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
A7 F1 I1 R1 776 60.0 3074904 90.1% 2770488 104.4

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 2,484,897 (C)6→7 coding (524/3594 nt) evgS → hybrid sensory histidine kinase in two‑component regulatory system with EvgA

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009132,484,8911.C93.8% 156.6 / 3.2 48coding (518/3594 nt)evgShybrid sensory histidine kinase in two‑component regulatory system with EvgA
Reads supporting (aligned to +/- strand):  ref base . (2/1);  new base C (23/22);  total (25/23)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.05e-01

TTCGCCGCCTCTTAATAATGACATTGCTGCAACCAAACCATTGATAATTACCTTTCCGGCGCTGGTAACCACCCTTCACGACTCAATGCGACCGCTTACCTCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATT‑A‑‑CCCCCCAGACGAGGTAATTCATCAATCATTTCCAAAAGCAACAATTATCTCTTTTACAAATTTATATCAGGCATTAGCATCCGTCTCAGCTGGGCACAATGATTACTTTATTGGTAGTAACATCATTACCA  >  NC_000913/2484754‑2485022
                                                                                                                                           |                                                                                                                                    
ttCGCCGCCTCTTAATAATGACATTGCTGCAACCAAACCATTGATAATTACCTTTCCGGCGCTGGTAACCACCCTTCACGACTCAATGCGACCGCTTACCTCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATT‑A‑‑c                                                                                                                                    <  1:474815/139‑1 (MQ=255)
ttCGCCGCCTCTTAATAATGACATTGCTGCAACCAAACCATTGATAATTACCTTTCCGGCGCTGGTAACCACCCTTCACGACTCAATGCGACCGCTCACCTCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATT‑a                                                                                                                                       <  2:718900/138‑1 (MQ=255)
ttCGCCGCCTCTTAATAATGACATTGCTGCAACCAAACCATTGATAATTACCTTTCCGGCGCTGGTAACCACCCTTCACGACTCAATGCGACCGCTCACCTCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATT‑a                                                                                                                                       >  1:718900/1‑138 (MQ=255)
  cgccgcCTCTTAATAATGACATTGCTGCAACCAAACCATTGATAATTACCTTTCCGGCGCTGGTAACCACCCTTCACGACTCAATGCGACCGCTTACCTCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATT‑A‑‑ccc                                                                                                                                  >  1:632443/1‑139 (MQ=255)
    agacagctTAATAATGACATTGCTGCAACCAAACCATTGATAATTACCTTTCCGGCGCTGGTAACCCCCCTTCACGACTCAATGCGACCGCATACCTCGCCAAAACCAGTAAATATTGCTCGGGTAGCAAATT‑A‑‑ccccc                                                                                                                                <  1:798304/133‑1 (MQ=255)
                    aCATTGCTGCAACCAAACCATTGATAATTACCTTTCCGGCGCTGGTAACCACCCTTCACGACTCAATGCGACCGCTTACCTCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATT‑A‑‑c                                                                                                                                    >  2:1210026/1‑119 (MQ=255)
                    aCATTGCTGCAACCAAACCATTGATAATTACCTTTCCGGCGCTGGTAACCACCCTTCACGACTCAATGCGACCGCTTACCTCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATT‑A‑‑c                                                                                                                                    <  1:1210026/119‑1 (MQ=255)
                     cATTGCTGCAACCAAACCATTGATAATTACCTTTCCGGCGCTGGTAACCACCCTTCACGACTCAATGCGACCGCTTACCTCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATT‑AC‑CCCCCCAGACGAGGTAATtca                                                                                                                >  2:639887/1‑139 (MQ=255)
                     cATTGCTGCAACCAAACCATTGATAATTACCTTTCCGGCGCTGGTAACCACCCTTCACGACTCAATGCGACCGCTTACCTCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATT‑A‑‑ccccccca                                                                                                                             >  1:477208/1‑123 (MQ=255)
                     cATTGCTGCAACCAAACCATTGATAATTACCTTTCCGGCGCTGGTAACCACCCTTCACGACTCAATGCGACCGCTTACCTCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATT‑A‑‑ccccccca                                                                                                                             <  2:477208/125‑3 (MQ=255)
