTTCTAAAGCAGAAAATAAGATAGAAGATATCGGCCa                                                                         >  2:967243/1‑141 (MQ=255)
                                                                 aaTTAAATAGAAAGAAAGTGATTTCTATGATTAAAAATAAAA‑TATTAACAGCAACTTTAGCAGT‑TGGTTTAATATCCCCTTTAGCCAATCCATTTATAGAAATTTCTAAAGCAGAAAATAAGATAGAAGATATCGGCCAAg                                                                       >  1:267379/1‑141 (MQ=255)
                                                                 aaTTAAATAGAAAGAAAGTGATTTCTATGATTAAAAATAAAA‑TATTAACAGCAACTTTAGCAGT‑TGGTTTAATATCCCCTTTAGCCAATCCATTTATAGAAATTTCTAAAGCAGAAAATAAGATAGAAGATATCGGACAAg                                                                       >  2:641398/1‑141 (MQ=255)
                                                                 aaTTAAATAGAAAGAAAGTGATTTCTATGATTAAAAATAAAA‑TATTAACAGCAACTTTAGCAGT‑TGGTTTAATATCCCCTTTAGCCAATCCATTTATAGAAATTTCTAAAGCAGAAAATAAGATAGAAGATATCAGCCAAg                                                                       >  2:963510/1‑141 (MQ=255)
                                                                 aaTTAAATAGAAAGAAAGTGATTTCTATGATTAAAAATAAAA‑TATTAACAGCAACTTTAGCAGT‑TGGTTTAATATCCCCTTTAGCCAATCAATTTATAGAAATTTCTAACGCAGAAAATAAGATAGAAGCTATCACCCAAg                                                                       >  2:821335/1‑141 (MQ=255)
                                                                 aaTTAAATAGAAAGAAAGCGATTTCTATGATTAAAAATAAAA‑TATTAACAGCAACTTTAGCAGT‑TGGTTTAATATCCCCTTTAGCCAATCCATTTATAGAAATTTCTAAAGCAGACAATAAGATAGAAGTTATAGGCCAAg                                                                       >  2:829504/1‑141 (MQ=255)
                                                                  aTTAAATAGAAAGAAAGTGATTTCTATGATTAAAAATAAAA‑TATTAACAGCAACTTTAGCAGT‑TGGTTTAATATCCCCTTTAGCCAATCCATTTATAGAAATTTCTAAAGCAGAAAATAAGATAGAAGATATCGGCCAAgg                                                                      <  1:1092374/141‑1 (MQ=255)
                                                                  aTTAAATAGAAAGAAAGTGATTTCTATGATTAAAAATAAAA‑TATTAACAGCAACTTTAGCAGT‑TGGTTTAATATCCCCTTTAGCCAAGCCATTTATAGAAATTTCTAAAGCAGAAAATAAGATAGAAGATATCGGCCAAgg                                                                      <  1:763695/141‑1 (MQ=255)
                                                                   ttAAATAGAAAGAAAGTGATTTCTATGATTAAAAATAAAA‑TATTAACAGCAACTTTAGCAGT‑TGGTTTAATATCCCCTTTAGCCAATCCATTTATAGAAATTTCTAAAGCAGAAAATAAGATAGAAGATATCGGCCAAGGt                                                                     <  2:490315/141‑1 (MQ=255)
                                                                    tAAATAGAAAGAAAGTGATTTCTATGATTAAAAATAAAA‑TATTAACAGCAACTTTAGCAGT‑TGGTTTAATATCCCCTTTAGCCAATCCATTTATAGAAATTTCTAAAGCAGAAAATAAGATAGAAGATATCGGCCAAGGTg                                                                    <  1:355116/141‑1 (MQ=255)
                                                                        tAGAAAGACAGTGATTTCTATGATTAAAATTAAAA‑TATTAACAGCAACTTTAGCAGT‑TGGTTTAATAGCCCCTTTAGCCAATCCATTTATAGAAATTTCTAAAGCAGAAAATAAGATAGAAGATATCGGCCAAGGTGCAGa                                                                <  2:511610/141‑1 (MQ=255)
