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 F3 I160 R1 220 104.1 6051714 95.9% 5803593 84.4

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NZ_CP009273 4,367,563 T→C intergenic (‑24/+65) blc ← / ← ampC lipocalin Blc/BlaEC family class C beta‑lactamase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NZ_CP0092734,367,5630TC100.0% 359.1 / NA 94intergenic (‑24/+65)blc/ampClipocalin Blc/BlaEC family class C beta‑lactamase
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (33/61);  total (33/61)

GAGAACTGCAGGCAACGACCAGAAATGCAGCTGTCGCTGCGGCAACGAGAGGGAGCAGGCGCATAAATGTTTCCTTACTGGTTTTTTTCTAAGTGTAGATGACAGCAAGGAAAAGCGGAGAAAAGGTCCGAAAATTCGGACCCGATGGAATTTTACTGTAGAGCGTTAAGAATC  >  NZ_CP009273/4367476‑4367649
                                                                                       |                                                                                      
gagaACTGCAGGCAACGACCAGAAATGCAGCTGTCGCTGCGGCAACGAGAGGGAGCAGGCGCATAAATGTTTCCTTACTGGTTTTTTCCt                                                                                      <  2:2189906/90‑1 (MQ=255)
 agaACTGCAGGCAACGACCAGAAATGCAGCTGTCGCTGCGGCAACGAGAGGGAGCAGGCGCATAAATGTTTCCTTACTGGTTTTTTCCTa                                                                                     <  2:606955/90‑1 (MQ=255)
 agaACTGCAGGCAACGACCAGAAATGCAGCTGTCGCTGCGGCAACGAGAGGGAGCAGGCGCATAAATGTTTCCTTACTGGTTTTTTCCTa                                                                                     >  2:664297/1‑90 (MQ=255)
 agaACTGCAGGCAACGACCAGAAATGCAGCTGTCGCTGCGGCAACGAGAGGGAGCAGGCGCATAAATGTTTCCTTACTGGTTTTTTCCTa                                                                                     <  2:653821/90‑1 (MQ=255)
 agaACTGCAGGCAACGACCAGAAATGCAGCTGTCGCTGCGGCAACGAGAGGGAGCAGGCGCATAAATGTTTCCTTACTGGTTTTTTCCTa                                                                                     <  1:2586267/90‑1 (MQ=255)
 agaACTGCAGGCAACGACCAGAAATGCAGCTGTCGCTGCGGCAACGAGAGGGAGCAGGCGCATAAATGTTTCCTTACTGGTTTTTTCCTa                                                                                     <  1:2721253/90‑1 (MQ=255)
 agaACTGCAGGCAACGACCAGAAATGCAGCTGTCGCTGCGGCAACGAGAGGGAGCAGGCGCATAAATGTTTCCTTACTGGTTTTTTCCTa                                                                                     <  1:2977249/90‑1 (MQ=255)
 agaACTGCAGGCAACGACCAGAAATGCAGCTGTCGCTGCGGCAACGAGAGGGAGCAGGCGCATAAATGTTTCCTTACTGGTTTTTTCCTa                                                                                     <  1:2360885/90‑1 (MQ=255)
 agaACTGCAGGCAACGACCAGAAATGCAGCTGTCGCTGCGGCAACGAGAGGGAGCAGGCGCATAAATGTTTCCTTACTGGTTTTTTCCTa                                                                                     <  1:2320429/90‑1 (MQ=255)
 agaACTGCAGGCAACGACCAGAAATGCAGCTGTCGCTGCGGCAACGAGAGGGAGCAGGCGCATAAATGTTTCCTTACTGGTTTTTTCCTa                                                                                     <  1:299896/90‑1 (MQ=255)
 agaACTGCAGGCAACGACCAGAAATGCAGCTGTCGCTGCGGCAACGAGAGGGAGCAGGCGCATAAATGTTTCCTTACTGGTTTTTTCCTa                                                                                     <  1:511454/90‑1 (MQ=255)
 agaACTGCAGGCAACGACCAGAAATGCAGCTGTCGCTGCGGCAACGAGAGGGAGCAGGCGCATAAATGTTTCCTTACTGGTTTTTTCCTa                                                                                     <  1:953154/90‑1 (MQ=255)
 agaACTGCAGGCAACGACCAGAAATGCAGCTGTCGCTGCGGCAACGAGAGGGAGCAGGCGCATAAATGTTTCCTTACTGGTTTTTTCCTa                                                                                     <  2:2534899/90‑1 (MQ=255)
 agaACTGCAGGCAACGACCAGAAATGCAGCTGTCGCTGCGGCAACGAGAGGGAGCAGGCGCATAAATGTTTCCTTACTGGTTTTTTCCTa                                                                                     <  1:2111641/90‑1 (MQ=255)
 agaACTGCAGGCAACGACCAGAAATGCAGCTGTCGCTGCGGCAACGAGAGGGAGCAGGCGCATAAATGTTTCCTTACTGGTTTTTTCCTa                                                                                     <  2:1393939/90‑1 (MQ=255)
 agaACTGCAGGCAACGACCAGAAATGCAGCTGTCGCTGCGGCAACGAGAGGGAGCAGGCGCATAAATGTTTCCTTACTGGTTTTTTCCTa                                                                                     <  2:1404061/90‑1 (MQ=255)
 agaACTGCAGGCAACGACCAGAAATGCAGCTGTCGCTGCGGCAACGAGAGGGAGCAGGCGCATAAATGTTTCCTTACTGGTTTTTTCCTa                                                                                     <  2:1835941/90‑1 (MQ=255)
