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
A1 F999 I1 R1 225 156.4 11709729 83.8% 9812752 75.7

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 3,896,324 +G coding (698/711 nt) b3718 ← putative isomerase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009133,896,3241.G100.0% 302.8 / NA 110V233A (GTG→GCG) b3718putative isomerase
Reads supporting (aligned to +/- strand):  ref base . (0/0);  new base G (58/52);  total (58/52)

Only 100 of 117 total aligned reads displayed.

AATGAGAACAGGCCGGAGCGTAATTCACACATCCGGCCTTATTTCTTAAGCTTAACCGAGTGCTAATTCTGCGGCACGGCTTTATCAGCGATTACCATCAGCGAAGGATGCAGCTGCAACACGGAAGCTGGAACATCTTCGGTAA  >  NC_000913/3896249‑3896393
                                                                            |                                                                     
aatGAGAACAGGCCGGAGCGTAATTCACACATCCGGCCTTATTTCTTAAGCTTAACCGAGTGCTAATTCTGCGGCa                                                                        <  1:4499834/76‑1 (MQ=255)
aatGAGAACAGGCCGGAGCGTAATTCACACATCCGGCCTTATTTCTTAAGCTTAACCGAGTGCTAATTCTGCGGCa                                                                        <  1:2885309/76‑1 (MQ=255)
 atGAGAACAGGCCGGAGCGTAATTCACACATCCGGCCTTATTTCTTAAGCTTAACCGAGTGCTAATTCTGCGGCag                                                                       <  1:1540640/76‑2 (MQ=255)
 atGAGAACAGGCCGGAGCGTAATTCACACATCCGGCCTTATTTCTTAAGCTTAACCGAGTGCTAATTCTGCGGCag                                                                       >  1:2162125/1‑75 (MQ=255)
   gagaACAGGCCGGAGCGTAATTCACACATCCGGCCTTATTTCTTAAGCTTAACCGAGTGCTAATTCTGCGGCagcg                                                                     >  1:5393606/1‑73 (MQ=255)
   gagaACAGGCCGGAGCGTAATTCACACATCCGGCCTTATTTCTTAAGCTTAACCGAGTGCTAATTCTGCGGCagcg                                                                     <  1:5207209/76‑4 (MQ=255)
      agcAGGCCGGAGCGTAATTCACACATCCGGCCTTATTTCTTAAGCTTAACCGAGTGCTAATTCTGCGGCAGCGGCt                                                                  <  2:2412607/74‑1 (MQ=255)
      aaCAGGCCGGAGCGTAATTCACACATCCGGCCTTATTTCTTAAGCTTAACCGAGTGCTAATTCTGCGGCAGCGGCt                                                                  >  2:3662561/1‑76 (MQ=255)
       aCAGGCCGGAGCGTAATTCACACATCCGGCCTTATTTCTTAAGCTTAACCGAGTGCTAATTCTGCGGCAGCGGCtt                                                                 >  2:5055703/1‑76 (MQ=255)
       aCAGGCCGGAGCGTAATTCACACAGCCGGCCTTATTTCTTAAGCTTAACCGAGTGCTAATTCTGCGGCAGCGGCtt                                                                 >  2:1495736/1‑76 (MQ=255)
        cAGGCCGGAGCGTAATTCACACATCCGGCCTTATTTCTTAAGCTTAACCGAGTGCTAATTCTGCGGCAGCGGCttt                                                                >  2:5773624/1‑76 (MQ=255)
          ggCCGGAGCGTAATTCACACATCCGGCCTTATTTCTTAAGCTTAACCGAGTGCTAATTCTGCGGCAGCGGCTTTAt                                                              >  1:971364/1‑76 (MQ=255)
           gCCGGAGCGTAATTCGCCCATCCGGCCGTATTTCTTAATCTTAACCGTGTGCTAATTCTGCGGCAGCGGCTTTATc                                                             <  2:60509/76‑1 (MQ=255)
