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 1,196,508 C→A 100% intergenic (+2563/‑1229) ftsQ → / → USA300HOU_1125 cell division protein FtsQ/hypothetical protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*CP0007301,196,5080CA100.0% 173.9 / ‑6.5 57intergenic (+2563/‑1229)ftsQ/USA300HOU_1125cell division protein FtsQ/hypothetical protein
Reads supporting (aligned to +/- strand):  ref base C (0/1);  new base A (24/32);  total (24/33)
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.

TTTCGGTACAGTTATTAATCCTGAATTACAAGATGAGATTGTTGTAACAGTTATTGCAACTGGTTTTGATGACAAACCAACATCACATGGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTCTAGCAATGCAACTTCTAAAGATGAATCATTCACTTCAAATTCATCAAATGCACAAGCAACTGATAGTGTAAGTGAAAGAACACATACAACTAAAGAAGATGATATTCCTAGCTTCATTAGAAATAGAGAAGAAA  >  CP000730/1196374‑1196642
                                                                                                                                      |                                                                                                                                      
tttCGTGACAGTTATTAATCCTGAATTACAAGATGAGATTGTTGTAACAGTTATTGCAACTGGTTTTGATGACAAACCAACATCACATGGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTATAGCaa                                                                                                                                  <  2:69847/141‑1 (MQ=255)
tttCGGTACAGTTATTAATCCTGAATTACAAGATGAGATTGTTGTAACAGTTATTGCAACTGGTTTTGATGACAAACCAACATCACATGGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTATAGCaa                                                                                                                                  <  2:821698/141‑1 (MQ=255)
tttCGGTACAGTTATTAATCCTGAATTACAAGATGAGATTGTTGTAACAGTTATTGCAACTGGTTTTGATGACAAACCAACATCACATGGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTATAGCaa                                                                                                                                  <  2:437346/141‑1 (MQ=255)
      tACAGTTATTAATCCTGAATTACAAGATGAGATTGTTGTAACAGTTATTGCAACTGGTTTTGATGACAAACCAACATCACATGGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTATAGCAATGCAAc                                                                                                                            >  2:209894/1‑141 (MQ=255)
      tACAGTGATTAATCCTGAATTGCAAATAGACATAGTTGTAACAGTTATTGCAACTGGTTTGGATGACAAACCAACATCAGACGGGCGTAAATCTGGTAGCACTGGATTCGGATCAAGCGTAAATACTTATAGCAATGCAAc                                                                                                                            <  2:145124/141‑1 (MQ=255)
       aCAGTTATTAATCCTGAATTACAAGATGAGATTGTTGTAACGGTTATTGCAACTGGTTTTGATGACAAACCAACATCACATGGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTATAGCAATGCAACt                                                                                                                           <  2:561417/141‑1 (MQ=255)
        cAGTTATTAATCCTGAATTACAAGATGAGATTGTTGTAACAGTTATTGCAACTGGTTTTGATGACAAACCAACATCACATGGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTATAGCAATGCAACtt                                                                                                                          >  2:493517/1‑141 (MQ=255)
               taATCCTGAATTACAAGATGAGATTGTTGTAACAGTTATTGCAACTGGTTTTGATGACAAACCAACATCACATGGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTATAGCAATGCAACTTCTAAAGa                                                                                                                   <  1:243794/141‑1 (MQ=255)
                 aTCTTGAATTACAAGATGAGATTGTTGTAACAGTTATTGCAACTGGTTTTGATGACAAACCAACATCACATGGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTATAGCAATGCAACTTCTAAAGATg                                                                                                                 <  2:659361/141‑1 (MQ=255)
                 aTCCTGAATTACAAGATGAGATTGTTGTAACAGTTATTGCAACTGGTTTTGATGACAAACCAACATCACATGGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTATAGCAATGCAACTTCTAAAGATg                                                                                                                 <  2:363291/141‑1 (MQ=255)
                    cTGAATTACAAGATGAGATTGTTGTAACAGTTATTGCAACTGGTTTTGATGACAAACCAACATCACATGGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTATAGCAATGCAACTTCTAAAGATGAAt                                                                                                              >  1:202444/1‑141 (MQ=255)
                       aaTTACAAGATGAGATTGTTGTAACAGTTATTGCAACTGGTTTTGATGACAAACCAACATCACATGGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTATAGCAATGCAACTTCTAAAGATGaataat                                                                                                           >  2:206535/1‑141 (MQ=255)
