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 F1 I2 R1 1873 183.1 9376148 98.2% 9207377 93.0

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 3,755,517 T→C intergenic (‑63/+127) yiaY ← / ← selB putative oxidoreductase/selenocysteinyl‑tRNA‑specific translation factor

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009133,755,5170TC100.0% 453.7 / NA 142intergenic (‑63/+127)yiaY/selBputative oxidoreductase/selenocysteinyl‑tRNA‑specific translation factor
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (1/141);  total (1/141)

Only 100 of 144 total aligned reads displayed.

AAGGAATAAAGAACGTTGAAGCTGCCATAACACACTCCTGAAAGTGTAAAAAAGGGCGGGCAGCTTACTGAGGATTTTCATTCGAAAATATGATCAGTATTATTGATTATCAAAATTAATCTAATAAAAAGCACATTGTATTCATTAAACAATGTGCTTTTTTTAAATTCATAAGAATTT  >  NC_000913/3755427‑3755606
                                                                                          |                                                                                         
aaGGAATAAAGAACGTTGAAGCTGCCATAACACACTCCTGAAAGTGTAAAAAAGGGCGGGCAGCTTACTGAGGATTTTCATTCGAAAATACGa                                                                                         <  1:3282314/93‑1 (MQ=255)
aaGGAATAAAGAACGTTGAAGCTGCCATAACACACTCCTGAAAGTGTAAAAAAGGGCGGGCAGCTTACTGAGGATTTTCATTCGAAAATACGa                                                                                         <  1:1954587/93‑1 (MQ=255)
aaGAAATAAAGAACGTTGAAGCTGCCATAACACACTCCTGAAAGTGTAAAAAAGGGCGGGCAGCTTACTGAGGATTTTCATTCGAAAATACGa                                                                                         <  2:1224688/93‑1 (MQ=255)
aaGAAATAAAGAACGTTGAAGCTGCCATAACACACTCCTGAAAGTGTAAAAAAGGGCGGGCAGCTTACTGAGGATTTTCATTCGAAAATACGa                                                                                         <  2:1996497/93‑1 (MQ=255)
 aGGAATAAAGAACGTTGAAGCTGCCATAACACACTCCTGAAAGTGTAAAAAAGGGCGGGCAGCTTACTGAGGATTTTCATTCGAAAATACGAt                                                                                        <  1:1507934/93‑1 (MQ=255)
 aGGAATAAAGAACGTTGAAGCTGCCATAACACACTCCTGAAAGTGTAAAAAAGGGCGGGCAGCTTACTGAGGATTTTCATTCGAAAATACGAt                                                                                        <  1:3709050/93‑1 (MQ=255)
  ggAATAAAGAACGTTGAAGCTGCCATAACACACTCCTGAAAGTGTAAAAAAGGGCGGGCAGCTTACTGAGGATTTTCATTCGAAAATACGATc                                                                                       <  2:1019868/93‑1 (MQ=255)
  ggAATAAAGAACGTTGAAGCTGCCATAACACACTCCTGAAAGTGTAAAAAAGGGCGGGCAGCTTACTGAGGATTTTCATTCGAAAATACGATc                                                                                       <  1:2370767/93‑1 (MQ=255)
  ggAATAAAGAACGTTGAAGCTGCCATAACACACTCCTGAAAGTGTAAAAAAGGGCGGGCAGCTTACTGAGGATTTTCATTCGAAAATACGATc                                                                                       <  2:401053/93‑1 (MQ=255)
  ggAATAAAGAACGTTGAAGCTGCCATAACACACTCCTGAAAGTGTAAAAAAGGGCGGGCAGCTTACTGAGGATTTTCATTCGAAAATACGATc                                                                                       <  1:3574876/93‑1 (MQ=255)
  ggAATAAAGAACGTTGAAGCTGCCATAACACACTCCTGAAAGTGTAAAAAAGGGCGGGCAGCTTACTGAGGATTTTCATTCGAAAATACGATc                                                                                       <  2:3971488/93‑1 (MQ=255)
  ggAATAAAGAACATTGAAGCTGCCATAACACCCTCCTGAAAGTGTAAAAAAGGGCGGGCAGCTTACTGAGGATTTTCATTCGAAAATACGATc                                                                                       <  1:3012613/93‑1 (MQ=255)
   gAATAAAGAACGTTGAAGCTGCCATAACACACTCCTGAAAGTGTAAAAAAGGGCGGGCAGCTTACTGAGGATTTTCATTCGAAAATACGATCa                                                                                      <  1:2447424/93‑1 (MQ=255)
   gAATAAAGAACGTTGAAGCTGCCATAACACACTCCTGAAAGTGTAAAAAAGGGCGGGCAGCTTACTGAGGATTTTCATTCGAAAATACGATCa                                                                                      <  1:660230/93‑1 (MQ=255)
    aaTAAAGAACGTTGAAGCTGCCATAACACACTCCTGAAAGTGTAAAAAAGGGCGGGCAGCTTACTGAGGATTTTCATTCGAAAATACGATCAg                                                                                     <  2:2546004/93‑1 (MQ=255)
      tAAAGAACGTTGAAGCTGCCATAACACACTCCTGAAAGTGTAAAAAAGGGCGGGCAGCTTACTGAGGATTTTCATTCGAAAATACGATCAGta                                                                                   <  2:2971251/93‑1 (MQ=255)
      tAAAGAACGTTGAAGCTGCCATAACACACTCCTGAAAGTGTAAAAAAGGGCGGGCAGCTTACTGAGGATTTTCATTCGAAAATACGATCAGta                                                                                   <  1:1799902/93‑1 (MQ=255)
      aaaaGAACGTTGAAGCTGCCATAACACACTCCTGAAAGTGTAAAAAAGGGCGGGCAGCTTACTGAGGATTTTCATTCGAAAATACGATCAGta                                                                                   <  1:2404852/92‑1 (MQ=255)
       aaaGAACGTTGAAGCTGCCATAACACACTCCTGAAAGTGTAAAAAAGGGCGGGCAGCTTACTGAGGATTTTCATTCGAAAATACGATCAGtat                                                                                  <  1:3977790/93‑1 (MQ=255)
