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 1061 294.1 15065038 98.6% 14854127 93.0

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 3,795,756 A→G A394A (GCA→GCG)  rfaL → O‑antigen ligase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009133,795,7560AG87.6% 669.7 / 83.1 267A394A (GCA→GCG) rfaLO‑antigen ligase
Reads supporting (aligned to +/- strand):  ref base A (18/15);  new base G (106/128);  total (124/143)
Fisher's exact test for biased strand distribution p-value = 3.55e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.37e-01

Only 100 of 273 total aligned reads displayed.

TTTTATATAGCATATAAAAAACGAGCTTTGGGTTTGTTGATATTAACGCTTGGCATTGTGGGGATTGGACTCAGTGATGTGATCATATGGGCACGCAGCATTCCAATTATCATTATATCCGCTATAGTCCTCTTACTCGTCATTAATAATCGTAACAATACAATTAATTAAGAATAAACAAGT  >  NC_000913/3795664‑3795846
                                                                                            |                                                                                          
ttttATATAGCATATAAAAAACGAGCTTTGGGTTTGTTGATATTAACGCTTGGCATTGTGGGGATTGGACTCAGTGATGTGATCATATGGGCa                                                                                            >  2:3975294/1‑93 (MQ=255)
  ttATATAGCATATAAAAAACGAGCTTTGGGTTTGTTGATATTAACGCTTGGCATTGTGGGGATTGGACTCAGTGATGTGATCATATGGGcgcg                                                                                          <  1:230583/93‑1 (MQ=255)
   tatataGCATATAAAAAACGAGCTTTGGGTTTGTTGATATTAACGCTTGGCATTGTGGGGATTGGACTCAGTGATGTGATCATATGGgcgcgc                                                                                         >  2:2532829/1‑93 (MQ=255)
   tatataGCATATAAAAAACGAGCTTTGGGTTTGTTGATATTAACGCTTGGCATTGTGGGGATTGGACTCAGTGATGTGATCATATGGGCACgc                                                                                         >  1:4907990/1‑93 (MQ=255)
    atataGCATATAAAAAACGAGCTTTGGGTTTGTTGATATTAACGCTTGGCATTGTGGGGATTGGACTCAGTGATGTGATCATATGGGCGCgca                                                                                        <  1:6044852/93‑1 (MQ=255)
     tataGCATATAAAAAACGAGCTTTGGGTTTGTTGATATTAACGCTTGGCATTGTGGGGATTGGACTCAGTGATGTGATCATATGGGCGCgcag                                                                                       >  2:2465301/1‑93 (MQ=255)
     tataGCATATAAAAAACGAGCTTTGGGTTTGTTGATATTAACGCTTGGCATTGTGGGGATTGGACTCAGTGATGTGATCATATGGGCGCgcag                                                                                       >  1:2095602/1‑93 (MQ=255)
      ataGCATATAAAAAACGAGCTTTGGGTTTGTTGATATTAACGCTTGGCATTGTGGGGATTGGACTCAGTGATGTGATCATATGGGCGCgcagc                                                                                      <  1:2953408/93‑1 (MQ=255)
       taGCATATAAAAAACGAGCTTTGGGTTTGTTGATATTAACGCTTGGCATTGTGGGGATTGGACTCAGTGATGTGATCATATGGGCGCgcagca                                                                                     >  1:1123583/1‑93 (MQ=255)
       taGCATATAAAAAACGAGCTTTGGGTTTGTTGATATTAACGCTTGGCATTGTGGGGATTGGACTCAGTGATGTGATCATATGGGCACgcagca                                                                                     >  2:2028278/1‑93 (MQ=255)
        aGCATATAAAAAACGAGCTTTGGGTTTGTTGATATTAACGCTTGGCATTGTGGGGATTGGACTCAGTGATGTGATCATATGGGCGCGCAGCAt                                                                                    <  2:5129221/93‑1 (MQ=255)
           atatAAAAAACGAGCTTTGGGTTTGTTGATATTAACGCTTGGCATTGTGGGGATTGGACTCAGTGATGTGATCATATGGGCGCGCAGCATTcc                                                                                 <  2:945503/93‑1 (MQ=255)
           atatAAAAAACGAGCTTTGGGTTTGTTGATATTAACGCTTGGCATTGTGGGGATTGGACTCAGTGATGTGATCATATGGGCGCGCAGCATTcc                                                                                 >  2:7033367/1‑93 (MQ=255)
           atatAAAAAACGAGCTTTGGGTTTGTTGATATTAACGCTTGGCATTGTGGGGATTGGACTCAGTGATGTGATCATATGGGCGCGCAGCATTcc                                                                                 >  2:6564215/1‑93 (MQ=255)
            tataAAAAACGAGCTTTGGGTTTGTTGATATTAACGCTTGGCATTGTGGGGATTGGACTCAGTGATGTGATCATATGGGCGCGCAGCATTCCa                                                                                >  2:4514860/1‑93 (MQ=255)
            tataAAAAACGAGCTTTGGGTTTGTTGATATTAACGCTTGGCATTGTGGGGATTGGACTCAGTGATGTGATCATATGGGCGCGCAGCATTCCa                                                                                >  1:3419545/1‑93 (MQ=255)
            tataAAAAACGAGCTTTGGGTTTGTTGATATTAACGCTTGGCATTGTGGGGATTGGACTCAGTGATGTGATCATATGGGCGCGCAGCATTCCa                                                                                >  1:6317474/1‑93 (MQ=255)
            tataAAAAACGAGCTTTGGGTTTGTTGATATTAACGCTTGGCATTGTGGGGATTGGACTCAGTGATGTGATCATATGGGCACGCAGCATTCCa                                                                                >  1:2592150/1‑93 (MQ=255)
              taAAAAACGAGCTTTGGGTTTGTTGATATTAACGCTTGGCATTGTGGGGATTGGACTCAGTGATGTGATCATATGGGCGCGCAGCATTCCAAt                                                                              >  2:627436/1‑93 (MQ=255)
              taAAAAACGAGCTTTGGGTTTGTTGATATTAACGCTTGGCATTGTGGGGATTGGACTCAGTGATGTGATCATATGGGCGCGCAGCATTCCAAt                                                                              <  2:5012470/93‑1 (MQ=255)
              taAAAAACGAGCTTTGGGTTTGTTGATATTAACGCTTGGCATTGTGGGGATTGGACTCAGTGATGTGATCATATGGGCGCGCAGCATTCCAAt                                                                              <  2:1868354/93‑1 (MQ=255)
                aaaaaCGAGCTTTGGGTTTGTTGATATTAACGCTTGGCATTGTGGGGATTGGACTCAGTGATGTGATCATATGGGCGCGCAGCATTCCAATTa                                                                            >  1:2225296/1‑93 (MQ=255)
                 aaaaCGAGCTTTGGGTTTGTTGATATTAACGCTTGGCATTGTGGGGATTGGACTCAGTGATGTGATCATATGGGCGCGCAGCATTCCAATTAt                                                                           >  1:6890237/1‑93 (MQ=255)
                  aaaCGAGCTTTGGGTTTGTTGATATTAACGCTTGGCATTGTGGGGATTGGACTCAGTGATGTGATCATATGGGCGCGCAGCATTCCAATTATc                                                                          >  1:1039033/1‑93 (MQ=255)
                  aaaCGAGCTTTGGGTTTGTTGATATTAACGCTTGGCATTGTGGGGATTGGACTCAGTGATGTGATCATATGGGCGCGCAGCATTCCAATTATc                                                                          >  1:1887460/1‑93 (MQ=255)
                   aaCGAGCTTTGGGTTTGTTGATATTAACGCTTGGCATTGTGGGGATTGGACTCAGTGATGTGATCATATGGGCGCGCAGCATTCCAATTATCa                                                                         >  2:1297958/1‑93 (MQ=255)
                   aaCGAGCTTTGGGTTTGTTGATATTAACGCTTGGCATTGTGGGGATTGGACTCAGTGATGTGATCATATGGGCGCGCAGCATTCCAATTATCa                                                                         >  1:4229359/1‑93 (MQ=255)
                     cGAGCTTTGGGTTTGTTGATATTAACGCTTGGCATTGTGGGGATTGGACTCAGTGATGTGATCATATGGGCGCGCAGCATTCCAATTATCAtt                                                                       <  1:5288763/93‑1 (MQ=255)
                      gAGCTTTGGGTTTGTTGATATTAACGCTTGGCATTGTGGGGATTGGACTCAGTGATGTGATCATATGGGCGCGCAGCATTCCAATTATCATta                                                                      >  2:3582518/1‑93 (MQ=255)