                                                                        tAGAAAGAAAGTGATTTCTATGATTAAAAATAAAA‑TATTAACAGCAACTTTAGCAGT‑TGGTTTAATATCCCCTTTAGCCAATCCATTTATAGAAATTTCTAAAGCAGAAAATAAGATAGAAGATATCGGCCAAGGTGCAGa                                                                <  1:90973/141‑1 (MQ=255)
                                                                        tAGAAAGAAAGTGATTTCTATGATTAAAAATAAAA‑TATTAACAGCAACTTTAGCAGT‑TGGTTTAATATCCCCTTTAGCCAATCCATTTATAGAAATTTCTAAAGCAGAAAATAAGATAGAAGATATCGGCCAAGGTGCAGa                                                                <  1:982927/141‑1 (MQ=255)
                                                                          gaaagaaaGTGATTTCTATGATTAAAAATAAAA‑TATTAACAGCAACTTTAGCAGT‑TGGTTTAATATCCCCTTTAGCCAATCCATTTATAGAAATTTCTAAAGCAGAAAATAAGATAGAAGATATCGGCCAAGGTGCAGaaa                                                              <  2:574765/141‑1 (MQ=255)
                                                                          gaaagaaaGTGATTTCTATGATTAAAAATAAAA‑TATTAACAGCAACTTTAGCAGT‑CGGTAATAGAACCCCTTTAGCCAATCCATTTATAGAAATTTCTAAAGCAGAAAATAAGATAGAAGATATCGGCCAAGGTGCAGaaa                                                              <  1:275755/141‑1 (MQ=255)
                                                                           aaagaaagTGATTTCTATGATTAAAAATAAAA‑TATTAACAGCAACTTTAGCAGT‑TGGTTTAATATCCCCTTTAGCCAATCCATTTATAGAAATTTCTAAAGCAGAAAATAAGATAGAAGATATCGGCCAAGGTGCAGAAat                                                             >  2:106328/1‑141 (MQ=255)
                                                                            aagaaagTGATTTCTATGATTAAAAATAAAA‑TATTAACAGCAACTTTAGCAGT‑TGGTTTAATAGCCCCTTTAGCCAATCCATTTATAGAAATTTCTAAAGCAGAAAATAAGATAGAAGATATCGGCCAAGGTGCAGAAatc                                                            >  1:1064312/1‑141 (MQ=255)
                                                                             agaaagTGATTTCTATGATTAAAAATTAAA‑TGTTAAAAG‑GACCTCAGCACTGTGTTTGAATATCCCCTTTTGCCAGTCCATTTATAGAAATTTCTAAAGCAGAAAATAAGATAGAAGATATCGGCCAAGGTGCAGAAatca                                                           <  1:270104/141‑1 (MQ=255)
                                                                             agaaagTGATTTCTATGATTAAAAATAAAA‑TATTAACAGCCACTTTGGCCGT‑TGGATTGATATCCCCTTTAGCCAATACATTTATAGAAAGTTCTAAAGCAGAAAATAAGATAGAAGATATCGGCCAAGGTGCAGAAatca                                                           <  2:1149924/141‑1 (MQ=255)
                                                                             agaaagTGATGTCTATGATTAAAAATAAAA‑TATTAACAGCAACTTTAGCAGT‑TGGTTTAATAGCCCCTTTAGCCAATCCATTTATAGAAATTTCTAAAGCAGAAAATAAGATAGAAGATATCGGCCAAGGTGCAGAAatca                                                           <  2:1163711/141‑1 (MQ=255)
                                                                                  gTGATTTCTATGATTAAAAATAAAA‑TATTAACAGCAACTTTAGCAGT‑TGGTTTAATATCCCCTTTAGCCAATCCATTTATAGAAATTTCTAAAGCAGAAAATAAGATAGAAGATATCGGCCAAGGTGCAGAAATCATCaaa                                                      <  1:912664/141‑1 (MQ=255)
                                                                                     aTTTCTATGATTAAAAATAAAA‑TATTAACAGCAACTTTAGCAGT‑TGGTTTAATATCCCCTTTAGCCAATCCATTTATAGAAATTTCTAAAGCAGAAAATAAGATAGAAGATATCGGCCAAGGTGCAGAAATCATCAAAAGa                                                   <  2:1032165/141‑1 (MQ=255)
