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
A11 F28 I1 R1 228 65.7 2434974 91.7% 2232871 138.5

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 1,692,622 A→G V77A (GTT→GCT)  uidC ← outer membrane porin family protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009131,692,6220AG100.0% 200.8 / NA 56V77A (GTT→GCT) uidCouter membrane porin family protein
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base G (27/29);  total (27/29)

AGCAGGCTATTTTCACTGGGTTTTATTTTTACTGCCCCCAGGGCAAAGCCAAAACTTTTATCACCATCAAGATACCACCGGGTACTCATATCAGCACGAGCACCTAATTTATAAACATAATACGCCCCGCCTTCAACGCCAATAATATTGGAATAATAACCACTATTGAAATCGAGCAATCCTCCCTGTACCCATGCGTAAATATCTCTTCCCGCGCCAGCACTGGGCTTATCCGCCCTGCGCAATTCGTTTTTCAGTCTGATGCGTAGTCCCG  >  NC_000913/1692487‑1692760
                                                                                                                                       |                                                                                                                                          
aGCAGGCTATTTTCACTGGGTTTTATTTTTACTGCCCCCAGGGCAAAGCCAAAACTTTTATCACCATCAAGATACCACCGGGTACTCATATCAGCACGAGCACCTAATTTATAAACATAATACGCCCCGCCTTCAGCGcc                                                                                                                                        <  2:626302/140‑1 (MQ=255)
 gCAGGCTATTTTCACTGGGTTTTATTTTTACTGCCCCCAGGGCAAAGCCAAAACTTTTATCACCATCAAGATACCACCGGGTACTCATATCAGCACGAGCACCTAATTTATAAACATAATACGCCCCGCCTTCAGCGCCa                                                                                                                                       >  1:429507/1‑140 (MQ=255)
   aGGCTATTTTCACTGGGTTTTATTTTTACTGCCCCCAGGGCAAAGCCAAAACTTTTATCACCATCAAGATACCACCGGGTACTCATATCAGCACGAGCACCTAATTTATAAACATAATACGCCCCGCCTTCAGCGCCaat                                                                                                                                     <  2:1018475/140‑1 (MQ=255)
     gCTATTTTCACTGGGTTTTATTTTTACTGCCCCCAGGGCAAAGCCAAAACTTTTATCACCATCAAGATACCACCGGGTACTCATATCAGCACGAGCACCTAATTTATAAACATAATACGCCCCGCCTTCAGCGCCaa                                                                                                                                      <  1:1011637/137‑1 (MQ=255)
     gCTATTTTCACTGGGTTTTATTTTTACTGCCCCCAGGGCAAAGCCAAAACTTTTATCACCATCAAGATACCACCGGGTACTCATATCAGCACGAGCACCTAATTTATAAACATAATACGCCCCGCCTTCAGCGCCaa                                                                                                                                      >  2:1011637/1‑137 (MQ=255)
      cTATTTTCACTGGGTTTTATTTTTACTGCCCCCAGGGCAAAGCCAAAACTTTTATCACCATCAAGATACCACCGGGTACTCATATCAGCACGAGCACCTAATTTATAAACATAATACGCCCCGCCTTCAGCGCCaataat                                                                                                                                  <  2:635620/140‑1 (MQ=255)
          tttCACTGGGTTTTATTTTTACTGCCCCCAGGGCAAAGCCAAAACTTTTATCACCATCAAGATACCACCGGGTACTCATATCAGCACGAGCACCTAATTTATAAACATAATACGCCCCGCCTTCAGCGCCAATAATATTg                                                                                                                              <  2:233653/140‑1 (MQ=255)
