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 305,770 T→C L274L (TTA→TTG)  LLNZ_01670 ← Nisin biosynthesis two‑component system, sensor histidine kinase NisK

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*CP002094305,7700TC99.0% 424.3 / NA 104L274L (TTA→TTG) LLNZ_01670Nisin biosynthesis two‑component system, sensor histidine kinase NisK
Reads supporting (aligned to +/- strand):  ref base T (0/0);  major base C (54/49);  minor base A (0/1);  total (54/50)
Fisher's exact test for biased strand distribution p-value = 4.81e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

Only 100 of 104 total aligned reads displayed.

AAAATCCTCCAGGGAGATTCTCGCTTTGTAATCATTTTCATCATTCAAAAGTTTTGTATAACTAATCATTGTGTTAAAATACTTGTCAAAAACAGTTAAACTATTTTTCATTGACTCAATAAAATCAGCTTGTTGTTCATTTACTTCAGTCATCTCTAGCAGTTCAATATTTCCTTTTAATACTGTTAAAGG  >  CP002094/305674‑305865
                                                                                                |                                                                                               
aaaaTCCTCCAGGGAGATTATCGCTTTGTAATCATTTTCATCATTCAAAAGTTTTGTATAACTAATCATTGTGTTAAAATACTTGTCAAAAACAGTCaa                                                                                               >  2:1488276/1‑99 (MQ=255)
 aaaTCCTCCAGGGAGATTATCGCTTTGTAATCATTTTCATCATTCAAAAGTTTTGTATAACTAATCATTGTGTTAAAATACTTGTCAAAAACAGTCaaa                                                                                              <  1:1475497/99‑1 (MQ=255)
 aaaTCCTCCAGGGAGATTATCGCTTTGTAATCATTTTCATCATTCAAAAGTTTTGTATAACTAATCATTGTGTTAAAATACTTGTCAAAAACAGTCaaa                                                                                              <  2:752520/99‑1 (MQ=255)
    tcctccAGGGAGATTATCGCTTTGTAATCATTTTCATCATTCAAAAGTTTTGTATAACTAATCATTGTGTTAAAATACTTGTCAAAAACAGTCAAACTa                                                                                           <  1:964498/99‑1 (MQ=255)
    tcctccAGGGAGATTATCGCTTTGTAATCATTTTCATCATTCAAAAGTTTTGTATAACTAATCATTGTGTTAAAATACTTGTCAAAAACAGTCAAACTa                                                                                           <  2:1597538/99‑1 (MQ=255)
      ctccAGGGAGATTATCGCTTTGTAATCATTTTCATCATTCAAAAGTTTTGTATAACTAATCATTGTGTTAAAATACTTGTCAAAAACAGTCAAACTAtt                                                                                         <  1:577766/99‑1 (MQ=255)
       tccAGGGAGATTATCGCTTTGTAATCATTTTCATCATTCAAAAGTTTTGTATAACTAATCATTGTGTTAAAATACTTGTCAAAAACAGTCAAACTAttt                                                                                        <  2:364922/99‑1 (MQ=255)
       tccAGGGAGATTATCGCTTTGTAATCATTTTCATCATTCAAAAGTTTTGTATAACTAATCATTGTGTTAAAATACTTGTCAAAAACAGTCAAACTAttt                                                                                        >  1:1274204/1‑99 (MQ=255)
         cAGGGAGATTATCGCTTTGTAATCATTTTCATCATTCAAAAGTTTTGTATAACTAATCATTGTGTTAAAATACTTGTCAAAAACAGTCAAACTAttttt                                                                                      >  2:1264443/1‑99 (MQ=255)
           gggAGATTATCGCTTTGTAATCATTTTCATCATTCAAAAGTTTTGTATAACTAATCATTGTGTTAAAATACTTGTCAAAAACAGTCAAACTATTTTTCa                                                                                    >  2:1505725/1‑99 (MQ=255)
           gggAGATTATCGCTTTGTAATCATTTTCATCATTCAAAAGTTTTGTATAACTAATCATTGTGTTAAAATACTTGTCAAAAACAGTCAAACTATTTTTCa                                                                                    >  2:24643/1‑99 (MQ=255)
             gagaTTATCGCTTTGTAATCATTTTCATCATTCAAAAGTTTTGTATAACTAATCATTGTGTTAAAATACTTGTCAAAAACAGTCAAACTATTTTTCAtt                                                                                  <  2:1251334/99‑1 (MQ=255)
             gagaTTATCGCTTTGTAATCATTTTCATCATTCAAAAGTTTTGTATAACTAATCATTGTGTTAAAATACTTGTCAAAAACAGTCAAACTATTTTTCAtt                                                                                  >  2:23717/1‑99 (MQ=255)
             gagaTTATCGCTTTGTAATCATTTTCATCATTCAAAAGTTTTGTATAACTAATCATTGTGTTAAAATACTTGTCAAAAACAGTCAAACTATTTTTCAtt                                                                                  >  1:1603222/1‑99 (MQ=255)
               gaTTATCGCTTTGTAATCATTTTCATCATTCAAAAGTTTTGTATAACTAATCATTGTGTTAAAATACTTGTCAAAAACAGTCAAACTATTTTTCATTGa                                                                                <  2:1554757/99‑1 (MQ=255)
                  tatcGCTTTGTAATCATTTTCATCATTCAAAAGTTTTGTATAACTAATCATTGTGTTAAAATACTTGTCAAAAACAGTCAAACTATTTTTCATTGACTc                                                                             <  2:172969/97‑1 (MQ=255)
                   atcGCTTTGTAATCATTTTCATCATTCAAAAGTTTTGTATAACTAATCATTGTGTTAAAATACTTGTCAAAAACAGTCAAACTATTTTTCATTGACTCa                                                                            <  2:502187/98‑1 (MQ=255)