                        gCTTTGGGTTTGTTGATATTAACGCTTGGCATTGTGGGGATTGGACTCAGTGATGTGATCATATGGGCGCGCAGCATTCCAATTATCATtata                                                                    <  1:171649/93‑1 (MQ=255)
                        gCTTTGGGTTTGTTGATATTAACGCTTGGCATTGTGGGGATTGGACTCAGTGATGTGATCATATGGGCGCGCAGCATTCCAATTATCATtata                                                                    <  1:411724/93‑1 (MQ=255)
                        gCTTTGGGTTTGTTCATATTAACGCTTGGCATTGTGGGGATTGGACTCAGTGATGTGATCATATGGGCGCGCAGCATTCCAATTATCATtata                                                                    >  2:6454752/1‑93 (MQ=255)
                         cTTTGGGTTTGTTGATATTAACGCTTGGCATTGTGGGGATTGGACTCAGTGATGTGATCATATGGGCGCGCAGCATTCCAATTATCATTatat                                                                   <  1:368713/93‑1 (MQ=255)
                         cTTTGGGTTTGTTGATATTAACGCTTGGCATTGTGGGGATTGGACTCAGTGATGTGATCATATGGGCGCGCAGCATTCCAATTATCATTatat                                                                   <  2:1713129/93‑1 (MQ=255)
                          tttGGGTTTGTTGATATTAACGCTTGGCATTGTGGGGATTGGACTCAGTGATGTGATCATATGGGCGCGCAGCATTCCAATTATCATTATATc                                                                  <  2:4141226/93‑1 (MQ=255)
                          tttGGGTTTGTTGATATTAACGCTTGGCATTGTGGGGATTGGACTCAGTGATGTGATCATATGGGCGCGCAGCATTCCAATTATCATTATATc                                                                  <  2:5622198/93‑1 (MQ=255)
                             gggTTTGTTGATATTAACGCTTGGCATTGTGGGGATTGGACTCAGTGATGTGATCATATGGGCGCGCTGCATTCCAATTATCATTATATCCGc                                                               <  2:6026882/93‑1 (MQ=255)
                              ggTTTGTTGATATTAACGCTTGGCATTGTGGGGATTGGACTCAGTGATGTGATCATATGGGCGCGCAGCATTCCAATTATCATTATATCCGCt                                                              >  1:3287176/1‑93 (MQ=255)
                               gTTTGTTGATATTAACGCTTGGCATTGTGGGGATTGGACTCAGTGATGTGATCATATGGGCGCGCAGCATTCCAATTATCATTATATCCGCta                                                             <  1:4638672/93‑1 (MQ=255)
                                tttGTTGATATTAACGCTTGGCATTGTGGGGATTGGACTCAGTGATGTGATCATATGGGCGCGCAGCATTCCAATTATCATTATATCCGCtat                                                            <  2:1540281/93‑1 (MQ=255)
                                 ttgttgATATTAACGCTTGGCATTGTGGGGATTGGACTCAGTGATGTGATCATATGGGCGCGCAGCATTCCAATTATCATTATATCCGCtata                                                           >  2:4916257/1‑93 (MQ=255)
                                   gttgATATTAACGCTTGGCATTGTGGGGATTGGACTCAGTGATGTGATCATATGGGCGCGCAGCATTCCAATTATCATTATATCCGCTATAGt                                                         <  1:884066/93‑1 (MQ=255)
                                   gttgATATTAACGCTTGGCATTGTGGGGATTGGACTCAGTGATGTGATCATATGGGCGCGCAGCATTCCAATTATCATTATATCCGCTATAGt                                                         <  1:7061367/93‑1 (MQ=255)
                                   gttgATATTAACGCTTGGCATTGTGGGGATTGGACTCAGTGATGTGATCATATGGGCACGCAGCATTCCAATTATCATTATATCCGCTATAGt                                                         <  1:2421228/93‑1 (MQ=255)
                                      gATATTAACGCTTGGCATTGTGGGGATTGGACTCAGTGATGTGATCATATGGGCGCGCAGCATTCCAATTATCATTATATCCGCTATAGTCct                                                      <  1:2805991/93‑1 (MQ=255)
                                       atatTAACGCTTGGCATTGTGGGGATTGGACTCAGTGATGTGATCATATGGGCGCGCAGCATTCCAATTATCATTATATCCGCTATAGTCctc                                                     <  1:1476782/93‑1 (MQ=255)
                                       atatTAACGCTTGGCATTGTGGGGATTGGACTCAGTGATGTGATCATATGGGCGCGCAGCATTCCAATTATCATTATATCCGCTATAGTCctc                                                     <  1:563250/93‑1 (MQ=255)
                                        tatTAACGCTTGGCATTGTGGGGATTGGACTCAGTGATGTGATCATATGGGCGCGCAGCATTCCAATTATCATTATATCCGCTATAGTCctct                                                    >  2:330758/1‑93 (MQ=255)
                                        tatTAACGCTTGGCATTGTGGGGATTGGACTCAGTGATGTGATCATATGGGCGCGCAGCATTCCAATTATCATTATATCCGCTATAGTCctct                                                    >  1:198669/1‑93 (MQ=255)
                                          ttAACGCTTGGCATTGTGGGGATTGGACTCAGTGATGTGATCATATGGGCGCGCAGCATTCCAATTATCATTATATCCGCTATAGTCCTCTTa                                                  >  1:5223810/1‑93 (MQ=255)
                                          ttAACGCTTGGCATTGTGGGGATTGGACTCAGTGATGTGATCATATGGGCGCGCAGCATTCCAATTATCATTATATCCGCTATAGTCCTCTTa                                                  >  2:2312684/1‑93 (MQ=255)
                                          ttAACGCTTGGCATTGTGGGGATTGGACTCAGTGATGTGATCATATGGGCGCGCAGCATTCCAATTATCATTATATCCGCTATAGTCCTCTTa                                                  <  1:3050509/93‑1 (MQ=255)
                                            aaCGCTTGGCATTGTGGGGATTGGACTCAGTGATGTGATCATATGGGCGCGCAGCATTCCAATTATCATTATATCCGCTATAGTCCTCTTACt                                                >  2:1447587/1‑93 (MQ=255)
                                             aCGCTTGGCATTGTGGGGATTGGACTCAGTGATGTGATCATATGGGCGCGCAGCATTCCAATTATCATTATATCCGCTATAGTCCTCTTACTc                                               >  2:3064183/1‑93 (MQ=255)
                                             aCGCTTGGCATTGTGGGGATTGGACTCAGTGATGTGATCATATGGGCGCGCAGCATTCCAATTATCATTATATCCGCTATAGTCCTCTTACTc                                               >  2:516714/1‑93 (MQ=255)
                                             aCGCTTGGCATTGTGGGGATTGGACTCAGTGATGTGATCATATGGGCGCGCAGCATTCCAATTATCATTATATCCGCTATAGTCCTCTTACTc                                               <  1:4802460/93‑1 (MQ=255)
                                             aCGCTTGGCATTGTGGGGATTGGACTCAGTGATGTGATCATATGGGCGCGCAGCATTCCAATTATCATTATATCCGCTATAGTCCTCTTACTc                                               >  2:1082133/1‑93 (MQ=255)
                                             aCGCTTGGCATTGTGGGGATTGGACTCAGTGATGTGATCATATGGGCGCGCAGCATTCCAATTATCATTATATCCGCCATAGTCCTCTTACTc                                               >  1:4884683/1‑93 (MQ=255)
                                              cGCTTGGCATTGTGGGGATTGGACTCAGTGATGTGATCATATGGGCGCGCAGCATTCCAATTATCATTATATCCGCTATAGTCCTCTTACTCg                                              >  2:5577857/1‑93 (MQ=255)
                                                    gCATTGTGGGGATTGGACTCAGTGATGTGATCATATGGGCGCGCAGCATTCCAATTATCATTATATCCGCTATAGTCCTCTTACTCGTCATta                                        >  2:3858871/1‑93 (MQ=255)
                                                     cATTGTGGGGATTGGACTCAGTGATGTGATCATATGGGCGCGCAGCATTCCAATTATCATTATATCCGCTATAGTCCTCTTACTCGTCATtaa                                       >  1:3132220/1‑93 (MQ=255)
                                                      aTTGTGGGGATTGGACTCAGTGATGTGATCATATGGGCGCGCAGCATTCCAATTATCATTATATCCGCTATAGTCCTCTTACTCGTCATtaat                                      <  2:2974323/93‑1 (MQ=255)
