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
A9 F1 I1 R1 759 71.0 3673240 91.5% 3361014 104.6

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 3,892,455 G→A A281T (GCG→ACG)  mdtL → multidrug efflux system protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009133,892,4550GA100.0% 181.3 / NA 57A281T (GCG→ACG) mdtLmultidrug efflux system protein
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (30/27);  total (30/27)

CGGTGAATACGCCACCATTATGGCGCTGACCGCTGGCGTCAGCATGACCGTTTCATTCTCCACGCCATTTGCGCTGGGAATTTTTAAGCCACGTACGTTGATGATCACCTCGCAGGTGTTATTCCTGGCGGCGGGGATCACTCTTGCCGTTTCACCTTCCCATGCGGTTTCTCTGTTTGGTATCACGCTGATTTGCGCCGGTTTCTCGGTAGGTTTTGGTGTGGCGATGAGTCAGGCGTTAGGGCCGTTTTCATTACGCG  >  NC_000913/3892325‑3892584
                                                                                                                                  |                                                                                                                                 
cgGTGACTACGCCACCATTATGGCGCTGACCGCTGGCGTCAGCATGACCGTTTCATTCTCCACGCCATTTGCGCTGGGAATTTTTAAGCCACGTACGTTGATGATCACCTCGCAGGTGTTATTTCTGGCGACGGGGATc                                                                                                                           >  1:1604996/1‑139 (MQ=255)
      aTACGCCACCATTATGGCGCTGACCGCTGGCGTCAGCATGACCGTTTCATTCTCCACGCCATTTGCGCTGGGAATTTTTAAGCCACGTACGTTGATGATCACCTCGCAGGTGTTATTCCTGGCGACGGGGATCACTCtt                                                                                                                     <  1:1104010/139‑1 (MQ=255)
             accaTTATGGCGCTGACCGCTGGCGTCAGCATGACCGTTTCATTCTCCACGCCATTTGCGCTGGGAATTTTTAAGCCACGTACGTTGATGATCACCTCGCAGGTGTTATTCCTGGCGACGGGGATCACTCTTGCCGttt                                                                                                              >  2:1582129/1‑139 (MQ=255)
             accaTTATGGCGCTGACCGCTGGCGTCAGCATGACCGTTTCATTCTCCACGCCATTTGCGCTGGGAATTTTTAAGCCACGTACGTTGATGATCACCTCGCAGGTGTTATTCCTGGCGACGGGGATCACTCTTGCCGttt                                                                                                              >  2:753541/1‑139 (MQ=255)
               caTTATGGCGCTGACCGCTGGCGTCAGCATGACCGTTTCATTCTCCACGCCATTTGCGCTGGGAATTTTTAAGCCACGTACGTTGATGATCACCTCGCAGGTGTTATTCCTGGCGACGGGGAt                                                                                                                            >  2:1432673/1‑123 (MQ=255)
               caTTATGGCGCTGACCGCTGGCGTCAGCATGACCGTTTCATTCTCCACGCCATTTGCGCTGGGAATTTTTAAGCCACGTACGTTGATGATCACCTCGCAGGTGTTATTCCTGGCGACGGGGAt                                                                                                                            <  1:1432673/123‑1 (MQ=255)
                 ttATGGCGCTGACCGCTGGCGTCAGCATGACCGTTTCATTCTCCACGCCATTTGCGCTGGGAATTTTTAAGCCACGTACGTTGATGATCACCTCGCAGGTGTTATTCCTGGCGACGGGGATCACTCTTGCCGTTTCAcc                                                                                                          <  1:753541/139‑1 (MQ=255)
                         cTGACCGCTGGCGTCAGCATGACCGTTTCATTCTCCACGCCATTTGCGCTGGGAATTTTTAAGCCACGTACGTTGATGATCACCTCGCAGGTGTTATTCCTGGCGACGGGGATCACTCTTGCCGTTTCACCTTCCCATg                                                                                                  >  2:943032/1‑139 (MQ=255)
                           gACCGCTGGCGTCAGCATGACCGTTTCATTCTCCACGCCATTTGCGCTGGGAATTTTTAAGCCACGTACGTTGATGATCACCTCGCAGGTGTTATTCCTGGCGACGGGGATCACTCTTGCCGTTTCACCTTCCCATGCg                                                                                                >  2:565128/1‑139 (MQ=255)
                            accacTGGCGTCAGCATGACCGTTTCATTCTCCACGCCATTTGCGCTGGGAATTTTTAAGCCACGTACGTTGATGATCACCTCGCAGGTGTTATTCCTGGCGACGGGGATCACTCTTGCCGTTTCACCTTCCCATGCgg                                                                                               >  2:435718/5‑139 (MQ=255)
