Sample Resequencing Stats

Note: The mutation counts shown below represent unfiltered mutation sets.
ALE, Flask, Isolate Predicted Mutations Mean Coverage Total Reads Percent Mapped Mapped Reads Average Read Length
A1 F1 I1 R1 1357 179.3 9500450 96.1% 9129932 93.0

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 1,727,504 A→G T132A (ACT→GCT)  lhr → Lhr

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009131,727,5040AG99.0% 324.5 / ‑5.9 103T132A (ACT→GCT) lhrLhr
Reads supporting (aligned to +/- strand):  ref base A (1/0);  new base G (48/54);  total (49/54)
Fisher's exact test for biased strand distribution p-value = 4.76e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

Only 100 of 105 total aligned reads displayed.

GCAACTTGCAGATCCCGTTGAAGGGTATTGCCGATGAACGGCGGCGGCGCGGCGAAACGGAAGTCAATCTTCGCGTAGGGATCCGTACTGGCGATACGCCTGCACAGGAACGCAGCAAACTCACCCGTAATCCGCCGGATATTCTGATCACCACACCCGAATCACTCTATCTGATG  >  NC_000913/1727418‑1727593
                                                                                      |                                                                                         
gcAACTTGCAGATCCCGTTGAAGGGTATTGCCGATGAACGGCGGCGGCGCGGCGAAACGGAAGTCAATCTTCGCGTAGGGATCCGTGCTGGCg                                                                                     <  2:1232291/93‑1 (MQ=255)
 cAACTTGCAGATCCCGTTGAAGGGTATTGCCGATGAACGGCGGCGGCGCGGCGAAACGGAAGTCAATCTTCGCGTAGGGATCCGTGCTGGCGa                                                                                    <  1:4125627/93‑1 (MQ=255)
  aaCTTGCAGATCCCGTTGAAGGGTATTGCCGATGAACGGCGGCGGCGCGGCGAAACGGAAGTCAATCTTCGCGTAGGGATCCGTGCTGGCGAt                                                                                   >  2:628420/1‑93 (MQ=255)
  aaCTTGCAGATCCCGTTGAAGGGTATTGCCGATGAACGGCGGCGGCGCGGCGAAACGGAAGTCAATCTTCGCGTAGGGATCCGTGCTGGCGAt                                                                                   >  2:3024671/1‑93 (MQ=255)
   aCTTGCAGATCCCGTTGAAGGGTATTGCCGATGCACGGCGGCGGCGCGGCGAAACGGAAGTCAATCTTCGCGTAGGGATCCGTGCTGGCGATa                                                                                  <  1:4520029/93‑1 (MQ=255)
   aCTTGCAGATCCCGTTGAAGGGTATTGCCGATGAACGGCGGCGGCGCGGCGAAACGGAAGTCAATCTTCGCGTAGGGATCCGTGCTGGCGATa                                                                                  >  1:494539/1‑93 (MQ=255)
   aCTTGCAGATCCCGTTGAAGGGTATTGCCGATGAACGGCGGCGGCGCGGCGAAACGGAAGTCAATCTTCGCGTAGGGATCCGTGCTGGCGATa                                                                                  <  1:1833537/93‑1 (MQ=255)
   aCTTGCAGATCCCG‑TGAAAGGTAATTCCGATTAACCGCGGCGGCCGCGCCAAACGGAAATTCATTTTCCCCGAAGGATCCGTGCTGGCGATAc                                                                                 <  2:4619082/93‑1 (MQ=255)
    cTTGCAGATCCCGTTGAAGGGTATTGCCGATGAACGGCGGCGGCGCGGCGAAACGGAAGTCAATCTTCGCGTAGGGATCCGTGCTGGCGATAc                                                                                 <  2:1101942/93‑1 (MQ=255)
     ttGCAGATCCCGTTGAAGGGTATTGCCGATGAACGGCGGCGGCGCGGCGAAACGGAAGTCAATCTTCGCGTAGGGATCCGTGCTGGCGATACg                                                                                >  1:1615954/1‑93 (MQ=255)
        cAGATCCCGTTGAAGGGTATTGCCGATGAACGGCGGCGGCGCGGCGAAACGGAAGTCAATCTTCGCGTAGGGATCCGTGCTGGCGATACGCCt                                                                             >  2:2969787/1‑93 (MQ=255)
         aGATCCCGTTGAAGGGTATTGCCGATGAACGGCGGCGGCGCGGCGAAACGGAAGTCAATCTTCGCGTAGGGATCCGTGCTGGCGATACGCCTg                                                                            >  2:1216737/1‑93 (MQ=255)
            tCCCGTTGAAGGGTATTGCCGATGAACGGCGGCGGCGCGGCGAAACGGAAGTCAATCTTCGCGTAGGGATCCGTGCTGGCGATACGCCTGcac                                                                         <  1:1098522/93‑1 (MQ=255)
            tCCCGTTGAAGGGTATTGCCGATGAACGGCGGCGGCGCGGCGAAACGGAAGTCAATCTTCGCGTAGGGATCCGTGCTGGCGATAAGCCTGcac                                                                         >  2:2326650/1‑93 (MQ=255)
             cccGTTGAAGGGTATTGCCGATGAACGGCGGCGGCGCGGCGAAACGGAAGTCAATCTTCGCGTAGGGATCCGTGCTGGCGATACGCCTGcaca                                                                        <  1:4726523/93‑1 (MQ=255)
             cccGTTGAAGGGTATTGCCGATGAACGGCGGCGGCGCGGCGAAACGGAAGTCAATCTTCGCGTAGGGATCCGTGCTGGCGATACGCCTGcaca                                                                        >  2:3264862/1‑93 (MQ=255)