                     cATTGCTGCAACCAAACCATTGATAATTACCTTTCCGGCGCTGGTAACCACCCTTCACGACTCAATGCGACCGCTTACCTCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATT‑A‑‑c                                                                                                                                    <  1:1019973/118‑1 (MQ=255)
                     cATTGCTGCAACCAAACCATTGATAATTACCTTTCCGGCGCTGGTAACCACCCTTCACGACTCAATGCGACCGCTTACCTCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATT‑A‑‑c                                                                                                                                    >  2:1019973/1‑118 (MQ=255)
                     cATTGCTGCAACCAAACCATTGATAATTACATTTCCGCCGCTGGTAACCACCCTTCACGACTCAATGCGACCGCTTACCTCACCAAAACCAGTAAATATTTCTCGGGTACAAAATTAA‑‑CCCCCCAGACTAGGtctgtct                                                                                                                >  2:798304/1‑133 (MQ=255)
                             cAACCAAACCATTGATAATTACCTTTCCGGCGCTGGTAACCACCCTTCACGACTCAATGCGACCGCTTACCTCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATT‑AC‑CCCCCCAGACGAGGTAATTCATCAATCAt                                                                                                        >  2:111302/1‑139 (MQ=255)
                               accaaaccaTTGATAATTACCTTTCCGGCGCTGGTAACCACCCTTCACGACTCAATGCGACCGCTTACCTCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATT‑AC‑CCCCCCAGACGAGGTAATTCATCAATCAttt                                                                                                      >  1:614757/1‑139 (MQ=255)
                                        ttGATAATTACCTTTCCGGCGCTGGTAACCACCCTTCACGACTCAATGCGACCGCTTACCTCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATT‑AC‑CCCCCCAGACGAGGTAATTCATCAATCATTTCCAAAAGca                                                                                             >  2:195990/1‑139 (MQ=255)
                                          gATAATTACCTTTCCGGCGCTGGTAACCACCCTTCACGACTCAATGCGACCGCTTACCTCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATT‑AC‑CCCCCCAGACGAGGTAATTCATCAATCATTTCCAAAAGcaac                                                                                           >  1:219024/1‑139 (MQ=255)
                                                      tCCGGCGCTGGTAACCACCCTTCACGACTCAATGCGACCGCTTACCTCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATT‑AC‑CCCCCCAGACGAGGTAATtcat                                                                                                               <  1:338203/107‑1 (MQ=255)
                                                      tCCGGCGCTGGTAACCACCCTTCACGACTCAATGCGACCGCTTACCTCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATT‑AC‑CCCCCCAGACGAGGTAATtcat                                                                                                               >  2:338203/1‑107 (MQ=255)
                                                       ccGGCGCTGGTAACCACCCTTCACGACTCAATGCGACCGCTTACCTCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATT‑A‑‑ccccc                                                                                                                                <  1:131073/88‑1 (MQ=255)
                                                       ccGGCGCTGGTAACCACCCTTCACGACTCAATGCGACCGCTTACCTCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATT‑A‑‑ccccc                                                                                                                                >  2:131073/1‑88 (MQ=255)
                                                          gcgcTGGTAACCACCCTTCACGACTCAATGCGACCGCTTACCTCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATT‑AC‑CCCCCCAGACGAGGTAATTCATCAATCATTTCCAAAAGCAACAATTATCTCTTTTACa                                                                           <  2:219024/139‑1 (MQ=255)
                                                             cTGGTAACCACCCTTCACGACTCAATGCGACCGCTTACCTCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATT‑AC‑CCCCCCAGACGAGGTAATTCATCAATCATTTCCAAAAGCAACAATTATCTCTTTTACAAAt                                                                        >  1:331940/1‑139 (MQ=255)
                                                                gTAACCACCCTTCACGACTCAATGCGACCGCTTACCTCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATT‑AC‑CCCCCCAGACGAGGTAATTCATCAATCATTTCCAAAAGCAACAATTATCTCTTTTACAAATTta                                                                     >  1:34007/1‑139 (MQ=255)
