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 2,034,536 G→A pseudogene (486/663 nt) yedS → pseudogene, outer membrane protein homology, putative outer membrane protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009132,034,5360GA100.0% 194.0 / NA 60pseudogene (486/663 nt)yedSpseudogene, outer membrane protein homology, putative outer membrane protein
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (35/25);  total (35/25)

TATATGACGTAGAAGCATGGACCGATATGCTGCCAGAATTTGGTGGCGATACCTATGCTGGCGCTGACAACTTCATGAACGGTCGTGCTAATGGTGTTGCAACCTACCGTAACAATGGCTTCTTTGGTTAGGTCGATGGCTTGAACTTTGCTTTGCAATATCAGGGTAATAATGAAAGTGGTGGACCATTCGGGCAGGAAGGTTCCGGTAGTGGTGATGGCCGTAGCCTTTCCAAAGAAAATGGTGATGGTTTCGGTATGTCAACA  >  NC_000913/2034406‑2034671
                                                                                                                                  |                                                                                                                                       
tataTGACGTAGAAGCATGGACCGATATGCTGCCAGAATTTGGTGGCGATACCTATGCTGGCGCTGAC‑ACTTCATGAACGGTCGTGCTAATGGTGTTGCAACCTACCGTAACAATGGCTTCTTTGGTTAAGTCGATGGc                                                                                                                                <  2:1633606/139‑1 (MQ=255)
 atatGACGTAGAAGCATGGACCGATATGCTGCCAGAATTTGGTGGCGATACCTATGCTGGCGCTGACAACTTCATGAACGGTCGTGCTAATGGTGTTGCAACCTACCGTAACAATGGCTTCTTTGGTTAAGTCGATGGc                                                                                                                                <  1:1128523/139‑1 (MQ=255)
       cGTAGAAGCATGGACCGATATGCTGCCAGAATTTGGTGGCGATACCTATGCTGGCGCTGACAACTTCATGAACGGTCGTGCTAATGGTGTTGCAACCTACCGTAACAATGGCTTCTTTGGTTAAGTCGATGGCTTGAAc                                                                                                                          >  1:1645309/1‑139 (MQ=255)
             aGCATGGACCGATATGCTGCCAGAATTTGGTGGCGATACCTATGCTGGCGCTGACAACTTCATGAACGGTCGTGCTAATGGTGTTGCAACCTACCGTAACAATGGCTTCTTTGGTTAAGTCGATGGCTTGAActttgct                                                                                                                    <  1:1379179/139‑1 (MQ=255)
               cATGGACCGATATGCTGCCAGAATTTGGTGGCGATACCTATGCTGGCGCTGACAACTTCATGAACGGTCGTGCTAATGGTGTTGCAACCTACCGTAACAATGGCTTCTTTGGTTAAGTCg                                                                                                                                     >  1:130030/1‑120 (MQ=255)
               cATGGACCGATATGCTGCCAGAATTTGGTGGCGATACCTATGCTGGCGCTGACAACTTCATGAACGGTCGTGCTAATGGTGTTGCAACCTACCGTAACAATGGCTTCTTTGGTTAAGTCg                                                                                                                                     <  2:130030/120‑1 (MQ=255)
                        atatGCTGCCAGAATTTGGTGGCGATACCTATGCTGGCGCTGACAACTTCATGAACGGTCGTGCTAATGGTGTTGCAACCTACCGTAACAATGGCTTCTTTGGTTAAGTCGATGGCTTGAACTTTGCTTTGCAatat                                                                                                           <  1:1219159/137‑1 (MQ=255)
                        atatGCTGCCAGAATTTGGTGGCGATACCTATGCTGGCGCTGACAACTTCATGAACGGTCGTGCTAATGGTGTTGCAACCTACCGTAACAATGGCTTCTTTGGTTAAGTCGATGGCTTGAACTTTGCTTTGCAatat                                                                                                           >  2:1219159/1‑137 (MQ=255)
                        atatGCTGCCAGAATTTGGTGGCGATACCTATGCTGGCGCTGACAACTTCATGAACGGTCGTGCTAATGGTGTTGCAACCTACCGTAACAATGGCTTCTTTGGTTAAGTCGATGGCTTGAACTTTGCTTTGCAATATCa                                                                                                         >  2:1718849/1‑139 (MQ=255)
                                   gAATTTGGTGGCGATACCTATGCTGGCGCTGACAACTTCATGAACGGTCGTGCTAATGGTGTTGCAACCTACCGTAACAATGGCTTCTTTGGTTAAGTCGATGGCTTGAACTTTGCTTTGCAATATCAGGGTAATAATg                                                                                              >  1:1312666/1‑139 (MQ=255)