            tCACTGGGTTTTATTTTTACTGCCCCCAGGGCAAAGCCAAAACTTTTATCACCATCAAGATACCACCGGGTACTCATATCAGCACGAGCACCTAATTTATAAACATAATACGCCCCGCCTTCAGCGCCAATAATATTGGa                                                                                                                            >  2:753451/1‑140 (MQ=255)
               cTGGGTTTTATTTTTACTGCCCCCAGGGCAAAGCCAAAACTTTTATCACCATCAAGATACCACCGGGTACTCATATCAGCACGAGCACCTAATTTATAAACATAATACGCCCCGCCTTCAGCGCCAATAATATTGGaata                                                                                                                         <  2:429507/140‑1 (MQ=255)
               cTGGGTTTTATTTTTACTGCCCCCAGGGCAAAGCCAAAACTTTTATCACCATCAAGATACCACCGGGTACTCATATCAGCACGAGCACCTAATTTATAAACATAATACGCCCCGCCTTCAGCGCCAATAATATTGGaata                                                                                                                         <  2:401595/140‑1 (MQ=255)
                tGGGTTTTATTTTTACTGCCCCCAGGGCAAAGCCAAAACTTTTATCACCATCAAGATACCACCGGGTACTCATATCAGCACGAGCACCTAATTTATAAACATAATACGCCCCGCCTTCAGCGCCAATAATATTGGaataa                                                                                                                        >  1:649242/1‑140 (MQ=255)
                   gTTTTATTTTTACTGCCCCCAGGGCAAAGCCAAAACTTTTATCACCATCAAGATACCACCGGGTACTCATATCAGCACGAGCACCTAATTTATAAACATAATACGCCCCGCCTTCAGCGCCAATAATATTGGAAtaataa                                                                                                                     <  1:1176413/140‑1 (MQ=255)
                    ttttATTTTTACTGCCCCCAGGGCAAAGCCAAAACTTTTATCACCATCAAGATACCACCGGGTACTCATATCAGCACGAGCACCTAATTTATAAACATAATACGCCCCGCCTTCAGCGCCAATAATATTGGAATAATAAc                                                                                                                    <  2:799645/140‑1 (MQ=255)
                            ttACTGCCCCCAGGGCAAAGCCAAAACTTTTATCACCATCAAGATACCACCGGGTACTCATATCAGCACGAGCACCTAATTTATAAACATAATACGCCCCGCCTTCAGCGCCAATAATATTGGAATAATAACCACTATTg                                                                                                            >  2:204059/1‑140 (MQ=255)
                            ttACTGCCCCCAGGGCAAAGCCAAAACTTTTATCACCATCAAGATACCACCGGGTACTCATATCAGCACGAGCACCTAATTTATAAACATAATACGCCCCGCCTTCAGCGCCAATAATATTGGAATAATAACCACTATTg                                                                                                            <  1:300413/140‑1 (MQ=255)
                                 gCCCCCAGGGCAAAGCCAAAACTTTTATCACCATCAAGATACCACCGGGTACTCATATCAGCACGAGCACCTAATTTATAAACATAATACGCCCCGCCTTCAGCGCCAATAATATTGGAATAATAACCACTATTGAAATc                                                                                                       <  2:726190/140‑1 (MQ=255)
                                   ccccAGGGCAAAGCCAAAACTTTTATCACCATCAAGATACCACCGGGTACTCATATCAGCACGAGCACCTAATTTATAAACATAATACGCCCCGCCTTCAGCGCCAATAATATTGGAATAATAACCACTATTGAAATCGa                                                                                                     >  1:1071507/1‑140 (MQ=255)
                                         ggCAAAGCCAAAACTTTTATCACCATCAAGATACCACCGGGTACTCATATCAGCACGAGCACCTAATTTATAAACATAATACGCCCCGCCTTCAGCGCCAATAATATTGGAATAATAACCACTATTGAAATCGAGCAAtc                                                                                               <  1:894763/140‑1 (MQ=255)
