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 26 102.0 3326124 78.0% 2594376 98.8

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA CP002094 2,396,538 T→C D73G (GAC→GGC)  LLNZ_12635 ← hypothetical protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*CP0020942,396,5380TC100.0% 406.1 / NA 101D73G (GAC→GGC) LLNZ_12635hypothetical protein
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (52/49);  total (52/49)

Only 100 of 101 total aligned reads displayed.

TCAAAACACGCTCTGCTGACATTTTTAATAATTGAAATTTCTCAGGCTCTTTCGTCATCTTGATATTTTCCAAAATGACTTGTTGAGCTGCTCGGTCTTTTTCAACAAGAAGGGCATGATCCATTCCTCTTGAGACGGCTTCAATTGCCAAACTTCCTGACCCTGCAAATAAATCAAGAACACGACCTCCG  >  CP002094/2396443‑2396633
                                                                                               |                                                                                               
tCAAAACACGCTCTGCTGACATTTTTAATAATTGAAATTTCTCAGGCTCTTTCGTCATCTTGATATTTTCCAAAATGACTTGTTGAGCTGCTCGGCCtt                                                                                              >  1:806870/1‑99 (MQ=255)
tCAAAACACGCTCTGCTGACATTTTTAATAATTGAAATTTCTCAGGCTCTTTCGTCATCTTGATATTTTCCAAAATGACTTGTTGAGCTGCTCGGCCtt                                                                                              >  1:1078437/1‑99 (MQ=255)
tCAAAACACGCTCTGCTGACATTTTTAATAATTGAAATTTCTCAGGCTCTTTCGTCATCTTGATATTTTCCAAAATGACTTGTTGAGCTGCTCGGCCtt                                                                                              >  1:1548838/1‑99 (MQ=255)
  aaaaCACGCTCTGCTGACATTTTTAATAATTGAAATTTCTCAGGCTCTTTCGTCATCTTGATATTTTCCAAAATGACTTGTTGAGCTGCTCGGCCtttt                                                                                            >  2:24027/1‑99 (MQ=255)
   aaaCACGCTCTGCTGACATTTTTAATAATTGAAATTTCTCAGGCTCTTTCGTCATCTTGATATTTTCCAAAATGACTTGTTGAGCTGCTCGGCCttttt                                                                                           <  2:1468419/99‑1 (MQ=255)
   aaaCACGCTCTGCTGACATTTTTAATAATTGAAATTTCTCAGGCTCTTTCGTCATCTTGATATTTTCCAAAATGACTTGTTGAGCTGCTCGGCCttttt                                                                                           <  1:1331649/99‑1 (MQ=255)
     acacGCTCTGCTGACATTTTTAATAATTGAAATTTCTCAGGCTCTTTCGTCATCTTGATATTTTCCAAAATGACTTGTTGAGCTGCTCGGCCTTTTTca                                                                                         >  2:1586144/1‑99 (MQ=255)
          ctctGCTGACATTTTTAATAATTGAAATTTCTCAGGCTCTTTCGTCATCTTGATATTTTCCAAAATGACTTGTTGAGCTGCTCGGCCTTTGTCAACaag                                                                                    >  1:1564652/1‑99 (MQ=255)
             tgctgACATTTTTAATAATTGAAATTTCTCAGGCTCTTTCGTCATCTTGATATTTTCCAAAATGACTTGTTGAGCTGCTCGGCCTTTTTCAACaagaag                                                                                 <  2:67177/99‑1 (MQ=255)
              gctgACATTTTTAATAATTGAAATTTCTCAGGCTCTTTCGTCATCTTGATATTTTCCAAAATGACTTGTTGAGCTGCTCGGCCTTTTTCAACAAGAAgg                                                                                <  2:1399662/99‑1 (MQ=255)
              gctgACATTTTTAATAATTGAAATTTCTCAGGCTCTTTCGTCATCTTGATATTTTCCAAAATGACTTGTTGAGCTGCTCGGCCTTTTTCAACAAGAAgg                                                                                >  1:1506716/1‑99 (MQ=255)
               ctgACATTTTTAATAATTGAAATTTCTCAGGCTCTTTCGTCATCTTGATATTTTCCAAAATGACTTGTTGAGCTGCTCGGCCTTTTTCAACAAGAAggg                                                                               <  2:305658/99‑1 (MQ=255)
                  aCATTTTTAATAATTGAAATTTCTCAGGCTCTTTCGTCATCTTGATATTTTCCAAAATGACTTGTTGAGCTGCTCGGCCTTTTTCAACAAGAAGGGCAt                                                                            >  2:191263/1‑99 (MQ=255)
                  aCATTTTTAATAATTGAAATTTCTCAGGCTCTTTCGTCATCTTGATATTTTCCAAAATGACTTGTTGAGCTGCTCGGCCTTTTTCAACAAGAAGGGCAt                                                                            >  1:698196/1‑99 (MQ=255)
                  aCATTTTTAATAATTGAAATTTCTCAGGCTCTTTCGTCATCTTGATATTTTCCAAAATGACTTGTTGAGCTGCTCGGCCTTTTTCAACAAGAAGGGCAt                                                                            <  1:443329/99‑1 (MQ=255)
                    aTTTTTAATAATTGAAATTTCTCAGGCTCTTTCGTCATCTTGATATTTTCCAAAATGACTTGTTGAGCTGCTCGGCCTTTTTCAACAAGAAGGGCATGa                                                                          <  2:1609083/99‑1 (MQ=255)
