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
A12 F28 I1 R1 116 70.6 2404304 99.2% 2385069 138.7

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 2,737,713 (G)6→5 intergenic (+67/‑32) pheL → / → pheA phe operon leader peptide/fused chorismate mutase/prephenate dehydratase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009132,737,7080G.100.0% 229.2 / NA 53intergenic (+62/‑37)pheL/pheAphe operon leader peptide/fused chorismate mutase/prephenate dehydratase
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base . (27/26);  total (27/26)

GTACTAAAGTCACTTAAGGAAACAAACATGAAACACATACCGTTTTTCTTCGCATTCTTTTTTACCTTCCCCTGAATGGGAGGCGTTTCGTCGTGTGAAACAGAATGCGAAGACGAACAATAAGGCCTCCCAAATCGGGGGGCCTTTTTTATTGATAACAAAAAGGCAACACTATGACATCGGAAAACCCGTTACTGGCGCTGCGAGAGAAAATCAGCGCGCTGGATGAAAAATTATTAGCGTTACTGGCAGAACGGCGCGAACTGGCC  >  NC_000913/2737572‑2737840
                                                                                                                                        |                                                                                                                                    
gtactAAAGTCACTTAAGGAAACAAACATGAAACACATACCGTTTTTCTTCGCATTCTTTTTTACCTTCCCCTGAATGGGAGGCGTTTCGTCGTGTGAAACAGAATGCGAAGACGAACAATAAGGCCTCCCAAATCgggg                                                                                                                                   <  2:447620/140‑1 (MQ=255)
  actAAAGTCACTTAAGGAAACAAACATGAAACACATACCGTTTTTCTTCGCATTCTTTTTTACCTTCCCCTGAATGGGAGGCGTTTCGTCGTGTGAAACAGAATGCGAAGACGAACAATAAGGCCTCCCAAATCgggggc                                                                                                                                 <  2:969585/140‑2 (MQ=255)
    tAAAGTCACTTAAGGAAACAAACATGAAACACATACCGTTTTTCTTCGCATTCTTTTTTACCTTCCCCTGAATGGGAGGCGTTTCGTCGTGTGAAACAGAATGCGAAGACGAACAATAAGGCCTCCCAAATCgggggcct                                                                                                                               >  1:998608/1‑137 (MQ=255)
      aaGTCACTTAAGGAAACAAACATGAAACACATACCGTTTTTCTTCGCATTCTTTTTTACCTTCCCCTGAATGGGAGGCGTTTCGTCGTGTGAAACAGAATGCGAAGACGAACAATAAGGCCTCCCAAATC‑GGGGGCCttt                                                                                                                            >  1:308416/1‑140 (MQ=255)
        gTCACTTAAGGAAACAAACATGAAACACATACCGTTTTTCTTCGCATTCTTTTTTACCTTCCCCTGAATGGGAGGCGTTTCGTCGTGTGAAACAGAATGCGAAGACGAACAATAAGGCCTCCCAAATC‑GGGGGCCttttt                                                                                                                          >  2:750011/1‑140 (MQ=255)
         tCACTTAAGGAAACAAACATGAAACACATACCGTTTTTCTTCGCATTCTTTTTTACCTTCCCCTGAATGGGAGGCGTTTCGTCGTGTGAAACAGAATGCGAAGACGAACAATAAGGCCTCCCAAATC‑GGGGGCCtttttt                                                                                                                         >  1:53377/1‑140 (MQ=255)
         tCACTTAAGGAAACAAACATGAAACACATACCGTTTTTCTTCGCATTCTTTTTTACCTTCCCCTGAATGGGAGGCGTTTCGTCGTGTGAAACAGAATGCGAAGACGAACAATAAGGCCTCCCAAATC‑GGGGGCCtttttt                                                                                                                         >  2:1195193/1‑140 (MQ=255)
