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 1548 369.5 20095359 96.9% 19472402 93.0

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 4,008,411 +C coding (494/516 nt) b4555 → hypothetical protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009134,008,4101.C100.0% 500.8 / NA 154A165P (GCT→CCT) b4555hypothetical protein
Reads supporting (aligned to +/- strand):  ref base . (0/0);  new base C (63/91);  total (63/91)

Only 100 of 155 total aligned reads displayed.

TCTGGAAGTGATGGCGGGCGGC‑GTTTC‑AAAGGCCATGCGCTGGAAG‑GCTGGCG‑‑‑‑AACT‑GGCTACAG‑CTGAAGGATTG‑ATTGC‑GTT‑‑GTGACGGGATGAACGACGCCGAAATGCTGTCGATGGC‑GGGAAA‑GCTGCATTATGGGCAGTGGC  >  NC_000913/4008346‑4008492
                                                                         |                                                                                        
tCTGGAAGTGATGGCGGGCGGC‑GTTTCAAAAGGCCATGCGCTGGAAGCGGTGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGC‑Gtt                                                                     <  1:7177307/93‑1 (MQ=255)
tCTGGAAGTGATGGCGGGCGGC‑GTTTCAAAAGGCCATGCGCTGGAAGCGGTGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGC‑Gtt                                                                     <  1:2396856/93‑1 (MQ=255)
tCTGGAAGTGATGGCGGGCGGC‑GTTTCAAAAGGCCATGCGCTGGAAGCGGTGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGC‑Gtt                                                                     >  1:2676227/1‑93 (MQ=255)
tCTGGAAGTGATGGCGGGCGGC‑GTTTCAAAAGGCCATGCGCTGGAAGCGGTGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGC‑Gtt                                                                     <  2:6362410/93‑1 (MQ=255)
 cTGGAAGTGATGGCGGGCGGC‑GTTTCAAAAGGCCATGCGCTGGAAGCGGTGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGC‑Gttt                                                                    <  1:1148820/93‑2 (MQ=255)
 cTGGAAGTGATGGCGGGCGGC‑GTTTCAAAAGGCCATGCGCTGGAAGCGGTGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGC‑Gttt                                                                    >  2:2016160/1‑92 (MQ=255)
 cTGGAAGTGATGGCGGGCGGC‑GTTTCAAAAGGCCATGCGCTGGAAGCGGTGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGC‑Gttt                                                                    >  2:3112731/1‑92 (MQ=255)
  tGGAAGTGATGGCGGGCGGC‑GTTTCAAAAGGCCATGCGCTGGAAGCGGTGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGC‑Gtttg                                                                   >  1:6088940/1‑91 (MQ=255)
  tGGAAGTGATGGCGGGCGGC‑GTTTCAAAAGGCCATGCGCTGGAAGCGGTGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGC‑Gtttg                                                                   <  2:3652544/93‑3 (MQ=255)
  tGGAAGTGATGGCGGGCGGC‑GTTTCAAAAGGCCATGCGCTGGAAGCGGTGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGC‑Gtttg                                                                   >  1:9334969/1‑91 (MQ=255)
  tGGAAGTGATGGCGGGCGGC‑GTTTCAAAAGGCCATGCGCTGGAAGCGGTGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGC‑Gtttg                                                                   >  1:4350676/1‑91 (MQ=255)
   ggAAGTGATGGCGGGCGGC‑GTTTCAAAAGGCCATGCGCTGGAAGCGGTGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGC‑Gtttgg                                                                  <  2:5823044/93‑4 (MQ=255)
   ggAAGTGATGGCGGGCGGC‑GTTTCAAAAGGCCATGCGCTGGAAGCGGTGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGC‑Gtttgg                                                                  <  2:2132599/93‑4 (MQ=255)
   ggAAGTGATGGCGGGCGGC‑GTTTCAAAAGGCCATGCGCTGGAAGCGGTGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGC‑Gtttgg                                                                  <  2:5825414/93‑4 (MQ=255)
   ggAAGTGATGGCGGGCGGC‑GTTTCAAAAGGCCATGCGCTGGAAGCGGTGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGC‑Gtttgg                                                                  <  1:864717/93‑4 (MQ=255)
   ggAAGTGATGGCGGGCGGC‑GTTTCAAAAGGCCATGCGCTGGAAGCGGTGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGC‑Gtttgg                                                                  >  1:1532792/1‑90 (MQ=255)
    gAAGTGATGGCGGGCGGC‑GTTTCAAAAGGCCATGCGCTGGAAGCGGTGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGC‑Gtttggt                                                                 <  1:6889041/93‑5 (MQ=255)
    gAAGTGATGGCGGGCGGC‑GTTTCAAAAGGCCATGCGCTGGAAGCGGTGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGC‑Gtttggt                                                                 <  1:6573968/93‑5 (MQ=255)
    gAAGTGATGGCGGGCGGC‑GTTTCAAAAGGCCATGCGCTGGAAGCGGTGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGC‑Gtttggt                                                                 <  2:4966347/93‑5 (MQ=255)
    gAAGTGATGGCGGGCGGC‑GTGTCAAAAGGCCATGCGCTGGAAGCGGTGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGC‑Gtttggt                                                                 <  2:861771/93‑5 (MQ=255)
          aTGGCGGGCGGC‑GTTTCAAAAGGCCATGCGCTGGAAGCGGTGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGC‑GTTTGGTGACggg                                                           >  1:750883/1‑93 (MQ=255)
          aTGGCGGGCGGC‑GTTTCAAAAGGCCATGCGCTGGAAGCGGTGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGC‑GTTTGGTGACggg                                                           >  2:3448880/1‑93 (MQ=255)
           tGGCGGGCGGCAGTTCA‑AAAGGCCATGCGCTGGAAGCGGTGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGC‑GTTTGGTGACGGGa                                                          <  1:9596275/93‑1 (MQ=255)
           tGGCGGGCGGC‑GTTTCAAAAGGCCATGCGCTGGAAGCGGTGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGC‑GTTTGGTGACGGGa                                                          <  2:8409837/93‑1 (MQ=255)