                     tttttAATAATTGAAATTTCTCAGGCTCTTTCGTCATCTTGATATTTTCCAAAATGACTTGTTGAGCTGCTCGGCCTTTTTCAACAAGAAGGGCATGAt                                                                         >  1:218240/1‑99 (MQ=255)
                     tttttAATAATTGAAATTTCTCAGGCTCTTTCGTCATCTTGATATTTTCCAAAATGACTTGTTGAGCTGCTCGGCCTTTTTCAACAAGAAGGGCATGAt                                                                         <  2:1281312/99‑1 (MQ=255)
                      ttttAATAATTGAAATTTCTCAGGCTCTTTCGTCATCTTGATATTTTCCAAAATGAGTTGTTGAGCTGCTCGGCCTTTTTCAACAAGAAGGGCATGATc                                                                        >  1:1549646/1‑99 (MQ=255)
                      ttttAATAATTGAAATTTCTCAGGCTCTTTCGTCATCTTGATATTTTCCAAAATGACTTGTTGAGCTGCTCGGCCTTTTTCAACAAGAAGGGCATGATc                                                                        <  2:233055/99‑1 (MQ=255)
                      ttttAATAATTGAAATTTCTCAGGCTCTTTCGTCATCTTGATATTTTCCAAAATGACTTGTTGAGCTGCTCGGCCTTTTTCAACAAGAAGGGCATGATc                                                                        <  1:210613/99‑1 (MQ=255)
                       tttAATAATTGAAATTTCTCAGGCTCTTTCGTCATCTTGATATTTTCCAAAATGACTTGTTGAGCTGCTCGGCCTTTTTCAACAAGAAGGGCATGATcc                                                                       >  1:133124/1‑99 (MQ=255)
                       tttAATAATTGAAATTTCTCAGGCTCTTTCGTCATCTTGATATTTTCCAAAATGACTTGTTGAGCTGCTCGGCCTTTTTCAACAAGAAGGGCATGATcc                                                                       <  1:1108512/99‑1 (MQ=255)
                        ttAATAATTGAAATTTCTCAGGCTCTTTCGTCATCTTGATATTTTCCAAAATGACTTGTTGAGCTGCTCGGCCTTTTTCAACAAGAAGGGCATGATCCa                                                                      <  2:1338868/99‑1 (MQ=255)
                        ttAATAATTGAAATTTCTCAGGCTCTTTCGTCATCTTGATATTTTCCAAAATGACTTCTTGAGCTGCTCGGCCTTTTTCAACAAGAAGGGCATGATCCa                                                                      <  1:133658/99‑1 (MQ=255)
                         taataaTTGAAATTTCTCAGGCTCTTTCGTCATCTTGATATTTTCCAAAATGACTTGTTGAGCTGCTCGGCCTTTTTCAACAAGAAGGGCATGATCCAt                                                                     >  2:258176/1‑99 (MQ=255)
                         taataaTGGAAATTTCTCAGGCTCTTTCGTCATCTTGATATTTTCCAAAATGACTTGTTGAGCTGCTCGGCCTTTTTCAACAAGAAGGGCATGATCCAt                                                                     <  1:183910/99‑1 (MQ=255)
                          aataatTGAAATTTCTCAGGCTCTTTCGTCATCTTGATATTTTCCAAAATGACTTGTTGAGCTGCTCGGCCTTTTTCAACAAGAAGGGCATGATCCAtt                                                                    >  1:945910/1‑99 (MQ=255)
                          aataatTGAAATTTCTCAGGCTCTTTCGTCATCTTGATATTTTCCAAAATGACTTGTTGAGCTGCTCGGCCTTTTTCAACAAGAAGGGCATGATCCAtt                                                                    <  2:1282825/99‑1 (MQ=255)
                           ataatTGAAATTTCTCAGGCTCTTTCGTCATCTTGATATTTTCCAAAATGACTTGTTGAGCTGCTCGGCCTTTTTCAACAAGAAGGGCATGATCCATTc                                                                   >  1:1107254/1‑99 (MQ=255)
                           ataatTGAAATTTCTCAGGCTCTTTCGTCATCTTGATATTTTCCAAAATGACTTGTTGAGCTGCTCGGCCTTTTTCAACAAGAAGGGCATGATCCATTc                                                                   <  2:825806/99‑1 (MQ=255)
                               ttGAAATTTCTCAGGCTCTTTCGTCATCTTGATATTTTCCAAAATGACTTGTTGAGCTGCTCGGCCTTTTTCAACAAGAAGGGCATGATCCATTCctct                                                               >  2:1377556/1‑99 (MQ=255)
                               ttGAAATTTCTCAGGCTCTTTCGTCATCTTGATATTTTCCAAAATGACTTGTTGAGCTGCTCGGCCTTTTTCAACAAGAAGGGCATGATCCATTCctct                                                               >  1:1217774/1‑99 (MQ=255)
                               ttGAAATTTCTCAGGCTCTTTCGTCATCTTGATATTTTCCAAAATGACTTGTTGAGCTGCTCGGCCTTTTTCAACAAGAAGGGCATGATCCATTCctct                                                               <  2:32155/99‑1 (MQ=255)
                                    aTTTCTCAGGCTCTTTCGTCATCTTGATATTTTCCAAAATGACTTGTTGAGCTGCTCGGCCTTTTTCAACAAGAAGGGCATGATCCATTCCTCTTgaga                                                          >  2:818139/1‑99 (MQ=255)
                                     tttCTCAGGCTCTTTCGTCATCTTGATATTTTCCAAAATGACTTGTTGAGCTGCTCGGCCTTTTTCAACAAGAAGGGCATGATCCATTCCTCTTGAGAc                                                         >  2:1463336/1‑99 (MQ=255)
