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 2,816,585 C→A 34.0% P81P (CCC→CCA)  soxR → DNA‑binding transcriptional dual regulator, Fe‑S center for redox‑sensing

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,816,5850CA34.0% 148.8 / 89.0 129P81P (CCC→CCA) soxRDNA‑binding transcriptional dual regulator, Fe‑S center for redox‑sensing
Reads supporting (aligned to +/- strand):  ref base C (37/48);  new base A (25/19);  total (62/67)
Fisher's exact test for biased strand distribution p-value = 1.94e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 2.47e-02

Only 100 of 130 total aligned reads displayed.

TTATCAAAATTGCTCAGCGTATTGGCATTCCGCTGGCGACCATTGGTGAAGCGTTTGGCGTGTTGCCCGAAGGGCATACGTTAAGTGCGAAAGAGTGGAAACAGCTTTCGTCCCAATGGCGAGAAGAGTTGG  >  minE/2816518‑2816649
                                                                   |                                                                
ttATCAAAATTGCTCAGCGTATTGGCATTCCGCTGGCGACCATTGGTGAAGCGTTTGGCGTGTTGccct                                                                 <  1:798039/69‑2 (MQ=255)
ttATCAAAATTGCTCAGCGTATTGGCATTCCGCTGGCGACCATTGGTGAAGCGTTTGGCGTGTTGCCCg                                                                 <  1:926451/69‑1 (MQ=255)
ttATCAAAATTGCTCAGCGTATTGGCATTCCGCTGGCGACCATTGGTGAAGCGTTTGGCGTGTTGCCCg                                                                 <  1:1681349/69‑1 (MQ=255)
ttATCAAAATTGCTCAGCGTATTGGCATTCCGCTGGCGACCATTGGTGAAGCGTTTGGCGTGTTGCCCg                                                                 <  1:3149205/69‑1 (MQ=255)
ttATCAAAATTGCTCAGCGTATTGGCATTCCGCTGGCGACCATTGGTGAAGCGTTTGGCGTGTTGCCCg                                                                 <  1:2767766/69‑1 (MQ=255)
ttATCAAAATTGCTCAGCGTATTGGCATTCCGCTGGCGACCATTGGTGAAGCGTTTGGCGTGTTGCCCg                                                                 <  1:3360676/69‑1 (MQ=255)
ttATCAAAATTGCTCAGCGTATTGGCATTCCGCTGGCGACCATTGGTGAAGCGTTTGGCGTGTTGCCCg                                                                 <  1:1936821/69‑1 (MQ=255)
ttATCAAAATTGCTCAGCGTATTGGCATTCCGCTGGCGACCATTGGTGAAGCGTTTGGCGTGTTGCCCg                                                                 <  1:1943523/69‑1 (MQ=255)
ttATCAAAATTGCTCAGCGTATTGGCATTCCGCTGGCGACCATTGGTGAAGCGTTTGGCGTGTTGCCCg                                                                 <  1:2756331/69‑1 (MQ=255)
ttATCAAAATTGCTCAGCGTATTGGCATTCCGCTGGCGACCATTGGTGAAGCGTTTGGCGTGTTGCCCg                                                                 <  1:493999/69‑1 (MQ=255)
ttATCAAAATTGCTCAGCGTATTGGCATTCCGCTGGCGACCATTGGTGAAGCGTTTGGCGTGTTGCCCg                                                                 <  1:2081420/69‑1 (MQ=255)
ttATCAAAATTGCTCAGCGTATTGGCATTCCGCTGGCGACCATTGGTGAAGCGTTTGGCGTGTTGCCCg                                                                 <  1:2206613/69‑1 (MQ=255)
