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 2,671,973 T→A 21.2% P316P (CCT→CCA)  malQ → 4‑alpha‑glucanotransferase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,671,9730TA21.2% 214.7 / 50.6 118P316P (CCT→CCA) malQ4‑alpha‑glucanotransferase
Reads supporting (aligned to +/- strand):  ref base T (53/40);  new base A (17/8);  total (70/48)
Fisher's exact test for biased strand distribution p-value = 3.66e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

Only 100 of 119 total aligned reads displayed.

GGCAGCCTTTGATGCGCTACATGCCCAGCAAGTGAAAGAGGACGAAATGCGCTGGGGCTGGCCTGCATGGCCAGAGATGTATCAGAACGTGGATTCACCAGAAGTGCGTCAGTTCTGCGAAGAACATCGT  >  minE/2671910‑2672039
                                                               |                                                                  
ggcagCCTTTGATGCGCTACATGCCCAGCAAGTGAAAGAGGACGAAATGCGCTGGGGCTGGCCTGCATg                                                               <  1:1890032/69‑1 (MQ=255)
ggcagCCTTTGATGCGCTACATGCCCAGCAAGTGAAAGAGGACGAAATGCGCTGGGGCTGGCCTGCATg                                                               <  1:573006/69‑1 (MQ=255)
  cagCCTTTGATGCGCTACATGCCCAGCAAGTGAAAGAGGACGAAATGCGCTGGGGCTGGCCTGCATg                                                               >  1:2165749/1‑67 (MQ=255)
     ccTTTGATGCGCTACATGCCCAGCAAGTGAAAGAGGACGAAATGCGCTGGGGCTGGCCTGCATGGCCag                                                          <  1:2941645/69‑1 (MQ=255)
     ccTTTGATGCGCTACATGCCCAGCAAGTGAAAGAGGACGAAATGCGCTGGGGCTGGCCTGCATGGCCag                                                          <  1:1609748/69‑1 (MQ=255)
     ccTTTGATGCGCTACATGCCCAGCAAGTGAAAGAGGACGAAATGCGCTGGGGCTGGCCTGCATGGCCag                                                          <  1:1755517/69‑1 (MQ=255)
     ccTTTGATGCGCTACATGCCCAGCAAGTGAAAGAGGACGAAATGCGCTGGGGCTGGCCTGCATGGCCag                                                          <  1:318394/69‑1 (MQ=255)
      cTTTGATGCGCTACATGCCCAGCAAGTGAAAGAGGACGAAATGCGCTGGGGCTGGCCTGCATGGc                                                             >  1:2313102/1‑65 (MQ=255)
      cTTTGATGCGCTACATGCCCAGCAAGTGAAAGAGGACGAAATGCGCTGGGGCTGGCCTGCATGGc                                                             >  1:2083171/1‑65 (MQ=255)
      cTTTGATGCGCTACATGCCCAGCAAGTGAAAGAGGACGAAATGCGCTGGGGCTGGCCTGCATGGc                                                             >  1:3267114/1‑65 (MQ=255)
      cTTTGATGCGCTACATGCCCAGCAAGTGAAAGAGGACGAAATGCGCTGGGGCTGGCCTGAATGGc                                                             >  1:2014824/1‑65 (MQ=255)
      cTTTGATGCGCTACATGCCCAGCAAGTGAAAGAGGACGAAATGCGCTGGGCCTGGCCTGCATgg                                                              >  1:1244475/1‑64 (MQ=255)
       tttGATGCGCTACATGCCCAGCAAGTGAAAGAGGACGAAATGTGCTGGGGCTGGCCAGCATGGCCagag                                                        >  1:286395/1‑69 (MQ=255)
       tttGATGCGCTACATGCCCAGCAAGTGAAAGAGGACGAAATGTGCTGGGGCTGGCCAGCATGGCCagag                                                        >  1:1982756/1‑69 (MQ=255)
       tttGATGCGCTACATGCCCAGCAAGTGAAAGAGGACGAAATGTGCTGGGGCTGGCCAGCATGGCCagag                                                        >  1:2935111/1‑69 (MQ=255)
       tttGATGCGCTACATGCCCAGCAAGTGAAAGAGGACGAAATGTGCTGGGGCTGGCCAGCATGGCCagag                                                        >  1:3261080/1‑69 (MQ=255)