                                    aaTTTGGTGGCGATACCTATGCTGGCGCTGACAACTTCATGAACGGTCGTGCTAATGGTGTTGCAACCTACCGTAACAATGGCTTCTTTGGTTAAGTCGATGGCTTGAACTTTGCTTTGCAATATCAGGGTAATAATGa                                                                                             <  1:1718849/139‑1 (MQ=255)
                                        tggtggCGATACCTATGCTGGCGCTGACAACTTCATGAACGGTCGTGCTAATGGTGTTGCAACCTACCGTAACAATGGCTTCTTTGGTTAAGTCGATGGCTTGAACTTTGCTTTGCAATATCAGGGTAATAATGAAAgt                                                                                         >  1:616799/1‑139 (MQ=255)
                                                       tGCTGGCGCTGACAACTTCATGAACGGTCGTGCTAATGGTGTTGCAACCTACCGTAACAATGGCTTCTTTGGTTAAGTCGATGGCTTGAACTTTGCTTTGCAATATCa                                                                                                         >  1:404626/1‑108 (MQ=255)
                                                       tGCTGGCGCTGACAACTTCATGAACGGTCGTGCTAATGGTGTTGCAACCTACCGTAACAATGGCTTCTTTGGTTAAGTCGATGGCTTGAACTTTGCTTTGCAATATCa                                                                                                         >  2:1423283/1‑108 (MQ=255)
                                                       tGCTGGCGCTGACAACTTCATGAACGGTCGTGCTAATGGTGTTGCAACCTACCGTAACAATGGCTTCTTTGGTTAAGTCGATGGCTTGAACTTTGCTTTGCAATATCa                                                                                                         <  1:1423283/108‑1 (MQ=255)
                                                       tGCTGGCGCTGACAACTTCATGAACGGTCGTGCTAATGGTGTTGCAACCTACCGTAACAATGGCTTCTTTGGTTAAGTCGATGGCTTGAACTTTGCTTTGCAATATCa                                                                                                         <  2:404626/108‑1 (MQ=255)
                                                            gcgcTGACAACTTCATGAACGGTCGTGCTAATGGTGTTGCAACCTACCGTAACAATGGCTTCTTTGGTTAAGTCGATGGCTTGAACTTTGCTTTGCAATATCa                                                                                                         <  1:98928/103‑1 (MQ=255)
                                                            gcgcTGACAACTTCATGAACGGTCGTGCTAATGGTGTTGCAACCTACCGTAACAATGGCTTCTTTGGTTAAGTCGATGGCTTGAACTTTGCTTTGCAATATCa                                                                                                         >  2:98928/1‑103 (MQ=255)
                                                             cgcTGACAACTTCATGAACGGTCGTGCTAATGGTGTTGCAACCTACCGTAACAATGGCTTCTTTGGTTAAGTCGATGGc                                                                                                                                >  2:1707989/1‑79 (MQ=255)
                                                             cgcTGACAACTTCATGAACGGTCGTGCTAATGGTGTTGCAACCTACCGTAACAATGGCTTCTTTGGTTAAGTCGATGGc                                                                                                                                <  1:1707989/79‑1 (MQ=255)
                                                             cgcTGACAACTTCATGAACGGTCGTGCTAATGGTGTTGCAACCTACCGTAACAATGGCTTCTTTGGTTAAGTCGATGGCTTGAActttgc                                                                                                                     >  2:1598951/1‑90 (MQ=255)
                                                             cgcTGACAACTTCATGAACGGTCGTGCTAATGGTGTTGCAACCTACCGTAACAATGGCTTCTTTGGTTAAGTCGATGGCTTGAActttgc                                                                                                                     >  2:104794/1‑90 (MQ=255)
                                                             cgcTGACAACTTCATGAACGGTCGTGCTAATGGTGTTGCAACCTACCGTAACAATGGCTTCTTTGGTTAAGTCGATGGCTTGAActttgc                                                                                                                     <  1:104794/90‑1 (MQ=255)
