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
A5 F50 I1 R1 10 71.6 2231174 98.9% 2206631 150.4

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 3,377,150 C→A V91F (GTT→TTT)  sspA ← stringent starvation protein A, phage P1 late gene activator, RNAP‑associated acid‑resistance protein, inactive glutathione S‑transferase homolog

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009133,377,1500CA100.0% 203.6 / NA 53V91F (GTT→TTT) sspAstringent starvation protein A, phage P1 late gene activator, RNAP‑associated acid‑resistance protein, inactive glutathione S‑transferase homolog
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base A (27/26);  total (27/26)

CCAGCAGTTCTTCGCGCAGTTGCTTACGTGCGGCATCTGCTTCAGAAGCTGAACCGTTGATGATGGTGTTCATCAGCGTGTACCAGTCTTTTTCGATGCGATGCATGTACAGACGGCTTTCACCGCGAGCTACCGGGTAAACAGGCATCAGTGGCGGATGCGGGAAACGCTCATCCAGATATTCCATAATGATGCGAGATTCCCACAGGGTCAGCTCACGATCCACCAGGGTCGGAACGCTCTGATTCGGGTTGAGGTCAATCAGATCCTGAGGCGGATTGTCC  >  NC_000913/3377009‑3377292
                                                                                                                                             |                                                                                                                                              
ccAGCAGTTCTTCGCGCAGTTGCTTACGTGCGGCATCTGCTTCAGAAGCTGAACCGTTGATGATGGTGTTCATCAGCGTGTACCAGTCTTTTTCGATGCGATGCATGTACAGACGGCTTTCACCGCGAGCTACCGGGTAAAAAGGCATc                                                                                                                                         >  1:523614/1‑149 (MQ=255)
     agTTCTTCGCGCAGTTGCTTACGTGCGGCATCTGCTTCAGAAGCTGAACCGTTGATGATGGTGTTCATCAGCGTGTACCAGTCTTTTTCGATGCGATGCATGTACAGACGGCTTTCACCGCGAGCTACCGGGTAAAAAGGCATCAGTGGCg                                                                                                                                  <  1:60054/151‑1 (MQ=255)
         cttcGCGCAGTTGCTTACGTGCGGCATCTGCTTCAGAAGCTGAACCGTTGATGATGGTGTTCATCAGCGTGTACCAGTCTTTTTCGATGCGATGCATGTACAGACGGCTTTCACCGCGAGCTACCGGGTAAAAAGGCATCAGTGGCGGATg                                                                                                                              >  1:242071/1‑151 (MQ=255)
           tcGCGCAGTTGCTTACGTGCGGCATCTGCTTCAGAAGCTGAACCGTTGATGATGGTGTTCATCAGCGTGTACCAGTCTTTTTCGATGCGATGCATGTACAGACGGCTTTCACCGCGAGCTACCGGGTAAAAAGGCATCAGTGGCGGATGc                                                                                                                             <  2:684293/150‑1 (MQ=255)
           tcGCGCAGTTGCTTACGTGCGGCATCTGCTTCAGAAGCTGAACCGTTGATGATGGTGTTCATCAGCGTGTACCAGTCTTTTTCGATGCGATGCATGTACAGACGGCTTTCACCGCGAGCTACCGGGTAAAAAGGCATCAGTGGCGGATGc                                                                                                                             <  1:196236/150‑1 (MQ=255)
           tcGCGCAGTTGCTTACGTGCGGCATCTGCTTCAGAAGCTGAACCGTTGATGATGGTGTTCATCAGCGTGTACCAGTCTTTTTCGATGCGATGCATGTACAGACGGCTTTCACCGCGAGCTACCGGGTAAAAAGGCAGCAGTGGCGGATg                                                                                                                              <  2:890904/149‑1 (MQ=255)