                            aCCGCTGGCGTCAGCATGACCGTTTCATTCTCCACGCCATTTGCGCTGGGAATTTTTAAGCCACGTACGTTGATGATCACCTCGCAGGTGTTATTCCTGGCGACgggg                                                                                                                              >  2:1682760/1‑108 (MQ=255)
                            aCCGCTGGCGTCAGCATGACCGTTTCATTCTCCACGCCATTTGCGCTGGGAATTTTTAAGCCACGTACGTTGATGATCACCTCGCAGGTGTTATTCCTGGCGACgggg                                                                                                                              <  1:1682760/108‑1 (MQ=255)
                                 tGGCGTCAGCATGACCGTTTCATTCTCCACGCCATTTGCGCTGGGAATTTTTAAGCCACGTACGTTGATGATCACCTCGCAGGTGTTATTCCTGGCGACGGGGATCACTCTTGCCGTTTCACCTTCCCATGCGGTTtct                                                                                          <  1:251383/139‑1 (MQ=255)
                                 tGGCGTCAGCATGACCGTTTCATTCTCCACGCCATTTGCGCTGGGAATTTTTAAGCCACGTACGTTGATGATCACCTCGCAGGTGTTATTCCTGGCGACGGGGATCACTCTTGCCGTTTCACCTTCCCATGCGGTTtct                                                                                          <  1:943032/139‑1 (MQ=255)
                                      tCAGCATGACCGTTTCATTCTCCACGCCATTTGCGCTGGGAATTTTTAAGCCACGTACGTTGATGATCACCTCGCAGGTGTTATTCCTGGCGACGGGGATCACTCTTGCCGTTTCACCTTCCCATGCGGTTTCTCTGtt                                                                                     <  2:223539/139‑1 (MQ=255)
                                      tCAGCATGACCGTTTCATTCTCCACGCCATTTGCGCTGGGAATTTTTAAGCCACGTACGTTGATGATCACCTCGCAGGTGTTATTCCTGGCGACGGGGATCACTCTTGCCGTTTCACCTTCCCATGCGGTTTCTCTGtt                                                                                     >  2:159815/1‑139 (MQ=255)
                                           aTGACCGTTTCATTCTCCACGCCATTTGCGCTGGGAATTTTTAAGCCACGTACGTTGATGATCACCTCGCAGGTGTTATTCCTGGCGACGGGGATCACTCTTGCCGTTTCACCTTCCCATGCGGTTTCTCTGTTTGGTa                                                                                <  2:1604996/139‑1 (MQ=255)
                                             gACCGTTTCATTCTCCACGCCATTTGCGCTGGGAATTTTTAAGCCACGTACGTTGATGATCACCTCGCAGGTGTTATTCCTGGCGACGGGGa                                                                                                                             <  2:1509337/92‑1 (MQ=255)
                                             gACCGTTTCATTCTCCACGCCATTTGCGCTGGGAATTTTTAAGCCACGTACGTTGATGATCACCTCGCAGGTGTTATTCCTGGCGACGGGGa                                                                                                                             >  1:1509337/1‑92 (MQ=255)
                                                  tttCATTCTCCACGCCATTTGCGCTGGGAATTTTTAAGCCACGTACGTTGATGATCACCTCGCAGGTGTTATTCCTGGCGACGGGGATCACTCTTGCCg                                                                                                                 >  2:464444/1‑99 (MQ=255)
                                                  tttCATTCTCCACGCCATTTGCGCTGGGAATTTTTAAGCCACGTACGTTGATGATCACCTCGCAGGTGTTATTCCTGGCGACGGGGATCACTCTTGCCg                                                                                                                 <  1:464444/99‑1 (MQ=255)
                                                  tttCATTCTCCACGCCATTTGCGCTGGGAATTTTTAAGCCACGTACGTTGATGATCACCTCGCAGGTGTTATTCCTGGCGACGGGGATCACTCTTGCCGTTTCACCTTCCCATGCGGTTTCTCTGTTTGGTATCACGCt                                                                         >  2:280662/1‑139 (MQ=255)
                                                                 cATTTGCGCTGGGAATTTTTAAGCCACGTACGTTGATGATCACCTCGCAGGTGTTATTCCTGGCGACGGGGATCACTCTTGCCGTTTCACCTTCCCATGCGGt                                                                                              >  1:861440/1‑103 (MQ=255)
                                                                 cATTTGCGCTGGGAATTTTTAAGCCACGTACGTTGATGATCACCTCGCAGGTGTTATTCCTGGCGACGGGGATCACTCTTGCCGTTTCACCTTCCCATGCGGt                                                                                              <  2:861440/103‑1 (MQ=255)
