Sample Resequencing Stats

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

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 1,791,400 T→C Q61Q (CAA→CAG)  btuD ← ATP‑binding component of vitamin B12 transport system

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009131,791,4000TC99.0% 294.3 / ‑4.4 95Q61Q (CAA→CAG) btuDATP‑binding component of vitamin B12 transport system
Reads supporting (aligned to +/- strand):  ref base T (0/1);  new base C (48/46);  total (48/47)
Fisher's exact test for biased strand distribution p-value = 4.95e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.11e-01

CCAGACCGGCGTTGCAAACGGCGGCGTCTGCTGTTGTGAAAGATAGGCGCGATGCAGCGCGAGTTTTGTTGCGGACCATGCTTCCAGTGGTTGCCCCGCGAACTGAATGCTTCCCTTACCGCTGGTCATTCCGGCCATTCGCGCCAGTAAGGTACTCTTACCCGCGCCATTCGGCCCCAC  >  NC_000913/1791310‑1791489
                                                                                          |                                                                                         
ccAGACCGGCGTTGCAAACGGCGGCGTCTGCTGTTGTGAAAGATAGGCGCGATGCAGCGCGAGTTTTGTTGCGGACCATGCTTCCAGTGGCTg                                                                                         >  1:219175/1‑93 (MQ=255)
acAGACAGGCGTTGCAAACGGCGGCGTCTGCTGTTGTGAAAGATAGGCGCGATGCAGCGCGAGTTTTGTTGCGGACCATGCTTCCAGTGGCTg                                                                                         <  1:686352/92‑1 (MQ=255)
     ccGGCGTTGCAAACGGCGGCGTCTGCTGTTGTGAAAGATAGGCGCGATGCAGCGCGAGTTTTGTTGCGGACCATGCTTCCAGTGGCTGCCCcg                                                                                    >  2:4255940/1‑93 (MQ=255)
       ggCGTTGCAAACGGCGGCGTCTGCTGTTGTGAAAGATAGGCGCGATGCAGCGCGAGTTTTGTTGCGGACCATGCTTCCAGTGGCTGCCCcgcg                                                                                  >  1:2280718/1‑93 (MQ=255)
         cGTTGCAAACGGCGGCGTCTGCTGTTGTGAAAGATAGGCGCGATGCAGCGCGAGTTTTGTTGCGGACCATGCTTCCAGTGGCTGCCCCGCGaa                                                                                <  1:4303997/93‑1 (MQ=255)
         cGTTGCAAACGGCGGCGTCTGCTGTTGTGAAAGATAGGCGCGATGCAGCGCGAGTTTTGTTGCGGACCATGCTTCCAGTGGCTGCCCCGCGaa                                                                                >  1:3975720/1‑93 (MQ=255)
          gTTGCAAACGGCGGCGTCTGCTGTTGTGAAAGATAGGCGCGATGCAGCGCGAGTTTTGTTGCGGACCATGCTTCCAGTGGCTGCCCCGCGAAc                                                                               <  1:2781085/93‑1 (MQ=255)
          gTTGCAAACGGCGGCGTCTGCTGTTGTGAAAGATAGGCGCGATGCAGCGCGAGTTTTGTTGCGGACCATGCTTCCAGTGGCTGCCCCGCGAAc                                                                               >  2:2876040/1‑93 (MQ=255)
          gTTGCAAACGGCGGCGTCTGCTGTTGTGAAAGATAGGCGCGATGCAGCGCGAGTTTTGTTGCGGACCATGCTTCCAGTGGCTGCCCCGCGAAc                                                                               >  1:2112270/1‑93 (MQ=255)
             gCAAACGGCGGCGTCTGCTGTTGTGAAAGATAGGCGCGATGCAGCGCGAGTTTTGTTGCGGACCATGCTTCCAGTGGCTGCCCCGCGAACTGa                                                                            <  1:3231560/93‑1 (MQ=255)
              cAAACGGCGGCGTCTGCTGTTGTGAAAGATAGGCGCGATGCAGCGCGAGTTTTGTTGCGTACCATGCTTCCAGTGGCTGCCCCGCGAACTGaa                                                                           <  1:1082366/93‑1 (MQ=255)
              cAAACGGCGGCGTCTGCTGTTGTGAAAGATAGGCGCGATGCAGCGCGAGTTTTGTTGCGGACCATGCTTCCAGTGGCTGCCCCGCGAACTGaa                                                                           <  2:196740/93‑1 (MQ=255)
               aaaCGGCGGCGTCTGCTGTTGTGAAAGATAGGCGCGATGCAGCGCGAGTTTTGTTGCGGACCATGCTTCCAGTGGCTGCCCCGCGAACTGAAt                                                                          <  2:1079851/93‑1 (MQ=255)
                 aCGGCGGCGTCTGCTGTTGTGAAAGATAGGCGCGATGCAGCGCGAGTTTTGTTGCGTACCATGCTTCCAGTGGCTGCCCCGCGAACTGAATGc                                                                        >  1:3214944/1‑93 (MQ=255)
                 aCGGCGGCGTCTGCTGTTGTGAAAGATAGGCGCGATGCAGCGCGAGTTTTGTTGCGGACCATGCTTCCAGTGGCTGCCCCGCGAACTGAATGc                                                                        <  2:4573335/93‑1 (MQ=255)
                   ggcggcGTCTGCTGTTGTGAAAGATAGGCGCGATGCAGCGCGAGTTTTGTTGCGGACCATGCTTCCAGTGGCTGCCCCGCGAACTGAATGCtt                                                                      <  1:2353923/93‑1 (MQ=255)
                    gcggcgTCTGCTGTTGTGAAAGATAGGCGCGATGCAGCGCGAGTTTTGTTGCGGACCATGCTTCCAGTGGCTGCCCCGCGAACTGAATGCTTc                                                                     >  2:1218015/1‑93 (MQ=255)