           tGGCGGGCGGC‑GTTTCAAAAGGCCATGCGCTGGAAGCGGTGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGC‑GTTTGGTGACGGGa                                                          <  1:1803182/93‑1 (MQ=255)
           tGGCGGGCGGC‑GTTTCAAAAGGCCATGCGCTGGAAGCGGTGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGC‑GTTTGGTGACGGGa                                                          <  2:2881758/93‑1 (MQ=255)
            ggcgggcgGC‑GTTTCAAAAGGCCATGCGCTGGAAGCGGTGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGC‑GTTTGGTGACGGGAt                                                         <  2:1818924/93‑1 (MQ=255)
            ggcgggcgGC‑GTTTCAAAAGGCCATGCGCTGGAAGCGGTGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGC‑GTTTGGTGACGGGAt                                                         >  2:8863266/1‑93 (MQ=255)
             gcgggcggC‑GTTTCAAAAGGCCATGCGCTGGAAGCGGTGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGC‑GTTTGGTGACGGGATg                                                        <  2:6051594/93‑1 (MQ=255)
             gcgggcggC‑GTTTCAAAAGGCCATGCGCTGGAAGCGGTGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGC‑GTTTGGTGACGGGATg                                                        <  2:8626408/93‑1 (MQ=255)
               gggcggC‑GTTTCAAAAGGCCATGCGCTGGAAGCGGTGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGC‑GTTTGGTGACGGGATGaa                                                      <  1:8916742/93‑1 (MQ=255)
               gggcggC‑GTTTCAAAAGGCCATGCGCTGGAAGCGGTGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGC‑GTTTGGTGACGGGATGaa                                                      >  1:1242716/1‑93 (MQ=255)
               gggcggC‑GTTTCAAAAGGCCATGCGCTGGAAGCGGTGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGC‑GTTTGGTGACGGGATGaa                                                      <  2:7651843/93‑1 (MQ=255)
               gggcggC‑GTTTCAAAAGGCCATGCGCTGGAAGCGGTGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGC‑GTTTGGTGACGGGATGaa                                                      <  1:3076046/93‑1 (MQ=255)
                ggcggc‑GTTTCAAAAGGCCATGCGCTGGAAGCGGTGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGC‑GTTTGGTGACGGGATGAac                                                     >  1:8626918/1‑93 (MQ=255)
                ggcggc‑GTTTCAAAAGGCCATGCGCTGGAAGCGGTGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGC‑GTTTGGTGACGGGATGAac                                                     >  1:8626919/1‑93 (MQ=255)
                ggcggc‑GTTTCAAAAGGCCATGCGCTGGAAGCGGTGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGC‑GTTTGGTGACGGGATGAac                                                     >  1:5145751/1‑93 (MQ=255)
                ggcggc‑GTTTCAAAAGGCCATGCGCTGGAAGCGGTGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGC‑GTTTGGTGACGGGATGAac                                                     <  2:4349308/93‑1 (MQ=255)
                ggcggc‑GTTTCAAAAGGCCATGCGCTGGAAGCGGTGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGC‑GTTTGGTGACGGGATGAac                                                     <  1:10002085/93‑1 (MQ=255)
                 gcggc‑gTTTCAAAAGGCCATGCGCTGGAAGCGGTGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGC‑GTTTGGTGACGGGATGAacg                                                    <  2:5280233/93‑1 (MQ=255)
                 gcggc‑gTTTCAAAAGGCCATGCGCTGGAAGCGGTGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGC‑GTTTGGTGACGGGATGAacg                                                    >  1:2907039/1‑93 (MQ=255)
                 gcggc‑gTTTCAAAAGGCCATGCGCTGGAAGCGGTGGCGAAGAAACTGGGCTACAGCCTGAAGGAGTGTATTGCGGTTG‑GTGACGGGATGAacg                                                    >  1:6401998/1‑93 (MQ=255)
                  cggc‑gTTTCAAAAGGCCATGCGCTGGAAGCGGTGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGC‑GTTTGGTGACGGGATGAacga                                                   <  1:10033062/93‑1 (MQ=255)
                   ggc‑gTTTCAAAAGGCCATGCGCTGGAAGCGGTGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGC‑GTTTGGTGACGGGATGAacgac                                                  <  2:8753943/93‑1 (MQ=255)
                   ggc‑gTTTCAAAAGGCCATGCGCTGGAAGCGGTGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGC‑GTTTGGTGACGGGATGAacgac                                                  <  2:1182648/93‑1 (MQ=255)
                   ggc‑gTTTCAAAAGGCCATGCGCTGGAAGCGGGGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGC‑GTTTGGTGACGGGATGAacgac                                                  >  1:2868802/1‑93 (MQ=255)
                    gc‑gTTTCAAAAGGCCATGCGCTGGAAGCGGTGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGC‑GTTTGGTGACGGGATGAacgacg                                                 >  2:3783878/1‑93 (MQ=255)
                     c‑gTTTCAAAAGGCCATGCGCTGGAAGCGGTGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGC‑GTTTGGTGACGGGATGAACGACGc                                                <  1:4552484/93‑1 (MQ=255)
                       gTTTCAAAAGGCCATGCGCTGGAAGCGGTGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGC‑GTTTGGTGACGGGATGAACGACGcc                                               <  2:6448755/93‑1 (MQ=255)
                       gTTTCAAAAGGCCATGCGCTGGAAGCGGTGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGC‑GTTTGGTGACGGGATGAACGACGcc                                               <  1:6408410/93‑1 (MQ=255)
                       gTTTCAAAAGGCCATGCGCTGGAAGCGGTGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGC‑GTTTGGTGACGGGATGAACGACGcc                                               >  1:7202564/1‑93 (MQ=255)
                       gTTTCAAAAGGCCATGCGCTGGAAGCGGTGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGC‑GTTNGGTGACGGGATGAACGACGcg                                               >  1:8760513/1‑92 (MQ=255)
