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 4,061,961 Δ1 bp coding (1386/1458 nt) b3876 ← putative permease

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009134,061,9590C.99.6% 1289.0 / ‑3.9 282coding (1388/1458 nt)b3876putative permease
Reads supporting (aligned to +/- strand):  ref base C (1/0);  new base . (153/127);  total (155/127)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.97e-01

Only 100 of 296 total aligned reads displayed.

TTTTTCATAATAAGTCCATTTTTTAAACGTAGGGAGGCCGCCACCCACCAGGATGGAAATAGCGGCTATTGACATTTATAACGTTACGGAAGCCCGTTTTTTCTTCTGTCGCCATCTCTTTATTTTTGCGTTGGTTGATTTCCTCAATAATCAATGCAAACCGTTTTTCATTGAGTGTGTA  >  NC_000913/4061867‑4062047
                                                                                            |                                                                                        
    tCATAATAAGTCCATTTTTTAAACGTAGGGAGGCCGCCACCCACCAGGATGGAAATAGGGGCTATTGACATTTATAACGTTACGGAAGccgtt                                                                                      >  1:886821/1‑90 (MQ=255)
    tCATAATAAGTCCATTTTTTAAACGTAGGGAGGCCGCCACCCACCAGGATGGAAATAGCGGCTATTGACATTTATAACGTTACGGAAGccgtt                                                                                      <  2:1378858/93‑4 (MQ=255)
     cATAATAAGTCCATTTTTTAAACGTAGGGAGGCCGCCACCCACCAGGATGGAAATAGCGGCTATTGACATTTATAACGTTACGGAAGccgttt                                                                                     <  2:944478/93‑5 (MQ=255)
      ataataAGTCCATTTTTTAAACGTAGGGAGGCCGCCACCCACCAGGATGGAAATAGCGGCTATTGACATTTATAACGTTACGGAAG‑CCGtttt                                                                                   >  2:2958259/1‑93 (MQ=255)
      ataataAGTCCATTTTTTAAACGTAGGGAGGCCGCCACCCACCAGGATGGAAATAGCGGCTATTGACATTTATAACGTTACGGAAG‑CCGtttt                                                                                   >  2:5360607/1‑93 (MQ=255)
       taataaGTCCATTTTTTAAACGTAGGGAGGCCGCCACCCACCAGGATGGAAATAGCGGCTATTGACATTTATAACGTTACGGAAG‑CCGttttt                                                                                  <  1:5560134/93‑1 (MQ=255)
       taataaGTCCATTTTTTAAACGTAGGGAGGCCGCCACCCACCAGGATGGAAATAGCGGCTATTGACATTTATAACGTTACGGAAG‑CCGttttt                                                                                  >  2:7257887/1‑93 (MQ=255)
        aataaGTCCATTTTTTAAACGTAGGGAGGCCGCCACCCACCAGGATGGAAATAGCGGCTATTGACATTTATAACGTTACGGAAG‑CCGtttttt                                                                                 <  1:6640852/93‑1 (MQ=255)
         ataaGTCCATTTTTTAAACGTAGGGAGGCCGCCACCCACCAGGATGGAAATAGCGGCTATTGACATTTATAACGTTACGGAAG‑CCGTTTTttc                                                                                <  1:4994533/93‑1 (MQ=255)
         ataaGTCCATTTTTTAAACGTAGGGAGGCCGCCACCCACCAGGATGGAAATAGCGGCTATTGACATTTATAACGTTACGGAAG‑CCGTTTTttc                                                                                >  1:2016267/1‑93 (MQ=255)
          taaGTCCATTTTTTAAACGTAGGGAGGCCGCCACCCACCAGGATGGAAATAGCGGCTATTGACATTTATAACGTTACGGAAG‑CCGTTTTttct                                                                               <  1:6795813/93‑1 (MQ=255)
           aaGTCCATTTTTTAAACGTAGGGAGGCCGCCACCCACCAGGATGGAAATAGCGGCTATTGACATTTATAACGTTACGGAAG‑CCGTTTTttctt                                                                              <  2:6232562/93‑1 (MQ=255)
            aGTCCATTTTTTAAACGTAGGGAGGCCGCCACCCACCAGGATGGAAATAGCGGCTATTGACATTTATAACGTTACGGAAG‑CCGTTTTttcttc                                                                             <  1:5079263/93‑1 (MQ=255)
            aGTCCATTTTTTAAACGTAGGGAGGCCGCCACCCACCAGGATGGAAATAGCGGCTATTGACATTTATAACGTTACGGAAG‑CCGTTTTttcttc                                                                             <  1:1055420/93‑1 (MQ=255)
            aGTCCATTTTTTAAACGTAGGGAGGCCGCCACCCACCAGGATGGAAATAGCGGCTATTGACATTTATAACGTTACGGAAG‑CCGTTTTttcttc                                                                             <  2:7414953/93‑1 (MQ=255)
            aGTCCATTTTTTAAACGTAGGGAGGCCGCCACCCACCAGGATGGAAATAGCGGCTATTGACATTTATAACGTTACGGAAG‑CCGTTTTttcttc                                                                             >  1:3967459/1‑93 (MQ=255)
             gTCCATTTTTTAAACGTAGGGAGGCCGCCACCCACCAGGATGGAAATAGCGGCTATTGACATTTATAACGTTACGGAAG‑CCGTTTTTtcttct                                                                            >  2:1570838/1‑93 (MQ=255)
             gTCCATTTTTTAAACGTAGGGAGGCAGACACCCACCAGGATGGAAATAGCGGCTATTGACATTTATAACGTTACGGAAG‑CCGTTTTTtcttct                                                                            <  2:614987/93‑1 (MQ=255)
              tCCATTTTTTAAACGTAGGGAGGCCGCCACCCACCAGGATGGAAATAGCGGCTATTGACATTTATAACGTTACGGAAG‑CCGTTTTTTCTTCTg                                                                           >  1:3319031/1‑93 (MQ=255)
              tCCATTTTTTAAACGTAGGGAGGCCGCCACCCACCAGGATGGAAATAGCGGCTATTGACATTTATAACGTTACGGAAG‑CCGTTTTTTCTTCTg                                                                           <  1:1747435/93‑1 (MQ=255)
              tCCATTTTTTAAACGTAGGGAGGCCGCCACCCACCAGGATGGAAATAGCGGCTATTGACATTTATAACGTTACGGAAG‑CCGTTTTTTCTTCTg                                                                           >  1:151291/1‑93 (MQ=255)
                cATTTTTTAAACGTAGGGAGGCCGCCACCCACCAGGATGGAAATAGCGGCTATTGACATTTATAACGTTACGGAAG‑CCGTTTTTTCTTCTGTc                                                                         >  2:411843/1‑93 (MQ=255)
                cATTTTTTAAACGTAGGGAGGCCGCCACCCACCAGGATGGAAATAGCGGCTATTGACATTTATAACGTTACGGAAG‑CCGTTTTTTCTTCTGTc                                                                         >  1:4399280/1‑93 (MQ=255)
                cATTTTTTAAACGTAGGGAGGCCGCCACCCACCAGGATGGAAATAGCGGCTATTGACATTTATAACGTTACGGAAG‑CCGTTTTTTCTTCTGTc                                                                         >  1:4175622/1‑93 (MQ=255)
                cATTTTTTAAACGTAGGGAGGCCGCCACCCACCAGGATGGAAATAGCGGCTATTGACATTTATAACGTTACGGAAG‑CCGTTTTTTCTTCTGTc                                                                         <  2:2870551/93‑1 (MQ=255)
                 aTTTTTTAAACGTAGGGAGGCCGCCACCCACCAGGATGGAAATAGCGGCTATTGACATTTATAACGTTACGGAAG‑CCGTTTTTTCTTCTGTCg                                                                        >  1:4760162/1‑93 (MQ=255)
                     tttAAACGTAGGGAGGCCGCCACCCACCAGGATGGAAATAGCGGCTATTGACATTTATAACGTTACGGAAG‑CCGTTTTTTCTTCTGTCGCCAt                                                                    >  1:5989166/1‑93 (MQ=255)
                       tAAACGTAGGGAGGCCGCCACCCACCAGGATGGAAATAGCGGCTATTGACATTTATAACGTTACGGAAG‑CCGTTTTTTCTTCTGTCGCCAtct                                                                  <  2:1666226/93‑1 (MQ=255)
                       tAAACGTAGGGAGGCCGCCACCCACCAGGATGGAAATAGCGGCTATTGACATTTATAACGTTACGGAAG‑CCGTTTTTTCTTCTGTCGCCAtct                                                                  <  2:1072781/93‑1 (MQ=255)
                       tAAACGTAGGGAGGCCGCCACCCACCAGGATGGAAATAGCGGCTATTGACATTTATAACGTTACGGAAG‑CCGTTTTTTCTTCTGTCGCCAtct                                                                  >  1:2089727/1‑93 (MQ=255)