                     cggcgTCTGCTGTTGTGAAAGATAGGCGCGATGCAGCGCGAGTTTTGTTGCGGACCATGCTTCCAGTGGCTGCCCCGCGAACTGAATGCTTcc                                                                    <  2:657493/93‑1 (MQ=255)
                      ggcgTCTGCTGTTGTGAAAGATAGGCGCGATGCAGCGCGAGTTTTGTTGCGGACCATGCTTCCAGTGGCTGCCCCGCGAACTGAATGCTTccc                                                                   <  1:3476518/93‑1 (MQ=255)
                      ggcgTCTGCTGTTGTGAAAGATAGGCGCGATGCAGCGCGAGTTTTGTTGCGGACCATGCTTCCAGTGGCTGCCCCGCGAACTGAATGCTTccc                                                                   >  1:3509648/1‑93 (MQ=255)
                      ggcgTCTGCTGTTGTGAAAGATAGGCGCGATGCAGCGCGAGTTTTGTTGCGGACCATGCTTCCAGTGGCTGCCCCGCGAACTGAATGCTTccc                                                                   >  1:1629338/1‑93 (MQ=255)
                       gcgTCTGCTGTTGTGAAAGATAGGCGCGATGCAGCGCGAGTTTTGTTGCGGACCATGCTTCCAGTGGCTGCCCCGCGAACTGAATGCTTTCCt                                                                  >  1:62715/1‑93 (MQ=255)
                       gcgTCTGCTGTTGTGAAAGATAGGCGCGATGCAGCGCGAGTTTTGTTGCGGACCATGCTTCCAGTGGCTGCCCCGCGAACTGAATGCTTCCCt                                                                  <  2:2365021/93‑1 (MQ=255)
                       gcgTCTGCTGTTGTGAAAGATAGGCGCGATGCAGCGCGAGTTTTGTTGCGGACCATGCTTCCAGTGGCTGCCCCGCGAACTGAATGCTTCCCt                                                                  <  2:2855525/93‑1 (MQ=255)
                         gTCTGCTGTTGTGAAAGATAGGCGCGATGCAGCGCTAGTTTTGTTGCGGACCATGCTTCCAGTGGCTGCCCCGCGAACTGAATGCTTCCCTTa                                                                <  2:2948482/93‑1 (MQ=255)
                          tCTGCTGTTGTGAAAGATAGGCGCGATGCAGCGCGAGTTTTGTTGCGGACCATGCTTCCAGTGGCTGCCCCGCGAACTGAATGCTTCCCTTAc                                                               <  1:1640935/93‑1 (MQ=255)
                          tCTGCTGTTGTGAAAGATAGGCGCGATGCAGCGCGAGTTTTGTTGCGGACCATGCTTCCAGTGGCTGCCCCGCGAACTGAATGCTTCCCTTAc                                                               <  1:1640936/93‑1 (MQ=255)
                           ctgctgTTGTGAAAGATAGGCGCGATGCAGCGCGAGTTTTGTTGCGGACCATGCTTCCAGTGGCTGCCCCGCGAACTGAATGCTTCCCTTAcc                                                              <  2:1757332/93‑1 (MQ=255)
                            tgctgTTGTGAAAGATAGGCGCGATGCAGCGCGAGTTTTGTTGCGGACCATGCTTCCAGTGGCTGCCCCGCGAACTGAATGCTTCCCTTAccc                                                             >  2:1265792/1‑92 (MQ=255)
                              ctgTTGTGAAAGATAGGCGCGATGCAGCGCGAGTTTTGTTGCGGACCATGCTTCCAGTGGCTGCCCCGCGAACTGAATGCTTCCCTTACCGCt                                                           <  2:3642931/93‑1 (MQ=255)
                              ctgTTGTGAAAGATAGGCGCGATGCAGCGCGAGTTTTGTTGCGGACCATGCTTCCAGTGGCTGCCCCGCGAACTGAATGCTTCCCTTACCGCt                                                           >  2:351920/1‑93 (MQ=255)
                              ctgTTGTGAAAGATAGGCGCGATGCAGCGCGAGTTTTGTTGCGGACCATGCTTCCAGTGGCTGCCCCGCGAACTGAATGCTTCCCTTACCGCt                                                           >  2:3756121/1‑93 (MQ=255)
                                gttgtGAAAGATAGGCGCGATGCAGCGCGAGTTTTGTTGCGGACCATGCTTCCAGTGGCTGCCCCGCGAACTGAATGCTTCCCTTACCGCTgg                                                         <  2:191911/93‑1 (MQ=255)
                                gttgtGAAAGATAGGCGCGATGCAGCGCGAGTTTTGTTGCGGACCATGCTTCCAGTGGCTGCCCCGCGAACTGAATGCTTCCCTTACCGCTgg                                                         <  2:2780121/93‑1 (MQ=255)
                                  tgtgAAAGATAGGCGCGATGCAGCGCGAGTTTTGTTGCGGACCATGCTTCCAGTGGCTGCCCCGCGAACTGAATGCTTCCCTTACCGCTGGTc                                                       <  1:337892/93‑1 (MQ=255)
                                   gtgAAAGATAGGCGCGATGCAGCGCGAGTTTTGTTGCGGACCATGCTTCCAGTGGCTGCCCCGCGAACTGAATGCTTCCCTTACCGCTGGTCa                                                      >  1:1372451/1‑93 (MQ=255)
                                    tgAAAGATAGGCGCGATGCAGCGCGAGTTTTGTTGCGGACCATGCTTCCAGTGGCTGCCCCGCGAACTGAATGCTTCCCTTACCGCTGGTCAt                                                     >  1:4662115/1‑93 (MQ=255)
                                    tgAAAGATAGGCGCGATGCAGCGCGAGTTTTGTTGCGGACCATGCTTCCAGTGGCTGCCCCGCGAACTGAATGCTTCCCTTACCGCTGGTCAt                                                     >  1:326287/1‑93 (MQ=255)
                                    tgAAAGATAGGCGCGATGCAGCGCGAGTTTTGTTGCGGACCATGCTTCCAGTGGCTGCCCCGCGAACTGAATGCTTCCCTTACCGCTGGACAt                                                     >  1:3390795/1‑93 (MQ=255)