              ccGTTGAAGGGTATTGCCGATGAACGGCGGCGGCGCGGCGAAACGGAAGTCAATCTTCGCGTAGGGATCCGTGCTGGCGATACGCCTGCACAg                                                                       <  1:4277561/93‑1 (MQ=255)
              ccGTTGAAGGGTATTGCCGATGAACGGCGGCGGCGCGGCGAAACGGAAGTCAATCTTCGCGTAGGGATCCGTGCTGGCGATACGCCTGCACAg                                                                       <  1:3120328/93‑1 (MQ=255)
               cGTTGAAGGGTATTGCCGATGACCGGCGGCGGCGCGGCGAAACGGAAGTCAATCTTCGCGTAGGGATCCGTGCTGGCGATACGCCTGCACAgg                                                                      <  2:4393394/93‑1 (MQ=255)
               cGTTGAAGGGTATTGCCGATGAACGGCGGCGGCGCGGCGAAACGGAAGTCAATCTTCGCGTAGGGATCCGTGCTGGCGATACGCCTGCACAgg                                                                      <  1:1057843/93‑1 (MQ=255)
                gTTGAAGGGTATTGCCGATGAACGGCGGCGGCGCGGCGAAACGGAAGTCAATCTTCGCGTAGGGATCCGTGCTGGCGATACGCCTGCACAGGa                                                                     <  1:388399/93‑1 (MQ=255)
                gTTGAAGGGTATTGCCGATGAACGGCGGCGGCGCGGCGAAACGGAAGTCAATCTTCGCGTAGGGAGCCGTGCTGGCGATACGCCTGCAGAGGa                                                                     >  1:2899264/1‑93 (MQ=255)
                 ttGAAGGGTATTGCCGATGAACGGCGGCGGCGCGGCGAAACGGAAGTCAATCTTCGCGTAGGGATCCGTGCTGGCGATACGCCTGCACAGGaa                                                                    >  2:2302805/1‑93 (MQ=255)
                 ttGAAGGGTATTGCCGATGAACGGCGGCGGCGCGGCGAAACGGAAGTCAATCTTCGCGTAGGGATCCGTGCTGGCGATACGCCTGCACAGGaa                                                                    >  1:185848/1‑93 (MQ=255)
                  tGAAGGGTATTGCCGATGAACGGCGGCGGCGCGGCGAAACGGAAGTCAATCTTCGCGTAGGGATCCGTGCTGGCGATACGCCTGCACAGGAAc                                                                   >  1:1549863/1‑93 (MQ=255)
                   gAAGGGTATTGCCGATGAACGGCGGCGGCGCGGGGAAACGGAAGTCAATCTTCGCGTAGGGATCCGTACTGGCGATACGCCTGCACCGGAACg                                                                  >  2:3734092/1‑93 (MQ=255)
                   gAAGGGTATTGCCGATGAACGGCGGCGGCGCGGCGAAACGGAAGTCAATCTTCGCGTAGGGATCCGTGCTGGCGATACGCCTGCACAGGAACg                                                                  >  2:314035/1‑93 (MQ=255)
                    aaGGGTATTGCCGATGAACGGCGGCGGCGCGGCGAAACGGAAGTCAATCTTCGCGTAGGGATCCGTGCTGGCGATACGCCTGCACAGGAAGgc                                                                 >  1:349615/1‑93 (MQ=255)
                     aGGGTATTGCCGATGAACGGCGGCGGCGCGGCGAAACGGAAGTCAATCTTCGCGTAGGGATCCGTGCTGGCGATACGCCTGCACAGGAACgca                                                                >  1:3753459/1‑93 (MQ=255)
                     aGGGTATTGCCGATGAACGGCGGCGGCGCGGCGAAACGGAAGTCAATCTTCGCGTAGGGATCCGTGCTGGCGATACGCCTGCACAGGAACgca                                                                >  2:1489803/1‑93 (MQ=255)
                     aGGGTATTGCCGATGAACGGCGGCGGCGCGGCGAAACGGAAGTCAATCTTCGCGTAGGGATCCGTGCTGGCGATACGCCTGCACAGGAACgca                                                                <  1:1752515/93‑1 (MQ=255)
                      gggTATTGCCGATGAACGGCGGCGGCGCGGCGAAACGGAAGTCAATCTTCGCGTAGGGATCCGTGCTGGCGATACGCCTGCACAGGAACgcag                                                               >  2:629345/1‑93 (MQ=255)
                      gggTATTGCCGATGAACGGCGGCGGCGCGGCGAAACGGAAGTCAATCTTCGCGTAGGGATCCGTGCTGGCGATACGCCTGCACAGGAACgcag                                                               >  1:1447717/1‑93 (MQ=255)
                        gTATTGCCGATGAACGGCGGCGGCGCGGCGAAACGGAAGTCAATCTTCGCGTAGGGATCCGTGCTGGCGATACGCCTGCACAGGAACgcagca                                                             >  2:3942615/1‑93 (MQ=255)
                          aTTGCCGATGAACGGCGGCGGCGCGGCGAAACGGAAGTCAATCTTCGCGTAGGGATCCGTGCTGGGGGTACGCCTGCACAGGAACCGAGCaaa                                                           >  2:2990277/1‑93 (MQ=255)
                           ttGCCGATGAACGGCGGCGGCGCGGCGAAACGGAAGTCAATCTTCGCGTAGGGATCCGTGCTGGCGATACGCCTGCACAGGAACGCAGCAAAc                                                          >  1:3732449/1‑93 (MQ=255)
                           ttGCCGATGAACGGCGGCGGCGCGGCGAAACGGAAGTCAATCTTCGCGTAGGGATCCGTGCTGGCGATACGCCTGCACAGGAACGCAGCAAAc                                                          <  1:2786481/93‑1 (MQ=255)
                             gCCGATGAACGGCGGCGGCGCGGCGAAACGGAAGTCAATCTTCGCGTAGGGATCCGTGCTGGCGATACGCCTGCACAGGAACGCAGCAAACTc                                                        >  2:2977740/1‑93 (MQ=255)