 agaACTGCAGGCAACGACCAGAAATGCAGCTGTCGCTGCGGCAACGAGAGGGAGCAGGCGCATAAATGTTTCCTTACTGGTTTTTTCCTa                                                                                     <  1:1825444/90‑1 (MQ=255)
 agaACTGCAGGCAACGACCAGAAATGCAGCTGTCGCTGCGGCAACGAGAGGGAGCAGGCGCATAAATGTTTCCTTACTGGTTTTTTCCTa                                                                                     <  1:1389021/90‑1 (MQ=255)
 agaACTGCAGGCAACGACCAGAAATGCAGCTGTCGCTGCGGCAACGAGAGGGAGCAGGCGCATAAATGTTTCCTTACTGGTTTTTTCCTa                                                                                     <  2:499511/90‑1 (MQ=255)
 agaACTGCAGGCAACGACCAGAAATGCAGCTGTCGCTGCGGCAACGAGAGGGAGCAGGCGCATAAATGTTTCCTTACTGGTTTTTTCCTa                                                                                     <  2:2167750/90‑1 (MQ=255)
    aCTGCAGGCAACGACCAGAAATGCAGCTGTCGCTGCGGCAACGAGAGGGAGCAGGCGCATAAATGTTTCCTTACTGGTTTTTTCCTAAgt                                                                                  >  1:1675603/1‑90 (MQ=255)
    aCTGCAGGCAACGACCAGAAATGCAGCTGTCGCTGCGGCAACGAGAGGGAGCAGGCGCATAAATGTTTCCTTACTGGTTTTTTCCTAAgt                                                                                  >  2:2225410/1‑90 (MQ=255)
    aCTGCAGGCAACGACCAGAAATGCAGCTGTCGCTGCGGCAACGAGAGGGAGCAGGCGCATAAATGTTTCCTTACTGGTTTTTTCCTAAgt                                                                                  >  2:2088814/1‑90 (MQ=255)
    aCTGCACGCAACGACCAGAAATGCAGCTGTCGCTGCGGCAACGAGAGGGAGCAGGCGCATAAATGTTTCCTTACTGGGTTTTTCCTAAgt                                                                                  >  1:1612610/1‑90 (MQ=255)
       gCAGGCAACGACCAGAAATGCAGCTGTCGCTGCGGCAACGAGAGGGAGCAGGCGCATAAATGTTTCCTTACTGGTTTTTTCCTAAgtg                                                                                 <  1:1983924/88‑1 (MQ=255)
       gCAGGCAACGACCAGAAATGCAGCTGTCGCTGCGGCAACGAGAGGGAGCAGGCGCATAAATGTTTCCTTACTGGTTTTTTCCTAAgtg                                                                                 >  2:1983924/1‑88 (MQ=255)
       gCAGGCAACGACCAGAAATGCAGCTGTCGCTGCGGCAACGAGAGGGAGCAGGCGCATAAATGTTTCCTTACTGGTTTTTTCCTAAGTGTa                                                                               >  1:1952664/1‑90 (MQ=255)
         aGGCAACGACCAGAAATGCGGCTGTCGCTGCGGCAACGAGAGGGAGCAGGCGCATAAATGTTTCCTTACTGGTTTTTTCCTAAGTGTAGa                                                                             >  2:2103716/1‑90 (MQ=255)
         aGGCAACGACCAGAAATGCAGCTGTCGCTGCGGCAACGAGAGGGAGCAGGCGCATAAATGTTTCCTTACTGGTTTTTTCCTAAGTGTAGa                                                                             >  1:1900149/1‑90 (MQ=255)
         aGGCAACGACCAGAAATGCAGCTGTCGCTGCGGCAACGAGAGGGAGCAGGCGCATAAATGTTTCCTTACTGGTTTTTTCCTAAGTGTAGa                                                                             >  1:828806/1‑90 (MQ=255)
         aGGCAACGACCAGAAATGCAGCTGTCGCTGCGGCAACGAGAGGGAGCAGGCGCATAAATGTTTCCTTACTGGTTTTTTCCTAAGTGTAGa                                                                             >  2:1253674/1‑90 (MQ=255)
           gCAACGACCAGAAATGCGGCTGTCGCTGCGGCAACGAGAGGGAGCAGGCGCATAAATGTTTCCTTACTGGTTTTTTCCTAAGTGTAGATg                                                                           <  1:2103716/90‑1 (MQ=255)
           gCAACGACCAGAAATGCAGCTGTCGCTGCGGCAACGAGAGGGAGCAGGCGCATAAATGTTTCCTTACTGGTTTTTTCCTAAGTGTAGATg                                                                           <  1:1541926/90‑1 (MQ=255)
           gCAACGACCAGAAATGCAGCTGTCGCTGCGGCAACGAGAGGGAGCAGGCGCATAAATGTTTCCTTACTGGTTTTTTCCTAAGTGTAGATg                                                                           <  1:304318/90‑1 (MQ=255)
           gCAACGACCAGAAATGCAGCTGTCGCTGCGGCAACGAGAGGGAGCAGGCGCATAAATGTTTCCTTACTGGTTTTTTCCTAAGTGTAGATg                                                                           <  2:2517745/90‑1 (MQ=255)
            cAACGACCAGAAATGCAGCTGTCGCTGCGGCAACGAGAGGGAGCAGGCGCATAAATGTTTCCTTACTGGTTTTTTCCTAAGTGTAGATGa                                                                          >  2:2856440/1‑90 (MQ=255)
             aaCGACCAGAAATGCAGCTGTCGCTGCGGCAACGAGAGGGAGCAGGCGCATAAATGTTTCCTTACTGGTTTTTTCCTAAGTGTAGATGAc                                                                         <  1:2634343/90‑1 (MQ=255)
             aaCGACCAGAAATGCAGCTGTCGCTGCGGCAACGAGAGGGAGCAGGCGCATAAATGTTTCCTTACTGGTTTTTTCCTAAGTGTAGATGAc                                                                         <  2:2419831/90‑1 (MQ=255)