                                     tttCTCAGGCTCTTTCGTCATCTTGATATTTTCCAAAATGACTTGTTGAGCTGCTCGGCCTTTTTCAACAAGAAGGGCATGATCCATTCCTCTTGAGAc                                                         >  1:85454/1‑99 (MQ=255)
                                        ctcAGGCTCTTTCGTCATCTTGATATTTTCCAAAATGACTTGTTGAGCTGCTCGGCCTTTTTCAACAAGAAGGGCATGATCCATTCCTCTTGAGACGGc                                                      <  1:1010096/99‑1 (MQ=255)
                                         tcAGGCTCTTTCGTCATCTTGATATTTTCCAAAATGACTTGTTGAGCTGCTCGGCCTTTTTCAACAAGAAGGGCATGATCCATTCCTCTTGAGACGGCt                                                     <  2:1442101/99‑1 (MQ=255)
                                            ggCTCTTTCGTCATCTTGATATTTTCCAAAATGACTTGTTGAGCTGCTCGGCCTTTTTCAACAAGAAGGGCATGATCCATTCCTCTTGAGACGGCTTCa                                                  >  2:795981/1‑99 (MQ=255)
                                            ggCTCTTTCGTCATCTTGATATTTTCCAAAATGACTTGTTGAGCTGCTCGGCCTTTTTCAACAAGAAGGGCATGATCCATTCCTCTTGAGACGGCTTCa                                                  >  2:406242/1‑99 (MQ=255)
                                            gcctctTTCGTCATCTTGATATATTCCAAACTGACTTGTTGAGCTGCTCGGCCTTTTTCAACAAGAAGGGCATGATCCATTCCTCTTGAGACGGCTTCa                                                  >  2:779251/3‑99 (MQ=255)
                                             gCTCTTTCGTCATCTTGATATTTTCCAAAATGACTTGTTGAGCTGCTCGGCCTTTTTCAACAAGAAGGGCGTGATCCATTCCTCTTGAGACGGCTTCaa                                                 <  2:680365/99‑1 (MQ=255)
                                             gCTCTTTCGTCATCTTGATATTTTCCAAAATGACTTGTTGAGCTGCTCGGCCTTTTTCAACAAGAAGGGCATGATCCATTCCTCTTGAGACGGCTTCaa                                                 >  1:527633/1‑99 (MQ=255)
                                              ctctTTCGTCATCTTGATATTTTCCAAAATGACTTGTTGAGCTGCTCGGCCTTTTTCAACAAGAAGGGCATGATCCATTCCTCTTGAGACGGCTTCAAt                                                <  1:1215761/99‑1 (MQ=255)
                                              ctctTTCGTCATCTTGATATTTTCCAAAATGACTTGTTGAGCTGCTCGGCCTTTTTCAACAAGAAGGGCATGATCCATTCCTCTTGAGACGGCTTCAAt                                                <  2:1271241/99‑1 (MQ=255)
                                                ctTTCGTCATCTTGATATTTTCCAAAATGACTTGTTGAGCTGCTCGGCCTTTTTCAACAAGAAGGGCATGATCCATTCCTCTTGAGACGGCTTCACTTg                                              >  2:436959/1‑99 (MQ=255)
                                                ctTTCGTCATCTTGATATTTTCCAAAATGACTTGTTGAGCTGCTCGGCCTTTTTCAACAAGAAGGGCATGATCCATTCCTCTTGAGACGGCTTCAATTg                                              <  1:938867/99‑1 (MQ=255)
                                                 tttCGTCATCTTGATATTTTCCAAAATGACTTGTTGAGCTGCTCGGCCTTTTTCAACAAGAAGGGCATGATCCATTCCTCTTGAGACGGCTTCAATTGc                                             >  2:248891/1‑99 (MQ=255)
                                                      tCATCTTGATATTTTCCAAAATGACTTGTTGAGCTGCTCGGCCTTTTTCAACAAGAAGGGCATGATCCATTCCTCTTGAGACGGCTTCAATTGCCAAAc                                        >  1:1462780/1‑99 (MQ=255)
                                                       cATCTTGATATTTTCCAAAATGACTTGTTGAGCTGCTCGGCCTTTTTCAACAAGAAGGGCATGATCCATTCCTCTTGAGACGGCTTCAATTGCCAAACt                                       <  1:293066/99‑1 (MQ=255)
                                                       cATCTTGATATTTTCCAAAATGACTTGTTGAGCTGCTCGGCCTTTTTCAACAAGAAGGGCATGATCCATTCCTCTTGAGACGGCTTCAATTGCCAAACt                                       >  1:1468959/1‑99 (MQ=255)
                                                        aTCTTGATATTTTCCAAAATGACTTGTTGAGCTGCTCGGCCTTTTTCAACAAGAAGGGCATGATCCATTCCTCTTGAGACGGCTTCAATTGCCAAACtt                                      >  2:230027/1‑99 (MQ=255)
                                                        aTCTTGATATTTTCCAAAATGACTTGTTGAGCTGCTCGGCCTTTTTCAACAAGAAGGGCATGATCCATTCCTCTTGAGACGGCTTCAATTGCCAAACtt                                      >  2:278507/1‑99 (MQ=255)
                                                         tCTTGATATTTTCCAAAATGACTTGTTGAGCTGCTCGGCCTTTTTCAACAAGAAGGGCATGATCCATTCCTCTTGAGACGGCTTCAATTGCCAAACTTc                                     <  1:939650/99‑1 (MQ=255)
                                                         tCTTGATATTTTCCAAAATGACTTGTTGAGCTGCTCGGCCTTTTTCAACAAGAAGGGCATGATCCATTCCTCTTGAGACGGCTTCAATTGCCAAACTTc                                     >  1:1560860/1‑99 (MQ=255)
                                                          cTTGATATTTTCCAAAATGACTTGTTGAGCTGCTCGGCCTTTTTCAACAAGAAGGGCATGATCCATTCCTCTTGAGACGGCTTCAATTGCCAAACTTcc                                    <  1:869124/99‑1 (MQ=255)