                           aCAAGATGAGATTGTTGTAACAGTTATTGCAACTGGTTTTGATGACAAACCAACATCACATGGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTATAGCAATGCAACTTCTAAAGATGAATCATTCAc                                                                                                       >  1:129194/1‑141 (MQ=255)
                           aCAAGATGAGATTGTTGTAACAGTTATTGCAACTGGTTTTGATGACAAACCAACATCACATGGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTATAGCAATGCAACTTCTAAAGATGAATCATTCAc                                                                                                       <  1:216588/141‑1 (MQ=255)
                           aCAAGATGAGATTGTTGTAACAGTTATTGCAACTGGTTTTGATGACAAACCAACATCACATGGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTATAGCAATGCAACTTCTAAAGATGAATCATTCAc                                                                                                       >  2:664533/1‑141 (MQ=255)
                              aGATGAGATTGTTGTAACAGTTATTGCAACTGGTTTTGATGACAAACCAACATCACATGGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTATAGCAATGCAACTTCTAAAGATGAATCATTCACTTc                                                                                                    >  1:735789/1‑141 (MQ=255)
                                      ttgttgTAACAGTTATTGCAACTGGTTTTGATGACAAACCAACATCACAGGGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACGTATAGCAATGCAACTTCTAAAGATGAATCATTCACTTCAAATtgat                                                                                            >  1:401497/1‑141 (MQ=255)
                                        gttgtAACCGTTATTGCAACTGGTTTTGATGACAAACCAACATCACATGGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTATAGCAATGCAACTTCTAAAGATGAATCATTCACTTCAAATtcatca                                                                                          <  1:463219/141‑1 (MQ=255)
                                        gttgtAACAGTTATTGCAACTGGTTTTGATGACAAACCAACATCACATGGTCGTAAATCTGGTAGCACTGGATTCGGAGCAAGCGTAAATCCTTATAGCAATGCAACTTCTAAAGATGAATCGTTCAGTTCAGATtcagca                                                                                          >  1:410901/1‑141 (MQ=255)
                                        gttgtAACAGTTATTGCAACTGGTTTTGATGACAAACCAACATCACATGGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTATAGCAATGCAACTTCTAAAGATGACTCATTCACTTCAAATtcatca                                                                                          <  1:671512/141‑1 (MQ=255)
                                        gttgtAACAGTTATTGCAACTGGTTTTGATGACAAACCAACATCACATGGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTATAGCAATGCAACTTCTAAAGATGAATCATTCACTTCAAATtcatca                                                                                          <  1:771532/141‑1 (MQ=255)
                                        gttgtAACAGTTATTGCAACTGGTTTTGATGACAAACCAACATCACATGGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTATAGCAATGCAACTTCTAAAGATGAATCATTCACTTCAAATtcatca                                                                                          <  1:499791/141‑1 (MQ=255)
                                             aaCAGTTATTGCAACTGGTTTTGATGACAAACCAACATCACATGGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTATAGCAATGCAACTTCTAAAGATGAATCATTCACTTCAAATTCATCAAATGc                                                                                     >  2:671314/1‑141 (MQ=255)
                                             aaCAGTTATTGCAACTGGTTTTGATGACAAACCAACATCACATGGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTATAGCAATGCAACTTCTAAAGATGAATCATTCACTTCAAATTCATCAAATGc                                                                                     >  2:898459/1‑141 (MQ=255)
                                                    aTTGCAACTGGTTTTGATGACAAACCAACATCACATGGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTATAGCAATGCATCTGTTAAAGATGAATCATTCACTTCAAATTCATCAAATGCACAAGCa                                                                              >  1:751262/1‑141 (MQ=255)
                                                      tGCAACTGGTTTTGATGACAAACCAACATCACATGGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTATAGCAATGCAACTTCTAAAGATGAATCATTCACTTCAAATTCATCAAATGCACAAGCAAc                                                                            >  2:536997/1‑141 (MQ=255)
                                                         aaCTGGTTTTGATGACCAACCAACATCACAGGGTCGTAAATCTGGTAGCACTAGATGCTGAACAATTGTAAATACTTATAGCAATGCAACTTCTAAAGATGAATCATTCACTTCAAATTCATCAAATGCACAAGCAACTGa                                                                         <  1:209894/141‑1 (MQ=255)
                                                         aaCTGGATTTGATGACAAACCAACATCACATGGTCGTAAATCTGGTAGCACTGGCTTCGGAACAAGCGTAAATATTTATAGCAATGAAACTTCTAAAGATGAATCATTCACTTCAAACTCATCAATCGCACAAGCacatgt                                                                         >  2:62894/1‑136 (MQ=255)
