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
A3 F28 I1 R1 169 80.7 2736954 99.0% 2709584 138.6

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 3,415,885 C→T P285S (CCG→TCG)  acrF → multidrug efflux pump RND permease AcrF

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009133,415,8850CT100.0% 194.4 / NA 58P285S (CCG→TCG) acrFmultidrug efflux pump RND permease AcrF
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (32/26);  total (32/26)

TAAAAATCCGGAAGAATTCGGCAAAGTGACCCTGCGCGTAAACAGTGACGGCTCGGTGGTACGCCTGAAAGATGTCGCACGGGTTGAACTTGGCGGTGAAAACTATAACGTTATCGCTCGTATCAACGGAAAACCGGCGGCGGGCCTGGGGATTAAGCTGGCAACCGGCGCGAATGCTCTCGATACCGCGAAAGCCATTAAGGCAAAACTGGCGGAATTACAGCCATTCTTCCCGCAGGGAATGAAGGTTCTCTACCCTTAT  >  NC_000913/3415752‑3416013
                                                                                                                                     |                                                                                                                                
tAAAAATCCGGAAGAATTCGGCAAAGTGACCCTGCGCGTAAACAGTGACGGCTCGGTGGTACGCCTGAAAGATGTCGCACGGGTTGAACTTGGCGGTGAAAACTATAACGTTATCGCTCGTATCAACGGAAAATcggcgg                                                                                                                            <  2:657549/140‑1 (MQ=255)
                ttCGGCAAAGTGACCCTGCGCGTAAACAGTGACGGCTCGGTGGTACGCCTGAAAGATGTCGCACGGGTTGAACTTGGCGGTGAAAACTATAACGTTATCGCTCGTATCAACTGAAAATCGGCGGCGGGcc                                                                                                                      <  2:800064/130‑1 (MQ=255)
                ttCGGCAAAGTGACCCTGCGCGTAAACAGTGACGGCTCGGTGGTACGCCTGAAAGATGTCGCACGGGTTGAACTTGGCGGTGAAAACTATAACGTTATCGCTCGTATCAACTGAAAATCGGCGGCGGGcc                                                                                                                      >  1:800064/1‑130 (MQ=255)
                         gTGACCCTGCGCGTAAACAGTGACGGCTCGGTGGTACGCCTGAAAGATGTCGCACGGGTTGAACTTGGCGGTGAAAACTATAACGTTATCGCTCGTATCAACGGAAAATCGGCGGCGGGCCTGGGGATTAAGCTGGCAAc                                                                                                   <  2:1066700/140‑1 (MQ=255)
                          tGACCCTGCGCGTAAACAGTGACGGCTCGGTGGTACGCCTGAAAGATGTCGCACGGGTTGAACTTGGCGGTGAAAACTATAACGTTATCGCTCGTATCAACGGAAAATCGGCGGCGGGCCTGGGGATTAAGCTGGCAAcc                                                                                                  <  1:70104/140‑1 (MQ=255)
                                  cgcgTAAACAGTGACGGCTCGGTGGTACGCCTGAAAGATGTCGCACGGGTTGAACTTGGCGGTGAAAACTATAACCTTATCGCTCGTATCAACGGAAAATCGGCGGCGGGCCTGGGGATTAAGCTGGCAACCGGCGCGaa                                                                                          >  2:483902/1‑140 (MQ=255)
                                    cgTAAACAGTGACGGCTCGGTGGTACGCCTGAAAGATGTCGCACGGGTTGAACTTGGCGGTGAAAACTATAACGTTATCGCTCGTATCAACGGAAAATCGGCGGCGGGCCTGGGGATTAAGCTGGCAACCGGCGCGAATg                                                                                        >  1:126808/1‑140 (MQ=255)