                                                                    ttGCGCTGGGAATTTTTAAGCCACGTACGTTGATGATCACCTCGCAGGTGTTATTCCTGGCGACGGGGATCACTCTTGCCGTTTCACCTTCCCATGCGGTTTCTCTGTTTGGTATCACGCTGAtt                                                                     <  1:608943/125‑1 (MQ=255)
                                                                    ttGCGCTGGGAATTTTTAAGCCACGTACGTTGATGATCACCTCGCAGGTGTTATTCCTGGCGACGGGGATCACTCTTGCCGTTTCACCTTCCCATGCGGTTTCTCTGTTTGGTATCACGCTGAtt                                                                     >  2:608943/1‑125 (MQ=255)
                                                                    ttGCGCTGGGAATTTTTAAGCCACGTACGTTGATGATCACCTCGCAGGTGTTATTCCTGGCGACGGGGATCACTCTTGCCGTTTCACCTTCCCATGCGGTTTCTCTGTTTGGTATCACGCTGATTTGCGCCGGTTtctc                                                       >  1:1160163/1‑139 (MQ=255)
                                                                    ttGCGCTGGGAATTTTTAAGCCACGTACGTTGATGATCACCTCGCAGGTGTTATTCCTGGCGACGGGGATCACTCTTGCCGTTTCACCTTCCCATGCGGTTTCTCTGTTTGGTATCACGCTGATTTGCGCCGGTTtctc                                                       >  2:991369/1‑139 (MQ=255)
                                                                      gcgcTGGGAATTTTTAAGCCACGTACGTTGATGATCACCTCGCAGGTGTTATTCCTGGCGACGGGGATCACTCTTGCCGTTTCACCTTCCCATGCGGTTTCTCTGTTTGGTATCACGCTGATTTGCGCCGGTTTCTCgg                                                     <  1:565128/139‑1 (MQ=255)
                                                                       cgcTGGGAATTTTTAAGCCACGTACGTTGATGATCACCTCGCAGGTGTTATTCCTGGCGACGGGGATCACTCTTGCCGTTTCACCTTCCCATGCGGTTTCTCTGTTTGGTATCACGCTGATTTGCGCCGGTTTCTCGGt                                                    <  1:280662/139‑1 (MQ=255)
                                                                       cgcTGGGAATTTTTAAGCCACGTACGTTGATGATCACCTCGCAGGTGTTATTCCTGGCGACGGGGATCACTCTTGCCGTTTCACCTTCCCATGCGGTTTCTCTGTTTGGTATCACGCTGATTTGCGCCGGTTTCTCGGt                                                    <  1:991369/139‑1 (MQ=255)
                                                                             gAATTTTTAAGCCACGTACGTTGATGATCACCTCGCAGGTGTTATTCCTGGCGACGGGGATCACTCTTGCCGTTTCACCTTCCCATGCGGTTTCTCTGTTTGGTATCACGCTGATTTGCGCCGGTTTCTCGGTAGGttt                                              >  2:203010/1‑139 (MQ=255)
                                                                                        ccACGTACGTTGATGATCACCTCGCAGGTGTTATTCCTGGCGACGGGGATCACTCTTGCCGTTTCACCTTCCCATGCGGTTtct                                                                                          >  2:1015699/1‑84 (MQ=255)
                                                                                        ccACGTACGTTGATGATCACCTCGCAGGTGTTATTCCTGGCGACGGGGATCACTCTTGCCGTTTCACCTTCCCATGCGGTTtct                                                                                          <  1:1015699/84‑1 (MQ=255)
                                                                                           cgtacgtTGATGATCACCTCGCAGGTGTTATTCCTGGCGACGGGGATCACTCTTGCCGTTTCACCTTCCCATGCGGTTTCTCTGTTTGGTATCACGCTGATTTGCGCCGGTTTCTCGGTAGGTTTTGGTGTGGCGATGa                                >  2:1718582/1‑139 (MQ=255)
                                                                                               cgtTGATGATCACCTCGCAGGTGTTATTCCTGGCGACGGGGATCACTCTTGGCGTTTCACCTTCCCATGCGGTTTCTCTGTTTGGTATCACGCTGATTTGCGCCGGTTTCTCGGTAGGTTTTGGTGTGGCGATGAGTCa                            <  1:159815/139‑1 (MQ=255)
                                                                                                    atgatCACCTCGCAGGTGTTATTCCTGGCGACGGGGATCACTCTTGCCGTTTCACCtt                                                                                                        >  1:1438619/1‑58 (MQ=255)
                                                                                                    atgatCACCTCGCAGGTGTTATTCCTGGCGACGGGGATCACTCTTGCCGTTTCACCtt                                                                                                        <  2:1438619/58‑1 (MQ=255)
