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 F18 I0 R1 32 69.1 1533550 96.6% 1481409 141.0

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA USA300TCH1516_ALE 2,532,298 A→T 100% T15T (ACA→ACT)  femA_3 → Aminoacyltransferase FemA

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE2,532,2980AT100.0% 193.3 / NA 59T15T (ACA→ACT) femA_3Aminoacyltransferase FemA
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base T (14/45);  total (14/45)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

TGTGTATTTGTAATCAGTTTTTGATAAAATAAAAAAATAGCATTATTAATAAATTCAAAAATTATAGTTCAATTCAGAGAGGGATGGGAT‑AAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACAACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGCATCTTGTAGGGGTTAAAGATGACAATGGTCAAGTGATTGCAGGATGCTTATTGACAGAAGCA  >  USA300TCH1516_ALE/2532161‑2532433
                                                                                                                                          |                                                                                                                                       
tttgtATTTGTAATCAGTTTTTGATAAAATAAAAAAATAGCATGATTAATAAATTGAAAAATTAGAGTTCAATTCAGAGAGGGATGGGAT‑AAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTactaca                                                                                                                                      <  1:535671/139‑1 (MQ=255)
   ttATGTGTAATCAGTTTTTGATAAAATAAAAAAATAGCATTATTAATAAATTCAAAAATTATAGTTCAATTCAGAGAGGGATGGGAT‑AAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAg                                                                                                                                   <  2:53818/140‑1 (MQ=255)
   gtATTTGTAATCAGTTTTTGATAAAATAAAAAAATAGCATTATTAATAAATTCAAAAATTATAGTTCAATTCAGAGAGGGATGGGAT‑AAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAg                                                                                                                                   <  1:244078/141‑1 (MQ=255)
   gtATTTGTAATCAGTTTTTGATAAAATAAAAAAATAGCATTATTAATAAATTCAAAAATTATAGTTCAATTCAGAGAGGGATGGGAT‑AAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAg                                                                                                                                   <  1:325373/141‑1 (MQ=255)
    tATTTGTAATCAGTTTTTGATAAAATAAAAAAATAGCATTATTAATAAATTCAAAAATTATAGTTCAATTCAGAGAGGGATGGGAT‑AAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGc                                                                                                                                  <  2:62163/141‑1 (MQ=255)
          tAATCAGTTTTTGATAAAATAAAAAAATAGCATTATTAATAAATTCAAAAATTATAGTTCAATTCAGAGAGGGATGGGAT‑AAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCAttttt                                                                                                                            >  2:194730/1‑141 (MQ=255)
           aaTCAGTTTTTGATAAAATAAAAAAATAGCATTATTAATAAATTCAAAAATTATAGTTCAATTCAGAGAGGGATGGGAT‑AAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTc                                                                                                                           >  2:57119/1‑141 (MQ=255)
           aaTCAGTTTTTGATAAAATAAAAAAATAGCATTATTAATAAATTCAAAAATTATAGTTCAATTCAGAGAGGGATGGGAT‑AAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTc                                                                                                                           <  1:407849/141‑1 (MQ=255)
                 tttttGATAAAATAAAAAAATAGCATTATTAATAAATTCAAAAATTATAGTTCAATTCAGAGAGGGATGGGAT‑AAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTa                                                                                                                     <  1:501483/141‑1 (MQ=255)
                 tttttGATAAAATAAAAAAATAGCATTATTAATAAATTCAAAAATTATAGTTCAATTCAGAGAGGGATGGGAT‑AAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTa                                                                                                                     <  1:35135/141‑1 (MQ=255)
                      taaaaaataaaaAAATAGCATTATTAATAAATTCAAAAATTATAGTTCAATTCAGAGAGGGATGTGAT‑AAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAAGGCGTTTACTACAAAGCATTTTTCACATTacacac                                                                                                                <  2:554354/138‑1 (MQ=255)
                      gATAAAATAAAAAAATAGCATTATTAATAAATTCAAAAATTATAGTTCAATTCAGAGAGGGATGGGAT‑AAAATGAACTTTGTTACGTTGACTTCGGATGAGTTCACTGCGTTTACTACAAAGCATTTTGCACATTacccac                                                                                                                >  1:285871/1‑141 (MQ=255)
                      gATAAAATAAAAAAATAGCATTATTAATAAATTCAAAAATTATAGTTCAATTCAGAGAGGGATGGGAG‑AAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTacacac                                                                                                                <  2:462730/141‑1 (MQ=255)
                       ataaaagaaaAAAATAGCATTATTAATAAATTCAAAAATTATAGTTCAATTCAGAGAGGGATGGGAT‑AAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTAcacaca                                                                                                               <  2:346875/141‑1 (MQ=255)
                                aaaaaTAGCATTATTAATAAATTCAAAAATTATAGTTCAATTCAGAGAGGGATGGGAT‑AAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTAt                                                                                                      >  2:515791/1‑141 (MQ=255)
                                aaaaaTAGCATTATTAATAAATTCAAAAATTATAGTTCAATTCAGAGAGGGATGGGAT‑AAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTAt                                                                                                      <  1:325385/141‑1 (MQ=255)
                                 aaaaTAGCATTATTAATAAATTCAAAAATTATAGTTCAATTCAGAGAGGGATGGGAT‑AAAATGAACTTTGTAACGTTGACTTCGGATGAGTCCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTAtt                                                                                                     <  2:195929/141‑1 (MQ=255)
