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 1,941,424 G→A 58.2% A282T (GCG→ACG)  ygfZ → predicted folate‑dependent regulatory protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,941,4240GA58.2% 33.9 / 77.5 104A282T (GCG→ACG) ygfZpredicted folate‑dependent regulatory protein
Reads supporting (aligned to +/- strand):  ref base G (23/20);  new base A (21/39);  total (44/60)
Fisher's exact test for biased strand distribution p-value = 7.16e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

Only 100 of 111 total aligned reads displayed.

AGCTGGTGAAGACTTAGAGCTGAAAATGGGCGAGAACTGGCGTCGTACCGGTACGGTACTGGCTGCGGTAAAACTGGAAGATGGTCAGGTCGTGGTACAGGTCGTCATGAATAACGATATGGAACCGGATAGC  >  minE/1941360‑1941492
                                                                |                                                                    
aGCTGGTGAAGACTTAGAGCTGAAAATGGGCGAGAACTGGCGTCGTACCGGTACGGTGCTGGCTACgg                                                                   >  1:1015401/1‑68 (MQ=255)
aGCTGGTGAAGACTTAGAGCTGAAAATGGGCGAGAACTGGCGTCGTACCGGTACGGTGCTGGCTACgg                                                                   >  1:1920340/1‑68 (MQ=255)
aGCTGGTGAAGACTTAGAGCTGAAAATGGGCGAGAACTGGCGTCGTACCGGTACGGTGCTGGCTACgg                                                                   >  1:2328828/1‑68 (MQ=255)
aGCTGGTGAAGACTTAGAGCTGAAAATGGGCGAGAACTGGCGTCGTACCGGTACGGTGCTGGCTACgg                                                                   >  1:2349576/1‑68 (MQ=255)
aGCTGGTGAAGACTTAGAGCTGAAAATGGGCGAGAACTGGCGTCGTACCGGTACGGTGCTGGCTACgg                                                                   >  1:2447498/1‑68 (MQ=255)
aGCTGGTGAAGACTTAGAGCTGAAAATGGGCGAGAACTGGCGTCGTACCGGTACGGTGCTGGCTACgg                                                                   >  1:2532499/1‑68 (MQ=255)
aGCTGGTGAAGACTTAGAGCTGAAAATGGGCGAGAACTGGCGTCGTACCGGTACGGTGCTGGCTACgg                                                                   >  1:1645231/1‑68 (MQ=255)
aGCTGGTGAAGACTTAGAGCTGAAAATGGGCGAGAACTGGCGTCGTACCGGTACGGTGCTGGCTACgg                                                                   >  1:1434092/1‑68 (MQ=255)
aGCTGGTGAAGACTTAGAGCTGAAAATGGGCGAGAACTGGCGTCGTACCGGTACGGTGCTGGCTACgg                                                                   >  1:1167031/1‑68 (MQ=255)
aGCTGGTGAAGACTTAGAGCTGAAAATGGGCGAGAACTGGCGTCGTACCGGTACGGTGCTGGCTACgg                                                                   >  1:836894/1‑68 (MQ=255)
aGCTGGTGAAGACTTAGAGCTGAAAAAGGGCGAGAACTGGCGTCGTACCGGTACGGTGCTGGCTACgg                                                                   >  1:329645/1‑68 (MQ=255)
aGCTCGTGAAGACTTAGAGCTGAAAATGGGCGAGAACTGGCGTCGTACCGGTACGGTGCTGGCTACgg                                                                   >  1:781950/1‑68 (MQ=255)
  cTGGTGAAGACTTAGAGCTGAAAATGGGCGAGAACTGGCGTCGTACCGGTACGGTACTGGCTTCGGTaa                                                                <  1:4506/69‑1 (MQ=255)
  cTGGTGAAGACTTAGAGCTGAAAATGGGCGAGAACTGGCGTCGTACCGGTACGGTACTGGCTGCGGTaa                                                                <  1:1420527/69‑1 (MQ=255)
  cTGGTGAAGACTTAGAGCTGAAAATGGGCGAGAACTGGCGTCGTACCGGTACGGTACTGGCTGCGGTaa                                                                <  1:3091377/69‑1 (MQ=255)
  cTGGTGAAGACTTAGAGCTGAAAATGGGCGAGAACTGGCGTCGTACCGGTACGGTACTGGCTGCGGTaa                                                                <  1:1639558/69‑1 (MQ=255)
