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 F1 I2 R1 772 77.0 3769570 91.6% 3452926 105.3

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 3,854,092 T→C G57G (GGT→GGC)  emrD → multidrug efflux system protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009133,854,0920TC100.0% 230.4 / NA 64G57G (GGT→GGC) emrDmultidrug efflux system protein
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (33/31);  total (33/31)

TTGGTATTACTCGTGGCCGTCGGTCAGATGGCGCAAACCATTTATATTCCAGCTATTGCCGATATGGCGCGCGATCTCAACGTCCGTGAAGGGGCGGTGCAGAGCGTAATGGGCGCTTATCTGCTGACTTACGGTGTCTCACAGCTGTTTTATGGCCCGATTTCCGACCGCGTGGGCCGCCGACCGGTGATCCTCGTCGGAATGTCCATTTTTATGCTGGCAACGCTGGTCGCGGTCACGACCTCCAGTTTGACGGTGTTGATTGCCG  >  NC_000913/3853958‑3854225
                                                                                                                                      |                                                                                                                                     
ttGGTATTACTCGTGGCCGTCGGTCAGATGGCGCAAACCATTTATATTCCAGCTATTGCCGATATGGCGCGCGATCTCAACGTCCGTGAAGGGGCGGTGCAGAGCGTAATGGGCGCTTATCTGCTGACTTACGGCGtct                                                                                                                                   <  1:1260067/139‑1 (MQ=255)
 tGGTATTACTCGTGGCCGTCGGTCAGATGGCGCAAACCATTTATATTCCAGCTATTGCCGATATGGCGCGCGATCTCAACGTCCGTGAAGGGGCGGTGCAGAGCGTAATGGGCGCTTATCTGCTGACTTACGGCGtctc                                                                                                                                  >  2:1205946/1‑139 (MQ=255)
  ggTATTACTCGTGGCCGTCGGTCAGATGGCGCAAACCATTTATATTCCAGCTATTGCCGATATGGCGCGCGATCTCAACGTCCGTGAAGGGGCGGTGCAGAGCGTAATGGGCGCTTATCTGCTGACTTACGGCGTCTca                                                                                                                                 <  1:1205946/139‑1 (MQ=255)
  ggTATTACTCGTGGCCGTCGGTCAGATGGCGCAAACCATTTATATTCCAGCTATTGCCGATATGGCGCGCGATCTCAACGTCCGTGAAGGGGCGGTGCAGAGCGTAATGGGCGCTTATCTGCTGACTTACGGCGTCTca                                                                                                                                 <  2:1761072/139‑1 (MQ=255)
       tACTCGTGGCCGTCGGTCAGATGGCGCAAACCATTTATATTCCAGCTATTGCCGATATGGCGCGCGATCTCAACGTCCGTGAAGGGGCGGTGCAGAGCGTAATGGGCGCTTATCTGCTGACTTACGGCGTCTCACAGCt                                                                                                                            >  1:580331/1‑139 (MQ=255)
        aCTCGTGGCCGTCGGTCAGATGGCGCAAACCATTTATATTCCAGCTATTGCCGATATGGCGCGCGATCTCAACGTCCGTGAAGGGGCGGTGCAGAGCGTAATGGGCGCTTATCTGCTGACTTACGGCGTCTcac                                                                                                                                >  1:692325/1‑134 (MQ=255)
        aCTCGTGGCCGTCGGTCAGATGGCGCAAACCATTTATATTCCAGCTATTGCCGATATGGCGCGCGATCTCAACGTCCGTGAAGGGGCGGTGCAGAGCGTAATGGGCGCTTATCTGCTGACTTACGGCGTCTcac                                                                                                                                <  2:692325/134‑1 (MQ=255)
         cTCGTGGCCGTCGGTCAGATGGCGCAAACCATTTATATTCCAGCTATTGCCGATATGGCGCGCGATCTCAACGTCCGTGAAGGGGCGGTGCAGAGCGTAATGGGCGCTTATCTGCTGACTTACGGCGtct                                                                                                                                   >  1:714911/1‑130 (MQ=255)