           gCCGGAGCGTAATTCACACATCCGGCCTTATTTCTTAAGCTTAACCGAGTGCTAATTCTGCGGCAGCGGCTTTATc                                                             >  2:2404909/1‑76 (MQ=255)
            ccGGAGCGTAATTCACACATCCGGCCTTATTTCTTAAGCTTAACCGAGTGCTAATTCTGCGGCAGCGGCTTTATCa                                                            <  1:5773625/76‑1 (MQ=255)
            ccGGAGCGTAATTCACACATCCGGCCTTATTTCTTAAGCTTAACCGAGTGCTAATTCTGCGGCAGCGGCTTTATCa                                                            <  2:4096967/76‑1 (MQ=255)
             cGGAGCGTAATTCACACATCCGGCCTTATTTCTTAAGCTTAACCGAGTGCTAATTCTGCGGCAGCGGCTTTATCAg                                                           >  1:881253/1‑76 (MQ=255)
             cGGAGCGTAATTCACACATCCGGCCTTATTTCTTAAGCTTAACCGAGTGCTAATTCTGCGGCAGCGGCTTTATCAg                                                           >  2:1573683/1‑76 (MQ=255)
              ggAGCGTAATTCACACATCCGGCCTTATTTCTTAAGCTTAACCGAGTGCTAATTCTGCGGCAGCGGCTTTATCAGc                                                          >  2:4306487/1‑76 (MQ=255)
               gAGCGTAATTCACACATCCGGCCTTATTTCTTAAGCTTAACCGAGTGCTAATTCTGCGGCAGCGGCTTTATCAGCg                                                         <  2:3968571/76‑1 (MQ=255)
                   gTAATTCACACATCCGGCCTTATTTCTTAAGCTTAACCGAGTGCTAATTCTGCGGCAGCGGCTTTATCAGCGATTa                                                     <  2:738767/76‑1 (MQ=255)
                    tAATTCACACATCCGGCCTTATTTCTTAAGCTTAACCGAGTGCTAATTCTGCGGCAGCGGCCTTATCAGCGATTAc                                                    >  2:1194760/1‑76 (MQ=255)
                     aaTTCACACATCCGGCCTTATTTCTTAAGCTTAACCGAGTGCTAATTCTGCGGCAGCGGCTTTATCAGCGATTTcc                                                   >  1:486549/1‑76 (MQ=255)
                     aaTTCACACATCCGGCCTTATTTCTTAAGCTTAACCGAGTGCTAATTCTGCGGCAGCGGCTTTATCAGCGATTAcc                                                   >  2:2640441/1‑76 (MQ=255)
                      aTTCACACATCCGGCCTTATTTCTTAAGCTTAACCGAGTGCTAATTCTGCGGCAGCGGCTTTATCAGCGATTACCa                                                  >  1:5398413/1‑76 (MQ=255)
                      aTTCACACATCCGGCCTTATTTCTTAAGCTTAACCGAGTGCTAATTCTGCGGCAGCGGCTTTATCAGCGATTACCa                                                  <  2:3859648/76‑1 (MQ=255)
                       ttCACACATCCGGCCTTATTTCTTAAGCTTAACCGAGTGCTAATTCTGCGGCAGCGGCTTTATCAGCGATTACCAt                                                 >  2:2737036/1‑76 (MQ=255)
                        tCACACATCCGGCCTTATTTCTTAAGCTTAACCGAGTGCTAATTCTGCGGCAGCGGCTTTATCAGCGATTACCATc                                                <  2:2426656/76‑1 (MQ=255)
                        tCACACATCCGGCCTTATTTCTTAAGCTTAACCGAGTGCTAATTCTGCGGCAGCGGCTTTATCAGCGATTACCATc                                                <  1:3781622/76‑1 (MQ=255)
                         cacacaTCCGGCCTTATTTCTTAAGCTTAACCGAGTGCTAATTCTGCGGCAGCGGCTTTATCAGCGATTACCCTCa                                               >  2:1576368/1‑76 (MQ=255)
                         cacacaTCCGGCCTTATTTCTTAAGCTTAACCGAGTGCTAATTCTGCGGCAGCGGCTTTATCAGCGATTACCAtta                                               <  1:976505/76‑3 (MQ=255)
