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
A1 F2 I199 R1 220 57.5 3163680 97.0% 3068769 86.1

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NZ_CP009273 3,624,386 T→C E522G (GAA→GGA)  yhiJ ← YhiJ/YhiL family protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NZ_CP0092733,624,3860TC99.1% 357.7 / ‑4.2 107E522G (GAA→GGA) yhiJYhiJ/YhiL family protein
Reads supporting (aligned to +/- strand):  ref base T (0/1);  new base C (68/38);  total (68/39)
Fisher's exact test for biased strand distribution p-value = 3.64e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.53e-01

Only 100 of 107 total aligned reads displayed.

GTAACATTAATATTCATGTTGTCTATGGTTCAGAGCTGTAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTTCATGCTGGTAAGACTTCCAGGGAGTGGTTATCTCAGGCCCTGCACCAGGGTTAATTTGGCAATTATGCATGCTGAACATTCT  >  NZ_CP009273/3624299‑3624468
                                                                                       |                                                                                  
gTAACATTAATATTCATGTTGTCTATGGTTCAGAGCTGTAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCa                                                                                  >  2:1007556/1‑90 (MQ=255)
  aaCATTAATATTCATGTTGTCTATGGTTCAGAGCTGTAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATg                                                                                >  2:476134/1‑90 (MQ=255)
  aaCATTAATATTCATGTTGTCTATGGTTCAGAGCTGTAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATg                                                                                <  1:106303/90‑1 (MQ=255)
  aaCATTAATATTCATGTTGTCTATGGTTCAGAGCTGTAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATg                                                                                <  2:1339764/90‑1 (MQ=255)
   aCATTAATATTCATGTTGTCTATGGTTCAGAGCTGTAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGc                                                                               <  1:477085/90‑1 (MQ=255)
      ttAATATTCATGTTGTCTATGGTTCAGAGCTGTAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTgg                                                                            >  2:850107/1‑90 (MQ=255)
      ttAATATTCATGTTGTCTATGGTTCAGAGCTGTAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTgg                                                                            >  2:624429/1‑90 (MQ=255)
      ttAATATTCATGTTGTCTATGGTTCAGAGCTGTAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTgg                                                                            >  2:304264/1‑90 (MQ=255)
        aaTATTCATGTTGTCTATGGTTCAGAGCTGTAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTa                                                                          >  1:441587/1‑90 (MQ=255)
        aaTATTCATGTTGTCTATGGTTCAGAGCTGTAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTa                                                                          <  2:1363481/90‑1 (MQ=255)
         atatTCATGTTGTCTATGGTTCAGAGCTGTAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCa                                                                                  >  1:543037/1‑81 (MQ=255)
         atatTCATGTTGTCTATGGTTCAGAGCTGTAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCa                                                                                  <  2:543037/81‑1 (MQ=255)
          tatTCATGTTGTCTATGGTTCAGAGCTGTAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTa                                                                          >  1:595817/1‑88 (MQ=255)
          tatTCATGTTGTCTATGGTTCAGAGCTGTAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTa                                                                          <  2:595817/88‑1 (MQ=255)
          tatTCATGTTGTCTATGGTTCAGAGCTGTAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAg                                                                        <  1:103526/90‑1 (MQ=255)
          tatTCATGTTGTCTATGGTTCAGAGCTGTAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAg                                                                        <  1:1374339/90‑1 (MQ=255)
            ttCATGTTGTCTATGGTTCAGAGCTGTAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGAc                                                                      <  2:829999/90‑1 (MQ=255)
              cATGTTGTCTATGGTTCAGAGCTGTAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACtt                                                                    >  2:251804/1‑90 (MQ=255)
              cATGTTGTCTATGGTTCAGAGCTGTAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACtt                                                                    >  1:572062/1‑90 (MQ=255)
              cATGTTGTCTATGGTTCAGAGCTGTAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACtt                                                                    >  2:1217822/1‑90 (MQ=255)
              cATGTTGTCTATGGTTCAGAGCTGTAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACtt                                                                    >  1:474209/1‑90 (MQ=255)
              cATGTTGTCTATGGTTCAGAGCTGTAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACtt                                                                    >  2:401690/1‑90 (MQ=255)
                   tgtCTATGGTTCAGAGCTGTAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAgg                                                               >  2:1529086/1‑90 (MQ=255)