         cTCGTGGCCGTCGGTCAGATGGCGCAAACCATTTATATTCCAGCTATTGCCGATATGGCGCGCGATCTCAACGTCCGTGAAGGGGCGGTGCAGAGCGTAATGGGCGCTTATCTGCTGACTTACGGCGtct                                                                                                                                   <  2:714911/130‑1 (MQ=255)
             tGGCCGTCGGTCAGATGGCGCAAACCATTTATATTCCAGCTATTGCCGATATGGCGCGCGATCTCAACGTCCGTGAAGGGGCGGTGCAGAGCGTAATGGGCGCTTATCTGCTGACTTACGGCGTCTCACAGCTGTTTTa                                                                                                                      >  1:1514058/1‑139 (MQ=255)
              ggCCGTCGGTCAGATGGCGCAAACCATTTATATTCCAGCTATTGCCGATATGGCGCGCGATCTCAACGTCCGTGAAGGGGCGGTGCAGAGCGTAATGGGCGCTTATCTGCTGACTTACGGCGTCTCACAGCTGTTTTAt                                                                                                                     >  1:1028087/1‑139 (MQ=255)
              ggCCGTCGGTCAGATGGCGCAAACCATTTATATTCCAGCTATTGCCGATATGGCGCGCGATCTCAACGTCCGTGAAGGGGCGGTGCAGAGCGTAATGGGCGCTTATCTGCTGACTTACGGCGTCTCACAGCTGTTTTAt                                                                                                                     >  1:642099/1‑139 (MQ=255)
                                  aaaCCATTTATATTCCAGCTATTGCCGATATGGCGCGCGATCTCAACGTCCGTGAAGGGGCGGTGCAGAGCGTAATGGGCGCTTATCTGCTGACTTACGGCGTCTCACAGCTGTTTTATGGCCCGATTTCCGACCGCGt                                                                                                 <  2:642099/139‑1 (MQ=255)
                                         ttATATTCCAGCTATTGCCGATATGGCGCGCGATCTCAACGTCCGTGAAGGGGCGGTGCAGAGCGTAATGGGCGCTTATCTGCTGACTTACGGCGTCTCACAGCTGTTTTATGGCCCGATTTCCGACCGCGTGGgc                                                                                             <  2:293962/136‑1 (MQ=255)
                                         ttATATTCCAGCTATTGCCGATATGGCGCGCGATCTCAACGTCCGTGAAGGGGCGGTGCAGAGCGTAATGGGCGCTTATCTGCTGACTTACGGCGTCTCACAGCTGTTTTATGGCCCGATTTCCGACCGCGTGGgc                                                                                             >  1:293962/1‑136 (MQ=255)
                                                ccAGCTATTGCCGATATGGCGCGCGATCTCAACGTCCGTGAAGGGGCGGTGCAGAGCGTAATGGGCGCTTATCTGCTGACTTACGGCGtct                                                                                                                                   <  1:943832/91‑1 (MQ=255)
                                                ccAGCTATTGCCGATATGGCGCGCGATCTCAACGTCCGTGAAGGGGCGGTGCAGAGCGTAATGGGCGCTTATCTGCTGACTTACGGCGtct                                                                                                                                   >  2:943832/1‑91 (MQ=255)
                                                ccAGCTATTGCCGATATGGCGCGCGATCTCAACGTCCGTGAAGGGGCGGTGCAGAGCGTAATGGGCGCTTATCTGCTGACTTACGGCGTCTCACAGCTGTTTTATGGCCCGATTTCCGACCGCGTGGGCCGCCGACCgg                                                                                   <  2:72497/139‑1 (MQ=255)
                                                  aGCTATTGCCGATATGGCGCGCGATCTCAACGTCCGTGAAGGGGCGGTGCAGAGCGTAATGGGCGCTTATCTGCTGACTTACGGCGTCTCACAGCTGTTTTATGGCCCGATTTCCGACCGCGTGGGCCGCCGACCGGTg                                                                                 >  2:404893/1‑139 (MQ=255)
                                                   gCTATTGCCGATATGGCGCGCGATCTCAACGTCCGTGAAGGGGCGGTGCAGAGCGTAATGGGCGCTTATCTGCTGACTTACGGCGTCTCACAGCTGTTTTATGGCCCGATTTCCGACCGCGTGGGCCGCCGACCGGTGa                                                                                >  2:656136/1‑139 (MQ=255)