ttATCAAAATTGCTCAGCGTATTGGCATTCCGCTGGCGACCATTGGTGAAGCGTTTGGCGTGTTGCCCg                                                                 <  1:719858/69‑1 (MQ=255)
ttATCAAAATTGCTCAGCGTATTGGCATTCCGCTGGCGACCATTGGTGAAGCGTTTGGCGTGTTGCCCg                                                                 <  1:742553/69‑1 (MQ=255)
ttATCAAAATTGCTCAGCGTATTGGCATTCCGCTGGCGACCATTGGTGAAGCGTTTGGCGTGTTGCCCg                                                                 <  1:798020/69‑1 (MQ=255)
ttATCAAAATTGCTCAGCGTATTGGCATTCCGCTGGCGACCATTGGTGAAGCGTTTGGCGTGTTGCCCg                                                                 <  1:1032589/69‑1 (MQ=255)
 tATCAAAATTGCTCAGCGTATTGGCATTCCGCTGGCGACCATTGGTGAAGCGTTTGGCGTGTTGCCCg                                                                 <  1:2375737/68‑1 (MQ=255)
       aaTTGCTCAGCGTATTGGCATTCCGCTGGCGACCATTGGTGAAGCGTTTGGCGTGTTGCCCGAAGGGCa                                                          <  1:2136370/69‑1 (MQ=255)
       aaTTGCTCAGCGTATTGGCATTCCGCTGGCGACCATTGGTGAAGCGTTTGGCGTGTTGCCCGAAGGGCa                                                          <  1:2629852/69‑1 (MQ=255)
       aaTTGCTCAGCGTATTGGCATTCCGCTGGCGACCATTGGTGAAGCGTTTGGCGTGTTGCCCGAAGGGCa                                                          <  1:1166214/69‑1 (MQ=255)
                     ttGGCATTCCGCTCGCAACCATTCGTGAAGCGTTTTGCGTGTTGCCAGAAGGGCATACGTTAAGTGCGa                                            <  1:2474811/69‑1 (MQ=255)
                     ttGGCATTCCGCTCGCAACCATTCGTGAAGCGTTTGGCGTGTTGCCAGAAGGGCATACGTTAAGTGCGa                                            <  1:2100571/69‑1 (MQ=255)
                     ttGGCATTCCGCTCGCAACCATTCGTGAAGCGTTTGGCGTGTTGCCAGAAGGGCATACGTTAAGTGCGa                                            <  1:2448765/69‑1 (MQ=255)
                     ttGGCATTCCGCTCGCAACCATTCGTGAAGCGTTTGGCGTGTTGCCAGAAGGGCATACGTTAAGTGCGa                                            <  1:2781181/69‑1 (MQ=255)
                     ttGGCATTCCGCTCGCAACCATTCGTGAAGCGTTTGGCGTGTTGCCAGAAGGGCATACGTTAAGTGCGa                                            <  1:2330365/69‑1 (MQ=255)
                     ttGGCATTCCGCTCGCAACCATTCGTGAAGCGTTTGGCGTGTTGCCAGAAGGGCATACGTTAAGTGCGa                                            <  1:3017266/69‑1 (MQ=255)
                     ttGGCATTCCGCTCGCAACCATTCGTGAAGCGTTTGGCGTGTTGCCAGAAGGGCATACGTTAAGTGCGa                                            <  1:389300/69‑1 (MQ=255)
                     ttGGCATTCCGCTCGCAACCATTCGTGAAGCGTTTGGCGTGTTGCCAGAAGGGCATACGTTAAGTGCGa                                            <  1:1451770/69‑1 (MQ=255)
                     ttGGCATTCCGCTCGCAACCATTCGTGAAGCGTTTGGCGTGTTGCCAGAAGGGCATACGTTAAGTGCGa                                            <  1:1628997/69‑1 (MQ=255)
                     ttGGCATTCCGCTCGCAACCATTCGTGAAGCGTTTGGCGTGTTGCCAGAAGGGCATACGTTAAGTGCGa                                            <  1:559051/69‑1 (MQ=255)