       tttGATGCGCTACATGCCCAGCAAGTGAAAGAGGACGAAATGTGCTGGGGCTGGCCAGCATGGCCagag                                                        >  1:2015832/1‑69 (MQ=255)
       tttGATGCGCTACATGCCCAGCAAGTGAAAGAGGACGAAATGTGCTGGGGCTGGCCAGCATGGCCagag                                                        >  1:1807662/1‑69 (MQ=255)
       tttGATGCGCTACATGCCCAGCAAGTGAAAGAGGACGAAATGTGCTGGGGCTGGCCAGCATGGCCagag                                                        >  1:3239146/1‑69 (MQ=255)
       tttGATGCGCTACATGCCCAGCAAGTGAAAGAGGACGAAATGTGCTGGGGCTGGCCAGCATGGCCagag                                                        >  1:2254536/1‑69 (MQ=255)
       tttGATGCGCTACATGCCCAGCAAGTGAAAGAGGACGAAATGTGCTGGGGCTGGCCAGCATGGCCagag                                                        >  1:869916/1‑69 (MQ=255)
       tttGATGCGCTACATGCCCAGCAAGTGAAAGAGGACGAAATGTGCTGGGGCTGGCCAGCATGGCCagag                                                        >  1:2675275/1‑69 (MQ=255)
       tttGATGCGCTACATGCCCAGCAAGTGAAAGAGGACGAAATGTGCTGGGGCTGGCCAGCATGGCCagag                                                        >  1:3380222/1‑69 (MQ=255)
       tttGATGCGCTACATGCCCAGCAAGTGAAAGAGGACGAAATGTGCTGGGGCTGGCCAGCATGGCCagag                                                        >  1:1151071/1‑69 (MQ=255)
       tttGATGCGCTACATGCCCAGCAAGTGAAAGAGGACGAAATGTGCTGGGGCTGGCCAGCATGGCCagag                                                        >  1:127451/1‑69 (MQ=255)
       tttGATGCGCTACATGCCCAGCAAGTGAAAGAGGACGAAATGTGCTGGGGCTGGCCAGCATGGCCagag                                                        >  1:727943/1‑69 (MQ=255)
       tttGATGCGCTACATGCCCAGCAAGTGAAAGAGGACGAAATGTGCTGGGGCTGGCCAGCATGGCCagag                                                        >  1:567381/1‑69 (MQ=255)
       tttGATGCGCTACATGCCCAGCAAGTGAAAGAGGACGAAATGCGCTGGGTCTGGCCTGCATGGCCagag                                                        <  1:2265412/69‑1 (MQ=255)
       tttGATGCGCTACATGCCCAGCAAGTGAAAGAGGACGAAATGCGCTGGGGCTGGCCTGCATGTCCagag                                                        <  1:5954/69‑1 (MQ=255)
       tttGATGCGCTACATGCCCAGCAAGTGAAAGAGGACGAAATGCGCTGGGGCTGGCCTGCATGGCCagag                                                        <  1:1634184/69‑1 (MQ=255)
       tttGATGCGCTACATGCCCAGCAAGTGAAAGAGGACGAAATGCGCTGGGGCTGGCCTGCATGGCCagag                                                        <  1:2120381/69‑1 (MQ=255)
       tttGATGCGCTACATGCCCAGCAAGTGAAAGAGGACGAAATGCGCTGGGGCTGGCCTGCATGGCCagag                                                        <  1:743438/69‑1 (MQ=255)
       tttGATGCGCTACATGCCCAGCAAGTGAAAGAGGACGAAATGCGCTGGGGCTGGCCTGCATGGCCagag                                                        <  1:1982792/69‑1 (MQ=255)
       tttGATGCGCTACATGCCCAGCAAGTGAAAGAGGACGAAATGCGCTGGGGCTGGCCTGCATGGCCagag                                                        <  1:725289/69‑1 (MQ=255)
       tttGATGCGCTACATGCCCAGCAAGTGAAAGAGGACGAAATGCGCTGGGGCTGGCCTGCATGGCCagag                                                        <  1:2951646/69‑1 (MQ=255)
       tttGATGCGCTACATGCCCAGCAAGTGAAAGAGGACGAAATGCGCTGGGGCTGGCCTGCATGGCCagag                                                        <  1:3214167/69‑1 (MQ=255)
       tttGATGCGCTACATGCCCAGCAAGTGAAAGAGGACGAAATGCGCTGGGGCTGGCCTGCATGGCCagag                                                        <  1:1686752/69‑1 (MQ=255)
          gATGCGCTACATGCCCAGCAAGTGAAAGAGGACGAAATGCGCTGGGGCTGGCCt                                                                    >  1:1485939/1‑54 (MQ=255)
