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 2,908,139 T→C 50.0% K164K (AAA→AAG)  treR ← DNA‑binding transcriptional repressor

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,908,1390TC50.0% ‑4.6 / 118.1 124K164K (AAA→AAG) treRDNA‑binding transcriptional repressor
Reads supporting (aligned to +/- strand):  ref base T (41/21);  new base C (30/32);  total (71/53)
Fisher's exact test for biased strand distribution p-value = 6.90e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

Only 100 of 125 total aligned reads displayed.

ACTGTGCGGCACGCCGAGATAACTGATATTACGATGCCCCTGGTCATACAGCCGTTGCATCAGGATTTTGATTGCCCCTTCGTCGTCATAACAGACCGAAGCAAAGCCTTTTGCGTCACGCGCCAGCAGAACCA  >  minE/2908073‑2908206
                                                                  |                                                                   
acTGTGCGGCACGCCGAGATAACTGATATTACGATG‑CCCTGGTCATACAGCCGTTGCATCAGGATTTTg                                                                  <  1:1756849/69‑1 (MQ=255)
  tgtgCGGCACGCCGAGATAACTGATATTACGATGCCCCTGGTCATACAGCCGTTGCATCAGGATTTTg                                                                  <  1:3178469/68‑1 (MQ=255)
  tgtgCGGCACGCCGAGATAACTGATATTACGATGCCCCTGGTCATACAGCCGTTGCATCAGGATTTTg                                                                  <  1:2063819/68‑1 (MQ=255)
  tgtgCGGCACGCCGAGATAACTGATATTACGATGCCCCTGGTCATACAGCCGTTGCATCAGGATTTTg                                                                  <  1:3257506/68‑1 (MQ=255)
  tgtgCGGCACGCCGAGATAACTGATATTACGATGCCCCTGGTCATACAGCCGTTGCATCAGGATTTTg                                                                  <  1:3207121/68‑1 (MQ=255)
          aagCCGAGATAGCTGATATTACGATGTCCCTGGTCATACAGCCGTTGCATCAGGATCTTGATTGCCCCt                                                         >  1:1030996/3‑69 (MQ=255)
          aCGCCGAGATAGGTGATATTACGATGTCCCTGGTCATACAGCCGTTGCATCAGGATCTTGATTGCCCCt                                                         >  1:2196456/1‑69 (MQ=255)
          aCGCCGAGATAGCTGATATTACGATGTCCCTGGTCATACAGCCGTTGCATCAGGATCTTGATTGCCCCt                                                         >  1:740528/1‑69 (MQ=255)
          aCGCCGAGATAGCTGATATTACGATGTCCCTGGTCATACAGCCGTTGCATCAGGATCTTGATTGCCCCt                                                         >  1:3228526/1‑69 (MQ=255)
          aCGCCGAGATAGCTGATATTACGATGTCCCTGGTCATACAGCCGTTGCATCAGGATCTTGATTGCCCCt                                                         >  1:29793/1‑69 (MQ=255)
          aCGCCGAGATAGCTGATATTACGATGTCCCTGGTCATACAGCCGTTGCATCAGGATCTTGATTGCCCCt                                                         >  1:1224592/1‑69 (MQ=255)
          aCGCCGAGATAGCTGATATTACGATGTCCCTGGTCATACAGCCGTTGCATCAGGATCTTGATTGCCCCt                                                         >  1:2686897/1‑69 (MQ=255)
          aCGCCGAGATAGCTGATATTACGATGTCCCTGGTCATACAGCCGTTGCATCAGGATCTTGATTGCCCCt                                                         >  1:2602683/1‑69 (MQ=255)
          aCGCCGAGATAGCTGATATTACGATGTCCCTGGTCATACAGCCGTTGCATCAGGATCTTGATTGCCCCt                                                         >  1:250545/1‑69 (MQ=255)
          aCGCCGAGATAGCTGATATTACGATGTCCCTGGTCATACAGCCGTTGCATCAGGATCTTGATTGCCCCt                                                         >  1:2341900/1‑69 (MQ=255)
          aCGCCGAGATAGCTGATATTACGATGTCCCTGGTCATACAGCCGTTGCATCAGGATCTTGATTGCCCCt                                                         >  1:1458577/1‑69 (MQ=255)