                                                           ttGATATTTTCCAAAATGACTTGTTGAGCTGCTCGGCCTTTTTCAACAAGAAGGGCATGATCCATTCCTCTTGAGACGGCTTCAATTGCCAAACTTCCt                                   >  2:285680/1‑99 (MQ=255)
                                                           ttGATATTTTCCAAAATGACTTGTTGAGCTGCTCGGCCTTTTTCAACAAGAAGGGCATGATCCATTCCTCTTGAGACGGCTTCAATTGCCAAACTTCCt                                   <  2:1229667/99‑1 (MQ=255)
                                                           ttGATATTTTCCAAAATGACTTGTTGAGCTGCTCGGCCTTTTTCAACAAGAAGGGCATGATCCATTCCTCTTGAGACGGCTTCAATTGCCAAACTTCCt                                   >  1:855039/1‑99 (MQ=255)
                                                            tGATATTTTCCAAAATGACTTGTTGAGCTGCTCGGCCTTTTTCAACAAGAAGGGCATGATCCATTCCTCTTGAGACGGCTTCAATTGCCAAACTTCCTg                                  >  2:1309467/1‑99 (MQ=255)
                                                             gATATTTTCCAAAATGACTTGTTGAGCTGCTCGGCCTTTTTCAACAAGAAGGGCATGATCCATTCCTCTTGAGACGGCTTCAATTGCCAAACTTCCTGa                                 >  2:707323/1‑99 (MQ=255)
                                                             gATATTTTCCAAAATGACTTGTTGAGCTGCTCGGCCTTTTTCAACAAGAAGGGCATGATCCATTCCTCTTGAGACGGCTTCAATTGCCAAACTTCCTGa                                 <  2:1490669/99‑1 (MQ=255)
                                                               tatTTTCCAAAATGACTTGTTGAGCTGCTCGGCCTTTTTCAACAAGAAGGGCATGATCCATTCCTCTTGAGACGGCTTCAATTGCCAAACTTCCTGAcc                               <  2:232413/99‑1 (MQ=255)
                                                               tatTTTCCAAAATGACTTGTTGAGCTGCTCGGCCTTTTTCAACAAGAAGGGCATGATCCATTCCTCTTGAGACGGCTTCAATTGCCAAACTTCCTGAcc                               >  2:1048106/1‑99 (MQ=255)
                                                                 ttttCCAAAATGACTTGTTGAGCTGCTCGGCCTTTTTCAACAAGAAGGGCATGATCCATTCCTCTTGAGACGGCTTCAATTGCCAAACTTCCTGAccca                             >  2:1120396/1‑98 (MQ=255)
                                                                 ttttCCAAAATGACTTGTTGAGCTGCTCGGCCTTTTTCAACAAGAAGGGCATGATCCATTCCTCTTGAGACGGCTTCAATTGCCAAACTTCCTGACCCt                             <  1:931197/99‑1 (MQ=255)
                                                                 ttttCCAAAATGACTTGTTGAGCTGCTCGGCCTTTTTCAACAAGAAGGGCATGATCCATTCCTCTTGAGACGGCTTCAATTGCCAAACTTCCTGACCCt                             >  2:732101/1‑99 (MQ=255)
                                                                 ttttCCAAAATGACTTGTTGAGCTGCTCGGCCTTTTTCAACAAGAAGGGCATGATCCATTCCTCTTGAGACGGCTTCAATTGCCAAACTTCCTGACCCt                             >  2:1033163/1‑99 (MQ=255)
                                                                  tttCCAAAATGACTTGTTTAGCTGCTCGGCCTTTGTCAACAAGAAGGGCATGATCCATTCCTCTTGAGACGGCTTCAATTGCCAAACTTCCTGACCCTg                            <  1:1548994/99‑1 (MQ=255)
                                                                  tttCCAAAATGACTTGTTGAGCTGCTCGGCCTTTTTCAACAAGAAGGGCATGATCCATTCCTCTTGAGACGGCTTCAATTGCCAAACTTCCTGACCCTg                            <  2:431578/99‑1 (MQ=255)
                                                                    tCCAAAATGACTTGTTGAGCTGCTCGGCCTTTTTCAACAAGAAGGGCATGATCCATTCCTCTTGAGACGGCTTCAATTGCCAAACTTCCTGACCCTGCa                          <  1:530770/99‑1 (MQ=255)
                                                                      cAAAATGACTTGTTGAGCTGCTCGGCCTTTTTCAACAAGAAGGGCATGATCCATTCCTCTTGAGACGGCTTCAATTGCCAAACTTCCTGACCCTGCaaa                        <  2:1653533/99‑1 (MQ=255)
                                                                      cAAAATGACTTGTTGAGCTGCTCGGCCTTTTTCAACAAGAAGAGAATGATCCATTCCTCTTGAGACGGCTTTAATTGCCAAGCTTCCTAACCCTGCaaa                        <  2:40289/99‑1 (MQ=255)
                                                                          aTGACTTGTTGAGCTGCTCGGCCTTTTTCAACAAGAAGGGCATGATCCATTCCTCTTGAGACGGCTTCAATTGCCAAACTTCCTGACCCTGCaaataaa                    <  2:1340419/99‑1 (MQ=255)
                                                                             aCTTGTTGAGCTGCTCGGCCTTTTTCAACAAGAAGGGCATGATCCATTCCTCTTGAGACGGCTTCAATTGCCAAACTTCCTGACCCTGCAAATAAATCa                 >  2:671386/1‑99 (MQ=255)
                                                                               ttgttgAGCTGCTCGGCCTTTTTCAACAAGAAGGGCATGATCCATTCCTCTTGAGACGGCTTCAATTGCCAAACTTCCTGACCCTGCAAATAAATCAAg               <  2:1272219/99‑1 (MQ=255)
