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 1,294,423 C→T 49.6% A274A (GCG→GCA)  nac ← DNA‑binding transcriptional dual regulator

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,294,4230CT49.6% ‑0.5 / 131.1 139A274A (GCG→GCA) nacDNA‑binding transcriptional dual regulator
Reads supporting (aligned to +/- strand):  ref base C (36/34);  new base T (37/32);  total (73/66)
Fisher's exact test for biased strand distribution p-value = 8.66e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.45e-01

Only 100 of 139 total aligned reads displayed.

ACTGGAGAACTAATCACTGACATTAACAACTCTTTCACTGCCTGTGCCTGTGGCGATAAGTTCGCTCTGGCGGGTAAATTTAATGACAAAGAGAGACTCATGGAAGGAGTGGTAATGCGTGACATCCA  >  minE/1294361‑1294488
                                                              |                                                                 
aCTGGAGAACTAATCACTGACATTAACAACTCTTTCACTGCCTGTGCCTGTGGCGATAAGTTCGCTCTg                                                             >  1:471948/1‑69 (MQ=255)
aCTGGAGAACTAATCACTGACATTAACAACTCTTTCACTGCCTGTGCCTGTGGCGATAAGTTCGCTCTg                                                             >  1:1374557/1‑69 (MQ=255)
           aaTCACTGACATTAACAACTCTTTCACTGCCTGTGCCTGTGGTGACAAGTTTGCTCTGGCg                                                          >  1:1345410/1‑61 (MQ=255)
           aaTCACTGACATTAACAACTCTTTCACTGCCTGTGCCTGTGGTGACAAGTTTGCTCTGGCGGGTaaa                                                    >  1:1887239/1‑67 (MQ=255)
           aaTCACTGACATTAACAACTCTTTCACTGCCTGTGCCTGTGGTGACAAGTTTGCTCTGGCGGGTaaa                                                    >  1:3240263/1‑67 (MQ=255)
           aaTCACTGACATTAACAACTCTTTCACTGCCTGTGCCTGTGGTGACAAGTTTGCTCTGGCGGGTaaa                                                    >  1:1985688/1‑67 (MQ=255)
           aaTCACTGACATTAACAACTCTTTCACTGCCTGTGCCTGTGGTGACAAGTTTGCTCTGGCGGGTaaa                                                    >  1:143635/1‑67 (MQ=255)
           aaTCACTGACATTAACAACTCTTTCACTGCCTGTGCCTGTGGTGACAAGTTTGCTCTGGCGGGTAAAt                                                   >  1:2200556/1‑68 (MQ=255)
           aaTCACTGACATTAACAACTCTTTCACTGCCTGTGCCTGTGGTGACAAGTTTGCTCTGGCGGGTAAAt                                                   >  1:2576803/1‑68 (MQ=255)
           aaTCACTGACATTAACAACTCTTTCACTGCCTGTGCCTGTGGTGACAAGTTTGCTCTGGCGGGTAAAt                                                   >  1:3383063/1‑68 (MQ=255)
           aaTCACTGACATTAACAACTCTTTCACTGCCTGTGCCTGTGGTGACAAGTTTGCTCTGGCGGGTAAAt                                                   >  1:2362576/1‑68 (MQ=255)
           aaTCACTGACATTAACAACTCTTTCACTGCCTGTGCCTGTGGTGACAAGTTTGCTCTGGCGGGTAAAt                                                   >  1:1141716/1‑68 (MQ=255)
           aaTCACTGACATTAACAACTCTTTCACTGCCTGTGCCTGTGGTGACAAGTTTGCTCTGGCGGGTAAAt                                                   >  1:765992/1‑68 (MQ=255)
           aaTCACTGACATTAACAACTCTTTCACTGCCTGTGCCTGTGGTGACAAGTTTGCTCTGGCGGGTAAAt                                                   >  1:1056387/1‑68 (MQ=255)
              cACTGACATTAACAACTCTTTCACTGCCTGTGCCTGTGGTGACAAGTTTGCTCTGGCGGGTAAAttt                                                 <  1:1831097/67‑1 (MQ=255)
              cACTGACATTAACAACTCTTTCACTGCCTGTGCCTGTGGTGACAAGTTTGCTCTGGCGGGTAAAttt                                                 <  1:2006242/67‑1 (MQ=255)
