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
A2 F1 I0 R1 4577 57.4 3436498 77.7% 2670158 63.4

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 2,637,188 G→A 68.1% T9T (ACG→ACA)  ugpE → glycerol‑3‑phosphate transporter subunit

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,637,1880GA68.1% 113.2 / 65.0 125T9T (ACG→ACA) ugpEglycerol‑3‑phosphate transporter subunit
Reads supporting (aligned to +/- strand):  ref base G (24/16);  new base A (33/52);  total (57/68)
Fisher's exact test for biased strand distribution p-value = 3.44e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.69e-01

Only 100 of 128 total aligned reads displayed.

GTGCAGTTCCGCTATGTTGAAAGCAAGGTGCGTTACCAATGATTGAGAACCGTCCGTGGCTGACGATATTCAGCCATACCATGCTGATCCTCGGGATCGCGGTGATCCTCTTCCCGCTGTACGTGGCGTTTGT  >  minE/2637124‑2637256
                                                                |                                                                    
gtgCAGTTCCGCTATGTTGAAAGCAAGGTGCGTTACCAATGATTGAGAACCGTCCGTGGCTGACGatat                                                                  <  1:1079891/69‑1 (MQ=255)
gtgCAGTTCCGCTATGTTGAAAGCAAGGTGCGTTACCAATGATTGAGAACCGTCCGTGGCTGACGa                                                                     >  1:1171506/1‑66 (MQ=255)
gcgCAGTTCCGCTATGTTGAAAGCAAGGGGCGTTACCAATGATTGAGAACCGTCCGTGGCTGACGatat                                                                  <  1:3354505/67‑1 (MQ=255)
  gCAGTTCCGCTATGTTGAAAGCAAGGTACGTTACC‑ATGATTGAGAACCGTCCGTGGCTGACAATATTCa                                                               <  1:295943/69‑1 (MQ=255)
   cAGTTCCGCTATGTTGAAAGCAAGGTACGTTACCAATGATTGAGAACCGTCCGTGGCTGACAATATTCa                                                               <  1:1998699/69‑1 (MQ=255)
   cAGTTCCGCTATGTTGAAAGCAAGGTACGTTACCAATGATTGAGAACCGTCCGTGGCTGACAATATTCa                                                               <  1:1735633/69‑1 (MQ=255)
   cAGTTCCGCTATGTTGAAAGCAAGGTACGTTACCAATGATTGAGAACCGTCCGTGGCTGACAATATTCa                                                               <  1:344382/69‑1 (MQ=255)
   cAGTTCCGCTATGTTGAAAGCAAGGTACGTTACCAATGATTGAGAACCGTCCGTGGCTGACAATATTCa                                                               <  1:1644233/69‑1 (MQ=255)
   cAGTTCCGCTATGTTGAAAGCAAGGTACGTTACCAATGATTGAGAACCGTCCGTGGCTGACAATATTCa                                                               <  1:3255807/69‑1 (MQ=255)
   cAGTTCCGCTATGTTGAAAGCAAGGTACGTTACCAATGATTGAGAACCGTCCGTGGCTGACAATATTCa                                                               <  1:1783685/69‑1 (MQ=255)
   cAGTTCCGCTATGTTGAAAGCAAGGTACGTTACCAATGATTGAGAACCGTCCGTGGCTGACAATATTCa                                                               <  1:1511660/69‑1 (MQ=255)
   cAGTTCCGCTATGTTGAAAGCAAGGTACGTTACCAATGATTGAGAACCGTCCGTGGCTGACAATATTCa                                                               <  1:324744/69‑1 (MQ=255)
   cAGTTCCGCTATGTTGAAAGCAAGGTACGTTACCAATGATTGAGAACCGTCCGTGGCTGACAATATTCa                                                               <  1:3178882/69‑1 (MQ=255)
   cAGTTCCGCTATGTTGAAAGCAAGGTACGTTACCAATGATTGAGAACCGTCCGTGGCTGACAATATTCa                                                               <  1:2030689/69‑1 (MQ=255)
   cAGTTCCGCTATGTTGAAAGCAAGGTACGTTACCAATGATTGAGAACCGTCCGTGGCTGACAATATTCa                                                               <  1:2767919/69‑1 (MQ=255)
   cAGTTCCGCTATGTTGAAAGCAAGGTACGTTACCAATGATTGAGAACCGTCCGTGGCTGACAATATTCa                                                               <  1:2692415/69‑1 (MQ=255)