                                                       ttGTGGGGATTGGACTCAGTGATGTGATCATATGGGCGCGCAGCATTCCAATTATCATTATATCCGCTATAGTCCTCTTACTCGTCATtaata                                     >  1:825108/1‑93 (MQ=255)
                                                         gtgGGGATTGGACTCAGTGATGTGATCATATGGGCGCGCAGCATTCCAATTATCATTATATCCGCTATAGTCCTCTTACTCGTCATTaataat                                   <  1:1433405/93‑1 (MQ=255)
                                                           ggggATTGGACTCAGTGATGTGATCATATGGGCGCGCAGCATTCCAATTATCATTATATCCGCTATAGTCCTCTTACTCGTCATTAATAATCg                                 <  1:486541/93‑1 (MQ=255)
                                                             ggATTGGACTCAGTGATGTGATCATATGGGCGCGCAGCATTCCAATTATCATTATATCCGCTATAGTCCTCTTACTCGTCATTAATAATCGTa                               <  2:4450189/93‑1 (MQ=255)
                                                              gATTGGACTCAGTGATGGGATCATATGGGCGCGCAGCATTCCAATTATCATTATATCCGCTATAGTCCTCTTACTCGTCATTAATAATCGTaa                              <  1:533663/93‑1 (MQ=255)
                                                               aTTGGACTCAGTGATGTGATCATATGGGCGCGCAGCATTCCAATTATCATTATATCCGCTATAGTCCTCTTACTCGTCATTAATAATCGTAac                             >  1:3529206/1‑93 (MQ=255)
                                                               aTTGGACTCAGTGATGTGATCATATGGGCACGCAGCATTCCAATTATCATTATATCCGCTAGAGTCCTCTTACTCGTCATTAATAATCGTAac                             <  1:4489811/93‑1 (MQ=255)
                                                                   gACTCAGTGATGTGATCATATGGGCACGCAGCATTCCAATTATCATTATATCCGCTATAGTCCTCTTACTCGTCATTAATAATCGTAacaata                         <  2:2837244/93‑1 (MQ=255)
                                                                    aCTCAGTGATGTGATCATATGGGCACGCAGCATTCCAATTATCATTATATCCGCTATAGTCCTCTTACTCGTCATTAATAATCGTAacaatac                        <  1:5409434/93‑1 (MQ=255)
                                                                       cAGTGATGTGATCATATGGGCGCGCAGCATTCCAATTATCATTATATCCGCTATAGTCCTCTTACTCGTCATTAATAATCGTAacaatacaat                     <  2:2593218/93‑1 (MQ=255)
                                                                        aGTGATGTGATCATATGGGCGCGCAGCATTCCAATTATCATTATATCCGCTATAGTCCTCTTACTCGTCATTAATAATCGTAACAATACaatt                    <  2:6109808/93‑1 (MQ=255)
                                                                         gtgatgtgatCATATGGGCACGCAGCATTCCAATTATCATTATATCCGCTATAGTCCTCTTACTCGTCATTAATAATCGTAACAATACaatta                   <  1:3885918/93‑1 (MQ=255)
                                                                           gatgtgatCATATGGGCACGCAGCATTCCAATTATCATTATATCCGCTATAGTCCTCTTACTCGTCATTAATAATCGTAACAATACaattaat                 >  2:4255648/1‑93 (MQ=255)
                                                                            atgtgatCATATGGGCGCGCAGCATTCCAATTATCATTATATCCGCTATAGTCTTCTTACTCGTCATTAATAATCGTAACAATACaattaatt                <  1:7508803/93‑1 (MQ=255)
                                                                            atgtgatCATATGGGCGCGCAGCATTCCAATTATCATTATATCCGCTATAGTCCTCTTACTCGTCATTAATAATCGTAACAATACaattaatt                <  2:1991098/93‑1 (MQ=255)
                                                                            atgtgatCATATGGGCGCGCAGCATTCCAATTATCATTATATCCGCTATAGTCCTCTTACTCGTCATTAATAATCGTAACAATACaattaatt                >  1:5889738/1‑93 (MQ=255)
                                                                            atgtgatCATATGGGCGCGCAGCATTCCAATTATCATTATATCCGCTATAGTCCTCTTACTCGTCATTAATAATCGTAACAATACaattaatt                <  2:5998928/93‑1 (MQ=255)
                                                                              gtgatCATATGGGCGCGCAGCATTCCAATTATCATTATATCCGCTATAGTCCTCTTACTCGTCATTAATAATCGTAACAATACAAttaattaa              <  2:3172162/93‑1 (MQ=255)
                                                                              gtgatCATATGGGCGCGCAGCATTCCAATTATCATTATATCCGCTATAGTCCTCTTACTCGTCATTAATAATCGTAACAATACAAttaattaa              <  1:3736447/93‑1 (MQ=255)
                                                                               tgatCATATGGGCGCGCAGCATTCCAATTATCATTATATCCGCTATAGTCCTCTTACTCGTCATTAATAATCGTAACAATACAATTAATTAAg             >  1:6443624/1‑93 (MQ=255)
                                                                               tgatCATATGGGCGCGCAGCATTCCAATTATCATTATATCCGCTATAGTCCTCTTACTCGTCATTAATAATCGTAACAATACAATTAATTAAg             >  2:7137473/1‑93 (MQ=255)
                                                                               tgatCATATGGGCGCGCAGCATTCCAATTATCATTATATCCGCTATAGTCCTCTTACTCGTCATTAATAATCGTAACAATACAATTAATTAAg             <  1:7206835/93‑1 (MQ=255)
                                                                               tgatCATATGGGCGCGCAGCATTCCAATTATCATTATATCCGCTATAGTCCTCTTACTCGTCATTAATAATCGTAACAATACAATTAATTAAg             >  1:1190771/1‑93 (MQ=255)
                                                                                 atCATATGGGCGCGCAGCATTCCAATTATCATTATATCCGCTATAGTCCTCTTACTCGTCATTAATAATCGTAACAATACAATTAATTAAGaa           <  2:4720909/93‑1 (MQ=255)
                                                                                  tCATATGGGCGCGCAGCATTCCAATTATCATTATATCCGCTATAGTCCTCTTACTCGTCATTAATAATCGTAACAATACAATTAATTAAGAAt          >  1:6788090/1‑93 (MQ=255)
                                                                                  tCATATGGGCGCGCAGCATTCCAATTATCATTATATCCGCTATAGTCCTCTTACTCGTCATTAATAATCGTAACAATACAATTAATTAAGAAt          <  1:1508246/93‑1 (MQ=255)
                                                                                  tCATATGGGCACGCAGCATTCCAATTATCATTATATCCGCTATAGTCCTCTTACTCGTCATTAATAATCGTAACAATACAATTAATTAAGAAt          >  1:6564936/1‑93 (MQ=255)
                                                                                  tCATATGGGCACGCAGCATTCCAATTATCATTATATCCGCTATAGTCCTCTTACTCGTCATTAATAATCGTAACAATACAATTAATTAAGAAt          >  2:5729313/1‑93 (MQ=255)
                                                                                    atatGGGCGCGCAGCATTCCAATTATCATTATATCCGCTATAGTCCTCTTACTCGTCATTAATAATCGTAACAATACAATTAATTAAGAATaa        >  2:5368499/1‑93 (MQ=255)
                                                                                    atatGGGCGCGCAGCATTCCAATTATCATTATATCCGCTATAGTCCTCTTACTCGTCATTAATAATCGTAACAATACAATTAATTAAGAATaa        <  1:5975623/93‑1 (MQ=255)
                                                                                    atatGGGCGCGCAGCATTCCAATTATCATTATATCCGCTATAGTCCTCTTACTCGTCATTAATAATCGTAACAATACAATTAATTAAGAATaa        >  2:6895406/1‑93 (MQ=255)
                                                                                     tatGGGCGCGCAGCATTCCAATTATCATTATATCCGCTATAGTCCTCTTACTCGTCATTAATAATCGTAACAATACAATTAATTAAGAATaaa       <  2:3743384/93‑1 (MQ=255)
                                                                                     tatGGGCACGCAGCATTCCAATTATCATTATATCCGCTATAGTCCTCTTACTCGTCATTAATAATCGTAACAATACAATTAATTAAGAATaaa       <  1:6664358/93‑1 (MQ=255)
                                                                                      atGGGCGCGCAGCATTCCAATTATCATTATATCCGCTATAGTCCTCTTACTCGTCATTAATAATCGTAACAATACAATTAATTAAGAATAAAc      <  2:733535/93‑1 (MQ=255)