                                            gTGACGGCTCGGTGGTACGCCTGAAAGATGTCGCACGGGTTGAACTTGGCGGTGAAAACTATAACGTTATCGCTCGTATCAACGGAAAATCGGCGGCGGGCCTGGGGATTAAGCTGGCAACCGGCGCGAATGCTCTCGAt                                                                                >  1:873114/1‑140 (MQ=255)
                                             tGACGGCTCGGTGGTACGCCTGAAAGATGTCGCACGGGTTGAACTTGGCGGTGAAAACTATAACGTTATCGCTCGTATCAACGGAAAATCGGCGGCGGGCCTGGGGATTAAGCTGGCAACCGGCGCGAATGCTCTCGATa                                                                               <  1:799518/140‑1 (MQ=255)
                                             tGACGGCTCGGTGGTACGCCTGAAAGATGTCGCACGGGTTGAACTTGGCGGTGAAAACTATAACGTTATCGCTCGTATCAACGGAAAATCGGCGGCGGGCCTGGGGATTAAGCTGGCAACCGGCGCGAATGCTCTCGATa                                                                               <  1:425883/140‑1 (MQ=255)
                                               aCGGCTCGGTGGTACGCCTGAGAGATGTCGCACGGGTTGAACTTGGCGGTGAAAACTATAACGTTATCGCTCGTATCAACGGAAAATCGGCGGCGGGCCTGGGGAATAAGCTGGCAACCGGCGCGAATGCTCTCGATaac                                                                             >  2:190929/1‑138 (MQ=255)
                                               aCGGCTCGGTGGTACGCCTGAAAGATGTCGCACGGGTTGAACTTGGCGGTGAAAACTATAACGTTATCGCTCGTATCAACGGAAAATCGGCGGCGGGCCTGGGGATTAAGCTGGCAACCGGCGCGAATGCTCTCGATAcc                                                                             >  2:988602/1‑140 (MQ=255)
                                                  gCTCGGTGGTACGCCTGAAAGATGTCGCACGGGTTGAACTTGGCGGTGAAAACTATAACGTTATCGCTCGTATCAACGGAAAATCGGCGGCGGGCCTGGGGATTAAGCTGGCAACCGGCGCGAATGCTCTCGATACcgcg                                                                          <  2:550697/140‑1 (MQ=255)
                                                   cTCGGTGGTACGCCTGAAAGATGTCGCACGGGTTGAACTTGGCGGTGAAAACTATAACGTTATCGCTCGTATCAACGGAAAATCGGCGGCGGGCCTGGGGATTAAGCTGGCAACCGGCGCGAAt                                                                                         <  1:1081951/124‑1 (MQ=255)
                                                   cTCGGTGGTACGCCTGAAAGATGTCGCACGGGTTGAACTTGGCGGTGAAAACTATAACGTTATCGCTCGTATCAACGGAAAATCGGCGGCGGGCCTGGGGATTAAGCTGGCAACCGGCGCGAAt                                                                                         >  2:1081951/1‑124 (MQ=255)
                                                   cTCGGTGGTACGCCTGAAAGATGTCGCACGGGTTGAACTTGGCGGTGAAAACTATAACGTTATCGCTCGTATCAACGGAAAATCGGCGGCGGGCCTGGGGATTAAGCTGGCAACCGGCGCGAATGCTCTCGATACCGCGa                                                                         >  1:301006/1‑140 (MQ=255)
                                                     cGGTGGTACGCCTGAAAGATGTCGCACGGGTTGAACTTGGCGGTGAAAACTATAACGTTATCGCTCGTATCAACGGAAAATCGGCGGCGGGCCTGGGGATTAAGCTGGCAACCGGCGCGAATGCTCTCGATACCGCGaaa                                                                       >  1:848278/1‑140 (MQ=255)
                                                       gtggtACGCCTGAAAGATGTCGCACGGGTTGAACTTGGCGGTGAAAACTATAACGTTATCGCTCGTATCAACGGAAAATCGGCGGCGGGCCTGGGGATTAAGCTGGCAACCGGCGCGAATGCTCTCGATACCGCGAAAGc                                                                     >  2:83179/1‑140 (MQ=255)