                          acacaTCCGGCCTTATTTCTTAAGCTTAACCGAGTGCTAATTCTGCGGCAGCGGCTTTATCAGCGATTACCATCAg                                              <  1:2187212/76‑1 (MQ=255)
                          acacaTCCGGCCTTATTTCTTAAGCTTAACCGAGTGCTAATTCTGCGGCAGCGGCTTTATCAGCGATTACCATCAg                                              >  2:4903258/1‑76 (MQ=255)
                          acacaTCCGGCCTTATTTCTTAAGCTTAACCGAGTGCTAATTCTGCGGCAGCGGCTTTATCAGCGATTACCATCAg                                              <  1:3823310/76‑1 (MQ=255)
                           cacaTCCGGCCTTATTTCTTAAGCTTAACCGAGTGCTAATTCTGCGGCAGCGGCTTTATCAGCGATTACCATCAGc                                             <  2:2331397/76‑1 (MQ=255)
                            acaTCCGGCCTTATTTCTTAAGCTTAACCGAGTGCTAATTCTGCGGCAGCGGCTTTATCAGCGATTACCATCAGCg                                            <  1:5612728/76‑1 (MQ=255)
                             caTCCGGCCTTATTTCTTAAGCTTAACCGAGTGCTAATTCTGCGGCAGCGGCTTTATCAGCGATTACCATCAGCGa                                           <  2:3489107/76‑1 (MQ=255)
                              aTCCGGCCTTATTTCTTAAGCTTAACCGAGTGCTAATTCTGCGGCAGCGGCTTTATCAGCGATTACCATCAGCGaa                                          >  1:1867795/1‑76 (MQ=255)
                               tCCGGCCTTATTTCTTAAGCTTAACCGAGTGCTAATTCTGCGGCAGCGGCTTTATCAGCGATTACCATCAGCGAAg                                         <  2:3881453/76‑1 (MQ=255)
                               tCCGGCCTTATTTCTTAAGCTTAACCGAGTGCTAATTCTGCGGCAGCCGCTTTATCAGCGATTACCATCCGCGaca                                         >  2:2339887/1‑74 (MQ=255)
                                ccGGCCTTATTTCTTAAGCTTAACCGAGTGCTAATTCTGCGGCAGCGGCTTTATCAGCGATTACCATCAGCGAAgg                                        >  1:3242619/1‑76 (MQ=255)
                                ccGGCCTTATTTCTTAAGCTTAACCGAGTGCTAATTCTGCGGCAGCGGCTTTATCAGCGATTACCATCAGCGAAgg                                        >  2:2943274/1‑76 (MQ=255)
                                  ggCCTTATTTCTTAAGCTTAACCGAGTGCTAATTCTGCGGCAGCGGCTTTATCAGCGATTACCATCAGCGAAGGAt                                      >  1:5410252/1‑76 (MQ=255)
                                  ggCCTTATTTCTTAAGCTTAACCGAGTGCTAATTCTGCGGCAGCGGCTTTATCAGCGATTACCATCAGCGAAGGAt                                      <  1:1503426/76‑1 (MQ=255)
                                  ggCCTTATTTCTTAAGCTTAACCGAGTGCTAATTCTGCGGCAGCGGCTTTATCAGCGATTACCATCAGCGAAGGAt                                      <  1:1569903/76‑1 (MQ=255)
                                    ccTTATTTCTTAAGCTTAACCGAGTGCTAATTCTGCGGCAGCGGCTTTATCAGCGATTACCATCAGCGAAGGATGc                                    <  1:710633/76‑1 (MQ=255)
                                    ccTTATTTCTTAAGCTTAACCGAGTGCTAATTCTGCGGCAGCGGCTTTATCAGCGATTAACATCAGCGAAGGATGc                                    >  1:1540371/1‑76 (MQ=255)
                                     cTTATTTCTTAAGCTTAACCGAGTGCTAATTCTGCGGCAGCGGCTTTATCAGCGATTACCATCAGCGAAGGATGCa                                   <  1:4673614/76‑1 (MQ=255)
                                      ttATTTCTTAAGCTTAACCGAGTGCTAATTCGGCGGCAGCGGCTTTATCAGCGATTACCATCAGCGAAGGATGCAg                                  >  2:2987272/1‑76 (MQ=255)