           aCTTAAGGAAACAAACATGAAACACATACCGTTTTTCTTCGCATTCTTTTTTACCTTCCCCTGAATGGGAGGCGTTTCGTCGTGTGAAACAGAATGCGAAGACGAACAATAAGGCCTCCCAAATC‑GGGGGCCTTTTTTAt                                                                                                                       >  1:1170933/1‑140 (MQ=255)
           aCTTAAGGAAACAAACATGAAACACATACCGTTTTTCTTCGCATTCTTTTTTACCTTCCCCTGAATGGGAGGCGTTTCGTCGTGTGAAACAGAATGCGAAGACGAACAATAAGGCCTCCCAAATC‑GGGGGCCTTTTTTAt                                                                                                                       >  2:556808/1‑140 (MQ=255)
           aCTTAAGGAAACAAACATGAAACACATACCGTTTTTCTTCGCATTCTTTTTTACCTTCCCCTGAATGGGAGGCGTTTCGTCGTGTGAAACAGAATGCGAAGACGAACAATAAGGCCTCCCAAATC‑GGGGGCCTTTTTTAt                                                                                                                       >  2:87838/1‑140 (MQ=255)
               aaGGAAACAAACATGAAACACATACCGTTTTTCTTCGCATTCTTTTTTACCTTCCCCTGAATGGGAGGCGTTTCGTCGTGTGAAACAGAATGCGAAGACGAACAATAAGGCCTCCCAAATC‑GGGGGCCTTTTTTATTGAt                                                                                                                   <  1:750011/140‑1 (MQ=255)
                  gAAACAAACATGAAACACATACCGTTTTTCTTCGCATTCTTTTTTACCTTCCCCTGAATGGGAGGCGTTTCGTCGTGTGAAACAGAATGCGAAGACGAACAATAAGGCCTCCCAAATC‑GGGGGCCTTTTTTATTGATAAc                                                                                                                >  1:223910/1‑140 (MQ=255)
                  gAAACAAACATGAAACACATACCGTTTTTCTTCGCATTCTTTTTTACCTTCCCCTGAATGGGAGGCGTTTCGTCGTGTGAAACAGAATGCGAAGACGAACAATAAGGCCTCCCAAATC‑GGGGGCCTTTTTTATTGATAAc                                                                                                                >  1:866568/1‑140 (MQ=255)
                    aacaaacaTGAAACACATACCGTTTTTCTTCGCATTCTTTTTTACCTTCCCCTGAATGGGAGGCGTTTCGTCGTGTGAAACAGAATGCGAAGACGAACAATAAGGCCTCCCAAATC‑GGGGGCCTTTTTTATTGATAACaa                                                                                                              <  1:99464/140‑1 (MQ=255)
                        aacaTGAAACACATACCGTTTTTCTTCGCATTCTTTTTTACCTTCCCCTGAATGGGAGGCGTTTCGTCGTGTGAAACAGAATGCGAAGACGAACAATAAGGCCTCCCAAATC‑GGGGGCCTTTTTTATTGATAACAAAAAg                                                                                                          <  2:338658/140‑1 (MQ=255)
                        aacaTGAAACACATACCGTTTTTCTTCGCATTCTTTTTTACCTTCCCCTGAATGGGAGGCGTTTCGTCGTGTGAAACAGAATGCGAAGACGAACAATAAGGCCTCCCAAATC‑GGGGGCCTTTTTTATTGATAACAAAAAg                                                                                                          <  1:1195193/140‑1 (MQ=255)
                         acaTGAAACACATACCGTTTTTCTTCGCATTCTTTTTTACCTTCCCCTGAATGGGAGGCGTTTCGTCGTGTGAAACAGAATGCGAAGACGAACAATAAGGCCTCCCAAATC‑GGGGGCCTTTTTTATTGATAACAAAAAgg                                                                                                         <  2:775821/140‑1 (MQ=255)