                    tcGCTTTGTAATCATTTTCATCATTCAAAAGTTTTGTATAACTAATCATTGTGTTAAAATACTTGTCAAAAACAGTCAAACTATTTTTCATTGACTCaa                                                                           <  1:119450/99‑1 (MQ=255)
                      gCTTTGTAATCATTTTCATCATTCAAAAGTTTTGTATAACTAATCATTGTGTTAAAATACTTGTCAAAAACAGTCAAACTATTTTTCATTGACTCAATa                                                                         >  1:1539156/1‑99 (MQ=255)
                      gCTTTGTAATCATTTTCATCATTCAAAAGTTTTGTATAACTAATCATTGTGTTAAAATACTTGTCAAAAACAGTCAAACTATTTTTCATTGACTCAATa                                                                         >  2:1148191/1‑99 (MQ=255)
                      gCTTTGTAATCATTTTCATCATTCAAAAGTTTTGTATAACTAATCATTGTGTTAAAATACTTGTCAAAAACAGTCAAACTATTTTTCATTGACTCAATa                                                                         <  2:864857/99‑1 (MQ=255)
                       cTTTGTAATCATTTTCATCATTCAAAAGTTTTGTATAACTAATCATTGTGTTAAAATACTTGTCATAAAGAGTCAAACTATTTTTCATTGACTCAATaa                                                                        >  1:780367/1‑99 (MQ=255)
                       cTTTGTAATCATTTTCATCATTCAAAAGTTTTGTATAACTAATCATTGTGTTAAAATACTTGTCAAAAACAGTCAAACTATTTTTCATTGACTCAATaa                                                                        >  1:1110789/1‑99 (MQ=255)
                          tGTAATCATTTTCATCATTCAAAAGTTTTGTATAACTAATCATTGTGTTAAAATACTTGTCAAAAACAGTCAAACTATTTTTCATTGACTCAATAAAAt                                                                     >  1:1326431/1‑99 (MQ=255)
                          tGTAATCATTTTCATCATTCAAAAGTTTTGTATAACTAATCATTGTGTTAAAATACTTGTCAAAAACAGTCAAACTATTTTTCATTGACTCAATAAAAt                                                                     <  2:862411/99‑1 (MQ=255)
                             aaTCATTTTCATCATTCAAAAGTTTTGTATAACTAATCATTGTGTTAAAATACTTGTCAAAAACAGTCAAACTATTTTTCATTGACTCAATAAAATCAg                                                                  <  1:1186658/99‑1 (MQ=255)
                              aTCATTTTCATCATTCAAAAGTTTTGTATAACTAATCATTGTGTTAAAATACTTGTCAAAAACAGTCAAACTATTTTTCATTGACTCAATAAAATCAGc                                                                 >  2:308405/1‑99 (MQ=255)
                               tCATTTTCATCATTCAAAAGTTTTGTATAACTAATCATTGTGTTAAAATACTTGTCAAAAACAGTCAAACTATTTTTCATTGACTCAATAAAATCAGCt                                                                >  2:1618358/1‑99 (MQ=255)
                               tCATTTTAATCATTTAAAAATTTTATATAACTAATCATTGTGTTAAAATAATTAACAAAAACATTCAATTTTTTTTTCATTGACTCAATAAAATCAGCt                                                                <  1:1618358/99‑1 (MQ=255)
                                cATTTTCATCATTCAAAAGTTTTGTATAACTAATCATTGTGTTAAAATACTTGTCAAAAACAGTCAAACTATTTTTCATTGACTCAATAAAATCAGCtt                                                               >  2:1634284/1‑99 (MQ=255)
                                 aTTTTCATCATTCAAAAGTTTTGTATAACTAATCATTGTGTTAAAATACTTGTCAAAAACAGTCAAACTATTTTTCATTGACTCAATAAAATCAGCttg                                                              <  1:725843/99‑1 (MQ=255)
                                  ttttCATCATTCAAAAGTTTTGTATAACTAATCATTGTGTTAAAATACTTGTCAAAAACAGTCAAACTATTTTTCATTGACTCAATAAAATCAGCttgt                                                             <  1:1063959/99‑1 (MQ=255)
                                  ttttCATCATTCAAAAGTTTTGTATAACTAATCATTGTGTTAAAATACTTGTCAAAAACAGTCAAACTATTTTTCATTGACTCAATAAAATCAGCttgt                                                             <  1:1121064/99‑1 (MQ=255)
                                   tttCATCATTCAAAAGTTTTGTATAACTAATCATTGTGTTAAAATACTTGTCAAAAACAGTCAAACTATTTTTCATTGACTCAATAAAATCAGCttgtt                                                            <  1:400743/99‑1 (MQ=255)
                                   tttCATCATTCAAAAGTTTTGTATAACTAATCATTGTGTTAAAATACTTGTCAAAAACAGTCAAACTATTTTTCATTGACTCAATAAAATCAGCttgtt                                                            >  1:766820/1‑99 (MQ=255)
                                     tcatcaATCAAAAGTTTTGTATAACTAATCATTGTGTTAAAATACTTGTCAAAAACAGTCAAACTATTTTTCATTGACTCAATAAAATCAGCTtgttgt                                                          <  2:592975/99‑1 (MQ=255)
                                      catcatTCAAAAGTTTTGTATAACTAATCATTGTGTTAAAATACTTGTCAAAAACAGTCAAACTATTTTTCATTGACTCAATAAAATCAGCTTgttgtt                                                         >  2:775204/1‑99 (MQ=255)
                                        tcatTCAAAAGTTTTGTATAACTAATCATTGTGTTAAAATACTTGTCAAAAACAGTCAAACTATTTTTCATTGACTCAATAAAATCAGCTTGTTGTTCa                                                       <  1:1526797/99‑1 (MQ=255)
                                        tcatTCAAAAGTTTTGTATAACTAATCATTGTGTTAAAATACTTGTCAAAAACAGTCAAACTATTTTTCATTGACTCAATAAAATCAGCTTGTTGTTCa                                                       >  2:1155830/1‑99 (MQ=255)