                                                    cTATTGCCGATATGGCGCGCGATCTCAACGTCCGTGAAGGGGCGGTGCAGAGCGTAATGGGCGCTTATCTGCTGACTTACGGCGTCTCACAGCTGTTTTATGGCCCGATTTCCGACCGCGTGGGCCGCCGACCGGTGAt                                                                               <  2:580331/139‑1 (MQ=255)
                                                      aTTGCCGATATGGCGCGCGATCTCAACGTCCGTGAAGGGGCGGTGCAGAGCGTAATGGGCGCTTATCTGCTGACTTACGGCGTCTCACAGCTGTTTTATGGCCCGATTTCCGACCGCGTGGGCCGCCGa                                                                                       <  2:1247202/129‑1 (MQ=255)
                                                      aTTGCCGATATGGCGCGCGATCTCAACGTCCGTGAAGGGGCGGTGCAGAGCGTAATGGGCGCTTATCTGCTGACTTACGGCGTCTCACAGCTGTTTTATGGCCCGATTTCCGACCGCGTGGGCCGCCGa                                                                                       >  1:1247202/1‑129 (MQ=255)
                                                       ttGCCGATATGGCGCGCGATCTCAACGTCCGTGAAGGGGCGGTGCAGAGCGTAATGGGCGCTTATCTGCTGACTTACGGCGTCTcac                                                                                                                                >  1:1037463/1‑87 (MQ=255)
                                                       ttGCCGATATGGCGCGCGATCTCAACGTCCGTGAAGGGGCGGTGCAGAGCGTAATGGGCGCTTATCTGCTGACTTACGGCGTCTcac                                                                                                                                <  2:1037463/87‑1 (MQ=255)
                                                         gCCGATATGGCGCGCGATCTCAACGTCCGTGAAGGGGCGGTGCAGAGCGTAATGGGCGCTTATCTGCTGACTTACGGCGTCTCACAGCTGTTTTATGGCCCGATTTCCGACCGCGTGGGCCGCCGACCGGTGATCCtcg                                                                          >  2:971717/1‑139 (MQ=255)
                                                                  gcgcgcGATCTCAACGTCCGTGAAGGGGCGGTGCAGAGCGTAATGGGCGCTTATCTGCTGACTTACGGCGTCTCACAGCTGTTTTATGGCCCGATTTCCGACCGCGTGGGCCGCCGACCGGTGATc                                                                              >  1:691629/1‑126 (MQ=255)
                                                                  gcgcgcGATCTCAACGTCCGTGAAGGGGCGGTGCAGAGCGTAATGGGCGCTTATCTGCTGACTTACGGCGTCTCACAGCTGTTTTATGGCCCGATTTCCGACCGCGTGGGCCGCCGACCGGTGATc                                                                              <  2:691629/126‑1 (MQ=255)
                                                                   cgcgcgATCTCAACGTCCGTGAAGGGGCGGTGCAGAGCGTAATGGGCGCTTATCTGCTGACTTACGGCGTCTCACAGCTGTTTTATGGCCCGATTTCCGACCGCGTGGGCCGCCGACCGGTGATCCtcgtcg                                                                       <  1:1603069/132‑1 (MQ=255)
                                                                   cgcgcgATCTCAACGTCCGTGAAGGGGCGGTGCAGAGCGTAATGGGCGCTTATCTGCTGACTTACGGCGTCTCACAGCTGTTTTATGGCCCGATTTCCGACCGCGTGGGCCGCCGACCGGTGATCCtcgtcg                                                                       >  2:1603069/1‑132 (MQ=255)
                                                                   cgcgcgATCTCAACGTCCGTGAAGGGGCGGTGCAGAGCGTAATGGGCGCTTATCTGCTGACTTACGGCGTCTCACAGCTGTTTTATGGCCCGATTTCCGACCGCGTGGGCCGCCGACCGGTGATCCTCGTCGGAATGTc                                                                <  1:1868983/139‑1 (MQ=255)
