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 2,071,763 A→G T735A (ACC→GCC)  b2000 → outer membrane fluffing protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009132,071,7630AG99.1% 341.3 / ‑4.8 110T735A (ACC→GCC) b2000outer membrane fluffing protein
Reads supporting (aligned to +/- strand):  ref base A (1/0);  new base G (49/60);  total (50/60)
Fisher's exact test for biased strand distribution p-value = 4.55e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.38e-01

Only 100 of 128 total aligned reads displayed.

GCTTATCGTGCAGAAGTCCCCCTGTATGCCTCCATGCTGACACAGGCAATGGACTATGACCGGATTGTGGCAGGCTCCCGCAGCCATCAGACCGGTGTAAATGGTGAAAACAACAGCGTCCGTCTCAGCATTCAGGGCGGTCATCTCGGTCACGATAACAATGGCGGTATTGCCCGTGG  >  NC_000913/2071673‑2071851
                                                                                          |                                                                                        
gCTTATCGTGCAGAAGTCCCCCTGTATGCCTCCATGCTGACACAGGCAATGGACTATGACCGGATTGTGGCAGGCTCCCGCAGCCATCAGGcc                                                                                        >  1:775505/1‑93 (MQ=255)
gCTTATCGTGCAGAAGTCCCCCTGTATGCCTCCATGCTGACACAGGCAATGGACTATGACCGGATTGTGGCAGGCTCCCGCAGCCATCAGGcc                                                                                        <  1:1869674/93‑1 (MQ=255)
  ttATCGTGCAGAAGTCCCCCTGTATGCCTCCATGCTGACACAGGCAATGGACTATGACCGGATTGTGGCAGGCTCCCGCAGCCATCAGGCCgg                                                                                      >  2:1259323/1‑93 (MQ=255)
  ttATCGTGCAGAAGTCCCCCTGTATGCCTCCATGCTGACACAGGCAATGGACTATGACCGGATTGTGGCAGGCTCCCGCAGCCATCAGGCCgg                                                                                      >  1:1253578/1‑93 (MQ=255)
   tATCGTGCAGAAGTCCCCCTGTATGCCTCCATGCTGACACAGGCAATGGACTATGACCGGATTGTGGCAGGCTCCCGCAGCCATCAGGCCGgt                                                                                     <  1:1374533/93‑1 (MQ=255)
   tATCGTGCAGAAGTCCCCCTGTATGCCTCCATGCTGACACAGGCAATGGACTATGACCGGATTGTGGCAGGCTCCCGCAGCCATCAGGCCGgt                                                                                     <  1:2112392/93‑1 (MQ=255)
    aTCGTGCAGAAGTCCCCCTGTATGCCTCCATGCTGACACAGGCAATGGACTATGACCGGATTGTGGCAGGCTCCCGCAGCCCTCAAGCCGgtg                                                                                    >  2:933647/1‑93 (MQ=255)
     tCGTGCAGAAGTCCCCCTGTATGCCTCCATGCTGACACAGGCAATGGACTATGACCGGATTGTGGCAGGCTCCCGCAGCCCTCAGGCCGgtgt                                                                                   >  1:2418515/1‑93 (MQ=255)
      cGTGCAGAAGTCCCCCTGTATGCCTCCATGCTGACACAGGCAATGGACTATGACCGGATTGTGGCAGGCTCCCGCAGCCATCAGGCCGGTGTa                                                                                  <  1:3948062/93‑1 (MQ=255)
        tGCAGAAGTCCCCCTGTATGCCTCCATGCTGACACAGGCAATGGACTATGACCGGATTGTGGCAGGCTCCCGCAGCCATCAGGCCGGTGTaaa                                                                                <  2:2520068/93‑1 (MQ=255)
        tGCAGAAGTCCCCCTGTATGCCTCCATGCTGACACAGGCAATGGACTATGACCGGATTGTGGCAGGCTCCCGCAGCCATCAGGCCGGTGTaaa                                                                                <  1:3710696/93‑1 (MQ=255)
        tGCAGAAGTCCCCCTGTATGCCTCCATGCTGACACAGGCAATGGACTATGACCGGATTGTGGCAGGCTCCCGCAGCCATCAGGCCGGTGTaaa                                                                                >  2:3302662/1‑93 (MQ=255)
        tGCAGAAGTCCCCCTGTATGCCTCCATGCTGACACAGGCAATGGACTATGACCGGATTGTGGCAGGCTCCCGCAGCCATCAGGCCGGTGTaaa                                                                                <  1:2931284/93‑1 (MQ=255)
         gCAGAAGTCCCCCTGTATGCCTCCATGCTGACACAGGCAATGGACTATGACCGGATTGTGGCAGGCTCCCGCAGCCATCAGGCCGGTGTAAAt                                                                               <  2:2545202/93‑1 (MQ=255)
          cAGAAGTCCCCCTGTATGCCTCCATGCTGACACAGGCAATGGACTATGACCGGATTGTGGCAGGCTCCCGCAGCCATCAGGCCGGTGTAAATg                                                                              <  2:1636474/93‑1 (MQ=255)
           aGAAGTCCCCCTGTATGCCTCCATGCTGACACAGGCAATGGACTATGACCGGATTGTGGCAGGCTCCCGCAGCCATCAGGCCGGTGTAAATgg                                                                             <  2:2849746/93‑1 (MQ=255)
            gAAGTCCCCCTGTATGCCTCCATGCTGACACAGGCAATGGACTATGACCGGATTGTGGCAGGCTCCCGCAGCCATCAGGCCGGTGTAAATGGt                                                                            >  1:4252834/1‑93 (MQ=255)
            gAAGTCCCCCTGTATGCCTCCATGCTGACACAGGCAATGGACTATGACCGGATTGTGGCAGGCTCCCGCAGCCATCAGGCCGGTGTAAATGGt                                                                            >  1:942195/1‑93 (MQ=255)