                                                             cgcTGACAACTTCATGAACGGTCGTGCTAATGGTGTTGCAACCTACCGTAACAATGGCTTCTTTGGTTAAGTCGATGGCTTGAActttgc                                                                                                                     <  1:1598951/90‑1 (MQ=255)
                                                             cgcTGACAACTTCATGAACGGTCGTGCTAATGGTGTTGCAACCTACCGTAACAATGGCTTCTTTGGTTAAGTCGATGGCTTGAACTTTGCTTTGCAatat                                                                                                           <  2:1595969/100‑1 (MQ=255)
                                                             cgcTGACAACTTCATGAACGGTCGTGCTAATGGTGTTGCAACCTACCGTAACAATGGCTTCTTTGGTTAAGTCGATGGCTTGAACTTTGCTTTGCAatat                                                                                                           >  1:1595969/1‑100 (MQ=255)
                                                             cgcTGACAACTTCATGAACGGTCGTGCTAATGGTGTTGCAACCTACCGTAACAATGGCTTCTTTGGTTAAGTCGATGGCTTGAACTTTGCTTTGCAATATCAGGGTAATAATGAAAGTGGTGGACCATTc                                                                             <  1:1035213/130‑1 (MQ=255)
                                                             cgcTGACAACTTCATGAACGGTCGTGCTAATGGTGTTGCAACCTACCGTAACAATGGCTTCTTTGGTTAAGTCGATGGCTTGAACTTTGCTTTGCAATATCAGGGTAATAATGAAAGTGGTGGACCATTc                                                                             >  2:1035213/1‑130 (MQ=255)
                                                              gcTGACAACTTCATGAACGGTCGTGCTAATGGTGTTGCAACCTACCGTAACAATGGCTTCTTTGGTTAAGTCGATGGCTTGAAct                                                                                                                         <  1:1151848/85‑1 (MQ=255)
                                                              gcTGACAACTTCATGAACGGTCGTGCTAATGGTGTTGCAACCTACCGTAACAATGGCTTCTTTGGTTAAGTCGATGGCTTGAAct                                                                                                                         >  2:1151848/1‑85 (MQ=255)
                                                                 gACAACTTCATGAACGGTCGTGCTAATGGTGTTGCAACCTACCGTAACAATGGCTTCTTTGGTTAAGTCGATGGCTTGAActttgc                                                                                                                     >  1:47719/1‑86 (MQ=255)
                                                                 gACAACTTCATGAACGGTCGTGCTAATGGTGTTGCAACCTACCGTAACAATGGCTTCTTTGGTTAAGTCGATGGCTTGAActttgc                                                                                                                     <  2:47719/86‑1 (MQ=255)
                                                                  aCAACTTCATGAACGGTCGTGCTAATGGTGTTGCAACCTACCGTAACAATGGCTTCTTTGGTTAAGTCGATGGCTTGAACTTTGCTTTGCAATATCAGGGTAATAATGAAAGTGGTGGACCATTCGGGCAGGAAGGTTc                                                               <  2:1256675/139‑1 (MQ=255)
                                                                      cTTCATGAACGGTCGTGCTAATGGTGTTGCAACCTACCGTAACAATGGCTTCTTTGGTTAAGTCGATGGCTTGAACTTTGCTTTGCAATATCAGGGTAATAATGAAAGTGGTGGACCATTCGGGCAGGAAGGTTCCGGt                                                           >  2:1136625/1‑139 (MQ=255)
                                                                                            ggTGTTGCAACCTACCGTAACAATGGCTTCTTTGGTTAAGTCGATGGGTTGAACTTTGCTTTGCAATATCAGGGTAATAATGAAAGTGGTGGACCATTCGGGCAGGAAGGTTCCGGTAGTGGTGATGGCCGTAGCCttt                                     >  2:992930/1‑139 (MQ=255)
                                                                                            ggTGTTGCAACCTACCGTAACAATGGCTTCTTTGGTTAAGTCGATGGCTTGAACTTTGCTTTGCAATATCAGGGTAATAATGAAAGTGGTGGACCATTCGGGCAgg                                                                      <  1:1477398/106‑1 (MQ=255)
