Sample Resequencing Stats

Note: The mutation counts shown below represent unfiltered mutation sets.
ALE, Flask, Isolate Predicted Mutations Mean Coverage Total Reads Percent Mapped Mapped Reads Average Read Length
A1 F1 I2 R1 1873 183.1 9376148 98.2% 9207377 93.0

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 1,962,070 A→T P335P (CCT→CCA)  flhA ← FlhA

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009131,962,0700AT99.1% 395.7 / ‑5.7 112P335P (CCT→CCA) flhAFlhA
Reads supporting (aligned to +/- strand):  ref base A (0/0);  major base T (57/54);  minor base C (0/1);  total (57/55)
Fisher's exact test for biased strand distribution p-value = 4.91e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.94e-01

Only 100 of 117 total aligned reads displayed.

CATTCCCAGAGAATCTTCCAGTTGTACATCGTTCCACGTCGCTTCGACAACGGTATTATTCTCTGCCATTTTTACCGGTTTGGGTTCGGCAGGCGCTTTTTGTTCGCGTCCGCGTATCCACCAGGCCAGCCCGAGCAATCCGGCAGTGAACAGCAAAAATACCAGGTTCGGCATTCCAG  >  NC_000913/1961980‑1962158
                                                                                          |                                                                                        
cATTCCCAGAGAATCTTCCAGTTGTACATCGTTCCACGTCGCTTCGACAACGGTATTATTCTCTGCCATTTTTACCGGTTTGGGTTCGGCTgg                                                                                        >  2:1031244/1‑93 (MQ=255)
 aTTCCCAGAGAATCTTCCAGTTGTACATCGTTCCACGTCGCTTCGACAACGGTATTATTCTCTGCCATTTTTACCGGTTTGGGTTCGGCTGgc                                                                                       >  2:4363223/1‑93 (MQ=255)
 aTTCCCAGAGAATCTTCCAGTTGTACATCGTTCCACGTCGCTTCGACAACGGTATTATTCTCTGCCATTTTTACCGGTTTGGGTTCGGCTGgc                                                                                       <  1:4226226/93‑1 (MQ=255)
 aTTCCCAGAGAATCTTCCAGTTGTACATCGTTCCACGTCGCTTCGACAACGGTATTATTCTCTGCCATTTTTACCGGTTTGGGTTCGGCTGgc                                                                                       <  2:3345648/93‑1 (MQ=255)
   tCCCAGAGAATCTTCCAGTTGTACATCGTTCCACGTCGCTTCGACAACGGTATTATTCTCTGCCATTTTTACCGGTTTGGGTTCGGCTGgcgc                                                                                     >  2:1778014/1‑93 (MQ=255)
    cccAGAGAATCTTCCAGTTGTACATCGGTCCACGTCGCTTCGACAACGGTATTATTCTCTGCCATTTTTATCGGTTTGGGTTCGGCTGgcggt                                                                                    >  2:762052/1‑91 (MQ=255)
     ccAGAGAATCTTCCAGTTGTACATCGTTCCACGTCGCTTCGACAACGGTATTATTCTCTGCCATTTTTACCGGTTTGGGTTCGGCTGGCGCtt                                                                                   <  2:226923/93‑1 (MQ=255)
        gagaATCTTCCAGTTGTACATCGTTCCACGTCGCTTCGACAACGGTATTATTCTCTGCCATTTTTACCGGTTTGGGTTCGGCTGGCGCttttt                                                                                >  2:1027945/1‑93 (MQ=255)
        gagaATCTTCCAGTTGTACATCGTTCCACGTCGCTTCGACAACGGTATTATTCTCTGCCATTTTTACCGGTTTGGGTTCGGCTGGCGCttttt                                                                                >  1:4405173/1‑93 (MQ=255)
           aaTCTTCCAGTTGTACATCGTTCCACGTCGCTTCGACAACGGTATTATTCTCTGCCATTTTTACCGGTTTGGGTTCGGCTGGCGCTTTTTGtt                                                                             >  1:1194591/1‑93 (MQ=255)
           aaTCTTCCAGTTGTACATCGTTCCACGTCGCTTCGACAACGGTATTATTCTCTGCCATTTTTACCGGTTTGGGTTCGGCTGGCGCTTTTTGtt                                                                             <  1:2945367/93‑1 (MQ=255)
            aTCTTCCAGTTGTACATCGTTCCACGTCGCTTCGACAACGGTATTATTCTCTGCCATTTTTACCGGTTTGGGTTCGGCTGGCGCTTTTTGTTc                                                                            <  1:1905121/93‑1 (MQ=255)
            aTCTTCCAGTTGTACATCGTTCCACGTCGCTTCGACAACGGTATTATTCTCTGCCATTTTTACCGGTTTGGGTTCGGCTGGCGCTTTTTGTTc                                                                            <  1:2405973/93‑1 (MQ=255)
             tCTTCCAGTTGTACATCGTTCCACGTCGCTTCGACAACGGTATTATTCTCTGCCATTTTTACCGGTTTGGGTTCGGCTGGCGCTTTTTGTTcg                                                                           >  2:865760/1‑93 (MQ=255)
             tCTTCCAGTTGTACATCGTTCCACGTCGCTTCGACAACGGTATTATTCTCTGCCATTTTTACCGGTTTGGGTTCGGCTGGCGCTTTTTGTTcg                                                                           >  1:3178974/1‑93 (MQ=255)
             tCTTCCAGTTGTACATCGTTCCACGTCGCTTCGACAACGGTATTATTCTCTGCCATTTTTACCGGTTTGGGTTCGGCTGGCGCTTTTTGTTcg                                                                           >  2:498875/1‑93 (MQ=255)
                tCCAGTTGTACATCGTTCCACGTCGCTTCGACAACGGTATTATTCTCTGCCATTTTTACCGGTTTGGGTTCGGCTGGCGCTTTTTGTTCGCGt                                                                        <  1:573033/93‑1 (MQ=255)