              cACTGACATTAACAACTCTTTCACTGCCTGTGCCTGTGGTGACAAGTTTGCTCTGGCGGGTAAAttt                                                 <  1:2002352/67‑1 (MQ=255)
              cACTGACATTAACAACTCTTTCACTGCCTGTGCCTGTGGTGACAAGTTTGCTCTGGCGGGTAAAttt                                                 <  1:2557345/67‑1 (MQ=255)
              cACTGACATTAACAACTCTTTCACTGCCTGTGCCTGTGGTGACAAGTTTGCTCTGGCGGGTAAAttt                                                 <  1:1614331/67‑1 (MQ=255)
              cACTGACATTAACAACTCTTTCACTGCCTGTGCCTGTGGTGACAAGTTTGCTCTGGCGGGTAAAttt                                                 <  1:2618313/67‑1 (MQ=255)
              cACTGACATTAACAACTCTTTCACTGCCTGTGCCTGTGGTGACAAGTTTGCTCTGGCGGGTAAAttt                                                 <  1:350005/67‑1 (MQ=255)
              cACTGACATTAACAACTCTTTCACTGCCTGTGCCTGTGGTGACAAGTTTGCTCTGGCGGGTAAAttt                                                 <  1:372293/67‑1 (MQ=255)
              cACTGACATTAACAACTCTTTCACTGCCTGTGCCTGTGGTGACAAGTTTGCTCTGGCGGGTAAAttt                                                 <  1:403133/67‑1 (MQ=255)
              cACTGACATTAACAACTCTTTCACTGCCTGTGCCTGTGGTGACAAGTTTGCTCTGGCGGGTAAAttt                                                 <  1:470355/67‑1 (MQ=255)
              cACTGACATTAACAACTCTTTCACTGCCTGTGCCTGTGGCGATAAGTTCGCTCTGGCGGGTAAAttt                                                 <  1:3297362/67‑1 (MQ=255)
              cACTGACATTAACAACTCTTTCACTGCCTGTGCCTGTGGCGATAAGTTCGCTCTGGCGGGTAAAttt                                                 <  1:450242/67‑1 (MQ=255)
              cACTGACATTAACAACTCTTTCACTGCCTGTGCCTGTGGCGATAAGTTCGCTCTGGCGGGTAAAttt                                                 <  1:1021220/67‑1 (MQ=255)
              cACTGACATTAACAACTCTTTCACTGCCTGTGCCTGTGGCGATAAGTTCGCTCTGGCGGGTAAAttt                                                 <  1:94592/67‑1 (MQ=255)
              cACTGACATTAACAACTCTTTCACTGCCTGTGCCTGTGGCGATAAGTTCGCTCTGGCGGGTAAAttt                                                 <  1:1662947/67‑1 (MQ=255)
              cACTGACATTAACAACTCTTTCACTGCCTGTGCCTGTGGCGATAAGTTCGCTCTGGAGGGTAAAttt                                                 <  1:2506822/67‑1 (MQ=255)
               aCTGACATTAACAACTCTTTCACTGCCTGTGCCTGTGGCGATAAGTTCGCTCTGGCGGGTAAATTTAAt                                              >  1:2229725/1‑69 (MQ=255)
               aCTGACATTAACAACTCTTTCACTGCCTGTGCCTGTGGCGATAAGTTCGCTCTGGCGGGTAAATTTAAt                                              >  1:2286988/1‑69 (MQ=255)
               aCTGACATTAACAACTCTTTCACTGCCTGTGCCTGTGGCGATAAGTTCGCTCTGGCGGGTAAATTTAAt                                              >  1:3407443/1‑69 (MQ=255)
                     aTTAACAACTCTTTCACTGCCTGTGCCTGTGGCGATAAGTTCGCTCTGGCGGGTAAATTTAATGACaaa                                        <  1:844453/69‑1 (MQ=255)
                     aTTAACAACTCTTTCACTGCCTGTGCCTGTGGCGATAAGTTCGCTCTGGCGGGTAAATTTAATGACaaa                                        <  1:3376550/69‑1 (MQ=255)
                     aTTAACAACTCTTTCACTGCCTGTGCCTGTGGCGATAAGTTCGCTCTGGCGGGTAAATTTAATGACaaa                                        <  1:371605/69‑1 (MQ=255)
                     aTTAACAACTCTTTCACTGCCTGTGCCTGTGGCGATAAGTTCGCTCTGGCGGGTAAATTTAATGACaaa                                        <  1:748245/69‑1 (MQ=255)
                     aTTAACAACTCTTTCACTGCCTGTGCCTGTGGCGATAAGTTCGCTCTGGCCGGTAAATTTAATGACaaa                                        <  1:2236309/69‑1 (MQ=255)
