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
A21 F20 I0 R1 109 83.9 1834642 93.1% 1708051 141.0

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA CP000730 973,213 C→A 100% E175* (GAG→TAG)  USA300HOU_0930 ← possible HAD superfamily hydrolase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*CP000730973,2130CA100.0% 186.3 / NA 59E175* (GAG→TAG) USA300HOU_0930possible HAD superfamily hydrolase
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base A (30/29);  total (30/29)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

TATCTTCATCACCGAATGCAATAATATTATTTCGGTCAATATTTAAAAATTGTCTAACTTGCTCAATGCCTCTTGCTTTATTAATACCAAGTTTTACAATTTCAATGACAGGGAATGGTGCGCCCCAGCGTCGATGCTCAATATGATCGGCATAAAAATGAGTAAGCATATTTTTGATTTCAGGTATTTTACTTTCTTCGGCTTCAATTAAAATTGAGGTAGGGGATTCTTTCAAGTGGACAAGTAAATTACCAGTTTGAATTCTTGGA  >  CP000730/973075‑973343
                                                                                                                                          |                                                                                                                                  
tATCTTCATCACCGAATGCAATAATATTATTTCGGTCAATATTTAAAAATTGTCTAACTTGCTCAATGCCTCTTGCTTTATTAATACCAAGTTTTACAATTTCAATGACAGGGAATGGTGCGCCCCAGCGTCGATGCTaaa                                                                                                                                  >  2:433720/1‑141 (MQ=255)
 ttCTTCATCACCGAATGCACTTATATTATTTCGGTCAATATTTAAAAGTTGTCTAACTTGCTCACTGCCTCTTGGTTTATTAATACCAAGTTTTACAATTTCAATGACAGGGAATGGTGCGCCCCAGCGTCGATGCTAAat                                                                                                                                 <  2:354262/140‑1 (MQ=255)
 aTCTTCATCACCGAATGCAATAATATTATTTCGGTCAATATTTAAAAATTGTCTAACTTGCTCAATGCCTCTTGCTTTATTAATACCAAGTTTTACAATTTCAATGACAGGGAATGGTGCGCCCCAGCGTCGATGCTAAat                                                                                                                                 <  2:743258/141‑1 (MQ=255)
      catcaCCGAATGCAATAATATTATTTCGGTCAATATTTAAAAATTGTCTAACTTGCTCAATGCCTCTTGCTTTATTAATACCAAGTTTTACAATTTCAATGACAGGGAATGGTGCGCCCCAGCGTCGATGCTAAATATGAt                                                                                                                            >  1:821818/1‑141 (MQ=255)
       atcaCCGAATGCAATAATATTATTTCGGTCAATATTTAAAAATTGTCTAACTTGCTCAATGCCTCTTGCTTTATTAATACCAAGTTTTACAATTTCAATGACAGGGAATGGTGCGCCCCAGCGTCGATGCTAAATATGATc                                                                                                                           >  1:706017/1‑141 (MQ=255)
         caCCGAATGCAATAATATTATTTCGGTCAATATTTAAAAATTGTCTAACTTGCTCAATGCCTCTTGCTTTATTAATACCAAGTTTTACAATTTCAATGACAGGGAATGGTGCGCCCCAGCGTCGATGCTAAATATGATCgg                                                                                                                         <  2:432337/141‑1 (MQ=255)
         caCCGAATGCAATAATATTATTTCGGTCAATATTTAAAAATTGTCTAACTTGCTCAATGCCTCTTGCTTTATTAATACCAAGTTTTACAATTTCAATGACAGGGAATGGTGCGCCCCAGCGTCGATGCTAAATATGATCgg                                                                                                                         <  2:432325/141‑1 (MQ=255)