                                                                               ttgttgAGCTGCTCGGCCTTTTTCAACAAGAAGGGCATGATCCATTCCTCTTGAGACGGCTTCAATTGCCAAACTTCCTGACCCTGCAAATAAATCAAg               >  1:479601/1‑99 (MQ=255)
                                                                               ttgttgAGCTGCTCGGCCTTTTTCAACAAGAAGGGCATGATCCATTCCTCTTGAGACGGCTTCAATTGCCAAACTTCCTGACCCTGCAAATAAATCAAg               >  1:273458/1‑99 (MQ=255)
                                                                                 gttgAGCTGCTCGGCCTTTTTCAACAAGAAGGGCATGATCCATTCCTCTTGAGACGGCTTCAATTGCCAAACTTCCTGACCCTGCAAATAAATCAAGaa             >  2:1018541/1‑99 (MQ=255)
                                                                                  ttgAGCTGCTCGGCCTTTTTCAACAAGAAGGGCATGATCCATTCCTCTTGAGACGGCTTCAATTGCCAAACTTCCTGACCCTGCAAATAAATCAAGAac            >  1:1036421/1‑99 (MQ=255)
                                                                                  ttgAGCTGCTCGGCCTTTTTCAACAAGAAGGGCATGATCCATTCCTCTTGAGACGGCTTCAATTGCCAAACTTCCTGACCCTGCAAATAAATCAAGAac            >  2:1074821/1‑99 (MQ=255)
                                                                                    gAGCTGCTCGGCCTTTTTCAACAAGAAGGGCATGATCCATTCCTCTTGAGACGGCTTCAATTGCCAAACTTCCTGACCCTGCAAATAAATCAAGAacac          >  1:502335/1‑99 (MQ=255)
                                                                                    gAGCTGCTCGGCCTTTTTCAACAAGAAGGGCATGATCCATTCCTCTTGAGACGGCTTCAATTGCCAAACTTCCTGACCCTGCAAATAAATCAAGAacac          <  2:801615/99‑1 (MQ=255)
                                                                                     aGCTGCTCGGCCTTTTTCAACAAGAAGGGCATGATCCATTCCTCTTGAGACGGCTTCAATTGCCAAACTTCCTGACCCTGCAAATAAATCAAGa              >  2:358104/1‑94 (MQ=255)
                                                                                     aGCTGCTCGGCCTTTTTCAACAAGAAGGGCATGATCCATTCCTCTTGAGACGGCTTCAATTGCCAAACTTCCTGACCCTGCAAATAAATCAAGa              <  1:358104/94‑1 (MQ=255)
                                                                                     aGCTGCTCGGCCTTTTTCAACAAGAAGGGCATGATCCATTCCTCTTGAGACGGCTTCAATTGCCAAACTTCCTGACCCTGCAAATAAATCAAGAACACg         >  1:298608/1‑99 (MQ=255)
                                                                                       ctgctCGGCCTTTTTCAACAAGAAGGGCATGATCCATTCCTCTTGAGACGGCTTCAATTGCCAAACTTCCTGACCCTGCACATAAATCAAGAACACGAc       >  2:1324965/1‑99 (MQ=255)
                                                                                        tgctCGGCCTTTTTCAACAAGAAGGGCATGATCCATTCCTCTTGAGACGGCTTCAATTGCCAAACTTCCTGACCCTGCAAATAAATCAAGAACACGAcc      <  2:670507/99‑1 (MQ=255)
                                                                                        tgctCGGCCTTTTTCAACAAGAAGGGCATGATCCATTCCTCTTGAGACGGCTTCAATTGCCAAACTTCCTGACCCTGCAAATAAATCAAGAACACAAcc      >  2:1164107/1‑99 (MQ=255)
                                                                                         gctCGGCCTTTTTCAACAAGAAGGGCATGATCCATTCCTCTTGAGACGGCTTCAATTGCCAAACTTCCTGACCCTGCAAATAAATCAAGAACACGACCt     <  2:85454/99‑1 (MQ=255)
                                                                                         gctCGGCCTTTTTCAACAAGAAGGGCATGATCCATTCCTCTTGAGACGGCTTCAATTGCCAAACTTCCTGACCCTGCAAATAAATCAAGAACACGACCt     <  2:1626870/99‑1 (MQ=255)
                                                                                          ctCGGCCTTTTTCAACAAGAAGGGCATGATCCATTCCTCTTGAGACGGCTTCAATTGCCAAACTTCCTGACCCTGCAAATAAATCAAGAACACGACCTc    <  2:554964/99‑1 (MQ=255)
                                                                                          ctCGGCCTTTTTCAACAAGAAGGGCATGATCCATTCCTCTTGAGACGGCTTCAATTGCCAAACTTCCTGACCCTGCAAATAAATCAAGAACACGACCTc    >  2:24312/1‑99 (MQ=255)
                                                                                          ctCGGCCTTTTTCAACAAGAAGGGCATGATCCATTCCTCTTGAGACGGCTTCAATTGCCAAACTTCCTGACCCTGCAAATAAATCAAGAACACGACCTc    <  2:15493/99‑1 (MQ=255)
                                                                                          ctCGGCCTTTTTCAACAAGAAGGGCATGATCCATTCCTCTTGAGACGGCTTCAATTGCCAAACTTCCTGACCCTGCAAATAAATCAAGAACACGACCTc    <  1:1262455/99‑1 (MQ=255)
                                                                                          ctCGGCCTTTTTCAACAAGAAGGGCATGATCCATTCCTCTTGAGACGGCTTCAATTGCCAAACTTCCTGACCCTGCAAATAAATCAAGAACACGACCTc    <  1:1022222/99‑1 (MQ=255)