                                                                                       tGGGCGCGCAGCATTCCAATTATCATTATATCCGCTATAGTCCTCTTACTCGTCATTAATAATCGTAACAATACAATTAATTAAGAATAAACa     >  2:435577/1‑93 (MQ=255)
                                                                                       tGGGCGCGCAGCATTCCAATTATCATTATATCCGCTATAGTCCTCTTACTCGTCATTAATAATCGTAACAATACAATTAATTAAGAATAAACa     >  1:6182758/1‑93 (MQ=255)
                                                                                       tGGGCACGCAGCATTCCAATTATCATTATATCCGCTATAGTCCTCTTACTCGTCATTAATAATCGTAACAATACAATTAATTAAGAATAAACa     <  1:5127224/93‑1 (MQ=255)
                                                                                        gggCGCGCAGCATTCCAATTATCATTATATCCGCTATAGTCCTCTTACTCGTCATTAATAATCGTAACAATACAATTAATTAAGAATAAACaa    <  2:7256833/93‑1 (MQ=255)
                                                                                            |                                                                                          
TTTTATATAGCATATAAAAAACGAGCTTTGGGTTTGTTGATATTAACGCTTGGCATTGTGGGGATTGGACTCAGTGATGTGATCATATGGGCACGCAGCATTCCAATTATCATTATATCCGCTATAGTCCTCTTACTCGTCATTAATAATCGTAACAATACAATTAATTAAGAATAAACAAGT  >  NC_000913/3795664‑3795846

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

BRESEQ :: bam2aln output
ATTTTATATAGCATATAAAAAACGAGCTTTGGGTTTGTTGATATTAACGCTTGGCATTGTGGGGATTGGACTCAGTGATGTGATCATATGGGCACGCAGCATTCCAATTATCATTATATCCGCTATAGTCCTCTTACTCGTCATTAATAATCGTAACAATACAATTAATTAAGAATAAACAAGTTTA  >  NC_000913/3795663‑3795849
                                                                                             |                                                                                             
ATTTTATATAGCATATAAAAAACGAGCTTTGGGTTTGTTGATATTAACGCTTGGCATTGTGGGGATTGGACTCAGTGATGTGATCATATGGGCG                                                                                               >  SRR4302542.3534775/1‑94 (MQ=60)
   TTATATAGCATATAAAAAACGAGCTTTGGGTTTGTTGATATTAACGCTTGGCATTGTGGGGATTGGACTCAGTGATGTGATCATATGGGCGCGC                                                                                            >  SRR4302542.3639410/1‑94 (MQ=60)
   TTATATAGCATATAAAAAACGAGCTTTGGGTTTGTTGATATTAACGCTTGGCATTGTGGGGATTGGACTCAGTGATGTGATCATATGGGCGCGC                                                                                            <  SRR4302542.232563/94‑1 (MQ=60)
   TTATATAGCATATAAAAAACGAGCTTTGGGTTTGTTGATATTAACGCTTGGCATTGTGGGGATTGGACTCAGTGATGTGATCATATGGGCACGC                                                                                            >  SRR4302542.4955726/1‑94 (MQ=60)
    TATATAGCATATAAAAAACGAGCTTTGGGTTTGTTGATATTAACGCTTGGCATTGTGGGGATTGGACTCAGTGATGTGATCATATGGGCGCGCA                                                                                           >  SRR4302542.7151294/1‑94 (MQ=60)
     ATATAGCATATAAAAAACGAGCTTTGGGTTTGTTGATATTAACGCTTGGCATTGTGGGGATTGGACTCAGTGATGTGATCATATGGGCGCGCAG                                                                                          >  SRR4302542.2113680/1‑94 (MQ=60)
     ATATAGCATATAAAAAACGAGCTTTGGGTTTGTTGATATTAACGCTTGGCATTGTGGGGATTGGACTCAGTGATGTGATCATATGGGCGCGCAG                                                                                          <  SRR4302542.1733209/94‑1 (MQ=60)
     ATATAGCATATAAAAAACGAGCTTTGGGTTTGTTGATATTAACGCTTGGCATTGTGGGGATTGGACTCAGTGATGTGATCATATGGGCGCGCAG                                                                                          <  SRR4302542.6103364/94‑1 (MQ=60)
     ATATAGCATATAAAAAACGAGCTTTGGGTTTGTTGATATTAACGCTTGGCATTGTGGGGATTGGACTCAGTGATGTGATCATATGGGCGCGCAG                                                                                          >  SRR4302542.6322706/1‑94 (MQ=60)
       ATAGCATATAAAAAACGAGCTTTGGGTTTGTTGATATTAACGCTTGGCATTGTGGGGATTGGACTCAGTGATGTGATCATATGGGCGCGCAGCA                                                                                        <  SRR4302542.2981680/94‑1 (MQ=60)
       ATAGCATATAAAAAACGAGCTTTGGGTTTGTTGATATTAACGCTTGGCATTGTGGGGATTGGACTCAGTGATGTGATCATATGGGCGCGCAGCA                                                                                        >  SRR4302542.1133179/1‑94 (MQ=60)
       ATAGCATATAAAAAACGAGCTTTGGGTTTGTTGATATTAACGCTTGGCATTGTGGGGATTGGACTCAGTGATGTGATCATATGGGCACGCAGCA                                                                                        >  SRR4302542.3991608/1‑94 (MQ=60)
        TAGCATATAAAAAACGAGCTTTGGGTTTGTTGATATTAACGCTTGGCATTGTGGGGATTGGACTCAGTGATGTGATCATATGGGCGCGCAGCAT                                                                                       >  SRR4302542.5762502/1‑94 (MQ=60)
        TAGCATATAAAAAACGAGCTTTGGGTTTGTTGATATTAACGCTTGGCATTGTGGGGATTGGACTCAGTGATGTGATCATATGGGCGCGCAGCAT                                                                                       <  SRR4302542.1169328/94‑1 (MQ=60)
         AGCATATAAAAAACGAGCTTTGGGTTTGTTGATATTAACGCTTGGCATTGTGGGGATTGGACTCAGTGATGTGATCATATGGGCGCGCAGCATT                                                                                      >  SRR4302542.5553779/1‑94 (MQ=60)
           CATATAAAAAACGAGCTTTGGGTTTGTTGATATTAACGCTTGGCATTGTGGGGATTGGACTCAGTGATGTGATCATATGGGCGCGCAGCATTCC                                                                                    <  SRR4302542.6649820/94‑1 (MQ=60)
           CATATAAAAAACGAGCTTTGGGTTTGTTGATATTAACGCTTGGCATTGTGGGGATTGGACTCAGTGATGTGATCATATGGGCGCGCAGCATTCC                                                                                    >  SRR4302542.3283351/1‑94 (MQ=60)
           CATATAAAAAACGAGCTTTGGGTTTGTTGATATTAACGCTTGGCATTGTGGGGATTGGACTCAGTGATGTGATCATATGGGCGCGCAGCATTCC                                                                                    >  SRR4302542.2073345/1‑94 (MQ=60)
           CATATAAAAAACGAGCTTTGGGTTTGTTGATATTAACGCTTGGCATTGTGGGGATTGGACTCAGTGATGTGATCATATGGGCACGCAGCATTCC                                                                                    >  SRR4302542.2137948/1‑94 (MQ=60)
            ATATAAAAAACGAGCTTTGGGTTTGTTGATATTAACGCTTGGCATTGTGGGGATTGGACTCAGTGATGTGATCATATGGGCGCGCAGCATTCCA                                                                                   >  SRR4302542.3451585/1‑94 (MQ=60)
            ATATAAAAAACGAGCTTTGGGTTTGTTGATATTAACGCTTGGCATTGTGGGGATTGGACTCAGTGATGTGATCATATGGGCGCGCAGCATTCCA                                                                                   >  SRR4302542.6379741/1‑94 (MQ=60)
            ATATAAAAAACGAGCTTTGGGTTTGTTGATATTAACGCTTGGCATTGTGGGGATTGGACTCAGTGATGTGATCATATGGGCGCGCAGCATTCCA                                                                                   >  SRR4302542.5014718/1‑94 (MQ=60)
            ATATAAAAAACGAGCTTTGGGTTTGTTGATATTAACGCTTGGCATTGTGGGGATTGGACTCAGTGATGTGATCATATGGGCACGCAGCATTCCA                                                                                   >  SRR4302542.2617254/1‑94 (MQ=60)
              ATAAAAAACGAGCTTTGGGTTTGTTGATATTAACGCTTGGCATTGTGGGGATTGGACTCAGTGATGTGATCATATGGGCGCGCAGCATTCCAAT                                                                                 <  SRR4302542.1940695/94‑1 (MQ=60)