                         ttcaaaaGGCCATGCGCTGGAAGCGGTGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGC‑GTTTGGTGACGGGATGAACGCCGCCGa                                             >  2:3275039/5‑93 (MQ=255)
                         ttcaaaaGGCCATGCGCTGGAAGCGGTGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGC‑GTTTGGTGACGGGATGAACGACGCCGa                                             >  1:4004406/5‑93 (MQ=255)
                         ttcaaaaGGCCATGCGCTGGAAGCGGTGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGC‑GTTTGGTGACGGGATGAACGACGCCGa                                             >  1:2638946/5‑93 (MQ=255)
                          tcaaaaGGCCATGCGCTGGAAGCGGTGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGC‑GTTTGGTGACGGGATGAACGACGCCGaa                                            >  2:7328160/4‑93 (MQ=255)
                          tcaaaaGGCCATGCGCTGGAAGCGGTGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGC‑GTTTGGTGACGGGATGAACGACGCCGaa                                            <  1:1680756/90‑1 (MQ=255)
                          tcaaaaGGCCATGCGCTGGAAGCGGTGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGC‑GTTTGGTGACGGGATGAACGACGCCGaa                                            <  2:776121/90‑1 (MQ=255)
                          tcaaaaGGCCATGCGCTGGAAGCGGTGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGC‑GTTTGGTGACGGGATGAACGACGCCGaa                                            >  2:7064425/4‑93 (MQ=255)
                          tcaaaaGGCCATGCGCTGGAAGCGGTGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGC‑GTTTGGTGACGGGATGAACGACGCCGaa                                            >  2:6112688/4‑93 (MQ=255)
                          tcaaaaGGCCATGCGCTGGAAGCGGTGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGC‑GTTTGGTGACGGGATGAACGACGCCGaa                                            >  2:5931017/4‑93 (MQ=255)
                           caaaaGGCCATGCGCTGGAAGCGGTGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGC‑GTTTGGTGACGGGATGAACGACGCCGaaa                                           <  2:6578560/91‑1 (MQ=255)
                           caaaaGGCCATGCGCTGGAAGCGGTGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGC‑GTTTGGTGACGGGATGAACGACGCCGaaa                                           <  2:318095/91‑1 (MQ=255)
                           caaaaGGCCATGCGCTGGAAGCGGTGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGC‑GTTTGGTGACGGGATGAACGACGCCGaaa                                           <  2:9396201/91‑1 (MQ=255)
                           caaaaGGCCATGCGCTGGAAGCGGTGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGC‑GTTTGGTGACGGGATGAACGACGCCGaaa                                           <  2:6411942/91‑1 (MQ=255)
                            aaaaGGCCATGCGCTGGAAGCGGTGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGC‑GTTTGGTGACGGGATGAACGACGCCGAAAt                                          >  1:798070/2‑93 (MQ=255)
                            aaaaGGCCATGCGCTGGAAGCGGTGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGC‑GTTTGGTGACGGGATGAACGACGCCGAAAt                                          >  1:865711/2‑93 (MQ=255)
                             aaaGGCCATGCGCTGGAAGCGGTGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGC‑GTTTGGTGACGGGATGAACGACGCCGAAATg                                         >  2:2286238/1‑93 (MQ=255)
                              aaGGCCATGCGCTGGAAGCGGTGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGC‑GTTTGGTGACGGGATGAACGACGCCGAAATGc                                        <  2:7954981/93‑1 (MQ=255)
                              aaGGCCATGCGCTGGAAGCGGTGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGC‑GTTTGGTGACGGGATGAACGACGCCGAAATGc                                        <  1:2939580/93‑1 (MQ=255)
                               aGGCCATGCGCTGGAAGCGGTGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGC‑GTTTGGTGACGGGATGAACGACGCCGAAATGCt                                       <  1:2133690/93‑1 (MQ=255)
                               aGGCCATGCGCTGGAAGCGGTGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGC‑GTTTGGTGACGGGATGAACGACGCCGAAATGCt                                       >  1:5588573/1‑93 (MQ=255)
                               aGGCCATGCGCTGGAAGCGGTGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGC‑GTTTGGTGACGGGATGAACGACGCCGAAATGCt                                       <  1:9889411/93‑1 (MQ=255)
                                ggCCATGCGCTGGAAGCGGTGGCGAAGAAACTGGGCTACAGCCTGAAGGATTGTATTGC‑GTTTGGTGACGGGATGAACGACGCCGAAATGCTg                                      <  2:7244493/93‑1 (MQ=255)
                                                             actgggCTACAGCCTGAAGGATTGTATTGC‑GTTTGGTGACGGGATGAACGACGCCGAAATGCTGTCGATGGCGGGGAAAGGCTGCATTATggg         <  2:635603/89‑1 (MQ=255)
                                                             actgggCTACAGCCTGAAGGATTGTATTGC‑GTTTGGTGACGGGATGAACGACGCCGAAATGCTGTCGATGGCGGGGAAAGGCTGCATTATggg         >  2:6918389/5‑93 (MQ=255)
                                                             actgggCTACAGCCTGAAGGATTGTATTGC‑GTTTGGTGACGGGATGAACGACGCCGAAATGCTGTCGATGGCGGGGAAAGGCTGCATTATggg         <  2:10047426/89‑1 (MQ=255)
                                                             actgggCTACAGCCTGAAGGATTGTATTGC‑GTTTGGTGACGGGATGAACGACGCCGAAATGCTGTCGATGGCGGGGAAAGGCTGCATTATggg         >  1:7427623/5‑93 (MQ=255)
                                                             actgggCTACAGCCTGAAGGATTGTATTGC‑GTTTGGTGACGGGATGAACGACGCCGAAATGCTGTCGATGGCGGGGAAAGGCTGCATTATggg         <  1:8996608/89‑1 (MQ=255)
                                                             actgggCTACAGCCTGAAGGATTGTATTGC‑GTTTGGTGACGGGATGAACGACGCCGAAATGCTGTCGATGGCGGGGAAAGGCTGCATTATggg         <  1:7457463/89‑1 (MQ=255)
                                                              ctgggCTACAGCCTGAAGGATTGTATTGC‑GTTTGGTGACGGGATGAACGACGCCGCAATGCTGTCGATGGCGGGGAAAGGCTGCATTATCGGc        >  2:7442846/4‑93 (MQ=255)