                                                                                                        tCACCTCGCAGGTGTTATTCCTGGCGACGGGGATCACTCTTGCCGTTTCACCTTCCCATGCGGTTTCTCTGTTTGGTATCACGCTGATTTGCGCCGGTTTCTCGGt                                                    >  2:265998/1‑106 (MQ=255)
                                                                                                        tCACCTCGCAGGTGTTATTCCTGGCGACGGGGATCACTCTTGCCGTTTCACCTTCCCATGCGGTTTCTCTGTTTGGTATCACGCTGATTTGCGCCGGTTTCTCGGt                                                    <  1:265998/106‑1 (MQ=255)
                                                                                                        tCACCTCGCAGGTGTTATTCCTGGCGACGGGGATCACTCTTGCCGTTTCACCTTCCCATGCGGTTTCTCTGTTTGGTATCACGCTGATTTGCGCCGGTTCCTCGGTAGGTTTTGGTGTGGCGATGAGTCAGGCGTTAgg                   <  1:435718/139‑1 (MQ=255)
                                                                                                          aCCTCGCAGGTGTTATTCCTGGCGACGGGGATCActct                                                                                                                      <  1:1814092/38‑1 (MQ=255)
                                                                                                          aCCTCGCAGGTGTTATTCCTGGCGACGGGGATCActct                                                                                                                      >  2:1814092/1‑38 (MQ=255)
                                                                                                            cTCGCAGGTGTTATTCCTGGCGACGGGGATCACTCTTGCCGTTTCACCTTCCCATGCGGTTTCTCTGTTTGGTATCACGCTGATTTGCGCCGGTTTCTCg                                                      >  2:640934/1‑100 (MQ=255)
                                                                                                            cTCGCAGGTGTTATTCCTGGCGACGGGGATCACTCTTGCCGTTTCACCTTCCCATGCGGTTTCTCTGTTTGGTATCACGCTGATTTGCGCCGGTTTCTCg                                                      <  1:640934/100‑1 (MQ=255)
                                                                                                              cGCAGGTGTTATTCCTGGCGACGGGGATCACTCTTGCCGTTTCACCTTCCCa                                                                                                    <  1:1046497/52‑1 (MQ=255)
                                                                                                              cGCAGGTGTTATTCCTGGCGACGGGGATCACTCTTGCCGTTTCACCTTCCCa                                                                                                    >  2:1046497/1‑52 (MQ=255)
                                                                                                              cGCAGGTGTTATTCCTGGCGACGGGGATCACTCTTGCCGTTTCACCTTCCCATGCGGTTTCTCTGTTTGGTATCACGCTGATTTGCGCCGGTTTCTCGGTAGGTTTTGGTGTGGCGATGAGTCAGGCGTTAGGGCCGtt             <  1:959476/139‑1 (MQ=255)
                                                                                                              cGCAGGTGTTATTCCTGGCGACGGGGATCACTCTTGCCGTTTCACCTTCCCATGCGGTTTCTCTGTTTGGTATCACGCTGATTTGCGCCGGTTTCTCGGTAGGTTTTGGTATGGCGATGAGTCAGGCGTTAGGGCCGtt             >  2:658548/1‑139 (MQ=255)
                                                                                                               gCAGGTGTTATTCCTGGCGACGGGGATCACTCTTGCCGTTTCACCTTCCCATGCGGTTTCTCTGTTTGGTATCACGCTGATTTGCGCCGGTTTCTCGGTAGGTTTTGGTGTGGCGATGAGTCAGGCGTTAGGGCCGttt            >  1:1336785/1‑139 (MQ=255)
                                                                                                                    tgtTATTCCTGGCGACGGGGATCACTCTTGCCGTTTCACCTTCCCATGCGGTTTCTCTGTTTGGTATCACGCTGATTTGCGCCGGTTTCTCGGTAGGTTTTGGTGTGGCGATGAGTCAGGCGTTAGGGCCGTTTTCAtt       >  2:523455/1‑139 (MQ=255)
