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 I1 R1 1357 179.3 9500450 96.1% 9129932 93.0

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 1,839,782 A→G H90R (CAC→CGC)  b1759 → hypothetical protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009131,839,7820AG100.0% 389.9 / NA 121H90R (CAC→CGC) b1759hypothetical protein
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base G (66/55);  total (66/55)

Only 100 of 126 total aligned reads displayed.

CGAAGCAACTGTGGGTGAATATGTTGCCAGCCATCAGCGAGAAGTTTCGGGGCGGATTATCCATCTTCATGCCTGGCACGTACCCGACTTCCACGGGACGTTACAGGCACATGAACATCAGGCGCTGGTCTGGTGCTCACCTGAAGAGGCGCTGCAATATCCGCTGGCCCCTGCTGACATT  >  NC_000913/1839690‑1839870
                                                                                            |                                                                                        
  aaGCAACTGTGGGTGAATATGTTGCCAGCCATCAGCGAGAAGTTTCGGGGCGGATTATCCATCTTCATGCCTGGCACGTACCCGACTTCcgcg                                                                                        >  1:1333908/1‑93 (MQ=255)
  aaGCAACTGTGGGTGAATATGTTGCCAGCCATCAGCGAGAAGTTTCGGGGCGGATTATCCATCTTCATGCCTGGCACGTACCCGACTTCcgcg                                                                                        >  1:2104058/1‑93 (MQ=255)
  aaGCAACTGTGGGTGAATATGTTGCCAGCCATCAGCGAGAAGTTTCGGGGCGGATTATCCATCTTCATGCCTGGCACGTACCCGACTTCcgcg                                                                                        <  1:2095652/93‑1 (MQ=255)
   aGCAACTGTGGGTGAATATGTTGCCAGCCATCAGCGAGAAGTTTCGGGGCGGATTATCCATCTTCATGCCTGGCACGTACCCGACTTCCGCgg                                                                                       >  2:3064398/1‑93 (MQ=255)
    gCAACTGTGGGTGAATATGTTGCCAGCCATCAGCGAGAAGTTTCGGGGCGGATTATCCATCTTCATGCCTGGCACGTACCCGACTTCCGCggg                                                                                      <  1:1223682/93‑1 (MQ=255)
     cAACTGTGGGTGAATATGTTGCCAGCCATCAGCGAGAAGTTTCGGGGCGGATTATCCATCTTCATGCCTGGCACGTACCCGACTTCCGCGGGa                                                                                     <  1:66412/93‑1 (MQ=255)
      aaCTGTGGGTGAATATGTTGCCAGCCATCAGCGAGAAGTTTCGGGGCGGATTATCCATCTTCATGCCTGGCACGTACCCGACTTCCGCGGGAc                                                                                    >  1:266641/1‑93 (MQ=255)
      aaCTGTGGGTGAATATGTTGCCAGCCATCAGCGAGAAGTTTCGGGGCGGATTATCCATCTTCATGCCTGGCACGTACCCGACTTCCGCGGGAc                                                                                    <  2:4556606/93‑1 (MQ=255)
       aCTGTGGGTGAATATGTTGCCAGCCATCAGCGAGAAGTTTCGGGGCGGATTATCCATCTTCATGCCTGGCACGTACCCGACTTCCGCGGGACg                                                                                   <  2:3155565/93‑1 (MQ=255)
        cTGTGGGTGAATATGTTGCCAGCCATCAGCGAGAAGTTTCGGGGCGGATTATCCATCTTCATGCCTGGCACGTACCCGACTTCCGCGGGACGt                                                                                  <  1:3472456/93‑1 (MQ=255)
        cTGTGGGTGAATATGTTGCCAGCCATCAGCGAGAAGTTTCGGGGCGGATTATCCATCTTCATGCCTGGCACGTACCCGACTTCCGCGGGACGt                                                                                  <  2:1226728/93‑1 (MQ=255)
        cTGTGGGTGAATATGTTGCCAGCCATCAGCGAGAAGTTTCGGGGCGGATTATCCATCTTCATGCCTGGCACGTACCCGACTTCCGCGGGACGt                                                                                  <  1:1399500/93‑1 (MQ=255)
           tgGGTGAATATGTTGCCAGCCATCAGCGAGAAGTTTCGGGGCGGATTATCCATCTTCATGCCTGGCACGTACCCGACTTCCGCGGGACGTTAc                                                                               <  1:1818811/93‑1 (MQ=255)
           tgGGTGAATATGTTGCCAGCCATCAGCGAGAAGTTTCGGGGCGGATTATCCATCTTCATGCCTGGCACGTACCCGACTTCCGCGGGACGTTAc                                                                               >  2:3418495/1‑93 (MQ=255)
             ggTGAATATGTTGCCAGCCATCAGCGAGAAGTTTCGGGGCGGATTATCCATCTTCATGCCTGGCACGTACCCGACTTCCGCGGGACGTTACAg                                                                             <  1:276685/93‑1 (MQ=255)
              gTGAATATGTTGCCAGCCATCAGCGAGAAGTTTCGGGGCGGATTATCCATCTTCATGCCTGGCACGTACCCGACTTCCGCGGGACGTTACAgg                                                                            >  2:3930666/1‑93 (MQ=255)
                gAATATGTTGCCAGCCATCAGCGAGAAGTTTCGGGGCGGATTATCCATCTTCATGCCTGGCACGTACCCGACTTCCGCGGGACGTTACAGGca                                                                          >  2:3483504/1‑93 (MQ=255)
                gAATATGTTGCCAGCCATCAGCGAGAAGTTTCGGGGCGGATTATCCATCTTCATGCCTGGCACGTACCCGACTTCCGCGGGACGTTACAGGca                                                                          >  1:845280/1‑93 (MQ=255)
                 aaTATGTTGCCAGCCATCAGCGAGAAGTTTCGGGGCGGATTATCCATCTTCATGCCTGGCACGTACCCGACTTCCGCGGGACGTTACAGGcac                                                                         <  1:3741388/93‑1 (MQ=255)