                         acaTGAAACACATACCGTTTTTCTTCGCATTCTTTTTTACCTTCCCCTGAATGGGAGGCGTTTCGTCGTGTGAAACAGAATGCGAAGACGAACAATAAGGCCTCCCAAATC‑GGGGGCC‑TTTTTATTGATAACAAAAAGGc                                                                                                        <  2:1172540/140‑1 (MQ=255)
                          caTGAAACACATACCGTTTTTCTTCGCATTCTTTTTTACCTTCCCCTGAATGGGAGGCGTTTCGTCGTGTGAAACAGAATGCGAAGACGAACAATAAGGCCTCCCAAATC‑GGGGGCCTTTTTTATTGATAACAAAAAGGc                                                                                                        <  2:629645/140‑1 (MQ=255)
                            tGAAACACATACCGTTTTTCTTCGCATTCTTTTTTACCTTCCCCTGAATGGGAGGCGTTTCGTCGTGTGAAACAGAATGCGAAGACGAACAATAAGGCCTCCCAAATC‑GGGGGCCTTTTTTATTGAt                                                                                                                   >  2:117369/1‑127 (MQ=255)
                            tGAAACACATACCGTTTTTCTTCGCATTCTTTTTTACCTTCCCCTGAATGGGAGGCGTTTCGTCGTGTGAAACAGAATGCGAAGACGAACAATAAGGCCTCCCAAATC‑GGGGGCCTTTTTTATTGAt                                                                                                                   <  1:117369/127‑1 (MQ=255)
                            tGAAACACATACCGTTTTTCTTCGCATTCTTTTTTACCTTCCCCTGAATGGGAGGCGTTTCGTCGTGTGAAACAGAATGCGAAGACGAACAATAAGGCCTCCCAAATC‑GGGGGCCTTTTTTATTGATAACAAAAAGGCaa                                                                                                      <  2:843/140‑1 (MQ=255)
                            tGAAACACATACCGTTTTTCTTCGCATTCTTTTTTACCTTCCCCTGAATGGGAGGCGTTTCGTCGTGTGAAACAGAATGCGAAGACGAACAATAAGGCCTCCCAAATC‑GGGGGCCTTTTTTATTGATAACAAAAAGGCaa                                                                                                      <  1:419507/140‑1 (MQ=255)
                            tGAAACACATACCGTTTTTCTTCGCATTCTTTTTTACCTTCCCCTGAATGGGAGGCGTTTCGTCGTGTGAAACAGAATGCGAAGACGAACAATAAGGCCTCCCAAATC‑GGGGGCCTTTTTTATTGATAACAAAAAGGCaa                                                                                                      <  1:24485/140‑1 (MQ=255)
                             gAAACACATACCGTTTTTCTTCGCATTCTTTTTTACCTTCCCCTGAATGGGAGGCGTTTCGTCGTGTGAAACAGAATGCGAAGACGAACAATAAGGCCTCCCAAATC‑GGGGGCCTTTTTTATTGATAACAAAAAGGCAac                                                                                                     <  2:590802/140‑1 (MQ=255)
                                 cacaTACCGTTTTTCTTCGCATTCTTTTTTACCTTCCCCTGAATGGGAGGCGTTTCGTCGTGTGAAACAGAATGCGAAGACGAACAATAAGGCCTCCCAAATC‑GGGGGCCTTTTTTATTGATAACAAAAAGGCAACACTa                                                                                                 <  2:234960/140‑1 (MQ=255)
                                       ccGTTTTTCTTCGCATTCTTTTTTACCTTCCCCTGAATGGGAGGCGTTTCGTCGTGTGAAACAGAATGCGAAGACGAACAATAAGGCCTCCCAAATC‑GGGGGCCTTTTTTATTGATAACAAAAAGGCAACACTATGACAt                                                                                           >  1:994496/1‑140 (MQ=255)
