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
A15 F59 I0 R1 41 74.1 1560052 97.4% 1519490 140.9

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA CP000730 1,274,207 T→A 7.3% S204T (TCA→ACA)  USA300HOU_1186 → CodY family transcriptional regulator

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*CP0007301,274,2070TA 7.3% 152.3 / 5.0 55S204T (TCA→ACA) USA300HOU_1186CodY family transcriptional regulator
Reads supporting (aligned to +/- strand):  ref base T (25/25);  new base A (2/2);  total (27/28)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.06e-01

GAAGCATAGTGAAGTAGAAAAAGAAGCGCGCGATAAAGCTGCTATTACAATGGCAATTAATTCATTATCTTATTCTGAAAAAGAAGCGATTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCATCAAAAGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCACTACGTAAATTAGAAAGTGCTGGTGTAATTGAATCACGTTCTTTAGGAATGAAAGGTACTTTCATTAAAGTTAAAAAAGAAAAATTCT  >  CP000730/1274068‑1274345
                                                                                                                                           |                                                                                                                                          
gaAGCATAGTGAAGTAGAAAAAGAAGCGCGCGATAAAGCTGCTATTACAATGGCAATTAATTCATTATCTTATTCTGAAAAAGAAGCGATTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCATc                                                                                                                                           >  2:304221/1‑141 (MQ=255)
 aagaagaGTTAAGTAGAAAAAGAAGCGCGCGATAAAGCTGCTTTTACGATGGCAATTAATTCATTATCTTAATCTGATAAAGAAGCGATTTAACATATATTTGAAGATCTTGGCGGTACGGAAAGCCTATTAATCGCATCa                                                                                                                                          <  2:62361/135‑1 (MQ=255)
 aaGCATAGTGAAGTAGAAAAAGAAGCGCGCGATAAAGCTGCTATTACAATGGCAATTAATTCATTATCTTATTCTGAAAAAGAAGCGATTGAACATATCTTTGAAGAACTTGGCCGTACGGAAGGCCTATTAATCGCATCa                                                                                                                                          <  2:481674/141‑1 (MQ=255)
   acATAGTGAAGTAGAAAAAGAAGCGCGCGATAAAGCTGCTATTACAATGGCAATTAATTCATTATCTTATTCTGAAAAAGAAGCGATTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCATCaaa                                                                                                                                        <  1:20691/140‑1 (MQ=255)
    cATAGAGAAGTAGAAAAAGAAGCGCGCGATAAAGCTGCTATTACAATGGCAATTAATTCATAATCTTATTCTGAAAAAGAACTGATTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCATCaaaa                                                                                                                                       <  2:688667/141‑1 (MQ=255)
         tGAAGTAGAAAAAGAAGCGCGCGATAAAGCTGCTATTACAATGGCAATTAATTCATTATCTTATTCTGAAAAAGAAGCGATTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCATCAAAAGTTGc                                                                                                                                  >  1:477433/1‑141 (MQ=255)
            aGTAGAAAAAGAAGCGCGCGATAAAGCTGCTATTACAATGGCAATTAATTCATTATCTTATTCTGAAAAAGAAGCGATTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCATCAAAAGTTGCAGa                                                                                                                               <  2:24953/141‑1 (MQ=255)
             gTAGAAAAAGAAGCGCGCGATAAAGCTGCTATTACAATGGCAATTAATTCATTATCTTATTCTGAAAAAGAAGCGATTGAACATATCTTTGAGGAACTTGGCGGTACGGAAGGCCTATTAATCGCATCAAAAGTTGCAGaa                                                                                                                              >  2:308218/1‑140 (MQ=255)
              tAGAAAAAGAAGCGCGCGATAAAGCTGCTATTACAATGGCAATTAATTCATTATCTTATTCTGAAAAAGAAGCGAGTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCATCAAAAGTTGCAGATa                                                                                                                             <  1:121900/141‑1 (MQ=255)
               aGAAAAAGAAGCGCGCGATAAAGCTGCTATTACAATGGCAATTAATTCATTATCTTATTCTGAAAAAGAAGCGATTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCATCAAAAGTTGCAGATag                                                                                                                            <  1:63755/141‑1 (MQ=255)
                gAAAAAGAAGCGCGCGATAAAGCTGCTATTACAATGGCAATTAATTCATTATCTTATTCTGAAAAAGAAGCGATTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCATCAAAAGTTGCAGATaga                                                                                                                           >  1:324049/1‑141 (MQ=255)
                    aagaagCGCGCGATAAAGCTGCTATTACAATGGCAATTAATTCATTATCTTATTCTGAAAAAGAAGCGATTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCATCAAAAGTTGCAGATAGAGTTg                                                                                                                       <  1:20371/141‑1 (MQ=255)