                                                              ctgggCTACAGCCTGAAGGATTGTATTGC‑GTTTGGTGACGGGATGAACGACGCCGAAATGCTGTCGATGGCGGGGAAAGGCTGCATTATGGGc        >  2:7442845/4‑93 (MQ=255)
                                                              ctgggCTACAGCCTGAAGGATTGTATTGC‑GTTTGGTGACGGGATGAACGACGCCGAAATGCTGTCGATGGCGGGGAAAGGCTGCATTATGGGc        >  1:5283558/4‑93 (MQ=255)
                                                              ctgggCTACAGCCTGAAGGATTGTATTGC‑GTTTGGTGACGGGATGAACGACGCCGAAATGCTGTCGATGGCGGGGAAAGGCTGCATTATGGGc        <  1:3790479/90‑1 (MQ=255)
                                                               tgggCTACAGCCTGAAGGATTGTATTGC‑GTTTGGTGACGGGATGAACGACGCCGAAATGCTGTCGATGGCGGGGAAAGGCTGCATTATGGGCa       <  1:3862419/91‑1 (MQ=255)
                                                               tgggCTACAGCCTGAAGGATTGTATTGC‑GTTTGGTGACGGGATGAACGACGCCGAAATGCTGTCGATGGCGGGGAAAGGCTGCATTATGGGCa       <  2:9225273/91‑1 (MQ=255)
                                                               tgggCTACAGCCTGAAGGATTGTATTGC‑GTTTGGTGACGGGATGAACGACGCCGAAATGCTGTCGATGGCGGGGAAAGGCTGCATTATGGGCa       >  2:9815504/3‑93 (MQ=255)
                                                               tgggCTACAGCCTGAAGGATTGTATTGC‑GTTTGGTGACGGGATGAACGACGCCGAAATGCTGTCGATGGCGGGGAAAGGCTGCATTATGGGCa       <  2:5431870/91‑1 (MQ=255)
                                                               tgggCTACAGCCTGAAGGATTGTATTGC‑GTTTGGTGACGGGATGAACGACGCCGAAATGCTGTCGATGGCGGGGAAAGGCTGCATTATGGGCa       <  1:6431365/91‑1 (MQ=255)
                                                                gggCTACAGCCTGAAGGATTGTATTGC‑GTTTGGTGACGGGATGAACGACGCCGAAATGCTGTCGATGGCGGGGAAAGGCTGCATTATGGGCAg      <  1:5581889/92‑1 (MQ=255)
                                                                 ggCTACAGCCTGAAGGATTGTATTGA‑GTTTGGTGACGGGATGAACGACGCCGAAATGCTGTCGATGGCGGGGAAAGGCTGCATTATGGGCAGt     <  2:5907352/93‑1 (MQ=255)
                                                                  gCTACAGCCTGAAGGATTGTATTGC‑GTTTGGTGACGGGATGAACGACGCCGAAATGCTGTCGATGGCGGGGAAAGGCTGCATTATGGGCAGTg    <  1:5093849/93‑1 (MQ=255)
                                                                  gCTACAGCCTGAAGGATTGTATTGC‑GTTTGGTGACGGGATGAACGACGCCGAAATGCTGTCGATGGCGGGGAAAGGCTGCATTATGGGCAGTg    <  1:1490113/93‑1 (MQ=255)
                                                                  gCTACAGCCTGAAGGATTGTATTGC‑GTTTGGTGAAGGGATGAACGACGCCGAAATGCTGTCGATGGCGGGGAAAGGCTGCATTATGGGCAGTg    <  1:6885365/93‑1 (MQ=255)
                                                                   cTACAGCCTGAAGGATTGTATTGC‑GTTTGGTGACGGGATGAACGACGCCGAAATGCTGTCGATGGCGGGGAAAGGCTGCATTATGGGCAGTgc   >  2:7560954/1‑92 (MQ=255)
                                                                   cTACAGCCTGAAGGATTGTATTGC‑GTTTGGTGACGGGATGAACGACGCCGAAATGCTGTCGATGGCGGGGAAAGGCTGCATTATGGGCAGTgc   >  2:3591843/1‑92 (MQ=255)
                                                                   cTACAGCCTGAAGGATTGTATTGC‑GTTTGGTGACGGGATGAACGACGCCGAAATGCTGTCGATGGCGGGGAAAGGCTGCATTATGGGCAGTgc   <  1:6556074/93‑2 (MQ=255)
                                                                   cTACAGCCTGAAGGATTGTATTGC‑GTTTGGTGACGGGATGAACGACGCCGAAATGCTGTCGATGGCGGGGAAAGGCTGCATTATGGGCAGTgc   <  2:1340347/93‑2 (MQ=255)
                                                                   cTACAGCCTGAAGGATTGTATTGC‑GTTTGGTGACGGGATGAACGACGCCGAAATGCTGTCGATGGCGGGGAAAGGCTGCATTATGGGCAGTgc   >  1:7893199/1‑92 (MQ=255)
                                                                    tACAGCCTGAAGGATTGTATTGC‑GTTTGGTGACGGGATGAACGACGCCGAAATGCTGTCGATGGCGGGGAAAGGCTGCATTATGGGCAGTgcg  >  1:2286645/1‑91 (MQ=255)
                                                                         |                                                                                        
TCTGGAAGTGATGGCGGGCGGC‑GTTTC‑AAAGGCCATGCGCTGGAAG‑GCTGGCG‑‑‑‑AACT‑GGCTACAG‑CTGAAGGATTG‑ATTGC‑GTT‑‑GTGACGGGATGAACGACGCCGAAATGCTGTCGATGGC‑GGGAAA‑GCTGCATTATGGGCAGTGGC  >  NC_000913/4008346‑4008492

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 20 ≤ ATCG/ATCG < 28 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

BRESEQ :: bam2aln output
TTCAAAGGCCATGCGCTGGAAG‑GCTGGCG‑‑‑‑AA‑‑‑‑CT‑GGCTACAG‑CTGAAGGATTG‑ATTGCGTT‑‑GTGACGGGATGAACGACGCCGAAATGCTGTCGATGGC‑GGG‑‑AAAGCTGCATTATGGGCAGTGGCCACCAGC  >  NC_000913/4008370‑4008499
                                                    |                                                                                              
tcaAAAGGCCATGCGCTGGAAGCGGTGGCGAAGAAA‑‑‑‑CTGGGCTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGCCGAAA                                                   <  SRR4302540.1699002/91‑1 (MQ=16)
 caAAAGGCCATGCGCTGGAAGCGGTGGCGAAGAAA‑‑‑‑CTGGGCTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGCCGAAAT                                                  >  SRR4302540.874903/3‑94 (MQ=18)
 caAAAGGCCATGCGCTGGAAGCGGTGGCGAAGAAA‑‑‑‑CTGGGCTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGCCGAAAT                                                  <  SRR4302540.2379168/92‑1 (MQ=18)
 caAAAGGCCATGCGCTGGAAGCGGTGGCGAAGAAA‑‑‑‑CTGGGCTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGCCGAAAT                                                  >  SRR4302540.806546/3‑94 (MQ=18)
 TAAAAGGCCATGCGCTGGAAGCGGTGGCGAAGAAA‑‑‑‑CTGGGCTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGCCGAAAT                                                  <  SRR4302540.8843161/94‑1 (MQ=18)
  AAAAGGCCATGCGCTGGAAGCGGTGGCGAAGAAA‑‑‑‑CTGGGCTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGCCGAAATG                                                 >  SRR4302540.161911/1‑94 (MQ=19)
   AAAGGCCATGCGCTGGAAGCGGTGGCG‑‑‑‑AAGAATCTGGGCTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGCCGAAATGC                                                <  SRR4302540.183462/94‑1 (MQ=21)