                        aaaCGTAGGGAGGCCGCCACCCACCAGGATGGAAATAGCGGCTATTGACATTTATAACGTTACGGAAG‑CCGTTTTTTCTTCTGTCGCCAtctc                                                                 >  1:4256740/1‑93 (MQ=255)
                        aaaCGTAGGGAGGCCGCCACCCACCAGGATGGAAATAGCGGCTATTGACATTTATAACGTTACGGAAG‑CCGTTTTTTCTTCTGTCGCCAtctc                                                                 <  1:2506967/93‑1 (MQ=255)
                        aaaCGTAGGGAGGCCGCCACCCACCAGGATGGAAATAGCGGCTATTGACATTTATAACGTTACGGAAG‑CCGTTTTTTCTTCTGTCGCCAtctc                                                                 <  2:7192777/93‑1 (MQ=255)
                         aaCGTAGGGAGGCCGCCACCCACCAGGATGGAAATAGCGGCTATTGACATTTATAACGTTACGGAAG‑CCGTTTTTTCTTCTGTCGCCATctct                                                                <  1:5310662/93‑1 (MQ=255)
                          aCGTAGGGAGGCCGCCACCCACCAGGATGGAAATAGCGGCTATTGACATTTATAACGTTACGGAAG‑CCGTTTTTTCTTCTGTCGCCATCTCtt                                                               <  2:247266/93‑1 (MQ=255)
                            gTAGGGAGGCCGCCACCCACCAGGATGGAAATAGCGGCTATTGACATTTATAACGTTACGGAAG‑CCGTTTTTTCTTCTGTCGCCATCTCTTTa                                                             <  1:1610529/93‑1 (MQ=255)
                            gTAGGGAGGCCGCCACCCACCAGGATGGAAATAGCGGCTATTGACATTTATAACGTTACGGAAG‑CCGTTTTTTCTTCTGTCGCCATCTCTTTa                                                             <  2:264898/93‑1 (MQ=255)
                             tAGGGAGGCCGCCACCCACCAGGATGGAAATAGCGGCTATTGACATTTATAACGTTACGGAAG‑CCGTTTTTTCTTCTGTCGCCATCTCTTTAt                                                            >  2:5294337/1‑93 (MQ=255)
                             tAGGGAGGCCGCCACCCACCAGGATGGAAATAGCGGCTATTGACATTTATAACGTTACGGAAG‑CCGTTTTTTCTTCTGTCGCCATCTCTTTAt                                                            >  1:5761640/1‑93 (MQ=255)
                             tAGGGAGGCCGCCACCCACCAGGATGGAAATAGCGGCTATTGACATTTATAACGTTACGGAAG‑CCGTTTTTTCTTCTGTCGCCATCTCTTTAt                                                            >  1:61878/1‑93 (MQ=255)
                              aGGGAGGCCGCCACCCACCAGGATGGAAATAGCGGCTATTGACATTTATAACGTTACGGAAG‑CCGTTTTTTCTTCTGTCGCCATCTCTTTAtt                                                           <  2:1028949/93‑1 (MQ=255)
                               gggAGGCCGCCACCCACCAGGATGGAAATAGCGGCTATTGACATTTATAACGTTACGGAAG‑CCGTTTTTTCTTCTGTCGCCATCTCTTTAttt                                                          >  2:5482590/1‑93 (MQ=255)
                                ggAGGCCGCCACCCACCAGGATGGAAATAGCGGCTATTGACATTTATAACGTTACGGAAG‑CCGTTTTTTCTTCTGTCGCCATCTCTTTAtttt                                                         >  2:4406672/1‑93 (MQ=255)
                                ggAGGCCGCCACCCACCAGGATGGAAATAGCGGCTATTGACATTTATAACGTTACGGAAG‑CCGTTTTTTCTTCTGTCGCCATCTCTTTAtttt                                                         >  2:5161148/1‑93 (MQ=255)
                                 gAGGCCGCCACCCACCAGGATGGAAATAGCGGCTATTGACATTTATAACGTTACGGAAG‑CCGTTTTTTCTTCTGTCGCCATCTCTTTAttttt                                                        <  1:7130940/93‑1 (MQ=255)
                                   ggCCGCCACCCACCAGGATGGAAATAGCGGCTATTGACATTTATAACGTTACGGAAG‑CCGTTTTTTCTTCTGTCGCCATCTCTTTATTTTTGc                                                      <  2:6821765/93‑1 (MQ=255)
                                     ccgccACCCACCAGGATGGAAATAGCGGCTATTGACATTTATAACGTTACGGAAG‑CCGTTTTTTCTTCTGTCGCCATCTCTTTATTTTTGCgt                                                    >  1:3365032/1‑93 (MQ=255)
                                     ccgccACCCACCAGGATGGAAATAGCGGCTATTGACATTTATAACGTTACGGAAG‑CCGTTTTTTCTTCTGTCGCCATCTCTTTATTTTTGCgt                                                    <  2:6278551/93‑1 (MQ=255)
                                      cgccACCCACCAGGATGGAAATAGCGGCTATTGACATTTATAACGTTACGGAAG‑CCGTTTTTTCTTCTGTCGCCATCTCTTTATTTTTGCgtt                                                   <  1:2450811/93‑1 (MQ=255)
                                      cgccACCCACCAGGATGGAAATAGCGGCTATTGACATTTATAACGTTACGGAAG‑CCGTTTTTTCTTCTGTCGCCATCTCTTTATTTTTGCgtt                                                   <  2:7336554/93‑1 (MQ=255)
                                       gccACCCACCAGGATGGAAATAGCGGCTATTGACATTTATAACGTTACGGAAG‑CCGTTTTTTCTTCTGTCGCCATCTCTTTATTTTTGCgttg                                                  <  1:6027366/93‑1 (MQ=255)
                                       gccACCCACCAGGATGGAAATAGCGGCTATTGACATTTATAACGTTACGGAAG‑CCGTTTTTTCTTCTGTCGCCATCTCTTTATTTTTGCgttg                                                  <  1:6150061/93‑1 (MQ=255)
                                       gccACCCACCAGGATGGAAATAGCGGCTATTGACATTTATAACGTTACGGAAG‑CCGTTTTTTCTTCTGTCGCCATCTCTTTATTTTTGCgttg                                                  <  2:566600/93‑1 (MQ=255)
                                         cacccaccAGGATGGAAATAGCGGCTATTGACATTTATAACGTTACGGAAG‑CCGTTTTTTCTTCTGTCGCCATCTCTTTATTTTTGCgttggt                                                >  1:6447431/1‑93 (MQ=255)
                                          acccaccAGGATGGAAATAGCGGCTATTGACATTTATAACGTTACGGAAG‑CCGTTTTTTCTTCTGTCGCCATCTCTTTATTTTTGCgttggtt                                               >  2:1216020/1‑93 (MQ=255)
                                             caccaGGATGGAAATAGCGGCTATTGACATTTATAACGTTACGGAAG‑CCGTTTTTTCTTCTGTCGCCATCTCTTTATTTTTGCGTTGGTTGAt                                            >  2:5044245/1‑93 (MQ=255)
                                             caccaGGATGGAAATAGCGGCTATTGACATTTATAACGTTACGGAAG‑CCGTTTTTTCTTCTGTCGCCATCTCTTTATTTTTGCGTTGGTTGAt                                            >  2:4313320/1‑93 (MQ=255)
                                             caccaGGATGGAAATAGCGGCTATTGACATTTATAACGTTACGGAAG‑CCGTTTTTTCTTCTGTCGCCATCTCTTTATTTTTGCGTTGGTTGAt                                            >  1:3473827/1‑93 (MQ=255)
                                               ccaGGATGGAAATAGCGGCTATTGACATTTATAACGTTACGGAAG‑CCGTTTTTTCTTCTGTCGCCATCTCTTTATTTTTGCGTTGGTTGAttt                                          >  1:6364672/1‑93 (MQ=255)
                                               ccaGGATGGAAATAGCGGCTATTGACATTTATAACGTTACGGAAG‑CCGTTTTTTCTTCTGTCGCCATCTCTTTATTTTTGCGTTGGTTGAttt                                          >  1:7019158/1‑93 (MQ=255)
                                               ccaGGATGGAAATAGCGGCTATTGACATTTATAACGTTACGGAAG‑CCGTTTTTTCTTCTGTCGCCATCTCTTTATTTTTGCGTTGGTTGAtct                                          >  2:2007100/1‑91 (MQ=255)
                                                caGGATGGAAATAGCGGCTATTGACATTTATAACGTTACGGAAG‑CCGTTTTTTCTTCTGTCGCCATCTCTTTATTTTTGCGTTGGTTGATTTc                                         >  1:4111634/1‑93 (MQ=255)
                                                      ggAAATAGCGGCTATTGACATTTATAACGTTACGGAAG‑CCGTTTTTTCTTCTGTCGCCATCTCTTTATTTTTGCGTTGGTTGATTTCCTCaat                                   <  2:7512549/93‑1 (MQ=255)