                                                          aCTGGTTTTGATGACAAACCAACATCACATGGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTATAGCAATGCAACTTCTAAAGATGAATCATTCACTTCAAATTCATCAAATGCACAAGCAACTGAt                                                                        >  1:801465/1‑141 (MQ=255)
                                                           cTGGTTTTGATGACAAACCAACATCACATGGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTATAGCAATGCAACTTCTAAAGATGAATCATTCACTTCAAATTCATCAAATGCACAAGCAACTGAtg                                                                       >  2:854502/1‑140 (MQ=255)
                                                           cTGGTTTTGATGACAAACCAACATCACATGGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTATAGCAATGCAACTTCTAAAGATGAATCATTCACTTCAAATTCATCAAATGCACAAGCAACTGATa                                                                       <  1:621666/141‑1 (MQ=255)
                                                              gTTTTGATGACAAACCAACATCACATGGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTATAGCAATGCAACTTCTAAAGATGAATCATTCACTTCAAATTCATCAAATGCACAAGCAACTGATAgtg                                                                    <  1:604219/141‑1 (MQ=255)
                                                              gTTTTGATGACAAACCAACATCACATGGTCGTAAATCTGGTAGCACTGGATTCGGAAAAAGCGTAAATACTTATAGCAATGCAACTTCTAAAGATGAATCATTCACTTCAAATTCATCAAATTCACAAACAACTGATAgtt                                                                    >  2:352449/1‑140 (MQ=255)
                                                               ttttGATGACAAACCAACATCACATGGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTATAGCAATGCAACTTCTAAAGATGAATCATTCACTTCAAATTCATCAAATGCACAAGCAACTGATAgtgt                                                                   >  1:324113/1‑141 (MQ=255)
                                                                tttGATGACAAACCAACATCACATGGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTATAGCAATGCCACTACAAAAGATGAACCATTAACTTCAAATCCATCAAATGCACAAGCAACTGATAGTGTa                                                                  >  2:593644/1‑141 (MQ=255)
                                                                tttGATGACAAACCAACATCACATGGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTATAGCAATGCAACTTCTAAAGATGAATCATTCACTTCAAATTCATCAAATGCACAAGCAACTGATAGTGTa                                                                  >  2:373043/1‑141 (MQ=255)
                                                                   gatgaCAAACCAACATCACATGGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTATAGCAATGCAACTTCTAAAGATGAATCATTCACTTCAAATTCATCAAATGCACAAGCAACTGATAGTGTAAGt                                                               <  1:878323/141‑1 (MQ=255)
                                                                     tgaCAAACCAACATCACATGGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTATAGCAATGCAACTTCTAAAGATGAATCATTCACTTCAAATTCATAAAATGCACAAGCAACTGATAGTGTAAGTGa                                                             >  1:335839/1‑141 (MQ=255)
                                                                      gaCAAACCAACATCACATGGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTATAGCAATGCAACTTCTAAAGATGAATCATTCACTTCAAATTCATCAAATGCACAAGCAACTGATAGTGTAAGTGaa                                                            <  2:269375/141‑1 (MQ=255)
                                                                           aCCAACATCACATGGTCGTAAATCTGGTAGCACTGGATCCGGAACAAGCGTAAATACTTCTAGCAATGCAACTTCTAAAGGTTAATCATTCACGTCAAATTCATCAAATGCACAAGCAACTGATAGTGTAAGTGAAAGAac                                                       <  2:369694/141‑1 (MQ=255)
                                                                                      aTGGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTATAGCAATGCAACTTCTAAAGATGAATCATTCACTTCAAATTCATCAAATGCACAAGCAACTGATAGTGTAAGTGAAAGAACACATACAACTa                                            >  2:900946/1‑141 (MQ=255)
                                                                                        gtacGTAAATCTGGTAGCACTTGATTCGGAACAAGCGTAAATACTTATAGCAATGCAACTTCTAAAGATGAATCATTCACTTCAAATTCATCAAATGCACAAGCAACTGATAGTGTAAGTGAAAGAACACATACAACTaaa                                          <  1:423916/138‑1 (MQ=255)
                                                                                              aaaTCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTATAGCAATGCAACTTCTAAAGATGAATCATTCACTTCAAATTCATCAAATGCACAAGCAACTGATAGTGTAAGTGAAAGAACACATACAACTAAAGAAgat                                    >  1:212328/1‑141 (MQ=255)