                                                                                           tCGGCCTTTTTCAACAAGAAGGGCATGATCCATTCCTCTTGAGACGGCTTCAATTGCCAAACTTCCTGACCCTGCAAATAAATCAAGAACACGACCTcc   >  2:130971/1‑99 (MQ=255)
                                                                                           tCGGCCTTTTTCAACAAGAAGGGCATGATCCATTCCTCTTGAGACGGCTTCAATTGCCAAACTTCCTGACCCTGCAAATAAATCAAGAACACGACCTcc   <  1:252594/99‑1 (MQ=255)
                                                                                            cGGCCTTTTTCAACAAGAAGGGCATGATCCATTCCTCTTGAGACGGCTTCAATTGCCAAACTTCCTGACCCTGCAAATAAATCAAGAACACGACCTCCg  <  1:1054705/99‑1 (MQ=255)
                                                                                               |                                                                                               
TCAAAACACGCTCTGCTGACATTTTTAATAATTGAAATTTCTCAGGCTCTTTCGTCATCTTGATATTTTCCAAAATGACTTGTTGAGCTGCTCGGTCTTTTTCAACAAGAAGGGCATGATCCATTCCTCTTGAGACGGCTTCAATTGCCAAACTTCCTGACCCTGCAAATAAATCAAGAACACGACCTCCG  >  CP002094/2396443‑2396633

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

BRESEQ :: bam2aln output
GTCAAAACACGCTCTGCTGACATTTTTAATAATTGAAATTTCTCAGGCTCTTTCGTCATCTTGATATTTTCCAAAATGACTTGTTGAGCTGCTCGGTCTTTTTCAACAAGAAGGGCATGATCCATTCCTCTTGAGACGGCTTCAATTGCCAAACTTCCTGACCCTGCAAATAAATCAAGAACACGACCTCCGTCGA  >  CP002094/2396442‑2396637
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GTCAAAACACGCTCTGCTGACATTTTTAATAATTGAAATTTCTCAGGCTCTTTCGTCATCTTGATATTTTCCAAAATGACTTGTTGAGCTGCTCGGCCTT                                                                                                  >  SRR7892090.813290/1‑100 (MQ=60)
GTCAAAACACGCTCTGCTGACATTTTTAATAATTGAAATTTCTCAGGCTCTTTCGTCATCTTGATATTTTCCAAAATGACTTGTTGAGCTGCTCGGCCTT                                                                                                  >  SRR7892090.1085815/1‑100 (MQ=60)
GTCAAAACACGCTCTGCTGACATTTTTAATAATTGAAATTTCTCAGGCTCTTTCGTCATCTTGATATTTTCCAAAATGACTTGTTGAGCTGCTCGGCCTT                                                                                                  >  SRR7892090.1558351/1‑100 (MQ=60)
    AAACACGCTCTGCTGACATTTTTAATAATTGAAATTTCTCAGGCTCTTTCGTCATCTTGATATTTTCCAAAATGACTTGTTGAGCTGCTCGGCCTTTTTC                                                                                              <  SRR7892090.1339626/100‑1 (MQ=60)
          GCTCTGCTGACATTTTTAATAATTGAAATTTCTCAGGCTCTTTCGTCATCTTGATATTTTCCAAAATGACTTGTTGAGCTGCTCGGCCTTTGTCAACAAG                                                                                        >  SRR7892090.1574313/1‑100 (MQ=60)
              TGCTGACATTTTTAATAATTGAAATTTCTCAGGCTCTTTCGTCATCTTGATATTTTCCAAAATGACTTGTTGAGCTGCTCGGCCTTTTTCAACAAGAAGG                                                                                    >  SRR7892090.1515816/1‑100 (MQ=60)
                  GACATTTTTAATAATTGAAATTTCTCAGGCTCTTTCGTCATCTTGATATTTTCCAAAATGACTTGTTGAGCTGCTCGGCCTTTTTCAACAAGAAGGGCAT                                                                                >  SRR7892090.704051/1‑100 (MQ=60)
                   ACATTTTTAATAATTGAAATTTCTCAGGCTCTTTCGTCATCTTGATATTTTCCAAAATGACTTGTTGAGCTGCTCGGCCTTTTTCAACAAGAAGGGCATG                                                                               <  SRR7892090.447470/100‑1 (MQ=60)
                     ATTTTTAATAATTGAAATTTCTCAGGCTCTTTCGTCATCTTGATATTTTCCAAAATGACTTGTTGAGCTGCTCGGCCTTTTTCAACAAGAAGGGCATGAT                                                                             >  SRR7892090.220279/1‑100 (MQ=60)
                      TTTTTAATAATTGAAATTTCTCAGGCTCTTTCGTCATCTTGATATTTTCCAAAATGAGTTGTTGAGCTGCTCGGCCTTTTTCAACAAGAAGGGCATGATC                                                                            >  SRR7892090.1559165/1‑100 (MQ=60)
                       TTTTAATAATTGAAATTTCTCAGGCTCTTTCGTCATCTTGATATTTTCCAAAATGACTTGTTGAGCTGCTCGGCCTTTTTCAACAAGAAGGGCATGATCC                                                                           <  SRR7892090.212580/100‑1 (MQ=60)
                       TTTTAATAATTGAAATTTCTCAGGCTCTTTCGTCATCTTGATATTTTCCAAAATGACTTGTTGAGCTGCTCGGCCTTTTTCAACAAGAAGGGCATGATCC                                                                           >  SRR7892090.134299/1‑100 (MQ=60)
                        TTTAATAATTGAAATTTCTCAGGCTCTTTCGTCATCTTGATATTTTCCAAAATGACTTGTTGAGCTGCTCGGCCTTTTTCAACAAGAAGGGCATGATCCA                                                                          <  SRR7892090.1115989/100‑1 (MQ=60)