                                                      ggAAATAGCGGCTATTGACATTTATAACGTTACGGAAG‑CCGTTTTTTCTTCTGTCGCCATCTCTTTATTTTTGCGTTGGTTGATCTCCTCaat                                   <  1:1830813/93‑1 (MQ=255)
                                                        aaaTAGCGGCTATTGACATTTATAACGTTACGGAAG‑CCGTTTTTTCTTCTGTCGCCATCTCTTTATTTTTGCGTTGGTTGATTTCCTCaataa                                 <  2:6541792/93‑1 (MQ=255)
                                                          aTAGCGGCTATTGACATTTATAACGTTACGGAAG‑CCGTTTTTTCTTCTGTCGCCATCTCTTTATTTTTGCGTTGGTTGATTTCCTCAATAATc                               <  2:6366584/93‑1 (MQ=255)
                                                          aTAGCGGCTATTGACATTTATAACGTTACGGAAG‑CCGTTTTTTCTTCTGTCGCCATCTCTTTATTTTTGCGTTGGTTGATCTCCTCAATAATc                               >  1:2468361/1‑93 (MQ=255)
                                                            aGCGGCTATTGACATTTATAACGTTACGGAAG‑CCGTTTTTTCTTCTGTCGCCATCTCTTTATTTTTGCGTTGGTTGATTTCCTCAATAATcga                             <  1:3205507/93‑3 (MQ=255)
                                                            aGCGGCTATTGACATTTATAACGTTACGGAAG‑CCGTTTTTTCTTCTGTCGCCATCTCTTTATTTTTGCGTTGGTTGATTTCCTCAATAATCaa                             >  2:6027960/1‑93 (MQ=255)
                                                            aGCGGCTATTGACATTTATAACGTTACGGAAG‑CCGTTTTTTCTTCTGTCGCCATCTCTTTATTTTTGCGTTGGTTGATTTCCTCAATAATCaa                             <  2:6706461/93‑1 (MQ=255)
                                                            aGCGGCTATTGACATTTATAACGTTACGGAAG‑CCGTTTTTTCTTCTGTCGCCATCTCTTTATTTTTGCGTTGGTTGATTTCCTCAATAATCaa                             <  2:3176107/93‑1 (MQ=255)
                                                             gCGGCTATTGACATTTATAACGTTACGGAAG‑CCGTTTTTTCTTCTGTCGCCATCTCTTTATTTTTGCGTTGGTTGATTTCCTCAATAATCAAt                            <  2:5149586/93‑1 (MQ=255)
                                                              cGGCTATTGACATTTATAACGTTACGGAAG‑CCGTTTTTTCTTCTGTCGCCATCTCTTTATTTTTGCGTTGGTTGATTTCCTCAATAATCAATg                           <  2:338597/93‑1 (MQ=255)
                                                              cGGCTATTGACATTTATAACGTTACGGAAG‑CCGTTTTTTCTTCTGTCGCCATCTCTTTATTTTTGCGTTGGTTGATCTCCTCAATAATCAATg                           <  2:6623585/93‑1 (MQ=255)
                                                               ggCTATTGACATTTATAACGTTACGGAAG‑CCGTTTTTTCTTCTGTCGCCATCTCTTTATTTTTGCGTTGGTTGATTTCCTCAATAATCAATGc                          <  2:6937880/93‑1 (MQ=255)
                                                                gCTATTGACATTTATAACGTTACGGAAG‑CCGTTTTTTCTTCTGTCGCCATCTCTTTATTTTTGCGTTGGTTGATTTCCTCAATAATCAATGCa                         >  2:4535176/1‑93 (MQ=255)
                                                                 cTATTGACATTTATAACGTTACGGAAG‑CCGTTTTTTCTTCTGTCGCCATCTCTTTATTTTTGCGTTGGTTGATTTCCTCAATAATCAATGCaa                        >  1:3901778/1‑93 (MQ=255)
                                                                   aTTGACATTTATAACGTTACGGAAG‑CCGTTTTTTCTTCTGTCGCCATCTCTTTATTTTTGCGTTGGTTGATTTCCTCAATAATCAATGCAAAc                      >  2:3915285/1‑93 (MQ=255)
                                                                   aTTGACATTTATAACGTTACGGAAG‑CCGTTTTTTCTTCTGTCGCCATCTCTTTATTTTTGCGTTGGTTGATTTCCTCAATAATCAATGCAAAc                      >  1:125657/1‑93 (MQ=255)
                                                                   aTTGACATTTATAACGTTACGGAAG‑CCGTTTTTTCTTCTGTCGCCATCTCTTTATTTTTGCGTTGGTTGATTTCCTCAATAATCAATGCAAAc                      >  1:7403964/1‑93 (MQ=255)
                                                                   aTTGACATTTATAACGTTACGGAAG‑CCGTTTTTTCTTCTGTCGCCATCTCTTTATTTTTGCGTTGGTTGATTTCCTCAATAATCAATGCAAAc                      <  1:750354/93‑1 (MQ=255)
                                                                   aTTGACATTTATAACGTTACGGAAG‑CCGTTTTTTCTTCTGTCGCCATCTCTTTATTTTTGCGTTGGTTGATTTCCTCAATAATCAATGCAAAc                      >  2:710742/1‑93 (MQ=255)
                                                                   aTTGACATTTATAACGTTACGGAAG‑CCGTTTTTTCTTCTGTCGCCATCTCTTTATTTTTGCGTTGGTTGATTTCCTCAATAATCAATGCAAAc                      <  1:300320/93‑1 (MQ=255)
                                                                   aTTGACATTTATAACGTTACGGAAG‑CCGTTTTTTCTTCTGTCGCCATCTCTTTATTTTTGCGTTGGTTGATTTCCTCAATAATCAATGCAAAc                      <  2:1472633/93‑1 (MQ=255)
                                                                    ttGACATTTATAACGTTACGGAAG‑CCGTTTTTTCTTCTGTCGCCATCTCTTTATTTTTGCGTTGGTTGATTTCCTCAATAATCAATGCAAAcc                     >  2:1779477/1‑93 (MQ=255)
                                                                    ttGACATTTATAACGTTACGGAAG‑CCGTTTTTTCTTCTGTCGCCATCTCTTTATTTTTGCGTTGGTTGATTTCCTCAATAATCAATGCAAAcc                     <  2:369101/93‑1 (MQ=255)
                                                                       aCATTTATAACGTTACGGAAG‑CCGTTTTTTCTTCTGTCGCCATCTCTTTATTTTTGCGTTGGTTGATTTCCTCAATAATCAATGCAAACCGtt                  <  1:4885474/93‑1 (MQ=255)
                                                                         aTTTATAACGTTACGGAAG‑CCGTTTTTTCTTCTGTCGCCATCTCTTTATTTTTGCGTTGGTTGATTTCCTCAATAATCAATGCAAACCGtttt                >  2:6481675/1‑93 (MQ=255)
                                                                         aTTTATAACGTTACGGAAG‑CCGTTTTTTCTTCTGTCGCCATCTCTTTATTTTTGCGTTGGTTGATCTCCTCAATAATCAATGCAAACCGtttt                >  2:2727985/1‑93 (MQ=255)
                                                                            tataACGTTACGGAAG‑CCGTTTTTTCTTCTGTCGCCATCTCTTTATTTTTGCGTTGGTTGATTTCCTCAATAATCAATGCAAACCGTTTTTCa             <  1:3592067/93‑1 (MQ=255)
                                                                             ataACGTTACGGAAG‑CCGTTTTTTCTTCTGTCGCCATCTCTTTATTTTTGCGTTGGTTGATCTCCTCAATAATCAATGCAAACCGTTTTTCAt            >  2:6508426/1‑93 (MQ=255)
                                                                                aCGTTACGGAAG‑CCGTTTTTTCTTCTGTCGCCATCTCTTTATTTTTGCGTTGGTTGATTTCCTCAATAATCAATGCAAACCGTTTTTCATTGa         <  2:5740376/93‑1 (MQ=255)
                                                                                   ttACGGAAG‑CCGTTTTTTCTTCTGTCGCCATCTCTTTATTTTTGCGTTGGTTGATTTCCTCAATAATCAATGCAAACCGTTTTTCATTGAgtg      >  1:2294518/1‑93 (MQ=255)
                                                                                   ttACGGAAG‑CCGTTTTTTCTTCTGTCGCCATCTCTTTATTTTTGCGTTGGTTGATTTCCTCAATAATCAATGCAAACCGTTTTTCATTGAgtg      >  2:593464/1‑93 (MQ=255)
                                                                                    tACGGAAG‑CCGTTTTTTCTTCTGTCGCCATCTCTTTATTTTTGCGTTGGTTGATTTCCTCAATAATCAATGCAAACCGTTTTTCATTGAgtgt     <  1:2858513/93‑1 (MQ=255)
                                                                                    tACGGAAG‑CCGTTTTTTCTTCTGTCGCCATCTCTTTATTTTTGCGTTGGTTGATTTCCTCAATAATCAATGCAAACCGTTTTTCATTGAgtgt     <  1:5403883/93‑1 (MQ=255)
                                                                                     aCGGAAG‑CCGTTTTTTCTTCTGTCGCCATCTCTTTATTTTTGCGTTGGTTGATTTCCTCAATAATCAATGCAAACCGTTTTTCATTGAgtgtg    >  1:273129/1‑93 (MQ=255)