                                          atTCAAAAGTTTTGTATAACTAATCATTGTGTTAAAATACTTGTCAAAAACAGTCAAACTATTTTTCATTGACTCAATAAAATCAGCTTGTTGTTCAtt                                                     <  2:154310/99‑1 (MQ=255)
                                          atTCAAAAGTTTTGTATAACTAATCATTGTGTTAAAATACTTGTCAAAAACAGTCAAACTATTTTTCATTGACTCAATAAAATCAGCTTGTTGTTCAtt                                                     <  2:456969/99‑1 (MQ=255)
                                           ttCAAAAGTTTTGTATAACTAATCATTGTGTTAAAATACTTGTCAAAAACAGTCAAACTATTTTTCATTGACTCAATAAAATCAGCTTGTTGTTCAttt                                                    <  1:877733/99‑1 (MQ=255)
                                           ttCAAAAGTTTTGTATAACTAATCATTGTGTTAAAATACTTGTCAAAAACAGTCAAACTATTTTTCATTGACTCAATAAAATCAGCTTGTTGTTCAttt                                                    >  1:868080/1‑99 (MQ=255)
                                              aaaaGTTTTGTATAACTAATCATTGTGTTAAAATACTTGTCAAAAACAGTCAAACTATTTTTCATTGACTCAATAAAATCAGCTTGTTGTTCATTTACt                                                 >  1:82265/1‑99 (MQ=255)
                                               aaaGTTTTGTATAACTAATCATTGTGTTAAAATACTTGTCAAAAACAGTCAAACTATTTTTCATTGACTCAATAAAATCAGCTTGTTGTTCATTTACtt                                                >  2:920814/1‑99 (MQ=255)
                                               aaaGTTTTGTATAACTAATCATTGTGTTAAAATACTTGTCAAAAACAGTCAAACTATTTTTCATTGACTCAATAAAATCAGCTTGTTGTTCATTTACtt                                                >  2:1658728/1‑99 (MQ=255)
                                                aaGTTTTGTATAACTAATCATTGTGTTAAAATACTTGTCAAAAACAGTCAAACTATTTTTCATTGACTCAATAAAATCAGCTTGTTGTTCATTTACTTc                                               >  2:860760/1‑99 (MQ=255)
                                                aaGTTTTGTATAACTAATCATTGTGTTAAAATACTTGTCAAAAACAGTCAAACTATTTTTCATTGACTCAATAAAATCAGCTTGTTGTTCATTTACTTc                                               >  1:1147010/1‑99 (MQ=255)
                                                  gTTTTGTATATCTAATCATTGTGTTAAAATACTAGTCATAAAAAGTAAAATTATTATTCATTGGATTAATAAAATCATCTTTTAGTTCATTTACTACAg                                             <  2:73977/99‑1 (MQ=255)
                                                  gTTTTGTATAACTAATCATTGTGTTAAAATACTTGTCAAAAACAGTCAAACTATTTTTCATTGACTCAATAAAATCAGCTTGTTGTTCATTTACTTCAg                                             <  2:811505/99‑1 (MQ=255)
                                                  gTTTTGTATAACTAATCATTGTGTTAAAATACTTGTCAAAAACAGTCAAACTATTTTTCATTGACTCAATAAAATCAGCTTGTTGTTCATTTACTTCAg                                             <  1:1371242/99‑1 (MQ=255)
                                                  gTTTTGTATAACTAATCATTGTGTTAAAATACTTGTCAAAAACAGTCAAACTATTTTTCATTGACTCAATAAAATCAGCTTGTTGTTCATTTACTTCAg                                             >  1:490261/1‑99 (MQ=255)
                                                   ttttGTATAACTAATCATTGTGTTAAAATACTTGTCAAAAACAGTCAAACTATTTTTCATTGACTCAATAAAATCAGCTTGTTGTTCATTTACTTCAGt                                            <  1:1408733/99‑1 (MQ=255)
                                                   ttttGTATAACTAATCATTGTGTTAAAATACTTGTCAAAAACAGTCAAACTATTTTTCATTGACTCAATAAAATCAGCTTGTTGTTCATTTACTTCAGt                                            <  1:1443820/99‑1 (MQ=255)
                                                   tttaGTAGAACTAATCATTGTGTTAAAATACTTGTCAAAAACAGTCAAACTATTTTTCATTGACTCAATAAAATCAGCTTGTTGTTCATTTACTTCCGt                                            >  2:1363552/1‑99 (MQ=255)
                                                     ttGTATAACTAATCATTGTGTTAAAATACTTGTCAAAAACAGTCAAACTATTTTTCATTGACTCAATAAAATCAGCTTGTTGTTCATTTACTTCAGTCa                                          >  2:495290/1‑99 (MQ=255)
                                                      tGTATAACTAATCATTGTGTTAAAATACTTGTCAAAAACAGTCAAACTATTTTTCATTGACTCAATAAAATCAGCTTGTTGTTCATTTACTTCAGTCAt                                         <  1:1020416/99‑1 (MQ=255)
                                                      tGTATAACTAATCATTGTGTTAAAATACTTGTCAAAAACAGTCAAACTATTTTTCATTGACTCAATAAAATCAGCTTGTTGTTCATTTACTTCAGTCAt                                         >  1:1071570/1‑99 (MQ=255)
                                                       gTATAACTAATCATTGTGTTAAAATACTTGTCAAAAACAGTCAAACTATTTTTCATTGACTCAATAAAATCAGCTTGTTGTTCATTTACTTCAGTCAtc                                        >  2:330669/1‑99 (MQ=255)
                                                          caaCTAATCATTGTGTTAAAATACTTGTCAAAAACAGTCAAACTATTTTTCATTGACTCAATAAAATCAGCTTGTTGTTCATTTACTTCAGTCATctct                                     >  1:540650/2‑99 (MQ=255)
                                                           aaCTAATCATTGTGTTAAAATACTTGTCAAAAACAGTCAAACTATTTTTCATTGACTCAATAAAATCAGCTTGTTGTTCATTTACTTCAGTCATCTCTa                                    >  2:1141371/1‑99 (MQ=255)
