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 2,115,180 T→C Q416R (CAG→CGG)  wcaK ← putative galactokinase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009132,115,1800TC97.7% 397.8 / ‑0.7 129Q416R (CAG→CGG) wcaKputative galactokinase
Reads supporting (aligned to +/- strand):  ref base T (1/2);  new base C (71/55);  total (72/57)
Fisher's exact test for biased strand distribution p-value = 5.83e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.82e-01

Only 100 of 132 total aligned reads displayed.

GTTAAGGACGAAGGTTTCTGACGACAGCGGGAATTTCAGTAAAAAGAAGCCGACCTTCATTTCACCTCCCCGATGCGCTCAAGCACAGACTGCACCATCTGCATTCCTGTCTGACGCTCACGACTGACGGCTTCACTAAGTCGCGCATTCAGCGCCGGAAGCTGGCCTAAGGTATCCGC  >  NC_000913/2115090‑2115268
                                                                                          |                                                                                        
gTTAAGGACGAAGGTTTCTGACGACAGCGGGAATTTCAGTAAAAAGAAGCCGACCTTCATTTCACCTCCCCGATGCGCTCAAGCACAGACCGc                                                                                        >  2:4283860/1‑93 (MQ=255)
gTTAAGGACGAAGGTTTCTGACGACAGCGGGAATTTCAGTAAAAAGAAGCCGACCTTCATTTCACCTCCCCGATGCGCTCAAGCACAGACCGc                                                                                        <  1:1578900/93‑1 (MQ=255)
 ttAAGGACGAAGGTTTCTGACGACAGCGGGAATTTCAGTAAAAAGAAGCCGACCTTCATTTCACCTCCCCGATGCGCTCACGCACAGACCGCa                                                                                       >  2:4583751/1‑93 (MQ=255)
   aaGGACGAAGGTTTCTGACGACAGCGGGAATTTCAGTAAAAAGAAGCCGACCTTCATTTCACCTCCCCGATGCGCTCAAGCACAGACCGCAcc                                                                                     <  1:3494356/93‑1 (MQ=255)
    aGGACGAAGGTTTCTGACGACAGCGGGAATTTCAGTAAAAAGAAGCCGACCTTCATTTCACCTCCCCGATGCGCTCAAGCACAGACCGCACCa                                                                                    >  2:1169513/1‑93 (MQ=255)
     ggACGAAGGTTTCTGACGACAGCGGGAATTTCAGTAAAAAGAAGCCGACCTTCATTTCACCTCCCCGATGCGCTCAAGCACAGACCGCACCAt                                                                                   >  2:1311265/1‑93 (MQ=255)
      gACGAAGGTTTCTGACGACAGCGGGAATTTCAGTAAAAAGAAGCCGACCTTCATTTCACCTCCCCGATGCGCTCAAGCACAGACCGCACCATc                                                                                  <  1:1105874/93‑1 (MQ=255)
      gACGAAGGTTTCTGACGACAGCGGGAATTTCAGTAAAAAGAAGCCGACCTTCATTTCACCTCCCCGATGCGCTCAAGCACAGACCGCACCATc                                                                                  >  1:4389669/1‑93 (MQ=255)
      gACGAAGGTTTCTGACGACAGCGGGAATTTCAGTAAAAAGAAGCCGACCTTCATTTCACCTCCCCGATGCGCTCAAGCACAGACCGCACCATc                                                                                  <  2:1794632/93‑1 (MQ=255)
       aCGAAGGTTTCTGACGACAGCGGGAATTTCAGTAAAAAGAAGCCGACCTTCATTTCACCTCCCCGATGCGCTCCAGCACAGACCACACCctct                                                                                 >  2:498893/1‑93 (MQ=255)
       aCGAAGGTTTCTGACGACAGCGGGAATTTCAGTAAAAAGAAGCCGACCTTCATTTCACCTCCCCGATGCGCTCAAGCACAGACCGCACCATCt                                                                                 >  1:2152838/1‑93 (MQ=255)
        cGAAGGTTTCTGACGACAGCGGGAATTTCAGTAAAAAGAAGCCGACCTTCATTTCACCTCCCCGATGCGCTCAAGCACAGACCGCACCATCTg                                                                                <  2:3807477/93‑1 (MQ=255)
            ggTTTCTGACGACAGCGGGAATTTCAGTAAAAAGAAGCCGACCTTCATTTCACCTCCCCGATGCGCTCAAGCACAGACCGCACCATCTGCAtt                                                                            <  2:4709761/93‑1 (MQ=255)
             gTTTCTGACGACAGCGGGAATTTCAGTAAAAAGAAGCCGACCTTCATTTCACCTCCCCGATGCGCTCAAGCACAGACCGCACCATCTGCATTc                                                                           >  2:1938230/1‑93 (MQ=255)
               ttCTGACGACAGCGGGAATTTCAGTAAAAAGAAGCCGACCTTCATTTCACCTCCCCGATGCGCTCAAGCACAGACTGCACCATCTGCATTCCt                                                                         <  1:1575972/93‑1 (MQ=255)
               ttCTGACGACAGCGGGAATTTCAGTAAAAAGAAGCCGACCTTCATTTCACCTCCCCGATGCGCTCAAGCACAGACCGCACCATCTGCATTCCt                                                                         <  2:3217841/93‑1 (MQ=255)
               ttCTGACGACAGCGGGAATTTCAGTAAAAAGAAGCCGACCTTCATTTCACCTCCCCGATGCGCTCAAGCACAGACCGCACCATCTGCATTCCt                                                                         >  1:2282803/1‑93 (MQ=255)
                 cTGACGACAGCGGTAATTTCAGTAAAAAGAAGCCGACCTTCATTTCACCTCCCCGATGCGCTCAAGCACAGACCGCACCATCTGCATTCCTGt                                                                       >  2:3432451/1‑93 (MQ=255)
                  tGACGACAGCGGGAATTTCAGTAAAAAGAAGCCGACCTTCATTTCACCTCCCCGATGCGCTCAAGCACAGACCGCACCATCTGCATTCCTGTc                                                                      <  2:3406041/93‑1 (MQ=255)
