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 987,023 C→T 43.2% L422L (CTG→TTG)  ynfE → oxidoreductase subunit

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE987,0230CT43.2% 32.2 / 79.7 104L422L (CTG→TTG) ynfEoxidoreductase subunit
Reads supporting (aligned to +/- strand):  ref base C (44/15);  new base T (18/27);  total (62/42)
Fisher's exact test for biased strand distribution p-value = 5.53e-04
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.93e-01

Only 100 of 105 total aligned reads displayed.

TCGGCATCAGCGGCGGAAATAGTGGCGCGCGTGAATCGACCTATACCATTACCATAGAACGCCTGCCGGTGCTGGATAATCCGGTCAAAACGTCAATCTCCTGCTTCAGCTGGACAGATGCTATCGAT  >  minE/986961‑987088
                                                              |                                                                 
tCGGCATCAGCGGCGGAAATAGTGGCGCGCGTGAATCGACCTATACCATTACCATAGAACGCCTGCCgg                                                             >  1:923292/1‑69 (MQ=255)
tCGGCATCAGCGGCGGAAATAGTGGCGCGCGTGAATCGACCTATACCATTACCATAGAACGCCTGCCgg                                                             >  1:3052446/1‑69 (MQ=255)
tCGGCATCAGCGGCGGAAATAGTGGCGCGCGTGAATCGACCTATACCATTACCATAGAACGCCTGCCgg                                                             >  1:364525/1‑69 (MQ=255)
tCGGCATCAGCGGCGGAAATAGTGGCGCGCGTGAATCGACCTATACCATTACCATAGAACGCCTGCCg                                                              >  1:2258896/1‑68 (MQ=255)
tCGGCATCAGCGGCGGAAATAGTGGCGCGCGTGAATCGACCTATACCATTACCATAGAACGCCTGCCg                                                              >  1:3018501/1‑68 (MQ=255)
tCGGCATCAGCGGCGGAAATAGTGGCGCGCGTGAATCGACCTATACCATTACCATAGAACGCCTGCCg                                                              >  1:3234892/1‑68 (MQ=255)
   gCATCAGCGGCGGAAATAGTGGTGCGCGTGAATCGACCTACACCATTACCATCGATCGCTTGCCGGTg                                                           >  1:2361929/1‑68 (MQ=255)
   gCATCAGCGGCGGAAATAGTGGTGCGCGTGAATCGACCTACACCATTACCATCGAACGCTTGCCGGTg                                                           >  1:156274/1‑68 (MQ=255)
   gCATCAGCGGCGGAAATAGTGGTGCGCGTGAATCGACCTACACCATTACCATCGAACGCTTGCCGGTg                                                           >  1:2694390/1‑68 (MQ=255)
   gCATCAGCGGCGGAAATAGTGGTGCGCGTGAATCGACCTACACCATTACCATCGAACGCTTGCCGGTg                                                           >  1:2058107/1‑68 (MQ=255)
   gCATCAGCGGCGGAAATAGTGGTGCGCGTGAATCGACCTACACCATTACCATCGAACGCTTGCCGGTg                                                           >  1:2971573/1‑68 (MQ=255)
   gCATCAGCGGCGGAAATAGTGGTGCGCGTGAATCGACCTACACCATTACCATCGAACGCTTGCCGGTg                                                           >  1:1906135/1‑68 (MQ=255)
   gCATCAGCGGCGGAAATAGTGGTGCGCGTGAATCGACCTACACCATTACCATCGAACGCTTGCCGGTg                                                           >  1:3158266/1‑68 (MQ=255)
   gCATCAGCGGCGGAAATAGTGGTGCGCGTGAATCGACCTACACCATTACCATCGAACGCTTGCCGGTg                                                           >  1:3354771/1‑68 (MQ=255)
   gCATCAGCGGCGGAAATAGTGGTGCGCGTGAATCGACCTACACCATTACCATCGAACGCTTGCCGGTg                                                           >  1:3397748/1‑68 (MQ=255)
   gCATCAGCGGCGGAAATAGTGGTGCGCGTGAATCGACCTACACCATTACCATCGAACGCTTGCCGGTg                                                           >  1:1644527/1‑68 (MQ=255)