                  atatGTTGCCAGCCATCAGCGAGAAGTTTCGGGGCGGATTATCCATCTTCATGCCTGGCACGTACCCGACTTCCGCGGGACGTTACAGGcaca                                                                        >  1:1738559/1‑93 (MQ=255)
                  atatGTTGCCAGCCATCAGCGAGAAGTTTCGGGGCGGATTATCCATCTTCATGCCTGGCACGTACCCGACTTCCGCGGGACGTTACAGGcaca                                                                        <  1:2025934/93‑1 (MQ=255)
                  atatGTTGCCAGCCATCAGCGAGAAGTTTCGGGGCGGATTATCCATCTTCATGCCTGGCACGTACCCGACTTCCGCGGGACGTTACAGGcaca                                                                        <  2:2394295/93‑1 (MQ=255)
                   tatGTTGCCAGCCATCAGCGAGAAGTTTCGGGGCGGATTATCCATCTTCATGCCTGGCACGTACCCGACTTCCGCGGGACGTTACAGGCACAt                                                                       >  1:4335521/1‑93 (MQ=255)
                   tatGTTGCCAGCCATCAGCGAGAAGTTTCGGGGCGGATTATCCATCTTCATGCCTGGCACGTACCCGACTTCCGCGGGACGTTACAGGCACAt                                                                       >  1:1220318/1‑93 (MQ=255)
                     tGTTGCCAGCCATCAGCGAGAAGTTTCGGGGCGGATTATCCATCTTCATGCCTGGCACGTACCCGACTTCCGCGGGACGTTACAGGCACATGa                                                                     >  1:2967450/1‑93 (MQ=255)
                      gTTGCCAGCCATCAGCGAGAAGTTTCGGGGCGGATTATCCATCTTCATGCCTGGCACGTACCCGACTTCCGCGGGACGTTACAGGCACATGaa                                                                    <  2:1418574/93‑1 (MQ=255)
                      gTTGCCAGCCATCAGCGAGAAGTTTCGGGGCGGATTATCCATCTTCATGCCTGGCACGTACCCGACTTCCGCGGGACGTTACAGGCACATGaa                                                                    >  2:4210121/1‑93 (MQ=255)
                        tGCCAGCCATCAGCGAGAAGTTTCGGGGCGGATTATCCATCTTCATGCCTGGCACGTACCCGACTTCCGCGGGACGTTACAGGCACATGAACa                                                                  <  2:4140242/93‑1 (MQ=255)
                        tGCCAGCCATCAGCGAGAAGTTTCGGGGCGGATTATCCATCTTCATGCCTGGCACGTACCCGACTTCCGCGGGACGTTACAGGCACATGAACa                                                                  <  2:3400613/93‑1 (MQ=255)
                             gccaTCAGCGAGAAGTTTCGGGGCGGATTATCCATCTTCATGCCTGGCACGTACCCGACTTCCGCGGGACGTTACAGGCACATGAACATCAgg                                                             >  2:1212264/1‑93 (MQ=255)
                             gccaTCAGCGAGAAGTTTCGGGGCGGATTATCCATCTTCATGCCTGGCACGTACCCGACTTCCGCGGGACGTTACAGGCACATGAACATCAgg                                                             <  2:3143569/93‑1 (MQ=255)
                              ccaTCAGCGAGAAGTTTCGGGGCGGATTATCCATCTTCATGCCTGGCACGTACCCGACTTCCGCGGGACGTTACAGGCACATGAACATCAGgc                                                            <  2:208351/93‑1 (MQ=255)
                              ccaTCAGCGAGAAGTTTCGGGGCGGATTATCCATCTTCATGCCTGGCACGTACCCGACTTCCGCGGGACGTTACAGGCACATGAACATCAGgc                                                            >  1:1163285/1‑93 (MQ=255)
                                aTCAGCGAGAAGTTTCGGGGCGGATTATCCATCTTCATGCCTGGCACGTACCCGACTTCCGCGGGACGTTACAGGCACATGAACATCAGgcgc                                                          >  1:3507125/1‑93 (MQ=255)
                                aTCAGCGAGAAGTTTCGGGGCGGATTATCCATCTTCATGCCTGGCACGTACCCGACTTCCGCGGGACGTTACAGGCACATGAACATCAGgcgc                                                          >  1:4168205/1‑93 (MQ=255)
                                 tCAGCGAGAAGTTTCGGGGCGGATTATCCATCTTCATGCCTGGCACGTACCCGACTTCCGCGGGACGTTACAGGCACATGAACATCAGGCGct                                                         >  2:3317345/1‑93 (MQ=255)
                                 tCAGCGAGAAGTTTCGGGGCGGATTATCCATCTTCATGCCTGGCACGTACCCGACTTCCGCGGGACGTTACAGGCACATGAACATCAGGCGct                                                         >  2:664097/1‑93 (MQ=255)
                                    gCGAGAAGTTTCGGGGCGGATTATCCATCTTCATGCCTGGCACGTACCCGACTTCCGCGGGACGTTACAGGCACATGAACATCAGGCGctggc                                                      >  1:1286300/1‑92 (MQ=255)
                                       agaAGTTTCGGGGCGGATTATCCATCTTCATGCCTGGCACGTACCCGACTTCCGCGGGACGTTACAGGCACCTGAACAACAGGCGctggtctg                                                   >  2:1020845/1‑93 (MQ=255)
                                       agaAGTTTCGGGGCGGATTATCCATCTTCATGCCTGGCACGTACCCGACTTCCGCGGGACGTTACAGGCACATGAACATCAGGCGctggtctg                                                   >  2:1020846/1‑93 (MQ=255)
                                        gaAGTTTCGGGGCGGATTATCCATCTTCATGCCTTGCACGTACCCGACTTCCGCGGGACGTTACAGGCACATGAACATCAGGTGctggtctgg                                                  >  1:2901558/1‑93 (MQ=255)
                                        gaAGTTTCGGGGCGGATTATCCATCTTCATGCCTTGCACGTACCCGACTTCCGCGGGACGTTACAGGCACATGAACATCAGGCGctggtctgg                                                  >  1:2901557/1‑93 (MQ=255)