               TAAAAAACGAGCTTTGGGTTTGTTGATATTAACGCTTGGCATTGTGGGGATTGGACTCAGTGATGTGATCATATGGGCGCGCAGCATTCCAATT                                                                                <  SRR4302542.2437105/94‑1 (MQ=60)
                AAAAAACGAGCTTTGGGTTTGTTGATATTAACGCTTGGCATTGTGGGGATTGGACTCAGTGATGTGATCATATGGGCGCGCAGCATTCCAATTA                                                                               >  SRR4302542.2244443/1‑94 (MQ=60)
                 AAAAACGAGCTTTGGGTTTGTTGATATTAACGCTTGGCATTGTGGGGATTGGACTCAGTGATGTGATCATATGGGCGCGCAGCATTCCAATTAT                                                                              >  SRR4302542.6957907/1‑94 (MQ=60)
                  AAAACGAGCTTTGGGTTTGTTGATATTAACGCTTGGCATTGTGGGGATTGGACTCAGTGATGTGATCATATGGGCGCGCAGCATTCCAATTATC                                                                             >  SRR4302542.4939367/1‑94 (MQ=60)
                  AAAACGAGCTTTGGGTTTGTTGATATTAACGCTTGGCATTGTGGGGATTGGACTCAGTGATGTGATCATATGGGCGCGCAGCATTCCAATTATC                                                                             >  SRR4302542.1903799/1‑94 (MQ=60)
                  AAAACGAGCTTTGGGTTTGTTGATATTAACGCTTGGCATTGTGGGGATTGGACTCAGTGATGTGATCATATGGGCGCGCAGCATTCCAATTATC                                                                             >  SRR4302542.1047957/1‑94 (MQ=60)
                   AAACGAGCTTTGGGTTTGTTGATATTAACGCTTGGCATTGTGGGGATTGGACTCAGTGATGTGATCATATGGGCGCGCAGCATTCCAATTATCA                                                                            >  SRR4302542.4271018/1‑94 (MQ=60)
                   AAACGAGCTTTGGGTTTGTTGATATTAACGCTTGGCATTGTGGGGATTGGACTCAGTGATGTGATCATATGGGCGCGCAGCATTCCAATTATCA                                                                            <  SRR4302542.3420695/94‑1 (MQ=60)
                   AAACGAGCTTTGGGTTTGTTGATATTAACGCTTGGCATTGTGGGGATTGGACTCAGTGATGTGATCATATGGGCGCGCAGCATTCCAATTATCA                                                                            <  SRR4302542.4948612/94‑1 (MQ=60)
                    AACGAGCTTTGGGTTTGTTGATATTAACGCTTGGCATTGTGGGGATTGGACTCAGTGATGTGATCATATGGGCGCGCAGCATTCCAATTATCAT                                                                           <  SRR4302542.6774049/94‑1 (MQ=60)
                     ACGAGCTTTGGGTTTGTTGATATTAACGCTTGGCATTGTGGGGATTGGACTCAGTGATGTGATCATATGGGCGCGCAGCATTCCAATTATCATT                                                                          >  SRR4302542.6277132/1‑94 (MQ=60)
                      CGAGCTTTGGGTTTGTTGATATTAACGCTTGGCATTGTGGGGATTGGACTCAGTGATGTGATCATATGGGCGCGCAGCATTCCAATTATCATTA                                                                         <  SRR4302542.5358134/94‑1 (MQ=60)
                      CGAGCTTTGGGTTTGTTGATATTAACGCTTGGCATTGTGGGGATTGGACTCAGTGATGTGATCATATGGGCGCGCAGCATTCCAATTATCATTA                                                                         <  SRR4302542.5340171/94‑1 (MQ=60)
                      CGAGCTTTGGGTTTGTTGATATTAACGCTTGGCATTGTGGGGATTGGACTCAGTGATGTGATCATATGGGCGCGCAGCATTCCAATTATCATTA                                                                         >  SRR4302542.702535/1‑94 (MQ=60)
                        AGCTTTGGGTTTGTTGATATTAACGCTTGGCATTGTGGGGATTGGACTCAGTGATGTGATCATATGGGCGCGCAGCATTCCAATTATCATTATA                                                                       >  SRR4302542.3050793/1‑94 (MQ=60)
                         GCTTTGGGTTTGTTGATATTAACGCTTGGCATTGTGGGGATTGGACTCAGTGATGTGATCATATGGGCGCGCAGCATTCCAATTATCATTATAT                                                                      <  SRR4302542.415270/94‑1 (MQ=60)
                         GCTTTGGGTTTGTTGATATTAACGCTTGGCATTGTGGGGATTGGACTCAGTGATGTGATCATATGGGCGCGCAGCATTCCAATTATCATTATAT                                                                      <  SRR4302542.173096/94‑1 (MQ=60)
                          CTTTGGGTTTGTTGATATTAACGCTTGGCATTGTGGGGATTGGACTCAGTGATGTGATCATATGGGCGCGCAGCATTCCAATTATCATTATATC                                                                     <  SRR4302542.371921/94‑1 (MQ=60)
                          CTTTGGGTTTGTTGATATTAACGCTTGGCATTGTGGGGATTGGACTCAGTGATGTGATCATATGGGCGCGCAGCATTCCAATTATCATTATATC                                                                     >  SRR4302542.4014060/1‑94 (MQ=60)
                          CTTTGGGTTTGTTGATATTAACGCTTGGCATTGTGGGGATTGGACTCAGTGATGTGATCATATGGGCGCGCAGCATTCCAATTATCATTATATC                                                                     >  SRR4302542.6017417/1‑94 (MQ=60)
                           TTTGGGTTTGTTGATATTAACGCTTGGCATTGTGGGGATTGGACTCAGTGATGTGATCATATGGGCACGCAGCATTCCAATTATCATTATATCC                                                                    >  SRR4302542.813819/1‑94 (MQ=60)
                            TTGGGTTTGTTGATATTAACGCTTGGCATTGTGGGGATTGGACTCAGTGATGTGATCATATGGGCGCGCAGCATTCCAATTATCATTATATCCG                                                                   <  SRR4302542.5426365/94‑1 (MQ=60)
                            TTGGGTTTGTTGATATTAACGCTTGGCATTGTGGGGATTGGACTCAGTGATGTGATCATATGGGCGCGCAGCATTCCAATTATCATTATATCCG                                                                   <  SRR4302542.6790234/94‑1 (MQ=60)
                            TTGGGTTTGTTGATATTAACGCTTGGCATTGTGGGGATTGGACTCAGTGATGTGATCATATGGGCGCGCAGCATTCCAATTATCATTATATCCG                                                                   <  SRR4302542.2268372/94‑1 (MQ=60)
                              GGGTTTGTTGATATTAACGCTTGGCATTGTGGGGATTGGACTCAGTGATGTGATCATATGGGCGCGCAGCATTCCAATTATCATTATATCCGCT                                                                 >  SRR4302542.3318215/1‑94 (MQ=60)
                              GGGTTTGTTGATATTAACGCTTGGCATTGTGGGGATTGGACTCAGTGATGTGATCATATGGGCGCGCAGCATTCCAATTATCATTATATCCGCT                                                                 <  SRR4302542.6078463/94‑1 (MQ=60)
                              GGGTTTGTTGATATTAACGCTTGGCATTGTGGGGATTGGACTCAGTGATGTGATCATATGGGCGCGCAGCATTCCAATTATCATTATATCCGCT                                                                 <  SRR4302542.2577946/94‑1 (MQ=60)
                              GGGTTTGTTGATATTAACGCTTGGCATTGTGGGGATTGGACTCAGTGATGTGATCATATGGGCACGCAGCATTCCAATTATCATTATATCCGCT                                                                 <  SRR4302542.1584857/94‑1 (MQ=60)
                               GGTTTGTTGATATTAACGCTTGGCATTGTGGGGATTGGACTCAGTGATGTGATCATATGGGCGCGCAGCATTCCAATTATCATTATATCCGCTA                                                                <  SRR4302542.3765763/94‑1 (MQ=60)
                                GTTTGTTGATATTAACGCTTGGCATTGTGGGGATTGGACTCAGTGATGTGATCATATGGGCGCGCAGCATTCCAATTATCATTATATCCGCTAT                                                               <  SRR4302542.4683995/94‑1 (MQ=60)
                                GTTTGTTGATATTAACGCTTGGCATTGTGGGGATTGGACTCAGTGATGTGATCATATGGGCGCGCAGCATTCCAATTATCATTATATCCGCTAT                                                               <  SRR4302542.4826842/94‑1 (MQ=60)
                                  TTGTTGATATTAACGCTTGGCATTGTGGGGATTGGACTCAGTGATGTGATCATATGGGCGCGCAGCATTCCAATTATCATTATATCCGCTATAG                                                             <  SRR4302542.2265404/94‑1 (MQ=60)