         caCCGAATGCAATAATATTATTTCGGTCAATATTTAAAAATTGTCTAACTTGCTCAATGCATCTTGCTTTATTAATACCAAGTTTTACAATTTCAATGACAGGGAATGGTGCGCCCCAGCGTCGATGCTAAATATGATCgg                                                                                                                         >  2:139188/1‑141 (MQ=255)
           ccGAATGCAATAATATTATTTCGGTCAATATTTAAAAATTGTCTAACTTGCTCAATGCCTCTTGCTTTATTAATACCAAGTTTTACAATTTCAATGACAGGGAATGGTGCGCCCCAGCGTCGATGCTAAATATGATCGGCa                                                                                                                       <  1:646525/141‑1 (MQ=255)
           ccGAATGCAATAATATTATTTCGGTCAATATTTAAAAATTGTCTAACTTGCTCAATGCCTCTTGCTTTATTAATACCAAGTTTTACAATTTCAATGACAGGGAATGGTGCGCCCCAGCGTCGATGCTAAATATGATCGGCa                                                                                                                       <  2:266196/141‑1 (MQ=255)
            cGAATGCAATCATATTATTTCGGTCCATATTTAAACATTGTCTAACTTGCTAAATGCCTCTTGCTTTATTAATACCAAGTTTTACAATTTCAATGACAGGGAATGGTGCGCCCCAGCGTCGATGCTAAATATGATCGGCAt                                                                                                                      <  1:189251/141‑1 (MQ=255)
            cGAATGCAATAATATTATTTCGGTCAATATTTAAAAATTGTCTAACTTGCTCAATGCCCCTTGCTTTATTAATACCAATTTTTACAATTTCAATGACAGGGAATGGTGCGCCCCAACGTCGATGCTAAATATGATCGGCAt                                                                                                                      <  1:406772/141‑1 (MQ=255)
            cGAATGCAATAATATTATTTCCGTCAATATTTAAAAATTGTCTAACTTGCTCAATGCCTCTTGCTTTATTAATACCAAGTTTTACACATTCAAGGAATGGGCCTTATTCGCCCCAACGTCGATGCTAAATATGATCGGCAt                                                                                                                      <  1:214686/141‑1 (MQ=255)
             gAATGCAATAATAGTATTTCGGTCAATATTTAAAAATTGTCTAACTTGCTCAATGCCTCTTGCTTTATTAATACCAAGTTTTACAATTTCAATGACAGGGAATGGTGCGCCCCAGCGTCGATGCTAAATATGATCGGCATa                                                                                                                     <  2:108789/141‑1 (MQ=255)
               aTGCAATAATATTATTTCGGTCAATATTTAAAAATTGTCTAACTTGCTCAATGCCTCTTGCTTTATTAATACCAAGTTTTACAATTTCAATGACAGGGAATGGTGCGCCCCAGCGTCGATGCTAAATATGATCGGCATaaa                                                                                                                   <  2:870197/141‑1 (MQ=255)
                 gCAATAATATTATTTCGGTCAATATTTAAAAATTGTCTAACTTGCTCAATGCCTCTTGCTTTATTAATACCAAGTTTTACAATTTCAATGACAGGGAATGGTGCGCCCCAGCGTCGATGCTAAATATGATCGGCATaaaaa                                                                                                                 <  1:106382/141‑1 (MQ=255)
                 gCAATAATATTATTTCGGTCAATATTTAAAAATTGTCTAACTTGCTCAATGCCTCTTGCTTTATTAATACCAAGTTTTACAATTTCAATGACAGGGAATGGTGCGCCCCAGCGTCGATGCTAAATATGATCGGCATaaaaa                                                                                                                 >  1:367568/1‑141 (MQ=255)
                       atatTATTTCGGTCAATATTTAAAAATTGTCTAACTTGCTCAATGCCTCTTGCTTTATTAATACCAAGTTTTACAATTTCAATGACAGGGAATGGTGCGCCCCAGCGTCGATGCTAAATATGATCGGCATAAAAATGAGTa                                                                                                           <  1:239318/141‑1 (MQ=255)