                                        gaAGTTTCGGGGCGGATTATCCATCTTCATGCCTGGCACGTACCCGACTTCCGCGGGACGTTACAGGCACATGAACATCAGGCGctggtctgg                                                  <  2:2304185/93‑1 (MQ=255)
                                        gaAGTTTCGGGGCGGATTATCCATCTTCATGCCTGGCACGTACCCGACTTCCGCGGGACGTTACAGGCACATGAACATCAGGCGctggtctgg                                                  >  2:1684955/1‑93 (MQ=255)
                                        gaAGTTTCGCGTCGGATTATCCATCTCCATGCCTGGCACGCTCCCGACTTCCGCGGGACTTTACAGGCACATGAACATCAGGCGctggtctgg                                                  <  2:362871/93‑1 (MQ=255)
                                         aaGTTTCGTGGCGGATTATCCATCTTCATGCCTGGCACGTACCCGACTTCCGCGGGACGTTACGGGCACATGAACATCAGGCGctggtctggt                                                 <  2:1446479/93‑1 (MQ=255)
                                         aaGTTTCGGGGCGGATTATCCATCTTCATGCCTGGCACGTACCCGACTTCCGCGGGACGTTACAGGCACATGAACATCAGGCGctggtctggt                                                 <  2:3442693/93‑1 (MQ=255)
                                         aaGTTTCGGGGCGGATTATCCATCTTCATGCCTGGCACGTACCCGACTTCCGCGGGACGTTACAGGCACATGAACATCAGGCGctggtctggt                                                 <  1:710414/93‑1 (MQ=255)
                                          aGTTTCGGGGCGGATTATCCATCTTCATGCCTGGCACGTACCCGACTTCCGCGGGACGTTACAGGCACATGAACATCAGGCGCTGGTCTGGTg                                                >  2:2230291/1‑93 (MQ=255)
                                              tCGGGGCGGATTATCCATCTTCATGCCTGGCACGTACCCGACTTCCGCGGGACGTTACAGGCACATGAACATCAGGCGCTGGTCTGGTGCTCa                                            >  2:1868171/1‑93 (MQ=255)
                                                 gggCGGATTATCCATCTTCATGCCTGGCACGTACCCGACTTCCGCGGGACGTTACAGGCACATGAACATCAGGCGCTGGTCTGGTGCTCACCt                                         >  1:700904/1‑93 (MQ=255)
                                                 gggCGGATTATCCATCTTCATGCCTGGCACGTACCCGACTTCCGCGGGACGTTACAGGCACATGAACATCAGGCGCTGGTCTGGTGCTCACCt                                         >  2:2804323/1‑93 (MQ=255)
                                                   gCGGATTATCCATCTTCATGCCTGGCACGTACCCGACTTCCGCGGGACGTTACAGGCACATGAACATCAGGCGCTGGTCTGGTGCTCACCTGa                                       <  2:2840446/93‑1 (MQ=255)
                                                      gATTATCCATCTTCATGCCTGGCACGTACCCGACTTCCGCGGGACGTTACAGGCACATGAACATCAGGCGCTGGTCTGGTGCTCACCTGAaga                                    >  1:3741867/1‑93 (MQ=255)
                                                      gATTATCCATCTTCATGCCTGGCACGTACCCGACTTCCGCGGGACGTTACAGGCACATGAACATCAGGCGCTGGTCTGGTGCTCACCTGAaga                                    >  2:1973468/1‑93 (MQ=255)
                                                       aTTATCCATCTTCATGCCTGGCACGTACCCGACTTCCGCGGGACGTTACAGGCACATGAACATCAGGCGCTGGTCTGGTGCTCACCTGAagag                                   <  1:3268381/93‑1 (MQ=255)
                                                        ttATCCATCTTCATGCCTGGCACGTACCCGACTTCCGCGGGACGTTACAGGCACATGAACATCAGGCGCTGGTCTGGTGCTCACCTGAAGAgg                                  >  2:797127/1‑93 (MQ=255)
                                                        ttATCCATCTTCATGCCTGGCACGTACCCGACTTCCGCGGGACGTTACAGGCACATGAACATCAGGCGCTGGTCTGGTGCTCACCTGAAGAgg                                  >  2:2790454/1‑93 (MQ=255)
                                                         tATCCATCTTCATGCCTGGCACGTACCCGACTTCCGCGGGACGTTACAGGCACATGAACATCAGGCGCTTGTCTGGTGCTCACCTGAAGAGgc                                 <  2:130829/93‑1 (MQ=255)
                                                          aTCCATCTTCATGCCTGGCACGTACCCGACTTCCGCGGGACGTTACAGGCACATGAACATCAGGCGCTGGTCTGGTGCTCACCTGAAGAGgcg                                >  2:3691597/1‑93 (MQ=255)
                                                           tCCATCTTCATGCCTGGCACGTACCCGACTTCCGCGGGACGTTACAGGCACATGAACATCAGGCGCTGGTCTGGTGCTCACCTGAAGAGgcgc                               <  1:1218706/93‑1 (MQ=255)
                                                           tCCATCTTCATGCCTGGCACGTACCCGACTTCCGCGGGACGTTACAGGCACATGAACATCAGGCGCTGGTCTGGTGCTCACCTGAAGAGgcgc                               >  2:1076094/1‑93 (MQ=255)
                                                           tCCATCTTCATGCCTGGCACGTACCCGACTTCCGCGGGACGTTACAGGCACATGAACATCAGGCGCTGGTCTGGTGCTCACCTGAAGAGgcgc                               <  1:4438650/93‑1 (MQ=255)
                                                             cATCTTCATGCCTGGCACGTACCCGACTTCCGCGGGACGTTACAGGCACATGAACATCAGGCGCTGGTCTGGTGCTCACCTGAAGAGGCGCTg                             <  2:2428178/93‑1 (MQ=255)
                                                             cATCTTCATGCCTGGCACGTACCCGACTTCCGCGGGACGTTACAGGCACATGAACATCAGGCGCTGGGCTGGTGCTCACCTGAAGAGGCGCTg                             >  2:856771/1‑93 (MQ=255)