                         TTAATAATTGAAATTTCTCAGGCTCTTTCGTCATCTTGATATTTTCCAAAATGACTTCTTGAGCTGCTCGGCCTTTTTCAACAAGAAGGGCATGATCCAT                                                                         <  SRR7892090.134843/100‑1 (MQ=60)
                          TAATAATTGAAATTTCTCAGGCTCTTTCGTCATCTTGATATTTTCCAAAATGACTTGTTGAGCTGCTCGGCCTTTTTCAACAAGAAGGGCATGATCCATT                                                                        >  SRR7892090.952890/1‑100 (MQ=60)
                          TAATAATGGAAATTTCTCAGGCTCTTTCGTCATCTTGATATTTTCCAAAATGACTTGTTGAGCTGCTCGGCCTTTTTCAACAAGAAGGGCATGATCCATT                                                                        <  SRR7892090.185590/100‑1 (MQ=60)
                           AATAATTGAAATTTCTCAGGCTCTTTCGTCATCTTGATATTTTCCAAAATGACTTGTTGAGCTGCTCGGCCTTTTTCAACAAGAAGGGCATGATCCATTC                                                                       >  SRR7892090.1114727/1‑100 (MQ=60)
                               ATTGAAATTTCTCAGGCTCTTTCGTCATCTTGATATTTTCCAAAATGACTTGTTGAGCTGCTCGGCCTTTTTCAACAAGAAGGGCATGATCCATTCCTCT                                                                   >  SRR7892090.1225515/1‑100 (MQ=60)
                                     ATTTCTCAGGCTCTTTCGTCATCTTGATATTTTCCAAAATGACTTGTTGAGCTGCTCGGCCTTTTTCAACAAGAAGGGCATGATCCATTCCTCTTGAGAC                                                             >  SRR7892090.86194/1‑100 (MQ=60)
                                        ttttttcttttctttttttttttttttaaaaaaatgttttttgtgGAGCTGCTCGGCCTTTTTCAACAAGAAGGGCATGATCCATTCCTCTTGAGACGGC                                                          <  SRR7892090.1453204/55‑1 (MQ=60)
                                         ttttttttctgttttttttttttttttccaaaaatgtctTTGTTGAGCTGCTCGGCCTTTTTCAACAAGAAGGGCATGATCCATTCCTCTTGAGACGGCT                                                         <  SRR7892090.150150/61‑1 (MQ=60)
                                         CTCAGGCTCTTTCGTCATCTTGATATTTTCCAAAATGACTTGTTGAGCTGCTCGGCCTTTTTCAACAAGAAGGGCATGATCCATTCCTCTTGAGACGGCT                                                         <  SRR7892090.1017263/100‑1 (MQ=60)
                                          tttggcaacgataatattccattttttatattcagggtcaagTGAGCTGCTCGGCCTTTTTCAACAAGAAGGGCATGATCCATTCCTCTTGAGACGGCTT                                                        <  SRR7892090.606398/58‑1 (MQ=60)
                                             GGCTCTTTCGTCATCTTGATATTTTCCAAAATGACTTGTTGAGCTGCTCGGCCTTTTTCAACAAGAAGGGCATGATCCATTCCTCTTGAGACGGCTTCAA                                                     >  SRR7892090.532426/1‑100 (MQ=60)
                                               CTCTTTCGTCATCTTGATATTTTCCAAAATGACTTGTTGAGCTGCTCGGCCTTTTTCAACAAGAAGGGCATGATCCATTCCTCTTGAGACGGCTTCAATT                                                   <  SRR7892090.1223498/100‑1 (MQ=60)
                                                 CTTTCGTCATCTTGATATTTTCCAAAATGACTTGTTGAGCTGCTCGGCCTTTTTCAACAAGAAGGGCATGATCCATTCCTCTTGAGACGGCTTCAATTGC                                                 <  SRR7892090.945840/100‑1 (MQ=60)
                                                      GTCATCTTGATATTTTCCAAAATGACTTGTTGAGCTGCTCGGCCTTTTTCAACAAGAAGGGCATGATCCATTCCTCTTGAGACGGCTTCAATTGCCAAAC                                            >  SRR7892090.1471442/1‑100 (MQ=60)
                                                       TCATCTTGATATTTTCCAAAATGACTTGTTGAGCTGCTCGGCCTTTTTCAACAAGAAGGGCATGATCCATTCCTCTTGAGACGGCTTCAATTGCCAAACT                                           >  SRR7892090.1477686/1‑100 (MQ=60)
                                                        CATCTTGATATTTTCCAAAATGACTTGTTGAGCTGCTCGGCCTTTTTCAACAAGAAGGGCATGATCCATTCCTCTTGAGACGGCTTCAATTGCCAAACTT                                          <  SRR7892090.295887/100‑1 (MQ=60)
                                                         ATCTTGATATTTTCCAAAATGACTTGTTGAGCTGCTCGGCCTTTTTCAACAAGAAGGGCATGATCCATTCCTCTTGAGACGGCTTCAATTGCCAAACTTC                                         >  SRR7892090.1570477/1‑100 (MQ=60)
                                                          TCTTGATATTTTCCAAAATGACTTGTTGAGCTGCTCGGCCTTTTTCAACAAGAAGGGCATGATCCATTCCTCTTGAGACGGCTTCAATTGCCAAACTTCC                                        <  SRR7892090.946624/100‑1 (MQ=60)
                                                           CTTGATATTTTCCAAAATGACTTGTTGAGCTGCTCGGCCTTTTTCAACAAGAAGGGCATGATCCATTCCTCTTGAGACGGCTTCAATTGCCAAACTTCCT                                       <  SRR7892090.875816/100‑1 (MQ=60)