                                                                                                   cggTAGCACTGGATTCGGAACAAGCGTAAATACTTATAGCAATGCAACTTCTAAAGATGAATCATTCACTTCAAATTCATCAAATGCACAAGCAACTGATAGTGTAAGTGAAAGAACACATACAACTAAAGAAGATGatat                               <  1:43159/140‑1 (MQ=255)
                                                                                                   cggTAGCACTGGATTCGGAACAAGCGTAAATACTTATAGCAATGCAACTTCTAAAGATGAATCATTCACTTCAAATTCATCAAATGCACAAGCAACTGATAGTGTAAGTGAAAGAACACATACAACTAAAGAAGATGatat                               <  1:43102/140‑1 (MQ=255)
                                                                                                     gTAGCACTGGATTCGGAACAAGCGTAAATACTTATAGCAATGCAACTTCTAAAGATGAATCATTCACTTCAAATTCATCAAATGCACAAGCAACTGATAGTGTAAGTGAAAGAACACATACAACTAAAGAAGATGATATTc                             >  2:675352/1‑141 (MQ=255)
                                                                                                       aGCACTGGATTCGGAACAAGCGTAAATACTTATAGCAATGCAACTTCTAAAGATGAATCATTCACTTCAAATTCATCAAATGCACAAGCAACTGATAGTGTAAGTGAAAGAACACATACAACTAAAGAAGATGATATTCCt                           <  2:757805/141‑1 (MQ=255)
                                                                                                        gCACTGGATTCGGAACAAGCGTAAATACTTATAGCAATGCAACTTCTAAAGATGAATCATTCACTTCAAATTCATCAAATGCACAAGCAACTGATAGTGTAAGTGAAAGAACACATACAACTAAAGAAGATGATATTCCTa                          <  1:373043/141‑1 (MQ=255)
                                                                                                          aCTGGATTCGGAACAAGCGTAAATACTTATAGCAATGCAACTTCTAAAGATGAATCATTCACTTCAAATTCATCAAATGCACAAGCAACTGATAGTGTAAGTGAAAGAACACATACAACTAAAGAAGATGATATTCCTAGc                        <  1:536997/141‑1 (MQ=255)
                                                                                                               aatCGGAACAAGCGTAAATACTTATAGCAATGCAACTTCTAAAGATGAATCATTCACTTCAAATTCATCAAATGCACAAGCAACTGATAGTGTAAGTGAAAGAACACATACAACTAAAGAAGATGATATTCCTAGCTTCAt                   <  1:86650/139‑1 (MQ=255)
                                                                                                               aTTCGGAACAAGCGTAAATACTTATAGCAATGCAACTCTTAAAGATGAATCATTCACTGCAAATTCATCAAATGCACAAGCAACTGATAGTGTAAGTGAAAGAACACATACAACTAAAGAAGATGATATTCCTAGCTTCAt                   <  2:271425/141‑1 (MQ=255)
                                                                                                                ttCGGAACAAGCGTAAATACTTATAGCAATGCAACTTCTAAAGATGAATCATTCACTTCAAATTCATCAAATGCACAAGCAACTGATAGTGTAAGTGAAAGAACACATACAACTAAAGAAGATGATATTCCTAGCTTCAtt                  <  1:30009/141‑1 (MQ=255)
                                                                                                                          gCGTAAATACTTATAGCAATGCAACTTCTAAAGATGAATCATTCACTTCAAATTCATCAAATGCACAAGCAACTGATAGTGTAAGTGAAAGAACACATACAACTAAAGAAGATGATATTCCTAGCTTCATTAGAAATagag        <  2:650469/141‑1 (MQ=255)
                                                                                                                             tAAATACTTATAGCAATGCAACTTCTAAAGATGAATCATTCACTTCAAATTCATCAAATGCACAAGCAACTGATAGTGTAAGTGAAAGAACACATACAACTAAAGAAGATGATATTCCTAGCTTCATTAGAAATAGagaag     <  1:642122/141‑1 (MQ=255)
                                                                                                                             tAAATACTTATAGCAATGCAACTTCTAAAGATGAATCATTCACTTCAAATTCATCAAATGCACAAGCAACTGATAGTGTAAGTGAAAGAACACATACAACTAAAGAAGATGATATTCCTAGCTTCATTAGAAATAGagaag     <  2:329456/141‑1 (MQ=255)
                                                                                                                             tAAATACTTATAGCAATGCAACTTCTAAAGATGAATCATTCACTTCAAATTCATCAAATGCACAAGCAACTGATAGTGTAAGTGAAAGAACACATACAACTAAAGAAGATGATATTCCTAGCTTCATTAGAAATAGagaag     <  2:503966/141‑1 (MQ=255)
                                                                                                                                aTACTTATAGCAATGCAACTTCTAAAGATGAATCATTCACTTCAAATTCATCAAATGCACAACCAACTGATAGTGTAATTGAAAGAACACATACAACTAAAGAAGATGATATTCCTAGCTTCATTAGAAATAGAGaagaaa  <  2:304871/141‑1 (MQ=255)
                                                                                                                                      |                                                                                                                                      
TTTCGGTACAGTTATTAATCCTGAATTACAAGATGAGATTGTTGTAACAGTTATTGCAACTGGTTTTGATGACAAACCAACATCACATGGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTCTAGCAATGCAACTTCTAAAGATGAATCATTCACTTCAAATTCATCAAATGCACAAGCAACTGATAGTGTAAGTGAAAGAACACATACAACTAAAGAAGATGATATTCCTAGCTTCATTAGAAATAGAGAAGAAA  >  CP000730/1196374‑1196642

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A