    AAGGCCATGCGCTGGAAGCGGTGGCGAAGAAA‑‑‑‑CTGGGCTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGCCGAAATGCT                                               >  SRR4302540.5650078/1‑94 (MQ=21)
    AAGGCCATGCGCTGGAAGCGGTGGCGAAGAAA‑‑‑‑CTGGGCTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGCCGAAATGCT                                               >  SRR4302540.5650079/1‑94 (MQ=21)
    AAGGCCATGCGCTGGAAGCGGTGGCGAAGAAA‑‑‑‑CTGGGCTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGCCGAAATGCT                                               <  SRR4302540.2971856/94‑1 (MQ=21)
     AGGCCATGCGCTGGAAGCGGTGGCGAAGAAA‑‑‑‑CTGGGCTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGCCGAAATGCTG                                              >  SRR4302540.1359571/1‑94 (MQ=23)
     AGGCCATGCGCTGGAAGCGGTGGCGAAGAAA‑‑‑‑CTGGGCTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGCCGAAATGCTG                                              <  SRR4302540.2156594/94‑1 (MQ=23)
     AGGCCATGCGCTGGAAGCGGTGGCGAAGAAA‑‑‑‑CTGGGCTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGCCGAAATGCTG                                              <  SRR4302540.10004879/94‑1 (MQ=23)
     AGGCCATGCGCTGGAAGCGGTGGCGAAGAAA‑‑‑‑CTGGGCTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGCCGAAATGCTG                                              >  SRR4302540.8031009/1‑94 (MQ=23)
     AGGCCATGCGCTGGAAGCGGTGGCGAAGAAA‑‑‑‑CTGGGCTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGCCGAAATGCTG                                              >  SRR4302540.7715878/1‑94 (MQ=23)
       GCCATGCGCTGGAAGCGGTGGCGAAGAAA‑‑‑‑CTGGGCTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGCCGAAATGCTGTC                                            <  SRR4302540.3646314/94‑1 (MQ=26)
        CCATGCGCTGGAAGCGGTGGCGAAGAAA‑‑‑‑CTGGGCTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGCCGAAATGCTGTCG                                           >  SRR4302540.4238846/1‑94 (MQ=28)
           gccatgctctggaagcggtggcgaagaaactgGGCTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGCCGAAATGCTGTC                                            <  SRR4302540.7483348/62‑1 (MQ=38)
             catgcgctggaagcggtggcgaagaaactgGGCTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGCCGAAATGCTGTCGT                                          >  SRR4302540.508408/31‑94 (MQ=40)
             catgcgctggaagcggtggcgaagaaactgGGCTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGCCGAAATGCTGTCGA                                          >  SRR4302540.5324835/31‑94 (MQ=42)
             catgcgctggaagcggtggcgaagaaactgGGCTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGCCGAAATGCTGTCGA                                          <  SRR4302540.3364981/64‑1 (MQ=42)
             catgcgctggaagcggtggcgaagaaactgGGCTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGCCGAAATGCTGTCGA                                          >  SRR4302540.508409/31‑94 (MQ=42)
              atgcgctggaagcggtggcgaagaaactgGGCTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGCCGAAATGCTGTCGAT                                         >  SRR4302540.9128906/30‑94 (MQ=45)
              atgcgctggaagcggtggcgaagaaactgGGCTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGCCGAAATGCTGTCGAT                                         <  SRR4302540.4917563/65‑1 (MQ=45)
              atgcgctggaagcggtggcgaagaaactgGGCTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGCCGAAATGCTGTCGAT                                         <  SRR4302540.4349373/65‑1 (MQ=45)
              atgcgctggaagcggtggcgaagaaactgGGCTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGCCGAAATGCTGTCGAT                                         >  SRR4302540.7093685/30‑94 (MQ=45)
              atgcgctggaagcggtggcgaagaaactgGGCTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGCCGAAATGCTGTCGAT                                         >  SRR4302540.8436599/30‑94 (MQ=45)
              atgcgctggaagcggtggcgaagaaactgGGCTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGCCGAAATGCTGTCGAT                                         <  SRR4302540.9194727/65‑1 (MQ=45)
              atgcgctggaagcggtggcgaagaaactgGGCTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGCCGAAATGCTGTCGAT                                         >  SRR4302540.7519695/30‑94 (MQ=45)
              atgcgctggaagcggtggcgaagaaactgGGCTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGCCGAAATGCTGTCGAT                                         <  SRR4302540.9526765/65‑1 (MQ=45)
              atgcgctggaagcggtggcgaagaaactgGGCTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGCCGAAATGCTGTCGAT                                         <  SRR4302540.1732967/65‑1 (MQ=45)
              atgcgctggaagcggtggcgaagaaactgGGCTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGCCGAAATGCTGTAGAT                                         >  SRR4302540.2167333/30‑94 (MQ=34)
               tgcgctggaagcggtggcgaagaaactgGGCTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGCCGAAATGCTGTCGATG                                        <  SRR4302540.3355497/66‑1 (MQ=47)
               tgcgctggaagcggtggcgaagaaactgGGCTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGCCGAAATGCTGTCGATG                                        <  SRR4302540.73176/66‑1 (MQ=47)
                gcgctggaagcggtggcgaagaaactgGGCTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGCCGAAATGCTGTCGATGG                                       >  SRR4302540.332012/28‑94 (MQ=49)
                gcgctggaagcggtggcgaagaaactgGGCTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGCCGAAATGCTGTCGATGG                                       <  SRR4302540.8647840/67‑1 (MQ=49)
                 cgctggaagcggtggcgaagaaactgGGCTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGCCGAAATGCTGTCGATGGC                                      >  SRR4302540.4068506/27‑94 (MQ=51)
                  gctggaagcggtggcgaagaaactgGGCTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGCCGAAATGCTGTCGATGGC‑G                                    >  SRR4302540.2070543/26‑94 (MQ=53)