              cgcAGTTGCTTACGTGCGGCATCTGCTTCAGAAGCTGAACCGTTGATGATGGTGTTCATCAGCGTGTACCAGTCTTTTTCGATGCGATGCATGTACAGACGGCTTTCACCGCGAGCTACCGGGTAAAAAGGCATCAGTGGCGGATGCGGGa                                                                                                                         <  2:382831/151‑1 (MQ=255)
                  gTTGCTTACGTGCGGCATCTGCTTCAGAAGCTGAACCGTTGATGATGGTGTTCATCAGCGTGTACCAGTCTTTTTCGATGCGATGCATGTACAGACGGCTTTCACCGCGAGCTACCGGGTAAAAAGGCATCAGTGGCGGATGCGGGaaa                                                                                                                       >  2:85509/1‑149 (MQ=255)
                  gTTGCTTACGTGCGGCATCTGCTTCAGAAGCTGAACCGTTGATGATGGTGTTCATCAGCGTGTACCAGTCTTTTTCGATGCGATGCATGTACAGACGGCTTTCACCGCGAGCTACCGGGTAAAAAGGCATCAGTGGCGGATGCGGGAAACg                                                                                                                     <  1:479447/151‑1 (MQ=255)
                             gCGGCATCTGCTTCAGAAGCTGAACCGTTGATGATGGTGTTCATCAGCGTGTACCAGTCTTTTTCGATGCGATGCATGTACAGACGGCTTTCACCGCGAGCTACCGGGTAAAAAGGCATCAGTGGCGGATGCGGGAAACGCTCATcc                                                                                                              >  2:615945/1‑147 (MQ=255)
                                 cATCTGCTTCAGAAGCTGAACCGTTGATGATGGTGTTCATCAGCGTGTACCAGTCTTTTTCGATGCGATGCATGTACAGACGGCTTTCACCGCGAGCTACCGGGTAAAAAGGCATCAGTGGCGGATGCGGGAAACGCTCATCCAGATATTc                                                                                                      <  2:143288/151‑1 (MQ=255)
                                  aTCTGCTTCAGAAGCTGAACCGTTGATGATGGTGTTCATCAGCGTGAACCAGTCTTTTTCGATGCGATGCATGTACAGACGGCTTTCACCGCGAGCTACCGGGTAAAAAGGCATCAGTGGCGGATGGGGGAAACGCTCATCCAGATAtt                                                                                                       >  1:229035/1‑149 (MQ=255)
                                   tCTGCTTCAGAAGCTGAACCGTTGATGATGGTGTTCATCAGCGTGTACCAGTCTTTTTCGATGCGATGCATGTACAGACGGCTTTCACCGCGAGCTACCGGGTAAAAAGGCATCAGTGGCGGATGCGGGAAACGCTCATCCAGATATTcc                                                                                                     >  1:823835/1‑150 (MQ=255)
                                      gCTTCAGAAGCTGAACCGTTGATGATGGTGTTCATCAGCGTGTACCAGTCTTTTTCGATGCGATGCATGTACAGACGGCTTTCACCGCGAGCTACCGGGTAAAAAGGCATCAGTGGCGGATGCGGGAAACGCTCATCCAGATATTCCAt                                                                                                   <  1:253676/149‑1 (MQ=255)
                                      gCTTCAGAAGCTGAACCGTTGATGATGGTGTTCATCAGCGTGTACCAGTCTTTTTCGATGCGATGCATGTACAGACGGCTTTCACCGCGAGCTACCGGGTAAAAAGGCATCAGTGGCGGATGCGGGAAACGCTCATCCAGATATTCCATa                                                                                                  >  1:1059341/1‑150 (MQ=255)
                                      gCTTCAGAAGCTGAACCGTTGATGATGGTGTTCATCAGCGTGTACCAGTCTTTTTCGATGCGATGCATGTACAGACGGCTTTCACCGCGAGCTACCGGGTAAAAAGGCATCAGTGGCGGATGCGGGAAACGCTCATCCAGATATTCCATa                                                                                                  <  1:1077014/150‑1 (MQ=255)