                   tgtCTATGGTTCAGAGCTGTAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAgg                                                               >  1:1315538/1‑90 (MQ=255)
                   tgtCTATGGTTCAGAGCTGTAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAgg                                                               >  1:1106501/1‑90 (MQ=255)
                   tgtCTATGGTTCAGAGCTGTAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAgg                                                               >  2:453031/1‑90 (MQ=255)
                    gtCTATGGTTCAGAGCTGTAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAggg                                                              <  2:1218668/90‑1 (MQ=255)
                    gtCTATGGTTCAGAGCTGTAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAggg                                                              <  2:441587/90‑1 (MQ=255)
                    gtCTATGGTTCAGAGCTGTAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAggg                                                              <  2:690918/90‑1 (MQ=255)
                     tCTATGGTTCAGAGCTGTAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAg                                                                        <  1:1043521/79‑1 (MQ=255)
                     tCTATGGTTCAGAGCTGTAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAg                                                                        >  2:1043521/1‑79 (MQ=255)
                      cTATGGTTCAGAGCTGTAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGAg                                                            <  1:314306/90‑1 (MQ=255)
                      cTATGGTTCAGAGCTGTAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGAg                                                            <  1:1089496/90‑1 (MQ=255)
                      cTATGGTTCAGAGCTGTAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGAg                                                            <  1:1180991/90‑1 (MQ=255)
                      cTATGGTTCAGAGCTGTAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGAg                                                            <  1:251804/90‑1 (MQ=255)
                      cTATGGTTCAGAGCTGTAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGAg                                                            >  2:49803/1‑90 (MQ=255)
                      cTATGGTTCAGAGCTGTAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGAg                                                            >  2:732872/1‑90 (MQ=255)
                        aTGGTTCAGAGCTGTAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGAGTg                                                          >  2:1237259/1‑90 (MQ=255)
                             tCAGAGCTGTAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCTGGGAGTGGTTAt                                                     >  1:1569701/1‑90 (MQ=255)
                             tCAGAGCTGTAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGAGTGGTTAt                                                     >  2:373864/1‑90 (MQ=255)
                              cAGAGCTGTAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTa                                                                          >  1:307088/1‑68 (MQ=255)
                              cAGAGCTGTAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTa                                                                          <  2:307088/68‑1 (MQ=255)
                              cAGAGCTGTAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGAGTGGTTAtc                                                    >  1:734924/1‑90 (MQ=255)
                              cAGAGCTGTAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGAGTGGTTAtc                                                    >  1:820311/1‑90 (MQ=255)
                              cAGAGCTGTAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGAGTGGTTAtc                                                    >  2:644417/1‑90 (MQ=255)
                              cAGAGCTGTAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGAGTGGTTAtc                                                    >  2:1389889/1‑90 (MQ=255)
                              cAGAGCTGTAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGAGTGGTTAtc                                                    >  2:1310441/1‑90 (MQ=255)
                              cAGAGCTGTAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGAAAGACTTCCAGGGAGGGGTTAtc                                                    >  1:466999/1‑90 (MQ=255)
                                gagCTGTAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGAGTGGTTAtctc                                                  >  2:203528/1‑90 (MQ=255)
                                gagCTGTAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGAGTGGTTAtctc                                                  >  2:555545/1‑90 (MQ=255)
                                 agCTGTAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGAGTGGTTATCTCa                                                 <  2:1580478/90‑1 (MQ=255)
                                 agCTGTAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGAGTGGTTATCTCa                                                 <  1:1200546/90‑1 (MQ=255)
                                 agCTGTAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGAGTGGTTATCTCa                                                 <  1:1033252/90‑1 (MQ=255)