                            attTCGGTCAATATTTAAAAATTGTCTAACTTGCTCAATGCCTCTTGCTTTATTAATACCAAGTTTTACAATTTCAATGACAGGGAATGGTGCGCCCCAGCGTCGATGCTAAATATGATCGGCATAAAAATGAGTAAGCat                                                                                                      >  1:909303/1‑141 (MQ=255)
                            attTCGGTCAATATATAAAAATTGTCTAGCTTGCTCAATGCCTCTTGCTTTATTAATACCAAGTTTTACAATTTCAATGACAGGGAATGGTGCGCCCCAGCGTCGATGCTAAATATGATCGGCATAAAAATGAGTAAGCat                                                                                                      >  1:594613/1‑141 (MQ=255)
                               tCGCTCAATATTTAAAAATTGTCTAAATTGATCAATGCCTCTTGCTTTATCAATACCAAGTTTTACAATTTCAATGACACGCAATGGTGCGCCCCAGCCTCGCTGCTAAATATGATCGGCATCCAAATGAGTAAGCATAtt                                                                                                   >  2:610889/1‑141 (MQ=255)
                                 ggTCAATATTTAAAAATTGTCTAACTTGCTCAATGCCTCTTGCTTTATTAATACCAAGTTTTACAATTTCAATGACAGGGAATGGTGCGCCCCAGCGTCGATGCTAAATATGATCGGCATAAAAATGAGTAAGCATAtttt                                                                                                 <  2:471281/141‑1 (MQ=255)
                                 ggTCAATATTTAAAAATTGTCTAACTTGCTCAATGCCTCTTGCTTTATTAATACCAAGTTTTACAATTTCAATGACAGGGAATGGTGCGCCCCAGCGTCGATGCTAAATATGATCGGCATAAAAATGAGTAAGCATAtttt                                                                                                 <  2:152620/141‑1 (MQ=255)
                                   tCAATATTTAAAAATTGTCTAACTTGCTCCATGCCTCTTGCTTCATTAATACCAAGCTTTACAATTTCAATGACAGGGAATGGTGCGCCGCCCCGTGGATGGTAAATTTGATCGGCATAAAAATGAGTAAGCATATTTTTg                                                                                               <  2:417338/141‑1 (MQ=255)
                                    cAATATTTAAAAATTGTCTAACTTGCTCAATGCCTCTTGCTTTATTAATACCAAGTTTTACAATTTCAATGACAGGGAATGGTGCGCCCTAGCGTCGATGCTAAATATGATCGGCATAAAAATGAGTAAGCATATTTTTGa                                                                                              <  2:51160/141‑1 (MQ=255)
                                     aaTATTTAAAAATTGTCTAACTTGCTCAATGCCTCTTGCTTTATTAATACCAAGTTTTACAATTTCAATGACAGGGAATGGTGCGCCCCAGCGTCGATGCTAAATATGATCGGCATAAAAATGAGTAAGCATATTTTTGAt                                                                                             >  1:3837/1‑141 (MQ=255)
                                     aaTATTTAAAAATTGTCTAACTTGCTCAATGCCTCTTGCTTTATTAATACCAAGTTTTACAATTTCAATGACAGGGAATGGTACGCCCCAGCGTCGATGCTAAATATGATCGGCCTAAAAATGATTAAGCCTAGTTTTGAt                                                                                             >  1:3922/1‑141 (MQ=255)
                                      atatTTAAAAATTGTCTAACTTGCTCAATGCCTCTTGCTTTATTAATACCAAGTTTTACAATTTCAATGACAGGGAATGGTGCGCCCCAGCGTCGATGCTAAATATGATCGGCATAAAAATGAGTAAGCATATTTTTGAtt                                                                                            <  1:103615/141‑1 (MQ=255)
                                      agatTTAAAAATTGTCGAGCTTGCTCGACGCCTCTTGCTTTATTAATACCGAGTTTTACAATTTCAATGACAGGGAATGGTGCGCGCCAGCGTCGATGCTAAATATGATCGGCATAAAAATGAGTAAGCATATTTTTGAtt                                                                                            <  1:545436/139‑1 (MQ=255)