                                                              aTCTTCATGCCTGGCACGTACCCGACTTCCGCGGGACGTTACAGGCACATGAACATCAGGCGCTGGTCTGGTGCTCACCTGAAGAGGCGCTGc                            <  1:273018/93‑1 (MQ=255)
                                                               tCTTCATGCCTGGCACGTACCCGACTTCCGCGGGACGTTACAGGCACATGAACATCAGGCGCTGGTCTGGTGCTCACCTGAAGAGGCGCTGCa                           >  2:2184891/1‑93 (MQ=255)
                                                               tCTTCATGCCTGGCACGTACCCGACTTCCGCGGGACGTTACAGGCACATGAACATCAGGCGCTGGTCTGGTGCTCACCTGAAGAGGCGCTGCa                           >  2:33625/1‑93 (MQ=255)
                                                               tCTTCATGCCTGGCACGTACCCGACTTCCGCGGGACGTTACAGGCACATGAACATCAGGCGCTGGTCTGGTGCTCACCTGAAGAGGCGCTGCa                           >  2:33622/1‑93 (MQ=255)
                                                               tCTTCATGCCTGGCACGTACCCGACTTCCGCGGGACGTTACAGGCACATGAACATCAGGCGCTGGTCTGGTGCTCACCTGAACAGGCGCTGCa                           >  2:33626/1‑93 (MQ=255)
                                                                 ttCATGCCTGGCACGTACCCGACTTCCGCGGGACGTTACAGGCACATGAACATCAGGCGCTGGTCTGGTGCTCACCTGAAGAGGCGCTGCact                         >  1:2306810/1‑91 (MQ=255)
                                                                 ttCATGCCTGGCACGTACCCGACTTCCGCGGGACGTTACAGGCACATGAACATCAGGCGCTGGTCTGGTGCTCACCTGAAGAGGCGCTGCAat                         >  1:2306811/1‑93 (MQ=255)
                                                                 ttCATGCCTGGCACGTACCCGACTTCCGCGGGACGTTACAGGCACATGAACATCAGGCGCTGGTCTGGTGCTCACCTGAAGAGGCGCTGCAat                         <  1:3828277/93‑1 (MQ=255)
                                                                  tCATGCCTGGCACGTACCCGACTTCCGCGGGACGTTACAGGCACATGAACATCAGGCGCTGGTCTGGTGCTCACCTGAAGAGGCGCTGCAata                        <  2:2066677/93‑1 (MQ=255)
                                                                  tCATGCCTGGCACGTACCCGACTTCCGCGGGACGTTACAGGCACATGAACATCAGGCGCTGGTCTGGTGCTCACCTGAAGAGGCGCTGCAata                        >  1:4153688/1‑93 (MQ=255)
                                                                  tCATGCCTGGCACGTACCCGACTTCCGCGGGACGTTACAGGCACATGAACATCAGGCGCTGGTCTGGTGCTCACCTGAAGAGGCGCTGCAata                        <  1:4602693/93‑1 (MQ=255)
                                                                   cATGCCTGGCACGTACCCGACTTCCGCGGGACGTTACAGGCACATGAACATCAGGCGCTGGTCTGGTGCTCACCTGAAGAGGCGCTGCAatat                       >  2:2566767/1‑93 (MQ=255)
                                                                   cATGCCTGGCACGTACCCGACTTCCGCGGGACGTTACAGGCACATGAACATCAGGCGCTGGTCTGGTGCTCACCTGAAGAGGCGCTGCAatat                       <  2:3961563/93‑1 (MQ=255)
                                                                   cATGCCTGGCACGTACCCGACTTCCGCGGGACGTTACAGGCACATGAACATCAGGCGCTGGTCTGGTGCTCACCTGAAGAGGCGCTGCAatat                       >  2:1486897/1‑93 (MQ=255)
                                                                    aTGCCTGGCACGTACCCGACTTCCGCGGGACGTTACAGGCACATGAACATCAGGCGCTGGTCTGGTGCTCACCTGAAGAGGCGCTGCAATATc                      <  1:4343317/93‑1 (MQ=255)
                                                                     tGCCTGGCACGTACCCGACTTCCGCGGGACGTTACAGGCACATGAACATCAGGCGCTGGTCTGGTGCTCACCTGAAGAGGCGCTGCAATATcc                     <  1:3706139/93‑1 (MQ=255)
                                                                      gCCTGGCACGTACCCGACTTCCGCGGGACGTTACAGGCACATGAACATCAGGCGCTGGTCTGGTGCTCACCTGAAGAGGCGCTGCAATATCCg                    >  1:3549847/1‑93 (MQ=255)
                                                                       ccTGGCACGTACCCGACTTCCGCGGGACGTTACAGGCACATGAACATCAGGCGCTGGTCTGGTGCTCACCTGAAGAGGCGCTGCAATATCCGc                   <  1:1777240/93‑1 (MQ=255)
                                                                          ggCACGTACCCGACTTCCGCGGGACGTTACAGGCACATGAACATCAGGCGCTGGTCTGGTGCTCACCTGAAGAGGCGCTGCAATATCCGCTgg                <  2:424772/93‑1 (MQ=255)
                                                                            cACGTACCCGACTTCCGCGGGACGTTACAGGCACATGAACATCAGGCGCTGGTCTGGTGCTCACCTGAAGAGGCGCTGCAATATCCGCTgggc              <  1:2426912/93‑3 (MQ=255)
                                                                            cACGTACCCGACTTCCGCGGGACGTTACAGGCACATGAACATCAGGCGCTGGTCTGGTGCTCACCTGAAGAGGCGCTGCAATATCCGCTGGcc              <  1:4216225/93‑1 (MQ=255)
                                                                             aCGTACCCGACTTCCGCGGGACGTTACAGGCACATGAACATCAGGCGCTGGTCTGGTGCTCACCTGAAGAGGCGCTGCAATATCCGCTGGccc             <  1:159526/93‑1 (MQ=255)
                                                                             aCGTACCCGACTTCCGCGGGACGTTACAGGCACATGAACATCAGGCGCTGGTCTGGTGCTCACCTGAAGAGGCGCTGCAATATCCGCTGGccc             >  2:3307372/1‑93 (MQ=255)