                                      aaaGATAGGCGCGATGCAGCGCGAGTTTTGTTGCGGACCATGCTTCCAGTGGCTGCCCCGCGAACTGAATGCTTCCCTTACCGCTGGTCATTc                                                   <  2:2196113/93‑1 (MQ=255)
                                      aaaGATAGGCGCGATGCAGCGCGAGTTTTGTTGCGGACCATGCTTCCAGTGGCTGCCCCGCGAACTGAATGCTTCCCTTACCGCTGGTCATTc                                                   <  2:3108737/93‑1 (MQ=255)
                                       aaGATAGGCGCGATGCAGCGCGAGTTTTGTTGCGGACCATGCTTCCAGTGGCTGCCCCGCGAACTGAATGCTTCCCTTACCGCTGGTCATTcc                                                  <  1:2713497/93‑1 (MQ=255)
                                       aaGATAGGCGCGATGCAGCGCGAGTTTTGTTGCGGACCATGCTTCCAGTGGCTGCCCCGCGAACTGAATGCTTCCCTTACCGCTGGTCATTcc                                                  <  1:134523/93‑1 (MQ=255)
                                        aGATAGGCGCGATGCAGCGCGAGTTTTGTTGCGGACCATGCTTCCAGTGGCTGCCCCGCGAACTGAATGCTTCCCTTACCGCTGGTCATTCCg                                                 <  2:4722525/93‑1 (MQ=255)
                                        aGATAGGCGCGATGCAGCGCGAGTTTTGTTGCGGACCATGCTTCCAGTGGCTGCCCCGCGAACTGAATGCTTCCCTTACCGCTGGTCATTCCg                                                 >  1:239352/1‑93 (MQ=255)
                                        aGATAGGCGCGATGCAGCGCGAGTGTTGGTCCAGATCATGCTTCCAGTGGCTGCCCCGCGAACTGAATGCTTCCCTTGCCGCTGGTCATTCCg                                                 <  2:3149316/93‑1 (MQ=255)
                                         gATAGGCGCGATGCAGCGCGAGTTTTGTTGCGGACCATGCTTCCAGTGGCTGCCCCGCGAACTGAATGCTTCCCTTACCGCTGGTCATTCCgg                                                >  1:3613206/1‑93 (MQ=255)
                                         gATAGGCGCGATGCAGCGCGAGTTTTGTTGCGGACCATGCTTCCAGTGGCTGCCCCGCGAACTGAATGCTTCCCTTACCGCTGGTCATTCCgg                                                >  2:4549466/1‑93 (MQ=255)
                                          aTAGGCGCGATGCAGCGCGAGTTTTGTTGCGGACCATGCTTCCAGTGGCTGCCCCGCGAACTGAATGCTTCCCTTACCGCTGGTCATTACGGc                                               >  2:3544385/1‑93 (MQ=255)
                                           tAGGCGCGATGCAGCGCGAGTTTTGTTGCGGACCATGCTTCCAGTGGTTGCCCCGCGAACTGAATGCTTCCCTTACCGCTGGTCATTCCGGcc                                              <  1:4043015/93‑1 (MQ=255)
                                            aGGCGCGATGCAGCGCGAGTTTTGTTGCGGACCATGCTTCCAGTGGCTGCCCCGCGAACTGAATGCTTCCCTTACCGCTGGTCATTCCGGCCa                                             >  1:2804602/1‑93 (MQ=255)
                                             ggCGCGATGCAGCGCGAGTTTTGTTGCGGACCATGCTTCCAGTGGCTGCCCCGCGAACTGAATGCTTCCCTTACCGCTGGTCATTCCGGCCAt                                            <  2:2976183/93‑1 (MQ=255)
                                             ggCGCGATGCAGCGCGAGTTTTGTTGCGGACCATGCTTCCAGTGGCTGCCCCGCGAACTGAATGCTTCCCTTACCGCTGGTCATTCCGGCCAt                                            >  2:2179715/1‑93 (MQ=255)
                                              gcgcGATGCAGCGCGAGTTTTGTTGCGGACCATGCTTCCAGTGGCTGCCCCGCGAACTGAATGCTTCCCTTACCGCTGGTCATTCCGGCCAtt                                           <  1:3469385/93‑1 (MQ=255)
                                               cgcgATGCAGCGCGAGTTTTGTTGCGGACCATGCTTCCAGTGGCTGCCCCGCGAACTGAATGCTTCCCTTACCGCTGGTCATTCCGGCCATTc                                          <  2:1002328/93‑1 (MQ=255)
                                                gcgATGCAGCGCGAGTTTTGTTGCGGACCATGCTTCCAGTGGCTGCCCCGCGAACTGAATGCTTCCCTTACCGCTGGTCATTCCGGCCATTcg                                         >  1:3740987/1‑93 (MQ=255)
                                                gcgATGCAGCGCGAGTTTTGTTGCGGACCATGCTTCCAGTGGCTGCCCCGCGAACTGAATGCTTCCCTTACCGCTGGTCATTCCGGCCATTcg                                         >  1:3740986/1‑93 (MQ=255)
                                                gcgATGCAGCGCGAGTTTTGTTGCGGACCATGCTTCCAGTGGCTGCCCCGCGAACTGAATGCTTCCCTTACCGCTGGTCATTCCGGCCATTcg                                         >  1:252572/1‑93 (MQ=255)
                                                 cgATGCAGCGCGAGTTTTGTTGCGGACCATGCTTCCAGTGGCTGCCCCGCGAACTGAATGCTTCCCTTACCGCTGGTCATTCCGGCCATTcgc                                        >  1:3277317/1‑93 (MQ=255)
                                                  gATGCAGCGCGAGTTTTGTTGCGGACCATGCTTCCAGTGGCTGCCCCGCGAACTGAATGCTTCCCTTACCGCTGGTCATTCCGGCCATTcgcg                                       <  1:1027319/93‑1 (MQ=255)
                                                     gCAGCGCGAGTTTTGTTGCGGACCATGCTTCCAGTGGCTGCCCCGCGAACTGAATGCTTCCCTTACCGCTGGTCATTCCGGCCATTCGCGCCa                                    >  1:2824276/1‑93 (MQ=255)