                                        atTTAAAAATTGTCTAACTTGCTCAATGCCTCTTGCTTTATTAATACCAAGTTTTACAATTTCAATGACAGGGAATGGTGCGCCCCAGCGTCGATGCTAAATATGATCGGCATAAAAATGAGTAAGCATATTTTTGAttta                                                                                          >  2:56822/1‑140 (MQ=255)
                                             aaaaTTGTCTAACTTGCTCAATGCCTCTTGCTTTATTAATACCAAGTTTTACAATTTCAATGACAGGGAATGGTGCGCCCCAGCGTCGATGCTAAATATGATCGGCATAAAAATGAGTAAGCATATTTTTGATTTCAGGTa                                                                                     <  2:586839/141‑1 (MQ=255)
                                                aTTGTCTAACTTCCTCAATGCCTCTTGCATTATTAATACCAAGGTTTACAATTTCAATGACAGGGAATGGTGCGCCCCACCGTCGATGCTAAATATGATCGGCATAAAAATGAGTAAGCATATTTTTGATTTCAGGTAttt                                                                                  <  1:514470/141‑1 (MQ=255)
                                                 ttGTCTAACTTGCTCAATGCCTCTTGCTTTATTAATACCAAGTTTTACAATTTCAATGACAGGGAATGGTGCGCCCCAGCGTCGATGCTAAATATGATCGGCATAAAAATGAGTAAGCATATTTTTGATTTCAGGTAtttt                                                                                 <  2:156679/141‑1 (MQ=255)
                                                             cTCAATGCCTCTTGCTTTATTAATACCACGTTTTACAATTTCAATGACAGGGCATGGTGCGCCCCAGCGTCGAGGCTAAATATGATCGGCATACAAATGAGTAAGCATATTTTTGGTTTCAGGGATTTTACTTTCTTCgac                                                                     >  2:793245/1‑139 (MQ=255)
                                                                 aTGCCTCTTGCTTTATTAATACCAAGTTTTACAATTTCAATGACAGGGAATGGTGCGCCCCAGCGTCGATGCTAAATATGATCGGCATAAAAATGAGTAAGCATATTTTTGATTTCAGGTATTTTACTTTCTTCGGCTTCa                                                                 >  1:390385/1‑141 (MQ=255)
                                                                    ccTCTTGCTTTATTAATACCAAGTTTTACAATTTCAATGACAGGGAATGGTGCGCCCCAGCGTCGATGCTAAATATGATCGGCATAAAAATGAGTAAGCATATTTTTGATTTCAGGTATTTTACTTTCTTCGGCTTCAAtt                                                              <  1:820390/141‑1 (MQ=255)
                                                                           cTTTATTAATACCAAGTTTTACAATTTCAATGACAGGGAATGGTGCGCCCCAGCGTCGATGCTAAATATGATCGGCATAAAAATGAGTAAGCATATTTTTGATTTCAGGTATTTTACTTTCTTCGGCTTCAATTAAAATTg                                                       <  2:179645/141‑1 (MQ=255)
                                                                           cTTTATTAATACCAAGTTTTACAATTTCAATGACAGGGAATGGTGCGCCCCAGCGTCGATGCTAAATATGATCGGCATAAAAATGAGTAAGCATATTTTTGATTTCAGGTATTTTACTTTCTTCGGCTTCAATTAAAATTg                                                       <  1:193109/141‑1 (MQ=255)
                                                                                ttaATACCAAGTTTTACAATTTCAATGACAGGGAATGGTGCGCCCCAGCGTCGATGCTAAATATGATCGGCATAAAAATGAGTAAGCATATTTTTGATTTCAGGTATTTTACTTTCTTCGGCTTCAATTAAAATTGAGGTa                                                  <  1:139188/141‑1 (MQ=255)
                                                                                    tACCAAGTTTTACAATTTCAATGACAGGGAATGGTGCGCCCCAGCGTCGATGCTAAATATGATCGGCATAAAAATGAGTAAGCATATTTTTGATTTCAGGTATTTTACTTTCTTCGGCTTCAATTAAAATTGAGGTAgggg                                              >  1:141069/1‑141 (MQ=255)