                                                            aCTAATCATTGTGTTAAAATACTTGTCAAAAACAGTCAAACTATTTTTCATTGACTCAATAAAATCAGCTTGTTGTTCATTTACTTCAGTCATCTCTAg                                   <  2:1636672/99‑1 (MQ=255)
                                                            aCTAATCATTGTGTTAAAATACTTGTCAAAAACAGTCAAACTATTTTTCATTGACTCAATAAAATCAGCTTGTTGTTCATTTACTTCAGTCATCTCTAg                                   >  2:34193/1‑99 (MQ=255)
                                                            aCTAATCATTGTGTTAAAATACTTGTCAAAAACAGTCAAACTATTTTTCATTGACTCAATAAAATCAGCTTGTTGTTCATTTACTTCAGTCATCTCTAg                                   <  1:290551/99‑1 (MQ=255)
                                                             cTAATCATTGTGTTAAAATACTTGTCAAAAACAGTCAAACTATTTTTCATTGACTCAATAAAATCAGCTTGTTGTTCATTTACTTCAGTCATCTCTAGc                                  >  1:179897/1‑99 (MQ=255)
                                                              tAATCATTGTGTTAAAATACTTGTCAAAAACAGTCAAACTATTTTTCATTGACTCAATAAAATCAGCTTGTTGTTCATTTACTTCAGTCATCTCTAGCa                                 <  2:727634/99‑1 (MQ=255)
                                                               aaTCATTGTGTTAAAATACTTGTCAAAAACAGTCAAACTATTTTTCATTGACTCAATAAAATCAGCTTGTTGTTCATTTACTTCAGTCATCTCTAGCAg                                <  1:730627/99‑1 (MQ=255)
                                                                aTCATTGTGTTAAAATACTTGTCAAAAACAGTCAAACTATTTTTCATTGACTCAATAAAATCAGCTTGTTGTTCATTTACTTCAGTCATCTCTAGCAGt                               >  1:822619/1‑99 (MQ=255)
                                                                   aTTGTGTTAAAATACTTGTCAAAAACAGTCAAACTATTTTTCATTGACTCAATAAAATCAGCTTGTTGTTCATTTACTTCAGTCATCTCTAGCAGTTCa                            >  1:37790/1‑99 (MQ=255)
                                                                    ttGTGTTAAAATACTTGTCAAAAACAGTCAAACTATTTTTCATTGACTCAATAAAATCAGCTTGTTGTTCATTTACTTCAGTCATCTCTAGCAGTTCaa                           <  2:975515/99‑1 (MQ=255)
                                                                    ttGTGTTAAAATACTTGTCAAAAACAGTCAAACTATTTTTCATTGACTCAATAAAATCAGCTTGTTGTTCATTTACTTCAGTCATCTCTAGCAGTTCaa                           >  1:1525809/1‑99 (MQ=255)
                                                                    ttGTGTTAAAATACTTGTCAAAAACAGTCAAACTATTTTTCATTGACTCAATAAAATCAGCTTGTTGTTCATTTACTTCAGTCATCTCTAGCAGTTCaa                           >  1:1545034/1‑99 (MQ=255)
                                                                     tgtgTTAAAATACTTGTCAAAAACAGTCAAACTATTTTTCATTGACTCAATAAAATCAGCTTGTTGTTCATTTACTTCAGTCATCTCTAGCAGTTCAat                          >  1:1182196/1‑99 (MQ=255)
                                                                      gtgtTAAAATACTTGTCAAAAACAGTCAAACTGTTTTTCATTGACTCAATAAAATCAGCTTGTTGTTCATTTACTTCAGTCATCTCTAGCAGTTCAata                         <  1:692547/99‑1 (MQ=255)
                                                                       tgtTAAAATACTTGTCAAAAACAGTCAAACTATTTTTCATTGACTCAATAAAATCAGCTTGTTGTTCATTTACTTCAGTCATCTCTAGCAGTTCAatat                        <  1:1511569/99‑1 (MQ=255)
                                                                       tgtTAAAATACTTGTCAAAAACAGTCAAACTATTTTTCATTGACTCAATAAAATCAGCTTGTTGTTCATTTACTTCAGTCATCTCTAGCAGTTCAatat                        <  1:1366725/99‑1 (MQ=255)
                                                                        gtTAAAATACTTGTCAAAAACAGTCAAACTATTTTTCATTGACTCAATAAAATCAGCTTGTTGTTCATTTACTTCAGTCATCTCTAGCAGTTCAATAtt                       >  1:1531809/1‑99 (MQ=255)
                                                                         ttAAAATACTTGTCAAAAACAGTCAAACTATTTTTCATTGACTCAATAAAATCAGCTTGTTGTTCATTTACTTCAGTCATCTCTAGCAGTTCAATAttt                      >  2:344022/1‑99 (MQ=255)
                                                                         ttAAAATACTTGTCAAAAACAGTCAAACTATTTTTCATTGACTCAATAAAATCAGCTTGTTGTTCATTTACTTCAGTCATCTCTAGCAGTTCAATAttt                      <  2:66792/99‑1 (MQ=255)
                                                                          tAAAATACTTGTCAAAAACAGTCAAACTATTTTTCATTGACTCAATAAAATCAGCTTGTTGTTCATTTACTTCAGTCATCTCTAGCAGTTCAATATTTc                     <  2:878433/99‑1 (MQ=255)
                                                                            aaaTACTTGTCAAAAACAGTCAAACTATTTTTCATTGACTCAATAAAATCAGCTTGTTGTTCATTTACTTCAGTCATCTCTAGCAGTTCAATATTTCCt                   <  1:135104/99‑1 (MQ=255)
                                                                            aaaTACTTGTCAAAAACAGTCAAACTATTTTTCATTGACTCAATAAAATCAGCTTGTTGTTCATTTACTTCAGTCATCTCTAGCAGTTCAATATTTCCt                   >  2:826971/1‑99 (MQ=255)