                                   aaTAGCATTATTAATAAATTCAAAAATTATAGTTCAATTCAGAGAGGGATGGGAT‑AAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCa                                                                                                   >  1:247830/1‑141 (MQ=255)
                                   aaTAGCATTATTAATAAATTCAAAAATTATAGTTCAATTCAGAGAGGGATGGGAT‑AAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCa                                                                                                   >  2:545254/1‑141 (MQ=255)
                                     aaGCATTATTAATAAATTCAAAAATTATAGTTCAATTCAGAGAGGGATGGGAT‑AAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCAtt                                                                                                 <  1:81078/140‑1 (MQ=255)
                                       gCATTATTAATAAATTCAAAAATTATAGTTCAATTCAGAGAGGGATGGGAT‑AAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTAc                                                                                               <  2:25197/141‑1 (MQ=255)
                                       gCATTATTAATAAATTCAAAAATTATAGTTCAATTCAGAGAGGGATGGGAT‑AAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTAc                                                                                               <  2:51002/141‑1 (MQ=255)
                                       gCATTATTAATAAATTAAAAAATTATAGTTCAATTCAGAGAGGGATGGGAT‑AAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTAc                                                                                               <  1:549427/141‑1 (MQ=255)
                                        cATTATTAATAAATTCAAAAATTATAGTTCAATTCAGAGAGGGATGGGAT‑AAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACa                                                                                              >  1:579845/1‑141 (MQ=255)
                                              taataaATTCAAAAATTATAGTTCAATTCAGAGAGGGATGGGAT‑AAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCATa                                                                                        <  2:95763/141‑1 (MQ=255)
                                                ataaATTCAAAAATTATAGTTCAATTCAGAGAGGGATGGGATAAAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCATag                                                                                       <  2:450211/141‑1 (MQ=255)
                                                  aaaTTCAAAAATTATAGTTCAATTCAGAGAGGGATGGGAT‑AAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGt                                                                                    <  1:313567/141‑1 (MQ=255)
                                                    aTTCAAAAATTATAGTTCAATTCAGAGAGGGATGGGAT‑AAAATGAACTTTATAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCAAGTTACACACAATCACCTATACATTACAGTCATAGAATTg                                                                                  >  2:71907/1‑141 (MQ=255)
                                                         aaaaTTATAGTTCAATTCAGAGAGGGATGGGAT‑AAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTCCACACAATCAGCTATTCATTACAATAATAGGCTTGCTTTa                                                                             >  2:666700/1‑141 (MQ=255)
                                                         aaaaTTATAGTTCAATTCAGAGAGGGATGGGAT‑AAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTa                                                                             <  1:685774/141‑1 (MQ=255)
                                                         aaaaTTATAGTTCAATTCAGAGAGGGATGGGAT‑AAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTa                                                                             <  1:455006/141‑1 (MQ=255)
                                                            aTTATAGTTCAAGTCAGAGAGGGATGGGAT‑AAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTaaaa                                                                          <  2:513150/141‑1 (MQ=255)
                                                                   ttCAATTCAGAGATGGATGGGAT‑AAAATGAACTTTGTAACGTTGACTTCGTATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGAtg                                                                   <  2:523665/141‑1 (MQ=255)
                                                                   ttCAATTCAGAGAGGGATGGGAT‑AAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGAtg                                                                   <  2:608936/141‑1 (MQ=255)
                                                                   gtCAATCCAGAGAGGGAAGGGAT‑AAAATGAACTTTGTAATGTTGACTTCGGCTGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGAtg                                                                   <  2:313703/140‑1 (MQ=255)
                                                                       aTTCAGAGAGGGATGGGAT‑AAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGGGTTGATTTAAAAGGCGATGTGcc                                                               >  1:229397/1‑140 (MQ=255)
                                                                         tCAGAGAGGGATGGGAT‑AAAATGAACTTTGGAACGTTGACTTCGGAAGAGTTCTATTCGTTTACTAAAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGCATc                                                             <  1:333270/141‑1 (MQ=255)
                                                                             agagGGATGGGAT‑AAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGCATCTTGt                                                         <  2:519604/141‑1 (MQ=255)
                                                                                     tggat‑CAAATGCAATTTGTGCCGTTGACTTCGGATGAGTTCAATGCGCTTGCTACGAAGCGTTTGTCACGTTACACGCAATCAGCTATTCATTGCAATCATAGTGGTGATTTAAAAGGCGATGTGCATCATGTAGGGGTTa                                                 <  2:750479/140‑1 (MQ=255)
                                                                                     gggat‑AAAATTAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGCATCTTGTAGGGGTTa                                                 <  2:435159/141‑1 (MQ=255)