                                                                                     aCGGAAG‑CCGTTTTTTCTTCTGTCGCCATCTCTTTATTTTTGCGTTGGTTGATTTCCTCAATAATCAATGCAAACCGTTTTTCATTGAgtgtg    <  1:955178/93‑1 (MQ=255)
                                                                                      cGGAAG‑CCGTTTTTTCTTCTGTCGCCATCTCTTTATTTTTGCGTTGGTTGATTTCCTCAATAATCAATGCAAACCGTTTTTCATTGAgtgtgt   <  1:2649978/93‑1 (MQ=255)
                                                                                       ggAAG‑CCGTTTTTTCTTCTGTCGCCATCTCTTTATTTTTGCGTTGGTTGATTTCCTCAATAATCAATGCAAACCGTTTTTCATTGAGTGTGTa  >  2:3058598/1‑93 (MQ=255)
                                                                                            |                                                                                        
TTTTTCATAATAAGTCCATTTTTTAAACGTAGGGAGGCCGCCACCCACCAGGATGGAAATAGCGGCTATTGACATTTATAACGTTACGGAAGCCCGTTTTTTCTTCTGTCGCCATCTCTTTATTTTTGCGTTGGTTGATTTCCTCAATAATCAATGCAAACCGTTTTTCATTGAGTGTGTA  >  NC_000913/4061867‑4062047

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

BRESEQ :: bam2aln output
TTTTCATAATAAGTCCATTTTTTAAACGTAGGGAGGCCGCCACCCACCAGGATGGAAATAGCGGCTATTGACATTTATAACGTTACGGAAGCCCGTTTTTTCTTCTGTCGCCATCTCTTTATTTTTGCGTTGGTTGATTTCCTCAATAATCAATGCAAACCGTTTTTCATTGAGTGTGTAAAAGAA  >  NC_000913/4061868‑4062053
                                                                                             |                                                                                            
TTTTCATAATAAGTCCATTTTTTAAACGTAGGGAGGCCGCCACCCACCAGGATGGAAATAGCGGCTATTGACATTTATAACGTTACGGAAGCCG                                                                                              <  SRR4302542.399599/94‑1 (MQ=60)
  TTCATAATAAGTCCATTTTTTAAACGTAGGGAGGCCGCCACCCACCAGGATGGAAATAGGGGCTATTGACATTTATAACGTTACGGAAG‑CCGTT                                                                                           >  SRR4302542.894486/1‑94 (MQ=60)
  TTCATAATAAGTCCATTTTTTAAACGTAGGGAGGCCGCCACCCACCAGGATGGAAATAGCGGCTATTGACATTTATAACGTTACGGAAG‑CCGTT                                                                                           <  SRR4302542.2918504/94‑1 (MQ=60)
  TTCATAATAAGTCCATTTTTTAAACGTAGGGAGGCCGCCACCCACCAGGATGGAAATAGCGGCTATTGACATTTATAACGTTACGGAAG‑CCGTT                                                                                           >  SRR4302542.7142056/1‑94 (MQ=60)
   TCATAATAAGTCCATTTTTTAAACGTAGGGAGGCCGCCACCCACCAGGATGGAAATAGCGGCTATTGACATTTATAACGTTACGGAAG‑CCGTTT                                                                                          <  SRR4302542.4023410/94‑1 (MQ=60)
    CATAATAAGTCCATTTTTTAAACGTAGGGAGGCCGCCACCCACCAGGATGGAAATAGCGGCTATTGACATTTATAACGTTACGGAAGCCCTTTT                                                                                          >  SRR4302542.1404776/1‑94 (MQ=60)
    CATAATAAGTCCATTTTTTAAACGTAGGGAGGCCGCCACCCACCAGGATGGAAATAGCGGCTATTGACATTTATAACGTTACGGAAG‑CCGTTTT                                                                                         >  SRR4302542.6083497/1‑94 (MQ=60)
     ATAATAAGTCCATTTTTTAAACGTAGGGAGGCCGCCACCCACCAGGATGGAAATAGCGGCTATTGACATTTATAACGTTACGGAAG‑CCGTTTTT                                                                                        >  SRR4302542.2693262/1‑94 (MQ=60)
     ATAATAAGTCCATTTTTTAAACGTAGGGAGGCCGCCACCCACCAGGATGGAAATAGCGGCTATTGACATTTATAACGTTACGGAAG‑CCGTTTTT                                                                                        >  SRR4302542.510628/1‑94 (MQ=60)
     ATAATAAGTCCATTTTTTAAACGTAGGGAGGCCGCCACCCACCAGGATGGAAATAGCGGCTATTGACATTTATAACGTTACGGAAG‑CCGTTTTT                                                                                        >  SRR4302542.423655/1‑94 (MQ=60)
     ATAATAAGTCCATTTTTTAAACGTAGGGAGGCCGCCACCCACCAGGATGGAAATAGCGGCTATTGACATTTATAACGTTACGGAAG‑CCGTTTTT                                                                                        >  SRR4302542.3907809/1‑94 (MQ=60)
      TAATAAGTCCATTTTTTAAACGTAGGGAGGCCGCCACCCACCAGGATGGAAATAGCGGCTATTGACATTTATAACGTTACGGAAG‑CCGTTTTTT                                                                                       <  SRR4302542.5614155/94‑1 (MQ=60)
       AATAAGTCCATTTTTTAAACGTAGGGAGGCCGCCACCCACCAGGATGGAAATAGCGGCTATTGACATTTATAACGTTACGGAAG‑CCGTTTTTTC                                                                                      <  SRR4302542.6706310/94‑1 (MQ=60)
       AATAAGTCCATTTTTTAAACGTAGGGAGGCCGCCACCCACCAGGATGGAAATAGCGGCTATTGACATTTATAACGTTACGGAAG‑CCGTTTTTTC                                                                                      >  SRR4302542.1926019/1‑94 (MQ=60)
       AATAAGTCCATTTTTTAAACGTAGGGAGGCCGCCACCCACCAGGATGGAAATAGCGGCTATTGACATTTATAACGTTACGGAAG‑CCGTTTTTTC                                                                                      >  SRR4302542.2033676/1‑94 (MQ=60)
        ATAAGTCCATTTTTTAAACGTAGGGAGGCCGCCACCCACCAGGATGGAAATAGCGGCTATTGACATTTATAACGTTACGGAAG‑CCGTTTTTTCT                                                                                     >  SRR4302542.6737879/1‑94 (MQ=60)
        ATAAGTCCATTTTTTAAACGTAGGGAGGCCGCCACCCACCAGGATGGAAATAGCGGCTATTGACATTTATAACGTTACGGAAG‑CCGTTTTTTCT                                                                                     <  SRR4302542.5043053/94‑1 (MQ=60)
         TAAGTCCATTTTTTAAACGTAGGGAGGCCGCCACCCACCAGGATGGAAATAGCGGCTATTGACATTTATAACGTTACGGAAG‑CCGTTTTTTCTT                                                                                    <  SRR4302542.6862637/94‑1 (MQ=60)
         TAAGTCCATTTTTTAAACGTAGGGAGGCCGCCACCCACCAGGATGGAAATAGCGGCTATTGACATTTATAACGTTACGGAAG‑CCGTTTTTTCTT                                                                                    >  SRR4302542.5418664/1‑94 (MQ=60)
          AAGTCCATTTTTTAAACGTAGGGAGGCCGCCACCCACCAGGATGGAAATAGCGGCTATTGACATTTATAACGTTACGGAAG‑CCGTTTTTTCTTC                                                                                   >  SRR4302542.4003030/1‑94 (MQ=60)
          AAGTCCATTTTTTAAACGTAGGGAGGCCGCCACCCACCAGGATGGAAATAGCGGCTATTGACATTTATAACGTTACGGAAG‑CCGTTTTTTCTTC                                                                                   >  SRR4302542.4006625/1‑94 (MQ=60)
           AGTCCATTTTTTAAACGTAGGGAGGCCGCCACCCACCAGGATGGAAATAGCGGCTATTGACATTTATAACGTTACGGAAG‑CCGTTTTTTCTTCT                                                                                  >  SRR4302542.2847450/1‑94 (MQ=60)
           AGTCCATTTTTTAAACGTAGGGAGGCCGCCACCCACCAGGATGGAAATAGCGGCTATTGACATTTATAACGTTACGGAAG‑CCGTTTTTTCTTCT                                                                                  <  SRR4302542.1064491/94‑1 (MQ=60)
           AGTCCATTTTTTAAACGTAGGGAGGCCGCCACCCACCAGGATGGAAATAGCGGCTATTGACATTTATAACGTTACGGAAG‑CCGTTTTTTCTTCT                                                                                  <  SRR4302542.5128627/94‑1 (MQ=60)
            GTCCATTTTTTAAACGTAGGGAGGCCGCCACCCACCAGGATGGAAATAGCGGCTATTGACATTTATAACGTTACGGAAG‑CCGTTTTTTCTTCTG                                                                                 >  SRR4302542.2269508/1‑94 (MQ=60)