          gATGCGCTACATGCCCAGCAAGTGAAAGAGGACGAAATGCGCTGGGGCTGGCCTGCATGGCCAGAGATg                                                     >  1:3177413/1‑69 (MQ=255)
          gATGCGCTACATGCCCAGCAAGTGAAAGAGGACGAAATGCGCTGGGGCTGGCCTGCATGGCCAGAGATg                                                     >  1:1788612/1‑69 (MQ=255)
          gATGCGCTACATGCCCAGCAAGTGAAAGAGGACGAAATGCGCTGGGGCTGGCCTGCATGGCCAGAGATg                                                     >  1:2002646/1‑69 (MQ=255)
          gATGCGCTACATGCCCAGCAAGTGAAAGAGGACGAAATGCGCTGGGGCTGGCCTGCATGGCCAGAGATg                                                     >  1:2777258/1‑69 (MQ=255)
           aTGCGCTACATGCCCAGCAAGTGAAAGAGGACGAAATGCGCTGGGGCTGGCCTGCATGGCCAGAGATg                                                     <  1:564706/68‑1 (MQ=255)
                cTACATGCCCAGCAAGTGAAAGAGGACGAAATGCGCTGGGGCTGGCCTGCATGGCCAGAGATGTATCAg                                               <  1:1538843/69‑1 (MQ=255)
                cTACATGCCCAGCAAGTGAAAGAGGACGAAATGCGCTGGGGCTGGCCTGCATGGCCAGAGATGTATCAg                                               <  1:1083777/69‑1 (MQ=255)
                     tGCCCAGCAAGTGAAAGAGGACGAAATGCGCTGGGGCTGGCCTGCATGGCCAGAGATGTATCAGAACg                                           >  1:2262945/1‑68 (MQ=255)
                     tGCCCAGCAAGTGAAAGAGGACGAAATGCGCTGGGGCTGGCCTGCATGGCCAGAGATGTATCAGAACg                                           >  1:3214650/1‑68 (MQ=255)
                     tGCCCAGCAAGTGAAAGAGGACGAAATGCGCTGGGGCTGGCCTGCATGGCCAGAGATGTATCAGAACg                                           >  1:2662840/1‑68 (MQ=255)
                     tGCCCAGCAAGTGAAAGAGGACGAAATGCGCTGGGGCTGGCCTGCATGGCCAGAGATGTATCAGAACg                                           >  1:2715118/1‑68 (MQ=255)
                      gCCCAGCAAGTGAAAGAGGACGAAATGCGCTGGGGCTGGCCTGCATGGCCAGAGATGTATCAGAACGTg                                         <  1:3303846/69‑1 (MQ=255)
                      gCCCAGCAAGTGAAAGAGGACGAAATGCGCTGGGGCTGGCCTGCATGGCCAGAGATGTATCAGAACGTg                                         <  1:1450498/69‑1 (MQ=255)
                      gCCCAGCAAGTGAAAGAGGACGAAATGCGCTGGGGCTGGCCTGCATGGCCAGAGATGTATCAGAACGTg                                         <  1:829482/69‑1 (MQ=255)
                      gCCCAGCAAGTGAAAGAGGACGAAATGCGCTGGGGCTGGCCTGCATGGCCAGAGATGTATCAGAACGTg                                         <  1:914898/69‑1 (MQ=255)
                         cAGCAAGTGAAAGAGGACGAAATGCGCTGGGGCTGGCCTGCATGGCCagag                                                        <  1:957442/51‑1 (MQ=255)
                             aaGTGAAAGAGGACGAAATGCGCTGGGGCTGGCCTg                                                                   >  1:187483/1‑36 (MQ=255)
                             aaGTGAAAGAGGACGAAATGCGCTGGGGCTGGCCTGCATGGCCAGAGATGTATCAGAACGTGGAtt                                     >  1:2401375/1‑66 (MQ=255)
                             aaGTGAAAGAGGACGAAATGCGCTGGGGCTGGCCTGCATGGCCAGAGATGTATCAGAACGTGGATTc                                    >  1:1267717/1‑67 (MQ=255)
                             aaGTGAAAGAGGACGAAATGCGCTGGGGCTGGCCTGCATGGCCAGAGATGTATCAGAACGTGGATTc                                    >  1:2339631/1‑67 (MQ=255)
                             aaGTGAAAGAGGACGAAATGCGCTGGGGCTGGCCTGCATGGCCAGAGATGTATCAGAACGTGGATTc                                    >  1:310243/1‑67 (MQ=255)