                  gctggaagcggtggcgaagaaactgGGCTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGCCGAAATGCTGTCGATGGC‑G                                    >  SRR4302540.1319173/26‑94 (MQ=53)
                  gctggaagcggtggcgaagaaactgGGCTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGCCGAAATGCTGTCGATGGC‑G                                    <  SRR4302540.4006010/69‑1 (MQ=53)
                  gctggaagcggtggcgaagaaactgGGCTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGCCGAAATGCTGTCGATGGC‑G                                    >  SRR4302540.3976907/26‑94 (MQ=53)
                  gctggaagcggtggcgaagaaactgGGCTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGCCGAAATGCTGTCGATGGC‑G                                    >  SRR4302540.3784977/26‑94 (MQ=53)
                  gctggaagcggtggcgaagaaactgGGCTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGCCGAAATGCTGTCGATGGC‑G                                    >  SRR4302540.1319175/26‑94 (MQ=53)
                   ctggaagcggtggcgaagaaactgGGCTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGCCGAAATGCTGTCGATGGC‑GG                                   >  SRR4302540.7373834/25‑94 (MQ=55)
                   ctggaagcggtggcgaagaaactgGGCTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGCCGAAATGCTGTCGATGGC‑GG                                   <  SRR4302540.1626527/70‑1 (MQ=55)
                   ctggaagcggtggcgaagaaactgGGCTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGCCGAAATGCTGTCGATGGC‑GG                                   >  SRR4302540.5805393/25‑94 (MQ=55)
                   ctggaagcggtggcgaagaaactgGGCTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGCCGAAATGCTGTCGATGGC‑GG                                   <  SRR4302540.3424547/70‑1 (MQ=55)
                   ctggaagcggtggcgaagaaactgGGCTACAGCCTGAAGGATTGTATTGCGTTTGGTGAAGGGATGAACGACGCCGAAATGCTGTCGATGGC‑GG                                   >  SRR4302540.5358055/25‑94 (MQ=41)
                    tggaagcggtggcgaagaaactgggctaccgcCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGCCGAAATGCTGTCGATGGC‑GGG                                  <  SRR4302540.6812653/62‑1 (MQ=60)
                    tggaagcggtggcgaagaaactgGGCTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGCCGAAATGCTGTCGATGGC‑GGG                                  >  SRR4302540.2788169/24‑94 (MQ=57)
                     ggaagcggtggcgaagaaactgGGCTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGCCGAAATGCTGTCGATGGC‑GGG‑‑G                               >  SRR4302540.9361108/23‑94 (MQ=56)
                     ggaagcggtggcgaagaaactgGGCTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGCCGAAATGCTGTCGATGGC‑GGG‑‑G                               <  SRR4302540.3583269/72‑1 (MQ=56)
                     ggaagcggtggcgaagaaactgGGCTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGCCGAAATGCTGTCGATGGC‑GGG‑‑G                               >  SRR4302540.5793723/23‑94 (MQ=56)
                     ggaagcggtggcgaagaaactgGGCTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGCCGAAATGCTGTCGATGGC‑GGG‑‑G                               <  SRR4302540.4837762/72‑1 (MQ=56)
                       aagcggtggcgaagaaactgGGCTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGCCGAAATGCTGTCGATGGC‑GGG‑‑GAA                             >  SRR4302540.4642256/21‑94 (MQ=55)
                        agcggtggcgaagaaactgGGCTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGCCGAAATGCTGTCGATGGCGGGG‑‑AAA                             <  SRR4302540.6008912/75‑1 (MQ=54)
                        agcggtggcgaagaaactgGGCTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGCCGAAATGCTGTCGATGGCGGGG‑‑AAA                             >  SRR4302540.5979359/20‑94 (MQ=54)
                        agcggtggcgaagaaactgGGCTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGCCGAAATGCTGTCGATGGCGGGG‑‑AAA                             <  SRR4302540.9853474/75‑1 (MQ=54)
                         gcggtggcgaagaaactgGGCTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGCCGAAATGCTGTCGATGGCGGGG‑‑AAAG                            <  SRR4302540.9762757/76‑1 (MQ=53)
                         gcggtggcgaagaaactgGGCTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGCCGAAATGCTGTCGATGGCGGGG‑‑AAAG                            <  SRR4302540.9634746/76‑1 (MQ=53)
                         gcggtggcgaagaaacggGGCTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGCCGAAATGCTGTCGATGGCGGGG‑‑AAAG                            <  SRR4302540.4477921/76‑1 (MQ=53)
                           ggtggcgaagaaactgGGCTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGCCGAAATGCTGTCGATGGC‑GGGgaaaggc                           <  SRR4302540.3329728/78‑8 (MQ=57)
                           ggtggcgaagaaactgGGCTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGCCGAAATGCTGTCGATGGC‑GGGgaaaggc                           <  SRR4302540.21553/78‑8 (MQ=57)
                             tggcgaagaaactgGGCTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGCCGAAATGCTGTCGATGGC‑GGGgaaaggctg                         >  SRR4302540.9804660/15‑85 (MQ=57)
                             tggcgaagaaactgGGCTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGCCGAAATGCTGTCGATGGC‑GGGgaaaggctg                         <  SRR4302540.9967425/80‑10 (MQ=57)
                               gcgaagaaactgGGCTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGCCGAAATGCTGTCGATGGC‑GGGGAAAGGCTGCA                       <  SRR4302540.5000314/82‑1 (MQ=50)
                                cgaagaaactgGGCTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGCCGAAATGCTGTCGATGGC‑GGGGAAAGGCTGCAT                      >  SRR4302540.6886699/12‑94 (MQ=49)
                                cgaagaaactgGGCTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGCCGAAATGCTGTCGATGGC‑GGGGAAAGGCTGCAT                      >  SRR4302540.8501557/12‑94 (MQ=49)