                                                               ccTGAAAGATGTCGCACGGGTTGAACTTGGCGGTGAAAACTATAACGTTATCGCTCGTATCAACGGAAAATCGGCGGCGGGCCTGGGGATTAAGCTGGCAACCGGCGCGAATGCTCTCGATACCGCGAAAGCCATTAAgg                                                             >  1:790922/1‑140 (MQ=255)
                                                                  gAAAGATGTCGCACGGGTTGAACTTGGCGGTGAAAACTATAACGTTATCGCTCGTATCAACGGAAAATCGGCGGCGGGCCTGGGGATTAAGCTGGCAACCGGCGCGAATGCTCTCGATACCGCGAAAGCCATTAAGGCaa                                                          >  2:1338188/1‑140 (MQ=255)
                                                                    aaGATGTCGCACGCGATGAACATGGTGGTGAAAACTATAACGTTATCGCTCGTATCAACGGAAAATCGGCGGCGGGCCTTGGGATTAAGCTGGGAACCGGCGCGAATGCTCTTGATACCCCGAAAGCCATTAAGGCaaaa                                                        >  2:211475/1‑140 (MQ=255)
                                                                        tGTCGCACGGGTTGAACTTGGTGGTGAAAACTATAACGTTATCGCTCGTATCAACGGAAAATCGGCGGCGGGCCTGGGGATTAAGCTGGCAACCGGCGCGAATGCTCTCGATACCGCGAAAGCCATTAAGGCAAAACTgg                                                    >  1:205417/1‑140 (MQ=255)
                                                                         gTCGCACGGGTTGAACTTGGCGGTGAAAACTATAACGTTATCGCTCGTATCAACGGAAAATCGGCGGCGGGCCTGGGGATTAAGCTGGCAACCGGCGCGAATGCTCTCGATACCGCGAAAGCCATTAAGGCAAAACTGGc                                                   <  2:790922/140‑1 (MQ=255)
                                                                          tCGCACGGGTTGAACTTGGCGGTGAAAACTATAACGTTATCGCTCGTATCAACGGAAAATCGGCGGCGGGCCTGGGGATTAAGCTGGCAACCGGCGCGAATGCTCTCGATACCGCGAAAGCCATTAAGGCAAAACTGGCg                                                  >  2:657856/1‑140 (MQ=255)
                                                                          tCGCACGGGTTGAACTTGGCGGTGAAAACTATAACGTTATCGCTCGTATCAACGGAAAATCGGCGGCGGGCCTGGGGATTAAGCTGGCAACCGGCGCGAATGCTCTCGATACCGCGAAAGCCATTAAGGCAAAACTGGCg                                                  >  2:518667/1‑140 (MQ=255)
                                                                                gggTTGAACTTGGCGGTGAAAACTATAACGTTATCGCTCGTATCAACGGAAAATCGGCGGCGGGCCTGGGGATTAAGCTGGCAACCGGCGCGAATGCTCTCGATACCGCGAAAGCCATTAAGGCAAAACTGGCGGAATTa                                            >  1:933093/1‑140 (MQ=255)
                                                                                       aCTTGGCGGTGAAAACTATAACGTTATCGCTCGTATCAACGGAAAATCGGCGGCGGGCCTGGGGATTAAGCTGGCAACCGGCGCGAATGCTCTCGATACCGCGAAAACCATTAAGGCAAAACTGGCGGAATTACAGCCAt                                     >  1:1365284/1‑140 (MQ=255)
                                                                                          tGGCGGTGAAAACTATAACGTTATCGCTCGTATCAACGGAAAATCGGCGGCGGGCCTGGGGATTAAGCTGGCAACCGGCGCGAATGCTCTCGATACCGCGAAAGCCATTAAGGCAAAACTGGCGGAATTACAGCCAttct                                  >  1:392094/1‑140 (MQ=255)
                                                                                           ggCGGTGAAAACTATAACGTTATCGCTCGTATCAACGGAAAATCGGCGGCGGGCCTGGGGATTAAGCTGGCAACCGGCGCGAATGCTCTCGATACCGCGAAAGCCATTAAGGCAAAACTGGCGGAATTACAGCCAttctt                                 >  1:722497/1‑140 (MQ=255)