                                        cGTTTTTCTTCGCATTCTTTTTTACCTTCCCCTGAATGGGAGGCGTTTCGTCGTGTGAAACAGAATGCGAAGACGAACAATAAGGCCTCCCAAATC‑GGGGGCCTTTTTTATTGATAACAAAAAgg                                                                                                         <  2:1034314/125‑1 (MQ=255)
                                        cGTTTTTCTTCGCATTCTTTTTTACCTTCCCCTGAATGGGAGGCGTTTCGTCGTGTGAAACAGAATGCGAAGACGAACAATAAGGCCTCCCAAATC‑GGGGGCCTTTTTTATTGATAACAAAAAgg                                                                                                         >  1:1034314/1‑125 (MQ=255)
                                            tttCTTCGCATTCTTTTTTACCTTCCCCTGAATGGGAGGCGTTTCGTCGTGTGAAACAGAATGCGAAGACGAACAATAAGGCCTCCCAAATC‑GGGGGCCTTTTTTATTGATAACAAAAAGGCAACACTATGACATCGGaa                                                                                      <  2:308416/140‑1 (MQ=255)
                                              tcttcGCATTCTTTTTTACCTTCCCCTGAATGGGAGGCGTTTCGTCGTGTGAAACAGAATGCGAAGACGAACAATAAGGCCTCCCAAATC‑GGGGGCCTTTTTTATTGATAACAAAAAGGCAACACTATGACATCGGaaaa                                                                                    >  1:302038/1‑140 (MQ=255)
                                                  cGCATTCTTTTTTACCTTCCCCTGAATGGGAGGCGTTTCGTCGTGTGAAACAGAATGCGAAGACGAACAATAAGGCCTCCCAAATC‑GGGGGCCTTTTTTATTGATAACAAAAAGGCAACACTATGACATCGGAAAACCCg                                                                                >  2:520596/1‑140 (MQ=255)
                                                  cGCATTCTTTTTTACCTTCCCCTGAATGGGAGGCGTTTCGTCGTGTGAAACAGAATGCGAAGACGAACAATAAGGCCTCCCAAATC‑GGGGGCCTTTTTTATTGATAACAAAAAGGCAACACTATGACATCGGAAAACCCg                                                                                >  1:497576/1‑140 (MQ=255)
                                                             ttACCTTCCCCTGAATGGGAGGCGTTTCGTCGTGTGAAACAGAATGCGAAGACGAACAATAAGGCCTCCCAAATC‑GGGGGCCTTTTTTATTGATAACAAAAAGGCAACACTATGACATCGGAAAACCCGTTACTGGCGCt                                                                     <  1:58931/140‑1 (MQ=255)
                                                               aCCTTCCCCTGAATGGGAGGCGTTTCGTCGTGTGAAACAGAATGCGAAGACGAACAATAAGGCCTCCCAAATC‑GGGGGCCTTTTTTATTGATAACAAAAAGGCAACACTATGACATCGGAAAACCCGTTACTGGCGCTGc                                                                   <  2:223910/140‑1 (MQ=255)
                                                                   tCCCCTGAATGGGAGGCGTTTCGTCGTGTGAAACAGAATGCGAAGACGAACAATAAGGCCTCCCAAATC‑GGGGGCCTTTTTTATTGATAACAAAAAGGCAACACTATGACATCGGAAAACCCGTTACTGGCGCTGCgaga                                                               >  2:246925/1‑140 (MQ=255)
                                                                   tCCCCTGAATGGGAGGCGTTTCGTCGTGTGAAACAGAATGCGAAGACGAACAATAAGGCCTCCCAAATC‑GGGGGCCTTTTTTATTGATAACAAAAAGGCAACACTATGACATCGGAAAACCCGTTACTGGCGCTGCgaga                                                               >  1:287082/1‑140 (MQ=255)
