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
A6 F8 I0 R1 22 59.8 3060272 94.8% 2901137 61.1

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 1,804,090 G→A 63.0% G52G (GGG→GGA)  mprA → DNA‑binding transcriptional regulator

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,804,0900GA63.0% 128.6 / 155.2 138G52G (GGG→GGA) mprADNA‑binding transcriptional regulator
Reads supporting (aligned to +/- strand):  ref base G (19/32);  new base A (46/41);  total (65/73)
Fisher's exact test for biased strand distribution p-value = 8.11e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.99e-01

Only 100 of 138 total aligned reads displayed.

TCGTCTTTGCATGCACATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACCACAGTATTCAGC  >  minE/1804024‑1804154
                                                                  |                                                                
tCGTCTTTGCATGCACATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAAtt                                                               >  1:62146/1‑70 (MQ=255)
tCGTCTTTGCATGCACATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAAt                                                                >  1:28501/1‑69 (MQ=255)
  gTCTTTGCATGCACATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAAc                                                            >  1:1348069/1‑71 (MQ=255)
  gTCTTTGCATGCACATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAAc                                                            >  1:457412/1‑71 (MQ=255)
   tCTTTGCATGCACATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACg                                                           <  1:2740713/71‑1 (MQ=255)
     tttGCATGCACATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAAc                                                            >  1:829275/1‑68 (MQ=255)
      ttGCATGCACATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAAc                                                            <  1:1835572/67‑1 (MQ=255)
       tgcatgcaCATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGAc                                                       >  1:1968594/1‑71 (MQ=255)
       tgcatgcaCATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACgag                                                         <  1:2419459/69‑1 (MQ=255)
       tgcatgcaCATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGAc                                                       >  1:2848138/1‑71 (MQ=255)
         catgcacatgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACgt                                                     <  1:802965/71‑1 (MQ=255)
             cacatgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAGGGCTCAGGGAATTAACGAGACgttgtt                                                 <  1:1756090/71‑1 (MQ=255)
             cacatgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACgttgtt                                                 <  1:800969/71‑1 (MQ=255)
             cacatgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACgttgtt                                                 <  1:1823839/71‑1 (MQ=255)
              acatgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTTAAGGCTCAGGGGATTAACGAGACGTTGttt                                                <  1:1180053/71‑1 (MQ=255)
                atgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTAt                                              <  1:1629404/71‑1 (MQ=255)
                atgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTAt                                              >  1:1369342/1‑71 (MQ=255)
                atgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTAt                                              >  1:1913305/1‑71 (MQ=255)
                atgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTAt                                              >  1:2360053/1‑71 (MQ=255)
                atgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTAt                                              >  1:410539/1‑71 (MQ=255)
                atgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTAt                                              >  1:1581676/1‑71 (MQ=255)
                 tgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATg                                             >  1:1063855/1‑71 (MQ=255)
                  gcaAAGCAAGCTGCTGGAGAACCGCAATAAAGTGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATgg                                            >  1:963012/1‑71 (MQ=255)
                  gcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACg                                                           >  1:1050423/1‑56 (MQ=255)
                  gcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACg                                                           >  1:672698/1‑56 (MQ=255)
                   caAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTa                                               >  1:1386/1‑67 (MQ=255)
                   caAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGc                                           >  1:2108294/1‑71 (MQ=255)
                   caAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTAt                                              >  1:2835616/1‑68 (MQ=255)
                      agcaagcTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGtt                                        <  1:1333786/71‑1 (MQ=255)
                      agcaagcTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGtt                                        <  1:1897842/71‑1 (MQ=255)
                       gcaagcTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGtt                                        <  1:1143784/70‑1 (MQ=255)
                       gcaagcTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGtt                                        >  1:2267155/1‑70 (MQ=255)
                        caagcTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATgg                                            >  1:367021/1‑65 (MQ=255)
                        caagcTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGa                                      >  1:1805637/1‑71 (MQ=255)
                         aagcTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGAt                                     <  1:1436854/71‑1 (MQ=255)
                         aagcTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACgaga                                                        >  1:608465/1‑52 (MQ=255)
                         aagcTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACgaga                                                        >  1:448898/1‑52 (MQ=255)
                         aagcTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGAt                                     <  1:1438428/71‑1 (MQ=255)
                            ctgctgGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTAc                                  <  1:122858/71‑1 (MQ=255)
                               ctgGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCt                               >  1:1028586/1‑71 (MQ=255)
                                tgGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTg                              >  1:1686662/1‑71 (MQ=255)
                                  gagaACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGGTTACGCTGGa                            <  1:1821041/71‑1 (MQ=255)
                                  gagaACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTg                              <  1:2558056/69‑1 (MQ=255)
                                  gagaACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTg                              <  1:306296/69‑1 (MQ=255)
                                  gagaACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTg                              >  1:478594/1‑69 (MQ=255)
                                  gagaACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTg                              <  1:2293213/69‑1 (MQ=255)
                                  gagaACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTg                              <  1:490704/69‑1 (MQ=255)
                                  gagaACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGa                            <  1:1424383/71‑1 (MQ=255)
                                  gagaACCGCAATAAAATGCTGAAGGCTCAGGGAATTaa                                                             >  1:312628/1‑38 (MQ=255)