                                       tATTTCTTAAGCTTAACCGAGTGCTAATTCTGCGGCAGCGGCTTTATCAGCGATTACCATCAGCGAAGGATGCAGc                                 <  2:1887886/76‑1 (MQ=255)
                                        aTTTCTTAAGCTTAACCGAGTGCTAATTCTGCGGCAGCGGCTTTATCAGCGATTACCATCAGCGAAGGATGCAGCt                                <  1:73614/76‑1 (MQ=255)
                                        aTTTCTTAAGCTTAACCGAGTGCTAATTCTGCGGCAGCGGCTTTATCAGCGATTACCATCAGCGAAGGATGCAGCt                                >  1:85746/1‑76 (MQ=255)
                                        aTTTCGTAAGCTTAACCGAGTGCTAATTCTGCGGCAGCGGCTTTTGTAGCGATTACCATCCGCGAAGGATGAAGCt                                >  1:5472108/1‑76 (MQ=255)
                                          ttCTTAAGCTTAACCGAGTGCTAATTCTGCGGCAGCGGCTTTATCAGCGATTACCATCAGCGAAGGATGCAGCTGc                              >  1:5826371/1‑76 (MQ=255)
                                          ttCTTAAGCTTAACCGAGTGCTAATTCTGCGGCAGCGGCTTTATCAGCGATTACCATCAGCGAAGGATGCAGCTGc                              <  1:4306488/76‑1 (MQ=255)
                                          ttCTTAAGCTTAACCGAGTGCTAATTCTGCGGCAGCGGCTTTATCAGCGATTACCATCAGCGAAGGATGCAGCTGc                              >  2:1926769/1‑76 (MQ=255)
                                            cTTAAGCTTAACCGAGTGCTAATTCTGCGGCAGCGGCTTTATCAGCGATTACCATCAGCGAAGGATGCAGCTGCaa                            <  2:2386443/76‑1 (MQ=255)
                                            cTTAAGCTTAACCGAGTGCTAATTCTGCGGCAGCGGCTTTATCAGCGATTACCATCAGCGAAGGATGCAGCTGCaa                            >  1:402694/1‑76 (MQ=255)
                                             ttAAGCTTAACCGAGTGCTAATTCTGCGGCAGCGGCTTTATCAGCGATTACCATCAGCGAAGGATGCAGCTGCAac                           <  1:2106336/76‑1 (MQ=255)
                                             ttAAGCTTAACCGAGTGCTAATTCTGCGGCAGCGGCTTTATCAGCGATTACCATCAGCGAAGGATGCAGCTGCAac                           >  2:2853598/1‑76 (MQ=255)
                                             ttAAGCTTAACCGAGTGCTAATTCTGCGGCAGCGGCTTTATCAGCGATTACCATCAGCGAAGGATGCAGCTGCAac                           >  2:5801556/1‑76 (MQ=255)
                                              tAAGCTTAACCGAGTGCTAATTCTGCGGCAGCGGCTTTATCAGCGATTACCATCAGCGAAGGATGCAGCTGCAaca                          <  1:4903259/76‑1 (MQ=255)
                                              tAAGCTTAACCGAGTGCTAATTCTGCGGCAGCGGCTTTATCAGCGATTACCATCAGCGAAGGATGCAGCTGCAaca                          <  2:3457258/76‑1 (MQ=255)
                                               aaGCTTAACCGAGTGCTAATTCTGCGGCAGCGGCTTTATCAGCGATTACCATCAGCGAAGGATGCAGCTGCAacac                         >  1:3390557/1‑76 (MQ=255)
                                               aaGCTTAACCGAGTGCTAATTCTGCGGCAGCGGCTTTATCAGCGATTACCATCAGCGAAGGATGCAGCTGCAacac                         <  2:5618341/76‑1 (MQ=255)
                                                aGCTTAACCGAGTGCTAATTCTGCGGCAGCGGCTTTATCAGCGATTACCATCAGCGAAGGATGCAGCTGCCACACg                        >  2:2416233/1‑76 (MQ=255)
                                                aGCTTAACCGAGTGCTAATTCTGCGGCAGCGGCTTTATCAGCGATTACCATCAGCGAAGGATGCAGCTGCAACACg                        >  1:4319411/1‑76 (MQ=255)
