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
A2 F17 I0 R1 43 55.2 1410130 81.3% 1146435 215.5

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_000913 2,132,787 A→C 100% I204S (ATC→AGC)  wcaA ← putative glycosyl transferase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009132,132,7870AC100.0% 179.5 / ‑6.7 62I204S (ATC→AGC) wcaAputative glycosyl transferase
Reads supporting (aligned to +/- strand):  ref base A (2/0);  new base C (27/32);  total (30/32)
Rejected as polymorphism: E-value score below prediction cutoff.
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

CCCGAATACCATCAGCCAGACGTTTGCCGTTACGCACCGACAGCAGCGTCAGCAAAGTGCGCCAGGTCATACGTTTATTGCGGATCTGGTAGAGGGTAAACAGCTGATATTTTTTGCTGGCGCGGTCGAATTTGTCTTTGTGCTTGCGGTAAAAGTGGAAGTACCCGGAGAATTTTTTCGGTGACGAGGTGATCTGCATTTCACCGTGATTGATATGCAGGATCTGCGTCGCCTCTTCTACTTTCCACGGTTCGCCGTACTCCACCACCATCCGCAGGAAGATGTCGTAATCCTGTGCCGCTTTCAGTTCGGTATCGAACAAACACTCTTTGAAACGCCATGCCCAGGTAAAGACCTGGTTGCCAATGATATTGCGTTTGTAGAACAGGCGGCGTGAATACGGCGATTTGGGATACAGCGGCAAGCTTGCCGGTTGGGA  >  NC_000913/2132566‑2133004
                                                                                                                                                                                                                             |                                                                                                                                                                                                                         
cccGAATACCATCAGCCAGACGTTTGCCGTTACGCACCGACAGCAGCGTCAGCAAAGTGCGCCAGGTCATACGTTTATTGCGGATCTGGTAGAGGGTAAACAGCTGATATTTTTTGCTGGCGCGGTCGAATTTGTCTTTGTGCTTGCGGTAAAAGTGGAAGTACCCGGAGAATTTTTTCGGTGACGAGGTGATCTGCATTTCACCGTGATTGATATGCAGGCTCTGc                                                                                                                                                                                                                      >  1:524721/1‑227 (MQ=255)
          aTCAGCCAGACGTTTGCCTTTTCGCACCGACAGCAGCGTCAGCAAAGTGCGCCAGGTCATAGGTTTATTGCGGATCTGGTAGAGGGTAAACAGATGATATTTTTTGCTGGCGCGGTCGAATTTGTCTTTGTGCTTGCGGTAAAAGTGGAAGTACCCGGAGAATTTTTTCGGTGACGAGGTGATCTGCATTTCACCGTGATTGATATGCAGGCTCTGCGTCGCCtctt                                                                                                                                                                                                            <  1:216179/227‑1 (MQ=255)
          aTCAGCCAGACGTTTGCCGTTACGCACCGGCAGCAGCGTCAGCAAAGTGCGCCAGGTCATACGTTTATTGCGGATCTGGTAGAGGGTAAACAGCTGATATTTTTTGCTGGCGCGGTCGAATTTGTCTTTGTGCTTGCGGTAAAAGTGGAAGTACCCGGAGAATTTTTTCGGTGACGAGGTGATCTGCATTTCACCGTGATTGATATGCAGGCTCTGCGTCGCCtctt                                                                                                                                                                                                            <  1:41345/227‑1 (MQ=255)
           tCAGCCAGACGTTTGCCGTTACGCACCGACAGCAGCGTCAGCAAAGTGCGCCAGGTCATACGTTTATTGCGGATCTGGTAGAGGGTAAACAGCTGATATTTTTTGCTGGCGCGGTCGAATTTGTCTTTGTGCTTGCGGTAAAAGTGGAAGTACCCGGAGAATTTTTTCGGTGACGAGGTGATCTGCATTTCACCGTGATTGATATGCAGGCTCTGCGTCGCCtcttct                                                                                                                                                                                                          >  1:348522/1‑228 (MQ=255)
           tCAGCCAGACGTTTGCCGTTACGCACCGACAGCAGCGTCAGCAAAGTGCGCCAGGTCATACGTTTATTGCGGATCTGGTAGAGGGTAAACAGCTGATATTTTTTGCTGGCGCGGTCGAATTTGTCTTTGTGCTTGCGGTAAAAGTGGAAGTACCCGGAGAATTTTTTCGGTGACGAGGTGATCTGCATTTCACCGTGATTGATATGCAGGCTCTGCGTCGCCtcttct                                                                                                                                                                                                          >  1:20033/1‑228 (MQ=255)
                  gACGTTTGCCGTTACGCACCGACAGCAGCGTCAGCAAAGTGCGCCAGGTCATACGTTTATTGCGGATCTGGGAGAGGGTAAACAGCTGATATTTTTTGCTGGCGCGGTCGAATTTGTCTTTGTGCTTGCGGTAAAAGTGGAAGTACCCGGAGAATTTTTTCGGTGACGAGGTGATCTGCATTTCACCGTGATTGATATGCAGGTTCTGCGTCGCATTTTCTACTTTcc                                                                                                                                                                                                   >  2:447713/1‑228 (MQ=255)
                   aCGTTTGCCTTTCCGCACCGACAGCAGCGTGAGCAAAGTGCGCCAGGTCATACGTTTATTGGGGATCTGGTAGAGGGTAAACAGCTGATATTTTTTGCTGGCGCGGTCGAATTTGTCTTTGTGCTTGCGGTAAAAGTGGAAGTACCCGGAGAATTTTTTCGGTGACGAGGTGATCTGCATTTCACCGTGATTTATATGCAGGCTCTGCGTCGCCTCTTCTACTTTCCa                                                                                                                                                                                                  <  1:133056/228‑1 (MQ=255)
                   aCGTTTGCCGTTACGCACCGACAGCAGCGTCAGCAAAGTGCGCCAGGTCATACGTTTATTGCGGATCTGGTAGAGGGTAAACAGCTGATATTTTTTGCTGGCGCGGTCGACTTTGTCTTTGTGCTTGCGGTAAAAGTGGAAGTACCCGGAGAATTTTTTCGGTGACGTGGGTATCTGCATTTCACCGTGATTGATAGGCAGGCTCTGGGTCGCCTCTTCTACTTTCCa                                                                                                                                                                                                  >  1:701305/1‑228 (MQ=255)
                       ttGCCGTTACGCACCGACAGCAGCGTCAGCAAAGTGCGCCAGGTCATACGTTTATTGCGGATCTGGTAGAGGGTAAACAGCTGATATTTTTTGCTGGCGCGGTCGAATTTGTCTTTGTGCTTGCGGTAAAAGTGGAAGTACCCGGAGAATTTTTTCGGTGACGAGGTGATCTGCATTTCACCGTGATTGATATGCAGGCTCTGCGCCGCCCCTTCTACTTTCCACgg                                                                                                                                                                                               >  1:505432/1‑227 (MQ=255)
                         gCCGTTACGCACCGACAGCAGCGTCAGCAAAGTGCGCCAGGTCATACGTTTATTGCGGATCTGGTAGAGGGTAAACAGCTGATATTTTTTGCTGGCGCGGTCGAATTTGTCTTTGTGCTTGCGGTAAAAGTGGAAGTACCCGGAGAATTTTTTCGGTGACGAGGTGATCTGCATTTCACCGTGATTGATATGCAGGACTGGCGGGGCCCCTTTTACTTTCCACgggt                                                                                                                                                                                             >  2:459865/1‑225 (MQ=255)
                             tttttaccgggcagcggCGTGAGCAAAGTGGCCTAGGTCATTCTTTTATGGGGGGTTTGGTAGAGGGTAAGCAGCTGATATTGTTGGCTGGCGCGGGCGAATTTGTCTTTGTGCTTGCGGTAAAAGTGGAAGTCCCCGGAGAATTTTTTCGGTGACGAGGTGATCTGCATTTCACCGTGATTGATATGCAGGCTCTGCGTCGCCTCTTCTACTTTCCACGGTTCGCCg                                                                                                                                                                                        <  2:227656/217‑1 (MQ=255)
                             ttcccccccGACAGCGGCGTCAGCAAAGTGCGCCAGGTCATACGTTTATTGCGGATCTGGTAGAGGGTAAACAGCTGATATTTTTTGCTGGCGCGGTCGAATTTGTCTTTGTGCTTGCGGTAAAAGTGGAAGTACCCGGAGAATTTTTTCGGTGACGAGGTGATCTGCATTTCACCGTGATTGATATGCAGGCTCTGCGTCGCCTCTTCTACTTTCCACGGTTCGCCg                                                                                                                                                                                        <  1:459865/221‑1 (MQ=255)
                             ttccGCTCCGACAGCAGGGTCAGCAAAGTGCGCCAGGTCATACGTTTATTGCGGATCTGGTAGAGGGTAAACAGCTGATATTTTTTGCTGGCGCGGTCGAATTTGTCTTTGTGCTTGCGGTAAAAGTGGAAGTACCCGGAGAATTTTTTCGGTGACGAGGTGATCTGCATTTCACCGTGATTGATATGCAGGCTCTGCGTCGCCTCTTCTACTTTCCACGGTTCGCCg                                                                                                                                                                                        <  1:568475/225‑1 (MQ=255)