            GTCCATTTTTTAAACGTAGGGAGGCCGCCACCCACCAGGATGGAAATAGCGGCTATTGACATTTATAACGTTACGGAAG‑CCGTTTTTTCTTCTG                                                                                 >  SRR4302542.3350296/1‑94 (MQ=60)
            GTCCATTTTTTAAACGTAGGGAGGCCGCCACCCACCAGGATGGAAATAGCGGCTATTGACATTTATAACGTTACGGAAG‑CCGTTTTTTCTTCTG                                                                                 >  SRR4302542.152576/1‑94 (MQ=60)
            GTCCATTTTTTAAACGTAGGGAGGCCGCCACCCACCAGGATGGAAATAGCGGCTATTGACATTTATAACGTTACGGAAG‑CCGTTTTTTCTTCTG                                                                                 >  SRR4302542.7006155/1‑94 (MQ=60)
            GTCCATTTTTTAAACGTAGGGAGGCCGCCACCCACCAGGATGGAAATAGCGGCTATTGACATTTATAACGTTACGGAAG‑CCGTTTTTTCTTCTG                                                                                 >  SRR4302542.5977502/1‑94 (MQ=60)
             TCCATTTTTTAAACGTAGGGAGGCCGCCACCCACCAGGATGGAAATAGCGGCTATTGACATTTATAACGTTACGGAAG‑CCGTTTTTTCTTCTGT                                                                                <  SRR4302542.1762597/94‑1 (MQ=60)
             TCCATTTTTTAAACGTAGGGAGGCCGCCACCCACCAGGATGGAAATAGCGGCTATTGACATTTATAACGTTACGGAAG‑CCGTTTTTTCTTCTGT                                                                                >  SRR4302542.3285268/1‑94 (MQ=60)
             TCCATTTTTTAAACGTAGGGAGGCCGCCACCCACCAGGATGGAAATAGCGGCTATTGACATTTATAACGTTACGGAAG‑CCGTTTTTTCTTCTGT                                                                                >  SRR4302542.5016909/1‑94 (MQ=60)
              CCATTTTTTAAACGTAGGGAGGCCGCCACCCACCAGGATGGAAATAGCGGCTATTGACATTTATAACGTTACGGAAG‑CCGTTTTTTCTTCTGTC                                                                               >  SRR4302542.4216802/1‑94 (MQ=60)
              CCATTTTTTAAACGTAGGGAGGCCGCCACCCACCAGGATGGAAATAGCGGCTATTGACATTTATAACGTTACGGAAG‑CCGTTTTTTCTTCTGTC                                                                               >  SRR4302542.4442478/1‑94 (MQ=60)
               CATTTTTTAAACGTAGGGAGGCCGCCACCCACCAGGATGGAAATAGCGGCTATTGACATTTATAACGTTACGGAAG‑CCGTTTTTTCTTCTGTCG                                                                              >  SRR4302542.4806577/1‑94 (MQ=60)
                ATTTTTTAAACGTAGGGAGGCCGCCACCCACCAGGATGGAAATAGCGGCTATTGACATTTATAACGTTACGGAAG‑CCGTTTTTTCTTCTGTCGC                                                                             >  SRR4302542.6478067/1‑94 (MQ=60)
                ATTTTTTAAACGTAGGGAGGCCGCCACCCACCAGGATGGAAATAGCGGCTATTGACATTTATAACGTTACGGAAG‑CCGTTTTTTCTTCTGTCGC                                                                             >  SRR4302542.5625937/1‑94 (MQ=60)
                ATTTTTTAAACGTAGGGAGGCCGCCACCCACCAGGATGGAAATAGCGGCTATTGACATTTATAACGTTACGGAAG‑CCGTTTTTTCTTCTGTCGC                                                                             >  SRR4302542.7586395/1‑94 (MQ=60)
                ATTTTTTAAACGTAGGGAGGCCGCCACCCACCAGGATGGAAATAGCGGCTATTGACATTTATAACGTTACGGAAG‑CCGTTTTTTCTTCTGTCGC                                                                             >  SRR4302542.992543/1‑94 (MQ=60)
                   TTTTAAACGTAGGGAGGCCGCCACCCACCAGGATGGAAATAGCGGCTATTGACATTTATAACGTTACGGAAG‑CCGTTTTTTCTTCTGTCGCCAT                                                                          >  SRR4302542.6047182/1‑94 (MQ=60)
                    TTTAAACGTAGGGAGGCCGCCACCCACCAGGATGGAAATAGCGGCTATTGACATTTATAACGTTACGGAAG‑CCGTTTTTTCTTCTGTCGCCATC                                                                         >  SRR4302542.5178245/1‑94 (MQ=60)
                     TTAAACGTAGGGAGGCCGCCACCCACCAGGATGGAAATAGCGGCTATTGACATTTATAACGTTACGGAAG‑CCGTTTTTTCTTCTGTCGCCATCT                                                                        >  SRR4302542.2107764/1‑94 (MQ=60)
                      TAAACGTAGGGAGGCCGCCACCCACCAGGATGGAAATAGCGGCTATTGACATTTATAACGTTACGGAAG‑CCGTTTTTTCTTCTGTCGCCATCTC                                                                       >  SRR4302542.4298663/1‑94 (MQ=60)
                       AAACGTAGGGAGGCCGCCACCCACCAGGATGGAAATAGCGGCTATTGACATTTATAACGTTACGGAAG‑CCGTTTTTTCTTCTGTCGCCATCTCT                                                                      <  SRR4302542.2531301/94‑1 (MQ=60)
                        AACGTAGGGAGGCCGCCACCCACCAGGATGGAAATAGCGGCTATTGACATTTATAACGTTACGGAAG‑CCGTTTTTTCTTCTGTCGCCATCTCTT                                                                     >  SRR4302542.3289355/1‑94 (MQ=60)
                        AACGTAGGGAGGCCGCCACCCACCAGGATGGAAATAGCGGCTATTGACATTTATAACGTTACGGAAG‑CCGTTTTTTCTTCTGTCGCCATCTCTT                                                                     <  SRR4302542.5362256/94‑1 (MQ=60)
                         ACGTAGGGAGGCCGCCACCCACCAGGATGGAAATAGCGGCTATTGACATTTATAACGTTACGGAAG‑CCGTTTTTTCTTCTGTCGCCATCTCTTT                                                                    <  SRR4302542.873155/94‑1 (MQ=60)
                          CGTAGGGAGGCCGCCACCCACCAGGATGGAAATAGCGGCTATTGACATTTATAACGTTACGGAAG‑CCGTTTTTTCTTCTGTCGCCATCTCTTTA                                                                   <  SRR4302542.4110296/94‑1 (MQ=60)
                           GTAGGGAGGCCGCCACCCACCAGGATGGAAATAGCGGCTATTGACATTTATAACGTTACGGAAG‑CCGTTTTTTCTTCTGTCGCCATCTCTTTAT                                                                  >  SRR4302542.5817567/1‑94 (MQ=60)
                           GTAGGGAGGCCGCCACCCACCAGGATGGAAATAGCGGCTATTGACATTTATAACGTTACGGAAG‑CCGTTTTTTCTTCTGTCGCCATCTCTTTAT                                                                  <  SRR4302542.1624437/94‑1 (MQ=60)
                           GTAGGGAGGCCGCCACCCACCAGGATGGAAATAGCGGCTATTGACATTTATAACGTTACGGAAG‑CCGTTTTTTCTTCTGTCGCCATCTCTTTAT                                                                  >  SRR4302542.62378/1‑94 (MQ=60)
                           GTAGGGAGGCCGCCACCCACCAGGATGGAAATAGCGGCTATTGACATTTATAACGTTACGGAAG‑CCGTTTTTTCTTCTGTCGCCATCTCTTTAT                                                                  >  SRR4302542.4268263/1‑94 (MQ=60)
                             AGGGAGGCCGCCACCCACCAGGATGGAAATAGCGGCTATTGACATTTATAACGTTACGGAAG‑CCGTTTTTTCTTCTGTCGCCATCTCTTTATTT                                                                <  SRR4302542.16477/94‑1 (MQ=60)
                             AGGGAGGCCGCCACCCACCAGGATGGAAATAGCGGCTATTGACATTTATAACGTTACGGAAG‑CCGTTTTTTCTTCTGTCGCCATCTCTTTATTT                                                                >  SRR4302542.750677/1‑94 (MQ=60)
                             AGGGAGGCCGCCACCCACCAGGATGGAAATAGCGGCTATTGACATTTATAACGTTACGGAAG‑CCGTTTTTTCTTCTGTCGCCATCTCTTTATTT                                                                <  SRR4302542.5564029/94‑1 (MQ=60)
                              GGGAGGCCGCCACCCACCAGGATGGAAATAGCGGCTATTGACATTTATAACGTTACGGAAG‑CCGTTTTTTCTTCTGTCGCCATCTCTTTATTTT                                                               >  SRR4302542.7333612/1‑94 (MQ=60)
                               GGAGGCCGCCACCCACCAGGATGGAAATAGCGGCTATTGACATTTATAACGTTACGGAAG‑CCGTTTTTTCTTCTGTCGCCATCTCTTTATTTTT                                                              >  SRR4302542.6208974/1‑94 (MQ=60)