             aaGTCCCCCTGTATGCCTCCATGCTGACACAGGCAATGGACTATGACCGGATTGTGGCAGGCTCCCGCAGGCATCAGGCCGGTGTAAATGGTg                                                                           >  2:4556882/1‑93 (MQ=255)
              aGTCCCCCTGTATGCCTCCATGCTGACACAGGCAATGGACTATGACCGAATTCGGGCAGGGTCACTCGGCCATCAGGCCGGTGTAAATGGTGa                                                                          <  2:2351700/93‑1 (MQ=255)
               gTCCCCCTGTATGCCTCCATGCTGACACAGGCAATGGACTATGACCGGATTGTGGCAGGCTCCCGCAGCCATCAGGCCGGTGTAAATGGTGaa                                                                         <  2:2019775/93‑1 (MQ=255)
               gTCCCCCTGTATGCCTCCATGCTGACACAGGCAATGGACTATGACCGGATTGTGGCAGGCTCCCGCAGCCATCAGGCCGGTGTAAATGGTGaa                                                                         >  1:2782957/1‑93 (MQ=255)
               gTCCCCCTGTATGCCTCCATGCTGACACAGGCAATGGACTATGACCGGATTGTGGCAGGCTCCCGCAGCCATCAGGCCGGTGTAAATGGTGaa                                                                         >  2:3971034/1‑93 (MQ=255)
                tCCCCCTGTATGCCTCCATGCTGACACAGGCAATGGACTATGACCGGATTGTGGCAGGCTCCCGCAGCCATCAGGCCGGTGTAAATGGTGaaa                                                                        <  2:3116288/93‑1 (MQ=255)
                tCCCCCTGTATGCCTCCATGCTGACACAGGCAATGGACTATGACCGGATTGTGGCAGGCTCCCGCAGCCATCAGGCCGGTGTAAATGGTGaaa                                                                        <  2:3705654/93‑1 (MQ=255)
                  ccccTGTATGCCTCCATGCTGACACAGGCAATGGACTATGACCGGATTGTGGCAGGCTCCCGCCGCCATCAGGGCGGTGTAAATGGTGAAaac                                                                      >  2:4131415/1‑93 (MQ=255)
                  ccccTGTATGCCTCCATGCTGACACAGGCAATGGACTATGACCGGATTGTGGCAGGCTCCCGCAGCCATCAGGGCGGTGTTCATGGTGaaaaa                                                                      >  2:3758011/1‑92 (MQ=255)
                  ccccTGTATGCCTCCATGCTGACACAGGCAATGGACTATGACCGGATTGTGGCAGGCTCCCGCAGCCATCAGGCCGGTGTAAATGGTGAAaac                                                                      >  2:1547994/1‑93 (MQ=255)
                  ccccTGTATGCCTCCATGCTGACACAGGCAATGGACTATGACCGGATTGTGGCAGGCTCCCGCAGCCATCAGGCCGGTGTAAATGGTGAAaac                                                                      >  2:1936828/1‑93 (MQ=255)
                   cccTGTATGCCTCCATGCTGACACAGGCAATGGACTATGACCGGATTGTGTGAGGCTCCCGCCGGCATCAGGCCGGTGTACATGGAGAAaaca                                                                     >  2:852480/1‑93 (MQ=255)
                   cccTGTATGCCTCCATGCTGACACAGGCAATGGACTATGACCGGATTGTGGCAGGCTCCCGCAGCCATCAGGCCGGTGTAAATGGTGAAaaca                                                                     >  1:3398890/1‑93 (MQ=255)
                    ccTGTATGCCTCCATGCTGACACAGTCAATGGACTATGACCGGATTGTGGCAGGCTCCCGCAGCCATCAGGCCGGTGTAAATGGTGAAaacaa                                                                    <  2:3137299/93‑1 (MQ=255)
                    ccTGTATGCCTCCATGCTGACACAGGCAATGGACTATGACCGGATTGTGGCAGGCTCCCGCAGCCATCAGGCCGGTGTAAATGGTGAAaacaa                                                                    >  1:3431578/1‑93 (MQ=255)
                     cTGTATGCCTCCATGCTGACACAGGCAATGGACTATGACCGGATTGTGGCAGGCTCCCGCAGCCATCAGGCCGGTGTAAATGGTGAAaacaac                                                                   >  1:1644780/1‑93 (MQ=255)
                     cTGTATGCCTCCATGCTGACACAGGCAATGGACTATGACCGGATTGTGGCAGGCTCCCGCAGCCATCAGGCCGGTGTAAATGGTGAAaacaac                                                                   <  1:4588878/93‑1 (MQ=255)
                      tGTATGCCTCCATGCTGACACAGGCAATGGACTATGACCGGATTGTGGCAGGCTCCCGCAGCCATCAGGCCGGTGTAAATGGTGAAAacaaca                                                                  <  1:717874/93‑1 (MQ=255)
                      tGTATGCCTCCATGCTGACACAGGCAATGGACTATGACCGGATTGTGGCAGGCTCCCGCAGCCATCAGGCCGGTGTAAATGGTGAAAacaaca                                                                  <  1:820534/93‑1 (MQ=255)
                       gTATGCCTCCATGCTGACACAGGCAATGGACTATGACCGGATTGTGGCAGGCTCCCGCAGCCATCAGGCCGGTGTAAATGGTGAAAACAACAg                                                                 >  2:4302130/1‑93 (MQ=255)
                        tATGCCTCCATGCTGACACAGGCAATGGACTATGACCGGATTGTGGCAGGCTCCCGCAGCCATCAGGCCGGTGTAAATGGTGAAAACAACAGc                                                                <  1:2102541/93‑1 (MQ=255)
                        tATGCCTCCATGCTGACACAGGCAATGGACTATGACCGGATTGTGGCAGGCTCCCGCAGCCATCAGGCCGGTGTAAATGGTGAAAACAACAGc                                                                >  2:3435900/1‑93 (MQ=255)