                                                                            aaaTACTTGTCAAAAACAGTCAAACTATTTTTCATTGACTCAATAAAATCAGCTTGTTGTTCATTTACTTCAGTCATCTCTAGCAGTTCAATATTTCCt                   <  1:1555411/99‑1 (MQ=255)
                                                                            aaaTACTTGTCAAAAACAGTCAAACTATTTTTCATTGACTCAATAAAATCAGCTTGTTGTTCATTTACTTCAGTCATCTCTAGCAGTTCAATATTTCCt                   >  2:1063210/1‑99 (MQ=255)
                                                                             aaTACTTGTCAAAAACAGTCAAACTATTTTTCATTGACTCAATAAAATCAGCTTGTTGTTCATTTACTTCAGTCATCTCTAGCAGTTCAATATTTCCtt                  <  2:593837/99‑1 (MQ=255)
                                                                              aTACTTGTCAAAAACAGTCAAACTATTTTTCATTGACTCAATAAAATCAGCTTGTTGTTCATTTACTTCAGTCATCTCTAGCAGTTCAATATTTCCttc                 >  1:573663/1‑98 (MQ=255)
                                                                                 cTTGTCAAAAACAGTCAAACTATTTTTCATTGACTCAATAAAATCAGCTTGTTGTTCATTTACTTCAGTCATCTCTAGCAGTTCAATATTTCCTTTTaa              <  2:65360/99‑1 (MQ=255)
                                                                                 cTTGTCAAAAACAGTCAAACTATTTTTCATTGACTCAATAAAATCAGCTTGTTGTTCATTTACTTCAGTCATCTCTAGCAGTTCAATATTTCCTTTTaa              <  2:694502/99‑1 (MQ=255)
                                                                                 cTTGTCAAAAACAGTCAAACTATTTTTCATTGACTCAATAAAATCAGCTTGTTGTTCATTTACTTCAGTCATCTCTAGCAGTTCAATATTTCCTTTTaa              >  1:450077/1‑99 (MQ=255)
                                                                                 cTTGTCAAAAACAGTCAAACTATTTTTCATTGACTCAATAAAATCAGCTTGTTGTTCATTTACTTCAGTCATCTCTAGCAGTTCAATATTTCCTTTTaa              >  1:1396478/1‑99 (MQ=255)
                                                                                   tGTCAAAAACAGTCAAACTATTTTTCATTGACTCAATAAAATCAGCTTGTTGTTCATTTACTTCAGTCATCTCTAGCAGTTCAATATTTCCTTTTAATa            >  2:19571/1‑99 (MQ=255)
                                                                                    gTCAAAAACAGTCAAACTATTTTTCATTGACTCAATAAAATCAGCTTGTTGTTCATTTACTTCAGTCATCTCTAGCAGTTCAATATTTCCTTTTAATAc           <  1:987422/99‑1 (MQ=255)
                                                                                     tCAAAAACAGTCAAACTATTTTTCATTGACTCAATAAAATCAGCTTGTTGTTCATTTACTTCAGTCATCTCTAGCAGTTCAATATTTCCTTTTAATACt          <  1:966352/99‑1 (MQ=255)
                                                                                       aaaaaCAGTCAAACTATTTTTCATTGACTCAATAAAATCAGCTTGTTGTTCATTTACTTCAGTCATCTCTAGCAGTTCAATATTTCCTTTTAATACTGt        <  1:350024/99‑1 (MQ=255)
                                                                                        aaaaCAGTCAAACTATTTTTCATTGACTCAATAAAATCAGCTTGTTGTTCATTTACTTCAGTCATCTCTAGCAGTTCAATATTTCCTTTTAATACTGtt       >  1:1382963/1‑99 (MQ=255)
                                                                                          aaCAGTCAAACTATTTTTCATTGACTCAATAAAATCAGCTTGTTGTTCATTTACTTCAGTCATCTCTAGCAGTTCAATATTTCCTTTTAATACTGTTaa     >  2:1181969/1‑99 (MQ=255)
                                                                                           aCAGTCAAACTATTTTTCATTGACTCAATAAAATCAGCTTGTTGTTCATTTACTTCAGTCATCTCTAGCAGTTCAATATTTCCTTTTAATACTGTTaaa    >  2:1315970/1‑99 (MQ=255)
                                                                                            cAGTCAAACTATTTTTCATTGACTCAATAAAATCAGCTTGTTGTTCATTTACTTCAGTCATCTCTAGCAGTTCAATATTTCCTTTTAATACTGTTAAAg   >  1:1572659/1‑99 (MQ=255)
                                                                                            cAGTCAAACTATTTTTCATTGACTCAATAAAATCAGCTTGTTGTTCATTTACTTCAGTCATCTCTAGCAGTTCAATATTTCCTTTTAATACTGTTAAAg   >  1:451764/1‑99 (MQ=255)
                                                                                             aGTCAAACTATTTTTCATTGACTCAATAAAATCAGCTTGTTGTTCATTTACTTCAGTCATCTCTAGCAGTTCAATATTTCCTTTTAATACTGTTAAAgg  >  1:1305704/1‑99 (MQ=255)
                                                                                                |                                                                                               
AAAATCCTCCAGGGAGATTCTCGCTTTGTAATCATTTTCATCATTCAAAAGTTTTGTATAACTAATCATTGTGTTAAAATACTTGTCAAAAACAGTTAAACTATTTTTCATTGACTCAATAAAATCAGCTTGTTGTTCATTTACTTCAGTCATCTCTAGCAGTTCAATATTTCCTTTTAATACTGTTAAAGG  >  CP002094/305674‑305865

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ 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
CAAAAAATCCTCCAGGGAGATTCTCGCTTTGTAATCATTTTCATCATTCAAAAGTTTTGTATAACTAATCATTGTGTTAAAATACTTGTCAAAAACAGTTAAACTATTTTTCATTGACTCAATAAAATCAGCTTGTTGTTCATTTACTTCAGTCATCTCTAGCAGTTCAATATTTCCTTTTAATACTGTTAAAGG  >  CP002094/305671‑305865
                                                                                                   |                                                                                               