   gCATCAGCGGCGGAAATAGTGGTGCGCGTGAATCGACCTACACCATTACCATCGAACGCTTGCCGGTg                                                           >  1:3434747/1‑68 (MQ=255)
   gCATCAGCGGCGGAAATAGTGGTGCGCGTGAATCGACCTACACCATTACCATCGAACGCTTGCCGGTg                                                           >  1:1459199/1‑68 (MQ=255)
   gCATCAGCGGCGGAAATAGTGGTGCGCGTGAATCGACCTACACCATTACCATCGAACGCTTGCCGGTg                                                           >  1:2280347/1‑68 (MQ=255)
   gCATCAGCGGCGGAAATAGTGGTGCGCGTGAATCGACCTACACCATTACCATCGAACGCTTGCCGGTg                                                           >  1:1411106/1‑68 (MQ=255)
   gCATCAGCGGCGGAAATAGTGGTGCGCGTGAATCGACCTACACCATTACCATCGAACGCTTGCCGGTg                                                           >  1:42134/1‑68 (MQ=255)
   gCATCAGCGGCGGAAATAGTGGTGCGCGTGAATCGACCTACACCATTACCATCGAACGCTTGCCGGTg                                                           >  1:1071032/1‑68 (MQ=255)
   gCATCAGCGGCGGAAATAGTGGTGCGCGTGAATCGACCTACACCATTACCATCGAACGCTTGCCGGTg                                                           >  1:81731/1‑68 (MQ=255)
   gCATCAGCGGCGGAAATAGTGGTGCGCGTGAATCGACCTACACCATTACCATCGAACGCTTGCCGGTg                                                           >  1:880039/1‑68 (MQ=255)
        aGCGGCGGAAATAGTGGCGCGCGTGAATCGACCTATACCATTACCATAGAACGCCTGCCGGTGCTGGAt                                                     >  1:2467098/1‑69 (MQ=255)
        aGCGGCGGAAATAGTGGCGCGCGTGAATCGACCTATACCATTACCATAGAACGCCTGCCGGTGCTGGAt                                                     >  1:2537457/1‑69 (MQ=255)
        aGCGGCGGAAATAGTGGCGCGCGTGAATCGACCTATACCATTACCATAGAACGCCTGCCGGTGCTGGAt                                                     >  1:2638183/1‑69 (MQ=255)
        aGCGGCGGAAATAGTGGCGCGCGTGAATCGACCTATACCATTACCATAGAACGCCTGCCGGTGCTGGAt                                                     >  1:2786974/1‑69 (MQ=255)
        aGCGGCGGAAATAGTGGCGCGCGTGAATCGACCTATACCATTACCATAGAACGCCTGCCGGTGCTGGAt                                                     >  1:2774995/1‑69 (MQ=255)
        aGCGGCGGAAATAGTGGCGCGCGTGAATCGACCTATACCATTACCATAGAACGCCTGCCGGTGCTGGAt                                                     >  1:2916048/1‑69 (MQ=255)
        aGCGGCGGAAATAGTGGCGCGCGTGAATCGACCTATACCATTACCATAGAACGCCTGCCGGTGCTGGAt                                                     >  1:2976249/1‑69 (MQ=255)
        aGCGGCGGAAATAGTGGCGCGCGTGAATCGACCTATACCATTACCATAGAACGCCTGCCGGTGCTGGAt                                                     >  1:379840/1‑69 (MQ=255)
        aGCGGCGGAAATAGTGGCGCGCGTGAATCGACCTATACCATTACCATAGAACGCCTGCCGGTGCTGGAt                                                     >  1:788588/1‑69 (MQ=255)
        aGCGGCGGAAATAGTGGCGCGCGTGAATCGACCTATACCATTACCATAGAACGCCTGCCGGTGCTGGAt                                                     >  1:901616/1‑69 (MQ=255)
        aGCGGCGGAAATAGTGGCGCGCGTGAATCGACCTATACCATTACCATAGAACGCCTGCCGGTGCTGGAt                                                     >  1:988580/1‑69 (MQ=255)
        aGCGGCGGAAATAGTGGCGCGCGTGAATCGACCTATACCATTACCATAGAACGCCTGCCGGTGCTGGAt                                                     >  1:1737155/1‑69 (MQ=255)
        aGCGGCGGAAATAGTGGCGCGCGTGAATCGACCTATACCATTACCATAGAACGCCTGCCGGTGCTGGAt                                                     >  1:1733176/1‑69 (MQ=255)
        aGCGGCGGAAATAGTGGCGCGCGTGAATCGACCTATACCATTACCATAGAACGCCTGCCGGTGCTGGAt                                                     >  1:1536816/1‑69 (MQ=255)