                          tGCCTCCATGCTGACACAGGCAATGGACTATGACCGGATTGTGGCAGGCTCCCGCAGCCATCAGGCCGGTGTAAATGGTGAAAACAACAGcgt                                                              >  2:2914346/1‑93 (MQ=255)
                          tGCCTCCATGCTGACACAGGCAATGGACTATGACCGGATTGTGGCAGGCTCCCGCAGCCATCAGGCCGGTGTAAATGGTGAAAACAACAGcgt                                                              >  2:945747/1‑93 (MQ=255)
                            ccTCCATGCTGACACAGGCAATGGCCTATGACCGGATTGTGGCAGGCTCCCGCAGCCATCAGGCCGGTGTAAATGGTGAAAACAACAGcgtcc                                                            <  1:4618064/93‑1 (MQ=255)
                             cTCCATGCTGACACAGGCAATGGACTATGACCGGATTGTGGCAGGCTCCCGCAGCCATCAGGCCGGTGTAAATGGTGAAAACAACAGcgtccg                                                           >  2:1006243/1‑93 (MQ=255)
                             cTCCATGCTGACACAGGCAATGGACTATGACCGGATTGTGGCAGGCTCCCGCAGCCATCAGGCCGGTGTAAATGGTGAAAACAACAGcgtccg                                                           >  1:2609395/1‑93 (MQ=255)
                                cATGCTGACACAGGCAATGGACTATGACCGGATTGTGGCAGGCTCCCGCAGCCATCAGGCCGGTGTAAATGGTGAAAACAACAGCGTCCGtct                                                        >  2:4484374/1‑93 (MQ=255)
                                cATGCTGACACAGGCAATGGACTATGACCGGATTGTGGCAGGCTCCCGCAGCCATCAGGCCGGTGTAAATGGTGAAAACAACAGCGGCCGtct                                                        >  2:1997256/1‑93 (MQ=255)
                                 aTGCTGACACAGGCAATGGACTATGACCGGATTGTGGCAGGCTCCCGCAGCCATCAGGCCGGTGTAAATGGTGAAAACAACAGCGTCCGtctc                                                       >  1:3553124/1‑93 (MQ=255)
                                 aTGCTGACACAGGCAATGGACTATGACCGGATTGTGGCAGGCTCCCGCAGCCATCAGGCCGGTGTAAATGGTGAAAACAACAGCGTCCGtctc                                                       >  2:3624198/1‑93 (MQ=255)
                                  tGCTGACACAGGCAATGGACTATGACCGGATTGTGGCAGGCTCCCGCAGCCATCAGGCCGGTGTAAATGGTGAAAACAACAGCGTCCGTCTCa                                                      <  2:1321693/93‑1 (MQ=255)
                                  tGCTGACACAGGCAATGGACTATGACCGGATTGTGGCAGGCTCCCGCAGCCATCAGGCCGGTGTAAATGGTGAAAACAACAGAGTCCGTCTCa                                                      >  1:3559617/1‑93 (MQ=255)
                                   gCTGACACAGGCAATGGACTATGACCGGATTGTGGCAGGCTCCCGCAGGCATCAGGCCGGTGTAAATGGTGAAAACAACAGCGTCCGTCTCAg                                                     >  2:3612581/1‑93 (MQ=255)
                                    cTGACACAGGCAATGGACTATGACCGGATTGTGGCAGGCTCCCGCAGCCATCAGGCCGGTGTAAATGGTGAAAACAACAGCGTCCGTCTCAGc                                                    <  2:3015917/93‑1 (MQ=255)
                                     tGACACAGGCAATGGACTATGACCGGATTGGGGCAGGCTCCCGCAGCCATCCGGCCGGTGTAAATGGTGAAAACAACAGCGTCGGTCTCAGCa                                                   >  1:1175400/1‑93 (MQ=255)
                                      gACACAGGCAATGGACTATGACCGGATTGTGGCAGGCTCCCGCAGCCATCAGGCCGGTGTAAATGGTGAAAACAACAGCGTCCGTCTCAGCAt                                                  <  1:3697026/93‑1 (MQ=255)
                                      gACACAGGCAATGGACTATGACCGGATTGTGGCAGGCTCCCGCAGCCATCAGGCCGGTGTAAATGGTGAAAACAACAGCGTCCGTCTCAGCAt                                                  <  1:50358/93‑1 (MQ=255)
                                        cacaGGCAATGGACTATGACCGGATTGTGGCAGGCTCCCGCAGCCATCAGGCCGGTGTAAATGGTGAAAACAACAGCGTCCGTCTCAGCATTc                                                >  1:2374432/1‑93 (MQ=255)
                                           aGGCAATGGACTATGACCGGATTGTGGCAGGCTCCCGCAGCCATCAGGCCGGTGTAAATGGTGAAAACAACAGCGTCCGTCTCAGCATTCAgg                                             <  1:1283920/93‑1 (MQ=255)
                                            ggCAATGGACTATGACCGGATTGTGGCAGGCTCCCGCGGCCATCAGGCCGGCGTAAATGGTGAAAACAACACCGGCCGTCTCAACAATAAggg                                            >  2:4492672/1‑93 (MQ=255)
                                             gCAATGGACTATGACCGGATTGTGGCAGGCTCCCGCAGCCATCAGGCCGGTGTAAATGGTGAAAACAACAGCGTCCGTCTCAGCATTCAGGGc                                           <  2:2205635/93‑1 (MQ=255)
                                               aaTGGACTATGACCGGATTGTGGCAGGCTCCCGCAGCCATCAGGGCGGTGTAAATGGTGAAAACAACAGCGTCCGTCTCAGCATTCAGGGCgg                                         >  2:2356745/1‑93 (MQ=255)
                                                aTGGACTATGACCGGATTGTGGCAGTCTCCCGCAGCCATCAGGCCGGTGTAAATGGTGAAAACAACAGCGTCCGTCTCAGCATTCAGGGCGGt                                        <  1:2472366/93‑1 (MQ=255)
                                                 tGGACTATGACCGGATTGTGGCAGGCTCCCGCAGCCATCAGGCCGGTGTAAATGGTGAAAACAACAGCGTCCGTCTCAGCATTCAGGGCGGTc                                       <  1:2961015/93‑1 (MQ=255)