                  tGACGACAGCGGGAATTTCAGTAAAAAGAAGCCGACCTTCATTTCACCTCCCCGATGCGCTCAAGCACAGACCGCACCATCTGCATTCCTGTc                                                                      <  1:4217842/93‑1 (MQ=255)
                   gacgacAGCGGGAATTTCAGTAAAAAGAAGCCGACCTTCATTTCACCTCCCCGATGCGCTCAAGCACAGACCGCACCATCTGCATTCCTGTCt                                                                     >  2:1452786/1‑93 (MQ=255)
                   gacgacAGCGGGAATTTCAGTAAAAAGAAGCCGACCTTCATTTCACCTCCCCGATGCGCTCAAGCACAGACCGCACCATCTGCATTCCTGTCt                                                                     >  2:3369734/1‑93 (MQ=255)
                   gacgacAGCGGGAATTTCAGTAAAAAGAAGCCGACCTTCATTTCACCTCCCCGATGCGCTCAAGCACAGACCGCACCATCTGCATTCCTGTCt                                                                     <  2:909614/93‑1 (MQ=255)
                    acgacAGCGGGAATTTCAGTAAAAAGAAGCCGACCTTCATTTCACCTCCCCGATGCGCTCAAGCACAGACCGCACCATCTGCATTCCTGTCTg                                                                    >  1:1392326/1‑93 (MQ=255)
                     cgacAGCGGGAATTTCAGTAAAAAGAAGCCGACCTTCATTTCACCTCCCCGATGCGCTCAAGCACAGACCGCACCATCTGCATTCCTGTCTGa                                                                   <  1:738171/93‑1 (MQ=255)
                     cgacAGCGGGAATTTCAGTAAAAAGAAGCCGACCTTCATTTCACCTCCCCGATGCGCTCAAGCACAGACCGCACCATCTGCATTCCTGTCTGa                                                                   <  2:375049/93‑1 (MQ=255)
                      gacAGCGGGAATTTCAGTAAAAAGAAGCCGACCTTCATTTCACCTCCCCGATGCGCTCAAGCACAGACCGCACCATCTGCATTCCTGTCTGAc                                                                  >  1:2556059/1‑93 (MQ=255)
                       acAGCGGGAATTTCAGTAAAAAGAAGCCGACCTTCATTTCACCTCCCCGATGCGCTCAAGCACAGACCGCACCATCTGCATTCCTGTCTGAct                                                                 >  2:1648461/1‑92 (MQ=255)
                        cAGCGGGAATTTGAGTAACAAGAAGCCGACCTTCCTTTCACCTCCCCGATGCGCTCTAGAACAGACCGCACCATCTGCATTCCTGTCTGTCGc                                                                >  2:3196033/1‑93 (MQ=255)
                        cAGCGGGAATTTCAGTAAAAAGAAGCCGACCTTCATTTCACCTCCCCGATGCGCTCAAGCACAGACCGCACCATCTGCATTCCTGTCTGACGc                                                                >  2:3196035/1‑93 (MQ=255)
                         aGCGGGAATTTCAGTAAAAAGAAGCCGACCTTCATTTCACCTCCCCGATGCGCTCAAGCACAGACCGCACCATCTGCATTCCTGTCTGACGCt                                                               >  2:2895680/1‑93 (MQ=255)
                          gCGGGAATTTCAGTAAAAAGAAGCCGGCCTTCATTTCACCTCCCCGATGCGCTCAAGCACAGACCGCACCATCTGCATTCCTGTCTGACGCTc                                                              <  1:3514438/93‑1 (MQ=255)
                          gCGGGAATTTCAGTAAAAAGAAGCCGACCTTCATTTCACCTCCCCGATGCGCTCAAGCACAGACCGCACCATCTGCATTCCTGTCTGACGCTc                                                              >  2:206042/1‑93 (MQ=255)
                            gggAATTTCAGTAAAAAGAAGCCGACCTTCATTTCACCTCCCCGATGCGCTCAAGCACAGACCGCACCATCTGCATTACTGTCTGACGCTCAc                                                            >  2:4395577/1‑93 (MQ=255)
                             ggAATTTCAGTAAAAAGAAGCCGACCTTCATTTCACCTCCCCGATGCGCTCAAGCACAGACCGCACCATCTGCATTCCTGTCTGACGCTCACg                                                           >  1:343240/1‑93 (MQ=255)
                             ggAATTTCAGTAAAAAGAAGCCGACCTTCATTTCACCTCCCCGATGCGCTCAAGCACAGACCGCACCATCTGCATTCCTGTCTGACGCTCACg                                                           >  2:4583244/1‑93 (MQ=255)
                             ggAATTTCAGTAAAAAGAAGCCGACCTTCATTTCACCTCCCCGATGCGCTCAAGCACAGACCGCACCATCTGCATTCCTGTCTGACGCTCACg                                                           >  1:1452818/1‑93 (MQ=255)
                               aaTTTCAGTAAAAAGAAGCCGACCTTCATTTCACCTCCCCGATGCGCTCAAGCACAGACCGCACCATCTGCATTCCTGTCTGACGCTCACGAc                                                         <  1:3460099/93‑1 (MQ=255)
                               aaTTTCAGTAAAAAGAAGCCGACCTTCATTTCACCTCCCCGATGCGCTCAAGCACAGACCGCACCATCTGCATTCCTGTCTGACGCTCACGAc                                                         <  2:1844967/93‑1 (MQ=255)
                                aTTTCAGTAAAAAGAAGCCGACCTTCATTTCACCTCCCCGATGCGCTCAAGCACAGACCGCACCATCTGCATTCCTGTCTGACGCTCACGACt                                                        >  1:3565252/1‑93 (MQ=255)
                                aTTTCAGTAAAAAGAAGCCGACCTTCATTTCACCTCCCCGATGCGCTCAAGCACAGACCGCACCATCTGCATTCCTGTCTGACGCTCACGACt                                                        >  2:13716/1‑93 (MQ=255)
                                 tttCAGTAAAAAGAAGCCGACCTTCATTTCACCTCCCCGATGCGCTCAAGCACAGACCGCACCATCTGCATTCCTGTCTGACGCTCACGACTg                                                       >  1:2141878/1‑93 (MQ=255)
                                 tttCAGTAAAAAGAAGCCGACCTTCATTTCACCTCCCCGATGCGCTCAAGCACAGACCGCACCATCTGCATTCCTGTCTGACGCTCACGACTg                                                       <  1:4456377/93‑1 (MQ=255)