        aGCGGCGGAAATAGTGGCGCGCGTGAATCGACCTATACCATTACCATAGAACGCCTGCCGGTGCTGGAt                                                     >  1:105766/1‑69 (MQ=255)
        aGCGGCGGAAATAGTGGCGCGCGTGAATCGACCTATACCATTACCATAGAACGCCTGCCGGTGCTGGAt                                                     >  1:2228971/1‑69 (MQ=255)
        aGCGGCGGAAATAGTGGCGCGCGTGAATCGACCTATACCATTACCATAGAACGCCTGCCGGTGCTGGAt                                                     >  1:1065414/1‑69 (MQ=255)
        aGCGGCGGAAATAGTGGCGCGCGTGAATCGACCTATACCATTACCATAGAACGCCTGCCGGTGCCGGAt                                                     >  1:2061500/1‑69 (MQ=255)
                   tAGTGGCGCGCGTGAATCGACCTATACCATTACCATAGAACGCCTGCCGGTGCTGGATAATCCGGTCaa                                          <  1:2402096/69‑1 (MQ=255)
                   tAGTGGCGCGCGTGAATCGACCTATACCATTACCATAGAACGCCTGCCGGTGCTGGATAATCCGGTCaa                                          <  1:169156/69‑1 (MQ=255)
                   tAGTGGCGCGCGTGAATCGACCTATACCATTACCATAGAACGCCTGCCGGTGCTGGATAATCCGGTCaa                                          <  1:579026/69‑1 (MQ=255)
                   tAGTGGCGCGCGTGAATCGACCTATACCATTACCATAGAACGCCTGCCGGTGCTGGATAATCCGGTCaa                                          <  1:2377472/69‑1 (MQ=255)
                   tAGTGGCGCGCGTGAATCGACCTATACCATTACCATAGAACGCCTGCCGGTGCTGGATAATCCGGTCaa                                          <  1:1058476/69‑1 (MQ=255)
                    aGTGGCGCGCGTGAATCGACCTATACCATTACCATAGAACGCCTGCCGGTGCTGGATAATCCGGTCaa                                          <  1:2853657/68‑1 (MQ=255)
                              gTGAATCGACCTATACCATTACCATAGAACGCCTGCCGGTGCTGGATAATCCGGTCAAAACGTCAAtct                               <  1:2200967/69‑1 (MQ=255)
                              gTGAATCGACCTATACCATTACCATAGAACGCCTGCCGGTGCTGGATAATCCGGTCAAAACGTCAAtct                               <  1:899998/69‑1 (MQ=255)
                              gTGAATCGACCTATACCATTACCATAGAACGCCTGCCGGTGCTGGATAATCCGGTCAAAACGTCAAtct                               <  1:2197022/69‑1 (MQ=255)
                                             ccattaccatCTAACGCTTGCCGGTGCTGGATAATCCGGTCAAAACGTCAATCTCCTGCTTCAGCTg                  <  1:766405/67‑1 (MQ=39)
                                             ccattaccatCGAACGCTTGCCGGTGCTGGATAATCCGGTCAAAACGTCTATCTCCTGCTTCAGCTg                  <  1:493315/67‑1 (MQ=39)
                                             ccattaccatCGAACGCTTGCCGGTGCTGGATAATCCGGTCAAAACGTCAATCTCCTGCTTCAGCTg                  <  1:7057/67‑1 (MQ=255)
                                             ccattaccatCGAACGCTTGCCGGTGCTGGATAATCCGGTCAAAACGTCAATCTCCTGCTTCAGCTg                  <  1:629074/67‑1 (MQ=255)
                                             ccattaccatCGAACGCTTGCCGGTGCTGGATAATCCGGTCAAAACGTCAATCTCCTGCTTCAGCTg                  <  1:836311/67‑1 (MQ=255)
                                             ccattaccatCGAACGCTTGCCGGTGCTGGATAATCCGGTCAAAACGTCAATCTCCTGCTTCAGCTg                  <  1:425602/67‑1 (MQ=255)
                                             ccattaccatCGAACGCTTGCCGGTGCTGGATAATCCGGTCAAAACGTCAATCTCCTGCTTCAGCTg                  <  1:1286666/67‑1 (MQ=255)
                                             ccattaccatCGAACGCTTGCCGGTGCTGGATAATCCGGTCAAAACGTCAATCTCCTGCTTCAGCTg                  <  1:906970/67‑1 (MQ=255)