CAAAAAATCCTCCAGGGAGATTATCGCTTTGTAATCATTTTCATCATTCAAAAGTTTTGTATAACTAATCATTGTGTTAAAATACTTGTCAAAAACAGTC                                                                                                 <  SRR7892090.213415/100‑1 (MQ=60)
    AAATCCTCCAGGGAGATTATCGCTTTGTAATCATTTTCATCATTCAAAAGTTTTGTATAACTAATCATTGTGTTAAAATACTTGTCAAAAACAGTCAAAC                                                                                             <  SRR7892090.1484284/100‑1 (MQ=60)
       TCCTCCAGGGAGATTATCGCTTTGTAATCATTTTCATCATTCAAAAGTTTTGTATAACTAATCATTGTGTTAAAATACTTGTCAAAAACAGTCAAACTAT                                                                                          <  SRR7892090.971532/100‑1 (MQ=60)
         CTCCAGGGAGATTATCGCTTTGTAATCATTTTCATCATTCAAAAGTTTTGTATAACTAATCATTGTGTTAAAATACTTGTCAAAAACAGTCAAACTATTT                                                                                        >  SRR7892090.1282061/1‑100 (MQ=60)
         CTCCAGGGAGATTATCGCTTTGTAATCATTTTCATCATTCAAAAGTTTTGTATAACTAATCATTGTGTTAAAATACTTGTCAAAAACAGTCAAACTATTT                                                                                        <  SRR7892090.582957/100‑1 (MQ=60)
               GGAGATTATCGCTTTGTAATCATTTTCATCATTCAAAAGTTTTGTATAACTAATCATTGTGTTAAAATACTTGTCAAAAACAGTCAAACTATTTTTCATT                                                                                  >  SRR7892090.1613260/1‑100 (MQ=60)
                 AGATTATCGCTTTGTAATCATTTTCATCATTCAAAAGTTTTGTATAACTAATCATTGTGTTAAAATACTTGTCAAAAACAGTCAAACTATTTTTCATTGA                                                                                >  SRR7892090.155650/1‑100 (MQ=60)
                       TCGCTTTGTAATCATTTTCATCATTCAAAAGTTTTGTATAACTAATCATTGTGTTAAAATACTTGTCAAAAACAGTCAAACTATTTTTCATTGACTCAAT                                                                          <  SRR7892090.120535/100‑1 (MQ=60)
                        CGCTTTGTAATCATTTTCATCATTCAAAAGTTTTGTATAACTAATCATTGTGTTAAAATACTTGTCAAAAACAGTCAAACTATTTTTCATTGACTCAATA                                                                         >  SRR7892090.1548583/1‑100 (MQ=60)
                         GCTTTGTAATCATTTTCATCATTCAAAAGTTTTGTATAACTAATCATTGTGTTAAAATACTTGTCATAAAGAGTCAAACTATTTTTCATTGACTCAATAA                                                                        >  SRR7892090.786555/1‑100 (MQ=60)
                         GCTTTGTAATCATTTTCATCATTCAAAAGTTTTGTATAACTAATCATTGTGTTAAAATACTTGTCAAAAACAGTCAAACTATTTTTCATTGACTCAATAA                                                                        >  SRR7892090.1118273/1‑100 (MQ=60)
                            TTGTAATCATTTTCATCATTCAAAAGTTTTGTATAACTAATCATTGTGTTAAAATACTTGTCAAAAACAGTCAAACTATTTTTCATTGACTCAATAAAAT                                                                     >  SRR7892090.1334398/1‑100 (MQ=60)
                             tttttttaaataataaaaaaaattttttttaaaAACTAATCATTGTGTTAAAATACTTGTCAAAAACAGTCAAACTATTTTTCATTGACTCAATAAAATC                                                                    <  SRR7892090.61082/67‑1 (MQ=60)
                                AATCATTTTCATCATTCAAAAGTTTTGTATAACTAATCATTGTGTTAAAATACTTGTCAAAAACAGTCAAACTATTTTTCATTGACTCAATAAAATCAGC                                                                 <  SRR7892090.1194322/100‑1 (MQ=60)
                                  TCATTTTAATCATTTAAAAATTTTATATAACTAATCATTGTGTTAAAATAATTAACAAAAACATTCAATTTTTTTTTCATTGACTCAATAAAATCAGCTT                                                               <  SRR7892090.1628563/100‑1 (MQ=32)
                                    ATTTTCATCATTCAAAAGTTTTGTATAACTAATCATTGTGTTAAAATACTTGTCAAAAACAGTCAAACTATTTTTCATTGACTCAATAAAATCAGCTTGT                                                             <  SRR7892090.731874/100‑1 (MQ=60)
                                     TTTTCATCATTCAAAAGTTTTGTATAACTAATCATTGTGTTAAAATACTTGTCAAAAACAGTCAAACTATTTTTCATTGACTCAATAAAATCAGCTTGTT                                                            >  SRR7892090.772968/1‑100 (MQ=60)
                                     TTTTCATCATTCAAAAGTTTTGTATAACTAATCATTGTGTTAAAATACTTGTCAAAAACAGTCAAACTATTTTTCATTGACTCAATAAAATCAGCTTGTT                                                            <  SRR7892090.1071287/100‑1 (MQ=60)
                                     TTTTCATCATTCAAAAGTTTTGTATAACTAATCATTGTGTTAAAATACTTGTCAAAAACAGTCAAACTATTTTTCATTGACTCAATAAAATCAGCTTGTT                                                            <  SRR7892090.1128559/100‑1 (MQ=60)
                                      TTTCATCATTCAAAAGTTTTGTATAACTAATCATTGTGTTAAAATACTTGTCAAAAACAGTCAAACTATTTTTCATTGACTCAATAAAATCAGCTTGTTG                                                           <  SRR7892090.404660/100‑1 (MQ=60)
                                         cgatcagtacttttttaaaatattatttgctttcttcAAAATACTTGTCAAAAACAGTCAAACTATTTTTCATTGACTCAATAAAATCAGCTTGTTGTTC                                                        <  SRR7892090.428693/63‑1 (MQ=60)