              aCGACCAGAAATGCAGCTGTCGCTGCGGCAACGAGAGGGAGCAGGCGCATAAATGTTTCCTTACTGGTTTTTTCCTAAGTGTAGATGACa                                                                        >  2:162856/1‑90 (MQ=255)
               cGACCAGAAATGCAGCTGTCGCTGCGGCAACGAGAGGGGGCAGGCGCATAAATGTTTCCTTACTGGTTTTTTCCTAAGTGTAGATGACAg                                                                       >  1:2946153/1‑90 (MQ=255)
                    aGAAATGCAGCTGTCGCTGCGGCAACGAGAGGGAGCAGGCGCATAAATGTTTCCTTACTGGTTTTTTCCTAAGTGTAGATGACAGCAAgg                                                                  >  2:1151650/1‑90 (MQ=255)
                       aaTGCAGCTGTCGCTGCGGCAACGAGAGGGAGCAGGCGCATAAATGTTTCCTTACTGGTTTTTTCCTAAGTGTAGATGACAGCAAGGaaa                                                               <  2:1882488/90‑1 (MQ=255)
                               tGTCGCTGCGGCAACGAGAGGGAGGAGGCGCATAAATGGTTCCTTGCTGGTTTTTTCCGAAGTGTAGATGGCAGGAGGGAAAAGCGgtga                                                       >  1:1829811/1‑90 (MQ=255)
                               tGTCGCTGCGGCAACGAGAGGGAGCAGGCGCATAAATGTTTCCTTACTGGTTTTTTCCTa                                                                                     <  2:2572351/60‑1 (MQ=255)
                               tGTCGCTGCGGCAACGAGAGGGAGCAGGCGCATAAATGTTTCCTTACTGGTTTTTTCCTa                                                                                     >  1:2572351/1‑60 (MQ=255)
                                gTCGCTGCGGCAACGAGAGGGAGCAGGCGCATAAATGTTTCCTTACTGGTTTTTTCCTAAGTGTAGATGACAGCAAGGAAAAGCGGAGaa                                                      >  2:1652831/1‑90 (MQ=255)
                                         gCAACGAGAGGGAGCAGGCGCATAAATGTTTCCTTACTGGTTTTTTCCTAAGTGTAGATGACAGCAAGGAAAAGCGGAGAAAAGGTCCGa                                             <  1:769249/90‑1 (MQ=255)
                                          cAACGAGAGGGAGCAGGCGCATAAATGTTTCCTTACTGGTTTTTTCCTAAGTGTAGATGACAGCAAGGAAAAGCGGAGAAAAGGTCCGaa                                            <  2:1555539/90‑1 (MQ=255)
                                              gagaGGGAGCAGGCGCATAAATGTTTCCTTACTGGTTTTTTCCTAAGTGTAGATGACAGCAAGGAAAAGCGGAGAAAAGGTCCGAAAAtt                                        >  1:2271963/1‑90 (MQ=255)
                                                   ggAGCAGGCGCATAAATGTTTCCTTACTGGTTTTTTCCTAAGTGTAGATGACAGCAAGGAAAAGCGGAGAAAAGGTCCGAAAATTCGGAc                                   <  1:151690/90‑1 (MQ=255)
                                                       cAGGCGCATAAATGTTTCCTTACTGGTTTTTTCCTAAGTGTAGATGACAGCAAGGAAAAGCGGAGAAAAGGTCCGAAAATTCGGACCCGa                               >  2:2736901/1‑90 (MQ=255)
                                                       cAGGCGCATAAATGTTTCCTTACTGGTTTTTTCCTAAGTGTAGATGACAGCAAGGAAAAGCGGAGAAAAGGTCCGAAAATTCGGACCCGa                               >  1:1241790/1‑90 (MQ=255)
                                                        aGGCGCATAAATGTTTCCTTACTGGTTTTTTCCTAAGTGTAGATGACAGCAAGGAAAAGCGGAGAAAAGGTCCGAAAATTCGGACCCGAt                              >  2:2277187/1‑90 (MQ=255)
                                                        aGGCGCATAAATGTTTCCTTACTGGTTTTTTCCTAAGTGTAGATGACAGCAAGGAAAAGCGGAGAAAAGGTCCGAAAATTCGGACCCGAt                              <  2:1989322/90‑1 (MQ=255)
                                                        aGGCGCATAAATGTTTCCTTACTGGTTTTTTCCTAAGTGTAGATGACAGCAAGGAAAAGCGGAGAAAAGGTCCGAAAATTCGGACCCGAt                              <  2:1168812/90‑1 (MQ=255)
                                                        aGGCGCATAAATGTTTCCTTACTGGTTTTTTCCTAAGTGTAGATGACAGCAAGGAAAAGCGGAGAAAAGGTCCGAAAATTCGGACCCGAt                              <  1:638156/90‑1 (MQ=255)
                                                        aGGCGCATAAATGTTTCCTTACTGGTTTTTTCCTAAGTGTAGATGACAGCAAGGAAAAGCGGAGAAAAGGTCCGAAAATTCGGACCCGAt                              <  2:785717/90‑1 (MQ=255)
                                                        aGGCGCATAAATGTTTCCTTACTGGTTTTTTCCTAAGTGTAGATGACAGCAAGGAAAAGCGGAGAAAAGGTCCGAAAATTCGGACCCGAt                              <  1:2746888/90‑1 (MQ=255)
                                                         ggCGCATAAATGTTTCCTTACTGGTTTTTTCCTAAGTGTAGATGACAGCAAGGAAAAGCGGAGAAAAGGTCCGAAAATTCGGACCCGATg                             >  1:2312498/1‑90 (MQ=255)
                                                         ggCGCATAAATGTTTCCTTACTGGTTTTTTCCTAAGTGTAGATGACAGCAAGGAAAAGCGGAGAAAAGGTCCGAAAATTCGGACCCGATg                             >  2:546746/1‑90 (MQ=255)