                                  gCTGTAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGAGTGGTTATCTCAg                                                <  2:1441420/90‑1 (MQ=255)
                                    tGTAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTTCATGCTGGTAAGACTTCCAGGGAGTGGTTATCTCAGGc                                              <  2:950299/90‑1 (MQ=255)
                                     gTAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGAGTGGTTATCTCAGGcc                                             >  2:1245061/1‑90 (MQ=255)
                                     gTAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGAGTGGTTATCTCAGGcc                                             >  2:375495/1‑90 (MQ=255)
                                     gTAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGAGTGGTTATCTCAGGcc                                             >  2:1337405/1‑90 (MQ=255)
                                     gTAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGAGTGGTTATCTCAGGcc                                             >  2:889451/1‑90 (MQ=255)
                                     gTAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGAGTGGTTATCTCAGGcc                                             >  2:306738/1‑90 (MQ=255)
                                     gTAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGAGTGGTTATCTCAGGcc                                             >  1:956182/1‑90 (MQ=255)
                                          aTTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGAGTGGTTATCTCAGGCCCTGCa                                        >  1:419685/1‑90 (MQ=255)
                                          aTTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGAGTGGTTATCTCAGGCCCTGCa                                        >  2:427861/1‑90 (MQ=255)
                                            tgtgCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGAGTGGTTATCTCAGGCCCTGCAcc                                      >  2:400032/1‑90 (MQ=255)
                                            tgtgCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGAGTGGTTATCTCAGGCCCTGCAcc                                      >  1:623494/1‑90 (MQ=255)
                                            tgtgCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGAGTGGTTATCTCAGGCCCTGCAcc                                      >  1:187389/1‑90 (MQ=255)
                                            tgtgCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGAGTGGTTATCTCAGGCCCTGCAcc                                      >  1:1320491/1‑90 (MQ=255)
                                            tgtgCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGAGTGGTTATCTCAGGCCCTGCAcc                                      >  2:1145002/1‑90 (MQ=255)
                                             gtgCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATg                                                                                <  2:685331/47‑1 (MQ=255)
                                             gtgCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATg                                                                                >  1:685331/1‑47 (MQ=255)
                                             gtgCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGAGTGGTTATCTCAGGccc                                            <  2:354120/83‑1 (MQ=255)
                                             gtgCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGAGTGGTTATCTCAGGCCCTGCACCa                                     >  2:859060/1‑90 (MQ=255)
                                             gtgCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGAGTGGTTATCTCAGGCCCTGCACCa                                     >  2:111307/1‑90 (MQ=255)
                                             gtgCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGAGTGGTTATCTCAGGCCCTGCACCa                                     >  1:318387/1‑90 (MQ=255)
                                             gtgCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGAGTGGTTATCTCAGGCCCTGCACCa                                     >  2:116231/1‑90 (MQ=255)
                                               gcgcCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGAGTGGTTATCTCAGGCCCTGCACCAgg                                   >  1:1040300/1‑90 (MQ=255)
                                               gcgcCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGAGTGGTTATCTCAGGCCCTGCACCAgg                                   >  2:1374662/1‑90 (MQ=255)
                                               gcgcCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGAGTGGTTATCTCAGGCCCTGCACCAgg                                   >  1:704261/1‑90 (MQ=255)
                                               gcgcCTTCTAATCAAAGGCATAAGTCCATTTCTG‑TTTTTCCATGCTGGTAAGACTTCCAGGGAGTGGTTATCTCAGGc                                              <  2:1344943/78‑1 (MQ=255)
                                               gcgcCTTCTAATCAAAGGCATAAGTCCATTTCTG‑TTTTTCCATGCTGGTAAGACTTCCAGGGAGTGGTTATCTCAGGc                                              >  1:1344943/1‑78 (MQ=255)
                                                     tCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGAGTGGTTATCTCAGGCCCTGCACCAGGGTTAAt                             <  1:859060/90‑1 (MQ=255)
                                                        aaTCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGAGTGGTTATCTCAGGCCCTGCACCAGGGTTAATTTg                          <  1:401690/90‑1 (MQ=255)