                                             ccattaccatCGAACGCTTGCCGGTGCTGGATAATCCGGTCAAAACGTCAATCTCCTGCTTCAGCTg                  <  1:1660828/67‑1 (MQ=255)
                                             ccattaccatCGAACGCTTGCCGGTGCTGGATAATCCGGTCAAAACGTCAATCTCCTGCTTCAGCTg                  <  1:794600/67‑1 (MQ=255)
                                             ccattaccatCGAACGCTTGCCGGTGCTGGATAATCCGGTCAAAACGTCAATCTCCTGCTTCAGCTg                  <  1:3350559/67‑1 (MQ=255)
                                             ccattaccatCGAACGCTTGCCGGTGCTGGATAATCCGGTCAAAACGTCAATCTCCTGCTTCAGCTg                  <  1:3275821/67‑1 (MQ=255)
                                             ccattaccatCGAACGCTTGCCGGTGCTGGATAATCCGGTCAAAACGTCAATCTCCTGCTTCAGCTg                  <  1:3259493/67‑1 (MQ=255)
                                             ccattaccatCGAACGCTTGCCGGTGCTGGATAATCCGGTCAAAACGTCAATCTCCTGCTTCAGCTg                  <  1:969146/67‑1 (MQ=255)
                                             ccattaccatCGAACGCTTGCCGGTGCTGGATAATCCGGTCAAAACGTCAATCTCCTGCTTCAGCTg                  <  1:242302/67‑1 (MQ=255)
                                             ccattaccatCGAACGCTTGCCGGTGCTGGATAATCCGGTCAAAACGTCAATCTCCTGCTTCAGCTg                  <  1:316882/67‑1 (MQ=255)
                                             ccattaccatCGAACGCTTGCCGGTGCTGGATAATCCGGTCAAAACGTCAATCTCCTGCTTCAGCTg                  <  1:3135185/67‑1 (MQ=255)
                                             ccattaccatCGAACGCTTGCCGGTGCTGGATAATCCGGTCAAAACGTCAATCTCCTGCTTCAGCTg                  <  1:1874744/67‑1 (MQ=255)
                                             ccattaccatCGAACGCTTGCCGGTGCTGGATAATCCGGTCAAAACGTCAATCTCCTGCTTCAGCTg                  <  1:1003873/67‑1 (MQ=255)
                                             ccattaccatCGAACGCTTGCCGGTGCTGGATAATCCGGTCAAAACGTCAATCTCCTGCTTCAGCTg                  <  1:2805870/67‑1 (MQ=255)
                                             ccattaccatCGAACGCTTGCCGGTGCTGGATAATCCGGTCAAAACGTCAATCTCCTGCTTCAGCTg                  <  1:2818019/67‑1 (MQ=255)
                                             ccattaccatCGAACGCTTGCCGGTGCTGGATAATCCGGTCAAAACGTCAATCTCCTGCTTCAGCTg                  <  1:2662775/67‑1 (MQ=255)
                                             ccattaccatCGAACGCTTGCCGGTGCTGGATAATCCGGTCAAAACGTCAATCTCCTGCTTCAGCTg                  <  1:266191/67‑1 (MQ=255)
                                             ccattaccatCGAACGCTTGCCGGTGCTGGATAATCCGGTCAAAACGTCAATCTCCTGCTTCAGCTg                  <  1:2348747/67‑1 (MQ=255)
                                             ccattaccatCGAACGCTTGCCGGTGCTGGATAATCCGGTCAAAACGTCAATCTCCTGCTTCAGCTg                  <  1:260053/67‑1 (MQ=255)
                                             ccattaccatCGAACGCTTGCCGGTGCTGGATAATCCGGTCAAAACGTCAATCTCCTGCTTCAGCTg                  <  1:2057380/67‑1 (MQ=255)
                                                ttaccatCGAACGCTTGCCGGTGCTGGATAATCCGGTCAAAACGTCAATCTCCTGCTTCAGCTg                  <  1:2703472/64‑1 (MQ=255)
                                                  accatAGAACGCCTGCCGGTGCTGGATAATCCGGTCAAAACGTCAATCTCCTGCTTCAGCTGGAc               >  1:63166/1‑65 (MQ=255)
                                                  accatAGAACGCCTGCCGGTGCTGGATAATCCGGTCAAAACGTCAATCTCCTGCTTCAGCTGGACAGa            >  1:2427075/1‑68 (MQ=255)
                                                  accatAGAACGCCTGCCGGTGCTGGATAATCCGGTCAAAACGTCAATCTCCTGCTTCAGCTGGACAGAt           >  1:2543242/1‑69 (MQ=255)