                 ccAGTTGTACATCGTTCCACGTCGCTTCGACAACGGTATTATTCTCTGCCATTTTTACCGGTTTGGGTTCGGCTGGCGCTTTTTGTTCGCGTc                                                                       <  2:2730469/93‑1 (MQ=255)
                 ccAGTTGTACATCGTTCCACGTCGCTTCGACAACGGTATTATTCTCTGCCATTTTTACCGGTTTGGGTTCGGCTGGCGCTTTTTGTTCGCGTc                                                                       <  2:3373856/93‑1 (MQ=255)
                   aGTTGTACATCGTTCCACGTCGCTTCGACAACGGTATTATTCTCTGCCATTTTTACCGGTTTGGGTTCGGCTGGCGCTTTTTGTTCGCGTCcg                                                                     >  1:223578/1‑93 (MQ=255)
                   aGTTGTACATCGTTCCACGTCGCTTCGACAACGGTATTATTCTCTGCCATTTTTACCGGTTTGGGTTCGGCTGGCGCTTTTTGTTCGCGTCcg                                                                     >  2:2244018/1‑93 (MQ=255)
                       ttACATCGTTCCACGTCGCTTCGACAACGGTATTATTCTCTGCCATTTTTACCGGTTTGGGTTCGGCTGGCGCTTTTTGTTCGCGTCCGCGTa                                                                 <  1:4088224/92‑1 (MQ=255)
                       gTACATCGTTCCACGTCGCTTCGACAACGGTATTATTCTCTGCCATTTTTACCGGTTTGGGTTCGGCTGGCGCTTTTTGTTCGCGTCCGCGTa                                                                 <  2:837785/93‑1 (MQ=255)
                         aCATCGTTCCACGTCGCTTCGACAACGGTATTATTCTCTGCCATTTTTACCGGTTTGGGTTCGGCTGGCGCTTTTTGTTCGCGTCCGCGTATc                                                               <  1:2192985/93‑1 (MQ=255)
                         aCATCGTTCCACGTCGCTTCGACAACGGTATTATTCTCTGCCATTTTTACCGGTTTGGGTTCGGCTGGCGCTTTTTGTTCGCGTCCGCGTATc                                                               <  1:3994019/93‑1 (MQ=255)
                          cATCGTTCCACGTCGCTTCGACAACGGTATTATTCTCTGCCATTTTTACCGGTTTGGGTTCGGCTGGCGCTTTTTGTTCGCGTCCGCGTATcc                                                              <  2:1907135/93‑1 (MQ=255)
                           aTCGTTCCACGTCGCTTCGACAACGGTATTATTCTCTGCCATTTTTACCGGTTTGGGTTCGGCTGGCGCTTTTTGTTCGCGTCCGCGTATccc                                                             >  2:1345412/1‑92 (MQ=255)
                           aTCGTTCCACGTCGCTTCGACAACGGTATTATTCTCTGCCATTTTTACCGGTTTGGGTTCGGCTGGCGCTTTTTGTTCGCGTCCGCGTATcca                                                             <  1:3616599/93‑1 (MQ=255)
                           aTCGTTCAACGTCGCTTCGACAACGGTATTATTCTCTGCCATTTTTACCGGTTTGGGTTCGGCTGGCGCTTTTTGTTCGCGTCCGCGTATcca                                                             >  1:1372194/1‑93 (MQ=255)
                              gTTCCACGTCGCTTCGACAACGGTATTATTCTCTGCCATTTTTACCGGTTTGGGTTCGGCTGGCGCTTTTTGTTCGCGTCCGCGTATccacca                                                          >  2:3040357/1‑93 (MQ=255)
                              gTTCCACGTCGCTTCGACAACGGTATTATTCTCTGCCATTTTTACCGGTTTGGGTTCGGCTGGCGCTTTTTGTTCGCGTCCGCGTATccacca                                                          >  2:1983304/1‑93 (MQ=255)
                              gTTCCACGTCGCTTCGACAACGGTATTATTCTCTGCCATTTTTACCGGTTTGGGTTCGGCTGGCGCTTTTTGTTCGCGTCCGCGTATccacca                                                          <  2:4255644/93‑1 (MQ=255)
                              gTTCCACGTCGCTTCGACAACGGTATTATTCTCTGCCATTTTTACCGGTTTGGGTTCGGCTGGCGCTTTTTGTTCGCGTCCGCGTATccacca                                                          <  1:1831640/93‑1 (MQ=255)
                              cttCCACGTCGCTTCGACAACGGTATTATTCTCTGCCATTTTTACCGGTTTGGGTTCGGCTGGCGCTTTTTGTTCGCGTCCGCGTATccacca                                                          <  2:1148851/92‑1 (MQ=255)
                              cttCCACGTCGCTTCGACAACGGTATTATTCTCTGCCATTTTTACCGGTTTGGGTTCGGCCGGCGCTTTTTGTTCGCGTCCGCGTATccacca                                                          <  1:1556898/92‑1 (MQ=255)
                                  cACGTCGCTTCGACAACGGTATTATTCTCTGCCATTTTTACCGGTTTGGGTTCGGCTGGCGCTTTTTGTTCGCGTCCGCGTATCCACCAggtc                                                      >  1:1309908/1‑91 (MQ=255)
                                   aCGTCGCTTCGACAACGGTATTATTCTCTGCCATTTTTACCGGTTTGGGTTCGGCTGGCGCTTTTTGTTCGCGTCCGCGTATCCACCAGGTCa                                                     >  2:3620700/1‑93 (MQ=255)
                                   aCGTCGCTTCGACAACGGTATTATTCTCTGCCATTTTTACCGGTTTGGGTTCGGCTGGCGCTTTTTGTTCGCGTCCGCGTATCCACCAGGTCa                                                     <  2:206559/93‑1 (MQ=255)
                                   aCGTCGCTTCGACAACGGGATTATTCTCTGCCATTTTTACCGGCTTGGGTTCGGCTGGCGCCTTTTGTTGGCGTCCGCGTCTCCACCCggtga                                                     >  2:3007894/1‑90 (MQ=255)
                                      tCGCTTCGACAACGGTATTATTCTCTGCCATTTTTACCGGTTTGGGTTCGGCTGGCGCTTTTTGTTCGCGTCCGCGTATCCACCAGGTCAGcc                                                  <  2:2825066/93‑1 (MQ=255)