                                                                                           ggCGGTGAAAACTATAACGTTATCGCTCGTATCAACGGAAAATCGGCGGCGGGCCTGGGGATTAAGCTGGCAACCGGCGCGAATGCTCTCGATACCGCGAAAGCCATTAAGGCAAAACTGGCGGAATTACAGCCAttctt                                 >  1:149234/1‑140 (MQ=255)
                                                                                            gCGGTGAAAACTATAACGTTATCGCTCGTATCAACGGAAAATCGGCGGCGGGCCTGGGGATTAAGCTGGCAACCGGCGCGAATGCTCTCGATACCGCGAAAGCCATTAAGGCAAAACTGGCGGAATTACAGCCAttcttc                                >  2:1329290/1‑140 (MQ=255)
                                                                                            gCGGTGAAAACTATAACGTTATCGCTCGTATCAACGGAAAATCGGCGGCGGGCCTGGGGATTAAGCTGGCAACCGGCGCGAATGCTCTCGATACCGCGAAAGCCATTAAGGCAAAACTGGCGGAATTACAGCCAttcttc                                >  1:1242315/1‑140 (MQ=255)
                                                                                            gCGGTGAAAACTATAACGTTATCGCTCGTATCAACGGAAAATCGGCGGCGGGCCTGGGGATTAAGCTGGCAACCGGCGCGAATGCTCTCGATACCGCGAAAGCCATTAAGGCAAAACTGGCGGAATTACAGCCAttcttc                                >  1:1203220/1‑140 (MQ=255)
                                                                                            gCGGTGAAAACTATAACGTTATCGCTCGTATCAACGGAAAATCGGCGGCGGGCCTGGGGATTAAGCTGGCAACCGGCGCGAATGCTCTCGATACCGCGAAAGCCATTAAGGCAAAACTGGCGGAATTACAGCCAttcttc                                >  1:685370/1‑140 (MQ=255)
                                                                                              ggTGAAAACTATAACGTTATCGCTCGTATCAACGGAAAATCGGCGGCGGGCCTGGGGATTAAGCTGGCAACCGGCGCGAATGCTCTCGATACCGCGAAAGCCATTAAGGCAAAACTGGCGGAATTACAGCCATTCTTccc                              <  2:304697/140‑1 (MQ=255)
                                                                                                  aaaaCTATAACGTTATCGCTCGTATCAACGGAAAATCGGCGGCGGGCCTGGGGATTAAGCTGGCAACCGGCGCGAATGCTCTCGATACCGCGAAAGCCATTAAGGCAAAACTGGCGGAATTACAGCCATTCTTCCCGCAg                          <  1:211475/140‑1 (MQ=255)
                                                                                                        ataACGTTATCGCTCGTATCAACGGAAAATCGGCGGCGGGCCTGGGGATTAAGCTGGCAACCGGCGCGAATGCTCTCGATACCGCGAAAGCCATTAAGGCAAAACTGGCGGAATTACAGCCATTCTTCCCGCAGGGAATg                    <  2:1348551/140‑1 (MQ=255)
                                                                                                          aaCGTTATCGCTCGTATCAACGGAAAATCGGCGGCGGGCCTGGGGATTAAGCTGGCAACCGGCGCGAATGCTCTCGATACCGCGAAAGCCATTAAGGCAAAACTGGCGGAATTACAGCCATTCTTCCCGCAGGGAATGaa                  >  2:1181182/1‑140 (MQ=255)
                                                                                                           aCGTTATCGCTCGTATCAACGGAAAATCGGCGGCGGGCCTGGGGATTAAGCTGGCAACCGGCGCGAATGCTCTCGATACCGCGAAAGCCATTAAGGCAAAACTGGCGGAATTACAGCCATTCTTCCCGCAGGGAATGAAg                 <  2:168626/140‑1 (MQ=255)
                                                                                                              ttATCGCTCGTATCAACGGAAAATCGGCGGCGGGCCTGGGGATTAAGCTGGCAACCGGCGCGAATGCTCTCGATATCGCGAAAGCCATTAAGGCAAAACTGGCGGAATTACAGCCATTCTTCCCGCAGGGAATGAAGGtt              <  2:933093/140‑1 (MQ=255)