                                          ATCATTCAAAAGTTTTGTATAACTAATCATTGTGTTAAAATACTTGTCAAAAACAGTCAAACTATTTTTCATTGACTCAATAAAATCAGCTTGTTGTTCA                                                       >  SRR7892090.703834/1‑100 (MQ=60)
                                           TCATTCAAAAGTTTTGTATAACTAATCATTGTGTTAAAATACTTGTCAAAAACAGTCAAACTATTTTTCATTGACTCAATAAAATCAGCTTGTTGTTCAT                                                      <  SRR7892090.1536097/100‑1 (MQ=60)
                                             ATTCAAAAGTTTTGTATAACTAATCATTGTGTTAAAATACTTGTCAAAAACAGTCAAACTATTTTTCATTGACTCAATAAAATCAGCTTGTTGTTCATTT                                                    >  SRR7892090.874771/1‑100 (MQ=60)
                                              TTCAAAAGTTTTGTATAACTAATCATTGTGTTAAAATACTTGTCAAAAACAGTCAAACTATTTTTCATTGACTCAATAAAATCAGCTTGTTGTTCATTTA                                                   <  SRR7892090.884436/100‑1 (MQ=60)
                                                CAAAAGTTTTGTATAACTAATCATTGTGTTAAAATACTTGTCAAAAACAGTCAAACTATTTTTCATTGACTCAATAAAATCAGCTTGTTGTTCATTTACT                                                 >  SRR7892090.82982/1‑100 (MQ=60)
                                                  AAAGTTTTGTATAACTAATCATTGTGTTAAAATACTTGTCAAAAACAGTCAAACTATTTTTCATTGACTCAATAAAATCAGCTTGTTGTTCATTTACTTC                                               >  SRR7892090.1154549/1‑100 (MQ=60)
                                                    AGTTTTGTATAACTAATCATTGTGTTAAAATACTTGTCAAAAACAGTCAAACTATTTTTCATTGACTCAATAAAATCAGCTTGTTGTTCATTTACTTCAG                                             >  SRR7892090.494684/1‑100 (MQ=60)
                                                     GTTTTGTATAACTAATCATTGTGTTAAAATACTTGTCAAAAACAGTCAAACTATTTTTCATTGACTCAATAAAATCAGCTTGTTGTTCATTTACTTCAGT                                            <  SRR7892090.1379293/100‑1 (MQ=60)
                                                      TTTTGTATAACTAATCATTGTGTTAAAATACTTGTCAAAAACAGTCAAACTATTTTTCATTGACTCAATAAAATCAGCTTGTTGTTCATTTACTTCAGTC                                           <  SRR7892090.1416849/100‑1 (MQ=60)
                                                      TTTTGTATAACTAATCATTGTGTTAAAATACTTGTCAAAAACAGTCAAACTATTTTTCATTGACTCAATAAAATCAGCTTGTTGTTCATTTACTTCAGTC                                           <  SRR7892090.1452288/100‑1 (MQ=60)
                                                        TTGTATAACTAATCATTGTGTTAAAATACTTGTCAAAAACAGTCAAACTATTTTTCATTGACTCAATAAAATCAGCTTGTTGTTCATTTACTTCAGTCAT                                         >  SRR7892090.1078928/1‑100 (MQ=60)
                                                         TGTATAACTAATCATTGTGTTAAAATACTTGTCAAAAACAGTCAAACTATTTTTCATTGACTCAATAAAATCAGCTTGTTGTTCATTTACTTCAGTCATC                                        <  SRR7892090.1027611/100‑1 (MQ=60)
                                                            ACAACTAATCATTGTGTTAAAATACTTGTCAAAAACAGTCAAACTATTTTTCATTGACTCAATAAAATCAGCTTGTTGTTCATTTACTTCAGTCATCTCT                                     >  SRR7892090.545543/1‑100 (MQ=60)
                                                              AACTAATCATTGTGTTAAAATACTTGTCAAAAACAGTCAAACTATTTTTCATTGACTCAATAAAATCAGCTTGTTttttttttttttttctctttctttt                                   >  SRR7892090.355055/1‑75 (MQ=60)
                                                               ACTAATCATTGTGTTAAAATACTTGTCAAAAACAGTCAAACTATTTTTCATTGACTCAATAAAATCAGCTTGTTGTTCATTTACTTCAGTCATCTCTAGC                                  <  SRR7892090.293347/100‑1 (MQ=60)
                                                               ACTAATCATTGTGTTAAAATACTTGTCAAAAACAGTCAAACTATTTTTCATTGACTCAATAAAATCAGCTTGTTGTTCATTTACTTCAGTCATCTCTAGC                                  >  SRR7892090.900884/1‑100 (MQ=60)
                                                               ACTAATCATTGTGTTAAAATACTTGTCAAAAACAGTCAAACTATTTTTCATTGACTCAATAAAATCAGCTTGTTGTTCATTTACTTCAGTCATCTCTAGC                                  >  SRR7892090.181528/1‑100 (MQ=60)
                                                                  AATCATTGTGTTAAAATACTTGTCAAAAACAGTCAAACTATTTTTCATTGACTCAATAAAATCAGCTTGTTGTTCATTTACTTCAGTCATCTCTAGCAGT                               >  SRR7892090.829108/1‑100 (MQ=60)
                                                                  AATCATTGTGTTAAAATACTTGTCAAAAACAGTCAAACTATTTTTCATTGACTCAATAAAATCAGCTTGTTGTTCATTTACTTCAGTCATCTCTAGCAGT                               <  SRR7892090.736667/100‑1 (MQ=60)
                                                                     CATTGTGTTAAAATACTTGTCAAAAACAGTCAAACTATTTTTCATTGACTCAATAAAATCAGCTTGTTGTTCATTTACTTCAGTCATCTCTAGCAGTTCA                            >  SRR7892090.38155/1‑100 (MQ=60)