  cTGGTGAAGACTTAGAGCTGAAAATGGGCGAGAACTGGCGTCGTACCGGTACGGTACTGGCTGCGGTaa                                                                <  1:829513/69‑1 (MQ=255)
          gACTTAGAGCTGAAAATGGGCGAGAACTGGCGTCGTACCGGTACGGTACTGGCTGCGGTAAAACTGGaa                                                        <  1:886637/69‑1 (MQ=255)
          gACTTAGAGCTGAAAATGGGCGAGAACTGGCGTCGTACCGGTACGGTACTGGCTGCGGTAAAACTGGaa                                                        <  1:2657853/69‑1 (MQ=255)
           aCTTAGAGCTGAAAATGGGCGAGAACTGGCGTCGTACCGGTACGGTACTGGCTGCGGTTAAACTGGAAg                                                       >  1:631966/1‑69 (MQ=255)
           aCTTAGAGCTGAAAATGGGCGAGAACTGGCGTCGTACCGGTACGGTACTGGCTGCGGTAAAACTGGAAg                                                       >  1:246204/1‑69 (MQ=255)
           aCTTAGAGCTGAAAATGGGCGAGAACTGGCGTCGTACCGGTACGGTACTGGCTGCGGTAAAACTGGAAg                                                       >  1:2082670/1‑69 (MQ=255)
           aCTTAGAGCTGAAAATGGGCGAGAACTGGCGTCGTACCGGTACGGTACTGGCTGCGGTAAAACTGGAAg                                                       >  1:2280483/1‑69 (MQ=255)
           aCTTAGAGCTGAAAATGGGCGAGAACTGGCGTCGTACCGGTACGGTACTGGCTGCGGTAAAACTGGAAg                                                       >  1:847450/1‑69 (MQ=255)
           aCTTAGAGCTGAAAATGGGCGAGAACTGGCGTCGTACCGGTACGGTACTGGCTGCGGTAAAACTGGAAg                                                       >  1:1004152/1‑69 (MQ=255)
           aCTTAGAGCTGAAAATGGGCGAGAACTGGCGTCGTACCGGTACGGTACTGGCTGCGGTAAAACTGGAAg                                                       >  1:2527073/1‑69 (MQ=255)
           aCTTAGAGCTGAAAATGGGCGAGAACTGGCGTCGTACCGGTACGGTACTGGCTGCGGTAAAACTGGAAg                                                       >  1:3417180/1‑69 (MQ=255)
           aCTTAGAGCTGAAAATGGGCGAGAACTGGCGTCGTACCGGTACGGTACTGGCTGCGGTAAAACTGGAAg                                                       >  1:464617/1‑69 (MQ=255)
           aCTTAGAGCTGAAAATGGGCGAGAACTGGCGTCGTACCGGTACGGTACTGGCTGCGGTAAAACTGGAAg                                                       >  1:557508/1‑69 (MQ=255)
           aCTTAGAGCTGAAAATGGGCGAGAACTGGCGTCGTACCGGTACGGTACTGGCTGCGGTAAAACTGGAAg                                                       >  1:579334/1‑69 (MQ=255)
           aCTTAGAGCTGAAAATGGGCGAGAACTGGCGTCGTACCGGTACGGTACTGGCTGCGGTAAAACTGGAAg                                                       >  1:1817069/1‑69 (MQ=255)
           aCTTAGAGCTGAAAATGGGCGAGAACTGGCGTCGTACCGGTACGGTACTGGCTGCGGTAAAACTGGAAg                                                       >  1:1759831/1‑69 (MQ=255)
                                    cTGGCGTCGTACCGGTACGGTGCTGTCTACGGTCAAACTGGAAGATGGTCAGGTTGTGGTGCAGgttgt                              <  1:519845/69‑1 (MQ=255)
                                    cTGGCGTCGTACCGGTACGGTGCTGGCTACGGTCAAACTGGAAGATGGTCAGGTTGTGGTGCAtgttgt                              <  1:1749150/69‑1 (MQ=255)
                                    cTGGCGTCGTACCGGTACGGTGCTGGCTACGGTCAAACTGGAAGATGGTCAGGTTGTGGTGCAGgttgt                              <  1:584760/69‑1 (MQ=255)
                                    cTGGCGTCGTACCGGTACGGTGCTGGCTACGGTCAAACTGGAAGATGGTCAGGTTGTGGTGCAGgttgt                              <  1:2642188/69‑1 (MQ=255)
                                    cTGGCGTCGTACCGGTACGGTGCTGGCTACGGTCAAACTGGAAGATGGTCAGGTTGTGGTGCAGgttgt                              <  1:1198866/69‑1 (MQ=255)
                                    cTGGCGTCGTACCGGTACGGTGCTGGCTACGGTCAAACTGGAAGATGGTCAGGTTGTGGTGCAGgttgt                              <  1:1152911/69‑1 (MQ=255)