                                   TGTTGATATTAACGCTTGGCATTGTGGGGATTGGACTCAGTGATGTGATCATATGGGCGCGCAGCATTCCAATTATCATTATATCCGCTATAGT                                                            >  SRR4302542.3090584/1‑94 (MQ=60)
                                    GTTGATATTAACGCTTGGCATTGTGGGGATTGGACTCAGTGATGTGATCATATGGGCGCGCAGCATTCCAATTATCATTATATCCGCTATAGTC                                                           <  SRR4302542.7130675/94‑1 (MQ=60)
                                    GTTGATATTAACGCTTGGCATTGTGGGGATTGGACTCAGTGATGTGATCATATGGGCGCGCAGCATTCCAATTATCATTATATCCGCTATAGTC                                                           >  SRR4302542.812499/1‑94 (MQ=60)
                                    GTTGATATTAACGCTTGGCATTGTGGGGATTGGACTCAGTGATGTGATCATATGGGCGCGCAGCATTCCAATTATCATTATATCCGCTATAGTC                                                           <  SRR4302542.891706/94‑1 (MQ=60)
                                    GTTGATATTAACGCTTGGCATTGTGGGGATTGGACTCAGTGATGTGATCATATGGGCACGCAGCATTCCAATTATCATTATATCCGCTATAGTC                                                           <  SRR4302542.2444767/94‑1 (MQ=60)
                                     TTGATATTAACGCTTGGCATTGTGGGGATTGGACTCAGTGATGTGATCATATGGGCGCGCAGCATTCCAATTATCATTATATCCGCTATAGTCC                                                          >  SRR4302542.4796270/1‑94 (MQ=60)
                                      TGATATTAACGCTTGGCATTGTGGGGATTGGACTCAGTGATGTGATCATATGGGCGCGCAGCATTCCAATTATCATTATATCCGCTATAGTCCT                                                         >  SRR4302542.1149334/1‑94 (MQ=60)
                                      TGATATTAACGCTTGGCATCGTGGGGATTGGACTCAGTGATGTGATCATATGGGCACGCAGCATTCCAATTATCATTATATCCGCTATAGTCCT                                                         <  SRR4302542.5648056/94‑1 (MQ=60)
                                       GATATTAACGCTTGGCATTGTGGGGATTGGACTCAGTGATGTGATCATATGGGCGCGCAGCATTCCAATTATCATTATATCCGCTATAGTCCTC                                                        <  SRR4302542.2833007/94‑1 (MQ=60)
                                        ATATTAACGCTTGGCATTGTGGGGATTGGACTCAGTGATGTGATCATATGGGCGCGCAGCATTCCAATTATCATTATATCCGCTATAGTCCTCT                                                       >  SRR4302542.200356/1‑94 (MQ=60)
                                        ATATTAACGCTTGGCATTGTGGGGATTGGACTCAGTGATGTGATCATATGGGCGCGCAGCATTCCAATTATCATTATATCCGCTATAGTCCTCT                                                       <  SRR4302542.568099/94‑1 (MQ=60)
                                        ATATTAACGCTTGGCATTGTGGGGATTGGACTCAGTGATGTGATCATATGGGCGCGCAGCATTCCAATTATCATTATATCCGCTATAGTCCTCT                                                       <  SRR4302542.1489520/94‑1 (MQ=60)
                                         TATTAACGCTTGGCATTGTGGGGATTGGACTCAGTGATGTGATCATATGGGCGCGCAGCATTCCAATTATCATTATATCCGCTATAGTCCTCTT                                                      >  SRR4302542.7296814/1‑94 (MQ=60)
                                          ATTAACGCTTGGCATTGTGGGGATTGGACTCAGTGATGTGATCATATGGGCGCGCAGCATTCCAATTATCATTATATCCGCTATAGTCCTCTTA                                                     >  SRR4302542.5274619/1‑94 (MQ=60)
                                           TTAACGCTTGGCATTGTGGGGATTGGACTCAGTGATGTGATCATATGGGCGCGCAGCATTCCAATTATCATTATATCCGCTATAGTCCTCTTAC                                                    >  SRR4302542.2105269/1‑94 (MQ=60)
                                           TTAACGCTTGGCATTGTGGGGATTGGACTCAGTGATGTGATCATATGGGCGCGCAGCATTCCAATTATCATTATATCCGCTATAGTCCTCTTAC                                                    <  SRR4302542.3079628/94‑1 (MQ=60)
                                            TAACGCTTGGCATTGTGGGGATTGGACTCAGTGATGTGATCATATGGGCGCGCAGCATTCCAATTATCATTATATCCGCTATAGTCCTCTTACT                                                   <  SRR4302542.2448932/94‑1 (MQ=60)
                                             AACGCTTGGCATTGTGGGGATTGGACTCAGTGATGTGATCATATGGGCGCGCAGCATTCCAATTATCATTATATCCGCCATAGTCCTCTTACTC                                                  >  SRR4302542.4932212/1‑94 (MQ=60)
                                              ACGCTTGGCATTGTGGGGATTGGACTCAGTGATGTGATCATATGGGCGCGCAGCATTCCAATTATCATTATATCCGCTATAGTCCTCTTACTCG                                                 <  SRR4302542.4535711/94‑1 (MQ=60)
                                              ACGCTTGGCATTGTGGGGATTGGACTCAGTGATGTGATCATATGGGCGCGCAGCATTCCAATTATCATTATATCCGCTATAGTCCTCTTACTCG                                                 <  SRR4302542.4849241/94‑1 (MQ=60)
                                               CGCTTGGCATTGTGGGGATTGGACTCAGTGATGTGATCATATGGGCGCGCAGCATTCCAATTATCATTATATCCGCTATAGTCCTCTTACTCGT                                                >  SRR4302542.5361827/1‑94 (MQ=60)
                                               CGCTTGGCATTGTGGGGATTGGACTCAGTGATGTGATCATATGGGCGCGCAGCATTCCAATTATCATTATATCCGCTATAGTCCTCTTACTCGT                                                <  SRR4302542.1503694/94‑1 (MQ=60)
                                                  TTGGCATTGTGGGGATTGGACTCAGTGATGTGATCATATGGGCGCGCAGCATTCCAATTATCATTATATCCGCTATAGTCCTCTTACTCGTCAT                                             <  SRR4302542.6942458/94‑1 (MQ=60)
                                                   TGGCATTGTGGGGATTGGACTCAGTGATGTGATCATATGGGCGCGCAGCATTCCAATTATCATTATATCCGCTATAGTCCTCTTACTCGTCATT                                            >  SRR4302542.1213640/1‑94 (MQ=60)
                                                    GGCATTGTGGGGATTGGACTCAGTGATGTGATCATATGGGCGCGCAGCATTCCAATTATCATTATATCCGCTATAGTCCTCTTACTCGTCATTA                                           <  SRR4302542.3697205/94‑1 (MQ=60)
                                                     GCATTGTGGGGATTGGACTCAGTGATGTGATCATATGGGCGCGCAGCATTCCAATTATCATTATATCCGCTATAGTCCTCTTACTCGTCATTAA                                          >  SRR4302542.3162006/1‑94 (MQ=60)
                                                      CATTGTGGGGATTGGACTCAGTGATGTGATCATATGGGCGCGCAGCATTCCAATTATCATTATATCCGCTATAGTCCTCTTACTCGTCATTAAT                                         <  SRR4302542.6500949/94‑1 (MQ=60)
                                                       ATTGTGGGGATTGGACTCAGTGATGTGATCATATGGGCGCGCAGCATTCCAATTATCATTATATCCGCTATAGTCCTCTTACTCGTCATTAATA                                        <  SRR4302542.6520496/94‑1 (MQ=60)
                                                       ATTGTGGGGATTGGACTCAGTGATGTGATCATATGGGCGCGCAGCATTCCAATTATCATTATATCCGCTATAGTCCTCTTACTCGTCATTAATA                                        >  SRR4302542.3288760/1‑94 (MQ=60)
                                                       ATTGTGGGGATTGGACTCAGTGATGTGATCATATGGGCGCGCAGCATTCCAATTATCATTATATCCGCTATAGTCCTCTTACTCGTCATTAATA                                        >  SRR4302542.832241/1‑94 (MQ=60)
                                                       ATTGTGGGGATTGGACTCAGTGATGTGATCATATGGGCACGCAGCATTCCAATTATCATTATATCCGCTATAGTCCTCTTACTCGTCATTAATA                                        >  SRR4302542.1807399/1‑94 (MQ=60)
                                                          GTGGGGATTGGACTCAGTGATGTGATCATATGGGCGCGCAGCATTCCAATTATCATTATATCCGCTATAGTCCTCTTACTCGTCATTAATAATC                                     <  SRR4302542.1445790/94‑1 (MQ=60)