                                 tttCAGTAAAAAGAAGCCGACCTTCATTTCACCTCCCCGATGCGCTCAAGCACAGACCGCACCATCTGCATTCCTGTCTGACGCTCACGACTg                                                       >  2:640095/1‑93 (MQ=255)
                                 tttCAGTAAAAAGAAGCCGACCTTCATTTCACCTCCCCGATGCGCTCAAGCACAGACCGCACCATCTGCATTCCTGTCTGACGCTCACGACTg                                                       <  1:2999752/93‑1 (MQ=255)
                                  ttCAGTAAAAAGAAGCCGACCTTCATTTCACCTCCCCGATGCGCTCAAGCACAGACCGCACCATCTGCATTCCTGTCTGACGCTCACGACTGa                                                      <  2:1105566/93‑1 (MQ=255)
                                   tCAGTAAAAAGAAGCCGACCTTCATTTCACCTCCCCGATGCGCTCAAGCACAGACCGCACCATCTGCATTCCTGTCTGACGCTCACGACTGAc                                                     <  2:1062222/93‑1 (MQ=255)
                                    cAGTAAAAAGAAGCCGACCTTCATTTCACCTCCCCGATGCGCTCAAGCACAGACCGCACCATCTGCATTCCTGTCTGACGCTCACGACTGACg                                                    >  1:199231/1‑93 (MQ=255)
                                    cAGTAAAAAGAAGCCGACCTTCATTTCACCTCCCCGATGCGCTCAAGCACAGACCGCACCATCTGCATTCCTGTCTGACGCTCACGACTGACg                                                    <  1:1655769/93‑1 (MQ=255)
                                    cAGTAAAAAGAAGCCGACCTTCATTTCACCTCCCCGATGCGCTCAAGCACAGACCGCACCATCTGCATTCCTGTCTGACGCTCACGACTGACg                                                    >  1:1923813/1‑93 (MQ=255)
                                     aGTAAAAAGAAGCCGACCTTCATTTCACCTCCCCGATGCGCTCAAGCACAGACCGCACCATCTGCATTCCTGTCTGACGCTCACGACTGACgg                                                   <  1:3188638/93‑1 (MQ=255)
                                      gTAAAAAGAAGCCGACCTTCATTTCACCTCCCCGATGCGCTCAAGCACAGACCGCACCATCTGCATTCCTGTCTGACGCTCACGACTGACGGc                                                  <  1:230650/93‑1 (MQ=255)
                                       tAAAAAGAAGCCGACCTTCATTTCACCTCCCCGATGCGCTCAAGCACAGACCGCACCATCTGCATTCCTGTCTGACGCTCACGACTGACGGCt                                                 >  1:951263/1‑93 (MQ=255)
                                       tAAAAAGAAGCCGACCTTCATTTCACCTCCCCGATGCGCTCAAGCACAGACCGCACCATCTGCATTCCTGTCTGACGCTCACGACTGACGGCt                                                 <  2:3970117/93‑1 (MQ=255)
                                        aaaaaGAAGCCGACCTTCATTTCACCTCCCCGATGCGCTCAAGCACAGACCGCACCATCTGCATTCCTGTCTGACGCTCACGACTGACGGCtt                                                <  2:2696922/93‑1 (MQ=255)
                                         aaaaGAAGCCGACCTTCATTTCACCTCCCCGATGCGCTCAAGCACAGACCGCACCATCTGCATTCCTGTCTGACGCTCACGACTGACGGCTTc                                               >  1:1045251/1‑93 (MQ=255)
                                           aagaagCCGACCTTCATTTCACCTCCCCGATGCGCTCAAGCACAGACCGCACCATCTGCATTCCTGTCTGACGCTCACGACTGACGGCTTCAc                                             >  2:3033442/1‑93 (MQ=255)
                                             gaagCCGACCTTCATTTCACCTCCCCGATGCGCTCAAGCACAGACCGCACCATCTGCATTCCTGTCTGACGCTCACGACTGACGGCTTCACTa                                           >  1:4701096/1‑93 (MQ=255)
                                             gaagCCGACCTTCATTTCACCTCCCCGATGCGCTCAAGCACAGACCGCACCATCTGCATTCCTGTCTGACGCTCACGACTGACGGCTTCACTa                                           >  2:576914/1‑93 (MQ=255)
                                               agCCGACCTTCATTTCACCTCCCCGATGCGCTCAAGCACAGACCGCACCATCTGCATTCCTGTCTGACGCTCACGACTGACGGCTTCACTAAg                                         >  2:3068351/1‑93 (MQ=255)
                                               agCCGACCTTCATTTCACCTCCCCGATGCGCTCAAGCACAGACCGCACCATCTGCATTCCTGTCTGACGCTCACGACTGACGGCTTCACTAAg                                         >  1:3949744/1‑93 (MQ=255)
                                                gCCGACCTTCATTTCACCTCCCCGATGCGCTCAAGCACAGACCGCACCATCTGCATTCCTGTCTGACGCTCACGACTGACGGCTTCACTAAGt                                        <  1:137314/93‑1 (MQ=255)
                                                gCCGACCTTCATTTCACCTCCCCGATGCGCTCAAGCACAGACCGCACCATCTGCATTCCTGTCTGACGCTCACGACTGACGGCTTCACTAAGt                                        <  2:3072680/93‑1 (MQ=255)
                                                gCCGACCTTCATTTCACCTCCCCGATGCGCTCAAGCACAGACCGCACCATCTGCATTCCTGTCTGACGCTCACGACTGACGGCTTCACTAAGt                                        <  1:2992459/93‑1 (MQ=255)
                                                 ccGACCTTCATTTCACCTCCCCGATGCGCTCAAGCACAGACCGCACCATCTGCATTCCTGTCTGACGCTCACGACTGACGGCTTCACTAAGTc                                       <  2:147259/93‑1 (MQ=255)
                                                    aCCTTCATTTCACCTCCCCGATGCGCTCAAGCACAGACCGCACCATCTGCATTCCTGTCTGACGCTCACGACTGACGGCTTCACTAAGTcgcc                                    >  2:2682622/1‑92 (MQ=255)