                                                           CTTGATATTTTCCAAAATGACTTGTTGAGCTGCTCGGCCTTTTTCAACAAGAAGGGCATGATCCATTCCTCTTGAGACGGCTTCAATTGCCAAACTTCCT                                       >  SRR7892090.861698/1‑100 (MQ=60)
                                                                 tttacaaaaaacaattttTTGAGCTGCTCGGCCTTTTTCAACAAGAAGGGCATGATCCATTCCTCTTGAGACGGCTTCAATTGCCAAACTTCCTGACCCT                                 <  SRR7892090.290309/82‑1 (MQ=60)
                                                                  TTTTCCAAAATGACTTGTTGAGCTGCTCGGCCTTTTTCAACAAGAAGGGCATGATCCATTCCTCTTGAGACGGCTTCAATTGCCAAACTTCCTGACCCTG                                <  SRR7892090.938143/100‑1 (MQ=60)
                                                                   TTTCCAAAATGACTTGTTTAGCTGCTCGGCCTTTGTCAACAAGAAGGGCATGATCCATTCCTCTTGAGACGGCTTCAATTGCCAAACTTCCTGACCCTGC                               <  SRR7892090.1558508/100‑1 (MQ=60)
                                                                     TCCAAAATGACTTGTTGAGCTGCTCGGCCTTTTTCAACAAGAAGGGCATGATCCATTCCTCTTGAGACGGCTTCAATTGCCAAACTTCCTGACCCTGCAA                             <  SRR7892090.535582/100‑1 (MQ=60)
                                                                               CTTGTTGAGCTGCTCGGCCTTTTTCAACAAGAAGGGCATGATCCATTCCTCTTGAGACGGCTTCAATTGCCAAACTTCCTGACCCTGCAAATAAATCAAG                   >  SRR7892090.276087/1‑100 (MQ=60)
                                                                               CTTGTTGAGCTGCTCGGCCTTTTTCAACAAGAAGGGCATGATCCATTCCTCTTGAGACGGCTTCAATTGCCAAACTTCCTGACCCTGCAAATAAATCAAG                   >  SRR7892090.483966/1‑100 (MQ=60)
                                                                                 atcTGAGCTGCTCGGCCTTTTTCAACAAGAAGGGCATGATCCATTCCTCTTGAGACGGCTTCAATTGCCAAACTTCCTGACCCTGCAAATAAATCAAGAA                 <  SRR7892090.361616/97‑1 (MQ=60)
                                                                                  GTTGAGCTGCTCGGCCTTTTTCAACAAGAAGGGCATGATCCATTCCTCTTGAGACGGCTTCAATTGCCAAACTTCCTGACCCTGCAAATAAATCAAGAAC                >  SRR7892090.1043654/1‑100 (MQ=60)
                                                                                    TGAGCTGCTCGGCCTTTTTCAACAAGAAGGGCATGATCCATTCCTCTTGAGACGGCTTCAATTGCCAAACTTCCTGACCCTGCAAATAAATCAAGAACAC              >  SRR7892090.506874/1‑100 (MQ=60)
                                                                                     GAGCTGCTCGGCCTTTTTCAACAAGAAGGGCATGATCCATTCCTCTTGAGACGGCTTCAATTGCCAAACTTCCTGACCCTGCAAATAAATCAAGAACACG             >  SRR7892090.301478/1‑100 (MQ=60)
                                                                                      AGCTGCTCGGCCTTTTTCAACAAGAAGGGCATGATCCATTCCTCTTGAGACGGCTTCAATTGCCAAACTTCCTGACCttgccaaaaaaaaaaaaaaaaaa            >  SRR7892090.210876/1‑77 (MQ=60)
                                                                                           CTCGGCCTTTTTCAACAAGAAGGGCATGATCCATTCCTCTTGAGACGGCTTCAATTGCCAAACTTCCTGACCCTGCAAATAAATCAAGAACACGACCTCC       <  SRR7892090.1270296/100‑1 (MQ=60)
                                                                                           CTCGGCCTTTTTCAACAAGAAGGGCATGATCCATTCCTCTTGAGACGGCTTCAATTGCCAAACTTCCTGACCCTGCAAATAAATCAAGAACACGACCTCC       <  SRR7892090.1029418/100‑1 (MQ=60)
                                                                                            TCGGCCTTTTTCAACAAGAAGGGCATGATCCATTCCTCTTGAGACGGCTTCAATTGCCAAACTTCCTGACCCTGCAAATAAATCAAGAACACGACCTCCG      <  SRR7892090.255010/100‑1 (MQ=60)
                                                                                             CGGCCTTTTTCAACAAGAAGGGCATGATCCATTCCTCTTGAGACGGCTTCAATTGCCAAACTTCCTGACCCTGCAAATAAATCAAGAACACGACCTCCGT     <  SRR7892090.1062006/100‑1 (MQ=60)
                                                                                              GGCCTTTTTCAACAAGAAGGGCATGATCCATTCCTCTTGAGACGGCTTCAATTGCCAAACTTCCTGACCCTGCAAATAAATCAAGAACACGACCTCCGTC    >  SRR7892090.1161632/1‑100 (MQ=60)
                                                                                                CCTTTTTCAACAAGAAGGGCATGATCCATTCCTCTTGAGACGGCTTCAATTGCCAAACTTCCTGACCCTGCAAATAAATCAAGAACACGACCTCCGTCGA  >  SRR7892090.470499/1‑100 (MQ=60)
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GTCAAAACACGCTCTGCTGACATTTTTAATAATTGAAATTTCTCAGGCTCTTTCGTCATCTTGATATTTTCCAAAATGACTTGTTGAGCTGCTCGGTCTTTTTCAACAAGAAGGGCATGATCCATTCCTCTTGAGACGGCTTCAATTGCCAAACTTCCTGACCCTGCAAATAAATCAAGAACACGACCTCCGTCGA  >  CP002094/2396442‑2396637

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