                                       cTTCAGAAGCTGAACCGTTGATGATGGTGTTCATCAGCGTGTACCAGTCTTTTTCGATGCGATGCATGTACAGACGGCTTTCACCGCGAGCTACCGGGTAAAAAGGCATCAGTGGCGGATGCGGGAAACGCTCATCCAGATATTCCATaa                                                                                                 >  1:628627/1‑150 (MQ=255)
                                         tCAGAAGCTGAACCGTTGATGATGGTGTTCATCAGCGTGTACCAGTCTTTTTCGATGCGATGCATGTACAGACGGCTTTCACCGCGAGCTACCGGGTAAAAAGGCATCAGTGGCGGATGCGGGAAACGCTCATCCAGATATTCCATAatg                                                                                               <  2:908559/150‑1 (MQ=255)
                                          cAGAAGCTGAACCGTTGATGATGGTGTTCATCAGCGTGTACCAGTCTTTTTCGATGCGATGCATGTACAGACGGCTTTCACCGCGAGCTACCGGGTAAAAAGGCATCAGTGGCGGATGCGGGAAACGCTCATCCAGATATTCCATAatgat                                                                                             <  2:53480/151‑1 (MQ=255)
                                           aGAAGCTGAACCGTTGATGATGGTGTTCATCAGCGTGTACCAGTCTTTTTCGATGCGATGCATGTACAGACGGCTTTCACCGCGAGCTACCGGGTAAAAAGGCATCAGTGGCGGATGCGGGAAAAGCTCATCAAGAGATTCCaaaa                                                                                                 >  1:848486/1‑146 (MQ=255)
                                                     ccGTTGATGATGGTGTTCATCAGCGTGTACCAGTCTTTTTCGATGCGATGCATGTACAGACGGCTTTCACCGCGAGCTACCGGGTAAAAAGGCATCAGTGGCGGATGCGGGAAACGCTCATCCAGATATTCCATAATGATGCGAGATTccc                                                                                  >  1:421567/1‑151 (MQ=255)
                                                     ccGTTGATGATGGTGTTCATCAGCGTGTACCAGTCTTTTTCGATGCGATGCATGTACAGACGGCTTTCACCGCGAGCTACCGGGTAAAAAGGCATCAGTGGCGGATGCGGGAAACGCTCATCCAGATATTCCATAATGATGCGAGATTccc                                                                                  <  2:204139/151‑1 (MQ=255)
                                                        ttGATGATGGTGTTCATCAGCGTGTACCAGTCTTTTTCGATGCGATGCATGTACAGACGGCTTTCACCGCGAGCTACCGGGTAAAAAGGCATCAGTGGCGGATGCGGGAAACGCTCATCCAGATATTCCATAATGATGCGAGATTCCcac                                                                                >  2:183910/1‑150 (MQ=255)
                                                         tgatgaTGGTGTTCATCAGCGTGTACCAGTCTTTTTCGATGCGATGCATGTACAGACGGCTTTCACCGCGAGCTACCGGGTAAAAAGGCATCAGTGGCGGATGCGGGAAACGCTCATCCAGATATTCCATAATGATGCGAGATTCCcaca                                                                               <  2:1094256/150‑1 (MQ=255)
                                                              atgGTGTTCATCAGCGTGTACCAGTCTTTTTCGATGCGATGCATGTACAGACGGCTTTCACCGCGAGCTACCGGGTAAAAAGGCATCAGTGGCGGATGCGGGAAACGCTCATCCAGATATTCCATAATGATGCGAGATTCCCACAGGGTCa                                                                         <  1:995579/151‑1 (MQ=255)