                                                                                                              ttATCGCTCGTATCAACGGAAAATCGGCGGCGGGCCTGGGGATTAAGCTGGCAACCGGCGCGAATGCTCTCGATACCGCGAAAGCCATTAAGGCAAAACTGGCGGAATTACAGCCATTCTTCCCGCAGGGAATGAAGGtt              <  1:518667/140‑1 (MQ=255)
                                                                                                              ttATCGCTCGTATCAACGGAAAATCGGCGGCGGGCCTGGGGATTAAGCTGGCAACCGGCGCGAATGCTCTCGATACCGCGAAAGCCATTAAGGCAAAACTGGCGGAATTACAGCCATTCTTCCCGCAGGGAATGAAGGtt              <  1:1338188/140‑1 (MQ=255)
                                                                                                              ttATCGCTCGTATCAACGGAAAATCGGCGGCGGGCCTGGGGATTAAGCTGGCAACCGGCGCGAATGCTCTCGATACCGCGAAAGCCATTAAGGCAAAACTGGCGGAATTACAGCCATTCTTCCCGCAGGGAATGAAGGtt              <  2:873114/140‑1 (MQ=255)
                                                                                                               tATCGCTCGTATCAACGGAAAATCGGCGGCGGGCCTGGGGATTAAGCTGGCAACCGGCGCGAATGCTCTCGATACCGCGAAAGCCATTAAGGCAAAACTGGCGGAATTACAGCCATTCTTCCCGCa                           <  2:1309259/126‑1 (MQ=255)
                                                                                                               tATCGCTCGTATCAACGGAAAATCGGCGGCGGGCCTGGGGATTAAGCTGGCAACCGGCGCGAATGCTCTCGATACCGCGAAAGCCATTAAGGCAAAACTGGCGGAATTACAGCCATTCTTCCCGCa                           >  1:1309259/1‑126 (MQ=255)
                                                                                                               tATCGCTCGTATCAACGGAAAATCGGCGGCGGGCCTGGGGATTAAGCTGGCAACCGGCGCGAATGCTCTCGATACCGCGAAAGCCATTAAGGCAAAACTGGCGGAATTACAGCCATTCTTCCCGCAGGGAATGAAGGTtc             >  1:28670/1‑140 (MQ=255)
                                                                                                                aTCGCTCGTATCAACGGAAAATCGGCGGCGGGCCTGGGGATTAAGCTGGCAACCGGCGCGAATGCTCTCGATACCGCGAAAGCCATTAAGGCAAAACTGGCGGAATTACAGCCATTCTTCCCGCAGGGAATGAAGGTtct            <  1:657856/140‑1 (MQ=255)
                                                                                                                aTCGCTCGTATCAACGGAAAATCGGCGGCGGGCCTGGGGATTAAGCTGGCAACCGGCGCGAATGCTCTCGATACCGCGAAAGCCATTAAGGCAAAACTGGCGGAATTACAGCCATTCTTCCCGCAGGGAATGAAGGTtct            >  1:1014003/1‑140 (MQ=255)
                                                                                                                 tCGCTCGTATCAACGGAAAATCGGCGGCGGGCCTGGGGATTAAGCTGGCAACCGGCGCGAATGCTCTCGATACCGCGAAAGCCATTAAGGCAAAACTGGCGGAATTACAGCCATTCTTCCCGCAGGGAATGAAGGTtctc           <  2:1242315/140‑1 (MQ=255)
                                                                                                                 tCGCTCGTATCAACGGAAAATCGGCGGCGGGCCTGGGGATTAAGCTGGCAACCGGCGCGAATGCTCTCGATACCGCGAAAGCCATTAAGGCAAAACTGGCGGAATTACAGCCATTCTTCCCGCAGGGAATGAAGGTtctc           >  2:1103508/1‑140 (MQ=255)