                    aagaagCGCGCGATAAAGCTGCTATTACAATGGCAATTAATTCATTATCTTATTCTGAAAAAGAAGCGATTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCATCAAAAGTTGCAGATAGAGTTg                                                                                                                       <  1:600318/141‑1 (MQ=255)
                              cgATAAAGCTGCTATTACAATGGCAATTAATTCATTATCTTATTCTGAAAAAGAAGCGATTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCATCAAAAGTTGCAGATAGAGTTGGTATTACTAg                                                                                                             <  1:304221/141‑1 (MQ=255)
                               gATAAAGCTGCTATTACAATGGCAATTAATTCATTATCTTATTCTGAAAAAGAAGCGATTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCATCAAAAGTTGCAGATAGAGTTGGTATTACTAGa                                                                                                            >  1:416973/1‑141 (MQ=255)
                                  aaaGCTTCTATTACAATGGCAATTAATTCATTATCTTATTCTGAAAAAGAAGCGATTGAACATATCTTTGAAGAACTTGGTGGTACGGAAGGCCTATTAATCGCATCAAAAGTTGCAGATAGAGTTGGTATTACTAGATCt                                                                                                         <  1:212837/141‑1 (MQ=255)
                                        gctATTACAATGGCAATTAATTCATTATCTTATTCTGAAAAAGAAGCGATTGAACATACCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCATCAAAAGTTGCAGATAGAGTTGGTATTACTAGATCTGTAAtt                                                                                                   >  2:492740/1‑141 (MQ=255)
                                              aCAATGGCAATTAATTCATTATCTTATTCTGAAAAAGAAGCGATTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCATCAAAAGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAAt                                                                                             >  2:306303/1‑141 (MQ=255)
                                              aCAATGGCAATTAATTCATTATCTTATTCTGAAAAAGAAGCGATTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCATCAAAAGTTGCAGATAGAGTTGGTATTACTAGATCTGTAAGTGTAAAt                                                                                             >  2:128098/1‑141 (MQ=255)
                                               cAATGGCAATTAATTCATTATCTTATTCTGAAAAAGAAGCGATTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGATTATTTTTTCGCATCAAAAGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAATg                                                                                            >  1:763685/1‑141 (MQ=255)
                                                  tGGCAATTAGTTCATTATCTTATTCTGAAAAAGAAGCGATTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCAACAAAAGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCAc                                                                                         >  1:569500/1‑141 (MQ=255)
                                                  tGGCAATTAATTCATTATCTTATTCTGAAAAAGAAGCGATTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCAACAAAAGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCAc                                                                                         >  2:318579/1‑141 (MQ=255)
                                                   ggCAATTAATTCATTATCTTATTCTGAAAAAGAAGCGATTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCATCAAAAGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCACt                                                                                        >  2:418905/1‑141 (MQ=255)
                                                      aattaattCATTATCTTATTCTGAAAAAGAAGCGATTTAACCTATCTTTGAAGAACTTGGCGGCACGGAAGGCCTATTAATCGCATCAAAAGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCACTACg                                                                                     <  1:524858/141‑1 (MQ=255)
                                                      aattaattCATTATCTTATTCTGAAAAAGAAGCGATTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCATCAAATGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCACTACg                                                                                     >  1:422028/1‑141 (MQ=255)
                                                            ttCATTATCTTATTCTGAAAAAGAAGCGATTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCATCAAAAGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCACTACGTAAAtt                                                                               >  2:37461/1‑141 (MQ=255)
                                                             ttaTTATCTTATTCTGAAAAAGAAGCGATTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCATCAAAAGTTGCAGATAGAGTTGGTAATACTAGATCTGTAATTGTAAATGCACTACGTAAATTa                                                                              <  1:301602/139‑1 (MQ=255)
                                                                            gAAAAAGAAGCGATTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCATCAAAAGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCACTACGTAAATTAGAAAGTGCTGGTGTa                                                               >  1:535440/1‑141 (MQ=255)
                                                                            gAAAAAGAAGCGATTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCATCAAAAGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCACTACGTAAATTAGAAAGTGCTGGTGTa                                                               >  1:535413/1‑141 (MQ=255)
                                                                            gAAAAAGAAGCGATTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTAATAATGGCATCAAAAGTTGCAGATAGAGTTGGTATTCCTGGGTCTGTAGTTGTAAATGAACTACGTAAATTAGAAAGTGCTGGGGTa                                                               >  1:333975/1‑141 (MQ=255)
                                                                             aaaaaGGAGCGATTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCATCAAAAGTTGCAGATAGAGTTGGTATTACTAGCTCTGTAATTGTAAATGCACTACGTAAATTAGAAAGTGCTGGTGTaa                                                              <  2:490459/141‑1 (MQ=255)
                                                                             aaaaaGAAGCGATTGAACAGATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCATCAAAAGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCACTACGTAAATTAGAAAGTGCTGGTGTaa                                                              <  1:289029/141‑1 (MQ=255)
                                                                                aagaagCGATTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCATCAAAAGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCACTACGTAAATTAGAAAGTGCTGGTGTAATTg                                                           >  1:65752/1‑141 (MQ=255)
                                                                                      cGATTGAACATATCTGTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCATCAAAAGTTGCAGATAGAGTTGGTATTACTAGATCTGTAACTGTAAATGCACTACGTAAATTAGAAAGTGCTGGTGTACTTGAATCAc                                                     <  2:498468/141‑1 (MQ=255)
                                                                                        aTTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCATCAAAAGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCACTACGTAAATTAGAAAGTGCTGGTGTAGTTGGATGACGt                                                   >  2:540812/1‑141 (MQ=255)
                                                                                              cATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCAGCAAAAGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCACTACGTAAATTAGAAAGTGCTGGTGTAATTGAATCACGTTCTTTa                                             <  1:104092/141‑1 (MQ=255)
                                                                                               atctccttGGAGAACTTGGCCGTACGGAAGGCCTATTAATCGCATCAAAAGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCACTACGTAAATTAGAAAGTGCTGGTGTAATTGAATCACGTTCTTTAg                                            <  1:309193/135‑1 (MQ=255)
                                                                                                  tCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCATCAAAAGTTGCAGATAGAGTTGGTATTACTAGAGCTGTAATTTGAAATGCACTACGTAAATTAGAAAGTGCTGGTGTAATTGAATCACGTTCTTTCGGaa                                         >  2:275748/1‑141 (MQ=255)
                                                                                                         agaaCTTGGCGGTACGGAAGGCCTATTAATCGCATCAAAAGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCACTACGTATATTAGAAAGTGCTGGTGTAATTGAATCACGTTCTTTAGGAATGAAAgg                                  <  1:339128/141‑1 (MQ=255)
                                                                                                          gaaCTGGGCGGTACGGAAGGCCTATTAATCGCATCAAAAGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCACTACGTAAATTAGAAAGTGCTGGTGTAATTGAATCACGTTCTTTAGGAATGAAAGGt                                 <  2:763685/141‑1 (MQ=255)
                                                                                                           aaCTTGGCTGTACGGAAGGTCTATTAATCGCAACAAAAGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCACTACGTAAATTAGAAAGTGCTGGTGTAATTGAATCACGTTCTTTAGGAATGAAAgtac                                <  1:632453/141‑4 (MQ=255)
                                                                                                             cTTGGCGGTACGGAAGGCCTATTAATCGCATCAAAAGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCACTACGTAAATTAGAAAGTGCTGGTGTAATTGAATCACGTTCTTTAGGAATGAAAGGTACt                              >  1:359429/1‑141 (MQ=255)
