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
A4 F8 I0 R1 23 95.3 4862342 97.3% 4731058 99.0

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_000913 3,535,733 A→C 100% F46V (TTT→GTT)  envZ ← sensory histidine kinase EnvZ

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009133,535,7330AC100.0% 265.9 / NA 71F46V (TTT→GTT) envZsensory histidine kinase EnvZ
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base C (31/40);  total (31/40)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

GGAAAGCGGGAGGCACAACCAACTGCGTGCCGTCCTCCAGTTGCAGTTTGTCGGTCATCAACATACGCACTTCGTACGCGAGGACTTTATTAAACTGCTGGAGGCTCGGCAAAATCGCGAAGTTCAGCACCACCAGATAAGTCGTCACCAGGCTGGCGAACAGCAAGGTGACGATGAGCAATAACGTA  >  NC_000913/3535640‑3535827
                                                                                             |                                                                                              
ggAAAGCGGGAGGCACAACCAACTGCGTGCCGTCCTCCAGTTGCAGTTTGTCGGTCATCAACATACGCACTTCGTACGCGAGGACTTTATTAACctgct                                                                                           <  1:2333340/99‑1 (MQ=255)
 gAAAGCGGGAGGCACAACCAACTGCGTGCCGTCCTCCAGTTGCAGTTTGTCGGTCATCAACATACGCACTTCGTACGCGAGGACTTTATTAACctgctg                                                                                          >  2:826607/1‑99 (MQ=255)
   aaGCGGGAGGCACAACCAACTGCGTGCCGTCCTCCAGTTGCAGTTTGTCGGTCATCAACATACGCACTTCGTACGCGAGGACTTTATTAACCTGCTGGa                                                                                        >  2:2360285/1‑99 (MQ=255)
     gCGGGAGGCACAACCAACTGCGTGCCGTCCTCCAGTTGCAGTTTGTCGGTCATCAACATACGCACTTCGTACGCGATGACTTTATTAACCTGCTGGAgg                                                                                      <  1:660630/99‑1 (MQ=255)
     gCGGGAGGCACAACCAACTGCGTGCCGTCCTCCAGTTGCAGTTTGTCGGTCATCAACATACGCACTTCGTACGCGAGGACTTTATTAACCTGCTGGAgg                                                                                      <  2:1955327/99‑1 (MQ=255)
        ggAGGCACAACCAACTGCGTGCCGTCCTCCAGTTGCAGTTTGTCGGTCATCAACATACGCACTTCGTACGCGAGGACTTTATTAACCTGCTGGAGGCTc                                                                                   >  2:980136/1‑99 (MQ=255)
        ggAGGCACAACCAACTGCGTGCCGTCCTCCAGTTGCAGTTTGTCGGTCATCAACATACGCACTTCGTACGCGAGGACTTTATTAACCTGCTGGAGGCTc                                                                                   <  2:1571069/99‑1 (MQ=255)
        ggAGGCACAACCAACTGCGTGCCGTCCTCCAGTTGCAGTTTGTCGGTCATCAACATACGCACTTCGTACGCGAGGACTTTATTAACCTGCTGGAGGCTc                                                                                   >  1:1788505/1‑99 (MQ=255)
         gAGGCACAACCAACTGCGTGCCGTCCTCCAGTTGCAGTTTGTCGGTCATCAACATACGCACTTCGTACGCGAGGACTTTATTAACCTCCTGGAGGCTCg                                                                                  >  2:600076/1‑99 (MQ=255)
           ggCACAACCAACTGCGTGCCGTCCTCCAGTTGCAGTTTGTCGGTCATCAACATACGCACTTCGTACGCGAGGACTTTATTAACCTGCTGGAGGCTCGGc                                                                                <  2:1031660/99‑1 (MQ=255)
             cacaACCAACTGCGTGCCGTCCTCCAGTTGCAGTTTGTCGGTCATCAACATACGCACTTCGTACGCGAGGACTTTATTAACCTGCTGGAGGCTCGGCaa                                                                              >  1:529342/1‑99 (MQ=255)