                                                     gCAGCGCGAGTTTTGTTGCGGACCATGCTTCCAGTGGCTGCCCCGCGAACTGAATGCTTCCCTTACCGCTGGTCATTCCGGCCATTCGCGCCa                                    <  1:1124961/93‑1 (MQ=255)
                                                     gCAGCGCGAGTTTTGTTGCGGACCATGCTTCCAGTGGCTGCCCCGCGAACTGAATGCTTCCCTTACCGCTGGTCATTCCGGCCATTCGCGCCa                                    <  1:2203257/93‑1 (MQ=255)
                                                     gCAGCGCGAGTTTTGTTGCGGACCATGCTTCCAGTGGCTGACCCGCGAACTGAATGCTTCCCTTACCGCTGGTCATTCCGGCCATTCGCGCCa                                    >  2:4438600/1‑93 (MQ=255)
                                                      cAGCGCGAGTTTTGTTGCGGACCATGCTTCCAGTGGCTGCCCCGCGAACTGAATGCTTCCCTTACCGCTGGTCATTCCGGCCATTCGCGCCAg                                   >  2:1090160/1‑93 (MQ=255)
                                                       aGCGCGAGTTTTGTTGCGGACCATGCTTCCAGTGGCTGCCCCGCGAACCGAATGCTTCCCTTACCGCTGGTCATTCCGGCCATTCGCGCCAga                                  >  1:1096918/1‑92 (MQ=255)
                                                        gcgcGAGTTTTGTTGCGGACCATGCTTCCAGTGGCTGCCCCGCGAACTGAATGCTTCCCTTACCGCTGGTCATTCCGGCCATTCGCGCCAGTa                                 >  1:4416188/1‑93 (MQ=255)
                                                         cgcgAGTTTTGTTGCGGACCATGCTTCCAGTGGCTGCCCCGCGAACTGAATGCTTCCCTTACCGCTGGTCATTCCGGCCATTCGCGCCAGTaa                                <  2:861976/93‑1 (MQ=255)
                                                          gcgAGTTTTGTTGCGGACCATGCTTCCAGTGGCTGCCCCGCGAACTGAATGCTTCCCTTACCGCTGGTCATTCCGGCCATTCGCGCCAGTAAg                               >  2:3462187/1‑93 (MQ=255)
                                                          ctgAGTTTTGTTGCGGACCATGCTTCCAGTGGCTGCCAGGCGAACTGAATGCTTCCCTCACCGCTGGTCATTCCGGCCATTCGCGCCAGTAAg                               <  2:197998/91‑1 (MQ=255)
                                                            gAGTTTTGTTGCGGACCATGCTTCCAGTGGCTGCCCCGCGAACTGAATGCTTCCCTTACCGCTGGTCATTCCGGCCATTCGCGCCAGTAAGGt                             >  2:4289793/1‑93 (MQ=255)
                                                                tttGTTGCGGACCATGCTTCCAGTGGCTGCCCCGCGAACTGAATTCTTCCCTTACCGCTGGGCATTCCGGCCATTCGCGCCAGTAAGGTActc                         <  1:1830639/93‑1 (MQ=255)
                                                                tttGTTGCGGACCATGCTTCCAGTGGCTGCCCCGCGAACTGAATGCTTCCCTTACCGCTGGTCATTCCGGCCATTCGCGCCAGTAAGGTActc                         >  1:736588/1‑93 (MQ=255)
                                                                 ttgttgCGGACCATGCTTCCAGTGGCTGCCCCGCGAACTGAATGCTTCCCTTACCGCTGGTCATTCCGGCCATTCGCGCCAGTAAGGTActct                        <  1:1827734/93‑1 (MQ=255)
                                                                 ttgttgCGGACCATGCTTCCAGTGGCTGCCCCGCGAACTGAATGCTTCCCTTACCGCTGGTCATTCCGGCCATTCGCGCCAGTAAGGTActct                        >  1:3552476/1‑93 (MQ=255)
                                                                  tgttgCGGCCCATGCTTCCAGTGGCTGCCCCGCGAACTGAATGCTTCCCTTACCGCTGGTCATTCCGGCCATTCGCGCCAGTAAGGTACTCtt                       <  2:468754/93‑1 (MQ=255)
                                                                  tgttgCGGACAATGCTTCCGGTGGCTGGCCCGCGAACTGAATGCTTCCCTTACCGCTGGTCATTCCGGCCATTCGCGCCAGTAAGGTACTCtt                       <  2:468753/93‑1 (MQ=255)
                                                                   gttgCGGACCATGCTTCCAGTGGCTGCCCCGCGAACTGGATGCTTCCCTTACCGCTGGTCATTCCGGCCATTCGCGCCAGTAAGGCACTGttc                      >  1:1410015/1‑92 (MQ=255)
                                                                   gttgCGGACCATGCTTCCAGTGGCTGCCCCGCGAACTGAATGCTTCCCTTACCGCTGGTCATTCCGGCCATTCGCGCCAGTAAGGTACTCTTa                      <  1:3904991/93‑1 (MQ=255)
                                                                   gttgCGGACCATGCTTCCAGTGGCTGCCCCGCGAACTGAATGCTTCCCTTACCGCTGGTCATTCCGGCCATTCGCGCCAGTAAGGTACTCTTa                      >  1:1410014/1‑93 (MQ=255)
                                                                    ttgCGGACCATGCTTCCAGTGGCTGCCCCGCGAACTGAATGCTTCCCTTACCGCTGGTCATTCCGGCCATTCGCGCCAGTAAGGTACTCTTAc                     <  1:4350811/93‑1 (MQ=255)
                                                                    ttgCGGACCATGCTTCCAGTGGCTGCCCCGCGAACTGAATGCTTCCCTTACCGCTGGTCATTCCGGCCATTCGCGCCAGTAAGGTACTCTTAc                     <  2:3451442/93‑1 (MQ=255)
                                                                        ggACCATGCTTCCAGTGGCTGCCCCGCGAACTGAATGCTTCCCTTACCGCTGGTCATTCCGGCCATTCGCGCCAGTAAGGTACTCTTACCcgc                 >  2:912238/1‑93 (MQ=255)