                                                                   gtTCATCAGCGTGTACCAGTCTTTTTCGATGCGATGCATGTACAGACGGCTTTCACCGCGAGCTACCGGGTAAAAAGGCATCAGTGGCGGATGCGGGAAACGCTCATCCAGATATTCCATAATGATGCGAGATTCCCACAGGGTCAGCTc                                                                     >  2:683748/1‑150 (MQ=255)
                                                                   gtTCATCAGCGTGTACCAGTCTTTTTCGATGCGATGCATGTACAGACGGCTTTCACCGCGAGCTACCGGGTAAAAAGGCATCAGTGGCGGATGCGGGAAACGCTCATCCAGATATTCCATAATGATGCGAGATTCCCACAGGGTCAGCTCa                                                                    <  2:928272/151‑1 (MQ=255)
                                                                    ttCATCAGCGTGTACCAGTCTTTTTCGATGCGATGCATGTACAGACGGCTTTCACCGCGAGCTACCGGGTAAAAAGGCATCAGTGGCGGATGCGGGAAACGCTCATCCAGATATTCCATAATGATGCGAGATTCCCACAGGGTCAGCTc                                                                     >  2:220871/1‑149 (MQ=255)
                                                                    ttCATCAGCGTGTACCAGTCTTTTTCGATGCGATGCATGTACAGACGGCTTTCACCGCGAGCTACCGGGTAAAAAGGCATCAGTGGCGGATGCGGGAAACGCTCATCCAGATATTCCATAATGATGCGAGATTCCCACAGGGTCAGCTCAc                                                                   >  2:819195/1‑151 (MQ=255)
                                                                    ttCATCAGCGTGTACCAGTCTTTTTCGATGCGATGCATGTACAGACGGCTTTCACCGCGAGCTACCGGGTAAAAAGGCATCAGTGGCGGATGCGGGAAACGCTCATCCAGATATTCCATAATGATGCGAGATTCCCACAGGGTCAGCTCAc                                                                   >  1:459668/1‑151 (MQ=255)
                                                                    ttCATCAGCGTGTACCAGTCTTTTTCGATGCGATGCATGTACAGACGGCTTTCACCGCGAGCTACCGGGTAAAAAGGCATCAGTGGCGGATGCGGGAAACGCTCATCCAGATATTCCATAATGATGCGAGATTCCCACAGGGTCAGCTCAc                                                                   >  1:912278/1‑151 (MQ=255)
                                                                         caGCGTGTACCAGTCTTTTTCGATGCGATGCATGTACAGACGGCTTTCACCGCGAGCTACCGGGTAAAAAGGCATCAGTGGCGGATGCGGGAAACGCTCATCCAGATATTCCATAATGATGCGAGATTCCCACAGGGTCAGCTCACGATcc                                                              >  2:1086121/1‑151 (MQ=255)
                                                                         caGCGTGTACCAGTCTTTTTCGATGCGATGCATGTACAGACGGCTTTCACCGCGAGCTACCGGGTAAAAAGGCATCAGTGGCGGATGCGGGAAACGCTCATCCAGATATTCCATAATGATGCGAGATTCCCACAGGGTCAGCTCACGATcc                                                              <  1:30095/151‑1 (MQ=255)
                                                                           gCGTGTACCAGTCTTTTTCGATGCGATGCATGTACAGACGGCTTTCACCGCGAGCTACCGGGTAAAAAGGCATCAGTGGCGGATGCGGGAAACGCTCATCCAGATATTCCATAATGATGCGAGATTCCCACAGGGTCAGCTCACGATccac                                                            <  2:334193/151‑1 (MQ=255)
                                                                               gtACCAGTCTTTTTCGATGCGATGCATGTACAGACGGCTTTCACCGCGAGCTACCGGGTAAAAAGGCATCAGTGGCGGATGCGGGAAACGCTCATCCAGATATTCCATAATGATGCGAGATTCCCACAGGGTCAGCTCACGATCCACCAgg                                                        <  2:749849/151‑1 (MQ=255)