   cAGTTCCGCTATGTTGAAAGCAAGGTACGTTACCAATGATTGAGAACCGTCCGTGGCTGACAATATTCa                                                               <  1:573790/69‑1 (MQ=255)
   cAGTTCCGCTATGTTGAAAGCAAGGTACGTTACCAATGATTGAGAACCGTCCGTGGCTGACAATATTCa                                                               <  1:2683645/69‑1 (MQ=255)
   cAGTTCCGCTATGTTGAAAGCAAGGTACGTTACCAATGATTGAGAACCGTCCGTGGCTGACAATATTCa                                                               <  1:2656014/69‑1 (MQ=255)
     gTTCCGCTATGTTGAAAGCAAGGTGCGTTACCAATGATTGAGAACCGTCCGTGGCTGACGATATTCAGc                                                             <  1:1140048/69‑1 (MQ=255)
       tCCGCTATGTTGAAAGCAAGGTGCGTTACCAATGATTGAGAACCGTCCGTGGCTGACGATATTCAGCCa                                                           >  1:2554838/1‑69 (MQ=255)
       tCCGCTATGTTGAAAGCAAGGTACGTTACCAATGATTGAGAACCGTCCGTGGCTGACAATATTCAGCCa                                                           <  1:1723964/69‑1 (MQ=255)
       tCCGCTATGTTGAAAGCAAGGTACGTTACCAATGATTGAGAACCGTCCGTGGCTGACAATATTCAGCCa                                                           <  1:2167269/69‑1 (MQ=255)
       tCCGCTATGTTGAAAGCAAGGTACGTTACCAATGATTGAGAACCGTCCGTGGCTGACAATATTCAGCCa                                                           <  1:2482268/69‑1 (MQ=255)
       tCCGCTATGTTGAAAGCAAGGTACGTTACCAATGATTGAGAACCGTCCGTGGCTGACAATATTCAGCCa                                                           <  1:1870471/69‑1 (MQ=255)
       tCCGCTATGTTGAAAGCAAGGTACGTTACCAATGATTGAGAACCGTCCGTGGCTGACAATATTCAGCCa                                                           <  1:503769/69‑1 (MQ=255)
       tCCGCTATGTTGAAAGCAAGGTACGTTACCAATGATTGAGAACCGTCCGTGGCTGACAATATTCAGCCa                                                           <  1:1478033/69‑1 (MQ=255)
       tCCGCTATGTTGAAAGCAAGGTACGTTACCAATGATTGAGAACCGTCCGTGGCTGACAATATTCAGCCa                                                           <  1:1287562/69‑1 (MQ=255)
       tCCGCTATGTTGAAAGCAAGGTACGTTACCAATGATTGAGAACCGTCCGTGGCTGACAATATTCAGCCa                                                           <  1:1385185/69‑1 (MQ=255)
        ccGCTATGTTGAAAGCAAGGTGCGTTACCAATGATTGAGAACCGTCCGTGGCTGACGATATTCAGCCAt                                                          <  1:2204758/69‑1 (MQ=255)
                ttGAAAGCAAGGTGCGTTACCAATGATTGAGAACCGTCCGTGGCTGACGATATTCAGCCATACCATGCt                                                  >  1:2357084/1‑69 (MQ=255)
                ttGAAAGCAAGGTGCGTTACCAATGATTGAGAACCGTCCGTGGCTGACGATATTCAGCCATACCATGCt                                                  >  1:2134500/1‑69 (MQ=255)
                  gAAAGCAAGGTGCGTTACCAATGATTGAGAACCGACCGTGGCTGACGATATTCAGCCATACCATGCTGa                                                >  1:551404/1‑69 (MQ=255)
                       cAAGGTGCGTTACCAATGATTGATAACCGTCCGAGGCTGACGATAtta                                                                >  1:2853547/1‑47 (MQ=255)
                       cAAGGTGCGTTACCAATGATTGAGACCCGTCCGTGGCTGACGATATTCAGCCATACCATGCTGATCCTc                                           >  1:2091064/1‑69 (MQ=255)
                       cAAGGTGCGTTACCAATGATTGAGAACCGTCCGTGGCTGACGATATTCAGCCATACCATGCTGATCCTc                                           >  1:239438/1‑69 (MQ=255)
                       cAAGGTGCGTTACCAATGATTGAGAACCGTCCGTGGCTGACGATATTCAGCCATACCATGCTGATCCTc                                           >  1:120045/1‑69 (MQ=255)