                                                                             aCGTACCCGACTTCCGCGGGACGTTACAGGCACATGAACATCAGGCGCTGGTCTGGTGCTCACCTGAAGAGGCGCTGCAATATCCGCTGGccc             >  2:2588505/1‑93 (MQ=255)
                                                                              cGTACCCGACTTCCGCGGGACGTTACAGGCACATGAACATCAGGCGCTGGTCTGGTGCTCACCTGAAGAGGCGCTGCAATATCCGCTGGcccc            <  1:3068711/93‑1 (MQ=255)
                                                                              cGTACCCGACTTCCGCGGGACGTTACAGGCACATGAACATCAGGCGCTGGTCTGGTGCTCACCTGAAGAGGCGCTGCAATATCCGCTGGcccc            <  1:4153449/93‑1 (MQ=255)
                                                                              cGTACCCGACTTCCGCGGGACGTTACAGGCACATGAACATCAGGCGCTGGTCTGGTGCTCACCTGAAGAGGCGCTGCAATATCCGCTGGcccc            <  1:159527/93‑1 (MQ=255)
                                                                               gTACCCGACTTCCGCGGGACGTTACAGGCACATGAACATCAGGCGCTGGTCTGGTGCTCACCTGAAGAGGCGCTGCAATATACGCTGGCCCct           >  1:2960847/1‑93 (MQ=255)
                                                                                tACCCGACTTCCGCGGGACGTTACAGGCACATGAACATCAGGCGCTGGTCTGGTGCTCACCTGAAGAGGCGCTGCAATATCCGCTGGCCCctg          >  1:2948074/1‑93 (MQ=255)
                                                                                  cccGACTTCCGCGGGACGTTACAGGCACATGAACATCAGGCGCTGGTCTGGTGCTCACCTGAAGAGGCGCTGCAATATCCGCTGGCCCctgct        >  1:1546209/1‑93 (MQ=255)
                                                                                   ccGACTTCCGCGGGACGTTACAGGCACATGAACATCAGGCGCTGGTCTGGTGCTCACCTGAAGAGGCGCTGCAATATCCGCTGGCCCctgctg       >  1:1267915/1‑93 (MQ=255)
                                                                                    cGACTTCCGCGGGACGTTACAGGCACATGAACATCAGGCGCTGGTCTGGTGCTCACCTGAAGAGGCGCTGCAATATCCGCTGGCCCCTGCTGa      >  1:3346893/1‑93 (MQ=255)
                                                                                      aCTTCCGCGGGACGTTACAGGCACATGAACATCAGGCGCTGGTCTGGTGCTCACCTGAAGAGGCGCTGCAATATCCGCTGGCCCCTGCTGACa    >  2:1960133/1‑93 (MQ=255)
                                                                                        ttCCGCGGGACGTTACAGGCACATGAACATCAGGCGCTGGTCTGGTGCTCACCTGAAGAGGCGCTGCAATATCCGCTGGCCCCTGCTGACAtt  >  1:1614360/1‑93 (MQ=255)
                                                                                        ttCCGCGGGACGTTACAGGCACATGAACATCAGGCGCTGGTCTGGTGCTCACCTGAAGAGGCGCTGCAATATCCGCTGGCCCCTGCTGACAtt  <  2:1151471/93‑1 (MQ=255)
                                                                                            |                                                                                        
CGAAGCAACTGTGGGTGAATATGTTGCCAGCCATCAGCGAGAAGTTTCGGGGCGGATTATCCATCTTCATGCCTGGCACGTACCCGACTTCCACGGGACGTTACAGGCACATGAACATCAGGCGCTGGTCTGGTGCTCACCTGAAGAGGCGCTGCAATATCCGCTGGCCCCTGCTGACATT  >  NC_000913/1839690‑1839870

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ 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: ‑

GATK/CNVnator alignment

BRESEQ :: bam2aln output
GAAGCAACTGTGGGTGAATATGTTGCCAGCCATCAGCGAGAAGTTTCGGGGCGGATTATCCATCTTCATGCCTGGCACGTACCCGACTTCCACGGGACGTTACAGGCACATGAACATCAGGCGCTGGTCTGGTGCTCACCTGAAGAGGCGCTGCAATATCCGCTGGCCCCTGCTGACATTCCA  >  NC_000913/1839691‑1839873
                                                                                           |                                                                                           
gaatgAACTGTGGGGGAATATGTTGCCAGCCATCAGCGGGAAGTTTCGGGGCGGATTATCCATCTTCATGCCTGGCACGTCCCCGACTTCCGCG                                                                                           <  SRR4302544.916673/89‑1 (MQ=60)
GAAGCAACTGTGGGTGAATATGTTGCCAGCCATCAGCGAGAAGTTTCGGGGCGGATTATCCATCTTCATGCCTGGCACGTACCCGACTTCCGCG                                                                                           >  SRR4302544.2124300/1‑94 (MQ=60)
GAAGCAACTGTGGGTGAATATGTTGCCAGCCATCAGCGAGAAGTTTCGGGGCGGATTATCCATCTTCATGCCTGGCACGTACCCGACTTCCGCG                                                                                           >  SRR4302544.1347047/1‑94 (MQ=60)
 AAGCAACTGTGGGTGAATATGTTGCCAGCCATCAGCGAGAAGTTTCGGGGCGGATTATCCATCTTCATGCCTGGCACGTACCCGACTTCCGCGG                                                                                          <  SRR4302544.2115818/94‑1 (MQ=60)
   GCAACTGTGGGTGAATATGTTGCCAGCCATCAGCGAGAAGTTTCGGGGCGGATTATCCATCTTCATGCCTGGCACGTACCCGACTTCCGCGGGA                                                                                        <  SRR4302544.1235787/94‑1 (MQ=60)
    CAACTGTGGGTGAATATGTTGCCAGCCATCAGCGAGAAGTTTCGGGGCGGATTATCCATCTTCATGCCTGGCACGTACCCGACTTCCGCGGGAC                                                                                       <  SRR4302544.67076/94‑1 (MQ=60)