                                                            aaaGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGAGTGGTTATCTCAGGCCCTGCACCAGGGTTAATTTGGCaa                      <  2:1295212/90‑1 (MQ=255)
                                                              aGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGAGTGGTTATCTCAGGCCCTGCACCAGGGTTAATTTGGCAAtt                    <  1:1085931/90‑1 (MQ=255)
                                                                gCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGAGTGGTTATCTCAGGCCCTGCACCAGGGTTAATTTGGCAATTat                  >  2:792905/1‑90 (MQ=255)
                                                                 cATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGAGTGGTTATCTCAGGCCCTGCACCAGGGTTAATTTGGCAATTatg                 <  2:851116/90‑1 (MQ=255)
                                                                 cATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGAGTGGTTATCTCAGGCCCTGCACCAGGGTTAATTTGGCAATTatg                 <  1:1403254/90‑1 (MQ=255)
                                                                   tAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGAGTGGTTATCTCAGGCCCTGCACCAGGGTTAATTTGGCAATTatgca               <  2:481458/90‑1 (MQ=255)
                                                                     aGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGAGTGGTTATCTCAGGCCCTGCACCAGGGTTAATTTGGCAATTatgcatg             <  1:306738/90‑1 (MQ=255)
                                                                      gTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGAGTGGTTATCTCAGGCCCTGCACCAGGGTTAATTTGGCAATTatgcatgc            <  1:316763/90‑1 (MQ=255)
                                                                         cATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGAGTGGTTATCTCAGGCCCTGCACCAGGGTTAATTTGGCAATTATGCATGCTGa         >  1:1108551/1‑90 (MQ=255)
                                                                         cATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGAGTGGTTATCTCAGGCCCTGCACCAGGGTTAATTTGGCAATTATGCATGCTGa         >  1:1384717/1‑90 (MQ=255)
                                                                         cATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGAGTGGTTATCTCAGGCCCTGCACCAGGGTTAATTTGGCAATTATGCATGCTGa         <  1:850107/90‑1 (MQ=255)
                                                                          aTTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGAGTGGTTATCTCAGGCCCTGCACCAGGGTTAATTTGGCAATTATGCATGCTGaa        >  2:629879/1‑90 (MQ=255)
                                                                          aTTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGAGTGGTTATCTCAGGCCCTGCACCAGGGTTAATTTGGCAATTATGCATGCTGaa        >  1:1413584/1‑90 (MQ=255)
                                                                          aTTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGAGTGGTTATCTCAGGCCCTGCACCAGGGTTAATTTGGCAATTATGCATGCTGaa        >  1:184441/1‑90 (MQ=255)
                                                                          aTTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGAGTGGTTATCTCAGGCCCTGCACCAGGGTTAATTTGGCAATTATGCATGCTGaa        >  2:484519/1‑90 (MQ=255)
                                                                          aTTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGAGTGGTTATCTCAGGCCCTGCACCAGGGTTAATTTGGCAATTATGCATGCTGaa        >  1:308224/1‑90 (MQ=255)
                                                                                gTTTTTTCCATGCTGGTAAGACTTCCAGGGAGTGGTTATCTCAGGCCCTGCACCAGGGTTAATTTGGCAATTATGCATGCTGAACAttct  >  1:1540124/1‑90 (MQ=255)
                                                                                gTTTTTTCCATGCTGGTAAGACTTCCAGGGAGTGGTTATCTCAGGCCCTGCACCAGGGTTAATTTGGCAATTATGCATGCTGAACAttct  >  1:675028/1‑90 (MQ=255)
                                                                                       |                                                                                  
GTAACATTAATATTCATGTTGTCTATGGTTCAGAGCTGTAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTTCATGCTGGTAAGACTTCCAGGGAGTGGTTATCTCAGGCCCTGCACCAGGGTTAATTTGGCAATTATGCATGCTGAACATTCT  >  NZ_CP009273/3624299‑3624468

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

BRESEQ :: bam2aln output
CTCAACCAGATAGTAACATTAATATTCATGTTGTCTATGGTTCAGAGCTGTAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTTCATGCTGGTAAGACTTCCAGGGAGTGGTTATCTCAGGCCCTGCACCAGGGTTAATTTGGCAATTATGCATGCTGAACATTCTTCC  >  NZ_CP009273/3624287‑3624471
                                                                                                   |                                                                                     
CTCAACCAGATAGTAACATTAATATTCATGTTGTCTATGGTTCAGAGCTGTAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTC                                                                                       >  SRR3722078.594877/1‑100 (MQ=60)
          TAGTAACATTAATATTCATGTTGTCTATGGTTCAGAGCTGTAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTA                                                                             >  SRR3722078.446882/1‑100 (MQ=60)
          TAGTAACATTAATATTCATGTTGTCTATGGTTCAGAGCTGTAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTA                                                                             <  SRR3722078.1522948/100‑1 (MQ=60)