                                                                    gcgcgATCTCAACGTCCGTGAAGGGGCGGTGCAGAGCGTAATGGGCGCTTATCTGCTGACTTACGGCGTCTCACAGCTGTTTTATGGCCCGATTTCCGACCGCGTGGGCCGCCGACCGGTGATCCTCGTCGGAATGTcc                                                               >  1:1519245/1‑139 (MQ=255)
                                                                          tctcAACGTCCGTGAAGGGGCGGTGCAGAGCGTAATGGGCGCTTATCTGCTGACTTACGGCGTCTCACAGCTGTTTTATGGCCCGATTTCCGACCGCGTGGGCCGCCGACCGGTGATCCTCGTCGGAATGTCCAttttt                                                         >  1:1252099/1‑139 (MQ=255)
                                                                                 gTCCGTGAAGGGGCGGTGCAGAGCGTAATGGGCGCTTATCTGCTGACTTACGGCGTCTCACAGCTGTTTTATGGCCCGATTTCCGACCGCGTGGGCCGCCGACCGGTGATCCTCGTCGGAATGTCCATTTTTATGCTgg                                                  <  2:1519245/139‑1 (MQ=255)
                                                                                    cGTGAAGGGGCGGTGCAGAGCGTAATGGGCGCTTATCTGCTGACTTACGGCGTCTCACAGCTGTTTTATGGCCCGATTTCCGACCGCGt                                                                                                 <  2:397196/89‑1 (MQ=255)
                                                                                    cGTGAAGGGGCGGTGCAGAGCGTAATGGGCGCTTATCTGCTGACTTACGGCGTCTCACAGCTGTTTTATGGCCCGATTTCCGACCGCGt                                                                                                 >  1:397196/1‑89 (MQ=255)
                                                                                    cGTGAAGGGGCGGTGCAGAGCGTAATGGGCGCTTATCTGCTGACTTACGGCGTCTCACAGCTGTTTTATGGCCCGATTTCCGACCGCGTGGGCCGCCGACCGGTGATCCTCGTCGGAATGTCCATTTTTAt                                                       >  1:360244/1‑131 (MQ=255)
                                                                                    cGTGAAGGGGCGGTGCAGAGCGTAATGGGCGCTTATCTGCTGACTTACGGCGTCTCACAGCTGTTTTATGGCCCGATTTCCGACCGCGTGGGCCGCCGACCGGTGATCCTCGTCGGAATGTCCATTTTTAt                                                       <  2:360244/131‑1 (MQ=255)
                                                                                    cGTGAAGGGGCGGTGCAGAGCGTAATGGGCGCTTATCTGCTGACTTACGGCGTCTCACAGCTGTTTTATGGCCCGATTTCCGACCGCGTGGGCCGCCGACCGGTGATCCTCGTCGGAATGTCCATTTTTATGCTGGCaa                                               >  2:1330854/1‑139 (MQ=255)
                                                                                      tGAAGGGGCGGTGCAGAGCGTAATGGGCGCTTATCTGCTGACTTACGGCGTCTCACAGCTGTTTTATGGCCCGATTTCCGACCGCGTGGGCCGCCGACCGGTGATCCTCGTCGGa                                                                     <  1:1640022/115‑1 (MQ=255)
                                                                                      tGAAGGGGCGGTGCAGAGCGTAATGGGCGCTTATCTGCTGACTTACGGCGTCTCACAGCTGTTTTATGGCCCGATTTCCGACCGCGTGGGCCGCCGACCGGTGATCCTCGTCGGa                                                                     >  2:1640022/1‑115 (MQ=255)
                                                                                      tGAAGGGGCGGTGCAGAGCGTAATGGGCGCTTATCTGCTGACTTACGGCGTCTCACAGCTGTTTTATGGCCCGATTTCCGACCGCGTGGGCCGCCGACCGGTGATCCTCGTCGGTATGTCCATTTTTATGCTGGCAACg                                             >  2:1049392/1‑139 (MQ=255)
                                                                                            ggCGGTGCAGAGCGTAATGGGCGCTTATCTGCTGACTTACGGCGTCTCACAGCTGTTTTATGGCCCGATTTCCGACCGCGTGGGCCGCCGACCGGTGATCCTCGTCGGa                                                                     <  2:23238/109‑1 (MQ=255)
