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 2,671,959 C→T 28.6% R312C (CGC→TGC)  malQ → 4‑alpha‑glucanotransferase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,671,9590CT28.6% 122.1 / 50.5 115R312C (CGC→TGC) malQ4‑alpha‑glucanotransferase
Reads supporting (aligned to +/- strand):  ref base C (50/32);  new base T (28/5);  total (78/37)
Fisher's exact test for biased strand distribution p-value = 1.52e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.94e-01

Only 100 of 127 total aligned reads displayed.

GCGACAGCCTGTTCTGGCAGGCAGCCTTTGATGCGCTACATGCCCAGCAAGTGAAAGAGGACGAAATGCGCTGGGGCTGGCCTGCATGGCCAGAGATGTATCAGAACGTGGATTCACCAGAAGTGCGTCAGTTC  >  minE/2671891‑2672024
                                                                    |                                                                 
gCGACAGCCTGTTCTGGCAGGCAGCCTTTGATGCGCTACATGCCCAGCAAGTGAAAGAGGACGAAATgc                                                                   >  1:1010376/1‑69 (MQ=255)
  gACAGCCTGTTCTGGCAGGCAGCCTTTGATGCGCTACATGCCCAGCAAGTGAAAGAGGACGAAATgcgc                                                                 <  1:2850394/69‑1 (MQ=255)
  gACAGCCTGTTCTGGCAGGCAGCCTTTGATGCGCTACATGCCCAGCAAGTGAAAGAGGACGAAATgcgc                                                                 <  1:1568684/69‑1 (MQ=255)
  gACAGCCTGTTCTGGCAGGCAGCCTTTGATGCGCTACATGCCCAGCAAGTGAAAGAGGACGAAATgcgc                                                                 <  1:1397122/69‑1 (MQ=255)
  gACAGCCTGTTCTGGCAGGCAGCCTTTGATGCGCTACATGCCCAGCAAGTGAAAGAGGACGAAATgcgc                                                                 <  1:547177/69‑1 (MQ=255)
  gACAGCCTGTTCTGGCAGGCAGCCTTTGATGCGCTACATGCCCAGCAAGTGAAAGAGGACGAAATgcgc                                                                 <  1:591964/69‑1 (MQ=255)
  gACAGCCTGTTCTGGCAGGCAGCCTTTGATGCGCTACATGCCCAGCAAGTGAAAGAGGACGAAATgcgc                                                                 <  1:607107/69‑1 (MQ=255)
  gACAGCCTGTTCTGGCAGGCAGCCTTTGATGCGCTACATGCCCAGCAAGTGAAAGAGGACGAAATgcgc                                                                 <  1:69779/69‑1 (MQ=255)
  gACAGCCTGTTCTGGCAGGCAGCCTTTGATGCGCTACATGCCCAGCAAGTGAAAGAGGACGAAATgcgc                                                                 <  1:1042019/69‑1 (MQ=255)
   aCAGCCTGTTCTAGCAGGCAGCCTTTGATGCGCTACATGCCCAGCAAGTGAAAGAGGACGAAATgcgc                                                                 <  1:449109/68‑1 (MQ=255)
     aGCCTGTTCTGGCAGGCAGCCTTTGATGCGCTACATGCCCAGCAAGTGAAAGAGGACGAAATGCGCTgg                                                              <  1:353772/69‑1 (MQ=255)
     aGCCTGTTCTGGCAGGCAGCCTTTGATGCGCTACATGCCCAGCAAGTGAAAGAGGACGAAATGCGCTgg                                                              <  1:3140243/69‑1 (MQ=255)
     aGCCTGTTCTGGCAGGCAGCCTTTGATGCGCTACATGCCCAGCAAGTGAAAGAGGACGAAATGCGCTgg                                                              <  1:1305631/69‑1 (MQ=255)
     aGCCTGTTCTGGCAGGCAGCCTTTGATGCGCTACATGCCCAGCAAGTGAAAGAGGACGAAATGCGCTgg                                                              <  1:2380334/69‑1 (MQ=255)
     aGCCTGTTCTGGCAGGCAGCCTTTGATGCGCTACATGCCCAGCAAGTGAAAGAGGACGAAATGCGCTgg                                                              <  1:2134348/69‑1 (MQ=255)