                                         ggCAAAGCCAAAACTTTTATCACCATCAAGATACCACCGGGTACTCATATCAGCACGAGCACCTAATTTATAAACATAATACGCCCCGCCTTCAGCGCCAATAATATTGGAATAATAACCACTATTGAAATCGAGCAAtc                                                                                               <  2:1017787/140‑1 (MQ=255)
                                         ggCAAAGCCAAAACTTTTATCACCATCAAGATACCACCGGGTACTCATATCAGCACGAGCACCTAATTTATAAACATAATACGCCCCGCCTTCAGCGCCAATAATATTGGAATAATAACCACTATTGAAATCGAGCAAtc                                                                                               <  2:946495/140‑1 (MQ=255)
                                           cAAAGCCAAAACTTTTATCACCATCAAGATACCACCGGGTACTCATATCAGCACGAGCACCTAATTTATAAACATAATACGCCCCGCCTTCAGCGCCAATAATATTGGAATAATAACCACTATTGAAATCGAGCAAtcct                                                                                             <  2:45604/140‑1 (MQ=255)
                                           cAAAGCCAAAACTTTTATCACCATCAAGATACCACCGGGTACTCATATCAGCACGAGCACCTAATTTATAAACATAATACGCCCCGCCTTCAGCGCCAATAATATTGGAATAATAACCACTATTGAAATCGAGCAAtcct                                                                                             <  2:419403/140‑1 (MQ=255)
                                           cAAAGCCAAAACTTTTATCACCATCAAGATACCACCGGGTACTCATATCAGCACGAGCACCTAATTTATAAACATAATACGCCCCGCCTTCAGCGCCAATAATATTGGAATAATAACCACTATTGAAATCGAGCAAtcct                                                                                             <  2:280312/140‑1 (MQ=255)
                                             aaGCCAAAACTTTTATCACCATCAAGATACCACCGGGTACTCATATCAGCACGAGCACCTAATTTATAAACATAATACGCCCCGCCTTCAGCGCCAATAATATTGGAATAATAACCACTATTGAAATCGAGCAAtcctcc                                                                                           >  2:1180530/1‑140 (MQ=255)
                                              aGCCAAAACTTTTATCACCATCAAGATACCACCGGGTACTCATATCAGCACGAGCACCTAATTTATAAACATAATACGCCCCGCCTTCAGCGCCAATAATATTGGAATAATAACCACTATTGAAATCGAg                                                                                                    <  2:517276/130‑1 (MQ=255)
                                              aGCCAAAACTTTTATCACCATCAAGATACCACCGGGTACTCATATCAGCACGAGCACCTAATTTATAAACATAATACGCCCCGCCTTCAGCGCCAATAATATTGGAATAATAACCACTATTGAAATCGAGCAATCCTccc                                                                                          >  2:314955/1‑140 (MQ=255)
                                              aGCCAAAACTTTTATCACCATCAAGATACCACCGGGTACTCATATCAGCACGAGCACCTAATTTATAAACATAATACGCCCCGCCTTCAGCGCCAATAATATTGGAATAATAACCACTATTGAAATCGAGCAATCCTccc                                                                                          >  1:1167552/1‑140 (MQ=255)
                                              aGCCAAAACTTTTATCACCATCAAGAAACCACCGGGTACTCATATCAGCACGAGCACCTAATTTATAAACATAATACGCCCCGCCTTCAGCGCCAATAATATTGGAATAATAACCACTATTGAAATCGAg                                                                                                    >  1:517276/1‑130 (MQ=255)
                                                    aaCTTTTATCACCATCAAGATACCACCGGGTACTCATATCAGCACGAGCACCTAATTTATAAACATAATACGCCCCGCCTTCAGCGCCAATAATATTGGAATAATAACCACTATTGAAATCGAGCAATCCTCCCTGTAcc                                                                                    <  1:717310/140‑1 (MQ=255)