          aCGCCGAGATAGCTGATATTACGATGTCCCTGGTCATACAGCCGTTGCATCAGGATCTTGATTGCCCCt                                                         >  1:2164532/1‑69 (MQ=255)
          aCGCCGAGATAGCTGATATTACGATGTCCCTGGTCATACAGCCGTTGCATCAGGATCTTGATTGCCCCt                                                         >  1:1597034/1‑69 (MQ=255)
          aCGCCGAGATAGCTGATATTACGATGTCCCTGGTCATACAGCCGTTGCATCAGGATCTTGATTGCCACt                                                         >  1:823466/1‑69 (MQ=255)
          aCGCCGAGATAGCTGATATTACGATGTCCCTGGTCATACAGCCGATGCATCAGGATCTTGATTGCCCCt                                                         >  1:2515056/1‑69 (MQ=255)
          aCGCCGAGATAGCCGATATTACGATGTCCCTGGTCATACAGCCGTTGCATCAGGATCTTGATTGCCCCt                                                         >  1:445306/1‑69 (MQ=255)
          aCGCCGAGATAACTGATATTACGATGCCCCTGGTCATACAGCCGTTGCATCAGGATTTTg                                                                  >  1:261586/1‑60 (MQ=255)
          aCGCCGAGATAACTGATATTACGATGCCCCTGGTCATACAGCCGTTGCATCAGGATTTTGATTGCCCCt                                                         >  1:460161/1‑69 (MQ=255)
          aCGCCGAGATAACTGATATTACGATGCCCCTGGTCATACAGCCGTTGCATCAGGATTTTGATTGCCCCt                                                         >  1:399885/1‑69 (MQ=255)
          aCGCCGAGATAACTGATATTACGATGCCCCTGGTCATACAGCCGTTGCATCAGGATTTTGATTGCCCCt                                                         >  1:2273217/1‑69 (MQ=255)
          aCGCCGAGATAACTGATATTACGATGCCCCTGGTCATACAGCCGTTGCATCAGGATTTTGATTGCCCCt                                                         >  1:1319195/1‑69 (MQ=255)
          aCGCCGAGATAACTGATATTACGATGCCCCTGGTCATACAGCCGTTGCATCAGGATTTTGATTGCCCCt                                                         >  1:2622180/1‑69 (MQ=255)
          aCGCCGAGATAACTGATATTACGATGCCCCTGGTCATACAGCCGTTGCATCAGGATTTTGATTGCCCCt                                                         >  1:1178214/1‑69 (MQ=255)
          aCGCCGAGATAACTGATATTACGATGCCCCTGGTCATACAGCCGTTGCATCAGGATTTTGATTGCCCCt                                                         >  1:334014/1‑69 (MQ=255)
          aCGCCGAGATAACTGATATTACGATGCCCCTGGTCATACAGCCGTTGCATCAGGATTTTGATTGCCCCt                                                         >  1:2045773/1‑69 (MQ=255)
          aCGCCGAGATAACTGATATTACGATGCCCCTGGTCATACAGCCGTTGCATCAGGATTTTGATTGCCCCt                                                         >  1:2910743/1‑69 (MQ=255)
          aCGCCGAGATAACTGATATTACGATGCCCCTGGTCATACAGCCGTTGCATCAGGATTTTGATTGCCCCt                                                         >  1:76710/1‑69 (MQ=255)
          aCGCCGAGATAACTGATATTACGATGCCCCTGGTCATACAGCCGTTGCATCAGGATTTTGATTGCCCCt                                                         >  1:1076738/1‑69 (MQ=255)
          aCGCCGAGATAACTGATATTACGATGCCCCTGGTCATACAGCCGTTGCATCAGGATTTTGATTGCCCCt                                                         >  1:1862027/1‑69 (MQ=255)
          aCGCCGAGATAACTGATATTACGATGCCCCTGGTCATACAGCCGTTGCATCAGGATTTTGATTGCCCCt                                                         >  1:1379940/1‑69 (MQ=255)
          aCGCCGAGATAACTGATATTACGATGCCCCTGGTCATACAGCCGTTGCATCAGGATTTTGATTGCCCCt                                                         >  1:1805378/1‑69 (MQ=255)
          aCGCCGAGATAACTGATATTACGATGCCCCTGGTCATACAGCCGTTGCATCAGGATTTTGATTGCCCCt                                                         >  1:1675246/1‑69 (MQ=255)
          aCGCCGAGATAACTGATATTACGATGCCCCTGGTCATACAGCCGTTGCATCAGGATTTTGATTGCCCCt                                                         >  1:2472591/1‑69 (MQ=255)