                                      tCGCTTCGACAACGGTATTATTCTCTGCCATTTTTACCGGTTTGGGTTCGGCTGGCGCTTTTTGTTCGCGTCCGCGTATCCACCAGGTCAGcc                                                  >  2:2249750/1‑93 (MQ=255)
                                       cGCTTCGACAACGGTATTATTCTCTGCCATTTTTACCGGTTTGGGTTCGGCTGGCGCTTTTTGTTCGCGTCCGCGTATCCACCAGGTCAGccc                                                 <  2:3426414/93‑1 (MQ=255)
                                         cTTCGACAACGGTATTATTCTCTGCCATTTTTACCGGTTTGGGTTCGGCTGGCGCTTTTTGTTCGCGTCCGCGTATCCACCAGGTCAGCCCGa                                               >  1:1501117/1‑93 (MQ=255)
                                          ttCGACAACGGTATTATTCTCTGCCATTTTTACCGGTTTGGGTTCGGCTGGCGCTTTTTGTTCGCGTCCGCGTATCCACCAGGTCAGCCCGAg                                              >  1:1004249/1‑93 (MQ=255)
                                          ttCGACAACGGTATTATTCTCTGCCATTTTTACCGGTTTGGGTTCGGCTGGCGCTTTTTGTTCGCGTCCGCGTATCCACCAGGTCAGCCCGAg                                              >  1:1249411/1‑93 (MQ=255)
                                              aCAACGGTATTATTCTCTGCCATTTTTACCGGTTTGGGTTCGGCTGGCGCTTTTTGTTCGCGTCCGCGTATCCACCAGGTCAGCCCGAGCaac                                          >  1:2995978/1‑92 (MQ=255)
                                              aCAACGGTATTATTCTCTGCCATTTTTACCGGTTTGGGTTCGGCTGGCGCTTTTTGTTCGCGTCCGCGTATCCACCAGGTCAGCCCGAGCAAt                                          >  2:466075/1‑93 (MQ=255)
                                               cAACGGTATTATTCTCTGCCATTTTTACCGGTTTGGGTTCGGCTGGCGCTTTTTGTTCGCGTCCGCGTATCCACCAGGTCAGCCCGAGCAATc                                         <  1:526810/93‑1 (MQ=255)
                                               cAACGGTATTATTCTCTGCCATTTTTACCGGTTTGGGTTCGGCTGGCGCTTTTTGTTCGCGTCCGCGTATCCACCAGGTCAGCCCGAGCAATc                                         <  1:3790242/93‑1 (MQ=255)
                                                aaCGGTATTATTCTCTGCCATTTTTACCGGTTTGGGTTCGGCTGGCGCTTTTTGTTCGCGTCCGCGTATCCACCAGGTCAGCCCGAGCAATcc                                        >  1:813074/1‑93 (MQ=255)
                                                aaCGGTATTATTCTCTGCCATTTTTACCGGTTTGGGTTCGGCTGGCGCTTTTTGTTCGCGTCCGCGTATCCACCAGGTCAGCCCGAGCAATcc                                        >  1:1695517/1‑93 (MQ=255)
                                                 aCGGTATTATTCTCTGCCATTTTTACCGGTTTGGGTTCGGCTGGCGCTTTTTGTTCGCGTCCGCGTATCCACCAGGTCAGCCCGAGCAATCCg                                       <  2:3845434/93‑1 (MQ=255)
                                                  cGGTATTATTCTCTGCCATTTTTACCGGTTTGGGTTCGGCTGGCGCTTTTTGTTCGCGTCCGCGTATCCACCAGGTCAGCCCGAGCAATCCgg                                      >  2:1928283/1‑93 (MQ=255)
                                                    gTATTATTCTCTGCCATTTTTACCGGTTTGGGTTCGGCTGGCGCTTTTTGTTCGCGTCCGCGTATCCACCAGGTCAGCCCGAGCAATCCGGCa                                    <  2:2693145/93‑1 (MQ=255)
                                                    gTATTATTCTCTGCCATTTTTACCGGTTTGGGTTCGGCTGGCGCTTTTTGTTCGCGTCCGCGTATCCACCAGGTCAGCCCGAGCAATCCGGCa                                    >  1:4663071/1‑93 (MQ=255)
                                                     tattatTCTCTGCCATTTTTACCGGTTTGGGTTCGGCTGGCGCTTTTTGTTCGCGTCCGCGTATCCACCAGGTCAGCCCGAGCAATCCGGCAg                                   >  1:37003/1‑93 (MQ=255)
                                                      attattCTCTGCCATTTTTACCGGTTTGGGTTCGGCTGGCGCTTTTTGTTCGCGTCCGCGTATCCACCAGGTCAGCCCGAGCAATCCgggcgg                                  >  2:4427305/1‑89 (MQ=255)
                                                      attattCTCTGCCATTTTTACCGGTTTGGGTTCGGCTGGCGCTTTTTGTTCGCGTCCGCGTATCCACCAGGTCAGCCCGAGCAATCCGGCAGt                                  >  2:1706850/1‑93 (MQ=255)
                                                      attattCTCTGCCATTTTTACCGGCTTGGGTTCGGCTGGCGCTTTTTGTTCGCGTTCGCGTATCCACCAGGTCAGCCCGCGCAATCCGGCCGt                                  >  1:2197499/1‑93 (MQ=255)
                                                       ttattCTCTGCCATTTTTACCGGTTTGGGTTCGGCTGGCGCTTTTTGTTCGCGTCCGCGTATCCACCAGGTCAGCCCGAGCAATCCGGCAGTg                                 >  1:777196/1‑93 (MQ=255)
                                                         attCTCTGCCATTTTTACCGGTTTGGGTTCGGCTGGCGCTTTTTGTTCGCGTCCGCGTATCCACCAGGTCAGCCCGAGCAATCCGGCAGTGaa                               >  1:1330252/1‑93 (MQ=255)
                                                         attCTCTGCCATTTTTACCGGTTTGGGTTCGGCTGGCGCTTTTTGTTCGCGTCCGCGTATCCACCAGGTCAGCCCGAGCAATCCGGCAGTGaa                               >  2:4621307/1‑93 (MQ=255)
                                                          ttCTCTGCCATTTTTACCGGTTTGGGTTCGGCTGGCGCTTTTTGTTCGCGTCCGCGTATCCACCAGGTCAGCCCGAGCAATCCGGCAGTGAAc                              <  1:3161781/93‑1 (MQ=255)