                                                                   tCCCCTGAATGGGAGGCGTTTCGTCGTGTGAAACAGAATGCGAAGACGAACAATAAGGCCTCCCAAATC‑GGGGGCCTTTTTTATTGATAACAAAAAGGCAACACTATGACATCGGAAAACCCGTTACTGGCGCTGCgaga                                                               >  1:586495/1‑140 (MQ=255)
                                                                    ccccTGAATGGGAGGCGTTTCGTCGTGTGAAACAGAATGCGAAGACGAACAATAAGGCCTCACAAATC‑GGGGGCCTTTTTTATTGATAACAAAAAGGCAACACTATGACATCGGAAAACCCGTTACTGGCGCTGCgagag                                                              >  2:1074957/1‑140 (MQ=255)
                                                                     cccTGAATGGGAGGCGTTTCGTCGTGTGAAACAGAATGCGAAGACGAACAATAAGGCCTCCCAAATC‑GGGGGCCTTTTTTATTGATAACAAAAAGGCAACACTATGACATCGGAAAACCCGTTACTGGCGCTGCgagaga                                                             >  2:401506/1‑140 (MQ=255)
                                                                               gAGGCGTTTCGTCGTGTGAAACAGAATGCGAAGACGAACAATAAGGCCTCCCAAATC‑GGGGGCCTTTTTTATTGATAACAAAAAGGCAACACTATGACATCGGAAAACCCGTTACTGGCGCTGCGAGAGAAAATCAgcgc                                                   >  2:595743/1‑140 (MQ=255)
                                                                                aGGCGTTTCGTCGTGTGAAACAGAATGCGAAGACGAACAATAAGGCCTCCCAAATC‑GGGGGCCTTTTTTATTGATAACAAAAAGGCAACACTATGACATCGGAAAACCCGTTACTGGCGCTGCGAGAGAAAATCAgcgcg                                                  <  2:998608/140‑1 (MQ=255)
                                                                                 ggCGTTTCGTCGTGTGAAACAGAATGCGAAGACGAACAATAAGGCCTCCCAAATC‑GGGGGCCTTTTTTATTGATAACAAAAAGGCAACACTATGACATCGGAAAACCCGTTACTGGCGCTGCGAGAGAAAATCAgcgcgc                                                 <  2:586495/140‑1 (MQ=255)
                                                                                     tttCGTCGTGTGAAACAGAATGCGAAGACGAACAATAAGGCCTCCCAAATC‑GGGGGCCTTTTTTATTGATAACAAAAAGGCAACACTATGACATCGGAAAACCCGTTACTGGCGCTGCGAGAGAAAATCAGCGCGCTGGa                                             >  1:358549/1‑140 (MQ=255)
                                                                                          tcgtGTGAAACAGAATGCGAAGACGAACAATAAGGCCTCCCAAATC‑GGGGGCCTTTTTTATTGATAACAAAAAGGCAACACTATGACATCGGAAAACCCGTTACTGGCGCTGCGAGAGAAAATCAGCGCGCTGGATGaaa                                        <  1:556808/140‑1 (MQ=255)
                                                                                                  aaCAGAATGCGAAGACGAACAATAAGGCCTCCCAAATC‑GGGGGCCTTTTTTATTGATAACAAAAAGGCAACACTATGACATCGGAAAACCCGTTACTGGCGCTGCGAGAGAAAATCAGCGCGCTGGATGAAAAAttatta                                <  2:232731/140‑1 (MQ=255)
                                                                                                    cAGAATGCGAAGACGAACAATAAGGCCTCCCAAATC‑GGGGGCCTTTTTTATTGATAACAAAAAGGCAACACTATGACATCGGAAAACCCGTTACTGGCGCTGCGAGAGAAAATCAGCGCGCTGGATGAAAAATTATTAGc                              <  2:287082/140‑1 (MQ=255)
                                                                                                     aGAATGCGAAGACGAACAATAAGGCCTCCCAAATC‑GGGGGCCTTTTTTATTGATAACAAAAAGGCAACACTATGACATCGGAAAACCCGTTACTGGCGCTGCGAGAGAAAATCAGCGCGCTGGATGAAAAATTATTAGCg                             <  2:994496/140‑1 (MQ=255)