    CAACTGTGGGTGAATATGTTGCCAGCCATCAGCGAGAAGTTTCGGGGCGGATTATCCATCTTCATGCCTGGCACGTACCCGACTTCCGCGGGAC                                                                                       >  SRR4302544.269455/1‑94 (MQ=60)
       CTGTGGGTGAATATGTTGCCAGCCATCAGCGAGAAGTTTCGGGGCGGATTATCCATCTTCATGCCTGGCACGTACCCGACTTCCGCGGGACGTT                                                                                    <  SRR4302544.3505573/94‑1 (MQ=60)
       CTGTGGGTGAATATGTTGCCAGCCATCAGCGAGAAGTTTCGGGGCGGATTATCCATCTTCATGCCTGGCACGTACCCGACTTCCGCGGGACGTT                                                                                    >  SRR4302544.1698188/1‑94 (MQ=60)
       CTGTGGGTGAATATGTTGCCAGCCATCAGCGAGAAGTTTCGGGGCGGATTATCCATCTTCATGCCTGGCACGTACCCGACTTCCGCGGGACGTT                                                                                    <  SRR4302544.1413446/94‑1 (MQ=60)
          TGGGTGAATATGTTGCCAGCCATCAGCGAGAAGTTTCGGGGCGGATTATCCATCTTCATGCCTGGCACGTACCCGACTTCCGCGGGACGTTACA                                                                                 <  SRR4302544.1836551/94‑1 (MQ=60)
            GGTGAATATGTTGCCAGCCATCAGCGAGAAGTTTCGGGGCGGATTATCCATCTTCATGCCTGGCACGTACCCGACTTCCGCGGGACGTTACAGG                                                                               <  SRR4302544.279581/94‑1 (MQ=60)
            GGTGAATATGTTGCCAGCCATCAGCGAGAAGTTTCGGGGCGGATTATCCATCTTCATGCCTGGCACGTACCCGACTTCCGCGGGACGTTACAGG                                                                               <  SRR4302544.1244238/94‑1 (MQ=60)
              TGAATATGTTGCCAGCCATCAGCGAGAAGTTTCGGGGCGGATTATCCATCTTCATGCCTGGCACGTACCCGACTTCCGCGGGACGTTACAGGCA                                                                             >  SRR4302544.853625/1‑94 (MQ=60)
                AATATGTTGCCAGCCATCAGCGAGAAGTTTCGGGGCGGATTATCCATCTTCATGCCTGGCACGTACCCGACTTCCGCGGGACGTTACAGGCACA                                                                           >  SRR4302544.1755584/1‑94 (MQ=60)
                AATATGTTGCCAGCCATCAGCGAGAAGTTTCGGGGCGGATTATCCATCTTCATGCCTGGCACGTACCCGACTTCCGCGGGACGTTACAGGCACA                                                                           <  SRR4302544.3778567/94‑1 (MQ=60)
                 ATATGTTGCCAGCCATCAGCGAGAAGTTTCGGGGCGGATTATCCATCTTCATGCCTGGCACGTACCCGACTTCCGCGGGACGTTACAGGCACAT                                                                          >  SRR4302544.4379651/1‑94 (MQ=60)
                 ATATGTTGCCAGCCATCAGCGAGAAGTTTCGGGGCGGATTATCCATCTTCATGCCTGGCACGTACCCGACTTCCGCGGGACGTTACAGGCACAT                                                                          <  SRR4302544.2045571/94‑1 (MQ=60)
                 ATATGTTGCCAGCCATCAGCGAGAAGTTTCGGGGCGGATTATCCATCTTCATGCCTGGCACGTACCCGACTTCCGCGGGACGTTACAGGCACAT                                                                          >  SRR4302544.1232388/1‑94 (MQ=60)
                   ATGTTGCCAGCCATCAGCGAGAAGTTTCGGGGCGGATTATCCATCTTCATGCCTGGCACGTACCCGACTTCCGCGGGACGTTACAGGCACATGA                                                                        >  SRR4302544.2995915/1‑94 (MQ=60)
                    AGTTGGCAGCTATCAGCGAGAAGTTTCGGGGCGGATTATCCATCTTCATGCCTGGCACGTACGCGAGTTCCGCGGGACGTTACAGGCACATGAA                                                                       <  SRR4302544.880221/94‑1 (MQ=60)
                          CAGCCATCAGCGAGAAGTTTCGTGGCGGATTATCCATCTTCATGCCTGCCACGTACCCGACTTCGGCGGGACGTTACAGGCACATGAACATCAG                                                                 >  SRR4302544.3303986/1‑94 (MQ=60)
                            GCCATCAGCGAGAAGTTTCGGGGCGGATTATCCATCTTCATGCCTGGCACGTACCCGACTTCCGCGGGACGTTACAGGCACATGAACATCAGGC                                                               >  SRR4302544.1174883/1‑94 (MQ=60)
                             CCATCAGCGAGAAGTTTCGGGGCGGATTATCCATCTTCATGCCTGGCACGTACCCGACTTCCGCGGGACGTTACAGGCACATTAACATCAGGCG                                                              <  SRR4302544.407042/94‑1 (MQ=60)
                             CCATCAGCGAGAAGTTTCGGGGCGGATTATCCATCTTCATGCCTGGCACGTACCCGACTTCCGCGGGACGTTACAGGCACATGAACATCAGGCG                                                              >  SRR4302544.2988229/1‑94 (MQ=60)
                              CATCAGCGAGAAGTTTCGGGGCGGATTATCCATCTTCATGCCTGGCACGTACCCGACTTCCGCGGGACGTTACAGGCACATGAACATCAGGCGC                                                             >  SRR4302544.4209498/1‑94 (MQ=60)
                              CATCAGCGAGAAGTTTCGGGGCGGATTATCCATCTTCATGCCTGGCACGTACCCGACTTCCGCGGGACGTTACAGGCACATGAACATCAGGCGC                                                             >  SRR4302544.3540578/1‑94 (MQ=60)
                               ttcagtgagcAGTTTCTGGGCGGATTCTCCTTCTTCATGCCTGGCTCGTTCCCTGTTTCCGCGGGACGTTACAGGCACATGAACATCAGGCGCT                                                            <  SRR4302544.3190919/84‑1 (MQ=35)