                                                                               gtACCAGTCTTTTTCGATGCGATGCATGTACAGACGGCTTTCACCGCGAGCTACCGGGTAAAAAGGCATCAGTGGCGGATGCGGGAAACGCTCATCCAGATATTCCATAATGATGCGAGATTCCCACAGGGTCAGCTCACGATCCACCAg                                                         <  2:787488/150‑1 (MQ=255)
                                                                                    aGTCTTTTTCGATGCGATGCATGTACAGACGGCTTTCACCGCGAGCTACCGGGTAAAAAGGCATCAGTGGCGGATGCGGGAAACGCTCATCCAGATATTCCATAATGATGCGAGATTCCCACAGGGTCAGCTCACGATCCACCAGGGTCgg                                                   <  2:168164/151‑1 (MQ=255)
                                                                                      tCTTTTTCGATGCGATGCATGTACAGACGGCTTTCACCGCGAGCTACCGGGTAAAAAGGCATCAGTGGCGGATGCGGGAAACGCTCATCCAGATATTCCATAATGATGCGAGATTCCCACAGGGTCAGCTCAc                                                                   >  2:805581/1‑133 (MQ=255)
                                                                                      tCTTTTTCGATGCGATGCATGTACAGACGGCTTTCACCGCGAGCTACCGGGTAAAAAGGCATCAGTGGCGGATGCGGGAAACGCTCATCCAGATATTCCATAATGATGCGAGATTCCCACAGGGTCAGCTCAc                                                                   <  1:805608/133‑1 (MQ=255)
                                                                                           ttCGATGCGATGCATGTACAGACGGCTTTCACCGCGAGCTACCGGGTAAAAAGGCATCAGTGGCGGATGCGGGAAACGCTCATCCAGATATTCCATAATGATGCGAGATTCCCACAGGGTCAGCTCACGATCCACCAGGGTCGGAACGctc                                            >  1:1100505/1‑151 (MQ=255)
                                                                                               atgcgatgcATGTACAGACGGCTTTCACCGCGAGCTACCGGGTAAAAAGGCATCAGTGGCGGATGCGGGAAACGCTCATCCAGATATTCCATAATGATGCGAGATTCCCACAGGGTCAGCTCACGATCCACCAGGGTCGGAACGCTCTGAt                                        >  2:78000/1‑151 (MQ=255)
                                                                                                           tACAGACGGCTTTCACCGCGAGCTACCGGGTAAAAAGGCATCAGTGGCGGATGCGGGAAACGCTCATCCAGATATTCCATAATGATGCGAGATTCCCACAGGGTCAGCTCACGATCCACCAGGGTCGGAACGCTCTGATTCGGGTTGAgg                             >  2:122269/1‑150 (MQ=255)
                                                                                                            aCAGACGGCTTTCACCGCGAGCTACCGGGTAAAAAGGCATCAGTGGCGGATGCGGGAAACGCTCATCCAGATATTCCATAATGATGCGAGATTCCCACAGGGTCAGCTCACGATCCACCAGGGTCGGAACGCTCTGATTCGGGTTGAGGt                            <  1:584902/150‑1 (MQ=255)
                                                                                                            aCAGACGGCTTTCACCGCGAGCTACCGGGTAAAAAGGCATCAGTGGCGGATGCGGGAAACGCTCATCCAGATATTCCATAATGATGCGAGATTCCCACAGGGTCAGCTCACGATCCACCAGGGTCGGAACGCTCTGATTCGGGTTGAGGt                            <  2:57227/150‑1 (MQ=255)
                                                                                                                   gCTTTCACCGCGAGCTACCGGGTAAAAAGGCATCAGTGGCGGATGCGGGAAACGCTCATCCAGATATTCCATAATGATGCGAGATTCCCACAGGGTCAGCTCACGATCCACCAGGGTCGGAACGCTCTGATTCGGGTTGAGGTCAATc                       >  1:652160/1‑148 (MQ=255)