                       tAACAACTCTTTCACTGCCTGTGCCTGTGGCGATAAGTTCGCTCTGGCGGGTAAATTTAATGACAAaga                                      <  1:1108862/69‑1 (MQ=255)
                        aacaacTCTTTCACTGCCTGTGCCTGTGGCGATAAGTTCGCTCTGGCGGGTAAATTTAATGACaaa                                        >  1:3302679/1‑66 (MQ=255)
                        aacaacTCTTTCACTGCCTGTGCCTGTGGCGATAAGTTCGCTCTGGCGGGTAAATTTAATGACaaa                                        >  1:2384591/1‑66 (MQ=255)
                        aacaacTCTTTCACTGCCTGTGCCTGTGGCGATAAGTTCGCTCTGGCGGGTAAATTTAATGACaaa                                        >  1:755710/1‑66 (MQ=255)
                        aacaacTCTTTCACTGCCTGTGCCTGTGGCGATAAGTTCGCTCTGGCGGGTAAATTTAATGACaaa                                        >  1:1751982/1‑66 (MQ=255)
                                 ttCACTGCCTGTGCCTGTGGCGATAAGTTCGCTCTGGCGGGTAAATTTAATGACAAAGAGAGACTCAt                             >  1:32009/1‑68 (MQ=255)
                                 ttCACTGCCTGTGCCTGTGGCGATAAGTTCGCTCTGGCGGGTAAATTTAATGACAAAGAGAGACTCAt                             >  1:1377795/1‑68 (MQ=255)
                                 ttCACTGCCTGTGCCTGTGGCGATAAGTTCGCTCTGGCGGGTAAATTTAATGACAAAGAGAGACTCAt                             >  1:2832004/1‑68 (MQ=255)
                                 ttCACTGCCTGTGCCTGTGGCGATAAGTTCGCTCTGGCGGGTAAATTTAATGACAAAGAGAGACTCAt                             >  1:2587328/1‑68 (MQ=255)
                                 ttCACTGCCTGTGCCTGTGGCGATAAGTTCGCTCTGGCGGGTAAATTTAATGACAAAGAGAGACTCAt                             >  1:649082/1‑68 (MQ=255)
                                 ttCACTGCCTGTGCCTGTGGCGATAAGTTCGCTCTGGCGGGTAAATTTAATGACAAAGAGAGACTCAt                             >  1:2110337/1‑68 (MQ=255)
                                 ttCACTGCCTGTGCCTGTGGCGATAAGTTCGCTCTGGCGGGTAAATTTAATGACAAAGAGAGACTCAt                             >  1:860750/1‑68 (MQ=255)
                                      tgcctgtgcctgTGGCGATAAGTTCGCTCTGGCGGGTAAATTTAATGACAAAGAGAGACTCATGGAAgg                       <  1:490750/69‑1 (MQ=255)
                                      tgcctgtgcctgTGGCGATAAGTTCGCTCTGGCGGGTAAATTTAATGACAAAGAGAGACTCATGGAAgg                       <  1:1480796/69‑1 (MQ=255)
                                      tgcctgtgcctgTGGCGATAAGTTCGCTCTGGCGGGTAAATTTAATGACAAAGAGAGACTCATGGAAgg                       <  1:1655149/69‑1 (MQ=255)
                                      tgcctgtgcctgTGGCGATAAGTTCGCTCTGGCGGGTAAATTTAATGACAAAGAGAGACTCATGGAAgg                       <  1:782788/69‑1 (MQ=255)
                                      tgcctgtgcctgTGGCGATAAGTTCGCTCTGGCGGGTAAATTTAATGACAAAGAGAGACTCATGGAAgg                       <  1:1141889/69‑1 (MQ=255)
                                      tgcctgtgcctgTGGCGATAAGTTCGCTCTGGCGGGTAAATTTAATGACAAAGAGAGACTCATGGAAgg                       <  1:2934565/69‑1 (MQ=255)
                                      tgcctgtgcctgTGGCGATAAGTTCGCTCTGGCGGGTAAATTTAATGACAAAGAGAGACTCATGGAAgg                       <  1:837029/69‑1 (MQ=255)
                                      tgcctgtgcctgTGGCGATAAGTTCGCTCTGGCGGGTAAATTTAATGACAAAGAGAGACTCATGGAAgg                       <  1:1726422/69‑1 (MQ=255)
                                              cctgtgGCGATAAGTTCGCTCTGGCGGGTAAATTTAATGACAAaga                                      <  1:586339/46‑1 (MQ=255)