                                    cTGGCGTCGTACCGGTACGGTGCTGGCTACGGTCAAACTGGAAGATGGTCAGGTTGTGGTGCAGgttgt                              <  1:3091334/69‑1 (MQ=255)
                                    cTGGCGTCGTACCGGTACGGTGCTGGCTACGGTCAAACTGGAAGATGGTCAGGTTGTGGTGCAGgttgt                              <  1:3137680/69‑1 (MQ=255)
                                    cTGGCGTCGTACCGGTACGGTGCTGGCTACGGTCAAACTGGAAGATGGTCAGGTTGTGGTGCAGgttgt                              <  1:1055925/69‑1 (MQ=255)
                                    cTGGCGTCGTACCGGTACGGTGCTGGCTACGGTCAAACTGGAAGATGGTCAGGTTGTGGTGCAGgttgt                              <  1:2270857/69‑1 (MQ=255)
                                    cTGGCGTCGTACCGGTACGGTGCTGGCTACGGTCAAACTGGAAGATGGTCAGGTTGTGGTGCAGgttgt                              <  1:2196679/69‑1 (MQ=255)
                                    cTGGCGTCGTACCGGTACGGTGCTGGCTACGGTCAAACTGGAAGATGGTCAGGTTGTGGTGCAGgttgt                              <  1:669316/69‑1 (MQ=255)
                                    cTGGCGTCGTACCGGTACGGTGCTGGCTACGGTCAAACTGGAAGATGGTCAGGTTGTGGTGCAGgttgt                              <  1:1365777/69‑1 (MQ=255)
                                    cTGGCGTCGTACCGGTACGGTGCTGGCTACGGTCAAACTGGAAGATGGTCAGGTTGTGGTGCAGgttgt                              <  1:2568220/69‑1 (MQ=255)
                                     tGGCGTCGTACCGGTACGGTGCTGGCTACGGTCAAACTGGAAGATGGTCAGGTTGTGGTGCAGgttgt                              <  1:2604550/68‑1 (MQ=255)
                                     tGGCGTCGTACCGGTACGGTGCTGGCTACGGTCAAACTGGAAGATGGTCAGGTTGTGGTGCAGgttgt                              <  1:3202088/68‑1 (MQ=255)
                                     tGGCGTCGTACCGGTACGGTGCTGGCTACGGTCAAACTGGAAGATGGTCAGGTTGTGGTGCAGgttgt                              <  1:2633593/68‑1 (MQ=255)
                                     tGGCGTCGTACCGGTACGGTGCTGGCTACGGTCAAACTGGAAGATGGTCAGGTTGTGGTGCAGgttgt                              <  1:610151/68‑1 (MQ=255)
                                     tGGCGTCGTACCGGTACGGTGCTGGCTACGGTCAAACTGGAAGATGGTCAGGTTGTGGTGCAGgttgt                              <  1:494346/68‑1 (MQ=255)
                                     tGGCGTCGTACCGGTACGGTGCTGGCTACGGTCAAACTGGAAGATGGTCAGGTTGTGGTGCAGgttgt                              <  1:1400513/68‑1 (MQ=255)
                                     tGGCGTCGTACCGGTACGGTGCTGGCTACGGTCAAACTGGAAGATGGTCAGGTTGTGGTGCAGgttgt                              <  1:3423880/68‑1 (MQ=255)
                                     tGGCGTCGTACCGGTACGGTGCTGGCTACGGTCAAACTGGAAGATGGTCAGGTTGTGGTGCAGgttgt                              <  1:1342832/68‑1 (MQ=255)
                                     tGGCGTCGTACCGGTACGGTGCTGGCTACGGTCAAACTGGAAGATGGTCAGGTTGTGGTGCAGgttgt                              <  1:49277/68‑1 (MQ=255)
                                     tGGCGTCGTACCGGTACGGTGCTGGCTACGGTCAAACTGGAAGATGGTCAGGTTGTGGTGCAGgttgt                              <  1:961952/68‑1 (MQ=255)
                                     tGGCGTCGTACCGGTACGGTGCTGGCTACGGTCAAACTGGAAGATGGTCAGGTTGTGGTGCAGgttgt                              <  1:918221/68‑1 (MQ=255)
                                     tGGCGTCGTACCGGTACGGTGCTGGCTACGGTCAAACTGGAAGATGGTCAGGTTGTGGTGCAGgttgt                              <  1:2157028/68‑1 (MQ=255)
                                     tGGCGTCGTACCGGTACGGTGCTGGCTACGGTCAAACTGGAAGATGGTCAGGTTGTGGTGCAGgttgt                              <  1:2302118/68‑1 (MQ=255)