                                                     aCTTTTATCACCATCAAGATACCACCGGGTACTCATATCAGCACGAGCACCTAATTTATAAACATAATACGCCCCGCCTTCAGCGCCAATAATATTGGAATAATAACCACTATTGAAATCGAGCAATCCTCCCTGTAccc                                                                                   <  2:649242/140‑1 (MQ=255)
                                                         ttATCACCATCAAGATACCACCGGGTACTCATATCAGCACGAGCACCTAATTTATAAACATAATACGCCCCGCCTTCAGCGCCAATAATATTGGAATAATAACCACTATTGAAATCGAGCAATCCTCCCTGTACCCATGc                                                                               <  1:834926/140‑1 (MQ=255)
                                                            tCACCATCAAGATACCACCGGGTACTCATATCAGCACGAGCACCTAATTTATAAACATAATACGCCCCGCCTTCAGCGCCAATAATATTGGAATAATAACCACTATTGAAATCGAGCAATCCTCCCTGTACCCATGCGTa                                                                            <  1:500043/140‑1 (MQ=255)
                                                                 aTCAAGATACCACCGGGTACTCATATCAGCACGAGCACCTAATTTATAAACATAATACGCCCCGCCTTCAGCGCCAATAATATTGGAATAATAACCACTATTGAAATCGAGCAATCCTCCCTGTACCCATGCGTAAatat                                                                       >  2:1208365/1‑140 (MQ=255)
                                                                           caccGGGTACTCATATCAGCACGAGCACCTAATTTATAAACATAATACGCCCCGCCTTCAGCGCCAATAATATTGGAATAATAACCACTATTGAAATCGAGCAATCCTCCCTGTACCCATGCGTAAATATCTCTTCCcgc                                                             >  2:381089/1‑140 (MQ=255)
                                                                            accGGGTACTCATATCAGCACGAGCACCTAATTTATAAACATAATACGCCCCGCCTTCAGCGCCAATAATATTGGAATAATAACCACTATTG‑AATCGAGCAATCCTCCCTGTACCCATGCGTAAATATCTCTTCCCgcgc                                                           <  2:636800/140‑1 (MQ=255)
                                                                             ccGGGTACTCATATCAGCACGAGCACCTAATTTATAAACATAATACGCCCCGCCTTCAGCGCCAATAATATTGGAATAATAACCACTATTGAAATCGAGCAATCCTCCCTGTACCCATGCGTAAATATCTCTTCCCgcgc                                                           <  1:510573/140‑1 (MQ=255)
                                                                                ggTACTCATATCAGCACGAGCACCTAATTTATAAACATAATACGCCCCGCCTTCAGCGCCAATAATATTGGAATAATAACCACTATTGAAATCGGGCAATCCTCCCTGTACCCATGCGTAAATATCTCTTCCCGCGCCAg                                                        >  1:98465/1‑140 (MQ=255)
                                                                                ggTACTCATATCAGCACGAGCACCTAATTTATAAACATAATACGCCCCGCCTTCAGCGCCAATAATATTGGAATAATAACCACTATTGAAATCGAGCAATCCTCCCTGTACCCATGCGTAAATATCTCTTCCCGCGCCAg                                                        >  1:356553/1‑140 (MQ=255)
                                                                                ggTACTCATATCAGCACGAGCACCTAATTTATAAACATAATACGCCCCGCCTTCAGCGCCAATAATATTGGAATAATAACCACTATTGAAATCGAGCAATCCTCCCTGTACCCATGCGTAAATATCTCTTCCCGCGCCAg                                                        >  2:733524/1‑140 (MQ=255)
                                                                                ggTACTCATATCAGCACGAGCACCTAATTTATAAACATAATACGCCCCGCCTTCAGCGCCAATAATATTGGAATAATAACCACTATTGAAATCGAGCAATCCTCCCTGTACCCATGCGTAAATATCTCTTCCCGCGCCAg                                                        >  1:1081356/1‑140 (MQ=255)