                             gCCGATGAACGGCGGCGGCGCGGCGAAACGGAAGTCAATCTTCGCGTAGGGATCCGTGCTGGCGATACGCCTGCACAGGAACGCAGCAAACTc                                                        <  2:4319231/93‑1 (MQ=255)
                               cGATGAACGGCGGCGGCGCGGCGAAACGGAAGTCAATCTTCGCGTAGGGATCCGTGCTGGCGATACGCCTGCACAGGAACGCAGCAAACTCAc                                                      <  1:1536664/93‑1 (MQ=255)
                               cGATGAACGGCGGCGGCGCGGCGAAACGGAAGTCAATCTTCGCGTAGGGATCCGTGCTGGCGATACGCCTGCACAGGAACGCAGCAAACTCAc                                                      <  2:1238798/93‑1 (MQ=255)
                                gATGAACGGCGGCGGCGCGGCGAAACGGAAGTCAATCTTCGCGTAGGGATCCGTGCTGGCGATACGCCTGCACAGGAACGCAGCAAACTCAcc                                                     <  1:3129763/93‑1 (MQ=255)
                                gATGAACGGCGGCGGCGCGGCGAAACGGAAGTCAATCTTCGCGTAGGGATCCGTGCTGGCGATACGCCTGCACAGGAACGCAGCAAACTCAcc                                                     >  1:1523610/1‑93 (MQ=255)
                                 aTGAACGGCGGCGGCGCGGCGAAACGGAAGTCAATCTTCGCGTAGGGATCCGTGCTGGCGATACGCCTGCACAGGAACGCAGCAAACTCAccc                                                    <  2:1235276/93‑1 (MQ=255)
                                   gAACGGCGGCGGCGCGGCGAAACGGAAGTCAATCTTTGCGTAGGGATCCGTGCTGGCGATACGCCTGCACAGGAAAGCAGCACACTCACCCGt                                                  >  2:568543/1‑93 (MQ=255)
                                   gAACGGCGGCGGCGCGGCGAAACGGAAGTCAATCTTCGCGTAGGGATCCGTGCTGGCGATACGCCTGCACAGGAACGCAGCAAACTCACCCGt                                                  <  2:492247/93‑1 (MQ=255)
                                   gAACGGCGGCGGCGCGGCGAAACGGAAGTCAATCTTCGCGTAGGGATCCGTGCTGGCGATACGCCTGCACAGGAACGCAGCAAACTCACCCGt                                                  <  2:4278544/93‑1 (MQ=255)
                                     aCGGCGGCGGCGCGGCGAAACGGAAGTCAATCTTCGCGTAGGGATCCGTGCTGGCGATACGCCTGCACAGGAACGCAGCAAACTCACCCGTaa                                                <  1:1409168/93‑1 (MQ=255)
                                     aCGGCGGCGGCGCGGCGAAACGGAAGTCAATCTTCGCGTAGGGATCCGTGCTGGCGATACGCCTGCACAGGAACGCAGCAAACTCACCCGTaa                                                <  2:3884200/93‑1 (MQ=255)
                                       gtcggcggcgCGGCGAAACGGTAGTCTATCTTCGCGTAGGGATCCTTGCTGGCGTTACGTCTGCACTGGAACGTAGCTAACTCACCCGTAATc                                              >  2:4216398/3‑93 (MQ=255)
                                       ggcggcggcGCGGCGAAACGGAAGTCAATCTTCGCGTAGGGATCCGTGCTGGCGATACGCCTGCACAGGAACGCAGCAAACTCACCCGTAATc                                              <  2:671182/93‑1 (MQ=255)
                                        gcggcggcgCGGCGAAACGGAAGTCAATCTTCGCGTAGGGATCCGTGCTGGCGATACGCCTGCACAGGAACGCAGCAAACTCACCCGTAATcc                                             >  1:4550162/1‑93 (MQ=255)
                                           gcggcgcggcGAAACGGAAGTCAATCTTCGCGTAGGGATCCGTGCTGGCGATACGCCTGCACAGGAACGCAGCAAACTCACCCGTAATccgcc                                          <  1:1367968/93‑1 (MQ=255)
                                           gcggcgcggcGAAACGGAAGTCAATCTTCGCGTAGGGATCCGTGCTGGCGATACGCCTGCACAGGAACGCAGCAAACTCACCCGTAATccgcc                                          <  2:1775626/93‑1 (MQ=255)
                                            cggcgcggcgAAACGGAAGTCAATCTTCGCGTAGGGATCCGTGCTGGCGATACGCCTGCACAGGAACGCAGCAAACTCACCCGTAATccgccg                                         <  1:2186152/93‑1 (MQ=255)
                                            cggcgcggcgAAACGGAAGTCAATCTTCGCGTAGGGATCCGTGCTGGCGATACGCCTGCACAGGAACGCAGCAAACTCACCCGTAATccgccg                                         <  2:1824611/93‑1 (MQ=255)
                                             ggcgcggcgAAACGGAAGTCAATCTTCGCGTAGGGATCCGTGCTGGCGATACGCCTGCACAGGAACGCAGCAAACTCACCCGTAATCCGCCgg                                        <  1:1718309/93‑1 (MQ=255)
                                             ggcgcggcgAAACGGAAGTCAATCTTCGCGTAGGGATCCGTGCTGGCGATACGCCTGCACAGGAACGCAGCAAACTCACCCGTAATCCGCCgg                                        >  2:1789249/1‑93 (MQ=255)
                                              gcgcggcgAAACGGAAGTCAATCTTCGCGTAGGGATCCGTGCTGGCGATACGCCTGCACAGGAACGCAGCAAACTCACCCGTAATCCGCCGGa                                       <  2:2967971/93‑1 (MQ=255)
                                               cgcggcgAAACGGAAGTCAATCTTCGCGTAGGGATCCGTGCTGGCGATACGCCTGCACAGGAACGCAGCAAACTCACCCGTAATCCGCCGGat                                      <  2:2954744/93‑1 (MQ=255)