                                                                                                      gAATGCGAAGACGAACAATAAGGCCTCCCAAATC‑GGGGGCCTTTTTTATTGATAACAAAAAGGCAACACTATGACATCGGAAAACCCGTTACTGGCGCTGCGAGAGAAAATCAGCGCGCTGGATGAAAAattatcatcca                            <  2:358549/140‑7 (MQ=255)
                                                                                                       aaTGCGAAGACGAACAATAAGGCCTCCCAAATC‑GGGGGCCTTTTTTATTGATAACAAAAAGGCAACACTATGACATCGGAAAACCCGTTACTGGCGCTGCGAGAGAAAATCAGCGCGCTGGATGAAAAAttatta                                >  1:274124/1‑135 (MQ=255)
                                                                                                       aaTGCGAAGACGAACAATAAGGCCTCCCAAATC‑GGGGGCCTTTTTTATTGATAACAAAAAGGCAACACTATGACATCGGAAAACCCGTTACTGGCGCTGCGAGAGAAAATCAGCGCGCTGGATGAAAAAttatta                                >  1:840887/1‑135 (MQ=255)
                                                                                                       aaTGCGAAGACGAACAATAAGGCCTCCCAAATC‑GGGGGCCTTTTTTATTGATAACAAAAAGGCAACACTATGACATCGGAAAACCCGTTACTGGCGCTGCGAGAGAAAATCAGCGCGCTGGATGAAAAAttatta                                <  2:274124/135‑1 (MQ=255)
                                                                                                       aaTGCGAAGACCAACAATAAGGCCTCCCAAATC‑GGGGGCCTTTTTTATTGATAACAAAAAGGCAACCCTATGACATCGGAAAACCCGTTACTGGCGCTGCGAGAGAAAATCAGCGCGCTGGATGAAAAAttatta                                <  2:840887/135‑1 (MQ=255)
                                                                                                                 cGAACAATAAGGCCTCCCAAATC‑GGGGGCCTTTTTTATTGATAACAAAAAGGCAACACTATGACATCGGAAAACCCGTTACTGGCGCTGCGAGAGAAAATCAGCGCGCTGGATGAAAAATTATTAGCGTTACTGGCAGaa                 >  2:622079/1‑140 (MQ=255)
                                                                                                                 cGAACAATAAGGCCTACCAAATC‑GGGGGCCTTTTTTATTGATAACAAAAAGGCAACACTATGACATCGGAAAACCCGTTACTGGCGCTGCGAGAGAAAATCAGCGCGCTGGATGAAAAATTATTAGCGTTACTGGCAGaa                 >  1:269922/1‑140 (MQ=255)
                                                                                                                                cccAAATC‑GGGGGCCTTTTTTATTGATAACAAAAAGGCAACACTATGACATCGGAAAACCCGTTACTGGCGCTGCGAGAGAAAATCAGCGCGCTGGATGAAAAATTATTAGCGTTACTGGCAGAACGGCGCGAACTGGcc  >  1:619093/1‑140 (MQ=255)
                                                                                                                                        |                                                                                                                                    
GTACTAAAGTCACTTAAGGAAACAAACATGAAACACATACCGTTTTTCTTCGCATTCTTTTTTACCTTCCCCTGAATGGGAGGCGTTTCGTCGTGTGAAACAGAATGCGAAGACGAACAATAAGGCCTCCCAAATCGGGGGGCCTTTTTTATTGATAACAAAAAGGCAACACTATGACATCGGAAAACCCGTTACTGGCGCTGCGAGAGAAAATCAGCGCGCTGGATGAAAAATTATTAGCGTTACTGGCAGAACGGCGCGAACTGGCC  >  NC_000913/2737572‑2737840

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A