                                                      cTTCATTTCACCTCCCCGATGCGCTCAAGCACAGACCGCACCATCTGCATTCCTGTCTGACGCTCACGACTGACGGCTTCACTAAGTCGCGCa                                  <  1:592987/93‑1 (MQ=255)
                                                       ttCATTTCACCTCCCCGATGCGCTCAAGCACAGACCGCACCATCTGCATTCCTGTCTGACGCTCACGACTGACGGCTTCACTAAGTCGCGCAt                                 >  2:238448/1‑93 (MQ=255)
                                                       ttCATTTCACCTCCCCGATGCGCTCAAGCACAGACCGCACCATCTGCATTCCTGTCTGACGCTCACGACTGACGGCTTCACTAAGTCGCGCAt                                 >  2:4009477/1‑93 (MQ=255)
                                                       ttCATTTCACCTCCCCGATGCGCTCAAGCACAGACCGCACCATCTGCATTCCTGTCTGACGCTCACGACTGACGGATTCACTAAGTCGCGCAt                                 >  2:3892044/1‑93 (MQ=255)
                                                        tCATTTCACCTCCCCGATGCGCTCAAGCACAGACCGCACCATCTGCATTCCTGTCTGACGCTCACGACTGACGGCTTCACTAAGTCGCGCAtt                                >  1:2138987/1‑93 (MQ=255)
                                                        tCATTTCACCTCCCCGATGCGCTCAAGCACAGACCGCACCATCTGCATTCCTGTCTGACGCTCACGACTGACGGCTTCACTAAGTCGCGCAtt                                <  1:1111277/93‑1 (MQ=255)
                                                         cATTTCACCTCCCCGATGCGCTCAAGCACAGACCGCACCATCTGCATTCCTGTCTGACGCTCACGACTGACGGCTTCACTAAGTCGCGCATTc                               <  1:3903863/93‑1 (MQ=255)
                                                          aTTTCACCTCCCCGATGCGCTCAAGCACAGACCGCACCATCTGCATTCCTGTCTGACGCTCACGACTGACGGCTTCACTAAGTCGCGCATTCa                              <  1:3093822/93‑1 (MQ=255)
                                                            ttCACCTCCCCGATGCGCTCAAGCACAGACCGCACCATCTGCATTCCTGTCTGACGCTCACGACTGACGGCTTCACTAAGTCGCGCATTCAgc                            >  1:2587355/1‑93 (MQ=255)
                                                            ttCACCTCCCCGATGCGCGCAAGCACAGACCGCACCATCTGCATTCCTGTCTGACGCTCACGACTGACGGCTTCACTAAGTCGCGCATTCAgc                            <  1:3146727/93‑1 (MQ=255)
                                                              cACCTCCCCGATGCGCTCAAGCACAGACCGCACCATCTGCATTCCTGTCTGACGCTCACGACTGACGGCTTCACTAAGTCGCGCATTCAgcgc                          >  1:495629/1‑93 (MQ=255)
                                                                ccTCCCCGATGCGCTCAAGCACAGACCGCACCATCTGCATTCCTGTCTGACGCTCACGACTGACGGCTTCACTAAGTCGCGCATTCAGCGCCg                        <  1:1436895/93‑1 (MQ=255)
                                                                  tCCCCGATGCGCTCAAGCACAGACCGCACCATCTGCATTCCTGTCTGACGCTCACGACTGACGGCTTCACTAAGTCGCGCATTCAGCGCCggc                      >  1:1797028/1‑92 (MQ=255)
                                                                  tCCCCGATGCGCTCAAGCACAGACCGCACCATCTGCATTCCTGTCTGACGCTCACGACTGACGGCTTCACTAAGTCGCGCATTCAGCGCCGGa                      >  2:2569202/1‑93 (MQ=255)
                                                                    cccGATGCGCTCAAGCACAGACCGCACCATCTGCATTCCTGTCTGACGCTCACGACTGACGGCTTCACTAAGTCGCGCATTCAGCGCCGGAAg                    <  1:458986/93‑1 (MQ=255)
                                                                     cccaTGCGCTCAAGCACAGACCGCACCATCTGCATTCCTGTCTGACGCTCACGACTGACGGCTTCACTAAGTCGCGCATTCAGCGCCGGAAGc                   >  1:3738398/4‑93 (MQ=255)
                                                                     ccGATGCGCTCAAGCACAGACCGCACCATCTGCATTCCTGTCTGACGCTCACGACTGACGGCTTCACTAAGTCGCGCATTCAGCGCCGGAAGc                   <  1:2530702/93‑1 (MQ=255)
                                                                     ccGATGCGCTCAAGCACAGACCGCACCATCTGCATTCCTGTCTGACGCTCACGACTGACGGCTTCACTAAGTCGCGCATTCAGCGCCGGAAGc                   >  2:2911290/1‑93 (MQ=255)
                                                                      cGATGCGCTCAAGCACAGACCGCACCATCTGCATTCCTGTCTGACGCTCACGACTGACGGCTTCACTAAGTCGCGCATTCAGCGCCGGAAGCt                  >  1:1068234/1‑93 (MQ=255)
                                                                      cGATGCGCTCAAGCACAGACCGCACCATCTGCATTCCTGTCTGACGCTCACGACTGACGGCTTCACTAAGTCGCGCATTCAGCGCCGGAAGCt                  >  2:3212930/1‑93 (MQ=255)
                                                                        aTGCGCTCAAGCACAGACCGCACCATCTGCATTCCTGTCTGACGCTCACGACTGACGGCTTCACTAAGTCGCGCATTCAGCGCCGGAAGCTgg                >  1:1420200/1‑93 (MQ=255)
                                                                         tGCGCTCAAGCACAGACCGCACCATCTGCATTCCTGTCTGACGCTCACGACTGACGGCTTCACTAAGTCGCGCATTCAGCGCCGGAAGCTGGc               <  2:2733783/93‑1 (MQ=255)
                                                                           cgcTCAAGCACAGACCGCACCATCTGCATTCCTGTCTGACGCTCACGACTGACGGCTTCACTAAGTCGCGCATTCAGCGCCGGAAGCTGGCCt             >  2:4294142/1‑93 (MQ=255)
                                                                            gcTCAAGCACAGACCGCACCATCTGCATTCCTGTCTGACGCTCACGACTGACGGCTTCACTAAGTCGCGCATTCAGCGCCGGAAGCTGGCCTa            <  1:1311265/93‑1 (MQ=255)