                                                  ggcgAAACGGAAGTCAATCTTCGCGTAGGGATCCGTGCTGGCGATACGCCTGCACAGGAACGCAGCAAACTCACCCGTAATCCGCCGGATAtt                                   >  2:1051689/1‑93 (MQ=255)
                                                  ggcgAAACGGAAGTCAATCTTCGCGTAGGGATCCGTGCTGGCGATACGCCTGCACAGGAACGCAGCAAACTCACCCGTAATCCGCCGGATAtt                                   <  1:1769560/93‑1 (MQ=255)
                                                  ggcgAAACGGAAGTCAATCTTCGCGTAGGGATCCGTGCTGGCGATACGCCTGCACAGGAACGCAGCAAACTCACCCGTAATCCGCCGGATAtt                                   <  1:910729/93‑1 (MQ=255)
                                                   gcgAAACGGAAGTCAATCTTCGCGTAGGGATCCGTGCTGGCGATACGCCTGCACAGGAACGCAGCAAACTCACCCGTAATCCGCCGGATATTc                                  <  2:3034515/93‑1 (MQ=255)
                                                   gcgAAACGGAAGTCAATCTTCGCGTAGGGATCCGTGCTGGCGATACGCCTGCACAGGAACGCAGCAAACTCACCCGTAATCCGCCGGATATTc                                  <  2:3506097/93‑1 (MQ=255)
                                                   gcgAAACGGAAGTCAATCTTCGCGTAGGGATCCGTGCTGGCGATACGCCTGCACAGGAACGCAGCAAACTCACCCGTAATCCGCCGGATATTc                                  >  1:96824/1‑93 (MQ=255)
                                                   gcgAAACGGAAGTCAATCTTCGCGTAGGGATCCGTGCTGGCGATACGCCTGCACAGGAACGCAGCAAACTCACCCGTAATCCGCCGGATATTc                                  >  2:2673696/1‑93 (MQ=255)
                                                    cgAAACGGAAGTCAATCTTCGCGTAGGGATCCGTGCTGGCGATACGCCTGCACAGGAACGCAGCAAACTCACCCGTAATCCGCCGGATATTCt                                 <  1:2888973/93‑1 (MQ=255)
                                                      aaaCGGAAGTCAATCTTCGCGTAGGGATCCGTGCTGGCGATACGCCTGCACAGGAACGCAGCAAACTCACCCGTACTCCGCCGGATATTCTGa                               >  2:2168558/1‑93 (MQ=255)
                                                      aaaCGGAAGTCAATCTTCGCGTAGGGATCCGTGCTGGCGATACGCCTGCACAGGAACGCAGCAAACTCACCCGTAATCCGCCGGATATTCTGa                               >  2:2462883/1‑93 (MQ=255)
                                                       aaCGGAAGTCAATCTTCGCGTAGGGATCCGTGCTGGCGATACGCCTGCACAGGAACGCAGCAAACTCACCCGTAATCCGCCGGATATTCTGAt                              <  1:862956/93‑1 (MQ=255)
                                                         cGGAAGTCAATCTTCGCGTAGGGATCCGTGCTGGCGATACGCCTGCACAGGAACGCAGCAAACTCACCCGTAATCCGCCGGATATTCTGATca                            <  2:1536484/93‑1 (MQ=255)
                                                          tgAAGTCAATCTTCGCGTAGGGATCCGTGCTGGCGATACGCCTGCACAGGAACGCAGCAAACTCACCCGTAATCCGCCGGATATTCTGATcac                           >  2:123633/2‑93 (MQ=255)
                                                           gAAGTCAATCTTCGCGTAGGGATCCGTGCTGGCGATACGCCTGCACAGGAACGCAGCAAACTCACCCGTAATCCGCCGGATATTCTGATcccc                          >  2:3831853/1‑93 (MQ=255)
                                                           gAAGTCAATCTTCGCGTAGGGATCCGTGCTGGCGATACGCCTGCACAGGAACGCAGCAAACTCACCCGTAATCCGCCGGATATTCTGATcacc                          <  2:448452/93‑1 (MQ=255)
                                                           gAAGTCAATCTTCGCGTAGGGATCCGTGCTGGCGATACGCCTGCACAGGAACGCAGCAAACTCACCCGTAATCCGCCGGATATTCTGATcacc                          >  2:3831854/1‑93 (MQ=255)
                                                            aaGTCAATCTTCGCGTAGGGATCCGTGCTGGCGATACGCCTGCACAGGAACGCAGCAAACTCACCCGTAATCCGCCGGATATTCTGATcacca                         >  1:2430030/1‑93 (MQ=255)
                                                             aGTCAATCTTCGCGTAGGGATCCGTGCTGGCGATACGCCTGCACAGGAACGCAGCAAACTCACCCGTAATCCGCCGGATATTCTGATcaccac                        <  1:2278623/93‑1 (MQ=255)
                                                             aGTCAATCTTCGCGTAGGGATCCGTGCTGGCGATACGCCTGCACAGGAACGCAGCAAACTCACCCGTAATCCGCCGGATATTCTGATcaccac                        >  2:4613999/1‑93 (MQ=255)
                                                              gTCAATCTTCGCGTAGGGATCCGTGCTGGCGATACGCCTGCACAGGAACGCAGCAAACTCACCCGTAATCCGCCGGATATTCTGATCACcaca                       <  1:2221486/93‑1 (MQ=255)
                                                              gTCAATCTTCGCGTAGGGATCCGTGCTGGCGATACGCCTGCACAGGAACGCAGCAAACTCACCCGTAATCCGCCGGATATTCTAATCACcaca                       <  1:119594/93‑1 (MQ=255)