                             ttACGGACCGACAGCAGCGTCAGCAAAGTGCGCCAGGTCATACGTTTATTGCGGATCTGGTAGAGGGTAAACAGCTGATATTTTTTGCTGGCGCGGTCGAATTTGTCTTTGTGCTTGCGGTAAAAGTGGAAGTACCCGGAGAATTTTTTCGGTGACGAGGTGATCTGCATTTCACCGTGATTGATATGCAGGCTCTGCGTCGCCTCTTCTACTTTCCACGGTTCGCCg                                                                                                                                                                                        <  1:512911/228‑1 (MQ=255)
                             ttACGCACCGACAGCAGCGTCAGCAAAGTGCGCCAGGTCATACGTTTATTGCGGATCTGGTAGAGGGTAAACAGCTGATATTTTTTGCTGGCGCGGTCGAATTTGTCTTTGTGCTTGCGGTAAAAGTGGAAGTACCCGGGGAATTTTTTCGGTGACTAGGTGATCTGCATTTCACCGTGTTTGATCTGCAGGCTCTGCGTCGCCTCTTCTCCTTTCCACGGTTCGcc                                                                                                                                                                                         >  1:702937/1‑227 (MQ=255)
                                    acgaaatcggcGTAAGCAAGGTGCGCCAGGTCATGCGTTTATTGCGGGTCTGGTAGAGGGTAAAAAGCTGATATTTTTTGCTGGCGCGGTCGAATTTGTCTTTGTGCTTGCGGTAAAAGTGGAAGTGCCCGGAGAATTTTTTCGGTGCCGAGGTGATCTGCATTTCACCGTGATTGATATGCAGGCTCTGCGTCGCCTCTTCTACTTTCCACGGTTCGCCGTACTcca                                                                                                                                                                                 <  1:297558/219‑1 (MQ=255)
                                       aCAGCAGCGTCAGCAAAGTGCGCCAGGTCATACGTTTATTGCGGATCTGGTAGAGGGTAAACAGCTGATATTTTTTGCTGGCGCGGTCGAATTTGTCTTTGTGCTTGCGGTAAAAGTGGAAGTACCCGGAGAATTTTTTCGGTGACGAGGTGATCTGCATTTCACCGTGATTGATATGCAGGCTCTGCGTCGCCTCTTCTACTTTCCACGGTTCGCCGTACTccacca                                                                                                                                                                              >  1:205796/1‑228 (MQ=255)
                                            agggacAGCAAAGTGGTCCTGGTCTATCGTTTATTGGGGTTTTTGTAGAGGTTAAACAGCTGATAGTTTTTGCTGGTGCGGTAGAATTTGTCTTTGTGTTTGCGGTAAAAGTGGACGTCCCCGGAGAATTTTTTCGGTTACGAGGTGATCTGCATTTCACCGTGATTGATATGCAGGCTCTGCGTCGCCTCTTCTACTTTCCACGGTTCGCCGTACGCCACCACCATc                                                                                                                                                                         <  2:702937/223‑1 (MQ=255)
                                              cGTCAGCAAAGTGCGCCAGGTCATACGTTTATTGCGGATCTGGTAGAGGGTAAACAGCTGATATTTTTTGCTGGCGCGGTCGAATTTGTCTTTGTGCTTGCGGTAAAAGTGGAAGTACCCGGAGAATTTTTTCGGTGACGAGGTGATCTGCATTTCACCGTGATTGATATGCAGGCTCTGCGTCGCCTCTTCTACTTTCCACGGTTCGCCGTACTCCACCACCATcc                                                                                                                                                                        >  1:15430/1‑227 (MQ=255)
                                                tCAGCAAAGTGCGCCAGGTCATACGTTTATTGCGGATCTGGTAGAGGGTAAACAGCTGATATTTTTTGCTGGCGCGGTCGAATTTGTCTTTGTGCTTGCGGTAAAAGTGGAAGTACCCGGAGAATTTTTTCGGTGACGAGGGGATCTGCATTTCACCGTGATTGATATGCAGGCTCTGCGTCGCCTCTTCTACTTTCCACGGTTCGCCGTACTCCACCACCACCCCCa                                                                                                                                                                     >  1:567879/1‑228 (MQ=255)
                                                  aGCAAAGTGCGCCAGGTCATACGTTTATTGCGGATCTGGTAGAGGGTAAACAGCTGATATTTTTTGCTGGCGCGGTCGAATTTGTCTTTGTGCTTGCGGTAAAAGTGGAAGTACCCGGAGAATTTTTTCGGTGACGAGGTGATCTGCATTTCACCGTGATTGATATTCAGGCTTTGCGTCGCCTCTTCTACTTTCCACGGTTCCCCGTACTCCACCACCACCCGCAgg                                                                                                                                                                   >  1:108087/1‑228 (MQ=255)
                                                   gCAAAGTGCACCAGGTCATGCGTTTAATGCGGATCTGGTAGAGGGTAAACAGCTGATATTTTTTGCTGGCTCGGTCGAATTTGTCTTTGTGCTTGCGGTAAAAGTGGAAGTACCCGGAGAATTTTTTCGGTGACGAGGTGATCTGCATTTCACCGTGATTGATATGCAGGCTCTGCGTCGCCTCTTCTACTTTCCACGGTTCGCCGTACTCCACCACCATCCGCAgg                                                                                                                                                                   <  1:126688/227‑1 (MQ=255)
                                                       atggcgcCAGGTCATACGTGTTTTGCGGATCTGGTAGAGGGTAAACAGCTGATATTTTTTGCTGGCGCGGTCGAATTTGTCTTTGTGCTTGCGGTAAAAGTGGAAGTACCCGGAGAATTTTTTCGGTGACGAGGTGATCTGCATTTCACCGTGATTGATATGCAGGCTCTGCGTCGCCTCTTCTACTTTCCACGGTTCGCCGTACTCCACCACCATCCGCAGGAAGa                                                                                                                                                               <  1:539099/224‑1 (MQ=255)
                                                       agggcgcCAGGTCATACGTTTATTGCGGATCTGGTAGAGGGTAAACAGCTGATATTTTTTGCTGGCGCGGTCGAATTTGTCTTTGTGCTTGCGGTAAAAGTGGAAGTACCCGGAGAATTTTTTCGGTGACGAGGTGATCTGCATTTCACCGTGATTGATATGCAGGCTCTGCGTCGCCTCTTCTACTTTCCACGGTTCGCCGTACTCCACCACCATCCGCAGGAAGa                                                                                                                                                               <  1:243878/224‑1 (MQ=255)
                                                       aGTGCGCCAGTTTATACGTTTATTGCGGATGCGGTAGAGGGTAAACAGCTTATATTTTTTGCTGGCGCGGTCGAATTTGTCTTTGTTCTTGCGGTAAAAGTGGAAGTTCCCGGAGAATTTTTTCGGTGACGAGGTGATCTGCATTTCACCGTGATTGATATGCAGGCTCTGCTGCGCCTCTTCTACTTTCCACGGTTCGCCGTACTCCACCACCATCCGCAGGAAGa                                                                                                                                                               <  1:292041/227‑1 (MQ=255)
                                                       aGTGCGCCAGGTCATACGTTTATTGCGGATCTTGTAGAGGGTAAACAGCTGATATTTTTTGCTGGCGCGGTCGAATTTGTCTTTGTGCTTGCGGTAAAAGTGGAAGTACCCGGAGAATTTTTTCGGTGACGAGGTGATCTGCATTTCACCGTGATTGATATGCAGGCTCTGCGTCGCCTCTTCTACTTTCCACGGTTCGCCGTACTCCACCACCATCCGCAGGAAGa                                                                                                                                                               <  1:447713/227‑1 (MQ=255)
                                                         tggtccAGGTTATACGTTTGTTGCGTATCTGGTTGAGGGTAAACATCTGATATTTTTTGCTGGCGCGGTCGAATTTGTCTTTGTGCTTGCGGTAAAAGTGGAAGTGCCCGGAGAATTTGTTCGGTGACGAGGTGATCTCCATTTCACCGTGATTGATATGCAGGCTCTGCGTCGCCTCTTCTACTTTCCACGGTTCGCCGTACTCCACCACCATCCGCAGGAAGATg                                                                                                                                                             <  2:478005/223‑1 (MQ=255)
                                                              cAGGTCATACGTTTATTGCGGATCTGGTAGAGGGTAAACAGCTGATATTTTTTGCTGGCGCGGTCGAATTTGTCTTTGTGCTTGCGGTAAAAGTGGAAGTACCCGGAGAATTTTTTCGGTGACGAGGGGATCTGCATTTCACCGGGATTGATATGCAGGCTCTGCGTAGCCTCTTCTACTTTCCACGGTTAGCCGAAATCCACCACCCTCCGCAGGAAGATGCCGt                                                                                                                                                         >  1:676408/1‑226 (MQ=255)
                                                                     gaggTTTATGTCGGATCTGGTTGAGGGTAAACAGCTGATATTTTTTGCTGGCGCGGTCGAATTTTTCTTTGTGCTTGCGGTAAAAGTGGAAGTACCCGGAGAATTTTTTCGGTGACGAGGTGATCTGCATTTCACCGTGATTGATATGCAGGCTCTGCGTCGCCTCTTCTACTTTCCACGGTTCGCCGTACTCCACCACCATCCGCAGGAAGATGTCGTAATCCtgtg                                                                                                                                                <  1:574624/225‑1 (MQ=255)