                                                                  aaCCACCCTTCACGACTCAATGCGACCGCTTACCTCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATT‑AC‑CCCCCCAGACGAGGTAATTCATCAATCATTTCCAAAAGCAACAATTATCTCTTTTACAAATTtata                                                                   <  2:34007/139‑1 (MQ=255)
                                                                   accagcCTTCACGACTCAATGCGACCGCTTACCTCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATT‑AC‑CCCCCCAGACGAGGTAATTCATCAATCATTTCCAAAAGCAACAATTATCTCTTTTACAAATTTatat                                                                  <  1:821813/139‑1 (MQ=255)
                                                                     caccCTTCACGACTCAATGCGACCGCTTACCTCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATT‑A‑‑cccccccaga                                                                                                                           <  2:167567/79‑5 (MQ=255)
                                                                     caccCTTCACGACTCAATGCGACCGCTTACCTCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATT‑A‑‑cccccccaga                                                                                                                           >  1:167567/1‑75 (MQ=255)
                                                                        ccTTCACGACTCAATGCGACCGCTTACCTCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATT‑AC‑CCCCCCAGACGAGGTAATtcat                                                                                                               >  2:928684/1‑89 (MQ=255)
                                                                        ccTTCACGACTCAATGCGACCGCTTACCTCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATT‑AC‑CCCCCCAGACGAGGTAATtcat                                                                                                               <  1:928684/89‑1 (MQ=255)
                                                                          ttCACGACTCAATGCGACCGCTTACCTCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATT‑AC‑CCCCCCAGACGAGGTAATTCATCAATCATTTCCAAAAGCAACAATTATCTCTTTTACAAATTTATATCAGGCAt                                                           <  1:111302/139‑1 (MQ=255)
                                                                               gACTCAATGCGACCGCTTACCTCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATT‑ACCCCCCCCAGACGAGGTAATTCATCAATCATTTCCAAAAGCAACAATTATCTCTTTTACAAATTTATATCAGGCATTAGc                                                       >  2:500576/1‑139 (MQ=255)
                                                                               gACTCAATGCGACCGCTTACCTCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATT‑AC‑CCCCCCAGACGAGGTAATTCATCAATCATTTCCAAAAGCAACAATTATCTCTTTTACAAATTTATATCAGGCATTAGCa                                                      <  2:778726/139‑1 (MQ=255)
                                                                                      tGCGACCGCTTACCTCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATT‑AC‑CCCCCCAGACGAGGTAATTCATCAATCATTTCCAAAAGCAACAATTATCTCTTTTACAAATTTATATCAGGCATTAGCATCCGtct                                               >  2:86489/1‑139 (MQ=255)
                                                                                      tGCGACCGCTTACCTCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATT‑AC‑CCCCCCAGACGAGGTAATTCATCAATCATTTCCAAAAGCAACAATTATCTCTTTTACAAATTTATATCAGGCATTAGCATCCGtct                                               >  1:477797/1‑139 (MQ=255)
                                                                                            cGCTTACCTCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATT‑AC‑CCCCCCAGACGAGGTAATTCATCAATCATTTCCAAAAGCAACAATTATCTCTTTTACAAATTTATATCAGGCATTAGCATCCGTCTCAGCTg                                         >  2:622506/1‑139 (MQ=255)
                                                                                               ttACCTCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATT‑AC‑CCCCCCAGACGAGGTAATTCATCAATCATTTCCAAAAGCAACAATTATCTCTTTTACAAATTTATATCAGGCATTAGCATCCGTCTCAGCTGGGc                                      <  2:477797/139‑1 (MQ=255)
                                                                                                tACCTCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATT‑AC‑CCCCCCAGACGAGGTAATTCATCAATCATTTCCAAAAGCAACAATTATCTCTTTTACAAATTTATATCAGGCATTAGCATCCGTCTCAGCTGGGca                                     <  1:528350/139‑1 (MQ=255)