                                                                                                                       tCACCGCGAGCTACCGGGTAAAAAGGCATCAGTGGCGGATGCGGGAAACGCTCATCCAGATATTCCATAATGATGCGAGATTCCCACAGGGTCAGCTCACGATCCACCAGGGTCGGAACGCTCTGATTCGGGTTGAGGTCAATCAGATcc                 <  2:318715/150‑1 (MQ=255)
                                                                                                                        cACCGCGAGCTACCGGGTAAAAAGGCATCAGTGGCGGATGCGGGAAACGCTCATCCAGATATTCCATAATGATGCGAGATTCCCACAGGGTCAGCTCACGATCCACCAGGGTCGGAACGCTCTGATTCGGGTTGAGGTCAATCAGATCCTg               >  1:171958/1‑151 (MQ=255)
                                                                                                                           cgcgAGCTACCGGGTAAAAAGGCATCAGTGGCGGATGCGGGAAACGCTCATCCAGATATTCCATAATGATGCGAGATTCCCACAGGGTCAGCTCACGATCCACCAGGGTCGGAACGCTCTGATTCGGGTTGAGGTCAATCAGATCCTGAgg            >  1:810166/1‑151 (MQ=255)
                                                                                                                               aGCTACCGGGTAAAAAGGCATCAGTGGCGGATGCGGGAAACGCTCATCCAGATATTCCATAATGATGCGAGATTCCCACAGGGTCAGCTCACGATCCACCAGGGTCGGAACGCTCTGATTCGGGTTGAGGTCAATCAGATCCTGAGGCGGa        <  2:508615/151‑1 (MQ=255)
                                                                                                                                   aCCGGGTAAAAAGGCATCAGTGGCGGATGCGGGAAACGCTCATCCAGATATTCCATAATGATGCGAGATTCCCACAGGGTCAGCTCACGATCCACCAGGGTCGGAACGCTCTGATTCGGGTTGAGGTCAATCAGATCCTGAGGCGGAtt      <  1:278476/149‑1 (MQ=255)
                                                                                                                                   aCCGGGTAAAAAGGCATCAGTGGCGGATGCGGGAAACGCTCATCCAGATATTCCATAATGATGCGAGATTCCCACAGGGTCAGCTCACGATCCACCAGGGTCGGAACGCTCTGATTCGGGTTGAGGTCAATCAGATCCTGAGGCGGATTGt    >  2:1048906/1‑151 (MQ=255)
                                                                                                                                     cGGGTAAAAAGGCATCAGTGGCGGATGCGGGAAACGGTCATCCAGATATTCCAAAATGATGCGAGATTCCCACAGGGACAGCTCACGATCCACCAGGGTCGGAACGCTCTGATTCGGGGTGAGGTCAATCAGATCCTGAGGCGGAtt      >  1:758931/1‑147 (MQ=255)
                                                                                                                                     cGGGTAAAAAGGCATCAGTGGCGGATGCGGGAAACGCTCATCCAGATATTCCATAATGATGCGAGATTCCCACAGGGTCAGCTCACGATCCACCAGGGTCGGAACGCTCTGATTCGGGTTGAGGTCAATCAGATCCTGAGGCGGATTGTcc  >  2:986068/1‑151 (MQ=255)
                                                                                                                                             |                                                                                                                                              
CCAGCAGTTCTTCGCGCAGTTGCTTACGTGCGGCATCTGCTTCAGAAGCTGAACCGTTGATGATGGTGTTCATCAGCGTGTACCAGTCTTTTTCGATGCGATGCATGTACAGACGGCTTTCACCGCGAGCTACCGGGTAAACAGGCATCAGTGGCGGATGCGGGAAACGCTCATCCAGATATTCCATAATGATGCGAGATTCCCACAGGGTCAGCTCACGATCCACCAGGGTCGGAACGCTCTGATTCGGGTTGAGGTCAATCAGATCCTGAGGCGGATTGTCC  >  NC_000913/3377009‑3377292

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A