                                                                           tATTGCGGATCTGGTAGAGGGTAAACAGCTGATATTTTTTGCTGGCGCGGTCGAATTTGTCTTTGTGCTTGCGGTAAAAGTGGAAGTACCCGGAGAATTTTTTCGGTGACGAGGTGATCTGCATTTCACCGTGATTGATATGCAGGCTCTGCGTCGCCTCTTCTACTTTCCACGGTTCGCCGTACTCCACCACCATCCGCAGGAAGATGTCGTAATCCTGTCCCGCt                                                                                                                                           >  1:140993/1‑227 (MQ=255)
                                                                                  gATCTGGTAGAGGGTAAACAGCTGATATTTTTTGCTGGCGCGGTCGACTTTGTCTTTGTGCTTGCGGTAAAAGCGGAATTACCCGGAGAATTTTTTCGGTGACGAGGTGATCTGCATTTCACGGTGATTGATATGCAGGCTCTGCGTTGCCTCTTCTACTTTCAACGGTTCGCCGTACTCCACCCCCATCCGCAGGAAGATGTCGTAATCCTGTGCCGCTTTCAGTTc                                                                                                                                   >  1:17213/1‑228 (MQ=255)
                                                                                  gATCTGGTAGAGGGTAAACAGCTGATATTTTTTGCTGGCGCGGTCGAATTTGTCTTTGTGCTTGCGGTAAAAGTTGAAGTACCCGGAGAATTTTTTCGGTGACGAGGTGATCTGCATTTCACCGTGATTGATCTGCATGCTCTGCGACGCCTCTTCTACTTTCCACGGTTCGCCGTACTCCACCACCATCCGCAGGAAGCTGTCGTAATCCTGTTCACCTTTCAGTTc                                                                                                                                   >  2:695065/1‑228 (MQ=255)
                                                                                       tgtggggggTTAACCGCTTGTTTTTTTTGCTGGGGCGGTCGAATTTGTCTTTGTGCGTGCGGTAAAAGTGGAAGTTCCCGGAGAATTTTTTCGGTGACGAGGTGATCTGCATTTCCCCGTGATTGATATGCAGGCTCTGCGTCGCCTCTTCTACTTTCCACGGTTCGCCGTACTCCACCACCATCCGCAGGAAGATGTCGTAATCCTGTGCCGCTTTCAGTTCGGTAt                                                                                                                              <  2:20033/222‑1 (MQ=255)
                                                                                             gggTAAACAGCTGATATTTTTTGCTGGCGCGGTCGAATTTGTCTTTGTGCTTGCGGTAAAAGTGGAAGTACCCGGAGAATTTTTTCGGTGACGCGGTGATCTGCATTTCACCGTGATTGATATGCAGGAGCGTCGTCGCCTCTTCTACTTTCCACGGTTCGCCGTACTCCACACCCATCCGCCGGAAGCGTTCGGAATCTGTTGCCGCTTTCAGTCCGGGATCGacc                                                                                                                         >  2:516239/1‑225 (MQ=255)
                                                                                              gttAAACAGGTGATTTTTTTTGGTGGCGCGGTCGAATTTGTCTTTGTGCTTGCGGTAAAAGTGGAAGTACCCGGAGAATTTTTTCGGTGACGAGGTGATCTGCATTTCACCGTGATTGATATGCAGGCTCTGCGTCGCCTCTTCTACTTTCCACGGTTCGCCGTACTCCACCACCATCCGCAGGAAGATGTCGTAATCCTGTGCCGCTTTCAGTTCGGTATCGaaca                                                                                                                        <  2:140993/225‑1 (MQ=255)
                                                                                              ggTAAACAGGTGATATTTTGTGCTGGCGCGGTCGAATTTGTCTTTGTGCTTGCGGTAAAAGTGGAAGTACCCGGAGAATTTTTTCGGTGACGAGGTGATCTGCATTTCACCGTGATTGATATGCAGGCTCTGCGTCGCCTCTTCTACTTTCCACGGTTCGCCGTACTCCACCACCATCCGCAGGAAGATGTCGTAATCCTGTGCCGCTTTCAGTTCGGTAt                                                                                                                              <  1:516239/221‑1 (MQ=255)
                                                                                              ggTAAACAGCTGATATTTTTTGCTGGCGCGGTCGAATTTGTCTTTGTGCTTGCGGTAAAAGTGGAAGTACCCGGAGAATTTTTTCGGTGACGAGGTGATCTGCATTTCACCGTGATTGATATGCAGGCTCTGCGTCGCCTCTTCTACTTTCCACGGTTCGCCGTACTCCCCCACCACCCCCAGGAAGATGTCGTAATCCTGTGCCCCTTTCAGTTCGGTATCGaacaa                                                                                                                       >  1:380214/1‑228 (MQ=255)
                                                                                              ggTAAACAGCTGATATTTTTTGCTGGCGCGGTCGAATTTGTCTTTGTGCTTGCGGTAAAAGTGGAAGTACCCGGAGAATTTTTTCGGTGACGAGGTGATCTGCATTTCACCGTGATTGATATGCAGGCTCTGCGTCGCCTCTTCTACTTTCCACGGTTCGCCGTACTCCACCCCCATCCCCCGGAAGATGTCGTAATCCTGTGCCGCTTTCAGTTCCGTATCGaacaa                                                                                                                       >  2:465615/1‑228 (MQ=255)
                                                                                              ggTAAACAGCTGATATTTTTTGCTGGCGCGGTCGAATTTGTCTTTGTGCTTGCGGTAAAAGTGGAAGTACCCGGAGAATTTTTTCGGTGACGAGGTGATCTGCATTTCACAGTGATTGATATGCAGGCTCTGCGTCGCCGCTTCTACTTTCCACGGTTCGCCGGACTCCACCACCCTCGGCGGGAAGATGTCGTATTCCTTGGCGCCTTTCAGTTCGGCATCGaacaa                                                                                                                       >  2:604289/1‑228 (MQ=255)
                                                                                                 aaaaAGGTGATTTTTTTTTGGGGCGGGGTGGAATTTGTTTTTGTGCGTGGGGTAAAAGTGGAAGTACCGGGAGAATTTTTTCGGTGACGAGGTGATCTGCATTTCACCGTGATTGATATGCAGGCTCTGCGTCGCCTCTTCTACTTTCCACGGTTCGCCGTACTCCACCACCATCCGCAGGAAGATGTCGTAATCCTGTGCCGCTTTCAGTTCGGTATCGaacaaaca                                                                                                                    <  2:380214/228‑1 (MQ=255)
                                                                                                       cTGATATTTTTTGCTGGCGCGGTCGAATTTGTCTTTGTGCTTGCGGTAAAAGTGGAAGTACCCGGAGAATTTTTTCGGTGACGAGGTGATCTGCATTTCACCGTGATTGATATGCAGGCTCTGCGTCGCCTCTTCTACTTTCCACGGTTCGCCGTACTCCACCACCATCCGCAGGAAGCTGTCGTCATCCTGTGCCGCTTTCAGTTCGGCATCTAACAAACCCTCtt                                                                                                               >  1:3658/1‑227 (MQ=255)
                                                                                                        tGATATTTTTTGCTGGCGCGGTCGAATTTGTCTTTGTGCTTGCGGTAAAAGTGGAAGTACCCGGAGAATTTTTTCGGTGACGAGGTGATCTGCATTTCACCGTGATTGATATGCAGGCTCTGCGTCGCCTCTTCTACTTTCCACGGTTCGCCGTACTCCACCACCATCCGCAGGAAGATGTCGTAATCCTGTGCCGCTTTCAGTTCGGTATCGAACAAACACTCttt                                                                                                              >  1:281264/1‑227 (MQ=255)
                                                                                                           tatTTTTTGCTGGCGCGGTCGAATTTGTCTTTGTGCTTGCGGTAAAAGTGGAAGTACCCGGAGAATTTTTTCGGTGACGAGGTGATCTGCATTTCACCGTGATTGATATGCAGGCTCTGCGTCGCCTCTTCTACTTTCCACGGTTCGCCGTACTCCACCACCATCCGCAGGAAGATGTCGTAATCCTGTGCCGCTTTCAGTTCGGTATCGAACAAACACTCTTTGaa                                                                                                           <  1:604289/227‑1 (MQ=255)
                                                                                                           tatTTTTTGCGGGGGCGGTCGAATTTGTCTTTGTGCTTGCGGTAAACGTGGAAGTACCCGGAGAATTTTTTCGGTGACGAGGTGATCTGCATTTCACCGTGATTGATATGCAGGCTCTGCGTCGCCTCTTCTACTTTCCACGGTTCGCCGTACTCCACCACCATCCGCAGGAAGATGTCGTAATCCTGTGCCGCTTTCAGTTCGGTATCGAACAAACACTCTTTGaa                                                                                                           <  1:434523/227‑1 (MQ=255)
                                                                                                             ttttttGCGGGGGCGGGCGAATTTGTTGTTGGGGCTGCGGTAAAAGGGGAAGTACCCGGAGAATTTTTGCGGTGACGAGGTGATCTGCATTTCCCCGTGATTGATATGCAGGCTCTGCGTCGCCTCTTCTACTTTCCACGGTTCGCCGTACTCCACCACCATCCGCAGGAAGATGTCGTAATCCTGTGCCGCTTTCAGTTCGGTATCGAACAAACACTCTTTGAAACg                                                                                                        <  2:15430/228‑1 (MQ=255)