                                                                                  tACTCATATCAGCACGAGCACCTAATTTATAAACATAATACGCCCCGCCTTCAGCGCCAATAATATTGGAATAATAACCACTATTGAAATCGAGCAATCCTCCCTGTACCCATGCGTAAATATCTCTTCCCGCGCCAGCa                                                      <  1:733524/140‑1 (MQ=255)
                                                                                    cTCCTATCAGCACGAGCACCTAATTTATAGACCTAATACGCCCCGCCTTCACCGCCATTACTATTGGTATCATAACCACTTTTGACTTCGAGCAATCCTCCCTGTCCCCATCCGTCACTATCTCTTCCCGCGCCAGCACt                                                    >  2:264532/1‑140 (MQ=255)
                                                                                          tCAGCACGAGCACCTAATTTATAAACATAATACGCCCCGCCTTCAGCGCCAATAATATTGGAATAATAACCACTATTGAAATCGAGCAATCCTCCCTGTACCCATGCGTAAATATCTCTTCCCGCGCCAGCACTGGGCtt                                              >  2:959900/1‑140 (MQ=255)
                                                                                            aGCACGAGCACCTAATTTATAAACATAATACGCCCCGCCTTCAGCGCCAATAATATTGGAATAATAACCACTATTGAAATCGAGCAATCCTCCCTGTATCCACGCGTAAATAGCTCTAGCCGAGGCAGCACTGGGcagag                                            <  2:1071507/140‑5 (MQ=255)
                                                                                            aGCACGAGCACCTAATTTATAAACATAATACGCCCCGCCTTCAGCGCCAATAATATTGGAATAATAACCACTATTGAAATCGAGCAATCCTCCCTGTACCCATGCGTAAATATCTCTTCCCGCGCCAGCACTGGGCTTAt                                            >  2:925467/1‑140 (MQ=255)
                                                                                              cACGAGCACCTAATTTATAAACATAATACGCCCCGCCTTCAGCGCCAATAATATTGGAATAATAACCACTATTGAAATCGAGCAATCCTCCCTGTACCCATGCGTAAATATCTCTTCCCGCGCCAGCACTGGGCTTATcc                                          >  2:567656/1‑140 (MQ=255)
                                                                                              cACGAGCACCTAATTTATAAACATAATACGCCCCGCCTTCAGCGCCAATAATATTGGAATAATAACCACTATTGAAATCGAGCAATCCTCCCTGTACCCATGCGTAAATATCTCTTCCCGCGCCAGCACTGGGCTTATcc                                          >  1:946724/1‑140 (MQ=255)
                                                                                                      ccTAATTTATAAACATAATACGCCCCGCCTTCAGCGCCAATAATATTGGAATAATAACCACTATTGAAATCGAGCAATCCTCCCTGTACCCATGCGTAAATATCTCTTCCCGCGCCAGCACTGGGCTTATCCGCCCTgcg                                  >  2:695364/1‑140 (MQ=255)
                                                                                                        tAATTTATAAACATAATACGCCCCGCCTTCAGCGCCAATAATATTGGAATAATAACCACTATTGAAATCGAGCAATCCTCCCTGTACCCATGCGTAAATATCTCTTCCCGCGCCAGCACTGGGCTTATCCGCCCTGCGCa                                >  1:1008249/1‑140 (MQ=255)
                                                                                                                         aCGCCCCGCCTTCAGCGCCAATAATATTGGAATAATAACCACTATTGAAATCGAGCAATCCTCCCTGTACCCATGCGTAAATATCTCTTCCCGCGCCAGCACTGGGCTTATCCGCCCTGCGCAATTCGTTTTTCAGTCTg               <  1:567656/140‑1 (MQ=255)