                                                          gcgcATAAATGTTTCCTTACTGGTTTTTTCCTAAGTGTAGATGACAGCAAGGAAAAGCGGAGAAAAGGTCCGAAAATTCGGACCCGATgg                            <  1:1012358/90‑1 (MQ=255)
                                                             cATAAATGTTTCCTTACTGGTTTTTTCCTAAGTGTAGATg                                                                           <  2:1407912/40‑1 (MQ=255)
                                                             cATAAATGTTTCCTTACTGGTTTTTTCCTAAGTGTAGATg                                                                           >  1:1407912/1‑40 (MQ=255)
                                                             cATAAATGTTTCCTTACTGGTTTTTTCCTAAGTGTAGATGACAGCAAGGAAAAGCGGAGAAAAGGTCCGAAAATTCGGACCCGATGGAAt                         <  2:828806/90‑1 (MQ=255)
                                                             cATAAATGTTTCCTTACTGGTTTTTTCCTAAGTGTAGATGACAGCAAGGAAAAGCGGAGAAAAGGTCCGAAAATTCGGACCCGATGGAAt                         <  2:413546/90‑1 (MQ=255)
                                                             cATAAATGTTTCCTTACTGGTTTTTTCCTAAGTGTAGATGACAGCAAGGAAAAGCGGAGAAAAGGTCCGAAAATTCGGACCCGATGGAAt                         <  2:363380/90‑1 (MQ=255)
                                                             cATAAATGTTTCCTTACTGGTTTTTTCCTAAGTGTAGATGACAGCAAGGAAAAGCGGAGAAAAGGTCCGAAAATTCGGACCCGATGGAAt                         <  1:1051872/90‑1 (MQ=255)
                                                             cATAAATGTTTCCTTACTGGTTTTTTCCTAAGTGTAGATGACAGCAAGGAAAAGCGGAGAAAAGGTCCGAAAATTCGGACCCGATGGAAt                         <  2:1967585/90‑1 (MQ=255)
                                                             cATAAATGTTTCCTTACTGGTTTTTTCCTAAGTGTAGATGACAGCAAGGAAAAGCGGAGAAAAGGTCCGAAAATTCGGACCCGATGGAAt                         <  2:1335422/90‑1 (MQ=255)
                                                             cATAAATGTTTCCTTACTGGTTTTTTCCTAAGTGTAGATGACAGCAAGGAAAAGCGGAGAAAAGGTCCGAAAATTCGGACCCGATGGAAt                         <  1:843834/90‑1 (MQ=255)
                                                             cATAAATGTTTCCTTACTGGTTTTTTCCTAAGTGTAGATGACAGCAAGGAAAAGCGGAGAAAAGGTCCGAAAATTCGGACCCGATGGAAt                         <  1:859668/90‑1 (MQ=255)
                                                             cATAAATGTTTCCTTACCGGTTTTTTCCTAAGTGTAGATGACAGCAAGGAAAAGCGGAGAAAAGGTCCGAAAATTCGGACCCGATGGAAt                         <  2:2042533/90‑1 (MQ=255)
                                                              aTAAATGTTTCCTTACTGGTTTTTTCCTAAGTGTAGATGACAGCAAGGAAAAGCGGAGAAAAgg                                                  <  2:957727/64‑1 (MQ=255)
                                                              aTAAATGTTTCCTTACTGGTTTTTTCCTAAGTGTAGATGACAGCAAGGAAAAGCGGAGAAAAgg                                                  >  1:957727/1‑64 (MQ=255)
                                                              aTAAATGTTTCCTTACTGGTTTTTTCCTAAGTGTAGATGACAGCAAGGAAAAGCGGAGAAAAGGTCCGAAAATTCGGACCCGATGGAAt                         <  1:2400974/89‑1 (MQ=255)
                                                              aTAAATATTTCCTTACTGGTTTTTTCCTAAGTGTAGATGACAGCAAGGAAAAGCGGAGAAAAGGTCCGAAAATTCGGACCCGATGGAAt                         >  2:2400974/1‑89 (MQ=255)
                                                                  aTGTTTCCTTACTGGTTTTTTCCTAAGTGTAGATGACAGCAAGGAAAAGCGGAGAAAAGGTCCGAAAATTCGGACCCGATGGAATTTTAc                    <  2:2725407/90‑1 (MQ=255)
                                                                    gTTTCCTTACTGGTTTTTTCCTAAGTGTAGATGACAGCAAGGAAAAGCGGAGAAAAGGTCCGAAAATTCGGACCCGATGGAATTTTACTg                  <  1:1178027/90‑1 (MQ=255)
                                                                      ttCCTTACTGGTTTTTTCCTAAGTGTAGATGACAGCAAGGAAAAGCGGAGAAAAGGTCCGAAAATTCGGACCCGATGGAATTTTACTGTa                >  1:2604636/1‑90 (MQ=255)
                                                                      ttCCTTACTGGTTTTTTCCTAAGTGTAGATGACAGCAAGGAAAAGCGGAGAAAAGGTCCGAAAATTCGGACCCGATGGAATTTTACTGTa                <  1:1298304/90‑1 (MQ=255)
                                                                       tCCTTACTGGTTTTTTCCTAAGTGTAGATGACAGCAAGGAAAAGCGGAGAAAAGGTCCGAAAATTCGGACCCGATGGAATTTTACTGTag               <  1:2887545/90‑1 (MQ=255)
                                                                       tCCTTACTGGTTTTTTCCTAAGTGTAGATGACAGCAAGGAAAAGCGGAGAAAAGGTCCGAAAATTCGGACCCGATGGAATTTTACTGTag               <  1:2645622/90‑1 (MQ=255)