              acaACCAACTGCGTGCCGTCCTCCAGTTGCAGTTTGTCGGTCATCAACATACGCACTTCGTACGCGAGGACTTTATTAACCTGCTGGAGGCTCGGCaaa                                                                             >  2:2140382/1‑99 (MQ=255)
               caaccaacTGCGTGCCGTCCTCCAGTTGCAGTTTGTCGGTCATCAACATACGCACTTCGTACGCGAGGACTTTATTAACCTGCTGGAGGCTCGGCaaaa                                                                            <  1:2074268/99‑1 (MQ=255)
                aaccaacTGCGTGCCGTCCTCCAGTTGCAGTTTGTCGGTCATCAACATACGCACTTCGTACGCGAGGACTTTATTAACCTGCTGGAGGCTCGGCAAAAt                                                                           >  1:1512194/1‑99 (MQ=255)
                  ccaacTGCGTGCCGTCCTCCAGTTGCAGTTTGTCGGTCATCAACATACGCACTTCGTACGCGAGGACTTTATTAACCTGCTGGAGGCTCGGCAAAATcg                                                                         >  1:1165007/1‑99 (MQ=255)
                   caacTGCGTGCCGTCCTCCAGTTGCAGTTTGTCGGTCATCAACATACGCACTTCGTACGCGAGGACTTTATTAACCTGCTGGAGGCTCGGCAAAATcgc                                                                        <  2:520438/99‑1 (MQ=255)
                     acTGCGTGCCGTCCTCCAGTTGCAGTTTGTCGGTCATCAACATACGCACTTCGTACGCGAGGACTTTATTAACCTGCTGGAGGCTCGGCAAAATCGCGa                                                                      >  2:110066/1‑99 (MQ=255)
                       tGCGTGCCGTCCTCCAGTTGCAGTTTGTCGGTCATCAACATACGCACTTCGTACGCGAGGACTTTATTAACCTGCTGGAGGCTCGGCAAAATCGCGAAg                                                                    <  2:489300/99‑1 (MQ=255)
                       tGCGTGCCGTCCTCCAGTTGCAGTTTGTCGGTCATCAACATACGCACTTCGTACGCGAGGACTTTATTAACCTGCTGGAGGCTCGGCAAAATCGCGAAg                                                                    <  1:2137106/99‑1 (MQ=255)
                       tGCGTGCCGTCCTCCAGTTGCAGTTTGTCGGTCATCAACATACGCACTTCGTACGCGAGGACTTTATTAACCTGCTGGAGGCTCGGCAAAATCGCGAAg                                                                    <  2:1122574/99‑1 (MQ=255)
                        gCGTGCCGTCCTCCAGTTGCAGTTTGTCGGTCATCAACATACGCACTTCGTACGCGAGGACTTTATTAACCTGCTGGAGGCTCGGCAAAATCGCGAAGt                                                                   <  1:2074956/99‑1 (MQ=255)
                        gCGTGCCGTCCTCCAGTTGCAGTTTGTCGGTCATCAACATACGCACTTCGTACGCGAGGACTTTATTAACCTGCTGGAGGCTCGGCAAAATCGCGAAGt                                                                   <  1:2078107/99‑1 (MQ=255)
                        gCGTGCCGTCCTCCAGTTGCAGTTTGTCGGTCATCAACATACGCACTTCGTACGCGAGGACTTTATTAACCTGCTGGAGGCTCGGCAAAATCGCGAAGt                                                                   >  1:1551716/1‑99 (MQ=255)
                         cGTGCCGTCCTCCAGTTGCAGTTTGTCGGTCATCAACATACGCACTTCGTACGCGAGGACTTTATTAACCTGCTGGAGGCTCGGCAAAATCGCGAAGtt                                                                  <  2:190975/99‑1 (MQ=255)
                         cGTGCCGTCCTCCAGTTGCAGTTTGTCGGTCATCAACATACGCACTTCGTACGCGAGGACTTTATTAACCTGCTGGAGGCTCGGCAAAATCGCGAAGtt                                                                  <  2:964830/99‑1 (MQ=255)
                          gTGCCGTCCTCCAGTTGCAGTTTGTCGGTCATCAACATACGCACTTCGTACGCGAGGACTTTATTAACCTGCTGGAGGCTCGGCAAAATCGCGAAGTTc                                                                 <  1:1041711/99‑1 (MQ=255)
                           tGCCGTCCTCCAGTTGCAGTTTGTCGGTCATCAACATACGCACTTCGTACGCGAGGACTTTATTAACCTGCTGGAGGCTCGGCAAAATCGCGAAGTTCa                                                                >  2:822672/1‑99 (MQ=255)