                                                                                     aTTTCTATGATTAAAAATAAAA‑TATTAACAGCAACTTTAGCAGT‑TGGTTTAATATCCCCTTTAGCCAATCCATTTATAGAAATTTCTAAAGCAGAAAATAAGATAGAAGATATCGGCCAAGGTGCAGAAATCATCAAAAGa                                                   >  1:770010/1‑141 (MQ=255)
                                                                                       ttCTATGATTAAAAATAAAA‑TATTAACAGCAACTTTAGCAGT‑TGGTTTAATATCCCCTTTAGCCAATCCATTTATAGCAATTTCTAAAGCAGAAAATAAGATAGAAGATATCGGCCAAGGTGCAGAAATCATCAAAAGAac                                                 >  1:805089/1‑141 (MQ=255)
                                                                                       ttCTATGATTAAAAATAAAA‑TATTAACAGCAACTTTAGCAGT‑TGGTTTAATATCCCCTTTAGCCAATCCATTTATAGAAATTTCTAAAGCAGAAAATAAGATAGAAGATATCGGCCAAGGTGCAGAAATCATCAAAAGAac                                                 >  2:858571/1‑141 (MQ=255)
                                                                                       ttCTATGATTAAAAATAAAA‑TATTAACAGCAACTTTAGCAGT‑TGGTTTAATATCCCCTTTAGCCAATCCATTTATAGAAATTTCTAAAGCAGAAAATAAGATAGAAGATATCGGCCAAGGTGCAGAAATCATCAAAAGAac                                                 <  2:599484/141‑1 (MQ=255)
                                                                                       ttCTATGATTAAAAATAAAA‑TATTAACAGCAACTTTAGCAGT‑TGGTTTAATAGCCCCTTTAGCCAATCCATTTATAGAAATTTCTAAAGCAGAAAATAAGATAGAAGATATCGGCCAAGGTGCAGAACTCCTCAAAAGAac                                                 >  2:668765/1‑141 (MQ=255)
                                                                                            tGATTAAAAATAAAA‑TATTAACAGCAACTTTAGCAGT‑TGGTTTAATATCCCCTTTAGCCAATCCGTTTATAGAAATTTCTAAAGCAGAAAATAAGATAGAAGATATCGGCCAAGGTGCAGAAATCATCAAAAGAACACaaa                                            >  2:743905/1‑140 (MQ=255)
                                                                                            acaTTAAAAATAAAA‑TATTCACACCAACTTTAGCAGT‑TGGTTTAATACCCCCTTTAGCCAATCCATTTATAGAAATTTCTAAAGCAGAAAATAAGATAGAAGATATCGGCCAAGGTGCAGAAATCATCAAAAGAACACAAg                                            <  1:599928/139‑1 (MQ=255)
                                                                                             tgtgtaaaataaaagTATTAACAGCAACTTTAGCAGT‑TAGTTTAATAGCCCCTTTAGCCAATCCATTTATAGAAATTTCTAAATCAGAAACTAATATAGAAGATATCGGCCAAGGTGCAGAAATCATCAAAAGAACACAAg                                            <  2:838133/136‑1 (MQ=255)
                                                                                                  aaaataaaa‑tATTAACAGCAACCTTAGCAGT‑TGGTTTAATAGCCCCTTTAGCCAATCCATTTATAGAAATTTCTAAAGCAGAAAATAAGATAGAAGATATCGGCCAAGGTGCAGAAATCATCAAAAGAACACAAGACATTa                                      <  1:477474/141‑1 (MQ=255)
                                                                                                   aaataaaa‑taTTAACAGCAACTTTAGCAGT‑TGGTTTAATATCCCCTTTAGCCAATCCATTTATAGAAATTTCTAAAGCAGAAAATAAGATAGAAGATATCGGCCAAGGTGCAGAAATCATCAAAAGAACACAAGACATTAc                                     >  2:1192286/1‑141 (MQ=255)
                                                                                                       aaaa‑taTTAACAGCAACTTTAGCAGT‑TGGTTTAATATCCCCTTTAGCCAATCCATTTATAGAAATTTCTAAAGCAGAAAATAAGATAGAAGATATCGGCCAAGGTGCAGAAATCATCAAAAGAACACAAGACATTATTAGc                                 <  2:828937/141‑1 (MQ=255)