                                   agaACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAg                           <  1:231087/71‑1 (MQ=255)
                                    gaACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGt                          <  1:2735522/71‑1 (MQ=255)
                                     aaCCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCg                                          <  1:2154328/54‑1 (MQ=255)
                                     aaCCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCg                                          <  1:589001/54‑1 (MQ=255)
                                     aaCCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATgg                                            <  1:2215834/52‑1 (MQ=255)
                                     aaCCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATgg                                            <  1:886654/52‑1 (MQ=255)
                                      aCCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGtct                        <  1:2967286/71‑1 (MQ=255)
                                       ccGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGtct                        >  1:1675935/1‑70 (MQ=255)
                                       ccGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGtct                        >  1:2963762/1‑70 (MQ=255)
                                        cGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGttt                                                <  1:1741118/45‑1 (MQ=255)
                                          cAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTa                                   >  1:1761763/1‑56 (MQ=255)
                                          cAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAg                     >  1:878624/1‑70 (MQ=255)
                                          cAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTAGAGTCTCAg                     >  1:2617432/1‑70 (MQ=255)
                                          cAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAg                     >  1:1023323/1‑70 (MQ=255)
                                           aaTAAAATTCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGa                   <  1:1532666/71‑1 (MQ=255)
                                           aaTAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACg                                 <  1:1247295/57‑1 (MQ=255)
                                           aaTAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACg                                 <  1:2796116/57‑1 (MQ=255)
                                           aaTAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGAt                                     <  1:1617021/53‑1 (MQ=255)
                                           aaTAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGa                   <  1:1361706/71‑1 (MQ=255)
                                            aTAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTAc                                  <  1:2835224/55‑1 (MQ=255)
                                            aTAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGa                   >  1:1934730/1‑70 (MQ=255)
                                              aaaaTGCTGAAGGCTCAGTGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGaaaa                >  1:2444064/1‑71 (MQ=255)
                                              aaaaTGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGc                                >  1:11846/1‑55 (MQ=255)
                                              aaaaTGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGc                                >  1:784897/1‑55 (MQ=255)
                                               aaaTGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAAc               <  1:2675712/71‑1 (MQ=255)
                                               aaaTGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAAc               <  1:1610761/71‑1 (MQ=255)
                                               aaaTGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACg                                 >  1:1495495/1‑53 (MQ=255)
                                               aaaTGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACg                                 >  1:1291362/1‑53 (MQ=255)
                                               aaaTGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGaaaa                <  1:2679175/70‑1 (MQ=255)
                                               aaaTGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAAc               <  1:408886/71‑1 (MQ=255)
                                                aaTGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTa                                               >  1:1885580/1‑38 (MQ=255)
                                                aaTGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGTGTCTCAGGAAAAcc              <  1:448858/71‑1 (MQ=255)
                                                aaTGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAAcc              <  1:106944/71‑1 (MQ=255)
                                                aaTGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAAcc              <  1:103372/71‑1 (MQ=255)
                                                 aTGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACca             <  1:1541059/71‑1 (MQ=255)
                                                  tGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACca             >  1:2062611/1‑70 (MQ=255)
                                                    cTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACCACAg          >  1:2143284/1‑71 (MQ=255)
                                                     tGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCg                                          <  1:2338208/38‑1 (MQ=255)
                                                     tGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGtt                                        <  1:1232446/40‑1 (MQ=255)
                                                     tGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACCACAg          >  1:1414697/1‑70 (MQ=255)
                                                     tGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACCACAg          >  1:2721621/1‑70 (MQ=255)
                                                      gagggCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACCACAGTa        >  1:1110777/4‑71 (MQ=255)
                                                       aaGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACCACAGTAt       >  1:2359380/1‑71 (MQ=255)
                                                       aaGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTg                              <  1:667622/48‑1 (MQ=255)
                                                       aaGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACCACAGTAt       >  1:1662203/1‑71 (MQ=255)
                                                       aaGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACCACAGTAt       >  1:2574739/1‑71 (MQ=255)
                                                        aGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACCACAGTAt       <  1:29775/70‑1 (MQ=255)
                                                         ggCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTg                              <  1:2331486/46‑1 (MQ=255)
                                                          gCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGa                                      >  1:2542763/1‑37 (MQ=255)
                                                           cTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACCACAGTATTCAg   <  1:1112801/71‑1 (MQ=255)
                                                              aGGGGATTAACGAGACGTTGTTTATGGCGTTGATTGCGCTGGAGTCTCAGGAAAACCACAGTATTCAGc  <  1:955115/69‑1 (MQ=255)
                                                                  |                                                                
TCGTCTTTGCATGCACATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACCACAGTATTCAGC  >  minE/1804024‑1804154

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A