                     ttGGCATTCCGCTCGCAACCATTCGTGAAGCGTTTGGCGTGTTGCCAGAAGGGCAAACGTTAAGTGCGa                                            <  1:3035956/69‑1 (MQ=255)
                     attgCATTCCGCTCGCAACCATTCGTGAAGCGTTTGGCGTGTTGCCAGAAGGGCATACGTTAAGTGCGa                                            <  1:164504/66‑1 (MQ=255)
                      tGGCATTCCGCTCGCAACCATTCGTGAAGCGTTTGGCGTGTTGCCAGAAGGGCATACGTTAAGTGCGa                                            <  1:1304045/68‑1 (MQ=255)
                      tGGCATTCCGCTCGCAACCATTCGTGAAGCGTTTGGCGTGTTGCCAGAAGGGCATACGTTAAGTGCGa                                            <  1:1338610/68‑1 (MQ=255)
                         cATTCCGCTGGCGACCATTGGTGAAGCGTTTGGCGTGTTGCCCg                                                                 <  1:1284860/44‑1 (MQ=255)
                         cATTCCGCTGGCGACCATTGGTGAAGCGTTTGGCGTGTTGCCCGAAGGGCATACGTTAAGTGCGAAag                                         <  1:273465/68‑1 (MQ=255)
                         cATTCCGCTGGCGACCATTGGTGAAGCGTTTGGCGTGTTGCCCGAAGGGCATACGTTAAGTGCGAAag                                         <  1:1102852/68‑1 (MQ=255)
                         cATTCCGCTGGCGACCATTGGTGAAGCGTTTGGCGTGTTGCCCGAAGGGCATACGTTAAGTGCGAAag                                         <  1:848364/68‑1 (MQ=255)
                         cATTCCGCTGGCGACCATTGGTGAAGCGTTTGGCGTGTTGCCCGAAGGGCATACGTTAAGTGCGAAag                                         <  1:1325157/68‑1 (MQ=255)
                         cATTCCGCTGGCGACCATTGGTGAAGCGTTTGGCGTGTTGCCCGAAGGGCATACGTTAAGTGCGAAag                                         <  1:2870671/68‑1 (MQ=255)
                          aTTCCGCTGGCGACCATTGGTTAAGCGTTTGGCGTGTTGCCCGAAGGGCATACGTTAAGTGCGAAagag                                       >  1:666309/1‑69 (MQ=255)
                          aTTCCGCTGGCGACCATTGGTGAAGCGTTTGGCGTGTTGCCCGAAGGGCATACGTTAAGTGCGAAagag                                       >  1:3416723/1‑69 (MQ=255)
                          aTTCCGCTGGCGACCATTGGTGAAGCGTTTGGCGTGTTGCCCGAAGGGCATACGTTAAGTGCGAAagag                                       >  1:706662/1‑69 (MQ=255)
                          aTTCCGCTGGCGACCATTGGTGAAGCGTTTGGCGTGTTGCCCGAAGGGCATACGTTAAGTGCGAAagag                                       >  1:3179089/1‑69 (MQ=255)
                            tCCGCTGGCGACCATTGGTGAAGCGTTTGGCGTGTTGCCCGAAGGGCATACGTTAAGTGCGAAAGAGt                                      >  1:2993096/1‑68 (MQ=255)
                            tCCGCTGGCGACCATTGGTGAAGCGTTTGGCGTGTTGCCCGAAGGGCATACGTTAAGTGCGAAAGAGt                                      >  1:2384717/1‑68 (MQ=255)
                             ccGCTGGCGACCATTGGTGAAGCGTTTGGCGTGTTGCCCGAAGGGCATACGtt                                                    >  1:235201/1‑53 (MQ=255)
                             ccGCTGGCGACCATTGGTGAAGCGTTTGGCGTGTTGCCCGAAGGGCATACGtt                                                    >  1:1734893/1‑53 (MQ=255)