                                                                                                        aaa‑taTTAACAGCAACTTTAGCAGT‑TGGTTTAATATCCCCTTTAGCCAATCCATTTATAGAAATTTCTAAAGCAGAAAATAAGATAGAAGATATCGGCCAAGGTGCAGACATCATCAAGAGAACACAAGACATTACTAGCa                                >  1:400874/1‑141 (MQ=255)
                                                                                                        aaa‑taTTAACAGCAACTTTAGCAGT‑TGGTTTAATATCCCCTTTAGCCAATCCATTTATAGAAATTTCTAAAGCAGAAAATAAGATAGAAGATATCGGCCAAGGTGCAGAAATCATCAAAAGAACACAAGACATTACTAGCa                                >  1:953070/1‑141 (MQ=255)
                                                                                                        aaa‑taTTAACAGCAACTTTAGCAGT‑TGGTTTAATATCCCCTTTAGCCAATCCATTTATAGAAATTTCTAAAGCAGAAAATAAGATAGAAGATATCGGCCAAGGTGCAGAAATCATCAAAAGAACACAAGACATTACTAGCa                                >  2:50272/1‑141 (MQ=255)
                                                                                                            tatTAACAGCAACTTTAGCAGT‑TGGTTTAATAGCCCCTTTAGCCAATCCATTTATAGAAATTTCTAAAGCAGAAAATAAGATAGAAGATATCGGCCAAGGTGCAGAAATCATCAAAAGAACACAAGACATTACTAGCAAAc                             <  1:742291/141‑1 (MQ=255)
                                                                                                             atTAACAGCAACTTTAGCAGT‑TGGTTTAATAGCCCCTTTAGCCAATCCATTTATAGAAATTTCTAAAGCAGAAAATAAGATAGAAGATATCGGCCAAGGTGCAGAAATCATCAAAAGAACACAAGACATTACTAGCAAACg                            <  2:1097586/141‑1 (MQ=255)
                                                                                                              ttAACAGCCACTTTAGCAGT‑TGGTTTAATAGCCCCTTTAGCCAATCCATTTATAGAAATTTCTAAAGCAGAAAATAAGATAGAAGATATCGTCCAAGGTGCAGAAATCATCAAAATAACACAAGACATTACTAGCAAACGa                           <  1:398188/141‑1 (MQ=255)
                                                                                                                   aGCAACTTTAGCAGT‑TGGTTTAATATCCCCTTTAGCCAATCCATTTATAGAAATTTCTAAAGCAGAAAATAAGATAGAAGATATCGGCCAAGGTGCAGAAATCATCAAAAGAACACAAGACATTACTAGCAAGCGATTAGc                      >  2:1198399/1‑141 (MQ=255)
                                                                                                                   aGCAACTTTAGCAGT‑TGGTTTAATATCCCCTTTAGCCAATCCATTTATAGAAATTTCTAAAGCAGAAAATAAGATAGAAGATATCGGCCAAGGTGCAGAAATCATCAAAAGAACACAAGACATTACTAGCAAACGATTAGc                      >  2:428050/1‑141 (MQ=255)
                                                                                                                    caaaCTTTAGCAAT‑TTGTTAAATATCCCCTTTAGCCAACGCATTTATAGAAATTTCTAAAGCAGAAAATAAGATAGAAGATATCCGCCAAGGTGCAGAAATCATCAAAAGAACACAAGACATTACTAGCAAACGATTAGCt                     <  1:829504/139‑1 (MQ=255)
                                                                                                                       aCTTTAGCAGT‑TGGTTTAATATCCCCTTTAGCCAATACATTTATAGAAATTTCTAAAGCAGAAAATAAGATAGAAGATATCGGCCAAGGTGCAGAAATCATCAAAAGAACACAAGACATTACTAGCAAACGATTAGCtata                  >  2:437274/1‑141 (MQ=255)
                                                                                                                         tttAGCAGT‑TGGTTTAATAGCCCCTTTAGCCAATCCATTTATAGAAATTTCTAAAGCAGAAAATAAGATAGAAGATATCGGCCAAGGTGCAGAAATCATCAAAAGAACACAAGACATTACTAGCAAACGATTAGCTATAAc                >  1:380918/1‑141 (MQ=255)