                                                                                                               ttttGCTGGCGCGGTCGAATTTGTCTTTGTGCTTGCGGTAAAAGTGGAAGTACCCGGAGAATTTTTTCGGTGACGAGGTGATCTGCATTTCACCGTGATTGATATGCAGGCTCTGCGTCGCCTCTTCTACTTTCCACGGTTCGCCGTACTCCACCACCATCCCCCGGAAGATGTTGTAATCCTGTGCCGTTTTCAGTTCGGTCTCGAACAAAAACCCTTTGAAACGcc                                                                                                      >  2:379335/1‑228 (MQ=255)
                                                                                                                    cTGGCGCGGTCGAATTTTGTTTTTTGCTTGCGGTAAAAGTGGAAGTCTCCGGAGAATTTTTTCGGTGACGAGGTGATCTGCATTTCCCCGTGATTGATATGCAGGCTCTGCGTCGCCTCTTCTACTTTCCACGGTTCGCCGTACTCCACCACCATCCGCAGGAAGATGTCGTAATCCTGTGCCGCTTTCAGTTCGGTATCGAACAAACACTCTTTGAAACGCCATGcc                                                                                                 <  2:205796/228‑1 (MQ=255)
                                                                                                                     tGGCGGGGTCGATTTTTTTTTTGGGCTTGCGGTAAAAGTTGAAGTTCCCGGAGAATTTTTTCGGTGACGAGGTGATCTGCATTTCCCCGTGATTGATATGCAGGCTCTGCGTCGCCTCTTCTACTTTCCACGGTTCGCCGTACTCCACCACCATCCGCAGGAAGATGTCGTAATCCTGTGCCGCTTTCAGTTCGGTATCGAACAAACACTCTTTGAAACGCCATGccc                                                                                                <  2:359052/228‑1 (MQ=255)
                                                                                                                     tGGCGCGGTCTAATTTGTTTGTGTGTTTGCGGTAAAATGTGAAGTCGCCGGAGAATTTTTTCGTTGACGAGGGGATCTGCATTTCCCCGGGATTGATATGCACGCTCTGCGTCGCCTCTTCTACTTTCCACGGTTCGGCGTACTCCACCGCCATCCGCAGGAAGATGTCGTAATCCTGTGCCGCTTTCAGTTCGGTATCGAACAAACACTCTTTGAAACGCCATGcc                                                                                                 <  2:108087/227‑1 (MQ=255)
                                                                                                                         gcgtgtgAATTTGTTTTTGTGCTTGCGGTAAAAGTGGAAGTACCCGGAGAATTTTTTCGGTGACGAGGTTATCTGCATTTCACCGTGATTGATATGCAGGCTCTGCGTCGCCTCTTCTACTTTCCACGGTTCGCCGTACTCCACCACCATCCGCAGGAAGATGTCGTAATCCTGTGCCGCTTTCAGTTCGGTATCGAACAAACACTCTTTGAAACGCCATGCCCAGGt                                                                                            <  1:99932/222‑1 (MQ=255)
                                                                                                                         gcgGTCGAATTTGGCTTTGTGCTTGCGGTAAAAGTGGAAGTACCCGGAGAATTTTTTCGGTGACGAGGTGATCTGCATTTCCCCGTGCTTGATATGCAGGCTCTGCGTCGCCTCTTCTACTTTCCACGGTTCGCCGAACTCCACCACCATCCGCAGGAAg                                                                                                                                                                >  1:95802/1‑160 (MQ=255)
                                                                                                                             tCGAATTTGTTGTTGTGCTTGCGGTAAAAGTGGAAGGCCCCGGAGAATTTTTTCGGTGACGAGGTGACCTGCATGTCCCCGGGATTGATATGCAGGCTCTGCGTCGCCTCTGCTACTTTCCACGGTTCGCCGTACTCCACCACCATCCGCAGGAAGATGTCGTAATCCTGTGCCGCTGTCAGTTCGGTATCGAACAAACTCTCTTTGAAACGCCATGCCCAGGTAAAg                                                                                        <  2:140272/228‑1 (MQ=255)
                                                                                                                                                             gAAGTACCCGGAGAATTTTTTCGGTGACGAGGTGATCTGCATTTCACCGTGATTGATATGCAGGCTCTGCGTCGCCTCTTCTACTTTCCACGGTTCGCCGTACTCCACCACCATCCGCAGGAAGATGTCGTAATCCTGTGCCGCTTTCAGTTCGGTATCGAACAAACACTCTTTGAAACGCCATGCCCAGGTAAAGACCTGGTTGCCAATGATATTGCGTTTGTAGaa                                                        >  2:191922/1‑228 (MQ=255)
                                                                                                                                                               aGTACCTGGAGAATTTTTTCGGTGACGAGGTGATCTGCATTTCACCGTGATTGATATGCAGGCTCTGCGTCGCCTCTTCTACTTTCCACGGTTCGCCGTACTCCACCACCATCCGCAGGAAGATGTCGTAATCCTGTGCCGCTTTCAGTTCGGTATCGAACAAACACTCCTTGAAACGCCATGCCCCGGTAAAGACCTGGTTGCCAATGATATTGCGTTTGTAGAACa                                                      >  1:421221/1‑228 (MQ=255)
                                                                                                                                                                                                  tGCATTTCACCGTGATTGATATGCAGGCTCTGCGTCGCCTCTTCTACTTTCCACGGTTCGCCGTACTCCACCACCATCCGCAGGAAGATGTCGTAATCCTGTTCCGCTTTCAGTTCGGTATCGAACAAACACTCTTTGAAACGCCATGCCCAGGTAAAGCCCTGGTTg                                                                               >  2:466933/1‑168 (MQ=255)
                                                                                                                                                                                                   gCATTTCACCGTGATTGATATGCAGGCTCTGCGTCGCCTCTTCTACTTTCCACGGTTCGCCGTACTCCACCACCATCCGCAGGAAGATGTCGTAATCCTGTGCCGCTTTCAGTTCGGTATCGAACAAACACTCTTTGAAACGCCATGCCCAGGTAAAGACCTGGTTGc                                                                              <  1:466933/168‑1 (MQ=255)
                                                                                                                                                                                                        tCACCTGGATTGGTATGCAGGCTTTGCGGCGCCTCTGCTACTTTCCACGGTTCGCCGTACTCCACCACCATCCGCAGGAAGATGTCGTAATCCTGTGCCGCTTTCAGTTCGGTATCGAACAAACACTCTTTGAAACGCCATGCCCAGGTAAAGACCTGGTTGCCAATGATATTGCGTTTGTAGAACAGGCGGCGTGAATACGGCGATTTGGGATACAGCGGCAAGCt              <  1:443997/227‑1 (MQ=255)
                                                                                                                                                                                                            cGTGATTGATATGCAGGCTCTGCGTCGCCTCTTCTACTTTCCACGGTTCGCCGTACTCCACCACCATCCGCAGGAAGATGTCGTAATCCTGTGCCGCTTTCAGTTCGGTATCGCACACACACTCTTTGAAACGCCATGCCCAGGTAACGACCTGGTTGCCAATGATATTGCGTTTGTAGAACACGCGGCGTGAAAACGGCGATTTGGGATACAGCGGCAAACTTGcc          >  1:226028/1‑227 (MQ=255)
                                                                                                                                                                                                            cGTGATTGATATGCAGGCTCTGCGTCGCCTCTTCTACTTTCCACGGTTCGCCGTACTCCACCACCATCCGCAGGAAGATGTCGTAATCCTGTGCCGCTTTCAGTTCGGTATCGAACAAACACTCTTTGAAACGCCATGc                                                                                                  >  2:90401/1‑139 (MQ=255)
                                                                                                                                                                                                             gTGATTGATATGCAGGCTCTGCGTCGCCTCTTCTACTTTCCACGGTTCGCCGTACTCCACCACCATCCGCAGGAAGATGTCGTAATCCTGTGCCGCTTTCAGTTCGGTATCGAACAAACACTCTTTGAAACGCCATGcc                                                                                                 <  1:90401/139‑1 (MQ=255)
                                                                                                                                                                                                              gttttgatATGCAGGCTTGGCGTCGCCCTTTCTACTTTCCACGGTTCGCCGTCCTCCACCCCCATCCGCAGGAAGATGTCGTAATCCTGGGCCGCTTTCAGTTCGGTATCGAACAAACACTCTTTGAAACGCCATGCCCAGGTAAAGACCTGGTTGCCAATGATATTGCGTTTGTAGAACAGGCGGCGTGAATACGGCGATTTGGGATACAGCGGCAAGCTTGCCGGt       <  2:348522/225‑1 (MQ=255)