                                                                                                               tGGCGGTACGGAAGGCCTATTAATCGCATCAAAAGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCACTACGTAAATTAGAAAGTGCTGGTGTAATTGAATCACGTTCTTTAGGAATGAAAGGTACttt                            >  2:36469/1‑141 (MQ=255)
                                                                                                               tGGCGGTACGGAAGGCCTATTAATCGCATCAAAAGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCACTACGTAAATTAGAAAGTGCTGGTGTAATTGAATCACGTTCTTTAGGAATGAAAGGTACttt                            >  2:616912/1‑141 (MQ=255)
                                                                                                               tGGCGGTACGGAAGGCCTATTAATCGCAACAAAAGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCACTACGTAAATTAGAAAGTGCTGGTGTAATTGAATCACGTTCTTTAGGAATGAAAGGTACttt                            <  1:508900/141‑1 (MQ=255)
                                                                                                                  ggggaCGGAAGGCCTATTAATCGCATCAAAAGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCACTACGTAAATTAGAAAGTGCTGGTGTAATTGAATCACGTTCTTTAGGAATGAAAGGTACTTTCAt                         <  2:310919/137‑1 (MQ=255)
                                                                                                                  cGGTACGGAAGGCCTATTAATCGCATCAAAAGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCACTACGTAAATTAGAAAGTGCTGGTGTAATTGAATCACGTTCTTTAGGAATGAAAGGTACTTTCAt                         >  1:399934/1‑141 (MQ=255)
                                                                                                                  cGGTACGGAAGGCCTATTAATCGCATCAAAAGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCACTACGTAAATTAGAAAGTGCTGGTGTAATTGAATCACGTTCTTTAGGAATGAAAGGCACTTTCAt                         >  2:651855/1‑141 (MQ=255)
                                                                                                                  cGGTACGGAAGGCCCATGAATCGCATCAAAAGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCACTACGTAAATTAGAAAGTGCTGGTGTAATTTAATCACGTTCTTTAGGAATGAAAGGTACTTTCAt                         <  2:311127/141‑1 (MQ=255)
                                                                                                                     tACGGAAGGCCTATTAATCGCATCAAAAGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCACTACGTAAATTAGAAAGTGCTGGTGTAATTGAGTCACGTTCTTTAGGAATGAAAGGTACTTTCTTTaa                      >  1:478608/1‑141 (MQ=255)
                                                                                                                                tATTAATCGCATCAAAAGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCACTACGTAAATTAGAAAGTGCTGGTCTAATTGAATCACGTTCTTTAGGAATGAAAGGTACTTTCATTAAAGTTAAAAAAg           <  1:516812/141‑1 (MQ=255)
                                                                                                                                   tAATCGCATCAAAAGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCACTACGTAAATTAGAAAGTGCTGGTGTAATTGAATCACGTTCTTTAGGAATGAAAGGTACTTTCTTTAAAGTTAAAAAAGaaa        >  1:152885/1‑141 (MQ=255)
                                                                                                                                     aTCGCATCAAAAGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCACTACGTAAATTAGAAAGTGCTGGTGTAATTGATTCACGTTCTTTAGGAATGAAAGGATTTTTTACTTAAGTTAAAAAAGaaaaa      <  2:551286/141‑1 (MQ=255)
                                                                                                                                        gCATCAAAAGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCACTACGTAAATTAGAAAGTGCTGGTGTAATTGAATCACGTTCTTTAGGAATGAAAGGTACTTTCATTAAAGTTAAAAAAGAAAAATTc   <  1:117385/141‑1 (MQ=255)
                                                                                                                                         cATCAAATGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCACTACGTAAATTAGAAAGTGCTGGTGTAATTGAATCACGTTCTTTAGGAATGAAAGGTACTTTCATTAAAGTTAAAAAAGAAAAATTCt  <  2:422028/141‑1 (MQ=255)
                                                                                                                                           |                                                                                                                                          
GAAGCATAGTGAAGTAGAAAAAGAAGCGCGCGATAAAGCTGCTATTACAATGGCAATTAATTCATTATCTTATTCTGAAAAAGAAGCGATTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCATCAAAAGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCACTACGTAAATTAGAAAGTGCTGGTGTAATTGAATCACGTTCTTTAGGAATGAAAGGTACTTTCATTAAAGTTAAAAAAGAAAAATTCT  >  CP000730/1274068‑1274345

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