          aCGCAGAGATAGCTGATATTACGATGTCCCTGGTCATACAGCCGTTGCATCAGGATCTTGATTGccc                                                           >  1:1722214/1‑67 (MQ=255)
                     aCTGATATTACGATGCCCCTGGTCATACAGCCGTTGCATCAGGATTTTGATTGCCCCTTCGTCGTCa                                                >  1:287365/1‑67 (MQ=255)
                     aCTGATATTACGATGCCCCTGGTCATACAGCCGTTGCATCAGGATTTTGATTGCCCCTTCGTCGTCAt                                               >  1:435710/1‑68 (MQ=255)
                              aCGATGCCCCTGGTCATACAGCCGTTGCATCAGGATTTTGATTGCCCCTTCgtcgtc                                                 <  1:313126/57‑1 (MQ=255)
                              aCGATGCCCCTGGTCATACAGCCGTTGCATCAGGATTTTGATTGCCCCTTCgtcgtc                                                 <  1:693097/57‑1 (MQ=255)
                                    tcccTGGTCATACAGCCGTTGCATCAGGATCTTGATTGCCCCTTCGTCGTCATAACAGACCGAAGCaaa                               <  1:47519/68‑1 (MQ=255)
                                    tcccTGGTCATACAGCCGTTGCATCAGGATCTTGATTGCCCCTTCGTCGTCATAACAGACCGAAGCaaa                               <  1:2417114/68‑1 (MQ=255)
                                    tcccTGGTCATACAGCCGTTGCATCAGGATCTTGATTGCCCCTTCGTCGTCATAACAGACCGAAGCaaa                               <  1:2944379/68‑1 (MQ=255)
                                    tcccTGGTCATACAGCCGTTGCATCAGGATCTTGATTGCCCCTTCGTCGTCATAACAGACCGAAGCaaa                               <  1:1592960/68‑1 (MQ=255)
                                    tcccTGGTCATACAGCCGTTGCATCAGGATCTTGATTGCCCCTTCGTCGTCATAACAGACCGAAGCaaa                               <  1:1192651/68‑1 (MQ=255)
                                    tcccTGGTCATACAGCCGTTGCATCAGGATCTTGATTGCCCCTTCGTCGTCATAACAGACCGAAGCaaa                               <  1:1531092/68‑1 (MQ=255)
                                    tcccTGGTCATACAGCCGTTGCATCAGGATCTTGATTGCCCCTTCGTCGTCATAACAGACCGAAGCaaa                               <  1:437165/68‑1 (MQ=255)
                                          gTCATACAGCCGTTGCATCAGGATTTTGATTGCCCCTTCGTCGTCAt                                               <  1:661233/47‑1 (MQ=255)
                                          gTCATACAGCCGTTGCATCAGGATTTTGATTGCCCCTTCGTCGTCAt                                               <  1:193021/47‑1 (MQ=255)
                                          gTCATACAGCCGTTGCATCAGGATTTTGATTGCCCCTTCGTCGTCAt                                               <  1:2653904/47‑1 (MQ=255)
                                          gTCATACAGCCGTTGCATCAGGATTTTGATTGCCCCTTCGTCGTCAt                                               <  1:1487548/47‑1 (MQ=255)
                                          gTCATACAGCCGTTGCATCAGGATTTTGATTGCCCCTTCGTCGTCAt                                               <  1:723136/47‑1 (MQ=255)
                                          gTCATACAGCCGTTGCATCAGGATTTTGATTGCCCCTTCGTCGTCAt                                               <  1:1425579/47‑1 (MQ=255)
                                          gTCATACAGCCGTTGCATCAGGATTTTGATTGCCCCTTCGTCGTCAt                                               <  1:2361695/47‑1 (MQ=255)
                                          gTCATACAGCCGTTGCATCAGGATTTTGATTGCCCCTTCGTCGTCAt                                               <  1:2435167/47‑1 (MQ=255)
                                          gTCATACAGCCGTTGCATCAGGATTTTGATTGCCCCTTCGTCGTCAt                                               <  1:2393976/47‑1 (MQ=255)