                                                                         gACCATGCTTCCAGTGGCTGCCCCGCGAACTGAATGCTTCCCTTACCGCTGGTCATTCCGGCCATTCGCGCCAGTAAGGTACTCTTACCcgcg                >  2:1984659/1‑93 (MQ=255)
                                                                          aCCATGCTTCCAGTGGCTGCCCCGCGAACTGAATGCTTCCCTTACCGCTGGTCATTCCGGCCATTCGCGCCAGTAAGGTACTCTTACCCgcgc               <  1:4675423/93‑1 (MQ=255)
                                                                           ccgtGCTTCCAGTGGCTGCCCCGCGAACTGAATGCTTCCCTTACCGCTGGTCATTCCGGCCATTCGCGCCAGTAAGGTACTCTTACCCGCGcc              <  1:4596245/90‑1 (MQ=255)
                                                                             aTGCTTCCAGTGGCTGCCCCGCGAACTGAATGCTTCCCTTACCGCTGGTCATTCCGGCCATTCGCGCCAGTAAGGTACTCTTACCCGCGCCAt            <  2:461370/93‑1 (MQ=255)
                                                                             aTGCTTCCAGTGGCTGCCCCGCGAACTGAATGCTTCCCTTACCGCTGGTCATTCCGGCCATTCGCGCCAGTAAGGTACTCTTACCCGCGCCAt            >  1:4239857/1‑93 (MQ=255)
                                                                               gCTTCCAGTGGCTGCCCCGCGAACTGAATGCTTCCCTTACCGCTGGTCATTCCGGCCATTCGCGCCAGTAAGGTACTCTTACCCGCGCCATTc          <  1:3987692/93‑1 (MQ=255)
                                                                               gCTTCCAGTGGCTGCCCCGCGAACTGAATGCTTCCCTTACCGCTGGTCATTCCGGCCATTCGCGCCAGTAAGGTACTCTTACCCGCGCCATTc          <  1:2841373/93‑1 (MQ=255)
                                                                                cTTCCAGTGGCTGCCCCGCGAACTGAATGCTTCCCTTACCGCTGGTCATTCCGGCCATTCGCGCCAGTAAGGTACTCTTACCCGCGCCATTCg         >  1:2735051/1‑93 (MQ=255)
                                                                                  tCCAGTGGCTGCCCCGCGAACTGAATGCTTCCCTTACCGCTGGTCATTCCGGCCATTCGCGCCAGTAAGGTACTCTTACCCGCGCCATTCGGc       >  2:2578434/1‑93 (MQ=255)
                                                                                   ccAGTGGCTGCCCCGCGAACTGAATGCTTCCCTTACCGCTGGTCATTCCGGCCATTCGCGCCAGTAAGGTACTCTTACCCGCGCCATTCGGcc      >  1:2397661/1‑93 (MQ=255)
                                                                                     aGTGGCTGCCCCGCGAACTGAATGCTTCCCTTACCGCTGGTCATTCCGGCCATTCGCGCCAGTAAGGTACTCTTACCCGCGCCATTCGGcccc    <  1:4487539/93‑1 (MQ=255)
                                                                                     aGTGGCTGCCCCGCGAACTGAATGCTTCCCTTACCGCTGGTCATTCCGGCCATTCGCGCCAGTAAGGTACTCTTACCCGCGCCATTCGGcccc    <  1:1807310/93‑1 (MQ=255)
                                                                                      gTGGCTGCCCCGCGAACTGAATGCTTCCCTTACCGCTGGTCATTCCGGCCATTCGCGCCAGTAAGGTACTCTTACCCGCGCCATTCGGCCcca   >  1:2860492/1‑93 (MQ=255)
                                                                                      gTGGCTGCCCCGCGAACTGAATGCTTCCCTTACCGCTGGTCATTCCGGCCATTCGCGCCAGTAAGGTACTCTTACCCGCGCCATTCGGCCcca   >  2:2774395/1‑93 (MQ=255)
                                                                                       tGGCTGCCCCGCGAACTGAATGCTTCCCTTACCGCTGGTCATTCCGGCCATTCGCGCCAGTAAGGTACTCTTACCCGCGCCATTCGGCCccac  >  1:1819751/1‑93 (MQ=255)
                                                                                          |                                                                                         
CCAGACCGGCGTTGCAAACGGCGGCGTCTGCTGTTGTGAAAGATAGGCGCGATGCAGCGCGAGTTTTGTTGCGGACCATGCTTCCAGTGGTTGCCCCGCGAACTGAATGCTTCCCTTACCGCTGGTCATTCCGGCCATTCGCGCCAGTAAGGTACTCTTACCCGCGCCATTCGGCCCCAC  >  NC_000913/1791310‑1791489

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

GATK/CNVnator alignment

BRESEQ :: bam2aln output
TGCCAGACCGGCGTTGCAAACGGCGGCGTCTGCTGTTGTGAAAGATAGGCGCGATGCAGCGCGAGTTTTGTTGCGGACCATGCTTCCAGTGGTTGCCCCGCGAACTGAATGCTTCCCTTACCGCTGGTCATTCCGGCCATTCGCGCCAGTAAGGTACTCTTACCCGCGCCATTCGGCCCCACCAGG  >  NC_000913/1791308‑1791493
                                                                                            |                                                                                             
TGCCAGACCGGCGTTGCAAACGGCGGCGTCTGCTGTTGTGAAAGATAGGCGCGATGCAGCGCGAGTTTTGTTGCGGACCATGCTTCCAGTGGCT                                                                                              <  SRR4302544.1766187/94‑1 (MQ=60)
 GCCAGACCGGCGTTGCAAACGGCGGCGTCTGCTGTTGTGAAAGATAGGCGCGATGCAGCGCGAGTTTTGTTGCGGACCATGCTTCCAGTGGCTG                                                                                             >  SRR4302544.221440/1‑94 (MQ=60)