                                                   gACTATGACCGGATTGTGGCAGGCTCCCGCAGCCATCAGGCCGGTGTAAATGGTGAAAACAACAGCGTCCGTCTCAGCATTCAGGGCGGTCAt                                     <  1:1767023/93‑1 (MQ=255)
                                                    aCTATGACCGGATTGTGGCAGGCTCCCGCAGCCATCAGGCCGGTGTAAATGGTGAAAACAACAGCGTCCGTCTCAGCATTCAGGGCGGTCAtc                                    >  2:1702077/1‑93 (MQ=255)
                                                    aCTATGACCGGATTGTGGCAGGCTCCCGCAGCCATCAGGCCGGTGTAAATGGTGAAAACAACAGCGTCCGTCTCAGCATTCAGGGCGGTCAtc                                    <  1:1352356/93‑1 (MQ=255)
                                                     cTATGACCGGATTGTGGCAGGCTCCCGCAGCCATCAGGCCGGTGTAAATGGTGAAAACAACAGCGTCCGTCTCAGCATTCAGGGCGGTCAtct                                   <  2:1791095/93‑1 (MQ=255)
                                                      tATGACCGGATTGTGGCAGGCTCCCGCCGCCATCAGGCCGGTGGAAATGGTGAAAATAACAGCGGCCGTCTCAGCATTCCGGGCGGTCAtctc                                  >  2:704815/1‑93 (MQ=255)
                                                      tATGACCGGATTGTGGCAGGCTCCCGCAGCCATCAGGCCGGTGTAAATGGTGAAAACAACAGCGTCCGTCTCAGCATTCAGGGCGGTCAtctc                                  <  1:951365/93‑1 (MQ=255)
                                                       aTGACCGGATGGTGGCAGGCTCCCGCAGCCATCAGGCCGGTGTAAATGGTGAAAACAACAGCGTCCGTCTCAGCATTCAGGGCGGTCATCTCg                                 <  2:1186368/93‑1 (MQ=255)
                                                        tGACCGGATTGTGGCAGGCTCCCGCAGCCATCAGGCCGGTGTAAATGGTGAAAACAACAGCGTCCGTCTCAGCATTCAGGGCGGTCATCTCgg                                >  2:2684031/1‑93 (MQ=255)
                                                         gACCGGATTGTGGCAGGCTCCCGCAGCCATCAGGCCGGTGTAAATGGTGAAAACAACAGCGTCCGTCTCAGCATTCAGGGCGGTCATCTCGGt                               <  1:182054/93‑1 (MQ=255)
                                                         gACCGGATTGTGGCAGGCTCCCGCAGCCATCAGGCCGGTGTAAATGGTGAAAACAACAGCGTCCGTCTCAGCATTCAGGGCGGTCATCTCGGt                               <  2:4347159/93‑1 (MQ=255)
                                                           ccGGATTGTGGCAGGCTCCCGCAGCCATCAGGCCGGTGTAAATGGTGAAAACAACCGCGTCCGTCTCAGCATTCAGGGCGGTCATCTCGGTCa                             >  2:2745175/1‑93 (MQ=255)
                                                              gATTGTGGCAGGCTCCCGCAGCCATCAGGCCGGTGTAAATGGTGAAAACAACAGCGTCCGTCTCAGCATTCAGGGCGGTCATCTCGGTCACGa                          >  2:4153424/1‑93 (MQ=255)
                                                               aTTGTGGCAGGCTCCCGCAGCCATCAGGCCGGTGTAAATGGTGAAAACAACAGCGTCCGTCTCAGCATTCAGGGCGGTCATCTCGGTCACGAt                         <  1:4424893/93‑1 (MQ=255)
                                                               aTTGTGGCAGGCTCCCGCAGCCAACAGGCCGGTGTAAATGGTGAAAACAACAGCGTCCGTCTCAGCATTCAGGGCGGTCATCTCGGTCACGAt                         >  1:4400580/1‑93 (MQ=255)
                                                                 tgtgGCAGGCTCCCGCAGCCATCAGGCCGGTGTAAATGGTGAAAACAACAGCGTCCGTCTCAGCATTCAGGGCGGTCATCTCGGTCACGATaa                       <  2:709433/93‑1 (MQ=255)
                                                                  gtgGCAGGCTCCCGCAGCCATCAGGCCGGTGTAAATGGTGAAAACAACAGCGTCCGTCTCAGCATTCAGGGCGGTCATCTCGGTCACGATAAc                      <  2:1818640/93‑1 (MQ=255)
                                                                   tgGCAGGCTCCCGCAGCCATCAGGCCGGTGTAAATGGTGAAAACAACAGCGTCCGTCTCAGCATTCAGGGCGGTCATCTCGGTCACGATAACa                     <  1:1223935/93‑1 (MQ=255)
                                                                    tgCAGGCGCCCGCAGCCATCAGGCCGGTGTAAATGGTGAAAACAACAGCGTCCGTCTCAGCATTCAGGGCGGTCATCTCGGTCCCGATAACaa                    <  1:1330530/92‑1 (MQ=255)
                                                                    ggCAGGCTCCCGCAGCCATCAGGCCGGTGTAAATGGTGAAAACAACAGCGTCCGTCTCAGCATTCAGGGCGGTCATCTCGGTCACGATAACaa                    <  1:1159845/93‑1 (MQ=255)
                                                                     gCAGGCTCCCGCAGCCATCAGGCCGGTGTAAATGGTGAAAACAACAGCGTCCGTCTCAGCATTCAGGGCGGTCATCTCGGTCACGATAACAAt                   >  1:879502/1‑93 (MQ=255)
                                                                      cAGGCTCCCGCAGCCATCAGGCCGGTGTAAATGGTGAAAACAACAGCGTCCGTCTCAGCATTCAGGGCGGTCATCTCGGTCACGATAACAATg                  <  1:3683502/93‑1 (MQ=255)
                                                                       aGGCTCCCGCAGCCATCAGGCCGGTGTAAATGGTGAAAACAACAGCGTCCGTCTCAGCATTCAGGGCGGTCATCTCGGTCACGATAACAATgg                 <  1:1905290/93‑1 (MQ=255)