       aaaGAACGTTGAAGCTGCCATAACACACTCCTGAAAGTGTAAAAAAGGGCGGGCAGCTTACTGAGGATTTTCATTCGAAAATACGATCAGtat                                                                                  <  1:1456616/93‑1 (MQ=255)
       aaaGAACGTTGAAGCTGCCATAACACACTCCTGAAAGTGTAAAAAAGGGCGGGCAGCTTACTGAGGATTTTCATTCGAAAATACGATCAGtat                                                                                  <  1:1095328/93‑1 (MQ=255)
       aaaGAACGTTGAAGCTGCCATAACACACTCCTGAAAGTGTAAAAAAGGGCGGGCAGCTTACTGAGGATTTTCATTCGAAAATACGATCAGtat                                                                                  <  2:2954415/93‑1 (MQ=255)
       aaaGAACGTGGAAGCTG‑CATAACACACTCCTGAAAGTGTAAAAAAGGGCGGGCAGCTTACTGAGGATTTTCATTCGAAAATACGATCAGtatt                                                                                 <  2:794916/93‑1 (MQ=255)
        aaGAACGTTGAAGCTGCCATAACACACTCCTGAAAGTGTAAAAAAGGGCGGGCAGCTTACTGAGGATTTTCATTCGAAAATACGATCAGtatt                                                                                 <  2:279533/93‑1 (MQ=255)
         aGAACGTTGAAGCTGCCATAACACACTCCTGAAAGTGTAAAAAAGGGCGGGCAGCTTACTGAGGATTTTCATTCGAAAATACGATCAGtatta                                                                                <  1:3881229/93‑1 (MQ=255)
         aGAACGTTGAAGCTGCCATAACACACTCCTGAAAGTGTAAAAAAGGGCGGGCAGCTTACTGAGGATTTTCATTCGAAAATACGATCAGtatta                                                                                <  1:2929264/93‑1 (MQ=255)
         aGAACGTTGAAGCTGCCATAACACACTCCTGAAAGTGTAAAAAAGGGCGGGCAGCTTACTGAGGATTTTCATTCGAAAATACGATCAGtatta                                                                                <  2:709709/93‑1 (MQ=255)
          gAACGTTGAAGCTGCCATAACACACTCCTGAAAGTGTAAAAAAGGGCGGGCAGCTTACTGAGGATTTTCATTCGAAAATACGATCAGtattat                                                                               <  1:2762612/93‑1 (MQ=255)
          gAACGTTGAAGCTGCCATAACACACTCCTGAAAGTGTAAAAAAGGGCGGGCAGCTTACTGAGGATTTTCATTCGAAAATACGATCAGtattat                                                                               <  1:1129249/93‑1 (MQ=255)
          gAACGTTGAAGCTGCCATAACACACTCCTGAAAGTGTAAAAAAGGGCGGGCAGCTTACTGAGGATTTTCATTCGAAAATACGATCAGtattat                                                                               <  2:3453532/93‑1 (MQ=255)
             cGTTGAAGCTGCCATAACACACTCCTGAAAGTGTAAAAAAGGGCGGGCAGCTTACTGAGGATTTTCATTCGAAAATACGATCAGTATTATTGa                                                                            <  2:2142061/93‑1 (MQ=255)
              gTTGAAGCTGCCATAACACACTCCTGAAAGTGTAAAAAAGGGCGGGCAGCTTACTGAGGATTTTCATTCGAAAATACGATCAGTATTATTGAt                                                                           <  1:1367530/93‑1 (MQ=255)
               ttGAAGCTGCCATAACACACTCCTGAAAGTGTAAAAAAGGGCGGGCAGCTTACTGAGGATTTTCATTCGAAAATACGATCAGTATTATTGAtt                                                                          <  2:3338211/93‑1 (MQ=255)
               ttGAAGCTGCCATAACACACTCCTGAAAGTGTAAAAAAGGGCGGGCAGCTTACTGAGGATTTTCATTCGAAAATACGATCAGTATTATTGAtt                                                                          <  2:3999822/93‑1 (MQ=255)
                tGAAGCTGCCATAACACACTCCTGAAAGTGTAAAAAAGGGCGGGCAGCTTACTGAGGATTTTCATTCGAAAATACGATCAGTATTATTGATTa                                                                         <  2:1558032/93‑1 (MQ=255)
                tGAAGCTGCCATAACACACTCCTGAAAGTGTAAAAAAGGGCGGGCAGCTTACTGAGGATTTTCATTCGAAAATACGATCAGTATTATTGATTa                                                                         <  1:3665670/93‑1 (MQ=255)
                 gAAGCTGCCATAACACACTCCTGAAAGTGTAAAAAAGGGCGGGCAGCTTACTGAGGATTTTCATTCGAAAATACGATCAGTATTATTGATTAt                                                                        <  1:494835/93‑1 (MQ=255)
                  aaGCTGCCATAACACACTCCTGAAAGTGTAAAAAAGGGCGGGCAGCTTACTGAGGATTTTCATTCGAAAATACGATCAGTATTATTGATTATc                                                                       <  1:433288/93‑1 (MQ=255)
                   aGCTGCCATAACACACTCCTGAAAGTGTAAAAAAGGGCGGGCAGCTTACTGAGGATTTTCATTCGAAAATACGATCAGTATTATTGATTATCa                                                                      <  1:3780367/93‑1 (MQ=255)
                   aGCTGCCATAACACACTCCTGAAAGTGTAAAAAAGGGCGGGCAGCTTACTGAGGATTTTCATTCGAAAATACGATCAGTATTATTGATTATCa                                                                      <  2:1787554/93‑1 (MQ=255)
                     cTGCCATAACACACTCCTGAAAGTGTAAAAAAGGGCGGGCAGCTTACTGAGGATTTTCATTCGAAAATACGATCAGTATTATTGATTATCaaa                                                                    <  2:4202695/93‑1 (MQ=255)
                      tGCCATAACACACTCCTGAAAGTGTAAAAAAGGGCGGGCAGCTTACTGAGGATTTTCATTCGAAAATACGATCAGTATTATTGATTATCaaaa                                                                   <  1:2008936/93‑1 (MQ=255)
                       gCCATAACACACTCCTGAAAGTGTAAAAAAGGGCGGGCAGCTTACTGAGGATTTTCATTCGAAAATACGATCAGTATTATTGATTATCAAAAt                                                                  <  1:2317613/93‑1 (MQ=255)