                                                                       tCCTTACTGGTTTTTTCCTAAGTGTAGATGACAGCAAGGAAAAGCGGAGAAAAGGTCCGAAAATTCGGACCCGATGGAATTTTACTGAag               >  2:208748/1‑90 (MQ=255)
                                                                        ccTTACTGGTTTTTTCCTAAGTGTAGATGACAGCAAGGAAAAGCGGAGAAAAGGTCCGAAAATTCGGACCCGATGGAATTTTACTGTaga              <  2:2644314/90‑1 (MQ=255)
                                                                        ccTTACTGGTTTTTTCCTAAGTGTAGATGACAGCAAGGAAAAGCGGAGAAAAGGTCCGAAAATTCGGACCCGATGGAATTTTACTGTaga              <  2:1698637/90‑1 (MQ=255)
                                                                         cTTACTGGTTTTTTCCTAAGTGTAGATGACAGCAAGGAAAAGCGGAGAAAAGGTCCGAAAATTCGGACCCGATGGAATTTTACTGTagag             <  2:1066557/90‑1 (MQ=255)
                                                                          ttACTGGTTTTTTCCTAAGTGTAGATGACAGCAAGGAAAAGCGGAGAAAAGGTCCGAAAATTCGGACCCGATGGAATTTTACTGTAGAGc            <  1:2309455/90‑1 (MQ=255)
                                                                           tACTGGTTTTTTCCTAAGTGTAGATGACAGCAAGGAAAAGCGGAGAAAAGGTCCGAAAATTCGGACCCGATGGAATTTTACTGTAGAGCg           >  2:2745657/1‑90 (MQ=255)
                                                                           tACTGGTTTTTTCCTAAGTGTAGATGACAGCAAGGAAAAGCGGAGAAAAGGTCCGAAAATTCGGACCCGATGGAATTTTACTGTAGAGCg           >  1:2963691/1‑90 (MQ=255)
                                                                           tACTGGTTTTTTCCTAAGTGTAGATGACAGCAAGGAAAAGCGGAGAAAAGGTCCGAAAATTCGGACCCGATGGAATTTTACTGTAAAGCg           >  2:963854/1‑90 (MQ=255)
                                                                              tGGTTTTTTCCTAAGTGTAGATGACAGCAAGGAAAAGCGGAGAAAAGGTCCGAAAATTCGGACCCGATGGAATTTTACTGTAGAGCGTTa        <  2:2913985/90‑1 (MQ=255)
                                                                              tGGTTTTTTCCTAAGTGTAGATGACAGCAAGGAAAAGCGGAGAAAAGGTCCGAAAATTCGGACCCGATGGAATTTTACTGTAGAGCGTTa        >  2:2837765/1‑90 (MQ=255)
                                                                              tGGTTTTTTCCTAAGTGTAGATGACAGCAAGGAAAAGCGGAGAAAAGGTCCGAAAATTCGGACCCGATGGAATTTTACTGTAGAGCGTTa        <  2:1241790/90‑1 (MQ=255)
                                                                                  tttttcCTAAGTGTAGATGACAGCAAGGAAAAGCGGAGAAAAGGTCCGAAAATTCGGACCCGATGGAATTTTACTGTAGAGCGTTAAGaa    >  2:2682628/1‑90 (MQ=255)
                                                                                  tttttcCTAAGTGTAGATGACAGCAAGGAAAAGCGGAGAAAAGGTCCGAAAATTCGGACCCGATGGAATTTTACTGTAGAGCGTTAAGaa    <  2:856914/90‑1 (MQ=255)
                                                                                  tttttcCTAAGTGTAGATGACAGCAAGGAAAAGCGGAGAAAAGGTCCGAAAATTCGGACCCGATGGAATTTTACTGTAGAGCGTTAAGaa    <  1:2260921/90‑1 (MQ=255)
                                                                                    tttcCTAAGTGTAGATGACAGCAAGGAAAAGCGGAGAAAAGGTCCGAAAATTCGGACCCGATGGAATTTTACTGTAGAGCGTTAAGAATc  <  2:2963691/90‑1 (MQ=255)
                                                                                       |                                                                                      
GAGAACTGCAGGCAACGACCAGAAATGCAGCTGTCGCTGCGGCAACGAGAGGGAGCAGGCGCATAAATGTTTCCTTACTGGTTTTTTTCTAAGTGTAGATGACAGCAAGGAAAAGCGGAGAAAAGGTCCGAAAATTCGGACCCGATGGAATTTTACTGTAGAGCGTTAAGAATC  >  NZ_CP009273/4367476‑4367649

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

BRESEQ :: bam2aln output
CGGCGGCGTAGGAGAACTGCAGGCAACGACCAGAAATGCAGCTGTCGCTGCGGCAACGAGAGGGAGCAGGCGCATAAATGTTTCCTTACTGGTTTTTTTCTAAGTGTAGATGACAGCAAGGAAAAGCGGAGAAAAGGTCCGAAAATTCGGACCCGATGGAATTTTACTGTAGAGCGTTAAGAATCTGCCAGGCGGCGT  >  NZ_CP009273/4367465‑4367662
                                                                                                  |                                                                                                   
CGGCGGCGTAGGAGAACTGCAGGCAACGACCAGAAATGCAGCTGTCGCTGCGGCAACGAGAGGGAGCAGGCGCATAAATGTTTCCTTACTGGTTTTTTCC                                                                                                    <  SRR3722030.1629609/100‑1 (MQ=60)
     GCGTAGGAGAACTGCAGGCAACGACCAGAAATGCAGCTGTCGCTGCGGCAACGAGAGGGAGCAGGCGCATAAATGTTTCCTTACTGGTTTTTTCCTAAGT                                                                                               >  SRR3722030.1702810/1‑100 (MQ=60)