                                                                        ggCTCCCGCAGCCATCAGGCCGGTGTAAATGGTGAAAACAACAGCGTCCGTCTCAGCATTCAGGGCGGTCATCTCGGTCACGATAACAATGGc                >  2:2167250/1‑93 (MQ=255)
                                                                             ccGCAGCCATCAGGCCGGTGTAAATGGTGAAAACAACAGCGTCCGTCTCAGCATTCAGGGCGGTCATCTCGGTCACGATAACAATGGCGGTAt           >  2:596294/1‑93 (MQ=255)
                                                                             ccGCAGCCATCAGGCCGGTGTAAATGGTGAAAACAACAGCGTCCGTCTCAGCATTCAGGGCGGTCATCTCGGTCACGATAACAATGGCGGTAt           <  1:4489582/93‑1 (MQ=255)
                                                                             ccGCAGCCATCAGGCCGGTGTAAATGGTGAAAACAACAGCGTCCGTCTCAGCATTCAGGGCGGTCATCTCGGTCACGATAACAATGGCGGTAt           >  2:736510/1‑93 (MQ=255)
                                                                               gCAGCCATCAGGCCGGTGTAAATGGTGAAAACAACAGCGTCCGTCTCAGCATTCAGGGCGGTCATCTCGGTCACGATAACAATGGCGGTATTg         >  2:3064129/1‑93 (MQ=255)
                                                                               gCAGCCATCAGGCCGGTGTAAATGGTGAAAACAACAGCGTCCGTCTCAGCATTCAGGGCGGTCATCTCGGTCACGATAACAATGGCGGTATTg         <  1:3799551/93‑1 (MQ=255)
                                                                                cAGCCATCAGGCCGGTGTAAATGGTGAAAACAACAGCGTCCGTCTCAGCATTCAGGGCGGTCATCTCGGTCACGATAACAATGGCGGTATTGc        <  1:1947029/93‑1 (MQ=255)
                                                                                 aGCCATCAGGCCGGTGTAAATGGTGAAAACAACAGCGTCCGTCTCAGCATTCAGGGCGGTCATCTCGGTCACGATAACAATGGCGGTATTGcc       >  2:1110548/1‑93 (MQ=255)
                                                                                  gCCATCAGGCCGGTGTAAATGGTGAAAACAACAGCGTCCGTCTCAGCATTCAGGGCGGTCATCTCGGTCACGATAACAATGGCGGTATTGccc      >  2:3803340/1‑93 (MQ=255)
                                                                                  gCCATCAGGCCGGTGTAAATGGTGAAAACAACAGCGTCCGTCTCAGCATTCAGGGCGGTCATCTCGGTCACGATAACAATGGCGGTATTGccc      >  1:1769834/1‑93 (MQ=255)
                                                                                  gCCATCAGGCCGGTGTAAATGGTGAAAACAACAGCGTCCGTCTCAGCATTCAGGGCGGTCATCTCGGTCACGATAACAATGGCGGTATTGccc      >  1:2964470/1‑93 (MQ=255)
                                                                                   ccATCAGGCCGGTGTAAATGGTGAAAACAACAGCGTCCGTCTCAGCATTCAGGGCGGTCATCTCGGTCACGATAACAATGGCGGTATTGCCCg     >  1:3895960/1‑93 (MQ=255)
                                                                                   ccATCAGGCCGGTGTAAATGGTGAAAACAACAGCGTCCGTCTCAGCATTCAGGGCGGTCATCTCGGTCACGATAACAATGGCGGTATTGCCCg     <  2:2091620/93‑1 (MQ=255)
                                                                                      tCAGGCCGGTGTAAATGGTGAAAACAACAGCGTCCGTCTCAGCATTCAGGGCGGTCATCTCGGTCACGATAACAATGGCGGTATTGCCCGTgg  >  1:3973336/1‑93 (MQ=255)
                                                                                      tCAGGCCGGTGTAAATGGTGAAAACAACAGCGTCCGTCTCAGCATTCAGGGCGGTCATCTCGGTCACGATAACAATGGCGGTATTGCCCGTgg  <  2:1615857/93‑1 (MQ=255)
                                                                                          |                                                                                        
GCTTATCGTGCAGAAGTCCCCCTGTATGCCTCCATGCTGACACAGGCAATGGACTATGACCGGATTGTGGCAGGCTCCCGCAGCCATCAGACCGGTGTAAATGGTGAAAACAACAGCGTCCGTCTCAGCATTCAGGGCGGTCATCTCGGTCACGATAACAATGGCGGTATTGCCCGTGG  >  NC_000913/2071673‑2071851

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 18 ≤ ATCG/ATCG < 26 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

BRESEQ :: bam2aln output
AATGCTTATCGTGCAGAAGTCCCCCTGTATGCCTCCATGCTGACACAGGCAATGGACTATGACCGGATTGTGGCAGGCTCCCGCAGCCATCAGACCGGTGTAAATGGTGAAAACAACAGCGTCCGTCTCAGCATTCAGGGCGGTCATCTCGGTCACGATAACAATGGCGGTATTGCCCGTGG  >  NC_000913/2071670‑2071851
                                                                                             |                                                                                        
AATGCTTATCGTGCAGAAGTCCGCCTGTATGCCTCCATGCTGACACAGGCAATGGACTATGACCGGATTGTGGCAGGCTCCCGCAGCCATCAGG                                                                                          <  SRR4302535.672631/94‑1 (MQ=60)
 ATGCTTAGCGTGCAGAAGTCACCCTGTAGGCCTCCATGCTGACACAGGCAATGGACTATGACCGGATTGTGGCAGGCTCCCGCAGCCATCAGGC                                                                                         <  SRR4302535.2155169/94‑1 (MQ=60)
  TGCTTATCGTGCAGAAGTCCCCCTGTATGCCTCCATGCTGACACAGGCAATGGACTATGACCGGATTGTGGCAGGCTCCCGCAGCCATCAGGCC                                                                                        >  SRR4302535.3267519/1‑94 (MQ=60)