                                  AGCGAGAAGTTTCGGGGCGGATTATCCATCTTCATGCCTGGCACGTACCCGACTTCCGCGGGACGTTACAGGCACATGAACATCAGGCGCTGGC                                                         >  SRR4302544.1298970/1‑94 (MQ=60)
                                      AGAAGTTTCGGGGCGGATTATCCATCTTCATGCCTTGCACGTACCCGACTTCCGCGGGACGTTACAGGCACATGAACATCAGGTGCTGGTCTGG                                                     >  SRR4302544.2929500/1‑94 (MQ=60)
                                      AGAAGTTTCGGGGCGGATTATCCATCTTCATGCCTTGCACGTACCCGACTTCCGCGGGACGTTACAGGCACATGAACATCAGGCGCTGGTCTGG                                                     >  SRR4302544.2929499/1‑94 (MQ=60)
                                        AAGTTTCGGGGCGGATTATCCATCTTCATGCCTGGCACGTACCCGACTTCCGCGGGACGTTACAGGCACATGAACATCAGGCGCTGGTCTGGTG                                                   <  SRR4302544.717459/94‑1 (MQ=60)
                                            TTCGGGGCGGATTATCCATCTTCATGCCTGGCACGTACCCGACTTCCGCGGGACGTTACAGGCACATGAACATCAGGCGCTGGTCTGGTGCTCA                                               >  SRR4302544.523575/1‑94 (MQ=60)
                                               GGGGCGGATTATCCATCTTCATGCCTGGCACGTACCCGACTTCCGCGGGACGTTACAGGCACATGAACATCAGGCGCTGGTCTGGTGCTCACCT                                            >  SRR4302544.707884/1‑94 (MQ=60)
                                                   CGGATTATCCATCTTCATGCCTGGCACGTACCCGACTTCCGCGGGACGTTACAGGCACATGAACATCAGGCGCTGGTCTGGTGCTCACCTGAAG                                        <  SRR4302544.206425/94‑1 (MQ=60)
                                                   CGGATTATCCATCTTCATGCCTGGCACGTACCCGACTTCCGCGGGACGTTACAGGCACATGAACATCAGGCGCTGGTCTGGTGCTCACCTGAAG                                        >  SRR4302544.2344983/1‑94 (MQ=60)
                                                    GGATTATCCATCTTCATGCCTGGCACGTACCCGACTTCCGCGGGACGTTACAGGCACATGAACATCAGGCGCTGGTCTGGTGCTCACCTGAAGA                                       >  SRR4302544.3779046/1‑94 (MQ=60)
                                                      ATTATCCATCTTCATGCCTGGCACGTACCCGACTTCCGCGGGACGTTACAGGCACATGAACATCAGGCGCTGGTCTGGTGCTCACCTGAAGAGG                                     <  SRR4302544.3299568/94‑1 (MQ=60)
                                                          TCCATCTTCATGCCTGGCACGTACCCGACTTCCGCGGGACGTTACAGGCACATGAACATCAGGCGCTGGTCTGGTGCTCACCTGAAGAGGCGCT                                 <  SRR4302544.1230765/94‑1 (MQ=60)
                                                          TCCATCTTCATGCCTGGCACGTACCCGACTTCCGCGGGACGTTACAGGCACATGAACATCAGGCGCTGGTCTGGTGCTCACCTGAAGAGGCGCT                                 <  SRR4302544.4483404/94‑1 (MQ=60)
                                                             ATCTTCATGCCTGGCACGTACCCGACTTCCGCGGGACGTTACAGGCACATGAACATCAGGCGCTGGTCTGGTGCTCACCTGAAGAGGCGCTGCA                              <  SRR4302544.275889/94‑1 (MQ=60)
                                                             ATCTTCATGCCTGGCACGTACCCGACTTCCGCGGGACGTTACAGGCACATGAACATCAGGCGCTGGTCTGGTGCTCACCTGAAGAGGCGCTGCA                              >  SRR4302544.2814028/1‑94 (MQ=60)
                                                               CTTCATGCCTGGCACGTACCCGACTTCCGCGGGACGTTACAGGCACATGAACATCAGGCGCTGGTCTGGTGCTCACCTGAAGAGGCGCTGCACT                            >  SRR4302544.2328609/1‑94 (MQ=60)
                                                               CTTCATGCCTGGCACGTACCCGACTTCCGCGGGACGTTACAGGCACATGAACATCAGGCGCTGGTCTGGTGCTCACCTGAAGAGGCGCTGCAAT                            >  SRR4302544.2328610/1‑94 (MQ=60)
                                                               CTTCATGCCTGGCACGTACCCGACTTCCACGGGACGTTACAGGCACATGAACATCAGGCGCTGGTCTGGTGCTCACCTGAAGAGGCGCTGCAAT                            <  SRR4302544.3575859/94‑1 (MQ=60)
                                                                TTCATGCCTGGCACGTACCCGACTTCCGCGGGACGTTACAGGCACATGAACATCAGGCGCTGGTCTGGTGCTCACCTGAAGAGGCGCTGCAATA                           >  SRR4302544.4194829/1‑94 (MQ=60)
                                                                TTCATGCCTGGCACGTACCCGACTTCCGCGGGACGTTACAGGCACATGAACATCAGGCGCTGGTCTGGTGCTCACCTGAAGAGGCGCTGCAATA                           <  SRR4302544.3866238/94‑1 (MQ=60)
                                                                 TCATGCCTGGCACGTACCCGACTTCCGCGGGACGTTACAGGCACATGAACATCAGGCGCTGGTCTGGTGCTCACCTGAAGAGGCGCTGCAATAT                          <  SRR4302544.4648441/94‑1 (MQ=60)
                                                                   ATGCCTGGCACGTACCCGACTTCCGCGGGACGTTACAGGCACATGAACATCAGGCGCTGGTCTGGTGCTCACCTGAAGAGGCGCTGCAATATCC                        <  SRR4302544.82269/94‑1 (MQ=60)
                                                                   ATGCCTGGCACGTACCCGACTTCCGCGGGACGTTACAGGCACATGAACATCAGGCGCTGGTCTGGTGCTCACCTGAAGAGGCGCTGCAATATCC                        <  SRR4302544.4387490/94‑1 (MQ=60)