                                                 gCTTAACCGAGTGCTAATTCTGCGGCAGCGGCTTTATCAGCGATTACCATCAGCGAAGGATGCAGCTGCAACACgg                       >  2:3685682/1‑76 (MQ=255)
                                                   ttAACCGAGTGCTAATTCTGCGGCAGCGGCTTTATCAGCGATTACCATCAGCGAAGGATGCAGCTGCAACACGGaa                     >  1:3746696/1‑76 (MQ=255)
                                                   ttAACCGAGTGCTAATTCTGCGGCAGCGGCTTTATCAGCGATTACCATCAGCGAAGGATGCAGCTGCAACACGGaa                     <  2:5225334/76‑1 (MQ=255)
                                                    tAACCGAGTGCTAATTCTGCGGCAGCGGCTTTATCAGCGATTACCATCAGCGAAGGATGCAGCTGCAACACGGAAg                    <  1:2301071/76‑1 (MQ=255)
                                                     aaCCGAGTGCTAATTCTGCGGCAGCGGCTTTATCAGCGATTACCATCAGCGAAGGATGCAGCTGCAACACGGAAGc                   >  1:850948/1‑76 (MQ=255)
                                                     aaCCGAGTGCTAATTCTGCGGCAGCGGCTTTATCAGCGATTACCATCAGCGAAGGATGCAGCTGCAACACGGAAGc                   <  1:5055704/76‑1 (MQ=255)
                                                     aaCCGAGTGCTAATTCTGCGGCAGCGGCTTTATCAGCGATTACCATCAGCGAAGGATGCAGCTGCAACACGGAAGc                   >  1:26879/1‑76 (MQ=255)
                                                      acagAGTGCTAATTCTGCGCCAGCGGCTTTATCAGCGATTACCATCAGCGAAGGATGCAGCTGCACCACGGAAGCt                  <  1:2694852/73‑1 (MQ=255)
                                                        cGAGTGCTAATTCTGCGGCAGCGGCTTTATCAGCGATTACCATCAGCGAAGGATGCAGCTGCAACACGGaa                     >  2:1815784/1‑71 (MQ=255)
                                                        cGAGTGCTAATTCTGCGGCAGCGGCTTTATCAGCGATTACCATCAGCGAAGGATGCAGCTGCAACACGGAAGGTgg                >  1:5788108/1‑76 (MQ=255)
                                                         gAGTGCTAATTCTGCGGCAGCGGCTTTATCAGCGATTACCATCAGCGAAGGATGCAGCTGCAACACGGAAGCTGGa               >  1:4297946/1‑76 (MQ=255)
                                                          aGTGCTAATTCTGCGGCAGCGGCTTTATCAGCGATTACCATCAGCGAAGGATGCAGCTGCAAAACGGGAGGTggga              >  1:436679/1‑74 (MQ=255)
                                                           gTGCTAATTCTGCGGCAGCGGCTTTATCAGCGATTACCATCAGCGAAGGATGCAGCTGCAACACGGAAGCTGGAAc             <  2:1552456/76‑1 (MQ=255)
                                                           gTGCTAATTCTGCGGCAGCGGCTTTATCAGCGATTACCATCAGCGAAGGATGCAGCTGCAACACGGAAGCTGGAAc             >  2:4497538/1‑76 (MQ=255)
                                                           gTGCTAATTCTGCGGCAGCGGCTTTATCAGCGATTACCATCAGCGAAGGATGCAGCTGCAACACGGAAGCTGGAAc             <  1:2082265/76‑1 (MQ=255)
                                                            tGCTAATTCTGCGGCAGCGGCTTTATCAGCGATTACCATCAGCGAAGGATGCAGCTGCAACACGGAAGCTGGAACa            <  1:1040422/76‑1 (MQ=255)
                                                            tGCTAATTCTGCGGCAGCGGCTTTAGCAGCGATTACCATCAGCGAAGGATGCAGCTGCAAAAAGGCAGATGGAACa            >  1:444731/1‑76 (MQ=255)
                                                            ggCTAATTCTGCGGCAGCGGCTTTATCAGCGATTACCATCAGCGAAGGATGCAGCTGCAACACGGAAGCTGGAACa            <  2:858893/75‑1 (MQ=255)