                       cAAGGTGCGTTACCAATGATTGAGAACCGTCCGTGGCTGACGATATTCAGCCATACCATGCTGATCCTc                                           >  1:2771041/1‑69 (MQ=255)
                       cAAGGTGCGTTACCAATGATTGAGAACCGTCCGTGGCTGACGATATTCAGCCATACCATGCTGATCCTc                                           >  1:2532896/1‑69 (MQ=255)
                       cAAGGTGCGTTACCAATGATTGAGAACCGTCCGTGGCTGACGATATTCAGCCATACCATGCTGATCCTc                                           >  1:3417591/1‑69 (MQ=255)
                       cAAGGTGCGTTACCAATGATTGAGAACCGTCCGTGGCTGACGATATTCAGCCATACCATGCTGATCCTc                                           >  1:2068343/1‑69 (MQ=255)
                       cAAGGTGCGTTACCAATGATTGAGAACCGTCCGTGGCTGACGATATTCAGCCATACCATGCTGATCCTc                                           >  1:2064330/1‑69 (MQ=255)
                       cAAGGTGCGTTACCAATGATTGAGAACCGTCCGTGGCTGACGATATTCAGCCATACCATGCTGATCCTc                                           >  1:519378/1‑69 (MQ=255)
                       cAAGGTGCGTTACCAATGATTGAGAACCGTCCGTGGCTGACGATATTCAGCCATACCATGCTGATCCTc                                           >  1:2999676/1‑69 (MQ=255)
                       cAAGGTGCGTTACCAATGATTGAGAACCGTCCGTGGCTGACGATATTCAGCCATACCATGCTGATCCTc                                           >  1:1601172/1‑69 (MQ=255)
                       cAAGGTGCGTTACCAATGATTGAGAACCGTACGTGGCTGACGATATTCAGCCATACCAt                                                     >  1:2802841/1‑59 (MQ=255)
                       cAAGGTACGTTACCAATGATTGAGAACCGTCCGTGGCTGACAATATTCAGCCATACCATGCTGATCCTc                                           <  1:2755414/69‑1 (MQ=255)
                       cAAGGTACGTTACCAATGATTGAGAACCGTCCGTGGCTGACAATATTCAGCCATACCATGCTGATCCTc                                           <  1:2960289/69‑1 (MQ=255)
                       cAAGGTACGTTACCAATGATTGAGAACCGTCCGTGGCTGACAATATTCAGCCATACCATGCTGATCCTc                                           <  1:882813/69‑1 (MQ=255)
                       cAAGGTACGTTACCAATGATTGAGAACCGTCCGTGGCTGACAATATTCAGCCATACCATGCTGATCCTc                                           <  1:1005488/69‑1 (MQ=255)
                       cAAGGTACGTTACCAATGATTGAGAACCGTCCGTGGCTGACAATATTCAGCCATACCATGCTGATCCTc                                           <  1:443224/69‑1 (MQ=255)
                       cAAGGTACGTTACCAATGATTGAGAACCGTCCGTGGCTGACAATATTCAGCCATACCATGCTGATCCTc                                           <  1:2558760/69‑1 (MQ=255)
                       cAAGGTACGTTACCAATGATTGAGAACCGTCCGTGGCTGACAATATTCAGCCATACCATGCTGATCCTc                                           <  1:96800/69‑1 (MQ=255)
                       cAAGGTACGTTACCAATGATTGAGAACCGTCCGTGGCTGACAATATTCAGCCATACCATGCTGATCCTc                                           <  1:1708249/69‑1 (MQ=255)
                       cAAGGTACGTTACCAATGATTGAGAACCGTCCGTGGCTGACAATATTCAGCCATACCATGCTGATCCTc                                           <  1:1981381/69‑1 (MQ=255)
                       cAAGGTACGTTACCAATGATTGAGAACCGTCCGTGGCTGACAATATTCAGCCATACCATGCTGATCCTc                                           <  1:1980279/69‑1 (MQ=255)
                       cAAGGTACGTTACCAATGATTGAGAACCGTCCGTGGCTGACAATATTCAGCCATACCATGCTGATCCTc                                           <  1:1931440/69‑1 (MQ=255)
                       cAAGGTACGTTACCAATGATTGAGAACCGTCCGTGGCTGACAATATTCAGCCATACCATGCTGATCCTc                                           <  1:2331301/69‑1 (MQ=255)
                       cAAGGTACGTTACCAATGATTGAGAACCGTCCGTGGCTGACAATATTCAGCCATACCATGCTGATCCTc                                           <  1:2427355/69‑1 (MQ=255)