                                                                                                                         ccaaGCAGT‑CGGATTAATAACCCCTGTAGCCAATCCAGTTATACAAAATTCTAAAGCAGAAAACAAGATAGAAGATACCGTCCAACCTGCACAAATCATCAAAATAACACAAGACATTACTAGCAAACGATTAGCTATAAc                <  2:454739/138‑1 (MQ=255)
                                                                                                                          ttAGCAGT‑TGGTTTAATAGCCCCTTTAGCCAATCCATTTATAGAAATTTCTAAAGCAGAAAATAAGATAGAAGATATCGGCCAAGGTGCAGAAATCATCAAAAGAACACAAGACATTACTAGCAAACGATTAGCTATAAcc               >  2:30307/1‑140 (MQ=255)
                                                                                                                           tAGCAGT‑TGGTTTAATAGCCCCTTTAGCCAATCCATTTATAGAAATTACTAAAGCAGAAAATAAGATAGAAGATATCGGCCAAGGTGCAGAAATCATCAAAAGAACACAAGACATTACTAGCAAACGATTAGCTATAACTc              >  2:774665/1‑141 (MQ=255)
                                                                                                                            aGCAGT‑TGGTTTAATATCCCCTTTAGCCAATCCATTTATAGAAATTTCTAAAGCAGAAAATAAGATAGAAGATATCGGCCAAGGTGCAGAAATCATCAAAAGAACACAAGACATTACTAGCAAACGATTAGCTATAACTCa             >  1:1161788/1‑141 (MQ=255)
                                                                                                                              cAGT‑TGGTTTAATATCCCCTTTAGCCAATCCATTTATAGAAATTTCTAAAGCAGAAAATAAGATAGAAGATATCGGCCAAGGTGCAGAAATCATCAAAAGAACACAAGACATTACTAGCAAACGATTAGCTATAACTCaaa           <  1:462191/141‑1 (MQ=255)
                                                                                                                                     gTTTAATAGCCCCTTTAGCCAATCCATTTATAGAAATTTCTAAAGCAGCAACTCAGATAGAAGATATCGGCCAAGGTGCAGAAATCATCAAAAGAACACAAGACATTACTAGCAAACGATTAGCTATAACTCAAAACATTc     <  1:868542/141‑1 (MQ=255)
                                                                                                                                       ttAATAGCCCCTTTAGCCAATCCATTTATAGAAATTTCTAAAGCAGAAAATAAGATAGAAGATATCGGCCAAGGTGCAGAAATCATCAAAAGAACACAAGACATTACTAGCAAACTATTAGCTATAACTCAAAAAATTCaa   >  2:32464/1‑141 (MQ=255)
                                                                                                                                        tAATATCCCCTTTAGCCAATCCATTTATAGAAATTTCTAAAGCAGAAAATAAGATAGAAGATATCGGCCAAGGTGCAGAAATCATCAAAAGAACACAAGACATTACTAGCAAACGATTAGCTATAACTCAAAAAATTCAAt  >  2:368307/1‑141 (MQ=255)
                                                                                                                                        tAATAGCCCCTTTAGCAAATCCATTTATAGAAATTTCTAAAGCAGAAAATAAGATAGAAGATATCGGCCAAGGTGCAGAAATCATCAAAAGAACACAAGACATTACTAGCAAACGATTAGCTATAACTCAAAACATTCAAt  >  1:665236/1‑141 (MQ=255)
                                                                                                                                             |                                                                                                                                       
TTAACTTTTAACGAACAGTTAATTCGAAAACGCTTACAAATGGATTATTATATATATGAACTTAAAATTAAATAGAAAGAAAGTGATTTCTATGATTAAAAATAAAA‑TATTAACAGCAACTTTAGCAGT‑TGGTTTAATAGCCCCTTTAGCCAATCCATTTATAGAAATTTCTAAAGCAGAAAATAAGATAGAAGATATCGGCCAAGGTGCAGAAATCATCAAAAGAACACAAGACATTACTAGCAAACGATTAGCTATAACTCAAAACATTCAAT  >  USA300TCH1516_ALE/2542186‑2542460

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