                              cGTCCTCCAGTTGCAGTTTGTCGGTCATCAACATACGCACTTCGTACGCGAGGACTTTATTAACCTGCTGGAGGCTCGGCAAAATCGCGAAGTTCAGca                                                             <  2:1145686/99‑1 (MQ=255)
                               gTCCTCCAGTTGCAGTTTGTCGGTCATCAACATACGCACTTCGTACGCGAGGACTTTATTAACCTGCTGGAGGCTCGGCAAAATCGCGAAGTTCAGcac                                                            <  2:105982/99‑1 (MQ=255)
                               gTCCTCCAGTTGCAGTTTGTCGGTCATCAACATACGCACTTCGTACGCGAGGACTTTATTAACCTGCTGGAGGCTCGGCAAAATCGCGAAGTTCAGcac                                                            <  2:514946/99‑1 (MQ=255)
                                tcctccAGTTGCAGTTTGTCGGTCATCAACATACGCACTTCGTACGCGAGGACTTTATTAACCTGCTGGAGGCTCGGCAAAATCGCGAAGTTCAGcacc                                                           <  1:1244614/99‑1 (MQ=255)
                                  ctccAGTTGCAGTTTGTCGGTCATCAACATACGCACTTCGTACGCGAGGACTTTATTAACCTGCTGGAGGCTCGGCAAAATCGCGAAGTTCAGcaccac                                                         >  2:226322/1‑99 (MQ=255)
                                  ctccAGTTGCAGTTTGTCGGTCATCAACATACGCACTTCGTACGCGAGGACTTTATTAACCTGCTGGAGGCTCGGCAAAATCGCGAAGTTCAGcaccac                                                         >  2:1827409/1‑99 (MQ=255)
                                  ctccAGTTGCAGTTTGTCGGTCATCAACATACGCACTTCGTACGCGAGGACTTTATTAACCTGCTGGAGGCTCGGCAAAATCGCGAAGTTCAGcaccac                                                         <  2:2160490/99‑1 (MQ=255)
                                   tccAGTTGCAGTTTGTCGGTCATCAACATACGCACTTCGTACGCGAGGACTTTATTAACCTGCTGGAGGCTCGGCAAAATCGCGAAGTTCAGCaccacc                                                        >  1:1684046/1‑99 (MQ=255)
                                    ccAGTTGCAGTTTGTCGGTCATCAACATACGCACTTCGTACGCGAGGACTTTATTAACCTGCTGGAGGCTCGGCAAAATCGCGAAGTTCAGCAccacca                                                       <  2:49140/99‑1 (MQ=255)
                                    ccAGTTGCAGTTTGTCGGTCATCAACATACGCACTTCGTACGCGAGGACTTTATTAACCTGCTGGAGGCTCGGCAAAATCGCGAAGTTCAGCAccacca                                                       <  2:2269167/99‑1 (MQ=255)
                                     cAGTTGCAGTTTGTCGGTCATCAACATACGCACTTCGTACGCGAGGACTTTATTAACCTGCTGGAGGCTCGGCAAAATCGCGAAGTTCAGCACCACCAg                                                      >  1:1088732/1‑99 (MQ=255)
                                       gTTGCAGTTTGTCGGTCATCAACATACGCACTTCGTACGCGAGGACTTTATTAACCTGCTGGAGGCTCGGCAAAATCGCGAAGTTCAGCACCACCAGAt                                                    >  2:1514878/1‑99 (MQ=255)
                                       gTTGCAGTTTGTCGGTCATCAACATACGCACTTCGTACGCGAGGACTTTATTAACCTGCTGGAGGCTCGGCAAAATCGCGAAGTTCAGCACCACCAGAt                                                    <  2:2085973/99‑1 (MQ=255)
                                           cAGTTTGTCGGTCATCAACATACGCACTTCGTACGCGAGGACTTTATTAACCTGCTGGAGGCTCGGCAAAATCGCGAAGTTCAGCACCACCAGATAAgt                                                <  1:1140008/99‑1 (MQ=255)
                                           cAGTTTGTCGGTCATCAACATACGCACTTCGTACGCGAGGACTTTATTAACCTGCTGGAGGCTCGGCAAAATCACGAAGTTCAGCACCACCAGATAAgt                                                <  2:704117/99‑1 (MQ=255)