                        ccATAACACACTCCTGAAAGTGTAAAAAAGGGCGGGCAGCTTACTGAGGATTTTCATTCGAAAATACGATCAGTATTATTGATTATCAAAAtt                                                                 <  2:2111596/93‑1 (MQ=255)
                          aTAACACACTCCTGAAAGTGTAAAAAAGGGCGGGCAGCTTACTGAGGATTTTCATTCGAAAATACGATCAGTATTATTGATTATCAAAATTaa                                                               <  1:4347829/93‑1 (MQ=255)
                            aaCACACTCCTGAAAGTGTAAAAAAGGGCGGGCAGCTTACTGAGGATTTTCATTCGAAAATACGATCAGTATTATTGATTATCAAAATTAATc                                                             <  2:3025288/93‑1 (MQ=255)
                            aaCACACTCCTGAAAGTGTAAAAAAGGGCGGGCAGCTTACTGAGGATTTTCATTCGAAAATACGATCAGTATTATTGATTATCAAAATTAATc                                                             <  1:3642959/93‑1 (MQ=255)
                            aaCACACTCCTGAAAGTGTAAAAAAGGGCGGGCAGCTTACTGAGGATTTTCATTCGAAAATACGATCAGTATTATTGATTATCAAAATTAATc                                                             <  2:3453535/93‑1 (MQ=255)
                             acacacTCCTGAAAGTGTAAAAAAGGGCGGGCAGCTTACTGAGGATTTTCATTCGAAAATACGATCAGTATTATTGATTATCAAAATTAATCt                                                            <  2:2156750/93‑1 (MQ=255)
                             acacacTCCTGAAAGTGTAAAAAAGGGCGGGCAGCTTACTGAGGATTTTCATTCGAAAATACGATCAGTATTATTGATTATCAAAATTAATCt                                                            <  1:1857096/93‑1 (MQ=255)
                              cacacTCCTGAAAGTGTAAAAAAGGGCGGGCAGCTTACTGAGGATTTTCATTCGAAAATACGATCAGTATTATTGATTATCAAAATTAATCta                                                           <  2:2077556/93‑1 (MQ=255)
                              cacacTCCTGAAAGTGTAAAAAAGGGCGGGCAGCTTACTGAGGATTTTCATTCGAAAATACGATCAGTATTATTGATTATCAAAATTAATCta                                                           <  1:3891088/93‑1 (MQ=255)
                               acacTCCTGAAAGTGTAAAAAAGGGCGGTCAGCTTACTGAGTATTTTCATTCGAAAATACGATCAGTATTATTGATTATCAAAATTAATCtaa                                                          <  1:796351/93‑1 (MQ=255)
                               acacTCCTGAAAGTGTAAAAAAGGGCGGGCAGCTTACTGAGGATTTTCATTCGAAAATACGATCAGTATTATTGATTATCAAAATTAATCtaa                                                          <  2:50542/93‑1 (MQ=255)
                               acacTCCTGAAAGTGTAAAAAAGGGCGGGCAGCTTACTGAGGATTTTCATTCGAAAATACGATCAGTATTATTGATTATCAAAATTAATCtaa                                                          <  2:2323935/93‑1 (MQ=255)
                               acacTCCTGAAAGTGTAAAAAAGGGCGGGCAGCTTACTGAGGATTTTCATTCGAAAATACGATCAGTATTATTGATTATCAAAATTAATCtaa                                                          <  2:1715077/93‑1 (MQ=255)
                                cacTCCTGAAAGTGTAAAAAAGGGCGGGCAGCTTACTGAGGATTTTCATTCGAAAATACGATCAGTATTATTGATTATCAAAATTAATCtaat                                                         <  1:901008/93‑1 (MQ=255)
                                cacTCCTGAAAGTGTAAAAAAGGGCGGGCAGCTTACTGAGGATTTTCATTCGAAAATACGATCAGTATTATTGATTATCAAAATTAATCtaat                                                         <  1:632939/93‑1 (MQ=255)
                                cacTCCTGAAAGTGT‑AAAAAGGGCGGGCAGCTTACTGAGGATTTTCATTCGAAAATACGATCAGTATTATTGATTATCAAAATTAATCtaata                                                        <  2:380727/93‑1 (MQ=255)
                                 acTCCTGAAAGTGTAAAAAAGGGCGGGCAGCTTACTGAGGATTTTCATTCGAAAATACGATCAGTATTATTGATTATCAAAATTAATCtaata                                                        <  1:4235703/93‑1 (MQ=255)
                                  cTCCTGAAAGTGTAAAAAAGGGCGGGCAGCTTACTGAGGATTTTCATTCGAAAATACGATCAGTATTATTGATTATCAAAATTAATCtaataa                                                       <  2:29281/93‑1 (MQ=255)
                                   tCCTGAAAGTGTAAAAAAGGGCGGGCAGCTTACTGAGGATTTTCATTCGAAAATACGATCAGTATTATTGATTATCAAAATTAATCTAATaaa                                                      <  1:2021948/93‑1 (MQ=255)
                                    ccTGAAAGTGTAAAAAAGGGCGGGCAGCTTACTGAGGATTTTCATTCGAAAATACGATCAGTATTATTGATTATCAAAATTAATCTAATaaaa                                                     <  2:387024/93‑1 (MQ=255)
                                      tGAAAGTGTAAAAAAGGGCGGGCAGCTTACTGAGGATTTTCATTCGAAAATACGATCAGTATTATTGATTATCAAAATTAATCTAATAAAAAg                                                   <  2:2983332/93‑1 (MQ=255)
                                          aGTGTAAAAAAGGGCGGGCAGCTTACTGAGGATTTTCATTCGAAAATACGATCAGTATTATTGATTATCAAAATTAATCTAATAAAAAGcaca                                               <  1:2714803/93‑1 (MQ=255)
                                          aGTGTAAAAAAGGGCGGGCAGCTTACTGAGGATTTTCATTCGAAAATACGATCAGTATTATTGATTATCAAAATTAATCTAATAAAAAGcaca                                               <  2:189078/93‑1 (MQ=255)
                                          aGTGTAAAAAAGGGCGGGCAGCTTACTGAGGATTTTCATTCGAAAATACGATCAGTATTATTGATTATCAAAATTAATCTAATAAAAAGcaca                                               <  2:2034742/93‑1 (MQ=255)