             cTGGCAGGCAGCCTTTGATGCGCTACATGCCCAGCAAGTGAAAGAGGACGAAATGTGCTGGGGCTGGcc                                                      >  1:319352/1‑69 (MQ=255)
             cTGGCAGGCAGCCTTTGATGCGCTACATGCCCAGCAAGTGAAAGAGGACGAAATGTGCTGGGGCTGGcc                                                      >  1:2352084/1‑69 (MQ=255)
             cTGGCAGGCAGCCTTTGATGCGCTACATGCCCAGCAAGTGAAAGAGGACGAAATGTGCTGGGGCTGGcc                                                      >  1:2812506/1‑69 (MQ=255)
             cTGGCAGGCAGCCTTTGATGCGCTACATGCCCAGCAAGTGAAAGAGGACGAAATGTGCTGGGGCTGGcc                                                      >  1:2562371/1‑69 (MQ=255)
             cTGGCAGGCAGCCTTTGATGCGCTACATGCCCAGCAAGTGAAAGAGGACGAAATGTGCTGGGGCTGGcc                                                      >  1:2265170/1‑69 (MQ=255)
             cTGGCAGGCAGCCTTTGATGCGCTACATGCCCAGCAAGTGAAAGAGGACGAAATGTGCTGGGGCTGGcc                                                      >  1:222133/1‑69 (MQ=255)
             cTGGCAGGCAGCCTTTGATGCGCTACATGCCCAGCAAGTGAAAGAGGACGAAATGTGCTGGGGCTGGcc                                                      >  1:1531324/1‑69 (MQ=255)
             cTGGCAGGCAGCCTTTGATGCGCTACATGCCCAGCAAGTGAAAGAGGACGAAATGTGCTGGGGCTGGcc                                                      >  1:1562394/1‑69 (MQ=255)
             cTGGCAGGCAGACTTTGATGCGCTACATGCCCAGAAAGTGAAAGAGGACGAAATGTGCTGGGGCTGGcc                                                      >  1:299342/1‑69 (MQ=255)
                   ggcagCCTTTGATGCGCTACATGCCCAGCAAGTGAAAGAGGACGAAATGCGCTGGGGCTGGCCTGCGTg                                                <  1:243506/69‑1 (MQ=255)
                   ggcagCCTTTGATGCGCTACATGCCCAGCAAGTGAAAGAGGACGAAATGCGCTGGGGCTGGCCTGCATg                                                <  1:573006/69‑1 (MQ=255)
                     cagCCTTTGATGCGCTACATGCCCAGCAAGTGAAAGAGGACGAAATGCGCTGGGGCTGGCCTGCATg                                                >  1:2165749/1‑67 (MQ=255)
                        ccTTTGATGCGCTACATGCCCAGCAAGTGAAAGAGGACGAAATGCGCTGGGGCTGGCCTGCATGGCCag                                           <  1:2941645/69‑1 (MQ=255)
                         cTTTGATGCGCTACATGCCCAGCAAGTGAAAGAGGACGAAATGCGCTGGGGCTGGCCTGCATGGc                                              >  1:3267114/1‑65 (MQ=255)
                         cTTTGATGCGCTACATGCCCAGCAAGTGAAAGAGGACGAAATGCGCTGGGGCTGGCCTGCATGGc                                              >  1:2083171/1‑65 (MQ=255)
                         cTTTGATGCGCTACATGCCCAGCAAGTGAAAGAGGACGAAATGCGCTGGGGCTGGCCTGCATGGc                                              >  1:1167593/1‑65 (MQ=255)
                         cTTTGATGCGCTACATGCCCAGCAAGTGAAAGAGGACGAAATGCGCTGGGGCTGGCCTGCATGGc                                              >  1:2313102/1‑65 (MQ=255)
                         cTTTGATGCGCTACATGCCCAGCAAGTGAAAGAGGACGAAATGCGCTGGGGCTGGCCTGCATGGc                                              >  1:1451973/1‑65 (MQ=255)
                         cTTTGATGCGCTACATGCCCAGCAAGTGAAAGAGGACGAAATGCGCTGGGGCTGGCCTGAATGGc                                              >  1:2014824/1‑65 (MQ=255)
                         cTTTGATGCGCTACATGCCCAGCAAGTGAAAGAGGACGAAATACGCTGGGGCTGGCCTGCATGGc                                              >  1:2807035/1‑65 (MQ=255)
                          tttGATGCGCTACATGCCCAGCAAGTGAAAGAGGACGAAATGTGCTGGGGCTGGCCAGCATGGCCagag                                         >  1:3380222/1‑69 (MQ=255)