                                            aGTTTGTCGGTCATCAACATACGCACTTCGTACGCGAGGACTTTATTAACCTGCTGGAGGCTCGGCAAAATCGCGAAGTTCAGCACCACCAGATAAgtc                                               >  2:933615/1‑99 (MQ=255)
                                                tGTCGGTCATCAACATACGCACTTCGTACGCGAGGACTTTATTAACCTGCTGGAGGCTCGGCAAAATCGCGAAGTTCAGCACCACCAGATAAGTCGTCa                                           <  1:2371566/99‑1 (MQ=255)
                                                  tCGGTCATCAACATACGCACTTCGTACGCGAGGACTTTATTAACCTGCTGGAGGCTCGGCAAAATCGCGAAGTTCAGCACCACCAGATAAGTCGTCAcc                                         >  1:1012956/1‑99 (MQ=255)
                                                     gTCATCAACATACGCACTTCGTACGCGAGGACTTTATTAACCTGCTGGAGGCTCGGCAAAATCGCGAAGTTCAGCACCACCAGATAAGTCGTCACCAgg                                      >  2:1401315/1‑99 (MQ=255)
                                                     gTCATCAACATACGCACTTCGTACGCGAGGACTTTATTAACCTGCTGGAGGCTCGGCAAAATCGCGAAGTTCAGCACCACCAGATAAGTCGTCACCAgg                                      <  2:416486/99‑1 (MQ=255)
                                                        atcaACATACGCACTTCGTACGCGAGGACTTTATTAACCTGCTGGAGGCTCGGCAAAATCGCGAAGTTCAGCACCACCAGATAAGTCGTCACCAGGCTg                                   <  2:1952980/99‑1 (MQ=255)
                                                        atcaACATACGCACTTCGTACGCGAGGACTTTATTAACCTGCTGGAGGCTCGGCAAAATCGCGAAGTTCAGCACCACCAGATAAGTCGTCACCAGGCTg                                   <  2:1561668/99‑1 (MQ=255)
                                                         tcaACATACGCACTTCGTACGCGAGGACTTTATTAACCTGCTGGAGGCTCGGCAAAATCGCGAAGTTCAGCACCACCAGATAAGTCGTCACCAGGCTgg                                  <  1:472618/99‑1 (MQ=255)
                                                           aaCATACGCACTTCGTACGCGAGGACTTTATTAACCTGCTGGAGGCTCGGCAAAATCGCGAAGTTCAGCACCACCAGATAAGTCGTCACCAGGCTGGCg                                >  2:1203100/1‑99 (MQ=255)
                                                            aCATACGCACTTCGTACGCGAGGACTTTATTAACCTGCTGGAGGCTCGGCAAAATCGCGAAGTTCAGCACCACCAGATAAGTCGTCACCAGGCTGGCGa                               >  1:565829/1‑99 (MQ=255)
                                                             cATACGCACTTCGTACGCGAGGACTTTATTAACCTGCTGGAGGCTCGGCAAAATCGCGAAGTTCAGCACCACCAGATAAGTCGTCACCAGGCTGGCGaa                              <  2:959890/99‑1 (MQ=255)
                                                              aTACGCACTTCGTACGCGAGGACTTTATTAACCTGCTGGAGGCTCGGCAAAATCGCGAAGTTCAGCACCACCAGATAAGTCGTCACCAGGCTGGCGAAc                             >  1:896353/1‑99 (MQ=255)
                                                              aTACGCACTTCGTACGCGAGGACTTTATTAACCTGCTGGAGGCTCGGCAAAATCGCGAAGTTCAGCACCACCAGATAAGTCGTCACCAGGCTGGCGAAc                             >  2:2006220/1‑99 (MQ=255)
                                                               tACGCACTTCGTACGCGAGGACTTTATTAACCTGCTGGAGGCTCGGCAAAATCGCGAAGTTCAGCACCACCAGATAAGTCGTCACCAGGCTGGCGAACa                            <  2:580636/99‑1 (MQ=255)
                                                                      ttCGTACGCGAGGACTTTATTAACCTGCTGGAGGCTCGGCAAAATCGCGAAGTTCAGCACCACCAGATAAGTCGTCACCAGGCTGGCGAACAGCAAGGt                     <  2:551165/99‑1 (MQ=255)
                                                                         gTACGCGAGGACTTTATTAACCTGCTGGAGGCTCGGCAAAATCGCGAAGTTCAGCACCACCAGATAAGTCGTCACCAGGCTGGCGAACAGCAAGGTGAc                  <  1:553140/99‑1 (MQ=255)