  TGCTTATCGTGCAGAAGTCCCCCTGTATGCCTCCATGCTGACACAGGCAATGGACTATGACCGGATTGTGGCAGGCTCCCGCAGCCATCAGGCC                                                                                        >  SRR4302535.780959/1‑94 (MQ=60)
  TGCTTATCGTGCAGAAGCCCCCCTGTATGCCTCCATGCTGACACAGGCAATGGACTATGACCGGATTGTGGCAGGCTCCCGCAGCCATCAGGCC                                                                                        >  SRR4302535.4563399/1‑94 (MQ=60)
   GCTTATCGTGCAGAAGTCCCCCTGTATGCCTCCATGCTGACACAGGCAATGGACTATGACCGGATTGTGGCAGGCTCCCGCAGCCATCAGGCCG                                                                                       <  SRR4302535.928193/94‑1 (MQ=60)
   GCTTATCGTGCAGAAGTCCCCCTGTATGCCTCCATGCTGACACAGGCAATGGACTATGACCGGATTGTGGCAGGCTCCCGCAGCCATCAGGCCG                                                                                       <  SRR4302535.1883152/94‑1 (MQ=60)
    CTTATCGTGCAGAAGTCCCCCTGTATGCCTCCATGCTGACACAGGCAATGGACTATGACCGGATTGTGGCAGGCTCCCGCAGCCATCAGGCCGG                                                                                      >  SRR4302535.1262542/1‑94 (MQ=60)
      TATCGTGCAGAAGTCCCCCTGTATGCCTCCATGCTGACACAGGCAATGGACTATGACCGGATTGTGGCAGGCTCCCGCAGCCATCAGGCCGGTG                                                                                    <  SRR4302535.1384354/94‑1 (MQ=60)
      TATCGTGCAGAAGTCCCCCTGTATGCCTCCATGCTGACACAGGCAATGGACTATGACCGGATTGTGGCAGGCTCCCGCAGCCATCAGGCCGGTG                                                                                    <  SRR4302535.2127639/94‑1 (MQ=60)
       ATCGTGCAGAAGTCCCCCTGTATGCCTCCATGCTGACACAGGCAATGGACTATGACCGGATTGTGGCAGGCTCCCGCAGCCCTCAGGCCGGTGT                                                                                   >  SRR4302535.2435928/1‑94 (MQ=60)
         CGTGCAGAAGTCCCCCTGTATGCCTCCATGCTGACACAGGCAATGGACTATGACCGGATTGTGGCAGGCTCCCGCAGCCATCAGGCCGGTGTAA                                                                                 <  SRR4302535.3975015/94‑1 (MQ=60)
          GTGCAGAAGTCCCCCTGTATGCCTCCATGCTGACACAGGCAATGGACTATGACCGGATTGTGGCAGGCTCCCGCAGCCATCAGGCCGGTGTAAA                                                                                >  SRR4302535.126699/1‑94 (MQ=60)
           TGCAGAAGTCCCCCTGTATGCCTCCATGCTGACACAGGCAATGGACTATGACCGGATTGTGGCAGGCTCCCGCAGCCATCAGGCCGGTGTAAAT                                                                               <  SRR4302535.2951925/94‑1 (MQ=60)
           TGCAGAAGTCCCCCTGTATGCCTCCATGCTGACACAGGCAATGGACTATGACCGGATTGTGGCAGGCTCCCGCAGCCATCAGGCCGGTGTAAAT                                                                               <  SRR4302535.3736398/94‑1 (MQ=60)
              AGAAGTCCCCCTGTATGCCTCCATGCTGACACAGGCAATGGACTATGACCGGATTGTGGCAGGCTTCCGCAGCCATCAGGCCGGTGTAAATGGT                                                                            >  SRR4302535.716123/1‑94 (MQ=60)
              AGAAGTCCCCCTGTATGCCTCCATGCTGACACAGGCAATGGACTATGACCGGATTGTGGCAGGCTCCCGCAGCCATCAGGCCGGTGTAAATGGT                                                                            >  SRR4302535.948866/1‑94 (MQ=60)
              AGAAGTCCCCCTGTATGCCTCCATGCTGACACAGGCAATGGACTATGACCGGATTGTGGCAGGCTCCCGCAGCCATCAGGCCGGTGTAAATGGT                                                                            >  SRR4302535.4281973/1‑94 (MQ=60)
                 AGTCCCCCTGTATGCCTCCATGCTGACACAGGCAATGGACTATGACCGGATTGTGGCAGGCTCCCGCAGCCATCAGGCCGGTGTAAATGGTGAA                                                                         >  SRR4302535.2802763/1‑94 (MQ=60)
                     CCCCTGTATGCCTCCATGCTGACACAGGCAATGGACTATGACCGGATTGTGGCAGGCTCCCGCAGCCATCAGGCCGGTGTAAATGGTGAAAACA                                                                     >  SRR4302535.3422540/1‑94 (MQ=60)
                      CCCTGTATGCCTCCATGCTGACACAGGCAATGGACTATGACCGGATTGTGGCAGGCTCCCGCAGCCATCAGGCCGGTGTAAATGGTGAAAACAA                                                                    >  SRR4302535.3455427/1‑94 (MQ=60)
                       CCTGTATGCCTCCATGCTGACACAGGCAATGGACTATGACCGGATTGTGGCAGGCTCCCGCAGCCATCAGGCCGGTGTAAATGGTGAAAACAAC                                                                   >  SRR4302535.1656667/1‑94 (MQ=60)
                       CCTGTATGCCTCCATGCTGACACAGGCAATGGACTATGACCGGATTGTGGCAGGCTCCCGCAGCCATCAGGCCGGTGTAAATGGTGAAAACAAC                                                                   <  SRR4302535.1800894/94‑1 (MQ=60)
                        CTGTATGCCTCCATGCTGACACAGGCAATGGACTATGACCGGATTGTGGCAGGCTCCCGCAGCCATCAGGCCGGTGTAAATGGTGAAAACAACA                                                                  <  SRR4302535.4620120/94‑1 (MQ=60)