                                              cctgtgGCGATAAGTTCGCTCTGGCGGGTAAATTTAATGACAAaga                                      <  1:583241/46‑1 (MQ=255)
                                              cctgtgGCGATAAGTTCGCTCTGGCGGGTAAATTTAATGACAAaga                                      <  1:3408701/46‑1 (MQ=255)
                                              cctgtgGCGATAAGTTCGCTCTGGCGGGTAAATTTAATGACAAaga                                      <  1:873590/46‑1 (MQ=255)
                                              cctgtgGCGATAAGTTCGCTCTGGCGGGTAAATTTAATGACAAAGAGAGACTCATGGAAGGAGTGGt                 <  1:3282400/67‑1 (MQ=255)
                                                    gCGATAAGTTCGCTCTGGCGGGTAAATTTAATGACAAAGAGAGACTCATGGAAGGAGTGGt                 >  1:3127008/1‑61 (MQ=255)
                                                    gCGATAAGTTCGCTCTGGCGGGTAAATTTAATGACAAAGAGAGACTCATGGAAGGAGTGGTAATGCGt          <  1:1328243/68‑1 (MQ=255)
                                                       acaaGTTTGCTCTGGCGGGTAAATTTAAGGACAAAGAGAGACTc                               <  1:2910214/42‑1 (MQ=37)
                                                       acaaGTTTGCTCTGGCGGGTAAATTTAAGGACAAAGAGAGACTc                               <  1:2483998/42‑1 (MQ=37)
                                                       acaaGTTTGCTCTGGCGGGTAAATTTAAGGACAAAGAGAGACTc                               <  1:2422919/42‑1 (MQ=37)
                                                       acaaGTTTGCTCTGGCGGGTAAATTTAAGGACAAAGAGAGACTc                               <  1:2769092/42‑1 (MQ=37)
                                                       acaaGTTTGCTCTGGCGGGTAAATTTAAGGACAAAGAGAGACTc                               <  1:1079292/42‑1 (MQ=37)
                                                       acaaGTTTGCTCTGGCGGGTAAATTTAAGGACAAAGAGAGACTc                               <  1:386658/42‑1 (MQ=37)
                                                       acaaGTTTGCTCTGGCGGGTAAATTTAAGGACAAAGAGAGACTc                               <  1:210027/42‑1 (MQ=37)
                                                       acaaGTTTGCTCTGGCGGGTAAATTTAAGGACAAAGAGAGACTc                               <  1:1675773/42‑1 (MQ=37)
                                                       acaaGTTTGCTCTGGCGGGTAAATTTAAGGACAAAGAGAGACTc                               <  1:2949382/42‑1 (MQ=37)
                                                       acaaGTTTGCTCTGGCGGGTAAATTTAAGGACAAAGAGAGACTc                               <  1:2971157/42‑1 (MQ=37)
                                                       acaaGTTTGCTCTGGCGGGTAAATTTAAGGACAAAGAGAGACTc                               <  1:3071239/42‑1 (MQ=37)
                                                       acaaGTTTGCTCTGGCGGGTAAATTTAAGGACAAAGAGAGACTc                               <  1:940553/42‑1 (MQ=37)
                                                       acaaGTTTGCTCTGGCGGGTAAATTTAAGGACAAAGAGAGACTCATTGAAGGAGTGGTAAt              >  1:883800/3‑61 (MQ=255)
                                                       acaaGTTTGCTCTGGCGGGTAAATTTAAGGACAAAGAGAGACTCATTGAAGGAGTGGTAATGCGTGAc       >  1:110306/3‑68 (MQ=255)
                                                       acaaGTTTGCTCTGGCGGGTAAATTTAAGGACAAAGAGAGACTCATTGAAGGAGTGGTAATGCGTGACa      >  1:1780949/3‑69 (MQ=255)
                                                       acaaGTTTGCTCTGGCGGGTAAATTTAAGGACAAAGAGAGACTCATTGAAGGAGTGGTAATGCGTGACa      >  1:2291214/3‑69 (MQ=255)