                                                                           aCGCGAGGAATTTATTAACCTGCTGGAGGCTCGGCAAAATCGCGAAGTTCAGCACCACCAGATAAGTCGTCACCAGGCTGGCGAACAGCAAGGTGACGa                <  2:354377/99‑1 (MQ=255)
                                                                            cgcgAGGACTTTATTAACCTGCTGGAGGCTCGGCAAAATCGCGAAGTTCAGCACCACCAGATAAGTCGTCACCAGGCTGGCGAACAGCAAGGTGACGAt               <  2:2267313/99‑1 (MQ=255)
                                                                                aGGACTTTATTAACCTGCTGGATGCACGGCAAAATCGCGAAGTTCAGCACCACAAGATAAGTCGTCACCAGGCTGGCGACCAGCAAGGTGACGATGAGc           >  2:1261146/1‑99 (MQ=255)
                                                                                aGGACTGTATTAACCTGCTGGAGGCTCGGCAAAATCGCGAAGTTCAGCACCACCAGATAAGTCGACACCAGGCTAGCGAACAGCAAGGTGACGATGAGc           >  2:1930575/1‑99 (MQ=255)
                                                                                 ggACTTTATTAACCTGCTGGAGGCTCGGCAAAATCGCGAAGTTCAGCACCACCAGATAAGTCGTCACCAGGCTGGCGAACAGCAAGGTGACGATGAGCa          >  2:869644/1‑99 (MQ=255)
                                                                                 ggACTTTATTAACCTGCTGGAGGCTCGGCAAAATCGCGAAGTTCAGCACCACCAGATAAGTCGTCACCAGGCTGGCGAACAGCAAGGTGACGATGAGCa          >  2:1853126/1‑99 (MQ=255)
                                                                                 ggACTTTATTAACCTGCTGGAGGCTCGGCAAAATCGCGAAGTTCAGCACCACCAGATAAGTCGTCACCAGGCTGGCGAACAGCAAGGTGACGATGAGCa          >  1:1913566/1‑99 (MQ=255)
                                                                                    cTTTATTAACCTGCTGGAGGCTCGGCAAAATCGCGAAGTTCAGCACCACCAGATAAGTCGTCACCAGGCTGGCGAACAGCAAGGTGACGATGAGCAATa       >  1:2058908/1‑99 (MQ=255)
                                                                                      ttattaACCTGCTGGAGGCTCGGCAAAATCGCGAAGTTCAGCACCACCAGATAAGTCGTCACCCGGCTGGCGAACAGCACGGTGACGATGAGCAATAAc     <  2:2394142/99‑1 (MQ=255)
                                                                                      ttattaACCTGCTGGAGGCTCGGCAAAATCGCGAAGTTCAGCACCACCAGATAAGTCGTCACCAGGCTGGCGAACAGCAAGGTGACGATGAGCAATAAc     <  1:2294378/99‑1 (MQ=255)
                                                                                        attaACCTGCTGGAGGCTCGGCAAAATCGCGAAGTTCAGCACCACCAGATAAGTCGTCACCAGGCTGGCGAACAGCAAGGTGACGATGAGCAATAACGt   <  2:626093/99‑1 (MQ=255)
                                                                                         ttaACCTGCTGGAGGCTCGGCAAAATCGCGAAGTTCAGCACCACCAGATAAGTCGTCACCAGGCTGGCGAACAGCAAGGTGACGATGAGCAATAACGTa  <  2:70013/99‑1 (MQ=255)
                                                                                         ttaACCTGCTGGAGGCTCGGCAAAATCGCGAAGTTCAGCACCACCAGATAAGTCGTCACCAGGCTGGCGAACAGCAAGGTGACGATGAGCAATAACGTa  >  2:1289436/1‑99 (MQ=255)
                                                                                             |                                                                                              
GGAAAGCGGGAGGCACAACCAACTGCGTGCCGTCCTCCAGTTGCAGTTTGTCGGTCATCAACATACGCACTTCGTACGCGAGGACTTTATTAAACTGCTGGAGGCTCGGCAAAATCGCGAAGTTCAGCACCACCAGATAAGTCGTCACCAGGCTGGCGAACAGCAAGGTGACGATGAGCAATAACGTA  >  NC_000913/3535640‑3535827

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A