                                                              gTCAATCTTCGCGTAGGGATCCGTGCTGGCGATACGCCTGCACAGGAACGCAGCAAACTCACCCGGAATCCGCCGGATATCCTGATCACcaca                       >  1:4207405/1‑93 (MQ=255)
                                                               tCAATCTTCGCGTAGGGATCCGTGCTGGCGATACGCCTGCACAGGAACGCAGCAAACTCACCCGTAATCCGCCGGATATTCTGATCACCacac                      <  1:1114254/93‑1 (MQ=255)
                                                               tCAATCTTCGCGTAGGGATCCGTGCTGGCGATACGCCTGCACAGGAACGCAGCAAACTCACCCGTAATCCGCCGGATATTCTGATCACCacac                      >  1:1641868/1‑93 (MQ=255)
                                                                 aaTCTTCGCGTAGGGATCCGTGCTGGCGATACGCCTGCACAGGAACGCAGCAAACTCACCCGTAATCCGCCGGATATTCTGATCACCACAccc                    <  2:3288011/93‑1 (MQ=255)
                                                                 aaTCTTCGCGTAGGGATCCGTGCTGGCGATACGCCTGCACAGGAACGCAGCAAACTCACCCGTAATCCGCCGGATATTCTGATCACCACAccc                    <  1:3024442/93‑1 (MQ=255)
                                                                 aaTCTTCGCGTAGGGATCCGTGCTGGCGATACGCCTGCACAGGAACGCAGCAAACTCACCCGTAATCCGCCGGATATTCTGATCACCACAccc                    >  2:2469083/1‑93 (MQ=255)
                                                                   tCTTCGCGTAGGGATCCGTGCTGGCGATACGCCTGCACAGGAACGCAGCAAACTCACCCGTAATCCGCCGGATATTCTGATCACCACACCCGa                  >  1:4369234/1‑93 (MQ=255)
                                                                   tCTTCGCGTAGGGATCCGTGCTGGCGATACGCCTGCACAGGAACGCAGCAAACTCACCCGTAATCCGCCGGATATTCTGATCACCACACCCGa                  >  1:1809469/1‑93 (MQ=255)
                                                                    cTTCGCGTAGGGATCCGTGCTGGCGATACGCCTGCACAGGAACGCAGCAAACTCACCCGTAATCCGCCGGATATTCTGATCACCACACCCGaa                 <  2:2116095/93‑1 (MQ=255)
                                                                     ttCGCGTAGGGATCCGTGCTGGCGATACGCCTGCACAGGAACGCAGCAAACTCACCCGTAATCCGCCGGATATTCTGATCACCACACCCGAAt                >  1:4128214/1‑93 (MQ=255)
                                                                        gcgTAGGGATCCGTGCTGGCGATACGCCTGCACAGGAACGCAGCAAACTCACCCGTAATCCGCCGGATATTCTGATCACCACACCCGAATCAc             <  2:3731159/93‑1 (MQ=255)
                                                                         cgTAGGGATCCGTGCTGGCGATACGCCTGCACAGGAACGCAGCAAACTCACCCGTAATCCGCCGGATATTCTGATCACCACACCCGAATCAct            >  1:3181589/1‑93 (MQ=255)
                                                                          gTAGGGATCCGTGCTGGGGATACGCCTGCACAGGAACGCAGCAAACTCACCCGTAATCCGCCGGATATTCTGATCACCACACCCGAATCActc           <  1:434302/93‑1 (MQ=255)
                                                                          gTAGGGATCCGTGCTGGCGATACGCCTGCACAGGAACGCAGCAAACTCACCCGTAATCCGCCGGATATTCTGATCACCACACCCGAATCActc           >  1:682230/1‑93 (MQ=255)
                                                                            aGGGATCCGTGCTGGCGATACGCCTGCACAGGAACGCAGCAAACTCACCCGTAATCCGCCGGATATTCTGATCACCACACCCGCATCACTCTa         >  1:2370623/1‑93 (MQ=255)
                                                                              ggATCCGTGCTGGCGATACGCCTGCACAGGAACGCAGCAAACTCACCCGTAATCCGCCGGATATTCTGATCACCACACCCGAATCACTCTATc       <  2:1008364/93‑1 (MQ=255)
                                                                               gATCCGTGCTGGCGATACGCCTGCACAGGAACGCAGCAAACTCACCCGTAACCCGCCGGATATTCTGATCACCCCCCCCGAATCACTCTATCt      <  1:480723/93‑1 (MQ=255)
                                                                                 tCCGTGCTGGCGATACGCCTGCACAGGAACGCAGCAAACTCACCCGTAATCCGCCGGATATTCTGATCACCACACCCGAATCACTCTATCTGa    <  2:640136/93‑1 (MQ=255)
                                                                                   cGTGCTGGCGATACGCCTGCACAGGAACGCAGCAAACTCACCCGTAATCCGCCGGATATTCTGATCACCACACCCGAATCACTCTATCTGATg  <  1:923871/93‑1 (MQ=255)
                                                                                      |                                                                                         
GCAACTTGCAGATCCCGTTGAAGGGTATTGCCGATGAACGGCGGCGGCGCGGCGAAACGGAAGTCAATCTTCGCGTAGGGATCCGTACTGGCGATACGCCTGCACAGGAACGCAGCAAACTCACCCGTAATCCGCCGGATATTCTGATCACCACACCCGAATCACTCTATCTGATG  >  NC_000913/1727418‑1727593

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 18 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

BRESEQ :: bam2aln output