                       cAAGGTACGTTACCAATGATTGAGAACCGTCCGTGGCTGACAATATTCAGCCATACCATGCTGATCCTc                                           <  1:1382847/69‑1 (MQ=255)
                       cAAGGTACGTTACCAATGATTGAGAACCGTCCGTGGCTGACAATATTCAGCCATACCATGCTGATCCTc                                           <  1:1198930/69‑1 (MQ=255)
                        aaGGTACGTTACCAATGATTGAGAACCGTCCGTGGCTGACAATATTCAGCCATACCATGCTGATCCTc                                           <  1:2943356/68‑1 (MQ=255)
                             gCGTTACCAATGATTGAGAACCGTCCGTGGCTGACGATATTCAGCCATACCATGCTGATCCTCGGGATc                                     >  1:25959/1‑69 (MQ=255)
                                     aaTGATTGAGAACCGTCCGTGGCTGACGATATTCAGCCATACCATGCTTATCCTCGGGATCGCGGTGa                              <  1:229012/68‑1 (MQ=255)
                                     aaTGATTGAGAACCGTCCGTGGCTGACGATATTCAGCCATACCATGCTGATCCTCGGGATCGCGGTGa                              <  1:1485940/68‑1 (MQ=255)
                                     aaTGATTGAGAACCGTCCGTGGCTGACGATATTCAGCCATACCATGCTGATCCTCGGGATCGCGGTGa                              <  1:2588399/68‑1 (MQ=255)
                                     aaTGATTGAGAACCGTCCGTGGCTGACGATATTCAGCCATACCATGCTGATCCTCGGGATCGCGGTGa                              <  1:1917316/68‑1 (MQ=255)
                                     aaTGATTGAGAACCGTCCGTGGCTGACGATATTCAGCCATACCATGCTGATCCTCGGGATCGCGGTGa                              <  1:68467/68‑1 (MQ=255)
                                     aaTGATTGAGAACCGTCCGTGGCTGACGATATTCAGCCATACCATGCTGATCCTCGGGATCGCGGTGa                              <  1:3023620/68‑1 (MQ=255)
                                     aaTGATTGAGAACCGTCCGTGGCTGACGATATTCAGCCATACCATGCTGATCCTCGGGATCGCGGTGa                              <  1:707743/68‑1 (MQ=255)
                                     aaTGATTGAGAACCGTCCGTGGCTGACAATATTCAGCCATACCATGCTGATCCTCGGGAt                                      >  1:2282698/1‑60 (MQ=255)
                                     aaTGATTGAGAACCGTCCGTGGCTGACAATATTCAGCCATACCATGCTGATCCTCGGGATCGCGGTGa                              >  1:2863359/1‑68 (MQ=255)
                                     aaTGATTGAGAACCGTCCGTGGCTGACAATATTCAGCCATACCATGCTGATCCTCGGGATCGCGGTGAt                             >  1:1435887/1‑69 (MQ=255)
                                     aaTGATTGAGAACCGTCCGTGGCTGACAATATTCAGCCATACCATGCTGATCCTCGGGATCGCGGTGAt                             >  1:1014920/1‑69 (MQ=255)
                                     aaTGATTGAGAACCGTCCGTGGCTGACAATATTCAGCCATACCATGCTGATCCTCGGGATCGCGGTGAt                             >  1:965150/1‑69 (MQ=255)
                                     aaTGATTGAGAACCGTCCGTGGCTGACAATATTCAGCCATACCATGCTGATCCTCGGGATCGCGGTGAt                             >  1:952610/1‑69 (MQ=255)
                                     aaTGATTGAGAACCGTCCGTGGCTGACAATATTCAGCCATACCATGCTGATCCTCGGGATCGCGGTGAt                             >  1:11042/1‑69 (MQ=255)
                                     aaTGATTGAGAACCGTCCGTGGCTGACAATATTCAGCCATACCATGCTGATCCTCGGGATCGCGGTGAt                             >  1:876309/1‑69 (MQ=255)
                                     aaTGATTGAGAACCGTCCGTGGCTGACAATATTCAGCCATACCATGCTGATCCTCGGGATCGCGGTGAt                             >  1:875649/1‑69 (MQ=255)
                                     aaTGATTGAGAACCGTCCGTGGCTGACAATATTCAGCCATACCATGCTGATCCTCGGGATCGCGGTGAt                             >  1:8747/1‑69 (MQ=255)
                                     aaTGATTGAGAACCGTCCGTGGCTGACAATATTCAGCCATACCATGCTGATCCTCGGGATCGCGGTGAt                             >  1:2552/1‑69 (MQ=255)