                                                                                        taGTTTTACAATTTTAAGGATAGGGTATGGTGCGCCCCAGCGTCGATGCTAAATATGATCGGCATAAAAATGAGTAAGCATATTTTTGATTTCAGGTATTTTACTTTCTTCGGCTTCAATTAAAATTGAGGTAGGGGATTc                                          <  2:140135/140‑1 (MQ=255)
                                                                                            tttACAATTTCAATGACAGGGAATGGTGCGCCCCAGCGTCGATGCTAAATATGATCGGCATAAAAATGAGTAAGCATATTTTTGATTTCAGGTATTTTACTTTCTTGGGCTTCAATTAAAATTGAAGTAGGGGATTCttta                                      >  2:193844/1‑140 (MQ=255)
                                                                                            tttACAATTTCAATGACAGGGAATGGTGCGCCCCAGCGTCGATGCTAAATATGATCGGCATAAAAATGAGTAAGCATATTTTTGATTTCAGGTATTTTACTTTCTTCGGCTTCAATTAAAATTGAGGTAGGGGCTTCTTTc                                      >  1:622217/1‑141 (MQ=255)
                                                                                            tttACAATTTCAATGACAGGGAATGGTGCGCCCCAGCGTCGATGCTAAATATGATCGGCATAAAAATGAGTAAGCATATTTTTGATTTCAGGTATTTTACTTTCTTCGGCTTCAATTAAAATTGAGGGAGGGGATTCTTTc                                      >  2:303044/1‑141 (MQ=255)
                                                                                            tttACAATTTCAATGACAGGGAATGGTGCGCCCCAGCGGCGATGCTAAATATGATCGGCATAAAAATGAGTAAGCATATTTTTGATTTCAGGTATTTTACTTTCTTCGGCTTCAATTAAAATTGAGGTAGGGGATTCTTTc                                      >  1:575683/1‑141 (MQ=255)
                                                                                            tttACAATTTCAATGACAGGGAATGATGCGCCCCAGCGTCGATGCTAAATATGATCGGCATAAACATGCGTCAGCATATTTTTGATTTCGGGTATTTTCCTTTCTTCGGCTTCAATTAAAATTTAGGTGGGGGTTTCttta                                      >  2:39049/1‑140 (MQ=255)
                                                                                              tACAATTTCAATGACAGGGAATGGTGCGCCCCAGCGTCGATGCTAAATATGATCGGCATAAAAATGAGTAAGCATATTTTTGATTTCAGGTGTTTTACTTTCTTCGGGTTCAACTAACATTGAGGAAGGGGATTCTTTCaa                                    >  1:350247/1‑141 (MQ=255)
                                                                                              tACAATTTCAATGACAGGGAATGGTGCGCCCCAGCGTCGATGCTAAATATGATCGGCATAAAAATGAGTAAGCATATTTTTGATTTCAGGTATTTTACTTTCTTCGGCTTCAATTAAAATTGAGGTAGGGGATTCTTTCaa                                    >  1:765337/1‑141 (MQ=255)
                                                                                                    ttCAATGACAGGGAATGGTGCGCCCCAGCGTCGATGCTAAATATGATCGGCATAAAAATGAGTAAGCATATTTTTGATTTCAGGCTGCAGATTTTCTTCGGCTTCAATTAAAATTGAGGTAGGGGATTCTTTCAAGTGGAc                              >  1:253242/1‑141 (MQ=255)
                                                                                                       aaTGACAGGGAATGGTGCGCCCCAGCGTCGATGCTAAATATGATCGGCATAAAAATGAGTAAGCATATTTTTGATTTCAGGTATTTTACTTTCTTCGGCTTCAATTAAAATTGAGGTAGGGGATTCTTTCAAGTGGACAAg                           <  1:476167/141‑1 (MQ=255)
                                                                                                         tGACAGGGAATGGTGCGCCCCAGCGTCGATGCTAAATATGATCGGCATAAAAATGAGTAAGCATATTTTTGATTTCAGGTATTTTACTTTCTTCGGCTTCAATTAAAATTGAGGTAGGGGATTCTTTCAAGTGGACAAGTa                         >  1:599498/1‑141 (MQ=255)