                          tttGATGCGCTACATGCCCAGCAAGTGAAAGAGGACGAAATGTGCTGGGGCTGGCCAGCATGGCCagag                                         >  1:1151071/1‑69 (MQ=255)
                          tttGATGCGCTACATGCCCAGCAAGTGAAAGAGGACGAAATGTGCTGGGGCTGGCCAGCATGGCCagag                                         >  1:286395/1‑69 (MQ=255)
                          tttGATGCGCTACATGCCCAGCAAGTGAAAGAGGACGAAATGTGCTGGGGCTGGCCAGCATGGCCagag                                         >  1:3261080/1‑69 (MQ=255)
                          tttGATGCGCTACATGCCCAGCAAGTGAAAGAGGACGAAATGTGCTGGGGCTGGCCAGCATGGCCagag                                         >  1:567381/1‑69 (MQ=255)
                          tttGATGCGCTACATGCCCAGCAAGTGAAAGAGGACGAAATGTGCTGGGGCTGGCCAGCATGGCCagag                                         >  1:2082694/1‑69 (MQ=255)
                          tttGATGCGCTACATGCCCAGCAAGTGAAAGAGGACGAAATGTGCTGGGGCTGGCCAGCATGGCCagag                                         >  1:127451/1‑69 (MQ=255)
                          tttGATGCGCTACATGCCCAGCAAGTGAAAGAGGACGAAATGTGCTGGGGCTGGCCAGCATGGCCagag                                         >  1:1664544/1‑69 (MQ=255)
                          tttGATGCGCTACATGCCCAGCAAGTGAAAGAGGACGAAATGTGCTGGGGCTGGCCAGCATGGCCagag                                         >  1:1807662/1‑69 (MQ=255)
                          tttGATGCGCTACATGCCCAGCAAGTGAAAGAGGACGAAATGTGCTGGGGCTGGCCAGCATGGCCagag                                         >  1:869916/1‑69 (MQ=255)
                          tttGATGCGCTACATGCCCAGCAAGTGAAAGAGGACGAAATGCGCTGGGTCTGGCCTGCATGGCCagag                                         <  1:2265412/69‑1 (MQ=255)
                          tttGATGCGCTACATGCCCAGCAAGTGAAAGAGGACGAAATGCGCTGGGGCTGGCCTGCATGGCCagag                                         <  1:743438/69‑1 (MQ=255)
                          tttGATGCGCTACATGCCCAGCAAGTGAAAGAGGACGAAATGCGCTGGGGCTGGCCTGCATGGCCagag                                         <  1:3214167/69‑1 (MQ=255)
                          tttGATGCGCTACATGCCCAGCAAGTGAAAGAGGACGAAATGCGCTGGGGCTGGCCTGCATGGCCagag                                         <  1:725289/69‑1 (MQ=255)
                          tttGATGCGCTACATGCCCAGCAAGTGAAAGAGGACGAAATGCGCTGGGGCTGGCCTGCATGGCCagag                                         <  1:2951646/69‑1 (MQ=255)
                          tttGATGCGCTACATGCCCAGCAAGTGAAAGAGGACGAAATGCGCTGGGGCTGGCCTGCATGGCCagag                                         <  1:1982792/69‑1 (MQ=255)
                          tttGATGCGCTACATGCCCAGCAAGTGAAAGAGGACGAAATGCGCTGGGGCTGGCCTGCATGGCCagag                                         <  1:1686752/69‑1 (MQ=255)
                          tttGATGCGCTACATGCCCAGCAAGTGAAAGAGGACGAAATGCGCTGGGGCTGGCCTGCATGGCCagag                                         <  1:1634184/69‑1 (MQ=255)
                             gATGCGCTACATGCCCAGCAAGTGAAAGAGGACGAAATGCGCTGGGGCTGGCCt                                                     >  1:1485939/1‑54 (MQ=255)
                             gATGCGCTACATGCCCAGCAAGTGAAAGAGGACGAAATGCGCTGGGGCTGGCCTGCATGGCCAGAGATg                                      >  1:3177413/1‑69 (MQ=255)
                             gATGCGCTACATGCCCAGCAAGTGAAAGAGGACGAAATGCGCTGGGGCTGGCCTGCATGGCCAGAGATg                                      >  1:1788612/1‑69 (MQ=255)