                             aaGTGAAAGAGGACGAAATGCGCTGGGGCTGGCCTGCATGGCCAGAGATGTATCAGAACGTGGATTc                                    >  1:1999061/1‑67 (MQ=255)
                               gTGAAAGAGGACGAAATGCGCTGGGGCTGGCCTGCa                                                                 >  1:177596/1‑36 (MQ=255)
                               gTGAAAGAGGACGAAATGCGCTGGGGCTGGCCTGCATGGCCAGAGATGTATCAGAACGTGGATTCAcc                                 >  1:111679/1‑68 (MQ=255)
                               gTGAAAGAGGACGAAATGCGCTGGGGCTGGCCTGCATGGCCAGAGATGTATCAGAACGTGGATTCAcc                                 >  1:192830/1‑68 (MQ=255)
                                  aaaGAGGACGAAATGCGCTGGGGCTGGCCTGCATGGCCAGAGATGTATc                                                 >  1:149128/1‑49 (MQ=255)
                                  aaaGAGGACGAAATGCGCTGGGGCTGGCCTGCATGGCCAGAGATGTATCAGAACg                                           >  1:1055587/1‑55 (MQ=255)
                                  aaaGAGGACGAAATGCGCTGGGGCTGGCCTGCATGGCCAGAGATGTATCAGAACGTGGATTCACCAGaa                             >  1:2863515/1‑69 (MQ=255)
                                  aaaGAGGACGAAATGCGCTGGGGCTGGCCTGCATGGCCAGAGATGTATCAGAACGTGGATTCACCAGaa                             >  1:1979843/1‑69 (MQ=255)
                                  aaaGAGGACGAAATGCGCTGGGGCTGGCCTGCATGGCCAGAGATGTATCAGAACGTGGATTCACCAGaa                             >  1:871326/1‑69 (MQ=255)
                                  aaaGAGGACGAAATGCGCTGGGGCTGGCCTGCATGGCCAGAGATGTATCAGAACGTGGATTCACCAGaa                             >  1:1279981/1‑69 (MQ=255)
                                  aaaGAGGACGAAATGCGCTGGGGCTGGCCTGCATGGCCAGAGATGTATCAGAACGTGGATTCACCAGaa                             >  1:3156881/1‑69 (MQ=255)
                                  aaaGAGGACGAAATGCGCTGGGGCTGGCCTGCATGGCCAGAGATGTATCAGAACGTGGATTCACCAGaa                             >  1:1955518/1‑69 (MQ=255)
                                  aaaGAGGACGAAATGCGCTGGGGCTGGCCTGCATGGCCAGAGATGTATCAGAACGTGGATTCACCAGaa                             >  1:943149/1‑69 (MQ=255)
                                  aaaGAGGACGAAATGCGCTGGGGCTGGCCTGCATGGCCAGAGATGTATCAGAACGTGGATTCACCAGaa                             >  1:2571517/1‑69 (MQ=255)
                                  aaaGAGGACGAAATGCGCTGGGGCTGGCCTGCATGGCCAGAGATGTATCAGAACGTGGATTCACCAGaa                             >  1:2349858/1‑69 (MQ=255)
                                  aaaGAGGACGAAATGCGCTGGGGCTGGCCTGCATGGCCAGAGATGTATCAGAACGTGGATTCACCAGaa                             >  1:110414/1‑69 (MQ=255)
                                  aaaGAGGACGAAATGCGCTGGGGCTGGCCTGCATGGCCAGAGATGTATCAGAACGTGGATTCACCAGa                              >  1:524044/1‑68 (MQ=255)
                                  aaaGAGGACGAAATGCGCTGGGGCTGGCCTGCATGGCCAGAGATGTATCAGAACGTGGATTCACCAGa                              >  1:3399989/1‑68 (MQ=255)
                                  aaaGAGGACGAAATGCGCTGGGGCTGGCCTGCATGGCCAGAGATGTATCAGAACGTGGATTCACCAGa                              >  1:211141/1‑68 (MQ=255)
                                  aaaGAGGACGAAATGCGCTGGGGCTGGCCTGCATGGCCAGAGATGTATCAGAACGTGGATTCACCAGa                              >  1:3060374/1‑68 (MQ=255)
                                              aTGTGCTGGGGCTGGCCAGCATGGCCAGAGATGTATCAGAACGTGGATTCACCAGAAGTGCGCCAGTTc                 <  1:3301534/69‑1 (MQ=255)
                                              aTGTGCTGGGGCTGGCCAGCATGGCCAGAGATGTATCAGAACGTGGATTCACCAGAAGTGCGCCAGTTc                 <  1:1418553/69‑1 (MQ=255)