                                                       acaaGTTTGCTCTGGCGGGTAAATTTAAGGACAAAGAGAGACTCATTGAAGGAGTGGTAATGCGTGACa      >  1:1707178/3‑69 (MQ=255)
                                                       acaaGTTTGCTCTGGCGGGTAAATTTAAGGACAAAGAGAGACTCATTGAAGGAGTGGTAATGCGTGACa      >  1:2447406/3‑69 (MQ=255)
                                                       acaaGTTTGCTCTGGCGGGTAAATTTAAGGACAAAGAGAGACTCATTGAAGGAGTGGTAATGCGTGACa      >  1:2558939/3‑69 (MQ=255)
                                                       acaaGTTTGCTCTGGCGGGTAAATTTAAGGACAAAGAGAGACTCATTGAAGGAGTGGTAATGCGTGACa      >  1:1520693/3‑69 (MQ=255)
                                                       acaaGTTTGCTCTGGCGGGTAAATTTAAGGACAAAGAGAGACTCATTGAAGGAGTGGTAATGCGTGACa      >  1:47985/3‑69 (MQ=255)
                                                       acaaGTTTGCTCTGGCGGGTAAATTTAAGGACAAAGAGAGACTCATTGAAGGAGTGGTAATGCGTGACa      >  1:3027479/3‑69 (MQ=255)
                                                       acaaGTTTGCTCTGGCGGGTAAATTTAAGGACAAAGAGAGACTCATTGAAGGAGTGGTAATGCGTGACa      >  1:1251145/3‑69 (MQ=255)
                                                       acaaGTTTGCTCTGGCGGGTAAATTTAAGGACAAAGAGAGACTCATTGAAGGAGAGGTAATGCGTGACa      >  1:3345797/3‑69 (MQ=255)
                                                       acaaGTTTGATCTGGCGGGTAAATTTAAGGACAAAGAGAGACTCATTGAAGGAGTGGTAATGCGTGACa      >  1:1473342/3‑69 (MQ=255)
                                                        caaGTTTGCTCTGGCGTGTAAATTTAAGGACAAAGAGAGACTc                               <  1:1066452/42‑1 (MQ=255)
                                                         aaGTTCGCTCTGGCGGGTAAATTTAATGACAAAGAGAGACTCATGGAAGGAGTGGTAATGCGTGACATc    >  1:1248245/1‑69 (MQ=255)
                                                         aaGTTCGCTCTGGCGGGTAAATTTAATGACAAAGAGAGACTCATGGAAGGAGTGGTAATGCGTGACATc    >  1:1618141/1‑69 (MQ=255)
                                                           gTTCGCTCTGGCGGGTAAATTTAATGACAAAGAGAGACTCATGGAAGGAGTGGTaa               >  1:1253904/1‑56 (MQ=255)
                                                           gTTCGCTCTGGCGGGTAAATTTAATGACAAAGAGAGACTCATGGAAGGAGTGGTAATGCGTGACa      >  1:823143/1‑65 (MQ=255)
                                                           gTTCGCTCTGGCGGGTAAATTTAATGACAAAGAGAGACTCATGGAAGGAGTGGTAATGCGTGACATCCa  >  1:1896914/1‑69 (MQ=255)
                                                           gTTCGCTCTGGCGGGTAAATTTAATGACAAAGAGAGACTCATGGAAGGAGTGGTAATGCGTGACATCCa  >  1:2886081/1‑69 (MQ=255)
                                                           gTTCGCTCTGGCGGGTAAATTTAATGACAAAGAGAGACTCATGGAAGGAGTGGTAATGCGTGACATCCa  >  1:92052/1‑69 (MQ=255)
                                                           gTTCGCTCTGGCGGGTAAATTTAATGACAAAGAGAGACTCATGGAAGGAGTGGTAATGCGTGACATCCa  >  1:921735/1‑69 (MQ=255)
                                                           gTTCGCTCTGGCGGGTAAATTTAATGACAAAGAGAGACTCATGGAAGGAGTGGTAATGCGTGACATCCa  >  1:572479/1‑69 (MQ=255)
                                                              |                                                                 
ACTGGAGAACTAATCACTGACATTAACAACTCTTTCACTGCCTGTGCCTGTGGCGATAAGTTCGCTCTGGCGGGTAAATTTAATGACAAAGAGAGACTCATGGAAGGAGTGGTAATGCGTGACATCCA  >  minE/1294361‑1294488

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