                                                                              tCAAGCACAGACCGCACCATCTGCATTCCTGTCTGACGCTCACGACTGACGGCTTCACTAAGTCGCGCATTCAGCGCCGGAAGCTGGCCTAAg          >  2:3590850/1‑93 (MQ=255)
                                                                              tCAAGCACAGACCGCACCATCTGCATTCCTGTCTGACGCTCACGACTGACGGCTTCACTAAGTCGCGCATTCAGCGCCGGAAGCTGGCCTAAg          <  1:2377246/93‑1 (MQ=255)
                                                                               cAAGCACAGACCGCACCATCTGCATTCCTGTCTGACGCTCACGACTGACGGCTTCACTAAGTCGCGCATTCAGCGCCGGAAGCTGGCCTAAgg         >  1:326558/1‑93 (MQ=255)
                                                                                aaGCACAGACCGCACCATCTGCATTCCTGTCTGACGCTCACGACTGACGGCTTCACTAAGTCGCGCATTCAGCGCCGGAAGCTGGCCTAAGGt        <  2:4652806/93‑1 (MQ=255)
                                                                                 aGCACAGACCGCACCATCTGCATTCCTGTCTGACGCTCACGACTGACGGCTTCACTAAGCGGCGCATTCACGGCCGGAACCTGGCCTAAggaa       >  1:2801258/1‑91 (MQ=255)
                                                                                  gCACAGACTGCACCATCTGCATTCCTGTCTGACGCTCACGACTGACGGCTTCACTAAGTCGCGCATTCAGCGCCGGAAGCTGGCCTAAGGTAt      <  1:4036553/93‑1 (MQ=255)
                                                                                  gCACAGACCGCACCATCTGCATTCCTGTCTGACGCTCACGACTGACGGCTTCACTAAGTCGCGCATTCAGCGCCGGAAGCTGGCCTAAGGTAt      <  1:4617653/93‑1 (MQ=255)
                                                                                    acaGACCGCACCATCTGCATTCCTGTCTGACGCTCACGACTGACGGCTTCACTAAGTCGCGCATTCAGCGCCGGAAGCTGGCCTAAGGTATcc    >  2:71610/1‑93 (MQ=255)
                                                                                     caGACCGCACCATCTGCATTCCTGTCTGACGCTCACGACTGACGGCTTCACTAAGTCGCGCATTCAGCGCCGGAAGCTGGCCTAAGGTATCCg   >  1:2764049/1‑93 (MQ=255)
                                                                                      aGACCGCACCATCTGCATTCCTGTCTGACGCTCACGACTGACGGCTTCACTAAGTCGCGCATTCAGCGCCGGAAGCTGGCCTAAGGTATCCGc  <  2:2856337/93‑1 (MQ=255)
                                                                                          |                                                                                        
GTTAAGGACGAAGGTTTCTGACGACAGCGGGAATTTCAGTAAAAAGAAGCCGACCTTCATTTCACCTCCCCGATGCGCTCAAGCACAGACTGCACCATCTGCATTCCTGTCTGACGCTCACGACTGACGGCTTCACTAAGTCGCGCATTCAGCGCCGGAAGCTGGCCTAAGGTATCCGC  >  NC_000913/2115090‑2115268

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 23 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

BRESEQ :: bam2aln output
TTGGTTAAGGACGAAGGTTTCTGACGACAGCGGGAATTTCAGTAAAAAGAAGCCGACCTTCATTTCACCTCCCCGATGCGCTCAAGCACAGACTGCACCATCTGCATTCCTGTCTGACGCTCACGACTGACGGCTTCACTAAGTCGCGCATTCAGCGCCGGAAGCTGGCCTAAGGTATCCGCAACCA  >  NC_000913/2115087‑2115273
                                                                                             |                                                                                             
TTGGTTAAGGACGAAGGTTTCTGACGACAGCGGGAATTTCAGTAAAAAGAAGCCGACCTTCATTTCACCTCCCCGATGCGCTCAAGCACAGACC                                                                                               <  SRR4302544.3699960/94‑1 (MQ=60)
TTGGTTAAGGACGAAGGTTTCTGACGACAGCGGGAATTTCAGTAAAAAGAAGCCGACCTTCATTTCACCTCCCCGATGCGCTCAAGCACAGACC                                                                                               <  SRR4302544.1243795/94‑1 (MQ=60)
TTGGTTAAGGACGAAGGTTTCTGACGACAGCGGGAATTTCAGTAAAAAGAAGCCGACCTTCATTTCACCTCCCCGATGCGCTCAAGCACAGACC                                                                                               <  SRR4302544.2398580/94‑1 (MQ=60)
   GTTAAGGACGAAGGTTTCTGACGACAGCGGGAATTTCAGTAAAAAGAAGCCGACCTTCATTTCACCTCCCCGATGCGCTCAAGCACAGACCGCA                                                                                            <  SRR4302544.1594507/94‑1 (MQ=60)
      AAGGACGAAGGTTTCTGACGACAGCGGGAATTTCAGTAAAAAGAAGCCGACCTTCATTTCACCTCCCCGATGCGCTCAAGCACAGACCGCACCA                                                                                         <  SRR4302544.3527673/94‑1 (MQ=60)
        GGACGAAGGTTTCTGACGACAGCGGGAATTTCAGTAAAAAGAAGCCGACCTTCATTTCACCTCCCCGATGCGCTCAAGCACAGACCGCACCATC                                                                                       >  SRR4302544.4434094/1‑94 (MQ=60)
        GGACGAAGGTTTCTGACGACAGCGGGAATTTCAGTAAAAAGAAGCCGACCTTCATTTCACCTCCCCGATGCGCTCAAGCACAGACCGCACCATC                                                                                       >  SRR4302544.4435763/1‑94 (MQ=60)
         GACGAAGGTTTCTGACGACAGCGGGAATTTCAGTAAAAAGAAGCCGACCTTCATTTCACCTCCCCGATGCGCTCAAGCACAGACCGCACCATCT                                                                                      <  SRR4302544.1116896/94‑1 (MQ=60)