                               GGAGGCCGCCACCCACCAGGATGGAAATAGCGGCTATTGACATTTATAACGTTACGGAAG‑CCGTTTTTTCTTCTGTCGCCATCTCTTTATTTTT                                                              <  SRR4302542.682892/94‑1 (MQ=60)
                               GGAGGCCGCCACCCACCAGGATGGAAATAGCGGCTATTGACATTTATAACGTTACGGAAG‑CCGTTTTTTCTTCTGTCGCCATCTCTTTATTTTT                                                              <  SRR4302542.5810756/94‑1 (MQ=60)
                               GGAGGCCGCCACCCACCAGGATGGAAATAGCGGCTATTGACATTTATAACGTTACGGAAG‑CCGTTTTTTCTTCTGTCGCCATCTCTTTATTTTT                                                              <  SRR4302542.2339998/94‑1 (MQ=60)
                                GAGGCCGCCACCCACCAGGATGGAAATAGCGGCTATTGACATTTATAACGTTACGGAAG‑CCGTTTTTTCTTCTGTCGCCATCTCTTTATTTTTG                                                             <  SRR4302542.7200923/94‑1 (MQ=60)
                                GAGGCCGCCACCCACCAGGATGGAAATAGCGGCTATTGACATTTATAACGTTACGGAAG‑CCGTTTTTTCTTCTGTCGCCATCTCTTTATTTTTG                                                             <  SRR4302542.3584055/94‑1 (MQ=60)
                                  GGCCGCCACCCACCAGGATGGAAATAGCGGCTATTGACATTTATAACGTTACGGAAG‑CCGTTTTTTCTTCTGTCGCCATCTCTTTATTTTTGCG                                                           <  SRR4302542.6506341/94‑1 (MQ=60)
                                  GGCCGCCACCCACCAGGATGGAAATAGCGGCTATTGACATTTATAACGTTACGGAAG‑CCGTTTTTTCTTCTGTCGCCATCTCTTTATTTTTGCG                                                           <  SRR4302542.6649600/94‑1 (MQ=60)
                                   GCCGCCACCCACCAGGATGGAAATAGCGGCTATTGACATTTATAACGTTACGGAAG‑CCGTTTTTTCTTCTGTCGCCATCTCTTTATTTTTGCGT                                                          >  SRR4302542.3396637/1‑94 (MQ=60)
                                     CGCCACCCACCAGGATGGAAATAGCGGCTATTGACATTTATAACGTTACGGAAG‑CCGTTTTTTCTTCTGTCGCCATCTCTTTATTTTTGCGTTG                                                        >  SRR4302542.1603964/1‑94 (MQ=60)
                                     CGCCACCCACCAGGATGGAAATAGCGGCTATTGACATTTATAACGTTACGGAAG‑CCGTTTTTTCTTCTGTCGCCATCTCTTTATTTTTGCGTTG                                                        >  SRR4302542.5022086/1‑94 (MQ=60)
                                     CGCCACCCACCAGGATGGAAATAGCGGCTATTGACATTTATAACGTTACGGAAG‑CCGTTTTTTCTTCTGTCGCCATCTCTTTATTTTTGCGTTG                                                        <  SRR4302542.2474648/94‑1 (MQ=60)
                                     CGCCACCCACCAGGATGGAAATAGCGGCTATTGACATTTATAACGTTACGGAAG‑CCGTTTTTTCTTCTGTCGCCATCTCTTTATTTTTGCGTTG                                                        <  SRR4302542.3206115/94‑1 (MQ=60)
                                      GCCACCCACCAGGATGGAAATAGCGGCTATTGACATTTATAACGTTACGGAAG‑CCGTTTTTTCTTCTGTCGCCATCTCTTTATTTTTGCGTTGG                                                       <  SRR4302542.4614331/94‑1 (MQ=60)
                                      GCCACCCACCAGGATGGAAATAGCGGCTATTGACATTTATAACGTTACGGAAG‑CCGTTTTTTCTTCTGTCGCCATCTCTTTATTTTTGCGTTGG                                                       <  SRR4302542.6209566/94‑1 (MQ=60)
                                      GCCACCCACCAGGATGGAAATAGCGGCTATTGACATTTATAACGTTACGGAAG‑CCGTTTTTTCTTCTGTCGCCATCTCTTTATTTTTGCGTTGG                                                       <  SRR4302542.6277181/94‑1 (MQ=60)
                                      GCCACCCACCAGGATGGAAATAGCGGCTATTGACATTTATAACGTTACGGAAG‑CCGTTTTTTCTTCTGTCGCCATCTCTTTATTTTTGCGTTGG                                                       <  SRR4302542.6085732/94‑1 (MQ=60)
                                       CCACCCACCAGGATGGAAATAGCGGCTATTGACATTTATAACGTTACGGAAG‑CCGTTTTTTCTTCTGTCGCCATCTCTTTATTTTTGCGTTGGT                                                      >  SRR4302542.5901434/1‑94 (MQ=60)
                                       CCACCCACCAGGATGGAAATAGCGGCTATTGACATTTATAACGTTACGGAAG‑CCGTTTTTTCTTCTGTCGCCATCTCTTTATTTTTGCGTTGGT                                                      <  SRR4302542.4158840/94‑1 (MQ=60)
                                       CCACCCACCAGGATGGAAATAGCGGCTATTGACATTTATAACGTTACGGAAG‑CCGTTTTTTCTTCTGTCGCCATCTCTTTATTTTTGCGTTGGT                                                      >  SRR4302542.6510929/1‑94 (MQ=60)
                                           CCACCAGGATGGAAATAGCGGCTATTGACATTTATAACGTTACGGAAG‑CCGTTTTTTCTTCTGTCGCCATCTCTTTATTTTTGCGTTGGTTGAT                                                  >  SRR4302542.3506346/1‑94 (MQ=60)
                                            CACCAGGATGGAAATAGCGGCTATTGACATTTATAACGTTACGGAAG‑CCGTTTTTTCTTCTGTCGCCATCTCTTTATTTTTGCGTTGGTTGATT                                                 >  SRR4302542.7003978/1‑94 (MQ=60)
                                             ACCAGGATGGAAATAGCGGCTATTGACATTTATAACGTTACGGAAG‑CCGTTTTTTCTTCTGTCGCCATCTCTTTATTTTTGCGTTGGTTGATTT                                                >  SRR4302542.7088134/1‑94 (MQ=60)
                                             ACCAGGATGGAAATAGCGGCTATTGACATTTATAACGTTACGGAAG‑CCGTTTTTTCTTCTGTCGCCATCTCTTTATTTTTGCGTTGGTTGATTT                                                >  SRR4302542.2037675/1‑94 (MQ=60)
                                             ACCAGGATGGAAATAGCGGCTATTGACATTTATAACGTTACGGAAG‑CCGTTTTTTCTTCTGTCGCCATCTCTTTATTTTTGCGTTGGTTGATTT                                                >  SRR4302542.6427349/1‑94 (MQ=60)
                                             ACCAGGATGGAAATAGCGGCTATTGACATTTATAACGTTACGGAAG‑CCGTTTTTTCTTCTGTCGCCATCTCTTTATTTTTGCGTTGGTTGATTT                                                <  SRR4302542.2036901/94‑1 (MQ=60)
                                              CCAGGATGGAAATAGCGGCTATTGACATTTATAACGTTACGGAAG‑CCGTTTTTTCTTCTGTCGCCATCTCTTTATTTTTGCGTTGGTTGATTTC                                               >  SRR4302542.4152160/1‑94 (MQ=60)
                                              CCAGGATGGAAATAGCGGCTATTGACATTTATAACGTTACGGAAG‑CCGTTTTTTCTTCTGTCGCCATCTCTTTATTTTTGCGTTGGTTGATCTC                                               >  SRR4302542.6232788/1‑94 (MQ=60)
                                                AGGATGGAAATAGCGGCTATTGACATTTATAACGTTACGGAAG‑CCGTTTTTTCTTCTGTCGCCATCTCTTTATTTTTGCGTTGGTTGATTTCCT                                             >  SRR4302542.2693618/1‑94 (MQ=60)
                                                AGGATGGAAATAGCGGCTATTGACATTTATAACGTTACGGAAG‑CCGTTTTTTCTTCTGTCGCCATCTCTTTATTTTTGCGTTGGTTGATTTCCT                                             >  SRR4302542.5609157/1‑94 (MQ=60)
                                                 GGATGGAAATAGCGGCTATTGACATTTATAACGTTACGGAAG‑CCGTTTTTTCTTCTGTCGCCATCTCTTTATTTTTGCGTTGGTTGATTTCCTC                                            >  SRR4302542.2319370/1‑94 (MQ=60)
                                                 GGATGGAAATAGCGGCTATTGACATTTATAACGTTACGGAAG‑CCGTTTTTTCTTCTGTCGCCATCTCTTTATTTTTGCGTTGGTTGATTTCCTC                                            >  SRR4302542.7111806/1‑94 (MQ=60)
                                                    TGGAAATAGCGGCTATTGACATTTATAACGTTACGGAAG‑CCGTTTTTTCTTCTGTCGCCATCTCTTTATTTTTGCGTTGGTTGATTTCCTCAAT                                         <  SRR4302542.3577463/94‑1 (MQ=60)