                                                          GTGGGGATTGGACTCAGTGATGTGATCATATGGGCGCGCAGCATTCCAATTATCATTATATCCGCTATAGTCCTCTTACTCGTCATTAATAATC                                     <  SRR4302542.2703010/94‑1 (MQ=60)
                                                            GGGGATTGGACTCAGTGATGTGATCATATGGGCGCGCAGCATTCCAATTATCATTATATCCGCTATAGTCCTCTTACTCGTCATTAATAATCGT                                   <  SRR4302542.6092279/94‑1 (MQ=60)
                                                            GGGGATTGGACTCAGTGATGTGATCATATGGGCGCGCAGCATTCCAATTATCATTATATCCGCTATAGTCCTCTTACTCGTCATTAATAATCGT                                   <  SRR4302542.490755/94‑1 (MQ=60)
                                                             GGGATTGGACTCAGTGATGTGATCATATGGGCGCGCAGCATTCCAATTATCATTATATCCGCTATAGTCCTCTTACTCGTCATTAATAATCGTA                                  <  SRR4302542.1728239/94‑1 (MQ=60)
                                                             GGGATTGGACTCAGTGATGTGATCATATGGGCACGCAGCATTCCAATTATCATTATATCCGCTATAGTCCTCTTACTCGTCATTAATAATCGTA                                  <  SRR4302542.6907521/94‑1 (MQ=60)
                                                               GATTGGACTCAGTGATGTGATCATATGGGCGCGCAGCATTCCAATTATCATTATATCCGCTATAGTCCTCTTACTCGTCATTAATAATCGTAAC                                >  SRR4302542.3562191/1‑94 (MQ=60)
                                                               GATTGGACTCAGTGATGGGATCATATGGGCGCGCAGCATTCCAATTATCATTATATCCGCTATAGTCCTCTTACTCGTCATTAATAATCGTAAC                                <  SRR4302542.538274/94‑1 (MQ=60)
                                                                ATTGGACTCAGTGATGTGATCATATGGGCGCGCAGCATTCCAATTATCATTATATCCGCTATAGTCCTCTTACTCGTCATTAATAATCGTAACA                               <  SRR4302542.876700/94‑1 (MQ=60)
                                                                ATTGGACTCAGTGATGTGATCATATGGGCGCGCAGCATTCCAATTATCATTATATCCGCTATAGTCCTCTTACTCGTCATTAATAATCGTAACA                               >  SRR4302542.5137824/1‑94 (MQ=60)
                                                                ATTGGACTCAGTGATGTGATCATATGGGCGCGCAGCATTCCAATTATCATTATATCCGCTATAGTCCTCTTACTCGTCATTAATAATCGTAACA                               >  SRR4302542.662074/1‑94 (MQ=60)
                                                                ATTGGACTCAGTGATGTGATCATATGGGCGCGCAGCATTCCAATTATCATTATATCCGCTATAGTCCTCTTACTCGTCATTAATAATCGTAACA                               >  SRR4302542.2978380/1‑94 (MQ=60)
                                                                ATTGGACTCAGTGATGTGATCATATGGGCGCGCAGCATTCCAATTATCATTATATCCGCTATAGTCCTCTTACTCGTCATTAATAATCGTAACA                               <  SRR4302542.3816313/94‑1 (MQ=60)
                                                                ATTGGACTCAGTGATGTGATCATATGGGCACGCAGCATTCCAATTATCATTATATCCGCTAGAGTCCTCTTACTCGTCATTAATAATCGTAACA                               <  SRR4302542.4533868/94‑1 (MQ=60)
                                                                  TGGACTCAGTGATGTGATCATATGGGCGCGCAGCATTCCAATTATCATTATATCCGCTATAGTCCTCTTACTCGTCATTAATAATCGTAACAAT                             <  SRR4302542.4850903/94‑1 (MQ=60)
                                                                   GGACTCAGTGATGTGATCATATGGGCGCGCAGCATTCCAATTATCATTATATCCGCTATAGTCCTCTTACTCGTCATTAATAATCGTAACAATA                            >  SRR4302542.4896220/1‑94 (MQ=60)
                                                                   GGACTCAGTGATGTGATCATATGGGCGCGCAGCATTCCAATTATCATTATATCCGCTATAGTCCTCTTACTCGTCATTAATAATCGTAACAATA                            <  SRR4302542.6008698/94‑1 (MQ=60)
                                                                    GACTCAGTGATGTGATCATATGGGCGCGCAGCATTCCAATTATCATTATATCCGCTATAGTCCTCTTACTCGTCATTAATAATCGTAACAATAC                           >  SRR4302542.5187748/1‑94 (MQ=60)
                                                                    GACTCAGTGATGTGATCATATGGGCACGCAGCATTCCAATTATCATTATATCCGCTATAGTCCTCTTACTCGTCATTAATAATCGTAACAATAC                           >  SRR4302542.3495563/1‑94 (MQ=60)
                                                                     ACTCAGTGATGTGATCATATGGGCACGCAGCATTCCAATTATCATTATATCCGCTATAGTCCTCTTACTCGTCATTAATAATCGTAACAATACA                          <  SRR4302542.5461974/94‑1 (MQ=60)
                                                                      CTCAGTGATGTGATCATATGGGCGCGCAGCATTCCAATTATCATTATATCCGCTATAGTCCTCTTACTCGTCATTAATAATCGTAACAATACAA                         <  SRR4302542.7001238/94‑1 (MQ=60)
                                                                      CTCAGTGATGTGATCATATGGGCGCGCAGCATTCCAATTATCATTATATCCGCTATAGTCCTCTTACTCGTCATTAATAATCGTAACAATACAA                         >  SRR4302542.5262738/1‑94 (MQ=60)
                                                                        CAGTGATGTGATCATATGGGCGCGCAGCATTCCAATTATCATTATATCCGCTATAGTCCTCTTACTCGTCATTAATAATCGTAACAATACAATT                       <  SRR4302542.1478937/94‑1 (MQ=60)
                                                                         AGTGATGTGATCATATGGGCGCGCAGCATTCCAATTATCATTATATCCGCTATAGTCCTCTTACTCGTCATTAATAATCGTAACAATACAATTA                      <  SRR4302542.1275012/94‑1 (MQ=60)
                                                                         AGTGATGTGATCATATGGGCGCGCAGCATTCCAATTATCATTATATCCGCTATAGTCCTCTTACTCGTCATTAATAATCGTAACAATACAATTA                      <  SRR4302542.4158240/94‑1 (MQ=60)
                                                                          GTGATGTGATCATATGGGCGCGCAGCATTCCAATTATCATTATATCCGCTATAGTCCTCTTACTCGTCATTAATAATCGTAACAATACAATTAA                     >  SRR4302542.4272891/1‑94 (MQ=60)
                                                                          GTGATGTGATCATATGGGCACGCAGCATTCCAATTATCATTATATCCGCTATAGTCCTCTTACTCGTCATTAATAATCGTAACAATACAATTAA                     <  SRR4302542.3924285/94‑1 (MQ=60)
                                                                            GATGTGATCATATGGGCGCGCAGCATTCCAATTATCATTATATCCGCTATAGTCCTCTTACTCGTCATTAATAATCGTAACAATACAATTAATT                   >  SRR4302542.5946816/1‑94 (MQ=60)
                                                                             ATGTGATCATATGGGCGCGCAGCATTCCAATTATCATTATATCCGCTATAGTCTTCTTACTCGTCATTAATAATCGTAACAATACAATTAATTA                  <  SRR4302542.7582656/94‑1 (MQ=60)
                                                                             ATGTGATCATATGGGCGCGCAGCATTCCAATTATCATTATATCCGCTATAGTCCTCTTACTCGTCATTAATAATCGTAACAATACAATTAATTA                  <  SRR4302542.4635766/94‑1 (MQ=60)
                                                                              TGTGATCATATGGGCGCGCAGCATTCCAATTATCATTATATCCGCTATAGTCCTCTTACTCGTCATTAATAATCGTAACAATACAATTAATTAA                 >  SRR4302542.3148641/1‑94 (MQ=60)
                                                                              TGTGATCATATGGGCGCGCAGCATTCCAATTATCATTATATCCGCTATAGTCCTCTTACTCGTCATTAATAATCGTAACAATACAATTAATTAA                 <  SRR4302542.6127220/94‑1 (MQ=60)