                                                                                            ggCGGTGCAGAGCGTAATGGGCGCTTATCTGCTGACTTACGGCGTCTCACAGCTGTTTTATGGCCCGATTTCCGACCGCGTGGGCCGCCGACCGGTGATCCTCGTCGGa                                                                     >  1:23238/1‑109 (MQ=255)
                                                                                             gCGGTGCAGAGCGTAATGGGCGCTTATCTGCTGACTTACGGCGTCTCACAGCTGTTTTATGGCCCGATTTCCGACCGCGt                                                                                                 <  2:744785/80‑1 (MQ=255)
                                                                                             gCGGTGCAGAGCGTAATGGGCGCTTATCTGCTGACTTACGGCGTCTCACAGCTGTTTTATGGCCCGATTTCCGACCGCGt                                                                                                 >  1:744785/1‑80 (MQ=255)
                                                                                             gCGGTGCAGAGCGTAATGGGCGCTTATCTGCTGACTTACGGCGTCTCACAGCTGTTTTATGGCCCGATTTCCGACCGCGTGGGCCGCCGACCGGTGATCCTCGTCGGAATGTCCATTTTTATGCTGGCAACGCTGGTcg                                      >  1:250818/1‑139 (MQ=255)
                                                                                              cGGTGCAGAGCGTAATGGGCGCTTATCTGCTGACTTACGGCGTCTca                                                                                                                                 <  2:1593282/47‑1 (MQ=255)
                                                                                              cGGTGCAGAGCGTAATGGGCGCTTATCTGCTGACTTACGGCGTCTca                                                                                                                                 >  1:1593282/1‑47 (MQ=255)
                                                                                                   cAGAGCGTAATGGGCGCTTATCTGCTGACTTACGGCGTCTCACAGCTGTTTTATGGCCCGATTTCCGACCGCGTGGGCCGCCGACCGGTGATCCTCGTCGGAATGTCCATTTTTATGCTGGCAACGCTGGTCGCGGTCa                                <  1:656136/139‑1 (MQ=255)
                                                                                                      agCGTAATGGGCGCTTATCTGCTGACTTACGGCGTCTCACAGCTGTTTTATGGCCCGATTTCCGACCGCGTGGGCCGCCGACCGGTGACCCTCGTCGGAATGTCCATTTTTATGCTGGCAACGCTGGTCGCGGTCACGa                             >  1:81447/1‑139 (MQ=255)
                                                                                                               ggCGCTTATCTGCTGACTTACGGCGTCTCACAGCTGTTTTATGGCCCGATTTCCGACCGCGTGGGCCGCCGACCGGTGATCCTCGTCGGAATGTCCATTTTTATGCTGGCAACGCTGGTCGCGGTCACGACCTCCAGtt                    <  1:971717/139‑1 (MQ=255)
                                                                                                                gcgcTTATCTGCTGACTTACGGCGTCTCACAGCTGTTTTATGGCCCGATTTCCGACCGCGTGGGCCGCCGa                                                                                       <  2:86903/71‑1 (MQ=255)
                                                                                                                gcgcTTATCTGCTGACTTACGGCGTCTCACAGCTGTTTTATGGCCCGATTTCCGACCGCGTGGGCCGCCGa                                                                                       >  1:86903/1‑71 (MQ=255)
                                                                                                                  gcTTATCTGCTGACTTACGGCGTCTCACAGCTGTTTTATGGCCCGATTTCCGACCGCGTGGGCCGCCGACCGGTGAt                                                                               <  1:772144/77‑1 (MQ=255)