     GCGTAGGAGAACTGCAGGCAACGACCAGAAATGCAGCTGTCGCTGCGGCAACGAGAGGGAGCAGGCGCATAAATGTTTCCTTACTGG‑TTTTTCCTAAGTG                                                                                              >  SRR3722030.501264/1‑100 (MQ=60)
     GCGTAGGAGAACTGCACGCAACGACCAGAAATGCAGCTGTCGCTGCGGCAACGAGAGGGAGCAGGCGCATAAATGTTTCCTTACTGGGTTTTTCCTAAGT                                                                                               >  SRR3722030.1638751/1‑100 (MQ=60)
      CGTAGGAGAACTGCAGGCAACGACCAGAAATGCAGCTGTCGCTGCGGCAACGAGAGGGAGCAGGCGCATAAATGTTTCCTTACTGGTTTTTTCCTAAGTG                                                                                              >  SRR3722030.1548784/1‑100 (MQ=60)
       agcgtcagatgtgtataagagacagGAAATGCAGCTGTCGCTGCGGCAACGAGAGGGAGCAGGCGCATAAATGTTTCCTTACTGGTTTTTTCCTAAGTGT                                                                                             <  SRR3722030.2415623/75‑1 (MQ=60)
        TAGGAGAACTGCAGGCAACGACCAGAAATGCAGCTGTCGCTGCGGCAACGAGAGGGAGCAGGCGCATAAATGTTTCCTTACTGGTTTTTTCCTAAGTGTA                                                                                            >  SRR3722030.1986742/1‑100 (MQ=60)
          GGAGAACTGCAGGCAACGACCAGAAATGCAGCTGTCGCTGCGGCAACGAGAGGGAGCAGGCGCATAAATGTTTCCTTACTGGTTTTTTCCTAAGTGTAGA                                                                                          >  SRR3722030.1932951/1‑100 (MQ=60)
          GGAGAACTGCAGGCAACGACCAGAAATGCAGCTGTCGCTGCGGCAACGAGAGGGAGCAGGCGCATAAATGTTTCCTTACTGGTTTTTTCCTAAGTGTAGA                                                                                          >  SRR3722030.841528/1‑100 (MQ=60)
            agatctacactggccatgtcgtcggcagcgtcagatgtgtataagagacaGGAGCAGGCGCATAAATGTTTCCTTACTGGTTTTTTCCTAAGTGTAGATG                                                                                        <  SRR3722030.1780734/50‑1 (MQ=60)
            AGAACTGCAGGCAACGACCAGAAATGCAGCTGTCGCTGCGGCAACGAGAGGGAGCAGGCGCATAAATGTTTCCTTACTGGTTTTTTCCTAAGTGTAGATG                                                                                        <  SRR3722030.2149309/100‑1 (MQ=60)
            AGAACTGCAGGCAACGACCAGAAATGCAGCTGTCGCTGCGGCAACGAGAGGGAGCAGGCGCATAAATGTTTCCTTACTGGTTTTTTCCTAAGTGTAGATG                                                                                        <  SRR3722030.967695/100‑1 (MQ=60)
            AGAACTGCAGGCAACGACCAGAAATGCAGCTGTCGCTGCGGCAACGAGAGGGAGCAGGCGCATAAATGTTTCCTTACTGGTTTTTTCCTAAGTGTAGATG                                                                                        <  SRR3722030.304271/100‑1 (MQ=60)
            AGAACTGCAGGCAACGACCAGAAATGCAGCTGTCGCTGCGGCAACGAGAGGGAGCAGGCGCATAAATGTTTCCTTACTGGTTTTTTCCTAAGTGTAGATG                                                                                        <  SRR3722030.3032102/100‑1 (MQ=60)
            AGAACTGCAGGCAACGACCAGAAATGCAGCTGTCGCTGCGGCAACGAGAGGGAGCAGGCGCATAAATGTTTCCTTACTGGTTTTTTCCTAAGTGTAGATG                                                                                        <  SRR3722030.2362546/100‑1 (MQ=60)
            AGAACTGCAGGCAACGACCAGAAATGCAGCTGTCGCTGCGGCAACGAGAGGGAGCAGGCGCATAAATGTTTCCTTACTGGTTTTTTCCTAAGTGTAGATG                                                                                        <  SRR3722030.2403807/100‑1 (MQ=60)
            AGAACTGCAGGCAACGACCAGAAATGCAGCTGTCGCTGCGGCAACGAGAGGGAGCAGGCGCATAAATGTTTCCTTACTGGTTTTTTCCTAAGTGTAGATG                                                                                        <  SRR3722030.2633728/100‑1 (MQ=60)
            AGAACTGCAGGCAACGACCAGAAATGCAGCTGTCGCTGCGGCAACGAGAGGGAGCAGGCGCATAAATGTTTCCTTACTGGTTTTTTCCTAAGTGTAGATG                                                                                        <  SRR3722030.2771526/100‑1 (MQ=60)
            AGAACTGCAGGCAACGACCAGAAATGCAGCTGTCGCTGCGGCAACGAGAGGGAGCAGGCGCATAAATGTTTCCTTACTGGTTTTTTCCTAAGTGTAGATG                                                                                        <  SRR3722030.1856394/100‑1 (MQ=60)
            AGAACTGCAGGCAACGACCAGAAATGCAGCTGTCGCTGCGGCAACGAGAGGGAGCAGGCGCATAAATGTTTCCTTACTGGTTTTTTCCTAAGTGTAGATG                                                                                        <  SRR3722030.519293/100‑1 (MQ=60)
            AGAACTGCAGGCAACGACCAGAAATGCAGCTGTCGCTGCGGCAACGAGAGGGAGCAGGCGCATAAATGTTTCCTTACTGGTTTTTTCCTAAGTGTAGATG                                                                                        <  SRR3722030.1410816/100‑1 (MQ=60)