                                                                               GTGATCATATGGGCGCGCAGCATTCCAATTATCATTATATCCGCTATAGTCCTCTTACTCGTCATTAATAATCGTAACAATACAATTAATTAAG                >  SRR4302542.6507081/1‑94 (MQ=60)
                                                                               GTGATCATATGGGCGCGCAGCATTCCAATTATCATTATATCCGCTATAGTCCTCTTACTCGTCATTAATAATCGTAACAATACAATTAATTAAG                <  SRR4302542.5335616/94‑1 (MQ=60)
                                                                               GTGATCATATGGGCGCGCAGCATTCCAATTATCATTATATCCGCTATAGTCCTCTTACTCGTCATTAATAATCGTAACAATACAATTAATTAAG                >  SRR4302542.1201026/1‑94 (MQ=60)
                                                                               GTGATCATATGGGCGCGCAGCATTCCAATTATCATTATATCCGCTATAGTCCTCTTACTCGTCATTAATAATCGTAACAATACAATTAATTAAG                <  SRR4302542.3773437/94‑1 (MQ=60)
                                                                               GTGATCATATGGGCACGCAGCATTCCAATTATCATTATATCCGCTATAGTCCTCTTACTCGTCATTAATAATCGTAACAATACAATTAATTAAG                >  SRR4302542.4170770/1‑94 (MQ=60)
                                                                                TGATCATATGGGCGCGCAGCATTCCAATTATCATTATATCCGCTATAGTCCTCTTACTCGTCATTAATAATCGTAACAATACAATTAATTAAGA               <  SRR4302542.7277567/94‑1 (MQ=60)
                                                                                  ATCATATGGGCGCGCAGCATTCCAATTATCATTATATCCGCTATAGTCCTCTTACTCGTCATTAATAATCGTAACAATACAATTAATTAAGAAT             >  SRR4302542.1062889/1‑94 (MQ=60)
                                                                                  ATCATATGGGCGCGCAGCATTCCAATTATCATTATATCCGCTATAGTCCTCTTACTCGTCATTAATAATCGTAACAATACAATTAATTAAGAAT             >  SRR4302542.6854853/1‑94 (MQ=60)
                                                                                  ATCATATGGGCACGCAGCATTCCAATTATCATTATATCCGCTATAGTCCTCTTACTCGTCATTAATAATCGTAACAATACAATTAATTAAGAAT             >  SRR4302542.6629632/1‑94 (MQ=60)
                                                                                   TCATATGGGCGCGCAGCATTCCAATTATCATTATATCCGCTATAGTCCTCTTACTCGTCATTAATAATCGTAACAATACAATTAATTAAGAATA            <  SRR4302542.1521284/94‑1 (MQ=60)
                                                                                    NNTATGGGCGCGCAGCATTCCAATTATCATTATATCCGCTATAGTCCTCTTACTCGTCATTAATAATCGTAACAATACAATTAATTAAGAATAA           <  SRR4302542.2138076/94‑1 (MQ=60)
                                                                                     ATATGGGCGCGCAGCATTCCAATTATCATTATATCCGCTATAGTCCTCTTACTCGTCATTAATAATCGTAACAATACAATTAATTAAGAATAAA          >  SRR4302542.736562/1‑94 (MQ=60)
                                                                                     ATATGGGCGCGCAGCATTCCAATTATCATTATATCCGCTATAGTCCTCTTACTCGTCATTAATAATCGTAACAATACAATTAATTAAGAATAAA          >  SRR4302542.646815/1‑94 (MQ=60)
                                                                                     ATATGGGCGCGCAGCATTCCAATTATCATTATATCCGCTATAGTCCTCTTACTCGTCATTAATAATCGTAACAATACAATTAATTAAGAATAAA          <  SRR4302542.538758/94‑1 (MQ=60)
                                                                                     ATATGGGCGCGCAGCATTCCAATTATCATTATATCCGCTATAGTCCTCTTACTCGTCATTAATAATCGTAACAATACAATTAATTAAGAATAAA          >  SRR4302542.1500548/1‑94 (MQ=60)
                                                                                     ATATGGGCGCGCAGCATTCCAATTATCATTATATCCGCTATAGTCCTCTTACTCGTCATTAATAATCGTAACAATACAATTAATTAAGAATAAA          <  SRR4302542.6033455/94‑1 (MQ=60)
                                                                                      TATGGGCGCGCAGCATTCCAATTATCATTATATCCGCTATAGTCCTCTTACTCGTCATTAATAATCGTAACAATACAATTAATTAAGAATAAAC         >  SRR4302542.2715588/1‑94 (MQ=60)
                                                                                      TATGGGCGCGCAGCATTCCAATTATCATTATATCCGCTATAGTCCTCTTACTCGTCATTAATAATCGTAACAATACAATTAATTAAGAATAAAC         <  SRR4302542.3040504/94‑1 (MQ=60)
                                                                                      TATGGGCACGCAGCATTCCAATTATCATTATATCCGCTATAGTCCTCTTACTCGTCATTAATAATCGTAACAATACAATTAATTAAGAATAAAC         <  SRR4302542.6730015/94‑1 (MQ=60)
                                                                                       ATGGGCGCGCAGCATTCCAATTATCATTATATCCGCTATAGTCCTCTTACTCGTCATTAATAATCGTAACAATACAATTAATTAAGAATAAACA        >  SRR4302542.6242746/1‑94 (MQ=60)
                                                                                        TGGGCACGCAGCATTCCAATTATCATTATATCCGCTATAGTCCTCTTACTCGTCATTAATAATCGTAACAATACAATTAATTAAGAATAAACAA       <  SRR4302542.5177017/94‑1 (MQ=60)
                                                                                         GGGCGCGCAGCATTCCAATTATCATTATATCCGCTATAGTCCTCTTACTCGTCATTAATAATCGTAACAATACAATTAATTAAGAATAAACAAG      >  SRR4302542.3766156/1‑94 (MQ=60)
                                                                                          GGCGCGCAGCATTCCAATTATCATTATATCCGCTATAGTCCTCTTACTCGTCATTAATAATCGTAACAATACAATTAATTAAGAATAAACAAGT     <  SRR4302542.491034/94‑1 (MQ=60)
                                                                                           GCGCGCAGCATTCCAATTATCATTATATCCGCTATAGTCCTCTTACTCGTCATTAATAATCGTAACAATACAATTAATTAAGAATAAACAAGTT    <  SRR4302542.1039135/94‑1 (MQ=60)
                                                                                           GCGCGCAGCATTCCAATTATCATTATATCCGCTATAGTCCTCTTACTCGTCATTAATAATCGTAACAATACAATTAATTAAGAATAAACAAGTT    <  SRR4302542.4436806/94‑1 (MQ=60)
                                                                                           GCGCGCAGCATTCCAATTATCATTATATCCGCTATAGTCCTCTTACTCGTCATTAATAATCGTAACAATACAATTAATTAAGAATAAACAAGTT    <  SRR4302542.6909819/94‑1 (MQ=60)
                                                                                           GCACGCAGCATTCCAATTATCATTATATCCGCTATAGTCCTCTTACTCGTCATTAATAATCGTAACAATACAATTAATTAAGAATAAACAAGTT    <  SRR4302542.3514073/94‑1 (MQ=60)
                                                                                            CGCGCAGCATTCCAATTATCATTATATCCGCTATAGTCCTCTTACTCGTCATTAATAATCGTAACAATACAATTAATTAAGAATAAACAAGTTT   >  SRR4302542.5774421/1‑94 (MQ=60)
                                                                                            CGCGCAGCATTCCAATTATCATTATATCCGCTATAGTCCTCTTACTCGTCATTAATAATCGTAACAATACAATTAATTAAGAATAAACAAGTTT   <  SRR4302542.1254149/94‑1 (MQ=60)
                                                                                             GCGCAGCATTCCAATTATCATTATATCCGCTATAGTCCTCTTACTCGTCATTAATAATCGTAACAATACAATTAATTAAGAATAAACAAGTTTA  >  SRR4302542.6417546/1‑94 (MQ=60)
                                                                                             |                                                                                             
ATTTTATATAGCATATAAAAAACGAGCTTTGGGTTTGTTGATATTAACGCTTGGCATTGTGGGGATTGGACTCAGTGATGTGATCATATGGGCACGCAGCATTCCAATTATCATTATATCCGCTATAGTCCTCTTACTCGTCATTAATAATCGTAACAATACAATTAATTAAGAATAAACAAGTTTA  >  NC_000913/3795663‑3795849

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