                                                cAGCCGTTGCATCAGGATTTTGATTGCCCCTTCGTCGTCATAACAGACCGAAGCAAAGc                             >  1:510892/1‑59 (MQ=255)
                                                cAGCCGTTGCATCAGGATTTTGATTGCCCCTTCGTCGTCATAACAGACCGAAGCAAAGCCTTTTGCGTc                   >  1:3281962/1‑69 (MQ=255)
                                                cAGCCGTTGCATCAGGATTTTGATTGCCCCTTCGTCGTCATAACAGACCGAAGCAAAGCCTTTTGCGTc                   >  1:394358/1‑69 (MQ=255)
                                                cAGCCGTTGCATCAGGATTTTGATTGCCCCTTCGTCGTCATAACAGACCGAAGCAAAGCCTTTTGCGTc                   >  1:73994/1‑69 (MQ=255)
                                                cAGCCGTTGCATCAGGATTTTGATTGCCCCTTCGTCGTCATAACAGACCGAAGCAAAGCCTTTTGCGTc                   >  1:934629/1‑69 (MQ=255)
                                                cAGCCGTTGCATCAGGATTTTGATTGCCCCTTCGTCGTCATAACAGACCGAAGCAAAGCCTTTTGCGTc                   >  1:919945/1‑69 (MQ=255)
                                                cAGCCGTTGCATCAGGATTTTGATTGCCCCTTCGTCGTCATAACAGACCGAAGCAAAGCCTTTTGCGTc                   >  1:38939/1‑69 (MQ=255)
                                                cAGCCGTTGCATCAGGATTTTGATTGCCCCTTCGTCGTCATAACAGACCGAAGCAAAGCCTTTTGCGTc                   >  1:3066765/1‑69 (MQ=255)
                                                cAGCCGTTGCATCAGGATTTTGATTGCCCCTTCGTCGTCATAACAGACCGAAGCAAAGCCTTTTGCGTc                   >  1:1967556/1‑69 (MQ=255)
                                                cAGCCGTTGCATCAGGATTTTGATTGCCCCTTCGTCGTCATAACAGACCGAAGCAAAGCCTTTTGCGTc                   >  1:2266355/1‑69 (MQ=255)
                                                cAGCCGTTGCATCAGGATTTTGATTGCCCCTTCGTCGTCATAACAGACCGAAGCAAAGCCTTTTGCGTc                   >  1:2283985/1‑69 (MQ=255)
                                                cAGCCGTTGCATCAGGATTTTGATTGCCCCTTCGTCGTCATAACAGACCGAAGCAAAGCCTTTTGCGTc                   >  1:1819408/1‑69 (MQ=255)
                                                cAGCCGTTGCATCAGGATTTTGATTGCCCCTTCGTCGTCATAACAGACCGAAGCAAAGCCTTTTGCGTc                   >  1:1141864/1‑69 (MQ=255)
                                                            cAGGATTTTGATTGCCCCTTCGTCGTCATAACAGACCGAAGCAAAGCCTTTTGCGTCACGCGCcagcag       <  1:2753508/69‑1 (MQ=255)
                                                            cAGGATTTTGATTGCCCCTTCGTCGTCATAACAGACCGAAGCAAAGCCTTTTGCGTCACGCGCcagcag       <  1:2329997/69‑1 (MQ=255)
                                                            cAGGATCTTGATTGCCCCTTCGTCGTCATAACAGACCGa                                     <  1:797446/39‑1 (MQ=255)
                                                            cAGGATCTTGATTGCCCCTTCGTCGTCATAACAGACCGa                                     <  1:1121910/39‑1 (MQ=255)
                                                            cAGGATCTTGATTGCCCCTTCGTCGTCATAACAGACCGa                                     <  1:1033882/39‑1 (MQ=255)
                                                            cAGGATCTTGATTGCCCCTTCGTCGTCATAACAGACCGa                                     <  1:1369026/39‑1 (MQ=255)
                                                            cAGGATCTTGATTGCCCCTTCGTCGTCATAACAGACCGa                                     <  1:1744395/39‑1 (MQ=255)
                                                            cAGGATCTTGATTGCCCCTTCGTCGTCATAACAGACCGa                                     <  1:1033145/39‑1 (MQ=255)
                                                            cAGGATCTTGATTGCCCCTTCGTCGTCATAACAGACCGa                                     <  1:1868191/39‑1 (MQ=255)