                                              aTGTGCTGGGGCTGGCCAGCATGGCCAGAGATGTATCAGAACGTGGATTCACCAGAAGTGCGCCAGTTc                 <  1:1062787/69‑1 (MQ=255)
                                               tgtgcTGGGGCTGGCCAGCATGGCCAGAGATGTATCAGAACGTGGATTCACCAGAAGTGCGCCAGTTc                 <  1:2203210/65‑1 (MQ=255)
                                               tgtgcTGGGGCTGGCCAGCATGGCCAGAGATGTATCAGAACGTGGATTCACCAGAAGTGCGCCAGTTc                 <  1:2395338/65‑1 (MQ=255)
                                               tgtgcTGGGGCTGGCCAGCATGGCCAGAGATGTATCAGAACGTGGATTCACCAGAAGTGCGCCAGTTc                 <  1:1423309/65‑1 (MQ=255)
                                                          ttgCCTGCATGGCCAGAGATGTATCAGAACGTGGATTCACCAGAAGTGCGTCAGTTCTGCGAAGAACAt     <  1:1741562/67‑1 (MQ=255)
                                                          tGGCCTGCATGGCCAGAGATGTATCAGAACGTGGATTCACCAGAAGTGCGTCAGTTCTGCGAAGAACAt     <  1:175837/69‑1 (MQ=255)
                                                            gCCTGCATGGCCAGAGATGTATCAGAACGTGGATTCACCAGAAGTGCGTCAGTTCTGCGAAGAACATc    >  1:1429702/1‑68 (MQ=255)
                                                            gCCTGCATGGCCAGAGATGTATCAGAACGTGGATTCACCAGAAGTGCGTCAGTTCTGCGAAGAACATc    >  1:1581284/1‑68 (MQ=255)
                                                            gCCTGCATGGCCAGAGATGTATCAGAACGTGGATTCACCAGAAGTGCGTCAGTTCTGCGAAGAACATc    >  1:2774419/1‑68 (MQ=255)
                                                              cTGCATGGCCAGAGATGTATCAGAACGTGGATTCACCAGAAGTGCGTCAGTTCTGCGAAGAACATCGt  <  1:1440449/68‑1 (MQ=255)
                                                              cTGCATGGCCAGAGATGTATCAGAACGTGGATTCACCAGAAGTGCGTCAGTTCTGCGAAGAACATCGt  <  1:387511/68‑1 (MQ=255)
                                                              cTGCATGGCCAGAGATGTATCAGAACGTGGATTCACCAGAAGTGCGTCAGTTCTGCGAAGAACATCGt  <  1:1363451/68‑1 (MQ=255)
                                                              cTGCATGGCCAGAGATGTATCAGAACGTGGATTCACCAGAAGTGCGTCAGTTCTGCGAAGAACATCGt  <  1:1664577/68‑1 (MQ=255)
                                                              cTGCATGGCCAGAGATGTATCAGAACGTGGATTCACCAGAAGTGCGTCAGTTCTGCGAAGAACATCGt  <  1:760776/68‑1 (MQ=255)
                                                              cTGCATGGCCAGAGATGTATCAGAACGTGGATTCACCAGAAGTGCGTCAGTTCTGCGAAGAACATCGt  <  1:2372477/68‑1 (MQ=255)
                                                              cTGCATGGCCAGAGATGTATCAGAACGTGGATTCACCAGAAGTGCGTCAGTTCTGCGAAGAACATCGt  <  1:19784/68‑1 (MQ=255)
                                                              cTGCATGGCCAGAGATGTATCAGAACGTGGATTCACCAGAAGTGCGTCAGTTCTGCGAAGAACATCGt  <  1:198052/68‑1 (MQ=255)
                                                              cTGCATGGCCAGAGATGTATCAGAACGTGGATTCACCAGAAGTGCGTCAGTTCTGCGAAGAACATCGt  <  1:23877/68‑1 (MQ=255)
                                                              cTGCATGGCCAGAGATGTATCAGAACGTGGATTCACCAGAAGTGCGTCAGTCCTGCGAAGAACATCGt  <  1:3418466/68‑1 (MQ=255)
                                                               |                                                                  
GGCAGCCTTTGATGCGCTACATGCCCAGCAAGTGAAAGAGGACGAAATGCGCTGGGGCTGGCCTGCATGGCCAGAGATGTATCAGAACGTGGATTCACCAGAAGTGCGTCAGTTCTGCGAAGAACATCGT  >  minE/2671910‑2672039

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