                                                  accatAGAACGCCTGCCGGTGCTGGATAATCCGGTCAAAACGTCAATCTCCTGCTTCAGCTGGACAGAt           >  1:1043737/1‑69 (MQ=255)
                                                  accatAGAACGCCTGCCGGTGCTGGATAATCCGGTCAAAACGTCAATCTCCTGCTTCAGCTGGACAGAt           >  1:2470948/1‑69 (MQ=255)
                                                  accatAGAACGCCTGCCGGTGCTGGATAATCCGGTCAAAACGTCAATCTCCTGCTTCAGCTGGACAGAt           >  1:1030613/1‑69 (MQ=255)
                                                  accatAGAACGCCTGCCGGTGCTGGATAATCCGGTCAAAACGTCAATCTCCTGCTTCAGCTGGACAGAt           >  1:988268/1‑69 (MQ=255)
                                                  accatAGAACGCCTGCCGGTGCTGGATAATCCGGTCAAAACGTCAATCTCCTGCTTCAGCTGGACAGAt           >  1:1026674/1‑69 (MQ=255)
                                                  accatAGAACGCCTGCCGGTGCTGGATAATCCGGTCAAAACGTCAATCTCCTGCTTCAGCTGGACAGAt           >  1:544892/1‑69 (MQ=255)
                                                  accatAGAACGCCTGCCGGTGCTGGATAATCCGGTCAAAACGTCAATCTCCTGCTTCAGCTGGACAGAt           >  1:2863771/1‑69 (MQ=255)
                                                  accatAGAACGCCTGCCGGTGCTGGATAATCCGGTCAAAACGTCAATCTCCTGCTTCAGCTGGACAGAt           >  1:398627/1‑69 (MQ=255)
                                                  accatAGAACGCCTGCCGGTGCTGGATAATCCGGTCAAAACGTCAATCTCCTGCTTCAGCTGGACAGAt           >  1:1457598/1‑69 (MQ=255)
                                                  accatAGAACGCCTGCCGGTGCTGGATAATCCGGTCAAAACGTCAATCTCCTGCTTCAGCTGGACAGAt           >  1:1890798/1‑69 (MQ=255)
                                                  accatAGAACGCCTGCCGGTGCTGGATAATCCGGTCAAAACGTCAATCTCCTGCTTCAGCTGGACAGAt           >  1:3037859/1‑69 (MQ=255)
                                                  accatAGAACGCCTGCCGGTGCTGGATAATCCGGTCAAAACGTCAATCTCCTGCTTCAGCTGGACAGAt           >  1:304256/1‑69 (MQ=255)
                                                  accatAGAACGCCTGCCGGTGCTGGATAATCCGGTCAAAACGTCAATCTCCTGCTTCAGCTGGACAGAt           >  1:3142164/1‑69 (MQ=255)
                                                        gAACGCCTGCCGGTGCTGGATAATCCGGTCAAAACGTCAATCTCCTGCTTCAGCTGGACAGATGc         <  1:883089/65‑1 (MQ=255)
                                                        gAACGCCTGCCGGTGCTGGATAATCCGGTCAAAACGTCAATCTCCTGCTTCAGCTGGACAGATGc         <  1:1536297/65‑1 (MQ=255)
                                                           cGCCTGCCGGTGCTGGATAATCCGGTCAAAACGTCAATCTCCTGCTTCAGCTGGACAGATGCTATCGAt  <  1:2759873/69‑1 (MQ=255)
                                                           cGCCTGCCGGTGCTGGATAATCCGGTCAAAACGTCAATCTCCTGCTTCAGCTGGACAGATGCTATCGAt  <  1:2967564/69‑1 (MQ=255)
                                                           cGCCTGCCGGTGCTGGATAATCCGGTCAAAACGTCAATCTCCTGCTTCAGCTGGACAGATGCTATCGAt  <  1:1985362/69‑1 (MQ=255)
                                                             ccTGCCGGTGCTGGATAATCCGGTCAAAACGTCAATCTCCTGCTTCAGCTGGACAGATGCTATCGAt  <  1:883175/67‑1 (MQ=255)
                                                              |                                                                 
TCGGCATCAGCGGCGGAAATAGTGGCGCGCGTGAATCGACCTATACCATTACCATAGAACGCCTGCCGGTGCTGGATAATCCGGTCAAAACGTCAATCTCCTGCTTCAGCTGGACAGATGCTATCGAT  >  minE/986961‑987088

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A