GTTCAGCGCAACTTGCAGATCCCGTTGAAGGGTATTGCCGATGAACGGCGGCGGCGCGGCGAAACGGAAGTCAATCTTCGCGTAGGGATCCGTACTGGCGATACGCCTGCACAGGAACGCAGCAAACTCACCCGTAATCCGCCGGATATTCTGATCACCACACCCGAATCACTCTATCTGATGC  >  NC_000913/1727411‑1727594
                                                                                             |                                                                                          
GTTCAGCGCAACTTGCAGATCCCGTTGAAGGGTATTGCCGATGAACGGCGGCGGCGCGGCGAAACGGAAGTCAATCTTCGCGTAGGGATCCGTG                                                                                            <  SRR4302544.3317303/94‑1 (MQ=60)
GTTCAGCGCAACTTGCAGATCCCGTTGAAGGGTATTGCCGATGAACGGCGGCGGCGCGGCGAAACGGAAGTCAATCTTCGCGTAGGGATCCGTG                                                                                            <  SRR4302544.463209/94‑1 (MQ=60)
  TCAGCGCAACTTGCAGATCCCGTTGAAGGGTATTGCCGATGAACGGCGGCGGCGCGGCGAAACGGAAGTCAATCTTCGCGTAGGGATCCGTGCT                                                                                          <  SRR4302544.4316165/94‑1 (MQ=60)
        CAACTTGCAGATCCCGTTGAAGGGTATTGCCGATGAACGGCGGCGGCGCGGCGAAACGGAAGTCAATCTTCGCGTAGGGATCCGTGCTGGCGAT                                                                                    <  SRR4302544.4166551/94‑1 (MQ=60)
         AACTTGCAGATCCCGTTGAAGGGTATTGCCGATGAACGGCGGCGGCGCGGCGAAACGGAAGTCAATCTTCGCGTAGGGATCCGTGCTGGCGATA                                                                                   >  SRR4302544.499401/1‑94 (MQ=60)
          ACTTGCAGATCCCGTTGAAGGGTATTGCCGATGCACGGCGGCGGCGCGGCGAAACGGAAGTCAATCTTCGCGTAGGGATCCGTGCTGGCGATAC                                                                                  <  SRR4302544.4565284/94‑1 (MQ=60)
          ACTTGCAGATCCCGTTGAAGGGTATTGCCGATGAACGGCGGCGGCGCGGCGAAACGGAAGTCAATCTTCGCGTAGGGATCCGTGCTGGCGATAC                                                                                  <  SRR4302544.1851348/94‑1 (MQ=60)
           CTTGCAGATCCCGTTGAAGGGTATTGCCGATGAACGGCGGCGGCGCGGCGAAACGGAAGTCAATCTTCGCGTAGGGATCCGTGCTGGCGATACG                                                                                 >  SRR4302544.229447/1‑94 (MQ=60)
           CTTGCAGATCCCGTTGAAGGGTATTGCCGATGAACGGCGGCGGCGCGGCGAAACGGAAGTCAATCTTCGCGTAGGGATCCGTGCTGGCGATACG                                                                                 >  SRR4302544.1631884/1‑94 (MQ=60)
                   TCCCGTTGAAGGGTATTGCCGATGAACGGCGGCGGCGCGGCGAAACGGAAGTCAATCTTCGCGTAGGGATCCGTGCTGGCGATACGCCTGCACA                                                                         <  SRR4302544.1109454/94‑1 (MQ=60)
                    CCCGTTGAAGGGTATTGCCGATGAACGGCGGCGGCGCGGCGAAACGGAAGTCAATCTTCGCGTAGGGATCCGTGCTGGCGATACGCCTGCACAG                                                                        <  SRR4302544.4773171/94‑1 (MQ=60)
                     CCGTTGAAGGGTATTGCCGATGAACGGCGGCGGCGCGGCGAAACGGAAGTCAATCTTCGCGTAGGGATCCGTGCTGGCGATACGCCTGCACAGG                                                                       <  SRR4302544.3149994/94‑1 (MQ=60)
                     CCGTTGAAGGGTATTGCCGATGAACGGCGGCGGCGCGGCGAAACGGAAGTCAATCTTCGCGTAGGGATCCGTGCTGGCGATACGCCTGCACAGG                                                                       <  SRR4302544.4321245/94‑1 (MQ=60)
                      CGTTGAAGGGTATTGCCGATGAACGGCGGCGGCGCGGCGAAACGGAAGTCAATCTTCGCGTAGGGATCCGTGCTGGCGATACGCCTGCACAGGA                                                                      <  SRR4302544.1068345/94‑1 (MQ=60)
                      CGTTGAAGGGTATTGCCGATGAACGGCGGCGGCGCGGCGAAACGGAAGTCAATCTTCGCGTAGGGAGCCGTGCTGGCGATACGCCTGCAGAGGA                                                                      >  SRR4302544.2927186/1‑94 (MQ=60)
                       GTTGAAGGGTATTGCCGATGAACGGCGGCGGCGCGGCGAAACGGAAGTCAATCTTCGCGTAGGGATCCGTGCTGGCGATACGCCTGCACAGGAA                                                                     >  SRR4302544.187694/1‑94 (MQ=60)
                       GTTGAAGGGTATTGCCGATGAACGGCGGCGGCGCGGCGAAACGGAAGTCAATCTTCGCGTAGGGATCCGTGCTGGCGATACGCCTGCACAGGAA                                                                     <  SRR4302544.392345/94‑1 (MQ=60)
                        TTGAAGGGTATTGCCGATGAACGGCGGCGGCGCGGCGAAACGGAAGTCAATCTTCGCGTAGGGATCCGTGCTGGCGATACGCCTGCACAGGAAC                                                                    >  SRR4302544.1565299/1‑94 (MQ=60)
                          GAAGGGTATTGCCGATGAACGGCGGCGGCGCGGCGAAACGGAAGTCAATCTTCGCGTAGGGATCCGTGCTGGCGATACGCCTGCACAGGAAGGC                                                                  >  SRR4302544.353202/1‑94 (MQ=60)