                                 gaagaaactgGGCTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGCCGAAATGCTGTCGATGGC‑GGGGAAAGGCTGCATT                     >  SRR4302540.6413707/11‑94 (MQ=49)
                                 gaagaaactgGGCTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGCCGAAATGCTGTCGATGGC‑GGGGAAAGGCTGCATT                     >  SRR4302540.9574949/11‑94 (MQ=49)
                                 gaagaaactgGGCTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGCCGAAATGCTGTCGATGGC‑GGGGAAAGGCTGCATT                     >  SRR4302540.6413706/11‑94 (MQ=49)
                                 gaagaaactgGGCTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGCCGAAATGCTGTCGATGGC‑GGGGAAAGGCTGCATT                     >  SRR4302540.3392811/11‑94 (MQ=49)
                                 gaagaaactgGGCTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGCCGAAATGCTGTCGATGGC‑GGGGAAAGGCTGCATT                     >  SRR4302540.2835520/11‑94 (MQ=49)
                                 gaagaaactgGGCTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGCCGAAATGCTGTCGATGGC‑GGGGAAAGGCTGCATT                     >  SRR4302540.8099482/11‑94 (MQ=49)
                                  aagaaactgGGCTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACTACGCCGAAATGCTGTCGATGGG‑GGGGCAAGGCTGCATTA                    >  SRR4302540.1963660/10‑94 (MQ=29)
                                  aagaaactgGGCTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGCCGAAATGCTGTCGATGGC‑GGGgaaaggctgcattt                    >  SRR4302540.3078795/10‑80 (MQ=57)
                                  aagaaactgGGCTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGCCGAAATGCTGTCGATGGC‑GGGGAAAGGCTGCATTA                    <  SRR4302540.1162261/85‑1 (MQ=48)
                                  aagaaactgGGCTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGCCGAAATGCTGTCGATGGC‑GGGGAAAGGCTGCATTA                    <  SRR4302540.2005748/85‑1 (MQ=48)
                                  AA‑‑‑‑CTGGGCTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGCCGAAATGCTGTCGATGGC‑GGGGAAAGGCTGCATTATGGG                >  SRR4302540.7730494/1‑94 (MQ=50)
                                  AA‑‑‑‑CTGGGCTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGCCGAAATGCTGTCGATGGC‑GGGGAAAGGCTGCATTATGGG                >  SRR4302540.7510367/1‑94 (MQ=50)
                                  AA‑‑‑‑CTGGGCTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGCCGAAATGCTGTCGATGGC‑GGGGAAAGGCTGCATTATGGG                <  SRR4302540.6387578/94‑1 (MQ=50)
                                  AA‑‑‑‑CTGGGCTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGAGATGAACGACGCCGAAATGCTGTCGATGGC‑GGGGAAAGGCTGCATTATGGG                <  SRR4302540.4674009/94‑1 (MQ=40)
                                   agaaactgGGCTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGCCGAAATGCTGTCGATGGC‑GGGGAAAGGCTGCATTAT                   >  SRR4302540.1202810/9‑94 (MQ=48)
                                   agaaactgGGCTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGCCGAAATGCTGTCGATGGC‑GGGGAAAGGCTGCATTAT                   <  SRR4302540.4982966/86‑1 (MQ=48)
                                   agaaactgGGCTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGCCGAAATGCTGTCGATGGC‑GGGGAAAGGCTGCATTAT                   <  SRR4302540.6763216/86‑1 (MQ=48)
                                   agaaactgGGCTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGCCGAAATGCTGTCGATGGC‑GGGGAAAGGCTGCATTAT                   <  SRR4302540.5940236/86‑1 (MQ=48)
                                   acaaactgGGCTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGCCGAAATGCTGTCGATGGC‑GGGGAAAGGCTGCATTAT                   <  SRR4302540.4455428/86‑1 (MQ=48)
                                   A‑‑‑‑CTGGGCTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGCCGAAATGCTGTCGATGGC‑GGGGAAAGGCTGCATTATGGGC               <  SRR4302540.9104530/94‑1 (MQ=53)
                                   A‑‑‑‑CTGGGCTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGCCGAAATGCTGTCGATGGC‑GGGGAAAGGCTGCATTATGGGC               >  SRR4302540.5341293/1‑94 (MQ=53)
                                   A‑‑‑‑CTGGGCTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGCCGAAATGCTGTCGATGGC‑GGGGAAAGGCTGCATTATGGGC               <  SRR4302540.7540608/94‑1 (MQ=53)
                                    gaaactgGGCTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGCCGAAATGCTGTCGATGGC‑GGGGAAAGGCTGCATTATG                  <  SRR4302540.3106427/87‑1 (MQ=49)
                                    gaaactgGGCTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGCCGAAATGCTGTCGATGGC‑GGGGAAAGGCTGCATTATG                  >  SRR4302540.3805053/8‑94 (MQ=49)
                                    gaaactgGGCTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGCCGAAATGCTGTCGATGGC‑GGGGAAAGGCTGCATTATG                  >  SRR4302540.613597/8‑94 (MQ=49)
                                     aaactgGGCTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGCCGAAATGCTGTCGATGGC‑GGGGAAAGGCTGCATTATGG                 <  SRR4302540.5883232/88‑1 (MQ=51)
                                     aaactgGGCTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGCCGAAATGCTGTCGATGGC‑GGGGAAAGGCTGCATTATGG                 >  SRR4302540.3177008/7‑94 (MQ=51)
                                      atctgGGCTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGCCGAAATGCTGTCGATGGC‑GGGGAAAGGCTGCATTATGGG                <  SRR4302540.9105269/89‑1 (MQ=53)
                                        ctgGGCTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGCCGAAATGCTGTCGATGGC‑GGGGAAAGGCTGCATTATGGGCA              <  SRR4302540.1026428/91‑1 (MQ=57)
                                        ctgGGCTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGCCGAAATGCTGTCGATGGC‑GGGGAAAGGCTGCATTATGGGCA              <  SRR4302540.7427969/91‑1 (MQ=57)