                             ccGCTGGCGACCATTGGTGAAGCGTTTGGCGTGTTGCCCGAAGGGCATACGtt                                                    >  1:2239411/1‑53 (MQ=255)
                             ccGCTGGCGACCATTGGTGAAGCGTTTGGCGTGTTGCCCGAAGGGCATACGtt                                                    >  1:2525171/1‑53 (MQ=255)
                             ccGCTGGCGACCATTGGTGAAGCGTTTGGCGTGTTGCCCGAAGGGCATACGtt                                                    >  1:2104084/1‑53 (MQ=255)
                             ccGCTGGCGACCATTGGTGAAGCGTTTGGCGTGTTGCCCGAAGGGCATACGTTAAGTGCGAAAGAGTg                                     >  1:3109925/1‑68 (MQ=255)
                             ccGCTGGCGACCATTGGTGAAGCGTTTGGCGTGTTGCCCGAAGGGCATACGTTAAGTGCGAAAGAGTg                                     >  1:2958212/1‑68 (MQ=255)
                             ccGCTGGCGACCATTGGTGAAGCGTTTGGCGTGTTGCCCGAAGGGCATACGTTAAGTGCGAAAGAGTg                                     >  1:2849945/1‑68 (MQ=255)
                             ccGCTGGCGACCATTGGTGAAGCGTTTGGCGTGTTGCCCGAAGGGCATACGTTAAGTGCGAAAGAGTg                                     >  1:1490998/1‑68 (MQ=255)
                             ccGCTGGCGACCATTGGTGAAGCGTTTGGCGTGTTGCCCGAAGGGCATACGTTAAGTGCGAAAGAGTg                                     >  1:1489265/1‑68 (MQ=255)
                             ccGCTGGCGACCATTGGTGAAGCGTTTGGCGTGTTGCCCGAAGGGCATACGTTAAGTGCGAAAGAGTg                                     >  1:3322117/1‑68 (MQ=255)
                             ccGCTGGCGACCATTGGTGAAGCGTTTGGCGTGTTGCCCGAAGGGCATACGTTAAGTGCGAAAGAGTg                                     >  1:2746331/1‑68 (MQ=255)
                             ccGCTGGCGACCATTGGTGAAGCGTTTGGCGTGTTGCCCGAAGGGCATACGTTAAGTGCGAAAGAGTg                                     >  1:2729382/1‑68 (MQ=255)
                             ccGCTGGCGACCATTGGTGAAGCGTTTGGCGTGTTGCCCGAAGGGCATACGTTAAGTGCGAAAGAGTg                                     >  1:3390260/1‑68 (MQ=255)
                             ccGCTGGCGACCATTGGTGAAGCGTTTGGCGTGTTGCCCGAAGGGCATACGTTAAGTGCGAAAGAGTg                                     >  1:1470193/1‑68 (MQ=255)
                             ccGCTGGCGACCATTGGTGAAGCGTTTGGCGTGTTGCCCGAAGGGCATACGTTAAGTGCGAAAGAGTg                                     >  1:1415849/1‑68 (MQ=255)
                             ccGCTGGCGACCATTGGTGAAGCGTTTGGCGTGTTGCCCGAAGGGCATACGTTAAGTGCGAAAGAGTg                                     >  1:1158771/1‑68 (MQ=255)
                             ccGCTGGCGACCATTGGTGAAGCGTTTGGCGTGTTGCCCGAAGGGCATACGTTAAGTGCGAAAGAGTg                                     >  1:1128475/1‑68 (MQ=255)
                             ccGCTGGCGACCATTGGTGAAGCGTTTGGCGTGTTGCCCGAAGGGCATACGTTAAGTGCGAAAGAGTg                                     >  1:845242/1‑68 (MQ=255)
                             ccGCTGGCGACCATTGGTGAAGCGTTTGGCGTGTTGCCCGAAGGGCATACGTTAAGTGCGAAAGAGTg                                     >  1:2374068/1‑68 (MQ=255)