                           AAGGGTATTGCCGATGAACGGCGGCGGCGCGGCGAAACGGAAGTCAATCTTCGCGTAGGGATCCGTGCTGGCGATACGCCTGCACAGGAACGCA                                                                 >  SRR4302544.3790732/1‑94 (MQ=60)
                            AGGGTATTGCCGATGAACGGCGGCGGCGCGGCGAAACGGAAGTCAATCTTCGCGTAGGGATCCGTGCTGGCGATACGCCTGCACAGGAACGCAG                                                                >  SRR4302544.1462107/1‑94 (MQ=60)
                            AGGGTATTGCCGATGAACGGCGGCGGCGCGGCGAAACGGAAGTCAATCTTCGCGTAGGGATCCGTGCTGGCGATACGCCTGCACAGGAACGCAG                                                                <  SRR4302544.1769670/94‑1 (MQ=60)
                                 ATTGCCGATGAACGGCGGCGGCGCGGCGAAACGGAAGTCAATCTTCGCGTAGGGATCCGTGCTGGCGATACGCCTGCACAGGAACGCAGCAAAC                                                           >  SRR4302544.3769560/1‑94 (MQ=60)
                                  TTGCCGATGAACGGCGGCGGCGCGGCGAAACGGAAGTCAATCTTCGCGTAGGGATCCGTGCTGGCGATACGCCTGCACAGGAACGCAGCAAACT                                                          <  SRR4302544.2813300/94‑1 (MQ=60)
                                      CGATGAACGGCGGCGGCGCGGCGAAACGGAAGTCAATCTTCGCGTAGGGATCCGTGCTGGCGATACGCCTGCACAGGAACGCAGCAAACTCACC                                                      <  SRR4302544.1551930/94‑1 (MQ=60)
                                      CGATGAACGGCGGCGGCGCGGCGAAACGGAAGTCAATCTTCGCGTAGGGATCCGTGCTGGCGATACGCCTGCACAGGAACGCAGCAAACTCACC                                                      >  SRR4302544.1538729/1‑94 (MQ=60)
                                       GATGAACGGCGGCGGCGCGGCGAAACGGAAGTCAATCTTCGCGTAGGGATCCGTGCTGGCGATACGCCTGCACAGGAACGCAGCAAACTCACCC                                                     <  SRR4302544.3159500/94‑1 (MQ=60)
                                            ACGGCGGCGGCGCGGCGAAACGGAAGTCAATCTTCGCGTAGGGATCCGTGCTGGCGATACGCCTGCACAGGAACGCAGCAAACTCACCCGTAAT                                                <  SRR4302544.1423195/94‑1 (MQ=60)
                                              GGCGGCGGCGCGGCGAAACGGAAGTCAATCTTCGCGTAGGGATCCGTGCTGGCGATACGCCTGCACAGGAACGCAGCAAACTCACCCGTAATCC                                              >  SRR4302544.4595594/1‑94 (MQ=60)
                                                  GCGGCGCGGCGAAACGGAAGTCAATCTTCGCGTAGGGATCCGTGCTGGCGATACGCCTGCACAGGAACGCAGCAAACTCACCCGTAATCCGCCG                                          <  SRR4302544.1381569/94‑1 (MQ=60)
                                                   CGGCGCGGCGAAACGGAAGTCAATCTTCGCGTAGGGATCCGTGCTGGCGATACGCCTGCACAGGAACGCAGCAAACTCACCCGTAATCCGCCGG                                         <  SRR4302544.2206824/94‑1 (MQ=60)
                                                    GGCGCGGCGAAACGGAAGTCAATCTTCGCGTAGGGATCCGTGCTGGCGATACGCCTGCACAGGAACGCAGCAAACTCACCCGTAATCCGCCGGA                                        <  SRR4302544.1735198/94‑1 (MQ=60)
                                                         GGCGAAACGGAAGTCAATCTTCGCGTAGGGATCCGTGCTGGCGATACGCCTGCACAGGAACGCAGCAAACTCACCCGTAATCCGCCGGATATTC                                   <  SRR4302544.919733/94‑1 (MQ=60)
                                                         GGCGAAACGGAAGTCAATCTTCGCGTAGGGATCCGTGCTGGCGATACGCCTGCACAGGAACGCAGCAAACTCACCCGTAATCCGCCGGATATTC                                   >  SRR4302544.97710/1‑94 (MQ=60)
                                                         GGCGAAACGGAAGTCAATCTTCGCGTAGGGATCCGTGCTGGCGATACGCCTGCACAGGAACGCAGCAAACTCACCCGTAATCCGCCGGATATTC                                   <  SRR4302544.1786879/94‑1 (MQ=60)
                                                           CGAAACGGAAGTCAATCTTCGCGTAGGGATCCGTGCTGGCGATACGCCTGCACAGGAACGCAGCAAACTCACCCGTAATCCGCCGGATATTCTG                                 <  SRR4302544.2916821/94‑1 (MQ=60)
                                                             AAACGGAAGTCAATCTTCGCGTAGGGATCCGTGCTGGCGATACGCCTGCACAGGAACGCAGCAAACTCACCCGTAATCCGCCGGATATTCTGAT                               >  SRR4302544.4428179/1‑94 (MQ=60)
                                                              AACGGAAGTCAATCTTCGCGTAGGGATCCGTGCTGGCGATACGCCTGCACAGGAACGCAGCAAACTCACCCGTAATCCGCCGGATATTCTGATC                              <  SRR4302544.871493/94‑1 (MQ=60)
                                                                  GAAGTCAATCTTCGCGTAGGGATCCGTGCTGGCGATACGCCTGCACAGGAACGCAGCAAACTCACCCGTAATCCGCCGGATATTCTGATCACCA                          >  SRR4302544.2453172/1‑94 (MQ=60)