  ACAGACAGGCGTTGCAAACGGCGGCGTCTGCTGTTGTGAAAGATAGGCGCGATGCAGCGCGAGTTTTGTTGCGGACCATGCTTCCAGTGGCTGC                                                                                            <  SRR4302544.693184/94‑1 (MQ=60)
        CGGCGTTGCAAACGGCGGCGTCTGCTGTTGTGAAAGATAGGCGCGATGCAGCGCGTGCTTTGTTGCGGACCATGCTTCCAGTGTCTGCCCCGCG                                                                                      >  SRR4302544.1168349/1‑94 (MQ=60)
        CGGCGTTGCAAACGGCGGCGTCTGCTGTTGTGAAAGATAGGCGCGATGCAGCGCGAGTTTTGTTGCGGACCATGCTTCCAGTGGCTGCCCCGCG                                                                                      >  SRR4302544.2302209/1‑94 (MQ=60)
          GCGTTGCAAACGGCGGCGTCTGCTGTTGTGAAAGATAGGCGCGATGCAGCGCGAGTTTTGTTGCGGACCATGCTTCCAGTGGCTGCCCCGCGAA                                                                                    >  SRR4302544.4015280/1‑94 (MQ=60)
           CGTTGCAAACGGCGGCGTCTGCTGTTGTGAAAGATAGGCGCGATGCAGCGCGAGTTTTGTTGCGGACCATGCTTCCAGTGGCTGCCCCGCGAAC                                                                                   >  SRR4302544.2132577/1‑94 (MQ=60)
           CGTTGCAAACGGCGGCGTCTGCTGTTGTGAAAGATAGGCGCGATGCAGCGCGAGTTTTGTTGCGGACCATGCTTCCAGTGGCTGCCCCGCGAAC                                                                                   <  SRR4302544.4347894/94‑1 (MQ=60)
            GTTGCAAACGGCGGCGTCTGCTGTTGTGAAAGATAGGCGCGATGCAGCGCGAGTTTTGTTGCGGACCATGCTTCCAGTGGCTGCCCCGCGAACT                                                                                  <  SRR4302544.2807854/94‑1 (MQ=60)
               GCAAACGGCGGCGTCTGCTGTTGTGAAAGATAGGCGCGATGCAGCGCGAGTTTTGTTGCGGACCATGCTTCCAGTGGCTGCCCCGCGAACTGAA                                                                               <  SRR4302544.3262487/94‑1 (MQ=60)
                CAAACGGCGGCGTCTGCTGTTGTGAAAGATAGGCGCGATGCAGCGCGAGTTTTGTTGCGTACCATGCTTCCAGTGGCTGCCCCGCGAACTGAAT                                                                              <  SRR4302544.1093131/94‑1 (MQ=60)
                  AACGGCGGCGTCTGCTGTTGTGAAAGATAGGCGCGATGCAGCGCGAGTTTTGTTGCGTACCATGCTTCCAGTGGCTGCCCCGCGAACTGAATGC                                                                            >  SRR4302544.3245612/1‑94 (MQ=60)
                     GGCGGCGTCTGCTGTTGTGAAAGATAGGCGCGATGCAGCGCGAGTTTTGTTGCGGACCATGCTTCCAGTGGCTGCCCCGCGAACTGAATGCTTC                                                                         <  SRR4302544.2376224/94‑1 (MQ=60)
                       CGGCGTCTGCTGTTGTGAAAGATAGGCGCGATGCAGCGCGAGTTTTGTTGCGGACCATGCTTCCAGTGGCTGCCCCGCGAACTGAATGCTTCCC                                                                       >  SRR4302544.1645376/1‑94 (MQ=60)
                       CGGCGTCTGCTGTTGTGAAAGATAGGCGCGATGCAGCGCGAGTTTTGTTGCGGACCATGCTTCCAGTGGCTGCCCCGCGAACTGAATGCTTCCC                                                                       >  SRR4302544.3543131/1‑94 (MQ=60)
                        GGCGTCTGCTGTTGTGAAAGATAGGCGCGATGCAGCGCGAGTTTTGTTGCGGACCATGCTTCCAGTGGCTGCCCCGCGAACTGAATGCTTTCCT                                                                      >  SRR4302544.63354/1‑94 (MQ=60)
                        GGCGTCTGCTGTTGTGAAAGATAGGCGCGATGCAGCGCGAGTTTTGTTGCGGACCATGCTTCCAGTGGCTGCCCCGCGAACTGAATGCTTCCCT                                                                      <  SRR4302544.3509670/94‑1 (MQ=60)
                            TCTGCTGTTGTGAAAGATAGGCGCGATGCAGCGCGAGTTTTGTTGCGGACCATGCTTCCAGTGGCTGCCCCGCGAACTGAATGCTTCCCTTACC                                                                  <  SRR4302544.1657104/94‑1 (MQ=60)
                            TCTGCTGTTGTGAAAGATAGGCGCGATGCAGCGCGAGTTTTGTTGCGGACCATGCTTCCAGTGGCTGCCCCGCGAACTGAATGCTTCCCTTACC                                                                  <  SRR4302544.1657105/94‑1 (MQ=60)
                                    TGTGAAAGATAGGCGCGATGCAGCGCGAGTTTTGTTGCGGACCATGCTTCCAGTGGCTGCCCCGCGAACTGAATGCTTCCCTTACCGCTGGTCA                                                          >  SRR4302544.1386124/1‑94 (MQ=60)
                                    TGTGAAAGATAGGCGCGATGCAGCGCGAGTTTTGTTGCGGACCATGCTTCCAGTGGCTGCCCCGCGAACTGAATGCTTCCCTTACCGCTGGTCA                                                          <  SRR4302544.341397/94‑1 (MQ=60)
                                     GTGAAAGATAGGCGCGATGCAGCGCGAGTTTTGTTGCGGACCATGCTTCCAGTGGCTGCCCCGCGAACTGAATGCTTCCCTTACCGCTGGTCAT                                                         >  SRR4302544.329681/1‑94 (MQ=60)