                                                                                                      aCCAAAACCAGTAAATATTGCTCGGGTAGCAAATT‑AC‑CCCCCCAGACg                                                                                                                          <  2:355612/48‑1 (MQ=255)
                                                                                                      aCCAAAACCAGTAAATATTGCTCGGGTAGCAAATT‑AC‑CCCCCCAGACg                                                                                                                          >  1:355612/1‑48 (MQ=255)
                                                                                                        cAAAACCAGTAAATATTGCTCGGGTAGCAAATT‑A‑‑cccccccaga                                                                                                                           >  1:405269/1‑40 (MQ=255)
                                                                                                        cAAAACCAGTAAATATTGCTCGGGTAGCAAATT‑A‑‑cccccccaga                                                                                                                           <  2:405269/44‑5 (MQ=255)
                                                                                                          aaaCCAGTAAATATTGCTCGGGTAGCAAATT‑AC‑CCCCCCAGACGAGGTAATTCATCAATCATTTCCAAAAGCAACAATTATCTCTTTTACAAATTTATATCAGGCATTAGCATCCGTCTCAGCTGGGCACAATGATTAc                           <  2:331940/139‑1 (MQ=255)
                                                                                                            aCCAGTAAATATTGCTCGGGTAGCAAATT‑AC‑CCCCCCAGACGAGGTAATTCATCAATCATTTCCAAAAGCAACAATTATCTCTTTTACAAATTTATATCAGGCATTAGCa                                                      <  1:1258805/110‑1 (MQ=255)
                                                                                                            aCCAGTAAATATTGCTCGGGTAGCAAATT‑AC‑CCCCCCAGACGAGGTAATTCATCAATCATTTCCAAAAGCAACAATTATCTCTTTTACAAATTTATATCAGGCATTAGCa                                                      >  2:1258805/1‑110 (MQ=255)
                                                                                                                gTAAATATTGCTCGGGTAGCAAATT‑ACCCCCCCCAGACGAGGTAATTCATCAATCATTTCCAAAAGCAACAATTATCTCTTTTACAAATTTATATCAGGCATTAGCATCCGTCTCAGCTGGGCACAATGATTACTTTAt                      <  1:500576/139‑1 (MQ=255)
                                                                                                                gTAAATATTGCTCGGGTAGCAAATT‑AC‑CCCCCCAGACGAGGTAATTCATCAATCATTTCCAAAAGCAACAATTATCTCTTTTACAAATTTATATCAGGCATTAGCATCCGTCTCAGCTGGGcaca                                   <  1:355317/125‑1 (MQ=255)
                                                                                                                gTAAATATTGCTCGGGTAGCAAATT‑AC‑CCCCCCAGACGAGGTAATTCATCAATCATTTCCAAAAGCAACAATTATCTCTTTTACAAATTTATATCAGGCATTAGCATCCGTCTCAGCTGGGcaca                                   >  2:355317/1‑125 (MQ=255)
                                                                                                                 tAAATATTGCTCGGGTAGCAAATT‑AC‑CCCCCCAGACGAGGTAATTCATCAATCATTTCCAAAAGCAACAATTATCTCTTTTACAAATTTATATCAGGCATTAGCATCCGTCTCAg                                            >  1:1530683/1‑115 (MQ=255)
                                                                                                                 tAAATATTGCTCGGGTAGCAAATT‑AC‑CCCCCCAGACAAGGTAATTCATCAATCATTTCCAAAAGCAACAATTATCTCTTTTACAAATTTATATCAGGCATTAGCATCCGTCTCAg                                            <  2:1530683/115‑1 (MQ=255)
                                                                                                                      atTGCTCGGGTAGCAAATT‑AC‑CCCCCCAGACGAGGTAATTCATCAATCATTTCCAAAAGCAACAATTATCTCTTTTACAAATTTATATCAGGCATTAGCATCCGTCTCAGCTGGGCACAATGATTACTTTATTGgtagt               <  2:1301319/139‑1 (MQ=255)
                                                                                                                          cTCGGGTAGCAAATT‑AC‑CCCCCCAGACGAGGTAATTCATCAATCATTTCCAAAAGCAACAATTATCTCTTTTa                                                                             <  1:679054/73‑1 (MQ=255)