         GACGAAGGTTTCTGACGACAGCGGGAATTTCAGTAAAAAGAAGCCGACCTTCATTTCACCTCCCCGATGCGCTCAAGCACAGACCGCACCATCT                                                                                      >  SRR4302544.1411398/1‑94 (MQ=60)
         GACGAAGGTTTCTGACGACAGCGGGAATTTCAGTAAAAAGAAGCCGACCTTCATTTCACCTCCCCGATGCGCTCAAGCACAGACCGCACCATCT                                                                                      >  SRR4302544.2173320/1‑94 (MQ=60)
                 TTTCTGACGACAGCGGGAATTTCAGTAAAAAGAAGCCGACCTTCATTTCACCTCCCCGATGCGCTCAAGCACAGACCGCACCATCTGCATTCCT                                                                              >  SRR4302544.2304312/1‑94 (MQ=60)
                  TTCTGACGACAGCGGGAATTTCAGTAAAAAGAAGCCGACCTTCATTTCACCTCCCCGATGCGCTCAAGCACAGACTGCACCATCTGCATTCCTG                                                                             <  SRR4302544.1591553/94‑1 (MQ=60)
                     TGACGACAGCGGGAATTTCAGTAAAAAGAAGCCGACCTTCATTTCACCTCCCCGATGCGCTCAAGCACAGACCGCACCATCTGCATTCCTGTCT                                                                          <  SRR4302544.4260490/94‑1 (MQ=60)
                     TGACGACAGCGGGAATTTCAGTAAAAAGAAGCCGACCTTCATTTCACCTCCCCGATGCGCTCAAGCACAGACCGCACCATCTGCATTCCTGTCT                                                                          <  SRR4302544.2476334/94‑1 (MQ=60)
                     TGACGACAGCGGGAATTTCAGTAAAAAGAAGCCGACCTTCATTTCACCTCCCCGATGCGCTCAAGCACAGACCGCACCATCTGCATTCCTGTCT                                                                          >  SRR4302544.2039196/1‑94 (MQ=60)
                      GACGACAGCGGGAATTTCAGTAAAAAGAAGCCGACCTTCATTTCACCTCCCCGATGCGCTCAAGCACAGACCGCACCATCTGCATTCCTGTCTG                                                                         >  SRR4302544.1406224/1‑94 (MQ=60)
                        CGACAGCGGGAATTTCAGTAAAAAGAAGCCGACCTTCATTTCACCTCCCCGATGCGCTCAAGCACAGACCGCACCATCTGCATTCCTGTCTGAC                                                                       <  SRR4302544.745394/94‑1 (MQ=60)
                        CGACAGCGGGAATTTCAGTAAAAAGAAGCCGACCTTCATTTCACCTCCCCGATGCGCTCAAGCACAGACCGCACCATCTGCATTCCTGTCTGAC                                                                       >  SRR4302544.2580602/1‑94 (MQ=60)
                             GCGGGAATTTCAGTAAAAAGAAGCCGGCCTTCATTTCACCTCCCCGATGCGCTCAAGCACAGACCGCACCATCTGCATTCCTGTCTGACGCTCA                                                                  <  SRR4302544.3547977/94‑1 (MQ=60)
                               GGGAATTTCAGTAAAAAGAAGCCGACCTTCATTTCACCTCCCCGATGCGCTCAAGCACAGACCGCACCATCTGCATTCCTGTCTGACGCTCACG                                                                >  SRR4302544.1467253/1‑94 (MQ=60)
                               GGGAATTTCAGTAAAAAGAAGCCGACCTTCATTTCACCTCCCCGATGCGCTCAAGCACAGACCGCACCATCTGCATTCCTGTCTGACGCTCACG                                                                >  SRR4302544.346784/1‑94 (MQ=60)
                                  AATTTCAGTAAAAAGAAGCCGACCTTCATTTCACCTCCCCGATGCGCTCAAGCACAGACCGCACCATCTGCATTCCTGTCTGACGCTCACGACT                                                             >  SRR4302544.3599433/1‑94 (MQ=60)
                                  AATTTCAGTAAAAAGAAGCCGACCTTCATTTCACCTCCCCGATGCGCTCAAGCACAGACCGCACCATCTGCATTCCTGTCTGACGCTCACGACT                                                             <  SRR4302544.3510926/94‑1 (MQ=60)
                                  AATTTCAGTAAAAAGAAGCCGACCTTCATTTCACCTCCCCGATGCGCTCAAGCACAGACCGCACCATCTGCATTCCTGTCTGACGCTCACGACT                                                             <  SRR4302544.3493123/94‑1 (MQ=60)
                                   ATTTCAGTAAAAAGAAGCCGACCTTCATTTCACCTCCCCGATGCGCTCAAGCACAGACCGCACCATCTGCATTCCTGTCTGACGCTCACGACTG                                                            >  SRR4302544.2162317/1‑94 (MQ=60)
                                   ATTTCAGTAAAAAGAAGCCGACCTTCATTTCACCTCCCCGATGCGCTCAAGCACAGACCGCACCATCTGCATTCCTGTCTGACGCTCACGACTG                                                            <  SRR4302544.2707256/94‑1 (MQ=60)
                                    TTTCAGTAAAAAGAAGCCGACCTTCATTTCACCTCCCCGATGCGCTCAAGCACAGACCGCACCATCTGCATTCCTGTCTGACGCTCACGACTGA                                                           <  SRR4302544.3028509/94‑1 (MQ=60)
                                    TTTCAGTAAAAAGAAGCCGACCTTCATTTCACCTCCCCGATGCGCTCAAGCACAGACCGCACCATCTGCATTCCTGTCTGACGCTCACGACTGA                                                           <  SRR4302544.4501252/94‑1 (MQ=60)
                                      TCAGTAAAAAGAAGCCGACCTTCATTTCACCTCCCCGATGCGCTCAAGCACAGACCGCACCATCTGCATTCCTGTCTGACGCTCACGACTGACG                                                         >  SRR4302544.1942421/1‑94 (MQ=60)
                                      TCAGTAAAAAGAAGCCGACCTTCATTTCACCTCCCCGATGCGCTCAAGCACAGACCGCACCATCTGCATTCCTGTCTGACGCTCACGACTGACG                                                         >  SRR4302544.201249/1‑94 (MQ=60)