           AGTAACATTAATATTCATGTTGTCTATGGTTCAGAGCTGTAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAA                                                                            >  SRR3722078.549454/1‑100 (MQ=60)
            GTAACATTAATATTCATGTTGTCTATGGTTCAGAGCTGTAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAG                                                                           >  SRR3722078.602726/1‑100 (MQ=60)
              AACATTAATATTCATGTTGTCTATGGTTCAGAGCTGTAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGAC                                                                         <  SRR3722078.107562/100‑1 (MQ=60)
               ACATTAATATTCATGTTGTCTATGGTTCAGAGCTGTAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACT                                                                        <  SRR3722078.482744/100‑1 (MQ=60)
                CATTAATATTCATGTTGTCTATGGTTCAGAGCTGTAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTT                                                                       >  SRR3722078.479834/1‑100 (MQ=60)
                CATTAATATTCATGTTGTCTATGGTTCAGAGCTGTAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTT                                                                       >  SRR3722078.578754/1‑100 (MQ=60)
                     ATATTCATGTTGTCTATGGTTCAGAGCTGTAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGG                                                                  >  SRR3722078.1123384/1‑100 (MQ=60)
                     ATATTCATGTTGTCTATGGTTCAGAGCTGTAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGG                                                                  >  SRR3722078.1336562/1‑100 (MQ=60)
                      TATTCATGTTGTCTATGGTTCAGAGCTGTAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGGG                                                                 <  SRR3722078.104756/100‑1 (MQ=60)
                      TATTCATGTTGTCTATGGTTCAGAGCTGTAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGGG                                                                 <  SRR3722078.1396488/100‑1 (MQ=60)
                      GATTCATGTTGTCTATGGTTCAGAGCTGTAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGGG                                                                 <  SRR3722078.1059102/100‑1 (MQ=60)
                               TGTCTATGGTTCAGAGCTGTAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCTGGGAGTGGTTAT                                                        >  SRR3722078.1595253/1‑100 (MQ=60)
                                GTCTATGGTTCAGAGCTGTAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGctgtctcttata                                                       >  SRR3722078.310837/1‑88 (MQ=60)
                                GTCTATGGTTCAGAGCTGTAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGAGTGGTTATC                                                       >  SRR3722078.744145/1‑100 (MQ=60)
                                GTCTATGGTTCAGAGCTGTAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGAGTGGTTATC                                                       >  SRR3722078.802624/1‑100 (MQ=60)
                                GTCTATGGTTCAGAGCTGTAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGAGTGGTTATC                                                       >  SRR3722078.831163/1‑100 (MQ=60)
                                GTCTATGGTTCAGAGCTGTAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGAAAGACTTCCAGGGAGGGGTTATC                                                       >  SRR3722078.472565/1‑100 (MQ=60)
                                  CTATGGTTCAGAGCTGTAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGAGTGGTTATCTC                                                     <  SRR3722078.1199435/100‑1 (MQ=60)
                                  CTATGGTTCAGAGCTGTAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGAGTGGTTATCTC                                                     <  SRR3722078.1106027/100‑1 (MQ=60)
                                  CTATGGTTCAGAGCTGTAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGAGTGGTTATCTC                                                     <  SRR3722078.318148/100‑1 (MQ=60)
                                  CTATGGTTCAGAGCTGTAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGAGTGGTTATCTC                                                     <  SRR3722078.254889/100‑1 (MQ=60)
                                       GTTCAGAGCTGTAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGAGTGGTTATCTCAGGCC                                                >  SRR3722078.969690/1‑100 (MQ=60)
                                            GAGCTGTAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGAGTGGTTATCTCAGGCCCTGCA                                           >  SRR3722078.424753/1‑100 (MQ=60)
                                             AGCTGTAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGAGTGGTTATCTCAGGCCCTGCAC                                          <  SRR3722078.1048610/100‑1 (MQ=60)
                                             AGCTGTAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGAGTGGTTATCTCAGGCCCTGCAC                                          <  SRR3722078.1219378/100‑1 (MQ=60)
                                              GCTGTAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGAGTGGTTATCTCAGGCCCTGCACC                                         >  SRR3722078.189615/1‑100 (MQ=60)
                                              GCTGTAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGAGTGGTTATCTCAGGCCCTGCACC                                         >  SRR3722078.630676/1‑100 (MQ=60)