                                                                    AGTCAATCTTCGCGTAGGGATCCGTGCTGGCGATACGCCTGCACAGGAACGCAGCAAACTCACCCGTAATCCGCCGGATATTCTGATCACCACA                        <  SRR4302544.2300084/94‑1 (MQ=60)
                                                                    AGTCAATCTTCGCGTAGGGATCCGTGCTGGCGATACGCCTGCACAGGAACGCAGCAAACTCACCCGGAATCCGCCGGATATCCTGATCACCACA                        >  SRR4302544.4249653/1‑94 (MQ=60)
                                                                     GTCAATCTTCGCGTAGGGATCCGTGCTGGCGATACGCCTGCACAGGAACGCAGCAAACTCACCCGTAATCCGCCGGATATTCTGATCACCACAC                       <  SRR4302544.2242381/94‑1 (MQ=60)
                                                                     GTCAATCTTCGCGTAGGGATCCGTGCTGGCGATACGCCTGCACAGGAACGCAGCAAACTCACCCGTAATCCGCCGGATATTCTGATCACCACAC                       >  SRR4302544.1658050/1‑94 (MQ=60)
                                                                     GTCAATCTTCGCGTAGGGATCCGTGCTGGCGATACGCCTGCACAGGAACGCAGCAAACTCACCCGTAATCCGCCGGATATTCTAATCACCACAC                       <  SRR4302544.120680/94‑1 (MQ=60)
                                                                      TCAATCTTCGCGTAGGGATCCGTGCTGGCGATACGCCTGCACAGGAACGCAGCAAACTCACCCGTAATCCGCCGGATATTCTGATCACCACACC                      <  SRR4302544.1125370/94‑1 (MQ=60)
                                                                        AATCTTCGCGTAGGGATCCGTGCTGGCGATACGCCTGCACAGGAACGCAGCAAACTCACCCGTAATCCGCCGGATATTCTGATCACCACACCCG                    <  SRR4302544.3053422/94‑1 (MQ=60)
                                                                         ATCTTCGCGTAGGGATCCGTGCTGGCGATACGCCTGCACAGGAACGCAGCAAACTCACCCGTAATCCGCCGGATATTCTGATCACCACACCCGA                   >  SRR4302544.4413545/1‑94 (MQ=60)
                                                                         ATCTTCGCGTAGGGATCCGTGCTGGCGATACGCCTGCACAGGAACGCAGCAAACTCACCCGTAATCCGCCGGATATTCTGATCACCACACCCGA                   >  SRR4302544.1827148/1‑94 (MQ=60)
                                                                           CTTCGCGTAGGGATCCGTGCTGGCGATACGCCTGCACAGGAACGCAGCAAACTCACCCGTAATCCGCCGGATATTCTGATCACCACACCCGAAT                 >  SRR4302544.4169147/1‑94 (MQ=60)
                                                                               GCGTAGGGATCCGTGCTGGCGATACGCCTGCACAGGAACGCAGCAAACTCACCCGTAATCCGCCGGATATTCTGATCACCACACCCGAATCACT             >  SRR4302544.3211864/1‑94 (MQ=60)
                                                                                CGTAGGGATCCGTGCTGGCGATACGCCTGCACAGGAACGCAGCAAACTCACCCGTAATCCGCCGGATATTCTGATCACCACACCCGAATCACTC            >  SRR4302544.689012/1‑94 (MQ=60)
                                                                                 GTAGGGATCCGTGCTGGGGATACGCCTGCACAGGAACGCAGCAAACTCACCCGTAATCCGCCGGATATTCTGATCACCACACCCGAATCACTCT           <  SRR4302544.438682/94‑1 (MQ=60)
                                                                                  TAGGGATCCGTGCTGGCGATACGCCTGCACAGGAACGCAGCAAACTCACCCGTAATCCGCCGGATATTCTGATCACCACACCCGCATCACTCTA          >  SRR4302544.2393056/1‑94 (MQ=60)
                                                                                      GATCCGTGCTGGCGATACGCCTGCACAGGAACGCAGCAAACTCACCCGTAACCCGCCGGATATTCTGATCACCCCCCCCGAATCACTCTATCTG      <  SRR4302544.485429/94‑1 (MQ=60)
                                                                                          CGTGCTGGCGATACGCCTGCACAGGAACGCAGCAAACTCACCCGTAATCCGCCGGATATTCTGATCACCACACCCGAATCACTCTATCTGATGC  >  SRR4302544.3486782/1‑94 (MQ=60)
                                                                                          CGTGCTGGCGATACGCCTGCACAGGAACGCAGCAAACTCACCCGTAATCCGCCGGATATTCTGATCACCACACCCGAATCACTCTATCTGATGC  <  SRR4302544.932980/94‑1 (MQ=60)
                                                                                          CGTGCTGGCGATACGCCTGCACAGGAACGCAGCAAACTCACCCGTAATCCGCCGGATATTCTGATCACCACACCCGAATCACTCTATCTGATGC  >  SRR4302544.1048392/1‑94 (MQ=60)
                                                                                             |                                                                                          
GTTCAGCGCAACTTGCAGATCCCGTTGAAGGGTATTGCCGATGAACGGCGGCGGCGCGGCGAAACGGAAGTCAATCTTCGCGTAGGGATCCGTACTGGCGATACGCCTGCACAGGAACGCAGCAAACTCACCCGTAATCCGCCGGATATTCTGATCACCACACCCGAATCACTCTATCTGATGC  >  NC_000913/1727411‑1727594

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