                                            tgtAAAAAAGGGCGGGCAGCTTACTGAGGATTTTCATTCGAAAATACGATCAGTATTATTGATTATCAAAATTAATCTAATAAAAAGCACAtt                                             <  2:2081383/93‑1 (MQ=255)
                                            tgtAAAAAAGGGCGGGCAGCTTACTGAGGATTTTCATTCGAAAATACGATCAGTATTATTGATTATCAAAATTAATCTAATAAAAAGCACAtt                                             <  2:3762797/93‑1 (MQ=255)
                                             gtAAAAAAGGGCGGGCAGCTTACTGAGGATTTTCATTCGAAAATACGATCAGTATTATTGATTATCAAAATTAATCTAATAAAAAGCACATTg                                            <  1:1005386/93‑1 (MQ=255)
                                               aaaaaaGAGCGGGCAGCTTACTGAGGATTTTCATTCGAAAATACGATCAGTATTATTGATTATCAAAATTAATCTAATAAAAAGCACATTGTa                                          <  2:3959041/93‑1 (MQ=255)
                                                  aaaGGGCGGGCAGCTTACTGAGGATTTTCATTCGAAAATACGATCAGTATTATTGATTATCAAAATTAATCTAATAAAAAGCACATTGTATTc                                       <  1:1219401/93‑1 (MQ=255)
                                                   aaGGGCGGGCAGCTTACTGAGGATTTTCATTCGAAAATACGATCAGTATTATTGATTATCAAAATTAATCTAATAAAAAGCACATTGTATTCa                                      <  2:3000996/93‑1 (MQ=255)
                                                   aaGGGCGGGCAGCTTACTGAGGATTTTCATTCGAAAATACGATCAGTATTATTGATTATCAAAATTAATCTAATAAAAAGCACATTGTATTCa                                      >  1:1158178/1‑93 (MQ=255)
                                                   aaGGGCGGGCAGCTTACTGAGGATTTTCATTCGAAAATACGATCAGTATTATTGATTATCAAAATTAATCTAATAAAAAGCACATTGTATTCa                                      <  1:2133878/93‑1 (MQ=255)
                                                        cgggcAGCTTACTGAGGATTTTCATTCGAAAATACGATCAGTATTATTGATTATCAAAATTAATCTAATAAAAAGCACATTGTATTCATTaaa                                 <  1:3662645/93‑1 (MQ=255)
                                                         gggcAGCTTACTGAGGATTTTCATTCGAAAATACGATCAGTATTATTGATTATCAAAATTAATCTAATAAATAGCACATTGTATTCATTAAAc                                <  2:1269458/93‑1 (MQ=255)
                                                          ggcAGCTTACTGAGGATTTTCATTCGAAAATACGATCAGTATTATTGATTATCAAAATTAATCTAATAAAAAGCACATTGTATTCATTAAACa                               <  2:1343123/93‑1 (MQ=255)
                                                           gcAGCTTACTGAGGATTTTCATTCGAAAATACGATCAGTATTATTGATTATCAAAATTAATCTAATAAAAAGCACATTGTATTCATTAAACaa                              <  2:2510555/93‑1 (MQ=255)
                                                            cAGCTTACTGAGGATTTTCATTCGAAAATACGATCAGTATTATTGATTATCAAAATTAATCTAATAAAAAGCACATTGTATTCATTAAACAAt                             <  1:700138/93‑1 (MQ=255)
                                                            cAGCTTACTGAGGATTTTCATTCGAAAATACGATCAGTATTATTGATTATCAAAATTAATCTAATAAAAAGCACATTGTATTCATTAAACAAt                             <  2:1236041/93‑1 (MQ=255)
                                                            cAGCTTACTGAGGATTTTCATTCGAAAATACGATCAGTATTATTGATTATCAAAATTAATCTAATAAAAAGCACATTGTATTCATTAAACAAt                             <  1:2107065/93‑1 (MQ=255)
                                                             aGCTTACTGAGGATTTTCATTCGAAAATACGATCAGTATTATTGATTATCAAAATTAATCTAATAAAAAGCACATTGTATTCATTAAACAAtg                            <  2:363837/93‑1 (MQ=255)
                                                                ttACTGAGGATTTTCATTCGAAAATACGATCAGTATTATTGATTATCAAAATTAATCTAATAAAAAGCACATTGTATTCATTAAACAATGTGc                         <  1:1514715/93‑1 (MQ=255)
                                                                   cTGAGGATTTTCATTCGAAAATACGATCAGTATTATTGATTATCAAAATTAATCTAATAAAAAGCACATTGTATTCATTAAACAATGTGCttt                      <  2:1280274/93‑1 (MQ=255)
                                                                    tGAGGATTTTCATTCGAAAATACGATCAGTATTATTGATTATCAAAATTAATCTAATAAAAAGCACATTGTATTCATTAAACAATGTGCtttt                     <  1:2650418/93‑1 (MQ=255)
                                                                      aGGATTTTCATTCGAAAATACGATCAGTATTATTGATTATCAAAATTAATCTAATAAAAAGCACATTGTATTCATTAAACAATGTGCtttttt                   <  2:3573005/93‑1 (MQ=255)
                                                                         aTTTTCATTCGAAAATACGATCAGTATTATTGATTATCAAAATTAATCTAATAAAAAGCACATTGTATTCATTAAACAATGTGCTTTTTTTaa                <  1:3941208/93‑1 (MQ=255)
                                                                          ttttCATTCGAAAATACGATCAGTATTATTGATTATCAAAATTAATCTAATAAAAAGCACATTGTATTCATTAAACAATGTGCTTTTTTTaaa               <  1:2633021/93‑1 (MQ=255)
                                                                           tttCATTCGAAAATACGATCAGTATTATTGATTATCAAAATTAATCTAATAAAAAGCACATTGTATTCATTAAACAATGTGCTTTTTTTAAAt              <  1:1015929/93‑1 (MQ=255)
                                                                            ttCATTCGAAAATACGATCAGTATTATTGATTATCAAAATTAATCTAATAAAAAGCACATTGTATTCATTAAACAATGTGCTTTTTTTAAAtt             <  1:271034/93‑1 (MQ=255)