                             gATGCGCTACATGCCCAGCAAGTGAAAGAGGACGAAATGCGCTGGGGCTGGCCTGCATGGCCAGAGATg                                      >  1:327370/1‑69 (MQ=255)
                             gATGCGCTACATGCCCAGCAAGTGAAAGAGGACGAAATGCGCTGGGGCTGGCCTGCATGGCCAGAGATg                                      >  1:2002646/1‑69 (MQ=255)
                             gATGCGCTACATGCCCAGCAAGTGAAAGAGGACGAAATGCGCTGGGGCTGGCCTGCATGGCCAGAGATg                                      >  1:2777258/1‑69 (MQ=255)
                                   cTACATGCCCAGCAAGTGAAAGAGGACGAAATGCGCTGGGGCTGGCCTGCATGGCCAGAGATGTATCAg                                <  1:1538843/69‑1 (MQ=255)
                                        tGCCCAGCAAGTGAAAGAGGACGAAATGCGCTGGGGCTGGCCTGCATGGCCAGAGATGTATCAGAACg                            >  1:2715118/1‑68 (MQ=255)
                                        tGCCCAGCAAGTGAAAGAGGACGAAATGCGCTGGGGCTGGCCTGCATGGCCAGAGATGTATCAGAACg                            >  1:3214650/1‑68 (MQ=255)
                                        tGCCCAGCAAGTGAAAGAGGACGAAATGCGCTGGGGCTGGCCTGCATGGCCAGAGATGTATCAGAACg                            >  1:2662840/1‑68 (MQ=255)
                                        tGCCCAGCAAGTGAAAGAGGACGAAATGCGCTGGGGCTGGCCTGCATGGCCAGAGATGTATCAGAACg                            >  1:2262945/1‑68 (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)
                                                aaGTGAAAGAGGACGAAATGCGCTGGGGCTGGCCTGCATGGCCAGAGATGTATCAGAACGTGGATTc                     >  1:310243/1‑67 (MQ=255)
                                                aaGTGAAAGAGGACGAAATGCGCTGGGGCTGGCCTGCATGGCCAGAGATGTATCAGAACGTGGATTc                     >  1:1267717/1‑67 (MQ=255)
                                                aaGTGAAAGAGGACGAAATGCGCTGGGGCTGGCCTGCATGGCCAGAGATGTATCAGAACGTGGATTc                     >  1:1981217/1‑67 (MQ=255)
                                                aaGTGAAAGAGGACGAAATGCGCTGGGGCTGGCCTGCATGGCCAGAGATGTATCAGAACGTGGATTc                     >  1:1999061/1‑67 (MQ=255)
                                                  gTGAAAGAGGACGAAATGCGCTGGGGCTGGCCTGCa                                                  >  1:177596/1‑36 (MQ=255)
                                                  gTGAAAGAGGACGAAATGCGCTGGGGCTGGCCTGCATGGCCAGAGATGTATCAGAACGTGGATTCAcc                  >  1:192830/1‑68 (MQ=255)
                                                  gTGAAAGAGGACGAAATGCGCTGGGGCTGGCCTGCATGGCCAGAGATGTATCAGAACGTGGATTCAcc                  >  1:2244142/1‑68 (MQ=255)
                                                  gTGAAAGAGGACGAAATGCGCTGGGGCTGGCCTGCATGGCCAGAGATGTATCAGAACGTGGATTCAcc                  >  1:434200/1‑68 (MQ=255)
                                                  gTGAAAGAGGACGAAATGCGCTGGGGCTGGCCTGCATGGCCAGAGATGTATCAGAACGTGGATTCAcc                  >  1:111679/1‑68 (MQ=255)
                                                   tGAAAGAGGACGAAATGCGCTGGGGCTGGCCTGCATGGCCagag                                         <  1:614849/44‑1 (MQ=255)
                                                     aaaGAGGACGAAATGCGCTGGGGCTGGCCTGCATGGCCAGAGATGTATc                                  >  1:149128/1‑49 (MQ=255)
                                                     aaaGAGGACGAAATGCGCTGGGGCTGGCCTGCATGGCCAGAGATGTATCAGAACg                            >  1:1055587/1‑55 (MQ=255)