                                                                                            ggTGTTGCAACCTACCGTAACAATGGCTTCTTTGGTTAAGTCGATGGCTTGAACTTTGCTTTGCAATATCAGGGTAATAATGAAAGTGGTGGACCATTCGGGCAgg                                                                      >  2:1477398/1‑106 (MQ=255)
                                                                                            ggTGTTGCAACCTACCGTAACAATGGCTTCTTTGGTTAAGTCGATGGCTTGAACTTTGCTTTGCAATATCAGGGTAATAATGAAAGTGGTGGACCATTCGGGCAGGAAGGTTCCGGTAGTGGTGATGGCCGTAg                                          >  2:732941/1‑134 (MQ=255)
                                                                                            ggTGTTGCAACCTACCGTAACAATGGCTTCTTTGGTTAAGTCGATGGCTTGAACTTTGCTTTGCAATATCAGGGTAATAATGAAAGTGGTGGACCATTCGGGCAGGAAGGTTCCGGTAGTGGTGATGGCCGTAg                                          <  1:732941/134‑1 (MQ=255)
                                                                                            ggTGTTGCAACCTACCGTAACAATGGCTTCTTTGGTTAAGTCGATGGCTTGAACTTTGCTTTGCAATATCAGGGTAATAATGAAAGTGGTGGACCATTCGGGCAGGAAGGTTCCGGTAGTGGTGATGGCCGTAGCCttt                                     >  2:868470/1‑139 (MQ=255)
                                                                                                    aaCCTACCGTAACAATGGCTTCTTTGGTTAAGTCGATGGCTTGAACTTTGCTTTGCAATATCAGGGTAATAATGAAAGTGGTGGACCATTCGGGCAGGAAGGTTCCGGTAGTGGTGATGGCCGTAGCCTTTCCAAAGaa                             <  1:132997/139‑1 (MQ=255)
                                                                                                        tACCGTAACAATGGCTTCTTTGGTTAAGTCGATGGCTTGAACTTTGCTTTGCAATATCAGGGTACTAATGACAGTGGTGGACCATTCGGGCAGGAAGGTTCCGGTAGTGGTGATGGCCGTAGCCTTTCCAAAGAAAATg                         >  1:834560/1‑139 (MQ=255)
                                                                                                          ccGTAACAATGGCTTCTTTGGTTAAGTCGATGGCTTGAACTTTGCTTTGCAATATCAGGGta                                                                                                    <  1:23573/62‑1 (MQ=255)
                                                                                                          ccGTAACAATGGCTTCTTTGGTTAAGTCGATGGCTTGAACTTTGCTTTGCAATATCAGGGta                                                                                                    >  2:23573/1‑62 (MQ=255)
                                                                                                               aCAATGGCTTCTTTGGTTAAGTCGATGGCTTGAACTTTGCTTTGCAATATCAGGGTAATAATGAAAGTGGTGGACCATTCGGGCAGGAAGGTTCCGGTAGTGGTGATGGCCGTAGCCTTTCCAAAGAAAATGGTGATgg                  >  2:866222/1‑139 (MQ=255)
                                                                                                                  aTGGCTTCTTTGGTTAAGTCGATGGCTTGAACTTTGCTTTGCAATATCAGGGTAATAATGAAAGTGGTGGACCATTCGGGCAGGAAGGTTCCGGTAGTGGTGATGGCCGTAGCCTTTCCAAAGAAAATGGTGATGGttt               >  1:1182586/1‑139 (MQ=255)
                                                                                                                   tGGCTTCTTTGGTTAAGTCGATGGCTTGAACTTTGCTTTGCAATATCAGGGt                                                                                                     >  2:431775/1‑52 (MQ=255)
                                                                                                                   tGGCTTCTTTGGTTAAGTCGATGGCTTGAACTTTGCTTTGCAATATCAGGGt                                                                                                     <  1:431775/52‑1 (MQ=255)
                                                                                                                   tGGCTTCTTTGGTTAAGTCGATGGCTTGAACTTTGCTTTGCAATATCAGGGTAATAATGAAAGTGGTGGACCATTCGGGCAGGAAGGTTCCGGTAGTGGTGATGGCCGTAGCCTTTCCAAAGAAAATGGTGATGGTTTc              >  2:460307/1‑139 (MQ=255)