                                                                              cATTCGAAAATACGATCAGTATTATTGATTATCAAAATTAATCTAATAAAAAGCACATTGTATTCATTAAACAATGTGCTTTTTTTAAATTCa           <  2:4477451/93‑1 (MQ=255)
                                                                                ttCGAAAATACGATCAGTATTATTGATTATCAAAATTAATCTAATAAAAAGCACATTGTATTCATTAAACAATGTGCTTTTTTTAAATTCATa         <  2:1119546/93‑1 (MQ=255)
                                                                                 tCGAAAATACGATCAGTATTATTGATTATCAAAATTAATCTAATAAAAAGCACATTGTATTCATTAAACAATGTGCTTTTTTTAAATTCATaa        <  1:859721/93‑1 (MQ=255)
                                                                                   gAAAATACGATCAGTATTATTGATTATCAAAATTAATCTAATAAAAAGCACATTGTATTCATTAAACAATGTGCTTTTTTTAAATTCATAAGa      <  2:2420001/93‑1 (MQ=255)
                                                                                    aaaaTACGATCAGTATTATTGATTATCAAAATTAATCTAATAAAAAGCACATTGTATTCATTAAACAATGTGCTTTTTTTAAATTCATAAGaa     <  1:2064408/93‑1 (MQ=255)
                                                                                     aaaTACGATCAGTATTATTGATTATCAAAATTAATCTAATAAAAAGCACATTGTATTCATTAAACAATGTGCTTTTTTTAAATTCATAAGAAt    <  2:4335294/93‑1 (MQ=255)
                                                                                     aaaTACGATCAGTATTATTGATTATCAAAATTAATCTAATAAAAAGCACATTGTATTCATTAAACAATGTGCTTTTTTTAAATTCATAAGAAt    <  2:439550/93‑1 (MQ=255)
                                                                                      aaTACGATCAGTATTATTGATTATCAAAATTAATCTAATAAAAAGCACATTGTATTCATTAAACAATGTGCTTTTTTTAAATTCATAAGAAtt   <  2:3410395/93‑1 (MQ=255)
                                                                                       atacGATCAGTATTATTGATTATCAAAATTAATCTAATAAAAAGCACATTGTATTCATTAAACAATGTGCTTTTTTTAAATTCATAAGAAttt  <  1:1755570/93‑1 (MQ=255)
                                                                                          |                                                                                         
AAGGAATAAAGAACGTTGAAGCTGCCATAACACACTCCTGAAAGTGTAAAAAAGGGCGGGCAGCTTACTGAGGATTTTCATTCGAAAATATGATCAGTATTATTGATTATCAAAATTAATCTAATAAAAAGCACATTGTATTCATTAAACAATGTGCTTTTTTTAAATTCATAAGAATTT  >  NC_000913/3755427‑3755606

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

BRESEQ :: bam2aln output
CAGAAGGAATAAAGAACGTTGAAGCTGCCATAACACACTCCTGAAAGTGTAAAAAAGGGCGGGCAGCTTACTGAGGATTTTCATTCGAAAATATGATCAGTATTATTGATTATCAAAATTAATCTAATAAAAAGCACATTGTATTCATTAAACAATGTGCTTTTTTTAAATTCATAAGAATTTT  >  NC_000913/3755424‑3755607
                                                                                             |                                                                                          
AAGAAGAAATAAAGAACGTTGAAGCTGCCATAACACACTCCTGAAAGTGTAAAAAAGGGCGGGCAGCTTACTGAGGATTTTCATTCGAAAATAC                                                                                            <  SRR4302535.3301320/94‑1 (MQ=60)
 AGAAGGAATAAAGAACGTTGAAGCTGCCATAACACACTCCTGAAAGTGTAAAAAAGGGCGGGCAGCTTACTGAGGATTTTCATTCGAAAATACG                                                                                           <  SRR4302535.1068640/94‑1 (MQ=60)
 AGAAGGAATAAAGAACGTTGAAGCTGCCATAACACACTCCTGAAAGTGTAAAAAAGGGCGGGCAGCTTACTGAGGATTTTCATTCGAAAATACG                                                                                           <  SRR4302535.2802555/94‑1 (MQ=60)
   AAGGAATAAAGAACGTTGAAGCTGCCATAACACACTCCTGAAAGTGTAAAAAAGGGCGGGCAGCTTACTGAGGATTTTCATTCGAAAATACGAT                                                                                         <  SRR4302535.3305109/94‑1 (MQ=60)
   AAGGAATAAAGAACGTTGAAGCTGCCATAACACACTCCTGAAAGTGTAAAAAAGGGCGGGCAGCTTACTGAGGATTTTCATTCGAAAATACGAT                                                                                         <  SRR4302535.1968654/94‑1 (MQ=60)
    AGGAATAAAGAACGTTGAAGCTGCCATAACACACTCCTGAAAGTGTAAAAAAGGGCGGGCAGCTTACTGAGGATTTTCATTCGAAAATACGATC                                                                                        <  SRR4302535.2695217/94‑1 (MQ=60)
    AGGAATAAAGAACGTTGAAGCTGCCATAACACACTCCTGAAAGTGTAAAAAAGGGCGGGCAGCTTACTGAGGATTTTCATTCGAAAATACGATC                                                                                        <  SRR4302535.3734737/94‑1 (MQ=60)
    AGGAATAAAGAACGTTGAAGCTGCCATAACACACTCCTGAAAGTGTAAAAAAGGGCGGGCAGCTTACTGAGGATTTTCATTCGAAAATACGATC                                                                                        <  SRR4302535.1518775/94‑1 (MQ=60)
     GGAATAAAGAACGTTGAAGCTGCCATAACACACTCCTGAAAGTGTAAAAAAGGGCGGGCAGCTTACTGAGGATTTTCATTCGAAAATACGATCA                                                                                       <  SRR4302535.2387787/94‑1 (MQ=60)
     GGAATAAAGAACGTTGAAGCTGCCATAACACACTCCTGAAAGTGTAAAAAAGGGCGGGCAGCTTACTGAGGATTTTCATTCGAAAATACGATCA                                                                                       <  SRR4302535.3599662/94‑1 (MQ=60)