                                                                                                                                                                                                                    atatGCAGGCTCTGCGTCGCCTCTTCTACTTTCCACGGTTCGCCGTACTCCACCACCATCCGCAGGAAGATGTCGTAATCCTGTGCCGCTTTCAGTTCGGTATCGAACAAACAATCTTTGAAACGCCATGCCCAGGTATAGACCTGGTTTCCACTGCTATTGCGTTTGTAGACCAGGCGGCGTGAATCACGCGCTCTGGGATAACGGGGCAACCATGCCGGGTGGGa  >  2:295055/1‑227 (MQ=255)
                                                                                                                                                                                                                             |                                                                                                                                                                                                                         
CCCGAATACCATCAGCCAGACGTTTGCCGTTACGCACCGACAGCAGCGTCAGCAAAGTGCGCCAGGTCATACGTTTATTGCGGATCTGGTAGAGGGTAAACAGCTGATATTTTTTGCTGGCGCGGTCGAATTTGTCTTTGTGCTTGCGGTAAAAGTGGAAGTACCCGGAGAATTTTTTCGGTGACGAGGTGATCTGCATTTCACCGTGATTGATATGCAGGATCTGCGTCGCCTCTTCTACTTTCCACGGTTCGCCGTACTCCACCACCATCCGCAGGAAGATGTCGTAATCCTGTGCCGCTTTCAGTTCGGTATCGAACAAACACTCTTTGAAACGCCATGCCCAGGTAAAGACCTGGTTGCCAATGATATTGCGTTTGTAGAACAGGCGGCGTGAATACGGCGATTTGGGATACAGCGGCAAGCTTGCCGGTTGGGA  >  NC_000913/2132566‑2133004

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 26 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

BRESEQ :: bam2aln output
GCAGATCTTCCAGCATCTTTAGCGCCCCCGAATACCATCAGCCAGACGTTTGCCGTTACGCACCGACAGCAGCGTCAGCAAAGTGCGCCAGGTCATACGTTTATTGCGGATCTGGTAGAGGGTAAACAGCTGATATTTTTTGCTGGCGCGGTCGAATTTGTCTTTGTGCTTGCGGTAAAAGTGGAAGTACCCGGAGAATTTTTTCGGTGACGAGGTGATCTGCATTTCACCGTGATTGATATGCAGGATCTGCGTCGCCTCTTCTACTTTCCACGGTTCGCCGTACTCCACCACCATCCGCAGGAAGATGTCGTAATCCTGTGCCGCTTTCAGTTCGGTATCGAACAAACACTCTTTGAAACGCCATGCCCAGGTAAAGACCTGGTTGCCAATGATATTGCGTTTGTAGAACAGGCGGCGTGAATACGGCGATTTGGGATACAGCGGCAAGCTTGCCGGTTGGGAATAGACTTCGCCCTGGCAAACGTAGTCG  >  NC_000913/2132540‑2133032
                                                                                                                                                                                                                                                       |                                                                                                                                                                                                                                                     
GCAGATCTTCCAGCATCTTTAGCGCCCCCGAATTCCATCAGCCAGACGTTTGCCGTTACGCACCGACAGCAGCGTCAGCAAAGTGCGCCAGGTCATACGTTTATTGCGGATCTGGTAGAGGGTAAACAGCTGATATTTTTTGCTGGCGCGGTCGAATTTGTCTTTGTGCTTGCGGTAAAAGTGGAAGTACCCGGAGAATTTTTTCGGTGACGAGGTGATCTGCATTTCACCGTGATTGATATGCAGGCTC                                                                                                                                                                                                                                                     <  M01186:129:000000000‑A5M8V:1:2101:21198:11125/250‑1 (MQ=60)
    ATCTTCCAGCATCTTTAGCGCCCCCGAATACCATCAGCCAGACGTTTGCCGTTACGCACCGACAGCAGCGTCAGCAAAGTGCGCCAGGTCATACGTTTATTGCGGATCTGGTAGAGGGTAAACAGCTGATATTTTTTGCTGGCGCGGTCGAATTTGTCTTTGTGCTTGCGGTAAAAGTGGAAGTACCCGGAGAATTTTTTCGGTGACGAGGTGATCTGCATTTCACCGGGATTGATATGCAGGCTCTGCGT                                                                                                                                                                                                                                                >  M01186:129:000000000‑A5M8V:1:2101:20541:14564/1‑251 (MQ=60)
               TCTTTAGCGCCCCCGAATACCATCAGCCAGACGTTTGCCGTTACGCACCGACAGCAGCGTCAGCAAAGTGCGCCAGGTCATACGTTTATTGCGGATCTGGTAGAGGGTAAACAGCTGATATTTTTTGCTGGCGCGGTCGAATTTGTCTTTGTGCTTGCGGTAAAAGTGGAAGTACCCGGAGAATTTTTTCGGTGACGAGGTGATCTGCATTTCACCGTGATTGATATGCAGGCTCTGCGTCGCCTCTTCT                                                                                                                                                                                                                                      >  M01186:129:000000000‑A5M8V:1:2106:24954:20134/1‑250 (MQ=60)
                        CCCCCGAATCCCATCAGCCAGACGTTTGCCGTTACGCACCGGCAGCAGCGTCAGCAAAGTGCGCCAGGTCATACGTTTATTGCGGATCTGGTAGAGGGTAAACAGCTGATATTTTTTGCTGGCGCGGTCGAATTTGTCTTTGTGCTTGCGGTAAAAGTGGAAGTACCCGGAGAATTTTTTCGGTGACGAGGTGATCTGCATTTCACCGTGATTGATATGCAGGCTCTGCGTCGCCTCTTCTACTTTCCAC                                                                                                                                                                                                                             <  M01186:129:000000000‑A5M8V:1:1102:19366:9054/250‑1 (MQ=60)
                        CCACCGAATACCATCAGCCAGACGTTTGCCTTTTCGCACCGACAGCAGCGTCAGCAAAGTGCGCCAGGTCATAGGTTTATTGCGGATCTGGTAGAGGGTAAACAGATGATATTTTTTGCTGGCGCGGTCGAATTTGTCTTTGTGCTTGCGGTAAAAGTGGAAGTACCCGGAGAATTTTTTCGGTGACGAGGTGATCTGCATTTCACCGTGATTGATATGCAGGCTCTGCGTCGCCTCTTCTACTTTCCAC                                                                                                                                                                                                                             <  M01186:129:000000000‑A5M8V:1:1107:23449:23442/250‑1 (MQ=60)
                          CCCGAATACCATCAGCCAGACGTTTGCCGTTACGCACCGACAGCAGCGTCAGCAAAGTGCGCCAGGTCATACGTTTATTGCGGATCTGGTAGAGGGTAAACAGCTGATATTTTTTGCTGGCGCGGTCGAATTTGTCTTTGTGCTTGCGGTAAAAGTGGAAGTACCCGGAGAATTTTTTCGGTGACGAGGTGATCTGCATTTCACCGTGATTGATATGCAGGCTCTGCGTCGCCTCTTCTACTTTCCCCGGT                                                                                                                                                                                                                          >  M01186:129:000000000‑A5M8V:1:2101:22296:9739/1‑251 (MQ=60)
                          CCCGAATACCATCAGCCAGACGTTTGCCGTTACGCACCGACAGCAGCGTCAGCAAAGTGCGCCAGGTCATACGTTTATTGCGGATCTGGTAGAGGGTAAACAGCTGATATTTTTTGCTGGCGCGGTCGAATTTGTCTTTGTGCTTGCGGTAAAAGTGGAAGTACCCGGAGAATTTTTTCGGTGACGAGGTGATCTGCATTTCACCGTGATTGATATGCAGGCTCTGCGTCGCCTCTTCTACTTTCCACGGT                                                                                                                                                                                                                          >  M01186:129:000000000‑A5M8V:1:1101:14199:16416/1‑251 (MQ=60)
                                 tcactgagcctGACGTTTGCCTTTCCGCACCGACAGCAGCGTGAGCAAAGTGCGCCAGGTCATACGTTTATTGGGGATCTGGTAGAGGGTAAACAGCTGATATTTTTTGCTGGCGCGGTCGAATTTGTCTTTGTGCTTGCGGTAAAAGTGGAAGTACCCGGAGAATTTTTTCGGTGACGAGGTGATCTGCATTTCACCGTGATTTATATGCAGGCTCTGCGTCGCCTCTTCTACTTTCCACGGTTCGCCGT                                                                                                                                                                                                                   <  M01186:129:000000000‑A5M8V:1:1105:11694:4494/240‑1 (MQ=60)
                                  CCATCAGCCAGACGTTTGCCGTTACGCACCGACAGCAGCGTCAGCAAAGTGCGCCAGGTCATACGTTTATTGCGGATCTGGTAGAGGGTAAACAGCTGATATTTTTTGCTGGCGCGGTCGACTTTGTCTTTGTGCTTGCGGTAAAAGTGGAAGTACCCGGAGAATTTTTTCGGTGACGTGGGTATCTGCATTTCACCGTGATTGATAGGCAGGCTCTGGGTCGCCTCTTCTACTTTCCACGGTCTGCCGTA                                                                                                                                                                                                                  >  M01186:129:000000000‑A5M8V:1:2114:6721:18765/1‑251 (MQ=60)