                                     tGGCGTCGTACCGGTACGGTGCTGGCTACGGTCAAACTGGAAGATGGTCAGGTTGTGGTGCAGgttgt                              <  1:1772097/68‑1 (MQ=255)
                                     tGGCGTCGTACCGGTACGGTGCTGGCTACGGTCAAACTGGAAGATGGTCAGGTTGTGGTGCAGgttgt                              <  1:697855/68‑1 (MQ=255)
                                     tGGCGTCGTACCGGTACGGTGCTGGCTACGGTCAAACTGGAAGATGGTCAGGTTGTGGTGCAGgttgt                              <  1:236939/68‑1 (MQ=255)
                                                 ggtacggtacTGGCTGCGGTAAAACTGGAAGATGGTCAGGTCGTGGTACAGGTCGTCATGAATAACGa                  <  1:3204123/68‑1 (MQ=255)
                                                 ggtacggtacTGGCTGCGGTAAAACTGGAAGATGGTCAGGTCGTGGTACAGGTCGTCATGAATAACGa                  <  1:3153268/68‑1 (MQ=255)
                                                 ggtacggtacTGGCTGCGGTAAAACTGGAAGATGGTCAGGTCGTGGTACAGGTCGTCATGAATAACGa                  <  1:2966869/68‑1 (MQ=255)
                                                 ggtacggtacTGGCTGCGGTAAAACTGGAAGATGGGCAGGTCGTGGTACAGGTCGTCATGAATAACGa                  <  1:1100678/68‑1 (MQ=255)
                                                  gtacggtgcTGGCTACGGTCAAACTGGAAGATGGTCAGGt                                             >  1:2468555/1‑40 (MQ=25)
                                                  gtacggtgcTGGCTACGGTCAAACTGGAAGATGGTCAGGTTGTGGTGCAGGTTGTCATGAATAACGata                >  1:543725/1‑69 (MQ=255)
                                                     cggtacTGGCTGCGGTAAAACTGGAAGATGGTCAGGTCGTTGTACAGGTCGTCATGAATAACGATATgg             <  1:1510749/69‑1 (MQ=255)
                                                     cggtacTGGCTGCGGTAAAACTGGAAGATGGTCAGGTCGTGGTACAGGTCGTCATGAATAACGATATgg             >  1:3161361/1‑69 (MQ=255)
                                                     cggtacTGGCTGCGGTAAAACTGGAAGATGGTCAGGTCGTGGTACAGGTCGTCATGAATAACGATATgg             >  1:1231856/1‑69 (MQ=255)
                                                       gtacTGGCTGCTGTAAAACTGGAAGATGGTCAGGTCGTGGTACAGGTCGTCATGAATAACGATATGGa            <  1:2663567/68‑1 (MQ=255)
                                                       gtacTGGCTGCGGTAAAACTGGAAGATGGTCAGGTCGTGGTACAGGTCGTCATGAATAACGa                  <  1:1102767/62‑1 (MQ=255)
                                                       gtacTGGCTGCGGTAAAACTGGAAGATGGTCAGGTCGTGGTACAGGTCGTCATGAATAACGATATGGa            >  1:1480216/1‑68 (MQ=255)
                                                       gtacTGGCTGCGGTAAAACTGGAAGATGGTCAGGTCGTGGTACAGGTCGTCATGAATAACGATATGGa            >  1:1782332/1‑68 (MQ=255)
                                                       gtacTGGCTGCGGTAAAACTGGAAGATGGTCAGGTCGTGGTACAGGTCGTCATGAATAACGATATGGa            >  1:1786310/1‑68 (MQ=255)
                                                       gtacTGGCTGCGGTAAAACTGGAAGATGGTCAGGTCGTGGTACAGGTCGTCATGAATAACGATATGGa            >  1:2630163/1‑68 (MQ=255)
                                                       gtacTGGCTGCGGTAAAACTGGAAGATGGTCAGGTCGTGGTACAGGTCGTCATGAATAACGATATGGa            >  1:961915/1‑68 (MQ=255)
                                                       gtacTGGCTGCGGTAAAACTGGAAGATGGTCAGGTCGTGGTACAGGTCGTCATGAATAACGATATGGa            <  1:2040347/68‑1 (MQ=255)
                                                       gtacTGGCTGCGGTAAAACTGGAAGATGGTCAGGTCGTGGTACAGGTCGTCATGAATAACAATATGGa            <  1:2468377/68‑1 (MQ=255)
                                                        tacTGGCTGCGGTAAAACTGGAAGATGGTCAGGTCGTGGTACAGGTCGTCATGAATAACGATATGGa            <  1:1736467/67‑1 (MQ=255)