                         TGTATGCCTCCATGCTGACACAGGCAATGGACTATGACCGGATTGTGGCAGGCTCCCGCAGCCATCAGGCCGGTGTAAATGGTGAAAACAACAG                                                                 <  SRR4302535.722917/94‑1 (MQ=60)
                         TGTATGCCTCCATGCTGACACAGGCAATGGACTATGACCGGATTGTGGCAGGCTCCCGCAGCCATCAGGCCGGTGTAAATGGTGAAAACAACAG                                                                 <  SRR4302535.826291/94‑1 (MQ=60)
                           TATGCCTCCATGCTGACACAGGCAATGGACTATGACCGGATTGTGGCAGGCTCCCGCAGCCATCAGGCCGGTGTAAATGGTGAAAACAACAGCG                                                               <  SRR4302535.2117704/94‑1 (MQ=60)
                               CCTCCATGCTGACACAGGCAATGGCCTATGACCGGATTGTGGCAGGCTCCCGCAGCCATCAGGCCGGTGTAAATGGTGAAAACAACAGCGTCCG                                                           <  SRR4302535.4649447/94‑1 (MQ=60)
                               CCTCCATGCTGACACAGGCAATGGACTATGACCGGATTGTGGCAGGCTCCCGCAGCCATCAGGCCGGTGTAAATGGTGAAAACAACAGCGTCCG                                                           >  SRR4302535.2628119/1‑94 (MQ=60)
                                   CATGCTGACACAGGCAATGGACTATGACCGGATTGTGGCAGGCTCCCGCAGCCATCAGGCCGGTGTAAATGGTGAAAACAACAGCGTCCGTCTC                                                       >  SRR4302535.3577780/1‑94 (MQ=60)
                                    ATGCTGACACAGGCAATGGACTATGACCGGATTGTGGCAGGCTCCCGCAGCCATCAGGCCGGTGTAAATGGTGAAAACAACAGAGTCCGTCTCA                                                      >  SRR4302535.3584301/1‑94 (MQ=60)
                                       CTGACACAGGCAATGGACTATGACCGGATTGGGGCAGGCTCCCGCAGCCATCCGGCCGGTGTAAATGGTGAAAACAACAGCGTCGGTCTCAGCA                                                   >  SRR4302535.1183791/1‑94 (MQ=60)
                                         GACACAGGCAATGGACTATGACCGGATTGTGGCAGGCTCCCGCAGCCATCAGGCCGGTGTAAATGGTGAAAACAACAGCGTCCGTCTCAGCATT                                                 <  SRR4302535.3722610/94‑1 (MQ=60)
                                         GACACAGGCAATGGACTATGACCGGATTGTGGCAGGCTCCCGCAGCCATCAGGCCGGTGTAAATGGTGAAAACAACAGCGTCCGTCTCAGCATT                                                 <  SRR4302535.50731/94‑1 (MQ=60)
                                          ACACAGGCAATGGACTATGACCGGATTGTGGCAGGCTCCCGCAGCCATCAGGCCGGTGTAAATGGTGAAAACAACAGCGTCCGTCTCAGCATTC                                                >  SRR4302535.2391487/1‑94 (MQ=60)
                                            ACAGGCAATGGACTATGACCGGATTGTGGCAGGCTCCCGCAGCCATCAGGCCGGTGTAAATGGTGAAAACAACAGCGTCCGTCTCAGCATTCAG                                              <  SRR4302535.4243491/94‑1 (MQ=60)
                                              AGGCAATGGACTATGACCGGATTGTGGCAGGCTCCCGCAGCCATCAGGCCGGTGTAAATGGTGAAAACAACAGCGTCCGTCTCAGCATTCAGGG                                            <  SRR4302535.1293071/94‑1 (MQ=60)
                                                  AATGGACTATGACCGGATTGTGGCAGGCTCCCGCAGCCATCAGGCCGGTGTAAATGGTGAAAACAACAGCGTCCGTCTCAGCATTCAGGGCGGT                                        <  SRR4302535.1568354/94‑1 (MQ=60)
                                                   ATGGACTATGACCGGATTGTGGCAGTCTCCCGCAGCCATCAGGCCGGTGTAAATGGTGAAAACAACAGCGTCCGTCTCAGCATTCAGGGCGGTC                                       <  SRR4302535.2490191/94‑1 (MQ=60)
                                                    TGGACTATGACCGGATTGTGGCAGGCTCCCGCAGCCATCAGGCCGGTGTAAATGGTGAAAACAACAGCGTCCGTCTCAGCATTCAGGGCGGTCA                                      <  SRR4302535.2981800/94‑1 (MQ=60)
                                                      GACTATGACCGGATTGTGGCAGGCTCCCGCAGCCATCAGGCCGGTGTAAATGGTGAAAACAACAGCGTCCGTCTCAGCATTCAGGGCGGTCATC                                    <  SRR4302535.1779835/94‑1 (MQ=60)
                                                       ACTATGACCGGATTGTGGCAGGCTCCCGCAGCCATCAGGCCGGTGTAAATGGTGAAAACAACAGCGTCCGTCTCAGCATTCAGGGCGGTCATCT                                   <  SRR4302535.1362034/94‑1 (MQ=60)
                                                         TATGACCGGATTGTGGCAGGCTCCCGCAGCCATCAGGCCGGTGTAAATGGTGAAAACAACAGCGTCCGTCTCAGCATTCAGGGCGGTCATCTCG                                 <  SRR4302535.958098/94‑1 (MQ=60)
                                                           TGACCGGATTGTGGCAGGCTCCCGCAGCCATCAGGCCGGTGTAAATGGTGAAAACAACAGCGTCCGTCTCAGCATTCAGGGCGGTCATCTCGGT                               >  SRR4302535.2423698/1‑94 (MQ=60)
                                                            GACCGGATTGTGGCAGGCTCCCGCAGCCATCAGGCCGGTGTAAATGGTGAAAACAACAGCGTCCGTCTCAGCATTCAGGGCGGTCATCTCGGTC                              <  SRR4302535.183314/94‑1 (MQ=60)