                                                                                                                         aCGCCCCGCCTTCAGCGCCAATAATATTGGAATAATAACCACTATTGAAATCGAGCAATCCTCCCTGTACCCATGCGTAAATATCTCTTCCCGCGCCAGCACTGGGCTTATCCGCCCTGCGCAATTCGTTTTTCAGTCTg               >  2:889532/1‑140 (MQ=255)
                                                                                                                             cccGCCTTCAGCGCCAATAATATTGGAATAATAACCACTATTGAAATCGAGCAATCCTCCCTGTACCCATGCGTAAATATCTCTTCTCGCGCCAGCACTGGGCTTATCCGCCCTGCGCAATTCGTTTTTCAGTCTGATGc           >  2:1060687/1‑140 (MQ=255)
                                                                                                                             cccGCCTTCAGCGCCAATAATATTGGAATAATAACCACTATTGAAATCGAGCAATCCTCCCTGTACCCATGCGTAAATATCTCTTCCCGCGCCAGCACTGGGCTTATCCGCCCTGCGCAATTCGTTTTTCAGTCTg               <  2:1126239/136‑1 (MQ=255)
                                                                                                                             cccGCCTTCAGCGCCAATAATATTGGAATAATAACCACTATTGAAATCGAGCAATCCTCCCTGTACCCATGCGTAAATATCTCTTCCCGCGCCAGCACTGGGCTTATCCGCCCTGCGCAATTCGTTTTTCAGTCTg               >  1:1126239/1‑136 (MQ=255)
                                                                                                                             cccGCCTTCAGCGCCAATAATATTGGAATAATAACCACTATTGAAATCGAGCAATCCTCCCTGTACCCATGCGTAAATATCTCTTCCCGCGCCAGCACTGGGCTTATCCGCCCTGCGCAATTCGTTTTTCAGTCTGATGc           >  1:298357/1‑140 (MQ=255)
                                                                                                                             cccGCCTTCAGCGCCAATAATATTGGAATAATAACCACTATTGAAATCGAGCAATCCTCCCTGTACCCATGCGTAAATATCTCTTCCCGCGCCAGCACTGGGCTTATCCGCCCTGCGCAATTCGTTTTTCAGTCTGATGc           >  2:850045/1‑140 (MQ=255)
                                                                                                                                   ttCAGCGCCACTAATATTGGAATAATAACCACTATTGAAATCGAGCAATCCTCCCTGTACCCATGCGTAAATATCTCTTCCCGCGCCAGCACTGGGCTTATCCGCCCTGCGCAATTCGTTTTTCAGTCTGATGCGTAGTc     <  2:749299/140‑1 (MQ=255)
                                                                                                                                    tCAGCGCCAATAATATTGGAATAATAACCACTATTGAAATCGAGCAATCCTCCCTGTACCCATGCGTAAATATCTCTTCCCGCGCCAGCACTGGGCTTATCCGCCCTGCGCAATTCGTTTTTCAGTCTGATGCGTAGTcc    <  1:474918/140‑1 (MQ=255)
                                                                                                                                      aaCGCCAATAATATTGGAATAATAACCACTATTGAAATCGAGCAATCCTCCCTGTACCCATGCGTAAATATCTCTTCCCGCGCCAGCACTGGGCTTATCCGCCCTGCGCAATTCGTTTTTCAGTCTGATGCGTAGTCCCg  >  1:855562/1‑140 (MQ=255)
                                                                                                                                       |                                                                                                                                          
AGCAGGCTATTTTCACTGGGTTTTATTTTTACTGCCCCCAGGGCAAAGCCAAAACTTTTATCACCATCAAGATACCACCGGGTACTCATATCAGCACGAGCACCTAATTTATAAACATAATACGCCCCGCCTTCAACGCCAATAATATTGGAATAATAACCACTATTGAAATCGAGCAATCCTCCCTGTACCCATGCGTAAATATCTCTTCCCGCGCCAGCACTGGGCTTATCCGCCCTGCGCAATTCGTTTTTCAGTCTGATGCGTAGTCCCG  >  NC_000913/1692487‑1692760

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