                                                            cAGGATCTTGATTGCCCCTTCGTCGTCATAACAGACCGa                                     <  1:1915499/39‑1 (MQ=255)
                                                            cAGGATCTTGATTGCCCCTTCGTCGTCATAACAGACCGa                                     <  1:101135/39‑1 (MQ=255)
                                                            cAGGATCTTGATTGCCCCTTCGTCGTCATAACAGACCGa                                     <  1:3063364/39‑1 (MQ=255)
                                                            cAGGATCTTGATTGCCCCTTCGTCGTCATAACAGACCGa                                     <  1:2277362/39‑1 (MQ=255)
                                                            cAGGATCTTGATTGCCCCTTCGTCGTCATAACAGACCGa                                     <  1:425113/39‑1 (MQ=255)
                                                            cAGGATCTTGATTGCCCCTTCGTCGTCATAACAGACCGa                                     <  1:2377369/39‑1 (MQ=255)
                                                            cAGGATCTTGATTGCCCCTTCGTCGTCATAACAGACCGa                                     <  1:350820/39‑1 (MQ=255)
                                                            cAGGATCTTGATTGCCCCTTCGTCGTCATAACAGACCGa                                     <  1:3388071/39‑1 (MQ=255)
                                                            cAGGATCTTGATTGCCCCTTCGTCGTCATAACAGACCGa                                     <  1:3379471/39‑1 (MQ=255)
                                                            cAGGATCTTGATTGCCCCTTCGTCGTCATAACAGACCGa                                     <  1:2524941/39‑1 (MQ=255)
                                                            cAGGATCTTGATTGCCCCTTCGTCGTCATAACAGACCGa                                     <  1:2566066/39‑1 (MQ=255)
                                                             aGGATCTTGATTGCCCCTTCGTCGTCATAACAGACCGAAGCAAAGcc                            >  1:2955553/1‑47 (MQ=255)
                                                             aGGATCTTGATTGCCCCTTCGTCGTCATAACAGACCGAAGCAAAGCCTTTTGCGTCACGCGCcagcag       >  1:583726/1‑68 (MQ=255)
                                                             aGGATCTTGATTGCCCCTTCGTCGTCATAACAGACCGAAGCAAAGCCTTTTGCGTCACGCGCCAGCAGa      >  1:2083430/1‑69 (MQ=255)
                                                             aGGATCTTGATTGCCCCTTCGTCGTCATAACAGACCGAAGCAAAGCCTTTTGCGTCACGCGCCAGCAGa      >  1:481668/1‑69 (MQ=255)
                                                             aGGATCTTGATTGCCCCTTCGTCGTCATAACAGACCGAAGCAAAGCCTTTTGCGTCACGCGCCAGCAGa      >  1:1274783/1‑69 (MQ=255)
                                                             aGGATCTTGATTGCCCCTTCGTCGTCATAACAGACCGAAGCAAAGCCTTTTGCGTCACGCGCCAGCAGa      >  1:3380217/1‑69 (MQ=255)
                                                             aGGATCTTGATTGCCCCTTCGTCGTCATAACAGACCGAAGCAAAGCCTTTTGCGTCACGCGCCAGCAGa      >  1:2810281/1‑69 (MQ=255)
                                                                 ttttGATTGCCCCTTCGTCGTCATAACAGACCGAAGCAAAGCCTTTTGCGTCACGCGCCAGCAGAACCa  >  1:766017/1‑69 (MQ=255)
                                                                  |                                                                   
ACTGTGCGGCACGCCGAGATAACTGATATTACGATGCCCCTGGTCATACAGCCGTTGCATCAGGATTTTGATTGCCCCTTCGTCGTCATAACAGACCGAAGCAAAGCCTTTTGCGTCACGCGCCAGCAGAACCA  >  minE/2908073‑2908206

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