                                                          ttCTCTGCCATTTTTACCGGTTTGGGTTCGGCTGGCGCTTTTTGTTCGCGTCCGCGTATCCACCAGGTCAGCCCGAGCAATCCGGCAGTGAAc                              >  1:2132273/1‑93 (MQ=255)
                                                          ttCTCTGCCATTTTTACCGGTTTGGGTTCGGCTGGCGCTTTTTGTTCGCGTCCGCGTATCCACCAGGTCAGCCCGAGCAATCCGGCAGTGAAc                              <  2:2801868/93‑1 (MQ=255)
                                                           tctcTGCCATTTTTACCGGTTTGGGTTCGGCTGGCGCTTTTTGTTCGCGTCCGCGTATCCACCAGGTCAGCCCGAGCAATCCGGCAGTGAACa                             <  1:3118409/93‑1 (MQ=255)
                                                           tctcTGCCATTTTTACCGGTTTGGGTTCGGCTGGCGCTTTTTGTTCGCGTCCGCGTATCCACCAGGTCAGCCCGAGCAATCCGGCAGTGAACa                             <  1:3100287/93‑1 (MQ=255)
                                                           tctcTGCCATTTTTACCGGTTTGGGTTCGGCTGGCGCTTTTTGTTCGCGTCCGCGTATCCACCAGGTCAGCCCGAGCAATCCGGCAGTGAACa                             >  1:2357805/1‑93 (MQ=255)
                                                            ctctGCCATTTTTACCGGTTTGGGTTCGGCTGGCGCTTTTTGTTCGCGTCCGCGTATCCACCAGGTCAGCCCGAGCAATCCGGCAGTGAACAg                            <  1:1129266/93‑1 (MQ=255)
                                                            ctctGCCATTTTTACCGGTTTGGGTTCGGCTGGCGCTTTTTGTTCGCGTCCGCGTATCCACCAGGTCAGCCCGAGCAATCCGGCAGTGAACAg                            <  2:1517483/93‑1 (MQ=255)
                                                             tctGCCATTTTTACCGGTTTGGGTTCGGCTGGCGCTTTTTGTTCGCGTCCGCGTATCCACCCGGTCAGCCCGAGCAATCCGGCAGTGAACAGc                           >  2:1620526/1‑93 (MQ=255)
                                                             tctGCCATTTTTACCGGTTTGGGTTCGGCTGGCGCTTTTTGTTCGCGTCCGCGTATCCACCAGGTCAGCCCGAGCAATCCGGCAGTGAACAGc                           <  2:4510153/93‑1 (MQ=255)
                                                             tctGCCATTTTTACCGGTTTGGGTTCGGCTGGCGCTTTTTGTTCGCGTCCGCGTATCCACCAGGTCAGCCCGAGCAATCCGGCAGTGAACAGc                           >  2:876572/1‑93 (MQ=255)
                                                             tctGCCATTTTTACCGGTTTGGGTTCGGCTGGCGCTTTTTGTTCGCGTCCGCGTATCCACCAGGTCAGCCCGAGCAATCCGGCAGTGAACAGc                           <  1:2960668/93‑1 (MQ=255)
                                                               tGCCATTTTTACCGGTTTGGGTTCGGCTGGCGCTTTTTGTTCGCGTCCGCGTATCCACCAGGTCAGCCCGAGCAATCCGGCAGTGAACAGCaa                         >  2:644124/1‑93 (MQ=255)
                                                               tGCCATTTTTACCGGTTTGGGTTCGGCTGGCGCTTTTTGTTCGCGTCCGCGTATCCACCAGGTCAGCCCGAGCAATCCGGCAGTGAACAGCaa                         >  1:1190780/1‑93 (MQ=255)
                                                               tGCCATTTTTACCGGTTTGGGTTCGGCTGGCGCTTTTTGTTCGCGTCCGCGTATCCACCAGGTCAGCCCGAGCAATCCGGCAGTGAACAGCaa                         >  1:1240648/1‑93 (MQ=255)
                                                                   aTTTTTACCGGTTTGGGTTCGGCTGGCGCTTTTTGTTCGCGTCCGCGTATCCACCAGGTCAGCCCGAGCAATCCGGCAGTGAACAGCAAAAAt                     <  2:3372730/93‑1 (MQ=255)
                                                                   aTTTTTACCGGTTTGGGTTCGGCTGGCGCTTTTTGTTCGCGTCCGCGTATCCACCAGGTCAGCCCGAGCAATCCGGCAGTGAACAGCAAAAAt                     <  2:802292/93‑1 (MQ=255)
                                                                    tttttACCGGTTTGGGTTCGGCTGGCGCTTTTTGTTCGCGTCCGCGTATCCACCAGGTCAGCCCGAGCAATCCGGCAGTGAACAGCAAAAATa                    >  2:2536663/1‑93 (MQ=255)
                                                                    tttttACCGGTTTGGGTTCGGCTGGCGCTTTTTGTTCGCGTCCGCGTATCCACCAGGTCAGCCCGAGCAATCCGGCAGTGAACAGCAAAAATa                    >  1:4025489/1‑93 (MQ=255)
                                                                     ttttACCGGTTTGGGTTCGGCTGGCGCTTTTTGTTCGCGTCCGCGTATCCACCAGGTCAGCCCGAGCAATCCGGCAGTGAACAGCAAAAATAc                   <  2:376549/93‑1 (MQ=255)
                                                                      tttACCGGTTTGGGTTCGGCTGGCGCTTTTTGTTCGCGTCCGCGTATCCACCAGGTCAGCCCGAGCAATCCGGCAGTGAACAGCAAAAATAcc                  >  2:4263390/1‑93 (MQ=255)
                                                                      tttACCGGTTTGGGTTCGGCTGGCGCTTTTTGTTCGCGTCCGCGTATCCACCAGGTCAGCCCGAGCAATCCGGCAGTGAACAGCAAAAATAcc                  <  1:292637/93‑1 (MQ=255)
                                                                       ttACCGGTTTGGGTTCGGCTGGCGCTTTTTGTTCGCGTCCGCGTATCCACCAGGTCAGCCCGAGCAATCCGGCAGTGAACAGCAAAAATACCa                 <  2:2236660/93‑1 (MQ=255)