                                                             gCTAATTCTGCGGCAGCGGCTTTATCAGCGATTACCATCAGCGAAGGATGCAGCTGCAACACGGAAGCCGGGACAt           >  2:4842673/1‑76 (MQ=255)
                                                               tAATTCTGCGGCAGCGGCTTTATCAGCGATTACCATCAGCGAAGGATGCAGCTGCAACACGGAAGCTGGAACATCt         <  1:376232/76‑1 (MQ=255)
                                                                aaTTCTTCGGCAGCGGCTTTATCAGCGATTACCATCAGCGAAGGATGCAGCTGCAACACGGAAGCTGGAACATCtt        <  1:28368/76‑1 (MQ=255)
                                                                 aTTCTGCGGCAGCGGCTTTATCAGCGATTACCATCAGCGAAGGATGCAGCTGCAACACGGAAGCTGGAACATCTTc       <  1:5801557/76‑1 (MQ=255)
                                                                 aTTCTGCGGCAGCGGCTTTATCAGCGATTACCATCAGCGAAGGATGCAGCTGCAACACGGAAGCTGGAACATCTTc       <  1:4021719/76‑1 (MQ=255)
                                                                 aTTCTGCGGCAGCGGCTTTATCAGCGATTACCATCAGCGAAGGATGCAGCTGCAACACGGAACCTGGAAACTCTTc       >  2:4215286/1‑76 (MQ=255)
                                                                  ttCTGCGGCAGCGGCTTTATCAGCGATTACCATCAGCGAAGGATGCAGCTGCAACACGGAAGCTGGAACATCTTCg      <  2:3204062/76‑1 (MQ=255)
                                                                  ttCTGCGGCAGCGGCTTTATCAGCGATTACCATCAGCGAAGGATGCAGCTGCAACACGGAAGCTGGAACATCTTCg      >  1:4159247/1‑76 (MQ=255)
                                                                    cggCGGCAGCGGCTTTATCAGCGATTACCAGCAGCGAAGTATGCAGCGGCAACACGGAAGCTCAAACATCGTCCGt    >  1:1060010/3‑76 (MQ=255)
                                                                    cTGCGGCAGCGGCTTTATCAGCGATTACCATCAGCGAAGGATGCAGCTGCAACACGGAAGCTGGAACATCTTCgga    >  2:5120001/1‑75 (MQ=255)
                                                                    cTGCGGCAGCGGCTTTATCAGCGATTACCATCAGCGAAGGATGCAGCTGCAACACGGAAGCTGGAACATCTTCGGt    <  1:4132268/76‑1 (MQ=255)
                                                                      gCGGCAGCGGCTTTATCAGCGATTACCATCAGCGAAGGATGCAGCTGCAACACGGAAGCTGGAACATCTTCGGTaa  >  2:4295171/1‑76 (MQ=255)
                                                                      gCGGCAGCGGCTTTATCAGCGATTACCATCAGCGAAGGATGCAGCTGCAACACGGAAGCTGGAACATCTTCGGTaa  >  2:2821011/1‑76 (MQ=255)
                                                                      gCGGCAGCGGCTTTATCAGCGATTACCATCAGCGAAGGATGCAGCTGCAACACGGAAGCTGGAACATCTTCGGTaa  <  2:2048561/76‑1 (MQ=255)
                                                                      gCGGCAGCGGCTTTATCAGCGATTACCATCAGCGAAGGATGCAGCTGCAACACGGAAGCCGGGACACCCTCGGTac  >  2:1612359/1‑75 (MQ=255)
                                                                            |                                                                     
AATGAGAACAGGCCGGAGCGTAATTCACACATCCGGCCTTATTTCTTAAGCTTAACCGAGTGCTAATTCTGCGGCACGGCTTTATCAGCGATTACCATCAGCGAAGGATGCAGCTGCAACACGGAAGCTGGAACATCTTCGGTAA  >  NC_000913/3896249‑3896393

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 9 ≤ ATCG/ATCG < 19 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap:     Deleted base: 

GATK/CNVnator alignment

N/A