                                        ctgGGCTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGCCGAAATGCTGTCGATGGC‑GGGGAAAGGCTGCATTATGGGCA              <  SRR4302540.3831804/91‑1 (MQ=57)
                                         tgGGCTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGCCGAAATGCTGTCGATGGC‑GGGGAAAGGCTGCATTATGGGCAG             <  SRR4302540.3904400/92‑1 (MQ=58)
                                         tgGGCTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGCCGAAATGCTGTCGATGGC‑GGGGAAAGGCTGCATTATGGGCAG             <  SRR4302540.6502950/92‑1 (MQ=58)
                                         G‑GGCTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGCCGAAATGCTGTCGATGGC‑GGGGAAAGGCTGCATTATGGGCAGT            <  SRR4302540.5643333/94‑1 (MQ=60)
                                            GCTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGCCGAAATGCTGTCGATGGC‑GGGGAAAGGCTGCATTATGGGCAGTGC          <  SRR4302540.1506497/94‑1 (MQ=60)
                                            GCTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGCCGAAATGCTGTCGATGGC‑GGGGAAAGGCTGCATTATGGGCAGTGC          >  SRR4302540.7985307/1‑94 (MQ=60)
                                            GCTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGCCGAAATGCTGTCGATGGC‑GGGGAAAGGCTGCATTATGGGCAGTGC          <  SRR4302540.5148963/94‑1 (MQ=60)
                                            GCTACAGCCTGAAGGATTGTATTGCGTTTGGTGAAGGGATGAACGACGCCGAAATGCTGTCGATGGC‑GGGGAAAGGCTGCATTATGGGCAGTGC          <  SRR4302540.6961699/94‑1 (MQ=48)
                                             CTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGCCGAAATGCTGTCGATGGC‑GGGGAAAGGCTGCATTATGGGCAGTGcg         <  SRR4302540.6628771/94‑3 (MQ=60)
                                             CTACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGCCGAAATGCTGTCGATGGC‑GGGGAAAGGCTGCATTATGGGCAGTGcg         >  SRR4302540.2311232/1‑92 (MQ=60)
                                              TACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGCCGAAATGCTGTCGATGGC‑GGGGAAAGGCTGCATTATGGGCAGTGcgc        >  SRR4302540.2354290/1‑91 (MQ=60)
                                              TACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGCCGAAATGCTGTCGATGGC‑GGGGAAAGGCTGCATTATGGGCAGTGcgc        <  SRR4302540.6720099/94‑4 (MQ=60)
                                              TACAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGCCGAAATGCTGTCGATGGC‑GGGGAAAGGCTGCATTATGGGCAGTGcgc        >  SRR4302540.4795597/1‑91 (MQ=60)
                                                CAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGCCGAAATGCTGTCGATGGC‑GGGGAAAGGCTGCATTATGGGCAGTGcgcac      <  SRR4302540.9255566/94‑6 (MQ=60)
                                                CAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGCCGAAATGCTGTCGATGGC‑GGGGAAAGGCTGCATTATGGGCAGTGcgcac      >  SRR4302540.1811185/1‑89 (MQ=60)
                                                CAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGCCGAAATGCTGTCGATGGC‑GGGGAAAGGCTGCATTATGGGCAGTGcgcac      <  SRR4302540.2741885/94‑6 (MQ=60)
                                                CAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGCCGAAATGCTGTCGATGGC‑GGGGAAAGGCTGCATTATGGGCAGTGcgcac      <  SRR4302540.959455/94‑6 (MQ=60)
                                                CAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGCCGAAATGCTGTCGATGGC‑GGGGAAAGGCTGCATTATGGGCAGTGcgcac      >  SRR4302540.1519608/1‑89 (MQ=60)
                                                CAGCCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGCCGAAATGCTGTCGATGGC‑GGGGAAAGGCTGCATTATGGGCAGTGcgcac      >  SRR4302540.872566/1‑89 (MQ=60)
                                                  gcCTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGCCGAAATGCTGTCGATGGC‑GGGGAAAGGCTGCATTATGGGCAGTGCGCACCA    <  SRR4302540.2203366/92‑1 (MQ=60)
                                                  C‑CTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGCCGAAATGCTGTCGATGGC‑GGGGAAAGGCTGCATTATGGGCAGTGCGCACCAG   <  SRR4302540.4701207/94‑1 (MQ=60)
                                                    CTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGCCGAAATGCTGTCGATGGC‑GGGGAAAGGCTGCATTATGGGCAGTGCGCACCAGC  <  SRR4302540.9093719/94‑1 (MQ=60)
                                                    CTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGCCGAAATGCTGTCGATGGC‑GGGGAAAGGCTGCATTATGGGCAGTGCGCACCAGC  >  SRR4302540.4472460/1‑94 (MQ=60)
                                                    CTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGCCGAAATGCTGTCGATGGC‑GGGGAAAGGCTGCATTATGGGCAGTGCGCACCAGC  <  SRR4302540.472006/94‑1 (MQ=60)
                                                    CTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGCCGAAATGCTGTCGATGGC‑GGGGAAAGGCTGCATTATGGGCAGTGCGCACCAGC  >  SRR4302540.4441843/1‑94 (MQ=60)
                                                    CTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGCCGAAATGCTGTCGATGGC‑GGGGAAAGGCTGCATTATGGGCAGTGCGCACCAGC  <  SRR4302540.3419595/94‑1 (MQ=60)
                                                    CTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGCCGAAATGCTGTCGATGGC‑GGGGAAAGGCTGCATTATGGGCAGTGCGCACCAGC  >  SRR4302540.6890283/1‑94 (MQ=60)
                                                    CTGAAGGATTGTATTGCGTTTGGTGACGGGATGAACGACGCCGAAATGCTGTCGATGGC‑GGGGAAAGGCTGCATTATGGGCAGTGCGCACCAGC  >  SRR4302540.4441842/1‑94 (MQ=60)
                                                    |                                                                                              
TTCAAAGGCCATGCGCTGGAAG‑GCTGGCG‑‑‑‑AA‑‑‑‑CT‑GGCTACAG‑CTGAAGGATTG‑ATTGCGTT‑‑GTGACGGGATGAACGACGCCGAAATGCTGTCGATGGC‑GGG‑‑AAAGCTGCATTATGGGCAGTGGCCACCAGC  >  NC_000913/4008370‑4008499

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 19 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