                                                                                                                   tGGCTTCTTTGGTTAAGTCGATGGCTTGAACTTTGCTTTGCAATATCAGGGTAATAATGAAAGTGGTGGACCATTCGGGCAGGAAGGTTCCGGTAGTGGTGATGGCCGTAGCCTTTCCAAAGAAAATGGTGATGGTTTc              >  2:1028696/1‑139 (MQ=255)
                                                                                                                    ggCTTCTTTGGTTAAGTCGATGGCTTGAACTTTGCTTTGCAATATCAGGGTAATAATGAAAGTGGTGGACCATTCGGGCAGGAAGGTTCCGGTAGTGGTGATGGCCGTAGCCTTTCCAAAGAAAATGGTGATGGTTTCg             >  1:125083/1‑139 (MQ=255)
                                                                                                                     gCTTCTTTGGTTAAGTCGATGGCTTGAACTTTGCTTTGCAATATCAGGGTACTAATGAAAGTGGTGGACCATTCGGGCAGGAAGGTTCCGGTAgtg                                                       <  1:1790260/96‑1 (MQ=255)
                                                                                                                     gCTTCTTTGGTTAAGTCGATGGCTTGAACTTTGCTTTGCAATATCAGGGTAATAATGAAAGTGGTGGACCATTCGGGCAGGAAGGTTCCGGTAgtg                                                       >  2:1790260/1‑96 (MQ=255)
                                                                                                                     gCTTCTTTGGTTAAGTCGATGGCTTGAACTTTGCTTTGCAATATCAGGGTAATAATGAAAGTGGTGGACCATTCGGGCAGGAAGGTTCCGGTAGTGGTGATGGCCGTAGCCTTTCCAAAGAAAATGGTGATGGTTTCgg            >  2:148277/1‑139 (MQ=255)
                                                                                                                       ttcttTGGTTAAGTCGATGGCTTGAACTTTGCTTTGCAATATCAGGGTAATAATGAAAGTGGTGGACCATTCGGGCAGGAAGGTTCCGGTAGTGGTGATGGCCGTAGCCTTTCCAAAGAAAATGGTGATGGTTTCGGTa          >  1:143191/1‑139 (MQ=255)
                                                                                                                          tttGGTTAAGTCGATGGCTTGAACTTTGCTTTGCAATATc                                                                                                          <  2:811860/40‑1 (MQ=255)
                                                                                                                          tttGGTTAAGTCGATGGCTTGAACTTTGCTTTGCAATATc                                                                                                          >  1:811860/1‑40 (MQ=255)
                                                                                                                            tGGTTAAGTCGATGGCTTGATCTTTGCTTTGCAAGATCAGGGTAATAATGAAAGTGGTGGGCCCTTCGGGCAGGCAGGTTCCGGTAGCGGTAATGGCCGTAGCCTTTCCAAAGAAAAAGGTGATGGTCTCGGTATGTCa     <  1:378300/139‑1 (MQ=255)
                                                                                                                               ttAAGTCGATGGCTTGAACTTTGCTTTGCAATATCAGGGTAATAATGAAAGtggtgg                                                                                    >  1:1191175/1‑57 (MQ=255)
                                                                                                                               ttAAGTCGATGGCTTGAACTTTGCTTTGCAATATCAGGGTAATAATGAAAGTGGTGGACCATTCGGGCAGGAAGGTTCCGGTAGTGGTGATGGCCGTAGCCTTTCCAAAGAAAATGGTGATGGTTTCGGTATGTCAACa  >  2:441201/1‑139 (MQ=255)
                                                                                                                                  |                                                                                                                                       
TATATGACGTAGAAGCATGGACCGATATGCTGCCAGAATTTGGTGGCGATACCTATGCTGGCGCTGACAACTTCATGAACGGTCGTGCTAATGGTGTTGCAACCTACCGTAACAATGGCTTCTTTGGTTAGGTCGATGGCTTGAACTTTGCTTTGCAATATCAGGGTAATAATGAAAGTGGTGGACCATTCGGGCAGGAAGGTTCCGGTAGTGGTGATGGCCGTAGCCTTTCCAAAGAAAATGGTGATGGTTTCGGTATGTCAACA  >  NC_000913/2034406‑2034671

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A