                CTGCAGGCAACGACCAGAAATGCAGCTGTCGCTGCGGCAACGAGAGGGGGCAGGCGCATAAATGTTTCCTTACTGGTTTTTTCCTAAGTGTAGATGACAG                                                                                    >  SRR3722030.3000487/1‑100 (MQ=60)
                CTGCAGGCAACGACCAGAAATGCAGCTGTCGCTGCGGCAACGAGAGGGAGCAGGCGCATAAATGTTTCCTTACTGGTTTTTTCCTAAGTGTAGATGACAG                                                                                    <  SRR3722030.2018724/100‑1 (MQ=60)
                      GCAACGACCAGAAATGCGGCTGTCGCTGCGGCAACGAGAGGGAGCAGGCGCATAAATGTTTCCTTACTGGTTTTTTCCTAAGTGTAGATGACAGCAAGGA                                                                              <  SRR3722030.2141234/100‑1 (MQ=60)
                      GCAACGACCAGAAATGCAGCTGTCGCTGCGGCAACGAGAGGGAGCAGGCGCATAAATGTTTCCTTACTGGTTTTTTCCTAAGTGTAGATGACAGCAAGGA                                                                              <  SRR3722030.308757/100‑1 (MQ=60)
                      GCAACGACCAGAAATGCAGCTGTCGCTGCGGCAACGAGAGGGAGCAGGCGCATAAATGTTTCCTTACTGGTTTTTTCCTAAGTGTAGATGACAGCAAGGA                                                                              <  SRR3722030.1566858/100‑1 (MQ=60)
                        AACGACCAGAAATGCAGCTGTCGCTGCGGCAACGAGAGGGAGCAGGCGCATAAATGTTTCCTTACTGGTTTTTTCCTAAGTGTAGATGACAGCAAGGAAA                                                                            <  SRR3722030.2682827/100‑1 (MQ=60)
                                GAAATGCAGCTGTCGCTGCGGCAACGAGAGGGAGGAGGCGCATAAATGGTTCCTTGCTGGTTTTTTCCGAAGTGTAGATGGCAGGAGGGAAAAGCGGTGA                                                                    >  SRR3722030.1860870/1‑100 (MQ=60)
                                GAAATGCAGCTGTCGCTGCGGCAACGAGAGGGAGCAGGCGCATAAATGTTTCCTTACTGGTTTTTTCCTAAGTGTAGATGctgtctcttatacacatctg                                                                    >  SRR3722030.2619537/1‑80 (MQ=60)
                                               CTGCGGCAACGAGAGGGAGCAGGCGCATAAATGTTTCCTTACTGGTTTTTTCCTAAGTGTAGATGACAGCAAGGAAAAGCGGAGAAAAGGTCCGAAAATT                                                     >  SRR3722030.2313064/1‑100 (MQ=60)
                                                    GCAACGAGAGGGAGCAGGCGCATAAATGTTTCCTTACTGGTTTTTTCCTAAGTGTAGATGACAGCAAGGAAAAGCGGAGAAAAGGTCCGAAAATTCGGAC                                                <  SRR3722030.781092/100‑1 (MQ=60)
                                                       ACGAGAGGGAGCAGGCGCATAAATGTTTCCTTACTGGTTTTTTCCTAAGctgtctcttatacacatctgacgctgccgacgacatggccagtgtagatct                                             >  SRR3722030.138449/1‑49 (MQ=60)
                                                        CGAGAGGGAGCAGGCGCATAAATGTTTCCTTACTGGTTTTTTCCTAAGTGTAGATGACAGCAAGGAAAAGCGGAGAAAAGGTCCGAAAATTCGGACCCGA                                            >  SRR3722030.1260142/1‑100 (MQ=60)
                                                          AGAGGGAGCAGGCGCATAAATGTTTCCTTACTGGTTTTTTCCTAAGTGTAGATGACAGCAAGGAAAAGCGGAGAAAAGGTCCGAAAATTCGGACCCGATG                                          >  SRR3722030.2354439/1‑100 (MQ=60)
                                                              GGAGCAGGCGCATAAATGTTTCCTTACTGGTTTTTTCCTAAGTGTAGATGACAGCAAGGActgtctcttatacacatctgacgctgccgacgacatggcc                                      >  SRR3722030.1430122/1‑60 (MQ=60)
                                                              GGAGCAGGCGCATAAATGTTTCCTTACTGGTTTTTTCCTAAGTGTAGATGACAGCAAGGAAAAGCGGAGAAAAGGTCCGAAAATTCGGACCCGATGGAAT                                      <  SRR3722030.153886/100‑1 (MQ=60)
                                                               GAGCAGGCGCATAAATGTTTCCTTACTGGTTTTTTCCTAAGTGTAGATGACAGCAAGGAAAAGCGGAGAAAAGGTCCGAAAATTCtgtctcttatacaca                                     >  SRR3722030.972327/1‑85 (MQ=60)
                                                                   AGGCGCATAAATGTTTCCTTACTGGTTTTTTCCTAAGTGTAGATGACAGCAAGGAAAAGCGGAGAAAAGGTCCGAAAATTCGGACCCGATGGAATTTTAC                                 <  SRR3722030.2797605/100‑1 (MQ=60)
                                                                   AGGCGCATAAATGTTTCCTTACTGGTTTTTTCCTAAGTGTAGATGACAGCAAGGAAAAGCGGAGAAAAGGTCCGAAAATTCGGACCCGATGGAATTTTAC                                 <  SRR3722030.648063/100‑1 (MQ=60)
                                                                     GCGCATAAATGTTTCCTTACTGGTTTTTTCCTAAGTGTAGATGACAGCAAGGAAAAGCGGAGAAAAGGTCCGAAAATTCGGACCCGATGGAATTTTACTG                               <  SRR3722030.1027668/100‑1 (MQ=60)