                                       CAGTAAAAAGAAGCCGACCTTCATTTCACCTCCCCGATGCGCTCAAGCACAGACCGCACCATCTGCATTCCTGTCTGACGCTCACGACTGACGG                                                        <  SRR4302544.1672094/94‑1 (MQ=60)
                                        AGTAAAAAGAAGCCGACCTTCATTTCACCTCCCCGATGCGCTCAAGCACAGACCGCACCATCTGCATTCCTGTCTGACGCTCACGACTGACGGC                                                       <  SRR4302544.3219015/94‑1 (MQ=60)
                                         GTAAAAAGAAGCCGACCTTCATTTCACCTCCCCGATGCGCTCAAGCACAGACCGCACCATCTGCATTCCTGTCTGACGCTCACGACTGACGGCT                                                      <  SRR4302544.233052/94‑1 (MQ=60)
                                         GTAAAAAGAAGCCGACCTTCATTTCACCTCCCCGATGCGCTCAAGCACAGACCGCACCATCTGCATTCCTGTCTGACGCTCACGACTGACGGCT                                                      >  SRR4302544.960615/1‑94 (MQ=60)
                                           AAAAAGAAGCCGACCTTCATTTCACCTCCCCGATGCGCTCAAGCACAGACCGCACCATCTGCATTCCTGTCTGACGCTCACGACTGACGGCTTC                                                    >  SRR4302544.1055617/1‑94 (MQ=60)
                                               AGAAGCCGACCTTCATTTCACCTCCCCGATGCGCTCAAGCACAGACCGCACCATCTGCATTCCTGTCTGACGCTCACGACTGACGGCTTCACTA                                                >  SRR4302544.4747565/1‑94 (MQ=60)
                                                 AAGCCGACCTTCATTTCACCTCCCCGATGCGCTCAAGCACAGACCGCACCATCTGCATTCCTGTCTGACGCTCACGACTGACGGCTTCACTAAG                                              >  SRR4302544.3988997/1‑94 (MQ=60)
                                                   GCCGACCTTCATTTCACCTCCCCGATGCGCTCAAGCACAGACCGCACCATCTGCATTCCTGTCTGACGCTCACGACTGACGGCTTCACTAAGTC                                            <  SRR4302544.138610/94‑1 (MQ=60)
                                                   GCCGACCTTCATTTCACCTCCCCGATGCGCTCAAGCACAGACCGCACCATCTGCATTCCTGTCTGACGCTCACGACTGACGGCTTCACTAAGTC                                            <  SRR4302544.3021154/94‑1 (MQ=60)
                                                     CGACCTTCATTTCACCTCCCCGATGCGCTCAAGCACAGACCGCACCATCTGCATTCCTGTCTGACGCTCACGACTGACGGCTTCACTAAGTCGC                                          <  SRR4302544.1245201/94‑1 (MQ=60)
                                                       ACCTTCATTTCACCTCCCCGATGCGCTCAAGCACAGACCGCACCATCTGCATTCCTGTCTGACGCTCACGACTGACGGCTTCACTAAGTCGCGC                                        >  SRR4302544.469584/1‑94 (MQ=60)
                                                        CCTTCATTTCACCTCCCCGATGCGCTCAAGCACAGACCGCACCATCTGCATTCCTGTCTGACGCTCACGACTGACGGCTTCACTAAGTCGCGCA                                       >  SRR4302544.15775/1‑94 (MQ=60)
                                                         CTTCATTTCACCTCCCCGATGCGCTCAAGCACAGACCGCACCATCTGCATTCCTGTCTGACGCTCACGACTGACGGCTTCACTAAGTCGCGCAT                                      <  SRR4302544.598808/94‑1 (MQ=60)
                                                         CTTCATTTCACCTCCCCGATGCGCTCAAGCACAGACCGCACCATCTGCATTCCTGTCTGACGCTCACGACTGACGGCTTCACTAAGTCGCGCAT                                      >  SRR4302544.1713815/1‑94 (MQ=60)
                                                          TTCATTTCACCTCCCCGATGCGCTCAAGCACAGACCGCACCATCTGCATTCCTGTCTGACGCTCACGACTGACGGCTTCACTAAGTCGCGCATT                                     <  SRR4302544.3059478/94‑1 (MQ=60)
                                                          TTCATTTCACCTCCCCGATGCGCTCAAGCACAGACCGCACCATCTGCATTCCTGTCTGACGCTCACGACTGACGGCTTCACTAAGTCGCGCATT                                     >  SRR4302544.2159413/1‑94 (MQ=60)
                                                           TCATTTCACCTCCCCGATGCGCTCAAGCACAGACCGCACCATCTGCATTCCTGTCTGACGCTCACGACTGACGGCTTCACTAAGTCGCGCATTC                                    <  SRR4302544.1122362/94‑1 (MQ=60)
                                                            CATTTCACCTCCCCGATGCGCTCAAGCACAGACCGCACCATCTGCATTCCTGTCTGACGCTCACGACTGACGGCTTCACTAAGTCGCGCATTCA                                   <  SRR4302544.3942647/94‑1 (MQ=60)
                                                             ATTTCACCTCCCCGATGCGCTCAAGCACAGACCGCACCATCTGCATTCCTGTCTGACGCTCACGACTGACGGCTTCACTAAGTCGCGCATTCAG                                  <  SRR4302544.3123290/94‑1 (MQ=60)
                                                              TTTCACCTCCCCGATGCGCTCAAGCACAGACCGCACCATCTGCATTCCTGTCTGACGCTCACGACTGACGGCTTCACTAAGTCGCGCATTCAGC                                 >  SRR4302544.2612242/1‑94 (MQ=60)
                                                               TTCACCTCCCCGATGCGCGCAAGCACAGACCGCACCATCTGCATTCCTGTCTGACGCTCACGACTGACGGCTTCACTAAGTCGCGCATTCAGCG                                <  SRR4302544.3176644/94‑1 (MQ=60)
                                                                TCACCTCCCCGATGCGCTCAAGCACAGACCGCACCATCTGCATTCCTGTCTGACGCTCACGACTGACGGCTTCACTAAGTCGCGCATTCAGCGC                               >  SRR4302544.500502/1‑94 (MQ=60)