     GGAATAAAGAACATTGAAGCTGCCATAACACCCTCCTGAAAGTGTAAAAAAGGGCGGGCAGCTTACTGAGGATTTTCATTCGAAAATACGATCA                                                                                       <  SRR4302535.3033723/94‑1 (MQ=60)
      GAATAAAGAACGTTGAAGCTGCCATAACACACTCCTGAAAGTGTAAAAAAGGGCGGGCAGCTTACTGAGGATTTTCATTCGAAAATACGATCAG                                                                                      <  SRR4302535.2465055/94‑1 (MQ=60)
      GAATAAAGAACGTTGAAGCTGCCATAACACACTCCTGAAAGTGTAAAAAAGGGCGGGCAGCTTACTGAGGATTTTCATTCGAAAATACGATCAG                                                                                      <  SRR4302535.664837/94‑1 (MQ=60)
         TAAAGAACGTTGAAGCTGCCATAACACACTCCTGAAAGTGTAAAAAAGGGCGGGCAGCTTACTGAGGATTTTCATTCGAAAATACGATCAGTAT                                                                                   <  SRR4302535.1812915/94‑1 (MQ=60)
         AAAAGAACGTTGAAGCTGCCATAACACACTCCTGAAAGTGTAAAAAAGGGCGGGCAGCTTACTGAGGATTTTCATTCGAAAATACGATCAGTAT                                                                                   <  SRR4302535.2422156/94‑1 (MQ=60)
          AAAGAACGTTGAAGCTGCCATAACACACTCCTGAAAGTGTAAAAAAGGGCGGGCAGCTTACTGAGGATTTTCATTCGAAAATACGATCAGTATT                                                                                  <  SRR4302535.1467042/94‑1 (MQ=60)
          AAAGAACGTTGAAGCTGCCATAACACACTCCTGAAAGTGTAAAAAAGGGCGGGCAGCTTACTGAGGATTTTCATTCGAAAATACGATCAGTATT                                                                                  <  SRR4302535.4004969/94‑1 (MQ=60)
          AAAGAACGTTGAAGCTGCCATAACACACTCCTGAAAGTGTAAAAAAGGGCGGGCAGCTTACTGAGGATTTTCATTCGAAAATACGATCAGTATT                                                                                  <  SRR4302535.1103123/94‑1 (MQ=60)
           AAGAACGTTGAAGCTGCCATAACACACTCCTGAAAGTGTAAAAAAGGGCGGGCAGCTTACTGAGGATTTTCATTCGAAAATACGATCAGTATTA                                                                                 <  SRR4302535.2395979/94‑1 (MQ=60)
            AGAACGTTGAAGCTGCCATAACACACTCCTGAAAGTGTAAAAAAGGGCGGGCAGCTTACTGAGGATTTTCATTCGAAAATACGATCAGTATTAT                                                                                <  SRR4302535.2949903/94‑1 (MQ=60)
            AGAACGTTGAAGCTGCCATAACACACTCCTGAAAGTGTAAAAAAGGGCGGGCAGCTTACTGAGGATTTTCATTCGAAAATACGATCAGTATTAT                                                                                <  SRR4302535.4393739/94‑1 (MQ=60)
            AGAACGTTGAAGCTGCCATAACACACTCCTGAAAGTGTAAAAAAGGGCGGGCAGCTTACTGAGGATTTTCATTCGAAAATACGATCAGTATTAT                                                                                <  SRR4302535.3907865/94‑1 (MQ=60)
             GAACGTTGAAGCTGCCATAACACACTCCTGAAAGTGTAAAAAAGGGCGGGCAGCTTACTGAGGATTTTCATTCGAAAATACGATCAGTATTATT                                                                               <  SRR4302535.2782296/94‑1 (MQ=60)
             GAACGTTGAAGCTGCCATAACACACTCCTGAAAGTGTAAAAAAGGGCGGGCAGCTTACTGAGGATTTTCATTCGAAAATACGATCAGTATTATT                                                                               <  SRR4302535.1137311/94‑1 (MQ=60)
              AACGTGGAAGCTGCCATAACACACTCCTGAAAGTGTAAAAAAGGGCGGGCAGCTTACTGAGGATTTTCATTCGAAAATACGATCAGTATTATTG                                                                              <  SRR4302535.646564/94‑1 (MQ=60)
                 GTTGAAGCTGCCATAACACACTCCTGAAAGTGTAAAAAAGGGCGGGCAGCTTACTGAGGATTTTCATTCGAAAATACGATCAGTATTATTGATT                                                                           <  SRR4302535.1377305/94‑1 (MQ=60)
                   TGAAGCTGCCATAACACACTCCTGAAAGTGTAAAAAAGGGCGGGCAGCTTACTGAGGATTTTCATTCGAAAATACGATCAGTATTATTGATTAT                                                                         <  SRR4302535.3691051/94‑1 (MQ=60)
                    GAAGCTGCCATAACACACTCCTGAAAGTGTAAAAAAGGGCGGGCAGCTTACTGAGGATTTTCATTCGAAAATACGATCAGTATTATTGATTATC                                                                        <  SRR4302535.498307/94‑1 (MQ=60)
                     AAGCTGCCATAACACACTCCTGAAAGTGTAAAAAAGGGCGGGCAGCTTACTGAGGATTTTCATTCGAAAATACGATCAGTATTATTGATTATCA                                                                       <  SRR4302535.436306/94‑1 (MQ=60)
                     AAGCTGCCATAACACACTCCTGAAAGTGTAAAAAAGGGCGGGCAGCTTACTGAGGATTTTCATTCGAAAATACGATCAGTATTATTGATTATCA                                                                       <  SRR4302535.2536648/94‑1 (MQ=60)
                      AGCTGCCATAACACACTCCTGAAAGTGTAAAAAAGGGCGGGCAGCTTACTGAGGATTTTCATTCGAAAATACGATCAGTATTATTGATTATCAA                                                                      <  SRR4302535.3806459/94‑1 (MQ=60)
                        CTGCCATAACACACTCCTGAAAGTGTAAAAAAGGGCGGGCAGCTTACTGAGGATTTTCATTCGAAAATACGATCAGTATTATTGATTATCAAAA                                                                    <  SRR4302535.4078442/94‑1 (MQ=60)
                         TGCCATAACACACTCCTGAAAGTGTAAAAAAGGGCGGGCAGCTTACTGAGGATTTTCATTCGAAAATACGATCAGTATTATTGATTATCAAAAT                                                                   <  SRR4302535.2023403/94‑1 (MQ=60)