                                                                                      ggat‑AAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGCATCTTGTAGGGGTTaa                                                <  2:77279/141‑1 (MQ=255)
                                                                                      ggat‑AAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGCATCTTGTAGGGGTTaa                                                >  1:473749/1‑141 (MQ=255)
                                                                                        at‑AAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGCATCTTGTAGGGGTTAAAg                                              <  2:585835/141‑1 (MQ=255)
                                                                                            aaaTGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGCATCTTGTAGGGGTTAAAGATg                                           <  2:740830/141‑1 (MQ=255)
                                                                                            aaaTGAACTTTGTAACGTGGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGCATCTTGTAGGGGTTAAAGATg                                           <  2:227442/141‑1 (MQ=255)
                                                                                              acgAACTTTGTAACGTTTACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGCATCTTGTAGGGGTTAAAGATGAc                                         <  2:763285/139‑1 (MQ=255)
                                                                                               tGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTCATAAAAAGCATTTTTCACATTACATCCCATCATCTATTCATTAAAATTATGGAGGTGATTTAAAAGGCGATGTGCATCTTGTAGGGGTTAAAGATGACa                                        <  1:753981/141‑1 (MQ=255)
                                                                                                    tttGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGCATCTTGTAGGGGTTAAAGATGACAATGGt                                   <  1:682836/141‑1 (MQ=255)
                                                                                                            ggtGACTTCGGATGGGTGTGATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAAGCATAGAGTTGATTTAAAAGGCGATGTGCATCTTGTAGGGGTTAAAGATGACAATGGTCAAGTGAt                           <  2:290233/139‑1 (MQ=255)
                                                                                                            gTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGCATCTTGTAGGGGTTAAAGATGTGAATGGTCAAGTGAt                           <  2:87269/141‑1 (MQ=255)
                                                                                                            gTTGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGCATCTTGTAGGGGTTAAAGATGACAATGGTCAAGTGAt                           <  1:194730/141‑1 (MQ=255)
                                                                                                              tGACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGCATCTTGTAGGGGTTAAAGATGACAATGGTCAAGTGATTg                         <  1:515791/141‑1 (MQ=255)
                                                                                                              tGACTGCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTAAAATCATAGAGTTGATTTAAAAGGCGATGTGCATCTTGTAGGGGTTAAAGATGACAATGGTCAAGTGATTg                         <  2:283/141‑1 (MQ=255)
                                                                                                               gACTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGCATCTTGTAGGGGTTAAAGATGACAATGGTCAAGTGATTGc                        >  2:143250/1‑141 (MQ=255)
                                                                                                                aCTTCGGATGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGCATCTTGTAGGGGTTAAAGATGACAAGAGTCAAGTGATTGcg                       >  2:414450/1‑140 (MQ=255)
                                                                                                                  ttCGGAGGAGTTCATTTCGTTTACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTATAATCATAGAGTTGATTTAAAAGGCGATGTGCATCTTGTAGGGGTTAAAGATGACAATGGTCAAGTGATTGCAgg                     <  2:597556/141‑1 (MQ=255)
                                                                                                                     gaaTGAGTTCAATGCGTTTACTACAAAGCATTCTGCACATTACACACAATCAGCTATTCATTACAATCATAGGGTTGATTTAAAAGGCGATGTGCATCTTGTAGGGGTTAAAGATGACAATGGTCAAGTGATTGCAGGATg                  <  2:285871/139‑1 (MQ=255)
                                                                                                                        tGAGTTCAATGCGTTTACTACAAAGCATTTTTCACATTACACACAAACAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGCATCTTGTAGGGGTTAAAGATGACAATGGTCAAGTGATTGCAGGATGCtt               >  2:490609/1‑141 (MQ=255)
                                                                                                                                attcGTTTACTACAAAGCATTCTTCACATTACACACAATCAGCTACTTCTTACAATTCTAGAGTTGATTTAAAAGGCGACGTGCATCTTGTTGGGGGTAAAGATGACAATGGTCAAGCGATTGCCGGATGCTTATTGACAg       <  2:279680/138‑1 (MQ=255)
                                                                                                                                     tttACTACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGCATCTTGTAGGGGTTAAAGATGACAATGGTCAAGTGATTGCAGGATGCTTATTGACAGAAgca  <  1:349790/141‑1 (MQ=255)
                                                                                                                                          |                                                                                                                                       
TGTGTATTTGTAATCAGTTTTTGATAAAATAAAAAAATAGCATTATTAATAAATTCAAAAATTATAGTTCAATTCAGAGAGGGATGGGAT‑AAAATGAACTTTGTAACGTTGACTTCGGATGAGTTCAATGCGTTTACAACAAAGCATTTTTCACATTACACACAATCAGCTATTCATTACAATCATAGAGTTGATTTAAAAGGCGATGTGCATCTTGTAGGGGTTAAAGATGACAATGGTCAAGTGATTGCAGGATGCTTATTGACAGAAGCA  >  USA300TCH1516_ALE/2532161‑2532433

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A