                                                                       GCATAAATGTTTCCTTACTGGTTTTTTCCTAAGTGTAGATGACAGCAAGGAAAAGCGGAGAAAAGGTCCGAAAATTCGGACCCGATGGAATTTTACTGTA                             >  SRR3722030.2652469/1‑100 (MQ=60)
                                                                        CATAAATGTTTCCTTACTGGTTTTTTCCTAAGTGTAGATGACAGCAAGGAAAAGCGGAGAAAAGGTCCGAAAATTCGGACCCGATGGAATTTTACTGTAG                            <  SRR3722030.2444723/100‑1 (MQ=60)
                                                                        CATAAATGTTTCCTTACTGGTTTTTTCCTAAGTGTAGATGACAGCAAGGAAAAGCGGAGAAAAGGTCCGAAAATTCGGACCCGATGGAATTTTACTGTAG                            <  SRR3722030.1067676/100‑1 (MQ=60)
                                                                        CATAAATGTTTCCTTACTGGTTTTTTCCTAAGTGTAGATGACAGCAAGGAAAAGCGGAGAAAAGGTCCGAAAATTCGGACCCGATGGAATTTTACTGTAG                            <  SRR3722030.856762/100‑1 (MQ=60)
                                                                        CATAAATGTTTCCTTACTGGTTTTTTCCTAAGTGTAGATGACAGCAAGGAAAAGCGGAGAAAAGGTCCGAAAATTCGGACCCGATGGAATTTTACTGTAG                            <  SRR3722030.872856/100‑1 (MQ=60)
                                                                            AATGTTTCCTTACTGGTTTTTTCCTAAGTGTAGATGACAGCAAGGAAAAGCGGAGAAAAGGTCCGAAAATTCGGACCCGATGGAATTTTACTGTAGAGCG                        >  SRR3722030.3018322/1‑100 (MQ=60)
                                                                               GTTTCCTTACTGGTTTTTTCCTAAGTGTAGATGACAGCAAGGAAAAGCGGAGAAAAGGTCCGAAAATTCGGACCCGATGGAATTTTACTGTAGAGCGTTA                     <  SRR3722030.1195480/100‑1 (MQ=60)
                                                                                 TTCCTTACTGGTTTTTTCCTAAGTGTAGATGACAGCAAGGAAAAGCGGAGAAAAGGTCCGAAAATTCGGACCCGATGGAATTTTACTGTAGAGCGTTAAG                   <  SRR3722030.1317989/100‑1 (MQ=60)
                                                                                  TCCTTACTGGTTTTTTCCTAAGTGTAGATGACAGCAAGGAAAAGCGGAGAAAAGGTCCGAAAATTCGGACCCGATGGAATTTTACTGTAGAGCGTTAAGA                  <  SRR3722030.2940821/100‑1 (MQ=60)
                                                                                  TCCTTACTGGTTTTTTCCTAAGTGTAGATGACAGCAAGGAAAAGCGGAGAAAAGGTCCGAAAATTCGGACCCGATGGAATTTTACTGTAGAGCGTTAAGA                  <  SRR3722030.2694325/100‑1 (MQ=60)
                                                                                     TTACTGGTTTTTTCCTAAGTGTAGATGACAGCAAGGAAAAGCGGAGAAAAGGTCCGAAAATTCGGACCCGATGGAATTTTACTGTAGAGCGTTAAGAATC               <  SRR3722030.2351343/100‑1 (MQ=60)
                                                                                          GGTTTTTTCCTAAGTGTAGATGACAGCAAGGAAAAGCGGAGAAAAGGTCCGAAAATTCGGACCCGATGGAATTTTACTGTAGAGCGTctgtctcttatac          >  SRR3722030.411521/1‑87 (MQ=60)
                                                                                          GGTTTTTTCCTAAGTGTAGATGACAGCAAGGAAAAGCGGAGAAAAGGTCCGAAAATTCGGACCCGATGGAATTTTACTGTAGAGCGTTAAGAATCTGCCA          >  SRR3722030.1717140/1‑100 (MQ=60)
                                                                                             TTTTTCCTAAGTGTAGATGACAGCAAGGAAAAGCGGAGAAAAGGTCCGAAAATTCGGACCCGATGGAATTTTACTGTAGAGCGTTAAGAATCTGCCAGGC       <  SRR3722030.2301787/100‑1 (MQ=60)
                                                                                               TTTCCTAAGTGTAGATGACAGCAAGGAAAAGCGGAGAAAAGGTCCGAAAATTCGGACCCGATGGAATTTTACTGTctgtctcttatacacatctgacgct     >  SRR3722030.180068/1‑75 (MQ=60)
                                                                                                  CCTAAGTGTAGATGACAGCAAGGAAAAGCGGAGAAAAGGTCCGAAAATTCGGACCCGATGGAATTTTACTGTAGAGCGTTAAGAATCTGCCAGGCGGTGT  <  SRR3722030.59447/100‑1 (MQ=60)
                                                                                                  CCTAAGTGTAGATGACAGCAAGGAAAAGCGGAGAAAAGGTCCGAAAATTCGGACCCGATGGAATTTTACTGTAGAGCGTTAAGAATCTGCCAGGCGGCGT  >  SRR3722030.1059479/1‑100 (MQ=60)
                                                                                                  |                                                                                                   
CGGCGGCGTAGGAGAACTGCAGGCAACGACCAGAAATGCAGCTGTCGCTGCGGCAACGAGAGGGAGCAGGCGCATAAATGTTTCCTTACTGGTTTTTTTCTAAGTGTAGATGACAGCAAGGAAAAGCGGAGAAAAGGTCCGAAAATTCGGACCCGATGGAATTTTACTGTAGAGCGTTAAGAATCTGCCAGGCGGCGT  >  NZ_CP009273/4367465‑4367662

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