                                                              CCGGATTGTGGCAGGCTCCCGCAGCCATCAGGCCGGTGTAAATGGTGAAAACAACAGCGTCCGTCTCAGCATTCAGGGCGGTCATCTCGGTCAC                            <  SRR4302535.2088695/94‑1 (MQ=60)
                                                                 GATTGTGGCAGGCTCCCGCAGCCATCAGGCCGGTGTAAATGGTGAAAACAACAGCGTCCGTCTCAGCATTCAGGGCGGTCATCTCGGTCACGAT                         <  SRR4302535.3889422/94‑1 (MQ=60)
                                                                 GATTGTGGCAGGCTCCCGCAGCCAACAGGCCGGTGTAAATGGTGAAAACAACAGCGTCCGTCTCAGCATTCAGGGCGGTCATCTCGGTCACGAT                         >  SRR4302535.4430695/1‑94 (MQ=60)
                                                                  ATTGTGGCAGGCTCCCGCAGCCATCAGGCCGGTGTAAATGGTGAAAACAACAGCGTCCGTCTCAGCATTCAGGGCGGTCATCTCGGTCACGATA                        <  SRR4302535.4455200/94‑1 (MQ=60)
                                                                      TGGCAGGCTCCCGCAGCCATCAGGCCGGTGTAAATGGTGAAAACAACAGCGTCCGTCTCAGCATTCAGGGCGGTCATCTCGGTCACGATAACAA                    <  SRR4302535.1232691/94‑1 (MQ=60)
                                                                       TGCAGGCGCCCGCAGCCATCAGGCCGGTGTAAATGGTGAAAACAACAGCGTCCGTCTCAGCATTCAGGGCGGTCATCTCGGTCCCGATAACAAT                   <  SRR4302535.1340020/94‑1 (MQ=60)
                                                                       GGCAGGCTCCCGCAGCCATCAGGCCGGTGTAAATGGTGAAAACAACAGCGTCCGTCTCAGCATTCAGGGCGGTCATCTCGGTCACGATAACAAT                   <  SRR4302535.1168134/94‑1 (MQ=60)
                                                                       GGCAGGCTCCCGCAGCCATCAGGCCGGTGTAAATGGTGAAAACAACAGCGTCCGTCTCAGCATTCAGGGCGGTCATCTCGGTCACGATAACAAT                   >  SRR4302535.885731/1‑94 (MQ=60)
                                                                         CAGGCTCCCGCAGCCATCAGGCCGGTGTAAATGGTGAAAACAACAGCGTCCGTCTCAGCATTCAGGGCGGTCATCTCGGTCACGATAACAATGG                 <  SRR4302535.3708990/94‑1 (MQ=60)
                                                                          AGGCTCCCGCAGCCATCAGGCCGGTGTAAATGGTGAAAACAACAGCGTCCGTCTCAGCATTCAGGGCGGTCATCTCGGTCACGATAACAATGGC                <  SRR4302535.1919002/94‑1 (MQ=60)
                                                                           GGCTCCCGCAGCCATCAGGCCGGTGTAAATGGTGAAAACAACAGCGTCCGTCTCAGCATTCAGGGCGGTCATCTCGGTCACGATAACAATGGCG               <  SRR4302535.2886406/94‑1 (MQ=60)
                                                                                CCGCAGCCATCAGGCCGGTGTAAATGGTGAAAACAACAGCGTCCGTCTCAGCATTCAGGGCGGTCATCTCGGTCACGATAACAATGGCGGTATT          <  SRR4302535.4520399/94‑1 (MQ=60)
                                                                                 CGCAGCCATCAGGCCGGTGTAAATGGTGAAAACAACAGCGTCCGTCTCAGAATTCAGGGCGGTCATCTCGGTCACGGTAACAATGGAGGTACTG         >  SRR4302535.3661519/1‑94 (MQ=60)
                                                                                  GCAGCCATCAGGCCGGTGTAAATGGTGAAAACAACAGCGTCCGTCTCAGCATTCAGGGCGGTCATCTCGGTCACGATAACAATGGCGGTATTGC        <  SRR4302535.3825742/94‑1 (MQ=60)
                                                                                   CAGCCATCAGGCCGGTGTAAATGGTGAAAACAACAGCGTCCGTCTCAGCATTCAGGGCGGTCATCTCGGTCACGATAACAATGGCGGTATTGCC       <  SRR4302535.1961047/94‑1 (MQ=60)
                                                                                    AGCCATCAGGCCGGTGTAAATGGTGAAAACAACAGCGTCCGTCTCAGCATTCAGGGCGGTCATCTCGGTCACGATAACAATGGCGGTATTGCCC      >  SRR4302535.2985274/1‑94 (MQ=60)
                                                                                    AGCCATCAGGCCGGTGTAAATGGTGAAAACAACAGCGTCCGTCTCAGCATTCAGGGCGGTCATCTCGGTCACGATAACAATGGCGGTATTGCCC      >  SRR4302535.1782664/1‑94 (MQ=60)
                                                                                     GCCATCAGGCCGGTGTAAATGGTGAAAACAACAGCGTCCGTCTCAGCATTCAGGGCGGTCATCTCGGTCACGATAACAATGGCGGTATTGCCCG     >  SRR4302535.3922659/1‑94 (MQ=60)
                                                                                        ATCAGGCCGGTGTAAATGGTGAAAACAACAGCGTCCGTCTCAGCATTCAGGGCGGTCATCTCGGTCACGATAACAATGGCGGTATTGCCCGTGG  >  SRR4302535.4000476/1‑94 (MQ=60)
                                                                                             |                                                                                        
AATGCTTATCGTGCAGAAGTCCCCCTGTATGCCTCCATGCTGACACAGGCAATGGACTATGACCGGATTGTGGCAGGCTCCCGCAGCCATCAGACCGGTGTAAATGGTGAAAACAACAGCGTCCGTCTCAGCATTCAGGGCGGTCATCTCGGTCACGATAACAATGGCGGTATTGCCCGTGG  >  NC_000913/2071670‑2071851

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 2 ≤ ATCG/ATCG < 20 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