                                                     aaaGAGGACGAAATGCGCTGGGGCTGGCCTGCATGGCCAGAGATGTATCAGAACGTGGATTCACCAGaa              >  1:2863515/1‑69 (MQ=255)
                                                     aaaGAGGACGAAATGCGCTGGGGCTGGCCTGCATGGCCAGAGATGTATCAGAACGTGGATTCACCAGaa              >  1:3156881/1‑69 (MQ=255)
                                                     aaaGAGGACGAAATGCGCTGGGGCTGGCCTGCATGGCCAGAGATGTATCAGAACGTGGATTCACCAGaa              >  1:943149/1‑69 (MQ=255)
                                                     aaaGAGGACGAAATGCGCTGGGGCTGGCCTGCATGGCCAGAGATGTATCAGAACGTGGATTCACCAGaa              >  1:1955518/1‑69 (MQ=255)
                                                     aaaGAGGACGAAATGCGCTGGGGCTGGCCTGCATGGCCAGAGATGTATCAGAACGTGGATTCACCAGaa              >  1:1979843/1‑69 (MQ=255)
                                                     aaaGAGGACGAAATGCGCTGGGGCTGGCCTGCATGGCCAGAGATGTATCAGAACGTGGATTCACCAGaa              >  1:110414/1‑69 (MQ=255)
                                                     aaaGAGGACGAAATGCGCTGGGGCTGGCCTGCATGGCCAGAGATGTATCAGAACGTGGATTCACCAGaa              >  1:1279981/1‑69 (MQ=255)
                                                     aaaGAGGACGAAATGCGCTGGGGCTGGCCTGCATGGCCAGAGATGTATCAGAACGTGGATTCACCAGaa              >  1:2349858/1‑69 (MQ=255)
                                                     aaaGAGGACGAAATGCGCTGGGGCTGGCCTGCATGGCCAGAGATGTATCAGAACGTGGATTCACCAGaa              >  1:2571517/1‑69 (MQ=255)
                                                     aaaGAGGACGAAATGCGCTGGGGCTGGCCTGCATGGCCAGAGATGTATCAGAACGTGGATTCACCAGaa              >  1:1402298/1‑69 (MQ=255)
                                                     aaaGAGGACGAAATGCGCTGGGGCTGGCCTGCATGGCCAGAGATGTATCAGAACGTGGATTCACCAGa               >  1:211141/1‑68 (MQ=255)
                                                     aaaGAGGACGAAATGCGCTGGGGCTGGCCTGCATGGCCAGAGATGTATCAGAACGTGGATTCACCAGa               >  1:524044/1‑68 (MQ=255)
                                                     aaaGAGGACGAAATGCGCTGGGGCTGGCCTGCATGGCCAGAGATGTATCAGAACGTGGATTCACCAGa               >  1:3005907/1‑68 (MQ=255)
                                                     aaaGAGGACGAAATGCGCTGGGGCTGGCCTGCATGGCCAGAGATGTATCAGAACGTGGATTCACCAGa               >  1:3399989/1‑68 (MQ=255)
                                                     aaaGAGGACGAAATGCGCTGGGGCTGGCCTGCATGGCCAGAGATGTATCAGAACGTGGATTCACCAGa               >  1:319309/1‑68 (MQ=255)
                                                                 aTGTGCTGGGGCTGGCCAGCATGGCCAGAGATGTATCAGAACGTGGATTCACCAGAAGTGCGCCAGTTc  <  1:1062787/69‑1 (MQ=255)
                                                                 aTGTGCTGGGGCTGGCCAGCATGGCCAGAGATGTATCAGAACGTGGATTCACCAGAAGTGCGCCAGTTc  <  1:832707/69‑1 (MQ=255)
                                                                 aTGTGCTGGGGCTGGCCAGCATGGCCAGAGATGTATCAGAACGTGGATTCACCAGAAGTGCGCCAGTTc  <  1:1418553/69‑1 (MQ=255)
                                                                    |                                                                 
GCGACAGCCTGTTCTGGCAGGCAGCCTTTGATGCGCTACATGCCCAGCAAGTGAAAGAGGACGAAATGCGCTGGGGCTGGCCTGCATGGCCAGAGATGTATCAGAACGTGGATTCACCAGAAGTGCGTCAGTTC  >  minE/2671891‑2672024

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