                                     GTGAAAGATAGGCGCGATGCAGCGCGAGTTTTGTTGCGGACCATGCTTCCAGTGGCTGCCCCGCGAACTGAATGCTTCCCTTACCGCTGGTCAT                                                         >  SRR4302544.4708229/1‑94 (MQ=60)
                                     GTGAAAGATAGGCGCGATGCAGCGCGAGTTTTGTTGCGGACCATGCTTCCAGTGGCTGCCCCGCGAACTGAATGCTTCCCTTACCGCTGGACAT                                                         >  SRR4302544.3423202/1‑94 (MQ=60)
                                         AAGATAGGCGCGATGCAGCGCGAGTTTTGTTGCGGACCATGCTTCCAGTGGCTGCCCCGCGAACTGAATGCTTCCCTTACCGCTGGTCATTCCG                                                     <  SRR4302544.135786/94‑1 (MQ=60)
                                         AAGATAGGCGCGATGCAGCGCGAGTTTTGTTGCGGACCATGCTTCCAGTGGCTGCCCCGCGAACTGAATGCTTCCCTTACCGCTGGTCATTCCG                                                     >  SRR4302544.241837/1‑94 (MQ=60)
                                         AAGATAGGCGCGATGCAGCGCGAGTTTTGTTGCGGACCATGCTTCCAGTGGCTGCCCCGCGAACTGAATGCTTCCCTTACCGCTGGTCATTCCG                                                     <  SRR4302544.2739601/94‑1 (MQ=60)
                                          AGATAGGCGCGATGCAGCGCGAGTTTTGTTGCGGACCATGCTTCCAGTGGCTGCCCCGCGAACTGAATGCTTCCCTTACCGCTGGTCATTCCGG                                                    >  SRR4302544.3648658/1‑94 (MQ=60)
                                             TAGGCGCGATGCAGCGCGAGTTTTGTTGCGGACCATGCTTCCAGTGGTTGCCCCGCGAACTGAATGCTTCCCTTACCGCTGGTCATTCCGGCCA                                                 <  SRR4302544.4083276/94‑1 (MQ=60)
                                             TAGGCGCGATGCAGCGCGAGTTTTGTTGCGGACCATGCTTCCAGTGGCTGCCCCGCGAACTGAATGCTTCCCTTACCGCTGGTCATTCCGGCCA                                                 >  SRR4302544.2831641/1‑94 (MQ=60)
                                                GCGCGATGCAGCGCGAGTTTTGTTGCGGACCATGCTTCCAGTGGCTGCCCCGCGAACTGAATGCTTCCCTTACCGCTGGTCATTCCGGCCATTC                                              <  SRR4302544.3502472/94‑1 (MQ=60)
                                                 CGCGATGCAGCGCGAGTTTTGTTGCGGACCATGCTTCCAGTGGCTGCCCCGCGAACTGAATGCTTCCCTTACCGCTGGTCATTCCGGCCATTCG                                             >  SRR4302544.255224/1‑94 (MQ=60)
                                                 CGCGATGCAGCGCGAGTTTTGTTGCGGACCATGCTTCCAGTGGCTGCCCCGCGAACTGAATGCTTCCCTTACCGCTGGTCATTCCGGCCATTCG                                             >  SRR4302544.3778162/1‑94 (MQ=60)
                                                 CGCGATGCAGCGCGAGTTTTGTTGCGGACCATGCTTCCAGTGGCTGCCCCGCGAACTGAATGCTTCCCTTACCGCTGGTCATTCCGGCCATTCG                                             >  SRR4302544.3778161/1‑94 (MQ=60)
                                                  GCGATGCAGCGCGAGTTTTGTTGCGGACCATGCTTCCAGTGGCTGCCCCGCGAACTGAATGCTTCCCTTACCGCTGGTCATTCCGGCCATTCGC                                            >  SRR4302544.3308552/1‑94 (MQ=60)
                                                    GATGCAGCGCGAGTTTTGTTGCGGACCATGCTTCCAGTGGCTGCCCCGCGAACTGAATGCTTCCCTTACCGCTGGTCATTCCGGCCATTCGCGC                                          <  SRR4302544.1037565/94‑1 (MQ=60)
                                                      TGCAGCGCGAGTTTTGTTGCGGACCATGCTTCCAGTGGCTGCCCCGCGAACTGAATGCTTCCCTTACCGCTGGTCATTCCGGCCATTCGCGCCA                                        >  SRR4302544.2851565/1‑94 (MQ=60)
                                                       GCAGCGCGAGTTTTGTTGCGGACCATGCTTCCAGTGGCTGCCCCGCGAACTGAATGCTTCCCTTACCGCTGGTCATTCCGGCCATTCGCGCCAG                                       <  SRR4302544.1136167/94‑1 (MQ=60)
                                                       GCAGCGCGAGTTTTGTTGCGGACCATGCTTCCAGTGGCTGCCCCGCGAACTGAATGCTTCCCTTACCGCTGGTCATTCCGGCCATTCGCGCCAG                                       <  SRR4302544.2224010/94‑1 (MQ=60)
                                                        CAGCGCGAGTTTTGTTGCGGACCATGCTTCCAGTGGCTGCCCCGCGAACCGAATGCTTCCCTTACCGCTGGTCATTCCGGCCATTCGCGCCAGA                                      >  SRR4302544.1107827/1‑94 (MQ=60)
                                                         AGCGCGAGTTTTGTTGCGGACCATGCTTCCAGTGGCTGCCCCGCGAACTGAATGCTTCCCTTACCGCTGGTCATTCCGGCCATTCGCGCCAGTA                                     >  SRR4302544.4460767/1‑94 (MQ=60)
                                                                 TTTTGTTGCGGACCATGCTTCCAGTGGCTGCCCCGCGAACTGAATGCTTCCCTTACCGCTGGTCATTCCGGCCATTCGCGCCAGTAAGGTACTC                             >  SRR4302544.743792/1‑94 (MQ=60)
                                                                  TTTGTTGCGGACCATGCTTCCAGTGGCTGCCCCGCGAACTGAATTCTTCCCTTACCGCTGGGCATTCCGGCCATTCGCGCCAGTAAGGTACTCT                            <  SRR4302544.1848438/94‑1 (MQ=60)