                                                                       ttACCGGTTTGGGTTCGGCTGGCGCTTTTTGTTCGCGTCCGCGTATCCACCAGGTCAGCCCGAGCAATCCGGCAGTGAACAGCAAAAATACCa                 >  1:3509092/1‑93 (MQ=255)
                                                                       ttACCGGTTTGGGTTCGGCTGGCGCTTTTTGTTCGCGTCCGCGTATCCACCAGGTCAGCCCGAGCAATCCGGCAGTGAACAGCAAAAATACCa                 >  1:2038648/1‑93 (MQ=255)
                                                                        tACCGGTTTGGGTTCGGCTGGCGCTTTTTGTTCGCGTCCGCGTATCCACCAGGTCAGCCCGAGCAATCCGGCAGTGAACAGCAAAAATACCAg                <  2:4010951/93‑1 (MQ=255)
                                                                         tccGGTTTGGGTTCGGCTGGCGCTTTTTGTTCGCGTCCGCGTATCCACCAGGTCAGCCCGAGCAATCCGGCAGTGAACAGCAAAAATACCAgg               <  1:3853136/92‑1 (MQ=255)
                                                                         aCCGGTTTGGGTTCGGCTGGCGCTTTTTGTTCGCGTCCGCGTATCCACCAGGTCAGCCCGAGCAATCCGGCAGTGAACAGCAAAAATACCAgg               >  2:1855907/1‑93 (MQ=255)
                                                                          ccGGTTTGGGTTCGGCTGGCGCTTTTTGTTTGCGTCCGCGTATCCACCAGGTCAGCCCGAGCAATCCGGCAGTGAACAGCAAAAATACCAGGt              >  2:1446900/1‑93 (MQ=255)
                                                                            ggTTTGGGTTCGGCTGGCGCTTTTTGTTCGCGTCCGCGTATCCACCAGGTCAGCCCGAGCAATCCGGCAGTGAACAGCAAAAATACCAGGTTc            >  1:2272062/1‑93 (MQ=255)
                                                                             gTTTGGGTTCGGCTGGCGCTTTTTGTTCGCGTCCGCGTATCCACCAGGTCAGCCCGAGCAATCCGGCAGTGAACAGCAAAAATACCAGATTCg           >  1:1207521/1‑93 (MQ=255)
                                                                              tttGGGTTCGGCTGGCGCTTTTTGTTCGCGTCCGCGTATCCACCAGGTCAGCCCGAGCAATCCGGCAGTGAACAGCAAAAATACCAGGTTCgg          >  2:2486682/1‑93 (MQ=255)
                                                                                 gtgTTCGTCGGGCGCTTTTTGTTCGCGTCCGCGTATCCACGAGGTCAGCCCGAGCAATCCGGCAGTGAACAGCAAAAATACCAGGTTCGGCAt       <  2:1684941/91‑1 (MQ=255)
                                                                                 ggtttCGGCTGGCGCTTTTTGTTCGCGTCCGCGTATCCACCAGGTCAGCCCGAGCAATCCGGCAGTGAACAGCAAAAATACCAGGTTCGGCAt       <  2:1655996/90‑1 (MQ=255)
                                                                                 gggTTCGGCTGGCGCTTTTTGTTCGCGTCCGCGTATCCACCAGGTCAGCCCGAGCAATCCGGCAGTGAACAGCAAAAATACCAGGTTCGGCAt       <  2:4357274/93‑1 (MQ=255)
                                                                                   gTTGGGCTGGCGCTTTTTGTTCGCGTCCGCGTATCCACCAGGTCAGCCCGAGCAATCCGGCAGTGAACAGCAAAAATACCAGGTTCGGCATTc     <  2:1643167/93‑1 (MQ=255)
                                                                                    ttCGGCTGGCGCTTTTTGTTCGCGTCCGCGTATCCACCAGGTCAGCCCGAGCAATCCGGCAGTGAACAGCAAAAATACCAGGTTCGGCATTcc    <  1:4266719/93‑1 (MQ=255)
                                                                                      cGGCTGGCGCTTTTTGTTCGCGTCCGCGTATCCACCAGGTCAGCCCGAGCAATCCGGCAGTGAACAGCAAAAATACCAGGTTCGGCATTCCAg  <  1:1087092/93‑1 (MQ=255)
                                                                                          |                                                                                        
CATTCCCAGAGAATCTTCCAGTTGTACATCGTTCCACGTCGCTTCGACAACGGTATTATTCTCTGCCATTTTTACCGGTTTGGGTTCGGCAGGCGCTTTTTGTTCGCGTCCGCGTATCCACCAGGCCAGCCCGAGCAATCCGGCAGTGAACAGCAAAAATACCAGGTTCGGCATTCCAG  >  NC_000913/1961980‑1962158

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 18 ≤ ATCG/ATCG < 25 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

BRESEQ :: bam2aln output
TTCCATTCCCAGAGAATCTTCCAGTTGTACATCGTTCCACGTCGCTTCGACAACGGTATTATTCTCTGCCATTTTTACCGGTTTGGGTTCGGCAGGCGCTTTTTGTTCGCGTCCGCGTATCCACCAGGCCAGCCCGAGCAATCCGGCAGTGAACAGCAAAAATACCAGGTTCGGCATTCCAGGCACC  >  NC_000913/1961977‑1962163
                                                                                             |                                                                                             
TTCCATTCCCAGAGAATCTTCCAGTTGTACATCGTTCCACGTCGCTTCGACAACGGTATTATTCTCTGCCATTTTTACCGGTTTGGGTTCGGCT                                                                                               >  SRR4302535.1575966/1‑94 (MQ=60)
 TCCATTCCCAGAGAATCTTCCAGTTGTACATCGTTCCACGTCGCTTCGACAACGGTATTATTCTCTGCCATTTTTACCGGTTTGGGTTCGGCTG                                                                                              <  SRR4302535.3209445/94‑1 (MQ=60)
  CCATTCCCAGAGAATCTTCCAGTTGTACATCGTTCCACGTCGCTTCGACAACGGTATTATTCTCTGCCATTTTTACCGGTTTGGGTTCGGCTGG                                                                                             <  SRR4302535.3337769/94‑1 (MQ=60)