                                                          cTGGCTACGGTCAAACTGGAAGATGGTCAGGTTGTGGTGCAGGTTGTCATGAATAACGATATGGAACCg        <  1:3033774/69‑1 (MQ=255)
                                                          cTGGCTACGGTCAAACTGGAAGATGGTCAGGTTGTGGTGCAGGTTGTCATGAATAACGATATGGAACCg        <  1:1904611/69‑1 (MQ=255)
                                                          cTGGCTACGGTCAAACTGGAAGATGGTCAGGTTGTGGTGCAGGTTGTCATGAATAACGATATGGAACCg        <  1:262571/69‑1 (MQ=255)
                                                          cTGGCTACGGTCAAACTGGAAGATGGTCAGGTTGTGGTGCAGGTTGTCATGAATAACGATATGGAACCg        <  1:2427026/69‑1 (MQ=255)
                                                          cTGGCTACGGTCAAACTGGAAGATGGTCAGGTTGTGGTGCAGGTTGTCATGAATAACGATATGGAACCg        <  1:2409495/69‑1 (MQ=255)
                                                          cTGGCTACGGTCAAACTGGAAGATGGTCAGGTTGTGGTGCAGGTTGTCATGAATAACGATATGGAACCg        <  1:2367073/69‑1 (MQ=255)
                                                          cTGGCTACGGTCAAACTGGAAGATGGTCAGGTTGTGGTGCAGGTTGTCATGAATAACGATATGGAACCg        <  1:2355939/69‑1 (MQ=255)
                                                          cTGGCTACGGTCAAACTGGAAGATGGTCAGGTTATGGTGCAGGTTGTCATGAATAACGATATGGAACCg        <  1:1894921/69‑1 (MQ=255)
                                                           tGGCTACGGTCAAACTGGAAGATGGTCAGGTTGTGGTGCAGGTTGTCATGAATAACGATATGGAACCg        <  1:2602493/68‑1 (MQ=255)
                                                             gCTGCGGTAAAACTGGAAGATGGTCAGGTCGTGGTACAGGTCGTCATGAATAACGATATGGAACCGGAt     >  1:2344656/1‑69 (MQ=255)
                                                               tGCGGTAAAACTGGAAGATGGTCAGGTCGTGGTACAGGTCGTCATGAATAACGATATGGAACCGGATAg   <  1:134520/69‑1 (MQ=255)
                                                               tGCGGTAAAACTGGAAGATGGTCAGGTCGTGGTACAGGTCGTCATGAATAACGATATGGAACCGGATAg   <  1:2066487/69‑1 (MQ=255)
                                                                gCGGTAAAACTGGAAGATGGTCAGGTCGTGGTACAGGTCGTCATGAATAACGATATGGAACCGGATAg   <  1:437035/68‑1 (MQ=255)
                                                                gCGGTAAAACTGGAAGATGGTCAGGTCGTGGTACAGGTCGTCATGAATAACGATATGGAACCGGATAg   <  1:2401249/68‑1 (MQ=255)
                                                                gCGGTAAAACTGGAAGATGGTCAGGTCGTGGTACAGGTCGTCATGAATAACGATATGGAACCGGATAGc  <  1:2016852/69‑1 (MQ=255)
                                                                gCGGTAAAACTGGAAGATGGTCAGGTCGTGGTACAGGTCGTCATGAATAACGATATGGAACCGGATAGc  <  1:756168/69‑1 (MQ=255)
                                                                gCGGTAAAACTGGAAGATGGTCAGGTCGTGGTACAGGTCGTCATGAATAACGATATGGAACCGGATAGc  <  1:1390851/69‑1 (MQ=255)
                                                                gCGGTAAAACTGGAAGATGGTCAGGTCGTGGTACAGGTCGTCATGAATAACGATATGGAACCGGATAGc  <  1:1284198/69‑1 (MQ=255)
                                                                gCGGTAAAACTGGAAGATGGTCAGGTCGTGGTACAGGTCGTCATGAATAACGATATGGAACCGGATAGc  <  1:377724/69‑1 (MQ=255)
                                                                |                                                                    
AGCTGGTGAAGACTTAGAGCTGAAAATGGGCGAGAACTGGCGTCGTACCGGTACGGTACTGGCTGCGGTAAAACTGGAAGATGGTCAGGTCGTGGTACAGGTCGTCATGAATAACGATATGGAACCGGATAGC  >  minE/1941360‑1941492

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