                                                                  TTTGTTGCGGACCATGCTTCCAGTGGCTGCCCCGCGAACTGAATGCTTCCCTTACCGCTGGTCATTCCGGCCATTCGCGCCAGTAAGGTACTCT                            >  SRR4302544.3586503/1‑94 (MQ=60)
                                                                   TTGTTGCGGACCATGCTTCCAGTGGCTGCCCCGCGAACTGAATGCTTCCCTTACCGCTGGTCATTCCGGCCATTCGCGCCAGTAAGGTACTCTT                           <  SRR4302544.1845519/94‑1 (MQ=60)
                                                                    TGTTGCGGACCATGCTTCCAGTGGCTGCCCCGCGAACTGGATGCTTCCCTTACCGCTGGTCATTCCGGCCATTCGCGCCAGTAAGGcactgttc                          >  SRR4302544.1424054/1‑86 (MQ=60)
                                                                    TGTTGCGGACCATGCTTCCAGTGGCTGCCCCGCGAACTGAATGCTTCCCTTACCGCTGGTCATTCCGGCCATTCGCGCCAGTAAGGTACTCTTA                          >  SRR4302544.1424053/1‑94 (MQ=60)
                                                                     GTTGCGGACCATGCTTCCAGTGGCTGCCCCGCGAACTGAATGCTTCCCTTACCGCTGGTCATTCCGGCCATTCGCGCCAGTAAGGTACTCTTAC                         <  SRR4302544.3943790/94‑1 (MQ=60)
                                                                      TTGCGGACCATGCTTCCAGTGGCTGCCCCGCGAACTGAATGCTTCCCTTACCGCTGGTCATTCCGGCCATTCGCGCCAGTAAGGTACTCTTACC                        <  SRR4302544.4395016/94‑1 (MQ=60)
                                                                            ACCATGCTTCCAGTGGCTGCCCCGCGAACTGAATGCTTCCCTTACCGCTGGTCATTCCGGCCATTCGCGCCAGTAAGGTACTCTTACCCGCGCC                  <  SRR4302544.4721633/94‑1 (MQ=60)
                                                                             CCGTGCTTCCAGTGGCTGCCCCGCGAACTGAATGCTTCCCTTACCGCTGGTCATTCCGGCCATTCGCGCCAGTAAGGTACTCTTACCCGCGCCA                 <  SRR4302544.4641957/94‑1 (MQ=60)
                                                                              CATGCTTCCAGTGGCTGCCCCGCGAACTGAATGCTTCCCTTACCGCTGGTCATTCCGGCCATTCGCGCCAGTAAGGTACTCTTACCCGCGCCAT                >  SRR4302544.4283068/1‑94 (MQ=60)
                                                                                 GCTTCCAGTGGCTGCCCCGCGAACTGAATGCTTCCCTTACCGCTGGTCATTCCGGCCATTCGCGCCAGTAAGGTACTCTTACCCGCGCCATTCG             <  SRR4302544.2868803/94‑1 (MQ=60)
                                                                                 GCTTCCAGTGGCTGCCCCGCGAACTGAATGCTTCCCTTACCGCTGGTCATTCCGGCCATTCGCGCCAGTAAGGTACTCTTACCCGCGCCATTCG             <  SRR4302544.4027388/94‑1 (MQ=60)
                                                                                 GCTTCCAGTGGCTGCCCCGCGAACTGAATGCTTCCCTTACCGCTGGTCATTCCGGCCATTCGCGCCAGTAAGGTACTCTTACCCGCGCCATTCG             >  SRR4302544.2761416/1‑94 (MQ=60)
                                                                                    TCCAGTGGCTGCCCCGCGAACTGAATGCTTCCCTTACCGCTGGTCATTCCGGCCATTCGCGCCAGTAAGGTACTCTTACCCGCGCCATTCGGCC          >  SRR4302544.2420405/1‑94 (MQ=60)
                                                                                       AGTGGCTGCCCCGCGAACTGAATGCTTCCCTTACCGCTGGTCATTCCGGCCATTCGCGCCAGTAAGGTACTCTTACCCGCGCCATTCGGCCCCA       <  SRR4302544.4532614/94‑1 (MQ=60)
                                                                                       AGTGGCTGCCCCGCGAACTGAATGCTTCCCTTACCGCTGGTCATTCCGGCCATTCGCGCCAGTAAGGTACTCTTACCCGCGCCATTCGGCCCCA       <  SRR4302544.1824976/94‑1 (MQ=60)
                                                                                       AGTGGCTGCCCCGCGAACTGAATGCTTCCCTTACCGCTGGTCATTCCGGCCATTCGCGCCAGTAAGGTACTCTTACCCGCGCCATTCGGCCCCA       >  SRR4302544.2888103/1‑94 (MQ=60)
                                                                                        GTGGCTGCCCCGCGAACTGAATGCTTCCCTTACCGCTGGTCATTCCGGCCATTCGCGCCAGTAAGGTACTCTTACCCGCGCCATTCGGCCCCAC      >  SRR4302544.1837499/1‑94 (MQ=60)
                                                                                            CTGCCCCGCGAACTGAATGCTTCCCTTACCGCTGGTCATTCCGGCCATTCGCGCCAGTAAGGTACTCTTACCCGCGCCATTCGGCCCCACCAGG  >  SRR4302544.1817558/1‑94 (MQ=60)
                                                                                            |                                                                                             
TGCCAGACCGGCGTTGCAAACGGCGGCGTCTGCTGTTGTGAAAGATAGGCGCGATGCAGCGCGAGTTTTGTTGCGGACCATGCTTCCAGTGGTTGCCCCGCGAACTGAATGCTTCCCTTACCGCTGGTCATTCCGGCCATTCGCGCCAGTAAGGTACTCTTACCCGCGCCATTCGGCCCCACCAGG  >  NC_000913/1791308‑1791493

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 2 ≤ ATCG/ATCG < 24 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