                                                                                                                  gcTTATCTGCTGACTTACGGCGTCTCACAGCTGTTTTATGGCCCGATTTCCGACCGCGTGGGCCGCCGACCGGTGAt                                                                               >  2:772144/1‑77 (MQ=255)
                                                                                                                  gcTTATCTGCTGACTTACGGCGTCTCACAGCTGTTTTATGGCCCGATTTCCGACCGCGTGGGCCGCCGACCGGTGATCCTCGTCGGAATGTCCATTTTTATGCTGGCAACGCTGGTCGCGGTCACGACCTCCAGTTTGa                 <  1:404893/139‑1 (MQ=255)
                                                                                                                   cTTATCTGCTGACTTACGGCGTCTCACAGCTGTTTTATGGCCCGATTTCCGACCGCGTGGGCCGCCGACCGGTGATCCTCGTCGGAATGTCCATTTTTATGCTGGCAACGCTGGTCGCGGTCACGACCTCCAGTTTGAc                <  2:1028087/139‑1 (MQ=255)
                                                                                                                        ctgctgACTTACGGCGTCTCACAGCTGTTTTATGGCCCGATTTCCGACCGCGTGGGCCGCCGACCGGTGATCCTCGTCGGAATGTCCATTTTTATGCTGGCAACGCTGGTCGCGGTCACGACCTCCAGTTTGACGgtgt           <  2:513804/139‑1 (MQ=255)
                                                                                                                           ctgACTTACGGCGTCTCACAGCTGTTTTATGGCCCGATTTCCGACCGCGTGGGCCGCCGACCGGTGATCCTCGTCGGAATGTCCATTTTTATGCTGGCAACGCTGGTCGCGGTCAc                               <  2:1703898/116‑1 (MQ=255)
                                                                                                                           ctgACTTACGGCGTCTCACAGCTGTTTTATGGCCCGATTTCCGACCGCGTGGGCCGCCGACCGGTGATCCTCGTCGGAATGTCCATTTTTATGCTGGCAACGCTGGTCGCGGTCAc                               >  1:1703898/1‑116 (MQ=255)
                                                                                                                              aCTTACGGCGTCTCACAGCTGTTTTATGGCCCGATTTCCGACCGCGTGGGCCGCCGACCGGTGATCCTCGTCGGAATGTCCATTTTTATGCTGGCAACGCTGGTCGCGGTCACGACCTCCAGTTTGa                 >  2:997227/1‑127 (MQ=255)
                                                                                                                              aCTTACGGCGTCTCACAGCTGTTTTATGGCCCGATTTCCGACCGCGTGGGCCGCCGACCGGTGATCCTCGTCGGAATGTCCATTTTTATGCTGGCAACGCTGGTCGCGGTCACGACCTCCAGTTTGa                 <  1:997227/127‑1 (MQ=255)
                                                                                                                                 tACGGCGTCTCACAGCTGTTTTATGGCCCGATTTCCGACCGCGTGGGCCGCCGACCGGTGATCCTCGTCGGAATGTCCATTTTTATGCTGGCAACGCTGGTCGCGGTCACGACCTCCAGTTTGACGGTGTTGATTgccg  >  1:1826301/1‑139 (MQ=255)
                                                                                                                                      |                                                                                                                                     
TTGGTATTACTCGTGGCCGTCGGTCAGATGGCGCAAACCATTTATATTCCAGCTATTGCCGATATGGCGCGCGATCTCAACGTCCGTGAAGGGGCGGTGCAGAGCGTAATGGGCGCTTATCTGCTGACTTACGGTGTCTCACAGCTGTTTTATGGCCCGATTTCCGACCGCGTGGGCCGCCGACCGGTGATCCTCGTCGGAATGTCCATTTTTATGCTGGCAACGCTGGTCGCGGTCACGACCTCCAGTTTGACGGTGTTGATTGCCG  >  NC_000913/3853958‑3854225

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A