                                              GCTGTAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGAGTGGTTATCTCAGGCCCTGCACC                                         >  SRR3722078.1341596/1‑100 (MQ=60)
                                               CTGTAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACctgtctcttatacacatctgacgctgccgacga                                        >  SRR3722078.693379/1‑67 (MQ=60)
                                               CTGTAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGAGTGGTTATCTCAGGCCCTGCACCA                                        >  SRR3722078.322287/1‑100 (MQ=60)
                                               CTGTAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGAGTGGTTATCTCAGGCCCTGCACCA                                        >  SRR3722078.358439/1‑100 (MQ=60)
                                                 GTAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGAGTGGTTATCTCAGGCCCTGCACCAGG                                      >  SRR3722078.1055816/1‑100 (MQ=60)
                                                 GTAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGAGTGGTTATCTCAGGCCCTGCACCAGG                                      >  SRR3722078.712769/1‑100 (MQ=60)
                                                 GTAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTG‑TTTTTCCATGCTGGTAAGACTTCCAGGGAGTGGTTATCTCAGGCCCTGCACCAGct                                     >  SRR3722078.1366531/1‑98 (MQ=60)
                                                                 TCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGAGTGGTTATCTCAGGCCCTGCACCAGGGTTAATTTGGCAATTA                      <  SRR3722078.870553/100‑1 (MQ=60)
                                                                    AATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGAGTGGTTATCTCAGGCCCTGCACCAGGGTTAATTTGGCAATTATGC                   <  SRR3722078.406564/100‑1 (MQ=60)
                                                                      TCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGAGTGGTTATCTCAGGCCCTGCACCAGGGTTAATTTGGCAATTATGCAT                 <  SRR3722078.1402233/100‑1 (MQ=60)
                                                                          AGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGAGTGGTTATCTCAGGCCCTGCACCAGGGTTAATTTGGCAATTATGCATGCTG             <  SRR3722078.1102384/100‑1 (MQ=60)
                                                                           GGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGAGTGGTTATCTCAGGCCCTGCACCAGGGTTAATTTGGCAATTATGCATGCTGA            >  SRR3722078.1407077/1‑100 (MQ=60)
                                                                           GGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGAGTGGTTATCTCAGGCCCTGCACCAGGGTTAATTTGGCAATTATGCATGCTGA            >  SRR3722078.1125463/1‑100 (MQ=60)
                                                                            GCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGAGTGGTTATCTCAGGCCCTGCACCAGGGTTAATTTGGCAATTATGCATGCTGAA           >  SRR3722078.186634/1‑100 (MQ=60)
                                                                            GCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGAGTGGTTATCTCAGGCCCTGCACCAGGGTTAATTTGGCAATTATGCATGCTGAA           >  SRR3722078.311990/1‑100 (MQ=60)
                                                                            GCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGAGTGGTTATCTCAGGCCCTGCACCAGGGTTAATTTGGCAATTATGCATGCTGAA           >  SRR3722078.1436532/1‑100 (MQ=60)
                                                                             CATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGAGTGGTTATCTCAGGCCCTGCACCAGGGTTAATTTGGCAATTATGCATGCTGAAT          <  SRR3722078.1425995/100‑1 (MQ=60)
                                                                                 AGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGAGTGGTTATCTCAGGCCCTGCACCAGGGTTAATTTGGCAATTATGCATGCTGAACATTC      <  SRR3722078.310484/100‑1 (MQ=60)
                                                                                  GTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGAGTGGTTATCTCAGGCCCTGCACCAGGGTTAATTTGGCAATTATGCATGCTGAACATTCT     >  SRR3722078.682795/1‑100 (MQ=60)
                                                                                  GTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGAGTGGTTATCTCAGGCCCTGCACCAGGGTTAATTTGGCAATTATGCATGCTGAACATTCT     <  SRR3722078.320640/100‑1 (MQ=60)
                                                                                  GTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGAGTGGTTATCTCAGGCCCTGCACCAGGGTTAATTTGGCAATTATGCATGCTGAACATTCT     >  SRR3722078.1565232/1‑100 (MQ=60)
                                                                                     CATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGAGTGGTTATCTCAGGCCCTGCACCAGGGTTAATTTGGCAATTATGCATGCTGAACATTCTTCC  <  SRR3722078.861453/100‑1 (MQ=60)
                                                                                                   |                                                                                     
CTCAACCAGATAGTAACATTAATATTCATGTTGTCTATGGTTCAGAGCTGTAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTTCATGCTGGTAAGACTTCCAGGGAGTGGTTATCTCAGGCCCTGCACCAGGGTTAATTTGGCAATTATGCATGCTGAACATTCTTCC  >  NZ_CP009273/3624287‑3624471

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