                                     aaTGATTGAGAACCGTCCGTGGCTGACAATATTCAGCCATACCATGCTGATCCTCGGGATCGCGGTGAt                             >  1:2478033/1‑69 (MQ=255)
                                     aaTGATTGAGAACCGTCCGTGGCTGACAATATTCAGCCATACCATGCTGATCCTCGGGATCGCGGTGAt                             >  1:633872/1‑69 (MQ=255)
                                     aaTGATTGAGAACCGTCCGTGGCTGACAATATTCAGCCATACCATGCTGATCCTCGGGATCGCGGTGAt                             >  1:2669860/1‑69 (MQ=255)
                                     aaTGATTGAGAACCGTCCGTGGCTGACAATATTCAGCCATACCATGCTGATCCTCGGGATCGCGGTGAt                             >  1:2461944/1‑69 (MQ=255)
                                     aaTGATTGAGAACCGTCCGTGGCTGACAATATTCAGCCATACCATGCTGATCCTCGGGATCGCGGTGAt                             >  1:2958460/1‑69 (MQ=255)
                                     aaTGATTGAGAACCGTCCGTGGCTGACAATATTCAGCCATACCATGCTGATCCTCGGGATCGCGGTGAt                             >  1:513447/1‑69 (MQ=255)
                                     aaTGATTGAGAACCGTCCGTGGCTGACAATATTCAGCCATACCATGCTGATCCTCGGGATCGCGGTGAt                             >  1:2713214/1‑69 (MQ=255)
                                     aaTGATTGAGAACCGTCCGTGGCTGACAATATTCAGCCATACCATGCTGATCCTCGGGATCGCGGTGAt                             >  1:1622019/1‑69 (MQ=255)
                                     aaTGATTGAGAACCGTCCGTGGCTGACAATATTCAGCCATACCATGCTGATCCTCGGGATCGCGGTGAt                             >  1:1673970/1‑69 (MQ=255)
                                     aaTGATTGAGAACCGTCCGTGGCTGACAATATTCAGCCATACCATGCTGATCCTCGGGATCGCGGTGAt                             >  1:1681322/1‑69 (MQ=255)
                                     aaTGATTGAGAACCGTCCGTGGCTGACAATATTCAGCCATACCATGCTGATCCTCGGGATCGCGGTGAt                             >  1:1760978/1‑69 (MQ=255)
                                     aaTGATTGAGAACCGTCCGTGGCTGACAATATTCAGCCATACCATGCTGATCCTCGGGATCGCGGTGAt                             >  1:3213647/1‑69 (MQ=255)
                                     aaTGATTGAGAACCGTCCGTGGCTGACAATATTCAGCCATACCATGCTGATCCTCGGGATCGCGGTGAt                             >  1:2110587/1‑69 (MQ=255)
                                     aaTGATTGAGAACCGTCCGTGGCTGACAATATTCAGCCATACCATGCTGATCCTCGGGATCGCGGTGAt                             >  1:1933304/1‑69 (MQ=255)
                                     aaTGATTGAGAACCGTCCGTGGCTGACAATATTCAGCCATACCATGCTGATCCTCGGGATCGCGGTGAt                             >  1:2875864/1‑69 (MQ=255)
                                         aTTGAGAACCGTCCGTGGCTGACGATATTCAGCCATa                                                         >  1:791216/1‑37 (MQ=255)
                                         aTTGAGAACCGTCCGTGGCTGACGATATTCAGCCATACCATGCtt                                                 <  1:712770/45‑2 (MQ=255)
                                                                gATATTCAGCCATACCATGCTGATCCTCGGGATCGCGGTGATCCTCTTCCCGCTGTACGTGGCGTTTGt  >  1:370683/1‑69 (MQ=255)
                                                                gATATTCAGCCATACCATGCTGATCCTCGGGATCGCGGTGATCCTCTTCCCGCTGTACGTGGCGTTTGt  >  1:2344607/1‑69 (MQ=255)
                                                                |                                                                    
GTGCAGTTCCGCTATGTTGAAAGCAAGGTGCGTTACCAATGATTGAGAACCGTCCGTGGCTGACGATATTCAGCCATACCATGCTGATCCTCGGGATCGCGGTGATCCTCTTCCCGCTGTACGTGGCGTTTGT  >  minE/2637124‑2637256

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