                                                                                                          gACAGGGAATGGTGCGCCCCAGCGTCGATGCTAAATATGATCGGCATAAAGAGGAGTAAGCATATTTTTGATTTCAGGTATTTTACTTTCCTCGGCTTCAATTAAAATTTAGGTAGGGGATTCTTTCAAGTGGACAAGTaa                        >  1:304032/1‑141 (MQ=255)
                                                                                                          gACAGGGAATGGTGCGCCCCAGCGTCGATGCTAAATATGATCGGCATAAAAATGAGTAAGCATATTTTTGATTTCAGGTATTTTACTTTCTTCGGCTTCAATTAAAATTGAGGTAGGGGATTCTTTCAAGTGGACAAGTaa                        >  1:303923/1‑141 (MQ=255)
                                                                                                          gACAGGGAATGGTGCGCCCCAGCGTCGATGCTAAATATGATCGGCATAAAAATGAGTAAGCATATTTTTGATGTCAGGTATTTTACTTTCTTCGGCTTCAATTAAAATTGAGGTAGGGGATTCTTTCAAGTGGACAAGTaa                        >  2:450469/1‑141 (MQ=255)
                                                                                                            cAGGGAATGGTGCGCCCCAGCGTCGATGCTAAATATGATCGGCATAAAAATGAGTAAGCATATTTTTGATTTCAGGTATTTTACTTTCTTCGGCTTCAATTAAAATTGAGGTAGGGGATTCTTTCAAGTGGACAAGTAAAt                      >  2:170853/1‑141 (MQ=255)
                                                                                                                       gcgcCCCAGCGTCGATGCTAAATATGATCGGCATAAAAATGAGTAAGCATATTTTTGATTTCAGGTATTTTACTTTCTTCGGCTTCAATTAAAATTGAGGTAGGGGATTCTTTCAAGTGGACAAGTAAATTACCAGTTTGa           >  2:433285/1‑141 (MQ=255)
                                                                                                                       gcgcCCCAGCGTCGATGCTAAATATGATCGGCATAAAAATGAGTAAGCATATTTTTGATTTCAGGTATTTTACTTTCTTCGGCTTCAATTAAAATTGAGGTAGGGGATTCTTTCAAGTGGACAAGTAAATAACCAGTTTGa           >  2:257540/1‑141 (MQ=255)
                                                                                                                        cgcCCCAGCGTCGATGCTAAATATGATCGGCATAAAAATGAGTAAGCATATTTTTGATTTCAGGTATTTTACTTTCTTCGGCTTCAATTAAAATTGAGGTAGGGGATTCTTTCAAGTGGACAGGTAAATTACCAGTTTGaa          >  1:693619/1‑141 (MQ=255)
                                                                                                                             cAGCGTCGATGCTAAATATGATCGGCATAAAAATGAGTAAGCATATTTTTGATTTCAGGTATTTTACTTTCTTCGGCTTCAATTAAAATTGAGGTAGGGGATTCTTTCAAGTGGACAAGTAAATTACCAGTTTGAATTCtt     >  2:293588/1‑141 (MQ=255)
                                                                                                                                cGTCGATGCTAAATATGATCGGCATAAAAATGAGTAAGCATATTTTTGATTTCAGGTATTTTACTTTCTTCGGCTTCAATTAAAATTGAGGTAGGGGATTCTTTCAAGTGGACAAGTAAATTACCAGTTTGAATTCTTGGa  <  2:274830/141‑1 (MQ=255)
                                                                                                                                          |                                                                                                                                  
TATCTTCATCACCGAATGCAATAATATTATTTCGGTCAATATTTAAAAATTGTCTAACTTGCTCAATGCCTCTTGCTTTATTAATACCAAGTTTTACAATTTCAATGACAGGGAATGGTGCGCCCCAGCGTCGATGCTCAATATGATCGGCATAAAAATGAGTAAGCATATTTTTGATTTCAGGTATTTTACTTTCTTCGGCTTCAATTAAAATTGAGGTAGGGGATTCTTTCAAGTGGACAAGTAAATTACCAGTTTGAATTCTTGGA  >  CP000730/973075‑973343

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A