                                                                                                                 tCGCTCGTATCAACGGAAAATCGGCGGCGGGCCTGGGGATTAAGCTGGCAACCGGCGCGAATGCTCTCGATACCGCGAAAGCCATTAAGGCAAAACTGGCGGAATTACAGCCATTCTTCCCGCAGGGAATGAAGGTtctc           >  2:599165/1‑140 (MQ=255)
                                                                                                                 tCGCTCGTATCAACGGAAAATCGGCGGCGGGCCTGGGGATTAAGCTGGCAACCGGCGCGAATGCTCTCGATACCGCGAAAGCCATTAAGGCAAAACTGGCGGAATTACAGCCATTCTTCCCGCAGGGAATGAAGGTtctc           <  1:83179/140‑1 (MQ=255)
                                                                                                                  cGCTCGTATCAACGGAAAATCGGCGGCGGGCCTGGGGATTAAGCTGGCAACCGGCGCGAATGCTCTCGATACCGCGAAAGCCATTAAGGCAAAACTGGCGGAATTACAGCCATTCTTCCCGCAGGGAATGAAGGTTctct          <  2:205417/140‑1 (MQ=255)
                                                                                                                  cGCTCGTATCAACGGAAAATCGGCGGCGGGCCTGGGGATTAAGCTGGCAACCGGCGCGAATGCTCTCGATACCGCGAAAGCCATTAAGGCAAAACTGGCGGAATTACAGCCATTCTTCCCGCAGGGAATGAAGGTTctct          <  1:523683/140‑1 (MQ=255)
                                                                                                                    cTCGTATCAACGGAAAATCGGCGGCGGGCCTGGGGATTAAGCTGGCAACCGGCGCGAATGCTCTCGATACCGCGAAAGCCATTAAGGCAAAACTGGCGGAATTACAGCCATTCTTCCCGCAGGGAATGAAGGTTCTCTAc        <  2:848278/140‑1 (MQ=255)
                                                                                                                      cGTATCAACGGAAAATCGGCGGCGGGCCTGGGGATTAAGCTGGCAACCGGCGCGAATGCTCTCGATACCGCGAAAGCCATTAAGGCAAAACTGGCGGAATTACAGCCATTCTTCCCGCAGGGAATGAAGGTTCTCTAc        <  1:876229/138‑1 (MQ=255)
                                                                                                                      cGTATCAACGGAAAATCGGCGGCGGGCCTGGGGATTAAGCTGGCAACCGGCGCGAATGCTCTCGATACCGCGAAAGCCATTAAGGCAAAACTGGCGGAATTACAGCCATTCTTCCCGCAGGGAATGAAGGTTCTCTAc        >  2:876229/1‑138 (MQ=255)
                                                                                                                       gTATCAACGGAAAATCGGCGGCGGGCCTGGGGATTAAGCTGGCAACCGGCGCGAATGCTCTCGATACCGCGAAAGCCATTAAGGCAAAACTGGCGGAATTACAGCCATTCTTCCCGCAGGGAATGAAGGTTCTCTACCCt     >  1:84870/1‑140 (MQ=255)
                                                                                                                                  aaaTCGGCGGCGGGCCTGGGGATTAAGCTGGCAACCGGCGCGAATGCTCTCGATACCGCGAAAGCCATTAAGGCAAAACTGGCGGAATTACAGCCATTCTTCCCGCAGGGAATGATGGTTCTCTACCCTTAt  <  1:441442/132‑1 (MQ=255)
                                                                                                                                     |                                                                                                                                
TAAAAATCCGGAAGAATTCGGCAAAGTGACCCTGCGCGTAAACAGTGACGGCTCGGTGGTACGCCTGAAAGATGTCGCACGGGTTGAACTTGGCGGTGAAAACTATAACGTTATCGCTCGTATCAACGGAAAACCGGCGGCGGGCCTGGGGATTAAGCTGGCAACCGGCGCGAATGCTCTCGATACCGCGAAAGCCATTAAGGCAAAACTGGCGGAATTACAGCCATTCTTCCCGCAGGGAATGAAGGTTCTCTACCCTTAT  >  NC_000913/3415752‑3416013

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A