    ATTCCCAGAGAATCTTCCAGTTGTACATCGTTCCACGTCGCTTCGACAACGGTATTATTCTCTGCCATTTTTACCGGTTTGGGTTCGGCTGGCG                                                                                           <  SRR4302535.4255144/94‑1 (MQ=60)
          AGAGAATCTTCCAGTTGTACATCGTTCCACGTCGCTTCGACAACGGTATTATTCTCTGCCATTTTTACCGGTTTGGGTTCGGCTGGCGCTTTTT                                                                                     >  SRR4302535.4435321/1‑94 (MQ=60)
          AGAGAATCTTCCAGTTGTACATCGTTCCACGTCGCTTCGACAACGGTATTATTCTCTGCCATTTTTACCGGTTTGGGTTCGGCTGGCGCTTTTT                                                                                     <  SRR4302535.3168172/94‑1 (MQ=60)
             GAATCTTCCAGTTGTACATCGTTCCACGTCGCTTCGACAACGGTATTATTCTCTGCCATTTTTACCGGTTTGGGTTCGGCTGGCGCTTTTTGTT                                                                                  >  SRR4302535.1203148/1‑94 (MQ=60)
              AATCTTCCAGTTGTACATCGTTCCACGTCGCTTCGACAACGGTATTATTCTCTGCCATTTTTACCGGTTTGGGTTCGGCTGGCGCTTTTTGTTC                                                                                 <  SRR4302535.2966068/94‑1 (MQ=60)
               ATCTTCCAGTTGTACATCGTTCCACGTCGCTTCGACAACGGTATTATTCTCTGCCATTTTTACCGGTTTGGGTTCGGCTGGCGCTTTTTGTTCG                                                                                <  SRR4302535.2423289/94‑1 (MQ=60)
               ATCTTCCAGTTGTACATCGTTCCACGTCGCTTCGACAACGGTATTATTCTCTGCCATTTTTACCGGTTTGGGTTCGGCTGGCGCTTTTTGTTCG                                                                                >  SRR4302535.3200956/1‑94 (MQ=60)
               ATCTTCCAGTTGTACATCGTTCCACGTCGCTTCGACAACGGTATTATTCTCTGCCATTTTTACCGGTTTGGGTTCGGCTGGCGCTTTTTGTTCG                                                                                <  SRR4302535.1918833/94‑1 (MQ=60)
                   TCCAGTTGTACATCGTTCCACGTCGCTTCGACAACGGTATTATTCTCTGCCATTTTTACCGGTTTGGGTTCGGCTGGCGCTTTTTGTTCGCGTC                                                                            <  SRR4302535.577055/94‑1 (MQ=60)
                     CAGTTGTACATCGTTCCACGTCGCTTCGACAACGGTATTATTCTCTGCCATTTTTACCGGTTTGGGTTCGGCTGGCGCTTTTTGTTCGCGTCCG                                                                          >  SRR4302535.225117/1‑94 (MQ=60)
                          TTACATCGTTCCACGTCGCTTCGACAACGGTATTATTCTCTGCCATTTTTACCGGTTTGGGTTCGGCTGGCGCTTTTTGTTCGCGTCCGCGTAT                                                                     <  SRR4302535.4116197/94‑1 (MQ=60)
                            ACATCGTTCCACGTCGCTTCGACAACGGTATTATTCTCTGCCATTTTTACCGGTTTGGGTTCGGCTGGCGCTTTTTGTTCGCGTCCGCGTATCC                                                                   <  SRR4302535.4021342/94‑1 (MQ=60)
                            ACATCGTTCCACGTCGCTTCGACAACGGTATTATTCTCTGCCATTTTTACCGGTTTGGGTTCGGCTGGCGCTTTTTGTTCGCGTCCGCGTATCC                                                                   >  SRR4302535.2148095/1‑94 (MQ=60)
                            ACATCGTTCCACGTCGCTTCGACAACGGTATTATTCTCTGCCATTTTTACCGGTTTGGGTTCGGCTGGCGCTTTTTGTTCGCGTCCGCGTATCC                                                                   <  SRR4302535.4380510/94‑1 (MQ=60)
                            ACATCGTTCCACGTCGCTTCGACAACGGTATTATTCTCTGCCATTTTTACCGGTTTGGGTTCGGCTGGCGCTTTTTGTTCGCGTCCGCGTATCC                                                                   <  SRR4302535.2208614/94‑1 (MQ=60)
                             CATCGTTCAACGTCGCTTCGACAACGGTATTATTCTCTGCCATTTTTACCGGTTTGGGTTCGGCTGGCGCTTTTTGTTCGCGTCCGCGTATCCA                                                                  >  SRR4302535.1382000/1‑94 (MQ=60)
                              ATCGTTCCACGTCGCTTCGACAACGGTATTATTCTCTGCCATTTTTACCGGTTTGGGTTCGGCTGGCGCTTTTTGTTCGCGTCCGCGTATCCAC                                                                 <  SRR4302535.3641672/94‑1 (MQ=60)
                                 GTTCCACGTCGCTTCGACAACGGTATTATTCTCTGCCATTTTTACCGGTTTGGGTTCGGCTGGCGCTTTTTGTTCGCGTCCGCGTATCCACCAG                                                              <  SRR4302535.1844857/94‑1 (MQ=60)
                                 CTTCCACGTCGCTTCGACAACGGTATTATTCTCTGCCATTTTTACCGGTTTGGGTTCGGCCGGCGCTTTTTGTTCGCGTCCGCGTATCCACCAG                                                              <  SRR4302535.1568123/94‑1 (MQ=60)
                                    CCACGTCGCTTCGACAACGGTATTATTCTCTGCCATTTTTACCGGTTTGGGTTCGGCTGGCGCTTTTTGTTCGCGTCCGCGTATCCACCAGGTC                                                           >  SRR4302535.1319271/1‑94 (MQ=60)
                                     CACGTCGCTTCGACAACGGTATTATTCTCTGCCATTTTTACCGGTTTGGGTTCGGCTGGCGCTTTTTGTTCGCGTCCGCGTATCCACCAGGTCA                                                          >  SRR4302535.1244862/1‑94 (MQ=60)