                                               gAAGCGTTTGGCGTGTTGCCCGAAGGGCATACGTTAAGTGCGAAAGAGTGGAAACAGCTTTCGTCCCaa                  >  1:1557562/1‑69 (MQ=255)
                                                aaGCGTTTGGCGTGTTGCCAGAAGGGCATACGTTAAGTGCGa                                            <  1:332739/42‑1 (MQ=255)
                                                aaGCGTTTGGCGTGTTGCCAGAAGGGCATACGTTAAGTGCGAAAGAGt                                      >  1:3125038/1‑48 (MQ=255)
                                                aaGCGTTTGGCGTGTTGCCAGAAGGGCATACGTTAAGTGCGAAAGAGTGGAAACAGCTTTCGTccc                    >  1:2369278/1‑66 (MQ=255)
                                                aaGCGTTTGGCGTGTTGCCAGAAGGGCATACGTTAAGTGCGAAAGAGTGGAAACAGCTTTCGTCCCaa                  >  1:1110361/1‑68 (MQ=255)
                                                aaGCGTTTGGCGTGTTGCCAGAAGGGCATACGTTAAGTGCGAAAGAGTGGAAACAGCTTTCGTCCCaa                  >  1:677508/1‑68 (MQ=255)
                                                aaGCGTTTGGCGTGTTGCCAGAAGGGCATACGTTAAGTGCGAAAGAGTGGAAACAGCTTTCGTCCCAAt                 >  1:1294724/1‑69 (MQ=255)
                                                aaGCGTTTGGCGTGTTGCCAGAAGGGCATACGTTAAGTGCGAAAGAGTGGAAACAGCTTTCGTCCCAAt                 >  1:2323263/1‑69 (MQ=255)
                                                aaGCGTTTGGCGTGTTGCCAGAAGGGCATACGTTAAGTGCGAAAGAGTGGAAACAGCTTTCGTCCCAAt                 >  1:317927/1‑69 (MQ=255)
                                                aaGCGTTTGGCGTGTTGCCAGAAGGGCATACGTTAAGTGCGAAAGAGTGGAAACAGCTTTCGTCCCAAt                 >  1:3201774/1‑69 (MQ=255)
                                                aaGCGTTTGGCGTGTTGCCAGAAGGGCATACGTTAAGTGCGAAAGAGTGGAAACAGCTTTCGTCCCAAt                 >  1:3268746/1‑69 (MQ=255)
                                                aaGCGTTTGGCGTGTTGCCAGAAGGGCATACGTTAAGTGCGAAAGAGTGGAAACAGCTTTCGTCCCAAt                 >  1:2013236/1‑69 (MQ=255)
                                                aaGCGTTTGGCGTGTTGCCAGAAGGGCATACGTTAAGTGCGAAAGAGTGGAAACAGCTTTCGTCCCAAt                 >  1:1409512/1‑69 (MQ=255)
                                                aaGCGTTTGGCGTGTTGCCAGAAGGGCATACGTTAAGTGCGAAAGAGTGGAAACAGCTTTCGTCCCAAt                 >  1:3349528/1‑69 (MQ=255)
                                                aaGCGTTTGGCGTGTTGCCAGAAGGGCATACGTTAAGTGCGAAAGAGTGGAAACAGCTTTCGTCCCAAt                 >  1:1483544/1‑69 (MQ=255)
                                                aaGCGTTTGGCGTGTTGCCAGAAGGGCATACGTTAAGTGCGAAAGAGTGGAAACAGCTTTCGTCCCAAt                 >  1:126244/1‑69 (MQ=255)
                                                aaGCGTTTGGCGTGTTGCCAGAAGGGCATACGTTAAGTGCGAAAGAGTGGAAACAGCTTTCGTCCCAAt                 >  1:218984/1‑69 (MQ=255)
                                                aaGCGTTTGGCGTGTTGCCAGAAGGGCATACGTTAAGTGCGAAAGAGTGGAAACAGCTTTCGTCCCAAt                 >  1:1216933/1‑69 (MQ=255)