                                                                    TGCCTGGCACGTACCCGACTTCCGCGGGACGTTACAGGCACATGAACATCAGGCGCTGGTCTGGTGCTCACCTGAAGAGGCGCTGCAATATCCG                       <  SRR4302544.3743019/94‑1 (MQ=60)
                                                                    TGCCTGGCACGTACCCGACTTCCGCGGGACGTTACAGGCACATGAACATCAGGCGCTGGTCTGGTGCTCACCTGAAGAGGCGCTGCAATATCCG                       >  SRR4302544.3583845/1‑94 (MQ=60)
                                                                      CCTGGCACGTACCCGACTTCCGCGGGACGTTACAGGCACATGAACATCAGGCGCTGGTCTGGTGCTCACCTGAAGAGGCGCTGCAATATCCGCT                     <  SRR4302544.1794630/94‑1 (MQ=60)
                                                                          GCACGTACCCGACTTCCGCGGGACGTTACAGGCACATGAACATCAGGCGCTGGTCTGGTGCTCACCTGAAGAGGCGCTGCAATATCCGCTGGCC                 >  SRR4302544.4346654/1‑94 (MQ=60)
                                                                           CACGTACCCGACTTCCGCGGGACGTTACAGGCACATGAACATCAGGCGCTGGTCTGGTGCTCACCTGAAGAGGCGCTGCAATATCCGCTGGGCC                <  SRR4302544.2450010/94‑1 (MQ=60)
                                                                           CACGTACCCGACTTCCGCGGGACGTTACAGGCACATGAACATCAGGCGCTGGTCTGGTGCTCACCTGAAGAGGCGCTGCAATATCCGCTGGCCC                <  SRR4302544.4258810/94‑1 (MQ=60)
                                                                            ACGTACCCGACTTCCGCGGGACGTTACAGGCACATGAACATCAGGCGCTGGTCTGGTGCTCACCTGAAGAGGCGCTGCAATATCCGCTGGCCCC               <  SRR4302544.161085/94‑1 (MQ=60)
                                                                             CGTACCCGACTTCCGCGGGACGTTACAGGCACATGAACATCAGGCGCTGGTCTGGTGCTCACCTGAAGAGGCGCTGCAATATCCGCTGGCCCCT              <  SRR4302544.4194585/94‑1 (MQ=60)
                                                                             CGTACCCGACTTCCGCGGGACGTTACAGGCACATGAACATCAGGCGCTGGTCTGGTGCTCACCTGAAGAGGCGCTGCAATATCCGCTGGCCCCT              <  SRR4302544.3097957/94‑1 (MQ=60)
                                                                             CGTACCCGACTTCCGCGGGACGTTACAGGCACATGAACATCAGGCGCTGGTCTGGTGCTCACCTGAAGAGGCGCTGCAATATCCGCTGGCCCCT              <  SRR4302544.161086/94‑1 (MQ=60)
                                                                             CGTACCCGACTTCCGCGGGACGTTACAGGCACATGAACATCAGGCGCTGGTCTGGTGCTCACCTGAAGAGGCGCTGCAATATACGCTGGCCCCT              >  SRR4302544.2989269/1‑94 (MQ=60)
                                                                              GTACCCGACTTCCGCGGGACGTTACAGGCACATGAACATCAGGCGCTGGTCTGGTGCTCACCTGAAGAGGCGCTGCAATATCCGCTGGCCCCTG             >  SRR4302544.2976390/1‑94 (MQ=60)
                                                                                ACCCGACTTCCGCGGGACGTTACAGGCACATGAACATCAGGCGCTGGTCTGGTGCTCACCTGAAGAGGCGCTGCAATATCCGCTGGCCCCTGCT           <  SRR4302544.3705459/94‑1 (MQ=60)
                                                                                ACCCGACTTCCGCGGGACGTTACAGGCACATGAACATCAGGCGCTGGTCTGGTGCTCACCTGAAGAGGCGCTGCAATATCCGCTGGCCCCTGCT           <  SRR4302544.1538583/94‑1 (MQ=60)
                                                                                ACCCGACTTCCGCGGGACGTTACAGGCACATGAACATCAGGCGCTGGTCTGGTGCTCACCTGAAGAGGCGCTGCAATATCCGCTGGCCCCTGCT           >  SRR4302544.1561607/1‑94 (MQ=60)
                                                                                 CCCGACTTCCGCGGGACGTTACAGGCACATGAACATCAGGCGCTGGTCTGGTGCTCACCTGAAGAGGCGCTGCAATATCCGCTGGCCCCTGCTG          >  SRR4302544.1280383/1‑94 (MQ=60)
                                                                                  CCGACTTCCGCGGGACGTTACAGGCACATGAACATCAGGCGCTGGTCTGGTGCTCACCTGAAGAGGCGCTGCAATATCCGCTGGCCCCTGCTGA         >  SRR4302544.3378820/1‑94 (MQ=60)
                                                                                      CTTCCGCGGGACGTTACAGGCACATGAACATCAGGCGCTGGTCTGGTGCTCACCTGAAGAGGCGCTGCAATATCCGCTGGCCCCTGCTGACATT     >  SRR4302544.1630274/1‑94 (MQ=60)
                                                                                        TCCGCGGGACGTTACAGGCACATGAACATCAGGCGCTGGTCTGGTGCTCACCTGAAGAGGCGCTGCAATATCCGCTGGCCCCTGCTGACATTCC   >  SRR4302544.4680905/1‑94 (MQ=60)
                                                                                         CCGCGGGACGTTACAGGCACATGAACATCAGGCGCTGGTCTGGTGCTCACCTGAAGAGGCGCTGCAATATCCGCTGGCCCCTGCTGACATTCCA  <  SRR4302544.2019001/94‑1 (MQ=60)
                                                                                           |                                                                                           
GAAGCAACTGTGGGTGAATATGTTGCCAGCCATCAGCGAGAAGTTTCGGGGCGGATTATCCATCTTCATGCCTGGCACGTACCCGACTTCCACGGGACGTTACAGGCACATGAACATCAGGCGCTGGTCTGGTGCTCACCTGAAGAGGCGCTGCAATATCCGCTGGCCCCTGCTGACATTCCA  >  NC_000913/1839691‑1839873

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 2 ≤ ATCG/ATCG < 25 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