                          GCCATAACACACTCCTGAAAGTGTAAAAAAGGGCGGGCAGCTTACTGAGGATTTTCATTCGAAAATACGATCAGTATTATTGATTATCAAAATT                                                                  <  SRR4302535.2334201/94‑1 (MQ=60)
                             ATAACACACTCCTGAAAGTGTAAAAAAGGGCGGGCAGCTTACTGAGGATTTTCATTCGAAAATACGATCAGTATTATTGATTATCAAAATTAAT                                                               <  SRR4302535.4377574/94‑1 (MQ=60)
                              TAACACACTCCTGAAAGTGTAAAAAAGGGCGGGCAGCTTACTGAGGATTTTCATTCGAAAATACGATCAGTATTATTGATTATCAAAATTAATC                                                              <  SRR4302535.3649951/94‑1 (MQ=60)
                              TAACACACTCCTGAAAGTGTAAAAAAGGGCGGGCAGCTTACTGAGGATTTTCATTCGAAAATACGATCAGTATTATTGATTATCAAAATTAATC                                                              <  SRR4302535.866572/94‑1 (MQ=60)
                              TAACACACTCCTGAAAGTGTAAAAAAGGGCGGGCAGCTTACTGAGGATTTTCATTCGAAAATACGATCAGTATTATTGATTATCAAAATTAATC                                                              <  SRR4302535.1567695/94‑1 (MQ=60)
                               AACACACTCCTGAAAGTGTAAAAAAGGGCGGGCAGCTTACTGAGGATTTTCATTCGAAAATACGATCAGTATTATTGATTATCAAAATTAATCT                                                             <  SRR4302535.3668187/94‑1 (MQ=60)
                               AACACACTCCTGAAAGTGTAAAAAAGGGCGGGCAGCTTACTGAGGATTTTCATTCGAAAATACGATCAGTATTATTGATTATCAAAATTAATCT                                                             <  SRR4302535.3209202/94‑1 (MQ=60)
                                ACACACTCCTGAAAGTGTAAAAAAGGGCGGGCAGCTTACTGAGGATTTTCATTCGAAAATACGATCAGTATTATTGATTATCAAAATTAATCTA                                                            <  SRR4302535.1870470/94‑1 (MQ=60)
                                 CACACTCCTGAAAGTGTAAAAAAGGGCGGGCAGCTTACTGAGGATTTTCATTCGAAAATACGATCAGTATTATTGATTATCAAAATTAATCTAA                                                           <  SRR4302535.3917768/94‑1 (MQ=60)
                                  ACACTCCTGAAAGTGTAAAAAAGGGCGGTCAGCTTACTGAGTATTTTCATTCGAAAATACGATCAGTATTATTGATTATCAAAATTAATCTAAT                                                          <  SRR4302535.801941/94‑1 (MQ=60)
                                   CACTCCTGAAAGTGTAAAAAAGGGCGGGCAGCTTACTGAGGATTTTCATTCGAAAATACGATCAGTATTATTGATTATCAAAATTAATCTAATA                                                         <  SRR4302535.907387/94‑1 (MQ=60)
                                   CACTCCTGAAAGTGTAAAAAAGGGCGGGCAGCTTACTGAGGATTTTCATTCGAAAATACGATCAGTATTATTGATTATCAAAATTAATCTAATA                                                         <  SRR4302535.637349/94‑1 (MQ=60)
                                    ACTCCTGAAAGTGTAAAAAAGGGCGGGCAGCTTACTGAGGATTTTCATTCGAAAATACGATCAGTATTATTGATTATCAAAATTAATCTAATAA                                                        <  SRR4302535.4264692/94‑1 (MQ=60)
                                    ACTCCTGAAAGTGTAAAAAAGGGCGGGCAGCTTACTGAGGATTTTCATTCGAAAATACGATCAGTATTATTGATTATCAAAATTAATCTAATAA                                                        <  SRR4302535.2223807/94‑1 (MQ=60)
                                      TCCTGAAAGTGTAAAAAAGGGCGGGCAGCTTACTGAGGATTTTCATTCGAAAATACGATCAGTATTATTGATTATCAAAATTAATCTAATAAAA                                                      <  SRR4302535.2036522/94‑1 (MQ=60)
                                       CCTGAAAGTGTAAAAAAGGGCGGGCAGCTTACTGAGGATTTTCATTCGAAAATACGATCAGTATTATTGATTATCAAAATTAATCTAATAAAAA                                                     <  SRR4302535.387388/94‑1 (MQ=60)
                                          GAAAGTGTAAAAAAGGGCGGGCAGCTTACTGAGGATTTTCATTCGAAAATACGATCAGTATTATTGATTATCAAAATTAATCTAATAAAAAGCA                                                  <  SRR4302535.1412637/94‑1 (MQ=60)
                                             AGTGTAAAAAAGGGCGGGCAGCTTACTGAGGATTTTCATTCGAAAATACGATCAGTATTATTGATTATCAAAATTAATCTAATAAAAAGCACAT                                               <  SRR4302535.2734198/94‑1 (MQ=60)
                                                GTAAAAAAGGGCGGGCAGCTTACTGAGGATTTTCATTCGAAAATACGATCAGTATTATTGATTATCAAAATTAATCTAATAAAAAGCACATTGT                                            <  SRR4302535.1012531/94‑1 (MQ=60)
                                                  AAAAAAGGGCGGGCAGCTTACTGAGGATTTTCATTCGAAAATACGATCAGTATTATTGATTATCAAAATTAATCTAATAAAAAGCACATTGTAT                                          <  SRR4302535.3713008/94‑1 (MQ=60)
                                                     AAAGGGCGGGCAGCTTACTGAGGATTTTCATTCGAAAATACGATCAGTATTATTGATTATCAAAATTAATCTAATAAAAAGCACATTGTATTCA                                       <  SRR4302535.1116592/94‑1 (MQ=60)
                                                     AAAGGGCGGGCAGCTTACTGAGGATTTTCATTCGAAAATACGATCAGTATTATTGATTATCAAAATTAATCTAATAAAAAGCACATTGTATTCA                                       >  SRR4302535.1166459/1‑94 (MQ=60)
                                                     AAAGGGCGGGCAGCTTACTGAGGATTTTCATTCGAAAATACGATCAGTATTATTGATTATCAAAATTAATCTAATAAAAAGCACATTGTATTCA                                       <  SRR4302535.1228148/94‑1 (MQ=60)