                                           GCTTCGACAACGGTATTATTCTCTGCCATTTTTACCGGTTTGGGTTCGGCTGGCGCTTTTTGTTCGCGTCCGCGTATCCACCAGGTCAGCCCGA                                                    >  SRR4302535.1511916/1‑94 (MQ=60)
                                            CTTCGACAACGGTATTATTCTCTGCCATTTTTACCGGTTTGGGTTCGGCTGGCGCTTTTTGTTCGCGTCCGCGTATCCACCAGGTCAGCCCGAG                                                   >  SRR4302535.1258330/1‑94 (MQ=60)
                                            CTTCGACAACGGTATTATTCTCTGCCATTTTTACCGGTTTGGGTTCGGCTGGCGCTTTTTGTTCGCGTCCGCGTATCCACCAGGTCAGCCCGAG                                                   >  SRR4302535.1011379/1‑94 (MQ=60)
                                                GACAACGGTATTATTCTCTGCCATTTTTACCGGTTTGGGTTCGGCTGGCGCTTTTTGTTCGCGTCCGCGTATCCACCAGGTCAGCCCGAGCAAC                                               >  SRR4302535.3016979/1‑94 (MQ=60)
                                                  CAACGGTATTATTCTCTGCCATTTTTACCGGTTTGGGTTCGGCTGGCGCTTTTTGTTCGCGTCCGCGTATCCACCAGGTCAGCCCGAGCAATCC                                             <  SRR4302535.3816379/94‑1 (MQ=60)
                                                  CAACGGTATTATTCTCTGCCATTTTTACCGGTTTGGGTTCGGCTGGCGCTTTTTGTTCGCGTCCGCGTATCCACCAGGTCAGCCCGAGCAATCC                                             <  SRR4302535.530489/94‑1 (MQ=60)
                                                  CAACGGTATTATTCTCTGCCATTTTTACCGGTTTGGGTTCGGCTGGCGCTTTTTGTTCGCGTCCGCGTATCCACCAGGTCAGCCCGAGCAATCC                                             >  SRR4302535.1707774/1‑94 (MQ=60)
                                                  CAACGGTATTATTCTCTGCCATTTTTACCGGTTTGGGTTCGGCTGGCGCTTTTTGTTCGCGTCCGCGTATCCACCAGGTCAGCCCGAGCAATCC                                             >  SRR4302535.818774/1‑94 (MQ=60)
                                                      GGTATTATTCTCTGCCATTTTTACCGGTTTGGGTTCGGCTGGCGCTTTTTGTTCGCGTCCGCGTATCCACCAGGTCAGCCCGAGCAATCCGGCA                                         >  SRR4302535.4694603/1‑94 (MQ=60)
                                                       GTATTATTCTCTGCCATTTTTACCGGTTTGGGTTCGGCTGGCGCTTTTTGTTCGCGTCCGCGTATCCACCAGGTCAGCCCGAGCAATCCGGCAG                                        >  SRR4302535.37288/1‑94 (MQ=60)
                                                        TATTATTCTCTGCCATTTTTACCGGCTTGGGTTCGGCTGGCGCTTTTTGTTCGCGTTCGCGTATCCACCAGGTCAGCCCGCGCAATCCGGCCGT                                       >  SRR4302535.2213160/1‑94 (MQ=60)
                                                         ATTATTCTCTGCCATTTTTACCGGTTTGGGTTCGGCTGGCGCTTTTTGTTCGCGTCCGCGTATCCACCAGGTCAGCCCGAGCAATCCGGCAGTG                                      >  SRR4302535.782655/1‑94 (MQ=60)
                                                           TATTCTCTGCCATTTTTACCGGTTTGGGTTCGGCTGGCGCTTTTTGTTCGCGTCCGCGTATCCACCAGGTCAGCCCGAGCAATCCGGCAGTGAA                                    >  SRR4302535.1339740/1‑94 (MQ=60)
                                                            ATTCTCTGCCATTTTTACCGGTTTGGGTTCGGCTGGCGCTTTTTGTTCGCGTCCGCGTATCCACCAGGTCAGCCCGAGCAATCCGGCAGTGAAC                                   <  SRR4302535.1548924/94‑1 (MQ=60)
                                                            ATTCTCTGCCATTTTTACCGGTTTGGGTTCGGCTGGCGCTTTTTGTTCGCGTCCGCGTATCCACCAGGTCAGCCCGAGCAATCCGGCAGTGAAC                                   >  SRR4302535.2147645/1‑94 (MQ=60)
                                                             TTCTCTGCCATTTTTACCGGTTTGGGTTCGGCTGGCGCTTTTTGTTCGCGTCCGCGTATCCACCAGGTCAGCCCGAGCAATCCGGCAGTGAACA                                  >  SRR4302535.2374717/1‑94 (MQ=60)
                                                             TTCTCTGCCATTTTTACCGGTTTGGGTTCGGCTGGCGCTTTTTGTTCGCGTCCGCGTATCCACCAGGTCAGCCCGAGCAATCCGGCAGTGAACA                                  <  SRR4302535.3183713/94‑1 (MQ=60)
                                                              TCTCTGCCATTTTTACCGGTTTGGGTTCGGCTGGCGCTTTTTGTTCGCGTCCGCGTATCCACCAGGTCAGCCCGAGCAATCCGGCAGTGAACAG                                 <  SRR4302535.3140120/94‑1 (MQ=60)
                                                              TCTCTGCCATTTTTACCGGTTTGGGTTCGGCTGGCGCTTTTTGTTCGCGTCCGCGTATCCACCAGGTCAGCCCGAGCAATCCGGCAGTGAACAG                                 <  SRR4302535.3121871/94‑1 (MQ=60)
                                                               CTCTGCCATTTTTACCGGTTTGGGTTCGGCTGGCGCTTTTTGTTCGCGTCCGCGTATCCACCAGGTCAGCCCGAGCAATCCGGCAGTGAACAGC                                <  SRR4302535.1137328/94‑1 (MQ=60)
                                                                TCTGCCATTTTTACCGGTTTGGGTTCGGCTGGCGCTTTTTGTTCGCGTCCGCGTATCCACCAGGTCAGCCCGAGCAATCCGGCAGTGAACAGCA                               <  SRR4302535.2981452/94‑1 (MQ=60)