                                      CAGCCAGACGTTTGCCGTTACGCACCGACAGCAGCGTCAGCAAAGTGCGCCAGGTCATACGTTTATTGCGGATCTGGTAGAGGGTAAACAGCTGATATTTTTTGCTGGCGCGGTCGAATTTGTCTTTGTGCTTGCGGTAAAAGTGGAAGTACCCGGAGAATTTTTTCGGTGACGAGGTGATCTGCATTTCACCGTGATTGATATGCAGGCTCTGCGCCGCCCCTTCTACTTTCCACGGTTCGCCGTCCTC                                                                                                                                                                                                               >  M01186:129:000000000‑A5M8V:1:2106:23021:6688/1‑250 (MQ=60)
                                           cgcCGTTTGCCGTTCCCCCCCGACAGCGGCGTCAGCAAAGTGCGCCAGGTCATACGTTTATTGCGGATCTGGTAGAGGGTAAACAGCTGATATTTTTTGCTGGCGCGGTCGAATTTGTCTTTGTGCTTGCGGTAAAAGTGGAAGTACCCGGAGAATTTTTTCGGTGACGAGGTGATCTGCATTTCACCGTGATTGATATGCAGGCTCTGCGTCGCCTCTTCTACTTTCCACGGTTCGCCGTACTCCACCAC                                                                                                                                                                                                         <  M01186:129:000000000‑A5M8V:1:2104:27855:19388/248‑1 (MQ=60)
                                           atgcgttgggcgttccgctCCGACAGCAGGGTCAGCAAAGTGCGCCAGGTCATACGTTTATTGCGGATCTGGTAGAGGGTAAACAGCTGATATTTTTTGCTGGCGCGGTCGAATTTGTCTTTGTGCTTGCGGTAAAAGTGGAAGTACCCGGAGAATTTTTTCGGTGACGAGGTGATCTGCATTTCACCGTGATTGATATGCAGGCTCTGCGTCGCCTCTTCTACTTTCCACGGTTCGCCGTACTCCACCAC                                                                                                                                                                                                         <  M01186:129:000000000‑A5M8V:1:2108:23959:10444/232‑1 (MQ=60)
                                           CGACGTTTCCCGTTACGGACCGACAGCAGCGTCAGCAAAGTGCGCCAGGTCATACGTTTATTGCGGATCTGGTAGAGGGTAAACAGCTGATATTTTTTGCTGGCGCGGTCGAATTTGTCTTTGTGCTTGCGGTAAAAGTGGAAGTACCCGGAGAATTTTTTCGGTGACGAGGTGATCTGCATTTCACCGTGATTGATATGCAGGCTCTGCGTCGCCTCTTCTACTTTCCACGGTTCGCCGTACTCCACCAC                                                                                                                                                                                                         <  M01186:129:000000000‑A5M8V:1:2106:6681:12307/251‑1 (MQ=60)
                                            GACGTTTGCCGTTACGCACCGACAGCAGCGTCAGCAAAGTGCGCCAGGTCATACGTTTATTGCGGATCTGGTAGAGGGTAAACAGCTGATATTTTTTGCTGGCGCGGTCGAATTTGTCTTTGTGCTTGCGGTAAAAGTGGAAGTACCCGGGGAATTTTTTCGGTGACTAGGTGATCTGCATTTCACCGTGTTTGATCTGCAGGCTCTGCGTCGCCTCTTCTCCTTTCCACGGTTCGCCGGACTCCA‑CACC                                                                                                                                                                                                        >  M01186:129:000000000‑A5M8V:1:2114:12457:21405/1‑250 (MQ=60)
                                                  tgacgttacggcacgaaatcggcgtaAGCAAGGTGCGCCAGGTCATGCGTTTATTGCGGGTCTGGTAGAGGGTAAAAAGCTGATATTTTTTGCTGGCGCGGTCGAATTTGTCTTTGTGCTTGCGGTAAAAGTGGAAGTGCCCGGAGAATTTTTTCGGTGCCGAGGTGATCTGCATTTCACCGTGATTGATATGCAGGCTCTGCGTCGCCTCTTCTACTTTCCACGGTTCGCCGTACTCCACCACCATCCGC                                                                                                                                                                                                  <  M01186:129:000000000‑A5M8V:1:1111:19464:13574/225‑1 (MQ=60)
                                                      GTTACGCACCGACAGCAGCGTCAGCAAAGTGCGCCAGGTCATACGTTTATTGCGGATCTGGTAGAGGGTAAACAGCTGATATTTTTTGCTGGCGCGGTCGAATTTGTCTTTGTGCTTGCGGTAAAAGTGGAAGTACCCGGAGAATTTTTTCGGTGACGAGGTGATCTGCATTTCACCGTGATTGATATGCAGGCTCTGCGTCGCCTCTTCTACTTTCCACGGTTCGCCGTACTCCACCACCATCCGCAGGA                                                                                                                                                                                              >  M01186:129:000000000‑A5M8V:1:1107:11763:14775/1‑251 (MQ=60)
                                                             ACCGACAGCAGCGTCAGCAAAGTGCGCCAGGTCATACGTTTATTGCGGATCTGGTAGAGGGTAAACAGCTGATATTTTTTGCTGGCGCGGTCGAATTTGTCTTTGTGCTTGCGGTAAAAGTGGAAGTACCCGGAGAATTTTTTCGGTGACGAGGTGATCTGCATTTCACCGTGATTGATATGCAGGCTCTGCGTCGCCTCTTCTACTTTCCACGGTTCGCCGTACTCCACCACCATCCGCAGGAAGATGT                                                                                                                                                                                        >  M01186:129:000000000‑A5M8V:1:1101:26446:13691/1‑250 (MQ=60)
                                                               CGACAGCAGCGTCAGCAAAGTGCGCCAGGTCATACGTTTATTGCGGATCTGGTAGAGGGTAAACAGCTGATATTTTTTGCTGGCGCGGTCGAATTTGTCTTTGTGCTTGCGGTAAAAGTGGAAGTACCCGGAGAATTTTTTCGGTGACGAGGGGATCTGCATTTCACCGTGATTGATATGCAGGCTCTGCGTCGCCTCTTCTACTTTCCACGGTTCGCCGTACTCCACCACCACCCCCAGGCAGATGTCGA                                                                                                                                                                                     >  M01186:129:000000000‑A5M8V:1:2108:11992:9973/1‑251 (MQ=60)
                                                                 aaagcaggtTCAGCAAAGTGCACCAGGTCATGCGTTTAATGCGGATCTGGTAGAGGGTAAACAGCTGATATTTTTTGCTGGCTCGGTCGAATTTGTCTTTGTGCTTGCGGTAAAAGTGGAAGTACCCGGAGAATTTTTTCGGTGACGAGGTGATCTGCATTTCACCGTGATTGATATGCAGGCTCTGCGTCGCCTCTTCTACTTTCCACGGTTCGCCGTACTCCACCACCATCCGCAGGAAGATGTCGTA                                                                                                                                                                                    <  M01186:129:000000000‑A5M8V:1:1104:10194:22354/241‑1 (MQ=60)
                                                                 ACAGCAGCGTCAGCAAAGTGCGCCAGGTCATACGTTTATTGCGGATCTGGTAGAGGGTAAACAGCTGATATTTTTTGCTGGCGCGGTCGAATTTGTCTTTGTGCTTGCGGTAAAAGTGGAAGTACCCGGAGAATTTTTTCGGTGACGAGGTGATCTGCATTTCACCGTGATTGATATTCAGGCTTTGCGTCGCCTCTTCTACTTTCCACGGTTCCCCGTACTCCACCACCACCCGCAGGACGATGTCGAAA                                                                                                                                                                                   >  M01186:129:000000000‑A5M8V:1:1104:27302:10105/1‑251 (MQ=60)
                                                                     gcggGTCAGCAAAGTGCGCCAGGTCATACGTTTATTGCGGATCTTGTAGAGGGTAAACAGCTGATATTTTTTGCTGGCGCGGTCGAATTTGTCTTTGTGCTTGCGGTAAAAGTGGAAGTACCCGGAGAATTTTTTCGGTGACGAGGTGATCTGCATTTCACCGTGATTGATATGCAGGCTCTGCGTCGCCTCTTCTACTTTCCACGGTTCGCCGTACTCCACCACCATCCGCAGGAAGATGTCGTAATCC                                                                                                                                                                                <  M01186:129:000000000‑A5M8V:1:2104:15735:11777/246‑1 (MQ=60)
                                                                     gagggtcagacaatgGCGCCAGGTCATACGTGTTTTGCGGATCTGGTAGAGGGTAAACAGCTGATATTTTTTGCTGGCGCGGTCGAATTTGTCTTTGTGCTTGCGGTAAAAGTGGAAGTACCCGGAGAATTTTTTCGGTGACGAGGTGATCTGCATTTCACCGTGATTGATATGCAGGCTCTGCGTCGCCTCTTCTACTTTCCACGGTTCGCCGTACTCCACCACCATCCGCAGGAAGATGTCGTAATCC                                                                                                                                                                                <  M01186:129:000000000‑A5M8V:1:2107:14791:9745/235‑1 (MQ=60)