                                                                   CCTCCCCGATGCGCTCAAGCACAGACCGCACCATCTGCATTCCTGTCTGACGCTCACGACTGACGGCTTCACTAAGTCGCGCATTCAGCGCCGG                            <  SRR4302544.1451203/94‑1 (MQ=60)
                                                                    CTCGCCGATGGGCTCAAGGGCAGTCTGCACCTTCTGCATTCCTGTCTGACGCTCACGTCTGGCGGCTTCACTAAGGCGCGCATTCAGCGCCGGA                           <  SRR4302544.3456186/94‑1 (MQ=55)
                                                                    CTCCCCGATGCGCTCAAGCACAGACCGCACCATCTGCATTCCTGTCTGACGCTCACGACTGACGGCTTCACTAAGTCGCGCATTCAGCGCCGGC                           >  SRR4302544.1814600/1‑94 (MQ=60)
                                                                       CCCGATGCGCTCAAGCACAGACCGCACCATCTGCATTCCTGTCTGACGCTCACGACTGACGGCTTCACTAAGTCGCGCATTCAGCGCCGGAAGC                        >  SRR4302544.3775555/1‑94 (MQ=60)
                                                                       CCCGATGCGCTCAAGCACAGACCGCACCATCTGCATTCCTGTCTGACGCTCACGACTGACGGCTTCACTAAGTCGCGCATTCAGCGCCGGAAGC                        <  SRR4302544.463501/94‑1 (MQ=60)
                                                                       CCCCATGCGCTCAAGCACAGACCGCACCATCTGCATTCCTGTCTGACGCTCACGACTGACGGCTTCACTAAGTCGCGCATTCAGCGCCGGAAGC                        >  SRR4302544.3775556/1‑94 (MQ=60)
                                                                        CCGATGCGCTCAAGCACAGACCGCACCATCTGCATTCCTGTCTGACGCTCACGACTGACGGCTTCACTAAGTCGCGCATTCAGCGCCGGAAGCT                       >  SRR4302544.1078851/1‑94 (MQ=60)
                                                                        CCGATGCGCTCAAGCACAGACCGCACCATCTGCATTCCTGTCTGACGCTCACGACTGACGGCTTCACTAAGTCGCGCATTCAGCGCCGGAAGCT                       <  SRR4302544.2555011/94‑1 (MQ=60)
                                                                          GATGCGCTCAAGCACAGACCGCACCATCTGCATTCCTGTCTGACGCTCACGACTGACGGCTTCACTAAGTCGCGCATTCAGCGCCGGAAGCTGG                     >  SRR4302544.1434339/1‑94 (MQ=60)
                                                                             GCGCTCAAGCACAGACCGCACCATCTGCATTCCTGTCTGACGCTCACGACTGACGGCTTCACTAAGTCGCGCATTCAGCGCCGGAAGCTGGCCT                  <  SRR4302544.2236416/94‑1 (MQ=60)
                                                                              CGCTCAAGCACAGACCGCACCATCTGCATTCCTGTCTGACGCTCACGACTGACGGCTTCACTAAGTCGCGCATTCAGCGCCGGAAGCTGGCCTA                 >  SRR4302544.4067255/1‑94 (MQ=60)
                                                                               GCTCAAGCACAGACCGCACCATCTGCATTCCTGTCTGACGCTCACGACTGACGGCTTCACTAAGTCGCGCATTCAGCGCCGGAAGCTGGCCTAA                <  SRR4302544.1324157/94‑1 (MQ=60)
                                                                                 TCAAGCACAGACCGCACCATCTGCATTCCTGTCTGACGCTCACGACTGACGGCTTCACTAAGTCGCGCATTCAGCGCCGGAAGCTGGCCTAAGG              >  SRR4302544.329954/1‑94 (MQ=60)
                                                                                 TCAAGCACAGACCGCACCATCTGCATTCCTGTCTGACGCTCACGACTGACGGCTTCACTAAGTCGCGCATTCAGCGCCGGAAGCTGGCCTAAGG              <  SRR4302544.2399751/94‑1 (MQ=60)
                                                                                  CAAGCACAGACCGCACCATCTGCATTCCTGTCTGACGCTCACGACTGACGGCTTCACTAAGTCGCGCATTCAGCGCCGGAAGCTGGCCTAAGGT             <  SRR4302544.709663/94‑1 (MQ=60)
                                                                                   AAGCACAGACCGCACCATCTGCATTCCTGTCTGACGCTCACGACTGACGGCTTCACTAAGCGGCGCATTCACGGCCGGAACCTGGCCTAAGGAA            >  SRR4302544.2828252/1‑94 (MQ=60)
                                                                                     GCACAGACTGCACCATCTGCATTCCTGTCTGACGCTCACGACTGACGGCTTCACTAAGTCGCGCATTCAGCGCCGGAAGCTGGCCTAAGGTATC          <  SRR4302544.4076753/94‑1 (MQ=60)
                                                                                     GCACAGACCGCACCATCTGCATTCCTGTCTGACGCTCACGACTGACGGCTTCACTAAGTCGCGCATTCAGCGCCGGAAGCTGGCCTAAGGTATC          <  SRR4302544.4663487/94‑1 (MQ=60)
                                                                                       ACAGACCGCACCATCTGCATTCCTGTCTGACGCTCACGACTGACGGCTTCACTAAGTCGCGCATTCAGCGCCGGAAGCTGGCCTAAGGTATCCG        >  SRR4302544.2790635/1‑94 (MQ=60)
                                                                                             CGCACCATCTGCATTCCTGTCTGACGCTCACGACTGACGGCTTCACTAAGTCGCGCATTCAGCGCCGGAAGCTGGCCTAAGGTATCCGCAACCA  >  SRR4302544.1917022/1‑94 (MQ=60)
                                                                                             |                                                                                             
TTGGTTAAGGACGAAGGTTTCTGACGACAGCGGGAATTTCAGTAAAAAGAAGCCGACCTTCATTTCACCTCCCCGATGCGCTCAAGCACAGACTGCACCATCTGCATTCCTGTCTGACGCTCACGACTGACGGCTTCACTAAGTCGCGCATTCAGCGCCGGAAGCTGGCCTAAGGTATCCGCAACCA  >  NC_000913/2115087‑2115273

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