                                                                 CTGCCATTTTTACCGGTTTGGGTTCGGCTGGCGCTTTTTGTTCGCGTCCGCGTATCCACCAGGTCAGCCCGAGCAATCCGGCAGTGAACAGCAA                              >  SRR4302535.1199305/1‑94 (MQ=60)
                                                                 CTGCCATTTTTACCGGTTTGGGTTCGGCTGGCGCTTTTTGTTCGCGTCCGCGTATCCACCAGGTCAGCCCGAGCAATCCGGCAGTGAACAGCAA                              >  SRR4302535.1249506/1‑94 (MQ=60)
                                                                   GCCATTTTTACCGGTTTGGGTTCGGCTGGCGCTTTTTGTTCGCGTCCGCGTATCCACCAGGTCAGCCCGAGCAATCCGGCAGTGAACAGCAAAA                            <  SRR4302535.3821004/94‑1 (MQ=60)
                                                                      ATTTTTACCGGTTTGGGTTCGGCTGGCGCTTTTTGTTCGCGTCCGCGTATCCACCAGGTCAGCCCGAGCAATCCGGCAGTGAACAGCAAAAATA                         >  SRR4302535.4053032/1‑94 (MQ=60)
                                                                         TTTACCGGTTTGGGTTCGGCTGGCGCTTTTTGTTCGCGTCCGCGTATCCACCAGGTCAGCCCGAGCAATCCGGCAGTGAACAGCAAAAATACCA                      >  SRR4302535.2053328/1‑94 (MQ=60)
                                                                         TTTACCGGTTTGGGTTCGGCTGGCGCTTTTTGTTCGCGTCCGCGTATCCACCAGGTCAGCCCGAGCAATCCGGCAGTGAACAGCAAAAATACCA                      >  SRR4302535.3533478/1‑94 (MQ=60)
                                                                         TTTACCGGTTTGGGTTCGGCTGGCGCTTTTTGTTCGCGTCCGCGTATCCACCAGGTCAGCCCGAGCAATCCGGCAGTGAACAGCAAAAATACCA                      <  SRR4302535.294684/94‑1 (MQ=60)
                                                                            TCCGGTTTGGGTTCGGCTGGCGCTTTTTGTTCGCGTCCGCGTATCCACCAGGTCAGCCCGAGCAATCCGGCAGTGAACAGCAAAAATACCAGGT                   <  SRR4302535.3879642/94‑1 (MQ=60)
                                                                              CGGTTTGGGTTCGGCTGGCGCTTTTTGTTCGCGTCCGCGTATCCACCAGGTCAGCCCGAGCAATCCGGCAGTGAACAGCAAAAATACCAGGTTC                 >  SRR4302535.2288268/1‑94 (MQ=60)
                                                                               GGTTTGGGTTCGGCTGGCGCTTTTTGTTCGCGTCCGCGTATCCACCAGGTCAGCCCGAGCAATCCGGCAGTGAACAGCAAAAATACCAGATTCG                >  SRR4302535.1216201/1‑94 (MQ=60)
                                                                                      GTTCGGCTGGCGCTTTTTGTTCGCGTCCGCGTATCCACCAGGTCAGCCCGAGCAATCCGGCAGTGAACAGCAAAAATACCAGGTTCGGCATTCC         >  SRR4302535.931675/1‑94 (MQ=60)
                                                                                       TTCGGCTGGCGCTTTTTGTTCGCGTCCGCGTATCCACCAGGTCAGCCCGAGCAATCCGGCAGTGAACAGCAAAAATACCAGGTTCGGCATTCCA        <  SRR4302535.4295934/94‑1 (MQ=60)
                                                                                        TCGGCTGGCGCTTTTTGTTCGCGTCCGCGTATCCACCAGGTCAGCCCGAGCAATCCGGCAGTGAACAGCAAAAATACCAGGTTCGGCATTCCAG       <  SRR4302535.2500378/94‑1 (MQ=60)
                                                                                         CGGCTGGCGCTTTTTGTTCGCGTCCGCGTATCCACCAGGTCAGCCCGAGCAATCCGGCAGTGAACAGCAAAAATACCAGGTTCGGCATTCCAGG      <  SRR4302535.1094820/94‑1 (MQ=60)
                                                                                           GCTGGCGCTTTTTGTTCGCGTCCGCGTATCCACCAGGTCAGCCCGAGCAATCCGGCAGTGAACAGCAAAAATACCAGGTTCGGCATTCCAGGCA    <  SRR4302535.2179979/94‑1 (MQ=60)
                                                                                           GCTGGCGCTTTTTGTTCGCGTCCGCGTATCCACCAGGTCAGCCCGAGCAATCCGGCAGTGAACAGCAAAAATACCAGGTTCGGCATTCCAGGCA    >  SRR4302535.966881/1‑94 (MQ=60)
                                                                                            CTGGCGCTTTTTGTTCGCGTCCGCGTATCCACCAGGTCAGCCCGAGCAATCCGGCAGTGAACAGCAAAAATACCAGGTTCGGCATTCCAGGCAC   >  SRR4302535.3360279/1‑94 (MQ=60)
                                                                                             TGGCGCTTTTTGTTCGCGTCCGCGTATCCACCAGGTCAGCCCGAGCAATCCGGCAGTGAACAGCAAAAATACCAGGTTCGGCATTCCAGGCACC  <  SRR4302535.1782073/94‑1 (MQ=60)
                                                                                             TGGCGCTTTTTGTTCGCGTCCGCGTATCCACCAGGTCAGCCCGAGCAATCCGGCAGTGAACAGCAAAAATACCAGGTTCGGCATTCCAGGCACC  >  SRR4302535.1685718/1‑94 (MQ=60)
                                                                                             |                                                                                             
TTCCATTCCCAGAGAATCTTCCAGTTGTACATCGTTCCACGTCGCTTCGACAACGGTATTATTCTCTGCCATTTTTACCGGTTTGGGTTCGGCAGGCGCTTTTTGTTCGCGTCCGCGTATCCACCAGGCCAGCCCGAGCAATCCGGCAGTGAACAGCAAAAATACCAGGTTCGGCATTCCAGGCACC  >  NC_000913/1961977‑1962163

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 2 ≤ ATCG/ATCG < 24 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