                                                     GGAAATAGCGGCTATTGACATTTATAACGTTACGGAAG‑CCGTTTTTTCTTCTGTCGCCATCTCTTTATTTTTGCGTTGGTTGATTTCCTCAATA                                        <  SRR4302542.2640362/94‑1 (MQ=60)
                                                     GGAAATAGCGGCTATTGACATTTATAACGTTACGGAAG‑CCGTTTTTTCTTCTGTCGCCATCTCTTTATTTTTGCGTTGGTTGATCTCCTCAATA                                        <  SRR4302542.1846671/94‑1 (MQ=60)
                                                        AATAGCGGCTATTGACATTTATAACGTTACGGAAG‑CCGTTTTTTCTTCTGTCGCCATCTCTTTATTTTTGCGTTGGTTGATTTCCTCAATAATC                                     >  SRR4302542.897944/1‑94 (MQ=60)
                                                        AATAGCGGCTATTGACATTTATAACGTTACGGAAG‑CCGTTTTTTCTTCTGTCGCCATCTCTTTATTTTTGCGTTGGTTGATCTCCTCAATAATC                                     >  SRR4302542.2492322/1‑94 (MQ=60)
                                                         ATAGCGGCTATTGACATTTATAACGTTACGGAAG‑CCGTTTTTTCTTCTGTCGCCATCTCTTTATTTTTGCGTTGGTTGATTTCCTCAATAATCA                                    <  SRR4302542.5450467/94‑1 (MQ=60)
                                                           AGCGGCTATTGACATTTATAACGTTACGGAAG‑CCGTTTTTTCTTCTGTCGCCATCTCTTTATTTTTGCGTTGGTTGATTTCCTCAATAATCGAT                                  <  SRR4302542.3235875/94‑1 (MQ=60)
                                                           AGCGGCTATTGACATTTATAACGTTACGGAAG‑CCGTTTTTTCTTCTGTCGCCATCTCTTTATTTTTGCGTTGGTTGATTTCCTCAATAATCAAT                                  >  SRR4302542.462976/1‑94 (MQ=60)
                                                             CGGCTATTGACATTTATAACGTTACGGAAG‑CCGTTTTTTCTTCTGTCGCCATCTCTTTATTTTTGCGTTGGTTGATTTCCTCAATAATCAATGC                                <  SRR4302542.489337/94‑1 (MQ=60)
                                                             CGGCTATTGACATTTATAACGTTACGGAAG‑CCGTTTTTTCTTCTGTCGCCATCTCTTTATTTTTGCGTTGGTTGATTTCCTCAATAATCAATGC                                <  SRR4302542.2233563/94‑1 (MQ=60)
                                                             CGGCTATTGACATTTATAACGTTACGGAAG‑CCGTTTTTTCTTCTGTCGCCATCTCTTTATTTTTGCGTTGGTTGATTTCCTCAATAATCAATGC                                >  SRR4302542.4424118/1‑94 (MQ=60)
                                                              GGCTATTGACATTTATAACGTTACGGAAG‑CCGTTTTTTCTTCTGTCGCCATCTCTTTATTTTTGCGTTGGTTGATTTCCTCAATAATCAATGCA                               <  SRR4302542.4831679/94‑1 (MQ=60)
                                                              GGCTATTGACATTTATAACGTTACGGAAG‑CCGTTTTTTCTTCTGTCGCCATCTCTTTATTTTTGCGTTGGTTGATTTCCTCAATAATCAATGCA                               <  SRR4302542.5121891/94‑1 (MQ=60)
                                                               GCTATTGACATTTATAACGTTACGGAAGGCGGTTTTTT‑TTTTGTCGCCCTCTCTTTATTTTTTCGTTGGTTGATTTTCTCAATAATCAATGCAA                              >  SRR4302542.6230977/1‑94 (MQ=60)
                                                               GCTATTGACATTTATAACGTTACGGAAG‑CCGTTTTTTCTTCTGTCGCCATCTCTTTATTTTTGCGTTGGTTGATTTCCTCAATAATCAATGCAA                              >  SRR4302542.3940294/1‑94 (MQ=60)
                                                                CTATTGACATTTATAACGTTACGGAAG‑CCGTTTTTTCTTCTGTCGCCATCTCTTTATTTTTGCGTTGGTTGATTTCCTCAATAATCAATGCAAA                             >  SRR4302542.1736465/1‑94 (MQ=60)
                                                                CTATTGACATTTATAACGTTACGGAAG‑CCGTTTTTTCTTCTGTCGCCATCTCTTTATTTTTGCGTTGGTTGATTTCCTCAATAATCAATGCAAA                             >  SRR4302542.3389905/1‑94 (MQ=60)
                                                                CTATTGACATTTATAACGTTACGGAAG‑CCGTTTTTTCTTCTGTCGCCATCTCTTTATTTTTGCGTTGGTTGATTTCCTCAATAATCAATGCAAA                             >  SRR4302542.5291099/1‑94 (MQ=60)
                                                                 TATTGACATTTATAACGTTACGGAAG‑CCGTTTTTTCTTCTGTCGCCATCTCTTTATTTTTGCGTTGGTTGATTTCCTCAATAATCAATGCAAAC                            >  SRR4302542.7476423/1‑94 (MQ=60)
                                                                 TATTGACATTTATAACGTTACGGAAG‑CCGTTTTTTCTTCTGTCGCCATCTCTTTATTTTTGCGTTGGTTGATTTCCTCAATAATCAATGCAAAC                            >  SRR4302542.126683/1‑94 (MQ=60)
                                                                 TATTGACATTTATAACGTTACGGAAG‑CCGTTTTTTCTTCTGTCGCCATCTCTTTATTTTTGCGTTGGTTGATTTCCTCAATAATCAATGCAAAC                            >  SRR4302542.2530775/1‑94 (MQ=60)
                                                                  ATTGACATTTATAACGTTACGGAAG‑CCGTTTTTTCTTCTGTCGCCATCTCTTTATTTTTGCGTTGGTTGATTTCCTCAATAATCAATGCAAACC                           <  SRR4302542.3069535/94‑1 (MQ=60)
                                                                  ATTGACATTTATAACGTTACGGAAG‑CCGTTTTTTCTTCTGTCGCCATCTCTTTATTTTTGCGTTGGTTGATTTCCTCAATAATCAATGCAAACC                           <  SRR4302542.302935/94‑1 (MQ=60)
                                                                  ATTGACATTTATAACGTTACGGAAG‑CCGTTTTTTCTTCTGTCGCCATCTCTTTATTTTTGCGTTGGTTGATTTCCTCAATAATCAATGCAAACC                           <  SRR4302542.756844/94‑1 (MQ=60)
                                                                   TTGACATTTATAACGTTACGGAAG‑CCGTTTTTTCTTCTGTCGCCATCTCTTTATTTTTGCGTTGGTTGATTTCCTCAATAATCAATGCAAACCG                          <  SRR4302542.6055098/94‑1 (MQ=60)
                                                                    TGACATTTATAACGTTACGGAAG‑CCGTTTTTTCTTCTGTCGCCATCTCTTTATTTTTGCGTTGGTTGATTTCCTCAATAATCAATGCAAACCGT                         >  SRR4302542.7491355/1‑94 (MQ=60)
                                                                    TGACATTTATAACGTTACGGAAG‑CCGTTTTTTCTTCTGTCGCCATCTCTTTATTTTTGCGTTGGTTGATTTCCTCAATAATCAATGCAAACCGT                         >  SRR4302542.3732486/1‑94 (MQ=60)
                                                                    TGACATTTATAACGTTACGGAAG‑CCGTTTTTTCTTCTGTCGCCATCTCTTTATTTTTGCGTTGGTTGATCTCCTCAATAATCAATGCAAACCGT                         >  SRR4302542.1414155/1‑94 (MQ=60)
                                                                     GACATTTATAACGTTACGGAAG‑CCGTTTTTTCTTCTGTCGCCATCTCTTTATTTTTGCGTTGGTTGATTTCCTCAATAATCAATGCAAACCGTT                        <  SRR4302542.1942116/94‑1 (MQ=60)
                                                                      ACATTTATAACGTTACGGAAG‑CCGTTTTTTCTTCTGTCGCCATCTCTTTATTTTTGCGTTGGTTGATTTCCTCAATAATCAATGCAAACCGTTT                       <  SRR4302542.4933010/94‑1 (MQ=60)
                                                                       CATTTATAACGTTACGGAAG‑CCGTTTTTTCTTCTGTCGCCATCTCTTTATTTTTGCGTTGGTTGATTTCCTCAATAATCAATGCAAACCGTTTT                      <  SRR4302542.1845838/94‑1 (MQ=60)
                                                                       CATTTATAACGTTACGGAAG‑CCGTTTTTTCTTCTGTCGCCATCTCTTTATTTTTGCGTTGGTTGATTTCCTCAATAATCAATGCAAACCGTTTT                      >  SRR4302542.3464163/1‑94 (MQ=60)
                                                                       CATTTATAACGTTACGGAAG‑CCGTTTTTTCTTCTGTCGCCATCTCTTTATTTTTGCGTTGGTTGATTTCCTCAATAATCAATGCAAACCGTTTT                      <  SRR4302542.2937228/94‑1 (MQ=60)