                                                                      ATTGTGTTAAAATACTTGTCAAAAACAGTCAAACTATTTTTCATTGACTCAATAAAATCAGCTTGTTGTTCATTTACTTCAGTCATCTCTAGCAGTTCAA                           >  SRR7892090.1554511/1‑100 (MQ=60)
                                                                      ATTGTGTTAAAATACTTGTCAAAAACAGTCAAACTATTTTTCATTGACTCAATAAAATCAGCTTGTTGTTCATTTACTTCAGTCATCTCTAGCAGTTCAA                           >  SRR7892090.1535100/1‑100 (MQ=60)
                                                                       TTGTGTTAAAATACTTGTCAAAAACAGTCAAACTATTTTTCATTGACTCAATAAAATCAGCTTGTTGTTCATTTACTTCAGTCATCTCTAGCAGTTCAAT                          >  SRR7892090.1189846/1‑100 (MQ=60)
                                                                         GTGTTAAAATACTTGTCAAAAACAGTCAAACTGTTTTTCATTGACTCAATAAAATCAGCTTGTTGTTCATTTACTTCAGTCATCTCTAGCAGTTCAATAT                        <  SRR7892090.698357/100‑1 (MQ=60)
                                                                          TGTTAAAATACTTGTCAAAAACAGTCAAACTATTTTTCATTGACTCAATAAAATCAGCTTGTTGTTCATTTACTTCAGTCATCTCTAGCAGTTCAATATT                       <  SRR7892090.1374769/100‑1 (MQ=60)
                                                                          TGTTAAAATACTTGTCAAAAACAGTCAAACTATTTTTCATTGACTCAATAAAATCAGCTTGTTGTTCATTTACTTCAGTCATCTCTAGCAGTTCAATATT                       >  SRR7892090.1541156/1‑100 (MQ=60)
                                                                          TGTTAAAATACTTGTCAAAAACAGTCAAACTATTTTTCATTGACTCAATAAAATCAGCTTGTTGTTCATTTACTTCAGTCATCTCTAGCAGTTCAATATT                       <  SRR7892090.1520717/100‑1 (MQ=60)
                                                                               AAATACTTGTCAAAAACAGTCAAACTATTTTTCATTGACTCAATAAAATCAGCTTGTTGTTCATTTACTTCAGTCATCTCTAGCAGTTCAATATTTCCTT                  <  SRR7892090.1564976/100‑1 (MQ=60)
                                                                               AAATACTTGTCAAAAACAGTCAAACTATTTTTCATTGACTCAATAAAATCAGCTTGTTGTTCATTTACTTCAGTCATCTCTAGCAGTTCAATATTTCCTT                  <  SRR7892090.136300/100‑1 (MQ=60)
                                                                                AATACTTGTCAAAAACAGTCAAACTATTTTTCATTGACTCAATAAAATCAGCTTGTTGTTCATTTACTTCAGTCATCTCTAGCAGTTCAATATTTCCTTC                 >  SRR7892090.578825/1‑100 (MQ=60)
                                                                                   ACTTGTCAAAAACAGTCAAACTATTTTTCATTGACTCAATAAAATCAGCTTGTTGTTCATTTACTTCAGTCATCTCTAGCAGTTCAATATTTCCTTTTAA              >  SRR7892090.454244/1‑100 (MQ=60)
                                                                                   ACTTGTCAAAAACAGTCAAACTATTTTTCATTGACTCAATAAAATCAGCTTGTTGTTCATTTACTTCAGTCATCTCTAGCAGTTCAATATTTCCTTTTAA              >  SRR7892090.1404570/1‑100 (MQ=60)
                                                                                       GTCAAAAACAGTCAAACTATTTTTCATTGACTCAATAAAATCAGCTTGTTGTTCATTTACTTCAGTCATCTCTAGCAGTTCAATATTTCCTTTTAATACT          <  SRR7892090.994505/100‑1 (MQ=60)
                                                                                        TCAAAAACAGTCAAACTATTTTTCATTGACTCAATAAAATCAGCTTGTTGTTCATTTACTTCAGTCATCTCTAGCAGTTCAATATTTCCTTTTAATACTG         <  SRR7892090.973390/100‑1 (MQ=60)
                                                                                          AAAAACAGTCAAACTATTTTTCATTGACTCAATAAAATCAGCTTGTTGTTCATTTACTTCAGTCATCTCTAGCAGTTCAATATTTCCTTTTAATACTGTT       <  SRR7892090.353450/100‑1 (MQ=60)
                                                                                          AAAAACAGTCAAACTATTTTTCATTGACTCAATAAAATCAGCTTGTTGTTCATTTACTTCAGTCATCTCTAGCAGTTCAATATTTCCTTTTAATACTGTT       >  SRR7892090.1391029/1‑100 (MQ=60)
                                                                                              ACAGTCAAACTATTTTTCATTGACTCAATAAAATCAGCTTGTTGTTCATTTACTTCAGTCATCTCTAGCAGTTCAATATTTCCTTTTAATACTGTTAAAG   >  SRR7892090.455933/1‑100 (MQ=60)
                                                                                              ACAGTCAAACTATTTTTCATTGACTCAATAAAATCAGCTTGTTGTTCATTTACTTCAGTCATCTCTAGCAGTTCAATATTTCCTTTTAATACTGTTAAAG   >  SRR7892090.1582401/1‑100 (MQ=60)
                                                                                               CAGTCAAACTATTTTTCATTGACTCAATAAAATCAGCTTGTTGTTCATTTACTTCAGTCATCTCTAGCAGTTCAATATTTCCTTTTAATACTGTTAAAGG  >  SRR7892090.1313622/1‑100 (MQ=60)
                                                                                                   |                                                                                               
CAAAAAATCCTCCAGGGAGATTCTCGCTTTGTAATCATTTTCATCATTCAAAAGTTTTGTATAACTAATCATTGTGTTAAAATACTTGTCAAAAACAGTTAAACTATTTTTCATTGACTCAATAAAATCAGCTTGTTGTTCATTTACTTCAGTCATCTCTAGCAGTTCAATATTTCCTTTTAATACTGTTAAAGG  >  CP002094/305671‑305865

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