                                                                     aaagctggataagggatgcgctagattcccgtgggctcggagatgtgtataaggagcagggagatagTTTTTGCTGGCGCGGTCGAATTTGTCTTTGTGCGTGCGGTAAAAGTGGAAGTACCCGGATAATTTTTTCGGTGACGAGGTTATCTGCATTTCACCGTGATTGATATGCAGGCTCTGCGTCGCCTCTTCTACTTTCCACGGTTCGCCGTACTCCACCACCATCCGCAGGAAGATGTCGTAATCC                                                                                                                                                                                <  M01186:129:000000000‑A5M8V:1:2114:23831:10991/183‑1 (MQ=60)
                                                                     GAGCGTCAGGAAAGTGCGCCAGTTTATACGTTTATTGCGGATGCGGTAGAGGGTAAACAGCTTATATTTTTTGCTGGCGCGGTCGAATTTGTCTTTGTTCTTGCGGTAAAAGTGGAAGTTCCCGGAGAATTTTTTCGGTGACGAGGTGATCTGCATTTCACCGTGATTGATATGCAGGCTCTGCTGCGCCTCTTCTACTTTCCACGGTTCGCCGTACTCCACCACCATCCGCAGGAAGATGTCGTAATCC                                                                                                                                                                                <  M01186:129:000000000‑A5M8V:1:1111:6043:7168/250‑1 (MQ=60)
                                                                     CAGGGTCAACAAAGGGCGCCAGGTCATACGTTTATTGCGGATCTGGTAGAGGGTAAACAGCTGATATTTTTTGCTGGCGCGGTCGAATTTGTCTTTGTGCTTGCGGTAAAAGTGGAAGTACCCGGAGAATTTTTTCGGTGACGAGGTGATCTGCATTTCACCGTGATTGATATGCAGGCTCTGCGTCGCCTCTTCTACTTTCCACGGTTCGCCGTACTCCACCACCATCCGCAGGAAGATGTCGTAATCC                                                                                                                                                                                <  M01186:129:000000000‑A5M8V:1:1108:14223:25361/250‑1 (MQ=60)
                                                                             GCAAAGTGCGCCAGGTCATACGTTTATTGCGGATCTGGTAGAGGGTAAACAGCTGATATTTTTTGCTGGCGCGGTCGAATTTGTCTTTGTGCTTGCGGTAAAAGTGGAAGTACCCGGAGAATTTTTTCGGTGACGAGGGGATCTGCATTTCACCGGGATTGATATGCAGGCTCTGCGTAGCCTCTTCTACTTTCCACGGTTAGCCGAAATCCACCACCCTCCGCAGGAAGATGCCGTAATCCTGTGCCG                                                                                                                                                                         >  M01186:129:000000000‑A5M8V:1:2112:26395:23650/1‑249 (MQ=60)
                                                                                   TGCGCCCGGTCAGAGGTTTATGTCGGATCTGGTTGAGGGTAAACAGCTGATATTTTTTGCTGGCGCGGTCGAATTTTTCTTTGTGCTTGCGGTAAAAGTGGAAGTACCCGGAGAATTTTTTCGGTGACGAGGTGATCTGCATTTCACCGTGATTGATATGCAGGCTCTGCGTCGCCTCTTCTACTTTCCACGGTTCGCCGTACTCCACCACCATCCGCAGGAAGATGTCGTAATCCTGTGCCGCTTTCAGT                                                                                                                                                                 <  M01186:129:000000000‑A5M8V:1:2108:26168:14814/251‑1 (MQ=60)
                                                                                          GGTCATACGTTTATTGCGGATCTGGTAGAGGGTAAACAGCTGATATTTTTTGCTGGCGCGGTCGAATTTGTCTTTGTGCTTGCGGTAAAAGTGGAAGTACCCGGAGAATTTTTTCGGTGACGAGGTGATCTGCATTTCACCGTGATTGATATGCAGGCTCTGCGTCGCCTCTTCTACTTTCCACGGTTCGCCGTACTCCACCACCATCCGCAGGAAGATGTCGTAATCCTGTCCCGCTTTCAGTTCGGTA                                                                                                                                                           >  M01186:129:000000000‑A5M8V:1:1105:12677:10804/1‑250 (MQ=60)
                                                                                           GTCTTTCGTTTATTGCGGATCTGGTAGAGTGTTGACAGCAGATAGTTTTTGTGAGGGCGGTGTAATTTGTCTTTGTGATTGCGGTAAAAGTGTAAGTACCCGGATAATGTTTTCGGTGACCAGCTGATCTGCATTTCACCGTGATTGATATGCAGGCTCTGCGTCGCCTCTTCTTCTTTCCACGGTTCGCCGTTCTCCTCCACCATCCGCAGGAAGATGTCGTAATCCTGTGGCGCTTTCAGTTCGGTAT                                                                                                                                                          <  M01186:129:000000000‑A5M8V:1:2112:20733:4702/250‑1 (MQ=60)
                                                                                                 CGTTTATTGCGGATCTGGTAGAGGGTAAACAGCTGATATTTTTTGCTGGCGCGGTCGACTTTGTCTTTGTGCTTGCGGTAAAAGCGGAATTACCCGGAGAATTTTTTCGGTGACGAGGTGATCTGCATTTCACGGTGATTGATATGCAGGCTCTGCGTTGCCTCTTCTACTTTCAACGGTTCGCCGTACTCCACCCCCATCCGCAGGAAGATGTCGTAATCCTGTGCCGCTTTCAGTTCGGTATCGAACAA                                                                                                                                                   >  M01186:129:000000000‑A5M8V:1:1101:11082:14751/1‑251 (MQ=60)
                                                                                                            GATCGGGTAGAGGGTAAACAGGTGATATTTTGTGCTGGCGCGGTCGAATTTGTCTTTGTGCTTGCGGTAAAAGTGGAAGTACCCGGAGAATTTTTTCGGTGACGAGGTGATCTGCATTTCACCGTGATTGATATGCAGGCTCTGCGTCGCCTCTTCTACTTTCCACGGTTCGCCGTACTCCACCACCATCCGCAGGAAGATGTCGTAATCCTGTGCCGCTTTCAGTTCGGTATCGAACAAACAC                                                                                                                                               <  M01186:129:000000000‑A5M8V:1:2106:15062:14440/244‑1 (MQ=60)
                                                                                                             ATCTGGTAGAGGGTAAACAGCTGATATTTTTTGCTGGCGCGGTCGAATTTGTCTTTGTGCTTGCGGTAAAAGTGGAAGTACCCGGAGAATTTTTTCGGTGACGAGGTGATCTGCATTTCACCGTGATTGATATGCAGGCTCTGCGTCGCCTCTTCTACTTTCCACGGTTCGCCGTACTCCCCCACCACCCCCAGGAAGATGTCGTAATCCTGTGCCCCTTTCAGTTCGGTATCGAACAAACACTCTTTGAA                                                                                                                                       >  M01186:129:000000000‑A5M8V:1:2102:24494:9456/1‑251 (MQ=60)
                                                                                                                      cggggAAACAGCTGATATTTTTTGCTGGCGCGGTCGAATTTGTCTTTGTGCTTGCGGTAAAAGTGGAAGTACCCGGAGAATTTTTTCGGTGACGAGGTGATCTGCATTTCACCGTGATTGATATGCAGGCTCTGCGTCGCCTCTTCTACTTTCCACGGTTCGCCGTACTCCACCACCATCCGCAGGAAGCTGTCGTCATCCTGTGCCGCTTTCAGTTCGGCATCTAACAAACCCTCTTTGAAACGCCATG                                                                                                                               >  M01186:129:000000000‑A5M8V:1:1101:12582:6140/6‑250 (MQ=60)
                                                                                                                       GGGTAAACAGCTGATATTTTTTGCTGGCGCGGTCGAATTTGTCTTTGTGCTTGCGGTAAAAGTGGAAGTACCCGGAGAATTTTTTCGGTGACGAGGTGATCTGCATTTCACCGTGATTGATATGCAGGCTCTGCGTCGCCTCTTCTACTTTCCACGGTTCGCCGTACTCCACCACCATCCGCAGGAAGATGTCGTAATCCTGTGCCGCTTTCAGTTCGGTATCGAACAAACACTCTTTGAAACGCCATGC                                                                                                                              >  M01186:129:000000000‑A5M8V:1:1110:20123:16809/1‑250 (MQ=60)
                                                                                                                         GTAAACAGCTGATATTTTTTGCTGGCGCGGTCGAATTTGTCTTTGTGCTTGCGGTAAAAGTGGAAGTACCCGGAGAATTTTTTCGGTGACGAGGTGATCTGCATTTCACCGTGATTGATATGCAGGCTCTGCGTCGCCTCTTCTACTTTCCACGGTTCGCCGTACTCCACCACCATCCGCAGGAAGATGTCGTAATCCTGTGCCGCTTTCAGTTCGGTATCGAACAAACACTCTTTGAAACGCCATGCCC                                                                                                                            <  M01186:129:000000000‑A5M8V:1:2109:27339:16777/250‑1 (MQ=60)
                                                                                                                         GTAAACAGCTGATATTTTTTGCGGGGGCGGTCGAATTTGTCTTTGTGCTTGCGGTAAACGTGGAAGTACCCGGAGAATTTTTTCGGTGACGAGGTGATCTGCATTTCACCGTGATTGATATGCAGGCTCTGCGTCGCCTCTTCTACTTTCCACGGTTCGCCGTACTCCACCACCATCCGCAGGAAGATGTCGTAATCCTGTGCCGCTTTCAGTTCGGTATCGAACAAACACTCTTTGAAACGCCATGCCC                                                                                                                            <  M01186:129:000000000‑A5M8V:1:2103:18686:24704/250‑1 (MQ=60)