                                                                                                                      ttATTCCTGGCGACGGGGATCACTCTTGCCGTTTCACCTTCCCATg                                                                                                  >  1:615418/1‑46 (MQ=255)
                                                                                                                      ttATTCCTGGCGACGGGGATCACTCTTGCCGTTTCACCTTCCCATg                                                                                                  <  2:615418/46‑1 (MQ=255)
                                                                                                                      ttATTCCTGGCGACGGGGATCACTCTTGCCGTTTCACCTTCCCATGCGGTTTCTCTGTTTGGTATCACGCTGATTTGCGCCGGTTTCTCGGTAGGTTTTGGTGTTGCGATGAGTCAGGCGTTAGGGCCGTTTTCATTAc     >  2:884482/1‑139 (MQ=255)
                                                                                                                         ttCCTGGCGACGGGGATCACTCTTGCCGTTTCACCTTCCCa                                                                                                    <  2:164075/41‑1 (MQ=255)
                                                                                                                         ttCCTGGCGACGGGGATCACTCTTGCCGTTTCACCTTCCCa                                                                                                    >  1:164075/1‑41 (MQ=255)
                                                                                                                         ttCCTGGCGACGGGGATCACTCTTGCCGTTTCACCTTCCCATGCGGTTTCTCTTTTTGGTATCACGCTGATTTGCGCCGGTTTCTCGGTAGGTTTTGGTGTGGCGATGAGTCAGGTGTTAGGGCCGTTTTCATTAcgcg  <  1:1718582/139‑1 (MQ=255)
                                                                                                                              ggcgacGGGGATCACTCTTGCCGTTTCACCTTCCCATGCGGTTTCTCTGTTTGGTATCACGCTGATTTgcgc                                                                <  1:1383483/72‑1 (MQ=255)
                                                                                                                              ggcgacGGGGATCACTCTTGCCGTTTCACCTTCCCATGCGGTTTCTCTGTTTGGTATCACGCTGATTTgcgc                                                                >  2:1383483/1‑72 (MQ=255)
                                                                                                                              ggcgacGGGGATCACTCTTGCCGTTTCACCTTCCCATGCGGTTTCTCTGTTTGGTATCACGCTGATTTGCGCCGGTTTCTCGGt                                                    >  2:1443409/1‑84 (MQ=255)
                                                                                                                              ggcgacGGGGATCACTCTTGCCGTTTCACCTTCCCATGCGGTTTCTCTGTTTGGTATCACGCTGATTTGCGCCGGTTTCTCGGt                                                    <  1:1443409/84‑1 (MQ=255)
                                                                                                                              ggcgacGGGGATCACTCTTGCCGTTTCACCTTCCCATGCGGTTTCTCTGTTTGGTATCACGCTGATTTGCGCCGGTTTCTCGGTAGGTTTTGGTGTGGCGATGAGTCAGGCGTTAGGGCCg               <  2:651454/121‑1 (MQ=255)
                                                                                                                              ggcgacGGGGATCACTCTTGCCGTTTCACCTTCCCATGCGGTTTCTCTGTTTGGTATCACGCTGATTTGCGCCGGTTTCTCGGTAGGTTTTGGTGTGGCGATGAGTCAGGCGTTAGGGCCg               >  1:651454/1‑121 (MQ=255)
                                                                                                                                  |                                                                                                                                 
CGGTGAATACGCCACCATTATGGCGCTGACCGCTGGCGTCAGCATGACCGTTTCATTCTCCACGCCATTTGCGCTGGGAATTTTTAAGCCACGTACGTTGATGATCACCTCGCAGGTGTTATTCCTGGCGGCGGGGATCACTCTTGCCGTTTCACCTTCCCATGCGGTTTCTCTGTTTGGTATCACGCTGATTTGCGCCGGTTTCTCGGTAGGTTTTGGTGTGGCGATGAGTCAGGCGTTAGGGCCGTTTTCATTACGCG  >  NC_000913/3892325‑3892584

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A