                                                                                                                          cTCGGGTAGCAAATT‑AC‑CCCCCCAGACGAGGTAATTCATCAATCATTTCCAAAAGCAACAATTATCTCTTTTa                                                                             >  2:679054/1‑73 (MQ=255)
                                                                                                                               gTAGCAAATT‑AC‑CCCCCCAGACGAGGTAATTCatcaatca                                                                                                         <  2:399255/40‑1 (MQ=255)
                                                                                                                               gTAGCAAATT‑AC‑CCCCCCAGACGAGGTAATTCatcaatca                                                                                                         >  1:399255/1‑40 (MQ=255)
                                                                                                                               gTAGCAAATT‑AC‑CCCCCCAGACGAGGTAATTCATCAATCATTTCCAAAAGCAACAATTATCTCTTTTACAAATTTATATCAGGCATTAGCATCCGTCTCAGCTGGGca                                     <  2:900815/108‑1 (MQ=255)
                                                                                                                               gTAGCAAATT‑AC‑CCCCCCAGACGAGGTAATTCATCAATCATTTCCAAAAGCAACAATTATCTCTTTTACAAATTTATATCAGGCATTAGCATCCGTCTCAGCTGGGca                                     >  1:900815/1‑108 (MQ=255)
                                                                                                                               gTAGCAAATT‑AC‑CCCCCCAGACGAGGTAATTCATCAATCATTTCCAAAAGCAACAATTATCTCTTTTACAAATTTATATCAGGCATTAGCATCCGTCTCAGCTGGGCACAATGa                               >  2:1375807/1‑114 (MQ=255)
                                                                                                                               gTAGCAAATT‑AC‑CCCCCCAGACGAGGTAATTCATCAATCATTTCCAAAAGCAACAATTATCTCTTTTACAAATTTATATCAGGCATTAGCATCCGTCTCAGCTGGGCACAATGa                               <  1:1375807/114‑1 (MQ=255)
                                                                                                                                 aGCAAATT‑AC‑CCCCCCAGACGAGGTAATTCATCAATCATTTCCAAAAGCAACAATTATCTCTTTTACAAATTTATATCAGGCATTAGCATCCGTCTCAGCTGGGCACAATGATTACTTTATTGGTAGTAACATCATTAc    <  1:639887/139‑1 (MQ=255)
                                                                                                                                   cAAATT‑AC‑CCCCCCAGACGAGGTAATTCATCAATCATTTCCAAAAGCAACAATTATCTCTTTTACAAATTTATATCAGGCATTAGCATCCGTCTCAGCTGGGca                                     >  2:623325/1‑104 (MQ=255)
                                                                                                                                   cAAATT‑AC‑CCCCCCAGACGAGGTAATTCATCAATCATTTCCAAAAGCAACAATTATCTCTTTTACAAATTTATATCAGGCATTAGCATCCGTCTCAGCTGGGca                                     <  1:623325/104‑1 (MQ=255)
                                                                                                                                   cAAATT‑AC‑CCCCCCAGACGAGGTAATTCATCAATCATTTCCAAAAGCAACAATTATCTCTTTTACAAATTTATATCAGGCATTAGCATCCGTCTCAGCTGGGCACAATGATTACTTTATTGGTAGTAACATCATTAcaa  >  2:250942/1‑137 (MQ=255)
                                                                                                                                   cAAATT‑A‑‑CCCCCCAGACGAGGTAATTCATCAATCATTTCCAAAAGc                                                                                              <  1:1511509/46‑1 (MQ=255)
                                                                                                                                   cAAATT‑A‑‑CCCCCCAGACGAGGTAATTCATCAATCATTTCCAAAAGc                                                                                              >  2:1511509/1‑46 (MQ=255)
                                                                                                                                           |                                                                                                                                    
TTCGCCGCCTCTTAATAATGACATTGCTGCAACCAAACCATTGATAATTACCTTTCCGGCGCTGGTAACCACCCTTCACGACTCAATGCGACCGCTTACCTCACCAAAACCAGTAAATATTGCTCGGGTAGCAAATT‑A‑‑CCCCCCAGACGAGGTAATTCATCAATCATTTCCAAAAGCAACAATTATCTCTTTTACAAATTTATATCAGGCATTAGCATCCGTCTCAGCTGGGCACAATGATTACTTTATTGGTAGTAACATCATTACCA  >  NC_000913/2484754‑2485022

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A