                                                                                                                                  TGATATTTTTTGGTGGCGCGGTTGAATTTTGCTTGGGGCTGTCGGGTAAAGTTGAATTACCCGGAGAATTTTTTCGGTGTCGCGGTGATCTGCATCTCACCGTGATTGGTAGGCAGGCTCTGCGTCGCCTCTTCTACTTTCCAAGGTTCGCCGTACTCCACCACCATCCGCAGGAAGATGTCGTAATCCTGTGCCGCTTTCAGTTCGGTATCGAACAAACACTCTTTGAAACGCCATGCCCAGGTAAAGAC                                                                                                                  <  M01186:129:000000000‑A5M8V:1:1113:7998:13031/251‑1 (MQ=60)
                                                                                                                                       tgtggtggtggcgcgtgtGAATTTGTTTTTGTGCTTGCGGTAAAAGTGGAAGTACCCGGAGAATTTTTTCGGTGACGAGGTTATCTGCATTTCACCGTGATTGATATGCAGGCTCTGCGTCGCCTCTTCTACTTTCCACGGTTCGCCGTACTCCACCACCATCCGCAGGAAGATGTCGTAATCCTGTGCCGCTTTCAGTTCGGTATCGAACAAACACTCTTTGAAACGCCATGCCCAGGTAAAGACCTGGT                                                                                                             <  M01186:129:000000000‑A5M8V:1:1104:11718:2516/233‑1 (MQ=60)
                                                                                                                                        TTTTTGCTGGCGCGGTCGAATTTGGCTTTGTGCTTGCGGTAAAAGTGGAAGTACCCGGAGAATTTTTTCGGTGACGAGGTGATCTGCATTTCCCCGTGCTTGATATGCAGGCTCTGCGTCGCCTCTTCTACTTTCCACGGTTCGCCGAACTCCACCACCATCCGCAGGAAGATGCCGTAATCC                                                                                                                                                                                >  M01186:129:000000000‑A5M8V:1:1103:23704:23240/1‑183 (MQ=60)
                                                                                                                                                                              GTAAAAGTGGAAGTACCTGGAGAATTTTTTCGGTGACGAGGTGATCTGCATTTCACCGTGATTGATATGCAGGCTCTGCGTCGCCTCTTCTACTTTCCACGGTTCGCCGTACTCCACCACCATCCGCAGGAAGATGTCGTAATCCTGTGCCGCTTTCAGTTCGGTATCGAACAAACACTCCTTGAAACGCCATGCCCCGGTAAAGACCTGGTTGCCAATGATATTGCGTTTGTAGAACAGGGGGCGAGAAT                                                                      >  M01186:129:000000000‑A5M8V:1:2103:28958:15179/1‑251 (MQ=60)
                                                                                                                                                                                                                 ACGAGGTGATCTGCATTTCACCGTGATTGATATGCAGGCTCTGCGTCGCCTCTTCTACTTTCCACGGTTCGCCGTACTCCACCACCATCCGCAGGAAGATGTCGTAATCCTGTGCCGCTTTCAGGTCGGTATCGAACAAACACTCTTTGAAACGCCATGCCCAGGTAAAGACCTGGTTGCCAATGATATTG                                                                                               <  M01186:129:000000000‑A5M8V:1:2104:14360:24860/191‑1 (MQ=60)
                                                                                                                                                                                                                      gggacCTGCATTTCACCTGGATTGGTATGCAGGCTTTGCGGCGCCTCTGCTACTTTCCACGGTTCGCCGTACTCCACCACCATCCGCAGGAAGATGTCGTAATCCTGTGCCGCTTTCAGTTCGGTATCGAACAAACACTCTTTGAAACGCCATGCCCAGGTAAAGACCTGGTTGCCAATGATATTGCGTTTGTAGAACAGGCGGCGTGAATACGGCGATTTGGGATACAGCGGCAAGCTTGCCGGTTGGG                               <  M01186:129:000000000‑A5M8V:1:2104:28053:9348/245‑1 (MQ=60)
                                                                                                                                                                                                                           CTGCATTTCACCGTGATTGATATGCAGGCTCTGCGTCGCCTCTTCTACTTTCCACGGTTCGCCGTACTCCACCACCATCCGCAGGAAGATGTCGTAATCCTGTGCCGCTTTCAGTTCGGTATCGCACACACACTCTTTGAAACGCCATGCCCAGGTAACGACCTGGTTGCCAATGATATTGCGTTTGTAGAACACGCGGCGTGAAAACGGCGATTTGGGATACAGCGGCAAACTTGCCAGTTGGGAATAG                          >  M01186:129:000000000‑A5M8V:1:1108:24852:10486/1‑250 (MQ=60)
                                                                                                                                                                                                                           CTGCATTTCACCGTGATTGATATGCAGGCTCTGCGTCGCCTCTTCTACTTTCCACGGTTCGCCGTACTCCACCACCATCCGCAGGAAGATGTCGTAATCCTGTGCCGCTTTCAGTTCGGTATCGAACAAACACTCTTTGAAACGCCATGCCCAGGTAAAGAC                                                                                                                  <  M01186:129:000000000‑A5M8V:1:1103:19629:19239/162‑1 (MQ=60)
                                                                                                                                                                                                                                           TTGATATGCAGGCTCTGCGTCGCCTCTTCTACTTTCCACGGTTCGCCGTACTCCACCACCATCCGCAGGAAGATGTCGTAATCCTGTGCCGCTTTCAGTTCGGTATCGAACAAACACTCTTTGAAACGCCATGCCCAGGTAAAGACCTGGTTGCCAATGATATTGCGTTTGTAGAACAGGCGGCGTGAATACGGCGATTTGGGATACAGCGGCAAGCTTGCCGGTTGGGAATAGACTTTGCCCTGGCAAAG         >  M01186:129:000000000‑A5M8V:1:1109:25769:18230/1‑251 (MQ=60)
                                                                                                                                                                                                                                               TATGCAGGCTCTGCGTCGCCTCTTCTACTTTCCACGGTTCGCCGTACTCCACCACCATCCGCAGGAAGATGTCGTAATCCTGTGCCGCTTTCAGTTCGGTATCGAACAAACACTCTTTGAAACGCCATGCCCAGGTAAAGACCTGGTTGCCAATGATATTGCGTTTGTAGAACAGGCGGCGTGAATAAGGCGATTTGGGTTCAAGAGGCAAGCTTGCCGGTTGGGGATAGACTTCGCCCTGGCAAACGAAG     >  M01186:129:000000000‑A5M8V:1:2101:26053:13209/1‑251 (MQ=60)
                                                                                                                                                                                                                                                  TCAGGCTCTGCGTCGCCTCTTCTACTTTCCACGGTTCGCCGTACTCCCCCACCATCCGCAGGAAGATGTCGTAATCCTGTGCCGCTTTCAGTTCGGTATCGAACAAACACTCTTTGAAACGCCATGCCCAGGTAAAGACCTGGTTGCCAATGATATTGCGTTTGTAGAACAGGCGGCGTGAATACGGCGATTTGGGATACAGCGGCAAGCTTGCCGGTTGGGAATAGACTTCGCCCTGGCAAACGTAGTCG  <  M01186:129:000000000‑A5M8V:1:2106:19450:9139/251‑1 (MQ=60)
                                                                                                                                                                                                                                                       |                                                                                                                                                                                                                                                     
GCAGATCTTCCAGCATCTTTAGCGCCCCCGAATACCATCAGCCAGACGTTTGCCGTTACGCACCGACAGCAGCGTCAGCAAAGTGCGCCAGGTCATACGTTTATTGCGGATCTGGTAGAGGGTAAACAGCTGATATTTTTTGCTGGCGCGGTCGAATTTGTCTTTGTGCTTGCGGTAAAAGTGGAAGTACCCGGAGAATTTTTTCGGTGACGAGGTGATCTGCATTTCACCGTGATTGATATGCAGGATCTGCGTCGCCTCTTCTACTTTCCACGGTTCGCCGTACTCCACCACCATCCGCAGGAAGATGTCGTAATCCTGTGCCGCTTTCAGTTCGGTATCGAACAAACACTCTTTGAAACGCCATGCCCAGGTAAAGACCTGGTTGCCAATGATATTGCGTTTGTAGAACAGGCGGCGTGAATACGGCGATTTGGGATACAGCGGCAAGCTTGCCGGTTGGGAATAGACTTCGCCCTGGCAAACGTAGTCG  >  NC_000913/2132540‑2133032

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