                                                                        ATTTATAACGTTACGGAAG‑CCGTTTTTTCTTCTGTCGCCATCTCTTTATTTTTGCGTTGGTTGATTTCCTCAATAATCAATGCAAACCGTTTTT                     >  SRR4302542.7295879/1‑94 (MQ=60)
                                                                        ATTTATAACGTTACGGAAG‑CCGTTTTTTCTTCTGTCGCCATCTCTTTATTTTTGCGTTGGTTGATTTCCTCAATAATCAATGCAAACCGTTTTT                     >  SRR4302542.4167373/1‑94 (MQ=60)
                                                                        ATTTATAACGTTACGGAAG‑CCGTTTTTTCTTCTGTCGCCATCTCTTTATTTTTGCGTTGGTTGATTTCCTCAATAATCAATGCAAACCGTTTTT                     <  SRR4302542.2544731/94‑1 (MQ=60)
                                                                           TATAACGTTACGGAAG‑CCGTTTTTTCTTCTGTCGCCATCTCTTTATTTTTGCGTTGGTTGATTTCCTCAATAATCAATGCAAACCGTTTTTCAT                  <  SRR4302542.3625571/94‑1 (MQ=60)
                                                                             TAACGTTACGGAAG‑CCGTTTTTTCTTCTGTCGCCATCTCTTTATTTTTGCGTTGGTTGATCTCCTCAATAATCAATGCAAACCGTTTTTCATTG                >  SRR4302542.6123144/1‑94 (MQ=60)
                                                                             TAACGTTACAGAAG‑CCGTTTTTTCTTCTGTCGCCATCTCTTTATTTTTGCGTTGGTTGATTTCCTCAATAATCAATGCAAACCGTTTTTCATTG                >  SRR4302542.961393/1‑94 (MQ=60)
                                                                              AACGTTACGGAAG‑CCGTTTTTTCTTCTGTCGCCATCTCTTTATTTTTGCGTTGGTTGATTTCCTCAATAATCAATGCAAACCGTTTTTCATTGA               <  SRR4302542.1788614/94‑1 (MQ=60)
                                                                                CGTTACGGAAG‑CCGTTTTTTCTTCTGTCGCCATCTCTTTATTTTTGCGTTGGTTGATTTCCTCAATAATCAATGCAAACCGTTTTTCATTGAGT             >  SRR4302542.3429784/1‑94 (MQ=60)
                                                                                 GTTACGGAAG‑CCGTTTTTTCTTCTGTCGCCATCTCTTTATTTTTGCGTTGGTTGATTTCCTCAATAATCAATGCAAACCGTTTTTCATTGAGTG            >  SRR4302542.27616/1‑94 (MQ=60)
                                                                                 GTTACGGAAG‑CCGTTTTTTCTTCTGTCGCCATCTCTTTATTTTTGCGTTGGTTGATTTCCTCAATAATCAATGCAAACCGTTTTTCATTGAGTG            <  SRR4302542.1610576/94‑1 (MQ=60)
                                                                                 GTTACGGAAG‑CCGTTTTTTCTTCTGTCGCCATCTCTTTATTTTTGCGTTGGTTGATTTCCTCAATAATCAATGCAAACCGTTTTTCATTGAGTG            >  SRR4302542.3369655/1‑94 (MQ=60)
                                                                                 GTTACGGAAG‑CCGTTTTTTCTTCTGTCGCCATCTCTTTATTTTTGCGTTGGTTGATTTCCTCAATAATCAATGCAAACCGTTTTTCATTGAGTG            >  SRR4302542.2530653/1‑94 (MQ=60)
                                                                                 GTTACGGAAG‑CCGTTTTTTCTTCTGTCGCCATCTCTTTATTTTTGCGTTGGTTGATTTCCTCAATAATCAATGCAAACCGTTTTTCATTGAGTG            <  SRR4302542.247259/94‑1 (MQ=60)
                                                                                 GTTACGGAAG‑CCGTTTTTTCTTCTGTCGCCATCTCTTTATTTTTGCGTTGGTTGATTTCCTCAATAATCAATGCAAACCGTTTTTCATTGAGTG            >  SRR4302542.2314230/1‑94 (MQ=60)
                                                                                 GTTACGGAAG‑CCGTTTTTTCTTCTGTCGCCATCTCTTTATTTTTGCGTTGGTTGATCTCCTCAATAATCAATGCAAACCGTTTTTCATTGAGTG            >  SRR4302542.2478764/1‑94 (MQ=60)
                                                                                   TACGGAAG‑CCGTTTTTTCTTCTGTCGCCATCTCTTTATTTTTGCGTTGGTTGATTTCCTCAATAATCAATGCAAACCGTTTTTCATTGAGTGTG          >  SRR4302542.1258485/1‑94 (MQ=60)
                                                                                   TACGGAAG‑CCGTTTTTTCTTCTGTCGCCATCTCTTTATTTTTGCGTTGGTTGATTTCCTCAATAATCAATGCAAACCGTTTTTCATTGAGTGTG          >  SRR4302542.275470/1‑94 (MQ=60)
                                                                                   TACGGAAG‑CCGTTTTTTCTTCTGTCGCCATCTCTTTATTTTTGCGTTGGTTGATTTCCTCAATAATCAATGCAAACCGTTTTTCATTGAGTGTG          <  SRR4302542.2885979/94‑1 (MQ=60)
                                                                                   TACGGAAG‑CCGTTTTTTCTTCTGTCGCCATCTCTTTATTTTTGCGTTGGTTGATTTCCTCAATAATCAATGCAAACCGTTTTTCATTGAGTGTG          <  SRR4302542.5456375/94‑1 (MQ=60)
                                                                                    ACGGAAG‑CCGTTTTTTCTTCTGTCGCCATCTCTTTATTTTTGCGTTGGTTGATTTCCTCAATAATCAATGCAAACCGTTTTTCATTGAGTGTGT         <  SRR4302542.963379/94‑1 (MQ=60)
                                                                                     CGGAAG‑CCGTTTTTTCTTCTGTCGCCATCTCTTTATTTTTGCGTTGGTTGATTTCCTCAATAATCAATGCAAACCGTTTTTCATTGAGTGTGTA        <  SRR4302542.2675572/94‑1 (MQ=60)
                                                                                      GGAAG‑CCGTTTTTTCTTCTGTCGCCATCTCTTTATTTTTGCGTTGGTTGATTTCCTCAATAATCAATGCAAACCGTTTTTCATTGAGTGTGTAA       >  SRR4302542.3313287/1‑94 (MQ=60)
                                                                                          agCCGTTTTTTCTTCTGTCGCCATCTCTTTATTTTTGCGTTGGTTGATTTCCTCAATAATCAATGCAAACCGTTTTTCATTGAGTGTGTAAAAG    >  SRR4302542.5044845/3‑94 (MQ=60)
                                                                                          agCCGTTTTTTCTTCTGTCGCCATCTCTTTATTTTTGCGTTGGTTGATTTCCTCAATAATCAATGCAAACCGTTTTTCATTGAGTGTGTAAAAG    >  SRR4302542.6539734/3‑94 (MQ=60)
                                                                                           GCCGTTTTTTCTTCTGTCGCCATCTCTTTATTTTTGCGTTGGTTGATTTCCTCAATAATCAATGCAAACCGTTTTTCATTGAGTGTGTAAAAGA   >  SRR4302542.6040206/1‑94 (MQ=60)
                                                                                           GCCGTTTTTTCTTCTGTCGCCATCTCTTTATTTTTGCGTTGGTTGATTTCCTCAATAATCAATGCAAACCGTTTTTCATTGAGTGTGTAAAAGA   >  SRR4302542.2822963/1‑94 (MQ=60)
                                                                                           GCCGTTTTTTCTTCTGTCGCCATCTCTTTATTTTTGCGTTGGTTGATTTCCTCAATAATCAATGCAAACCGTTTTTCATTGAGTGTGTAAAAGA   >  SRR4302542.1721781/1‑94 (MQ=60)
                                                                                            CCGTTTTTTCTTCTGTCGCCATCTCTTTATTTTTGCGTTGGTTGATTTCCTCAATAATCAATGCAAACCGTTTTTCATTGAGTGTGTAAAAGAA  <  SRR4302542.7262246/94‑1 (MQ=60)
                                                                                            CCGTTTTTTCTTCTGTCGCCATCTCTTTATTTTTGCGTTGGTTGATTTCCTCAATAATCAATGCAAACCGTTTTTCATTGAGTGTGTAAAAGAA  >  SRR4302542.5408157/1‑94 (MQ=60)
                                                                                             |                                                                                            
TTTTCATAATAAGTCCATTTTTTAAACGTAGGGAGGCCGCCACCCACCAGGATGGAAATAGCGGCTATTGACATTTATAACGTTACGGAAGCCCGTTTTTTCTTCTGTCGCCATCTCTTTATTTTTGCGTTGGTTGATTTCCTCAATAATCAATGCAAACCGTTTTTCATTGAGTGTGTAAAAGAA  >  NC_000913/4061868‑4062053

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 26 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