                                                     AAAGGGCGGGCAGCTTACTGAGGATTGTCATTCGAAAAGACGATCAGTATTATTGATTATCAAAATTAATCTAATAAAAAGCACATTGTATTCA                                       <  SRR4302535.1228147/94‑1 (MQ=60)
                                                      AAGGGCGGGCAGCTTACTGAGGATTTTCATTCGAAAATACGATCAGTATTATTGATTATCAAAATTAATCTAATAAAAAGCACATTGTATTCAT                                      <  SRR4302535.2149256/94‑1 (MQ=60)
                                                        GGGCGGGCAGCTTACTGAGGATTTTCATTCGAAAATACGATCAGTATTATTGATTATCAAAATTAATCTAATAAAAAGCACATTGTATTCATTA                                    <  SRR4302535.2068430/94‑1 (MQ=60)
                                                           CGGGCAGCTTACTGAGGATTTTCATTCGAAAATACGATCAGTATTATTGATTATCAAAATTAATCTAATAAAAAGCACATTGTATTCATTAAAC                                 <  SRR4302535.3688006/94‑1 (MQ=60)
                                                              GCAGCTTACTGAGGATTTTCATTCGAAAATACGATCAGTATTATTGATTATCAAAATTAATCTAATAAAAAGCACATTGTATTCATTAAACAAT                              <  SRR4302535.3925105/94‑1 (MQ=60)
                                                               CAGCTTACTGAGGATTTTCATTCGAAAATACGATCAGTATTATTGATTATCAAAATTAATCTAATAAAAAGCACATTGTATTCATTAAACAATG                             <  SRR4302535.2122264/94‑1 (MQ=60)
                                                               CAGCTTACTGAGGATTTTCATTCGAAAATACGATCAGTATTATTGATTATCAAAATTAATCTAATAAAAAGCACATTGTATTCATTAAACAATG                             <  SRR4302535.705049/94‑1 (MQ=60)
                                                                   TTACTGAGGATTTTCATTCGAAAATACGATCAGTATTATTGATTATCAAAATTAATCTAATAAAAAGCACATTGTATTCATTAAACAATGTGCT                         <  SRR4302535.1525627/94‑1 (MQ=60)
                                                                       TGAGGATTTTCATTCGAAAATACGATCAGTATTATTGATTATCAAAATTAATCTAATAAAAAGCACATTGTATTCATTAAACAATGTGCTTTTT                     <  SRR4302535.2669395/94‑1 (MQ=60)
                                                                            ATTTTCATTCGAAAATACGATCAGTATTATTGATTATCAAAATTAATCTAATAAAAAGCACATTGTATTCATTAAACAATGTGCTTTTTTTAAA                <  SRR4302535.3968112/94‑1 (MQ=60)
                                                                            ATTTTCATTCGAAAATACGATCAGTATTATTGATTATCAAAATTAATCTAATAAAAAGCACATTGTATTCATTAAACAATGTGCTTTTTTTAAA                <  SRR4302535.725310/94‑1 (MQ=60)
                                                                             TTTTCATTCGAAAATACGATCAGTATTATTGATTATCAAAATTAATCTAATAAAAAGCACATTGTATTCATTAAACAATGTGCTTTTTTTAAAT               <  SRR4302535.1819447/94‑1 (MQ=60)
                                                                             TTTTCATTCGAAAATACGATCAGTATTATTGATTATCAAAATTAATCTAATAAAAAGCACATTGTATTCATTAAACAATGTGCTTTTTTTAAAT               <  SRR4302535.2651889/94‑1 (MQ=60)
                                                                              TTTCATTCGAAAATACGATCAGTATTATTGATTATCAAAATTAATCTAATAAAAAGCACATTGTATTCATTAAACAATGTGCTTTTTTTAAATT              <  SRR4302535.1023151/94‑1 (MQ=60)
                                                                               TTCATTCGAAAATACGATCAGTATTATTGATTATCAAAATTAATCTAATAAAAAGCACATTGTATTCATTAAACAATGTGCTTTTTTTAAATTC             <  SRR4302535.272921/94‑1 (MQ=60)
                                                                                    TCGAAAATACGATCAGTATTATTGATTATCAAAATTAATCTAATAAAAAGCACATTGTATTCATTAAACAATGTGCTTTTTTTAAATTCATAAG        <  SRR4302535.865790/94‑1 (MQ=60)
                                                                                     CGAAAATACGATCAGTATTATTGATTATCAAAATTAATCTAATAAAAAGCACATTGTATTCATTAAACAATGTGCTTTTTTTAAATTCATAAGA       <  SRR4302535.2017809/94‑1 (MQ=60)
                                                                                       AAAATACGATCAGTATTATTGATTATCAAAATTAATCTAATAAAAAGCACATTGTATTCATTAAACAATGTGCTTTTTTTAAATTCATAAGAAT     <  SRR4302535.2079289/94‑1 (MQ=60)
                                                                                       AAAATACGATCAGTATTATTGATTATCAAAATTAATCTAATAAAAAGCACATTGTATTCATTAAACAATGTGCTTTTTTTAAATTCATAAGAAT     <  SRR4302535.2927344/94‑1 (MQ=60)
                                                                                          ATACGATCAGTATTATTGATTATCAAAATTAATCTAATAAAAAGCACATTGTATTCATTAAACAATGTGCTTTTTTTAAATTCATAAGAATTTT  <  SRR4302535.1768257/94‑1 (MQ=60)
                                                                                             |                                                                                          
CAGAAGGAATAAAGAACGTTGAAGCTGCCATAACACACTCCTGAAAGTGTAAAAAAGGGCGGGCAGCTTACTGAGGATTTTCATTCGAAAATATGATCAGTATTATTGATTATCAAAATTAATCTAATAAAAAGCACATTGTATTCATTAAACAATGTGCTTTTTTTAAATTCATAAGAATTTT  >  NC_000913/3755424‑3755607

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 20 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