                                                aaGCGTTTGGCGTGTTGCCAGAAGGGCATACGTTAAGTGCGAAAGAGTGGAAACAGCTTTCGTCCCAAt                 >  1:468921/1‑69 (MQ=255)
                                                aaGCGTTTGGCCTGTTGCCAGAAGGGCATACGTTAAGTGCGAAAGAGTGGAAACAGCTTTCGTCCCAAt                 >  1:716418/1‑69 (MQ=255)
                                                 aGCGTTTGGCGTGTTGCCCGAAGGGCATACGTTAAGTGCGAAAGAGTGGAAACAGCTTTCGTCCCAATg                >  1:2705584/1‑69 (MQ=255)
                                                 aGCGTTTGGCGTGTTGCCCGAAGGGCATACGTTAAGTGCGAAAGAGTGGAAACAGCTTTCGTCCCAATg                >  1:1415457/1‑69 (MQ=255)
                                                 aGCGTTTGGCGTGTTGCCCGAAGGGCATACGTTAAGTGCGAAAGAGTGGAAACAGCTTTCGTCCCAATg                >  1:2404116/1‑69 (MQ=255)
                                                 aGCGTTTGGCGTGTTGCCCGAAGGGCATACGTTAAGTGCGAAAGAGTGGAAACAGCTTTCGTCCCAATg                >  1:1919047/1‑69 (MQ=255)
                                                 aGCGTTTGGCGTGTTGCCCGAAGGGCATACGTTAAGTGCGAAAGAGTGGAAACAGCTTTCGTCCCAATg                >  1:1521502/1‑69 (MQ=255)
                                                         gCGTGTTGCCCGAAGGGCATACGTTAAGTGCGAAag                                         <  1:1079073/36‑1 (MQ=255)
                                                                gCCCGAAGGGCATACGTTAAGTTCGAAAGAGTGGAAACAGCTTTCGTCCCAATGGCGAGAAGAGTTgg  <  1:786566/68‑1 (MQ=255)
                                                                gCCCGAAGGGCATACGTTAAGTGCGAAAGAGTGGAAACAGCTTTCGTCCCAATGGCGAGAAGAGTTgg  <  1:2110589/68‑1 (MQ=255)
                                                                gCCCGAAGGGCATACGTTAAGTGCGAAAGAGTGGAAACAGCTTTCGTCCCAATGGCGAGAAGAGTTgg  <  1:1466417/68‑1 (MQ=255)
                                                                gCCCGAAGGGCATACGTTAAGTGCGAAAGAGTGGAAACAGCTTTCGTCCCAATGGCGAGAAGAGTTgg  <  1:2584508/68‑1 (MQ=255)
                                                                gCCCGAAGGGCATACGTTAAGTGCGAAAGAGTGGAAACAGCTTTCGTCCCAATGGCGAGAAGAGTTgg  <  1:2064342/68‑1 (MQ=255)
                                                                gCCCGAAGGGCATACGTTAAGTGCGAAAGAGTGGAAACAGCTTTCGTCCCAATGGCGAGAAGAGTTgg  <  1:1894460/68‑1 (MQ=255)
                                                                gCCCGAAGGGCATACGTTAAGTGCGAAAGAGTGGAAACAGCTTTCGTCCCAATGGCGAGAAGAGTTgg  <  1:1720466/68‑1 (MQ=255)
                                                                gCCCGAAGGGCATACGTTAAGTGCGAAAGAGTGGAAACAGCTTTCGTCCCAATGGCGAGAAGAGTTgg  <  1:3116116/68‑1 (MQ=255)
                                                                   |                                                                
TTATCAAAATTGCTCAGCGTATTGGCATTCCGCTGGCGACCATTGGTGAAGCGTTTGGCGTGTTGCCCGAAGGGCATACGTTAAGTGCGAAAGAGTGGAAACAGCTTTCGTCCCAATGGCGAGAAGAGTTGG  >  minE/2816518‑2816649

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