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
A7 F80 I0 R1 1148 65.4 3296958 93.8% 3092546 131.2

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_002947 5,655,677:1 +A 13.2% intergenic (‑81/+71) epd ← / ← tktA D‑erythrose 4‑phosphate dehydrogenase/transketolase A

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0029475,655,6771.A13.2% 186.7 / 25.0 53intergenic (‑81/+71)epd/tktAD‑erythrose 4‑phosphate dehydrogenase/transketolase A
Reads supporting (aligned to +/- strand):  ref base . (21/25);  new base A (3/4);  total (24/29)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.89e-01

GCGCGCAGGACACAGCGGCCGATACGGCCATAACCGTTGAGTGCAACTTTGTAGGGACGGTGGGGCATTCGGGGCTCACGAGACAGTTCAATTGTCGTCAGCCTGCGGAATTTGCGGTGTGGCATTCGCGGGCAAGCCCGCTCCCACAG‑GGTTTCATGCAACCTCTGTGGGAGCGGGCTTGCCCGCGAATGAAGGCGACACCGCCCGCAGATCTTTAAATCAGTCTTCCAGCAGCTCTTCGGCAGTACCGAGGATGTTCTCCAGGGTGAAGCCAAACTCTTCGAACAATGCCGAAGC  >  NC_002947/5655529‑5655825
                                                                                                                                                     |                                                                                                                                                    
gcgcgcAGGACACAGCGGCCGATACGGCCATAACCGTTGAGTGCAACTTTGTAGGGACGGTGGGGCATTCGGGGCTCACGAGACAGTTCAATTGTCGTCAGCCTGCGGAATTTGCGGTGTGGCATTCGCGGGCAAGCCCGCTCCCACAg‑g                                                                                                                                                     <  1:171465/150‑1 (MQ=255)
     cAGGACACAGCGGCCGATACGGCCATAACCGTTGAGTGCAACTTTGTAGGGACGGTGGGGCATTCGGGGCTCACGAGACAGTTCAATTGTCGTCAGCCTGCGGAATTTGCGGTGTGGCATTCGCGGGCAAGCCCGCTCCCACAG‑GGTTTc                                                                                                                                                <  2:1181486/150‑1 (MQ=255)
      aGGACACAGCGGCCGATACGGCCATAACCGTTGAGTGCAAATTTGTAGGGACGGTGGGGCATTCGGGGCTCACGAGACAGTTCAATTGTCGTCAGCCTGCGGAATTTGCGGTGTGGCATTCGCGGGCAAGCCCGCTCCCACAG‑GGTTTCa                                                                                                                                               <  1:308898/150‑1 (MQ=255)
       ggACACAGCGGCCGATACGGCCATAACCGTTGAGTGCAACTTTGTAGGGACGGTGGGGCATTCGGGGCTCACGAGACAGTTCAATTGTCGTCAGCCTGCGGAATTTGCGGTGTGGCATGCGCGGGCAAGCCCGCTCCCACAG‑GGTTTCAt                                                                                                                                              <  2:1006704/150‑1 (MQ=255)
                  ccGATACGGCCATAACCGTTGAGTGCAACTTTGTAGGGACGGTGGGGCATTCGGGGCTCACGAGACAGTTCAATTGTCGTCAGCCTGCGGAATTTGCGGTGTGGCATTCGCGGGCAAGCCCGCTCCCACAG‑GGTTTCATGCAACCTCtgt                                                                                                                                   <  2:1436417/150‑1 (MQ=255)
                  ccGATACGGCCATAACCGTTGAGTGCAACTTTGTAGGGACGCTGGGGCATTCGGGGCTCACGAGACAGTTCAATTGTCGTCAGCCTGCGGAATTTGCGGTGTGGCATTCGCGGGCAAGCCCGCTCCCACAG‑GGTTTCATGCAACCTCtgt                                                                                                                                   <  2:1122077/150‑1 (MQ=255)
                   cGATACGGCCATAACCGTTGAGTGCAACTTTGTAGGGACGGTGGGGCATTCGGGGCTCACGAGACAGTTCAATTGGCGTCAGCCTGCGGAATTTGCGGTGTGGCATTCGCGGGCAAGCCCGCTCACACAG‑GGTTTCATGCAACCTCtgtg                                                                                                                                  <  1:1362809/150‑1 (MQ=255)
                    gATACGGCCATAACCGTTGAGTGCAACTTTGTAGGGACGGTGGGGCATTCGGGGCTCACGAGACAGTTCAATTGTCGTCAGCCTGCGGAATTTGCGGTGTGGCATTCGCGGGCAAGCCCGCTCCCACAGAGGTTGCATGAAACC‑CTGTgg                                                                                                                                 <  1:1398382/150‑1 (MQ=38)
                      tACGGCCATAACCGTTGAGTGCAACTTTGTAGGGACGGTGGGGCATTCGGGGCTCACGAGACAGTTCAATTGTCGTCAGCCTGCGGAATTTGCGGTGTGGCATTCGCGGGCAAGCCCGCTCCCACAT‑GGTTTCATGCAACCTCTGTggg                                                                                                                                <  1:631519/149‑1 (MQ=255)
                      tACGGCCATAACCGTTGAGTGCAACTTTGTAGGGACGGTGGGGCATTCGGGGCTCACGAGACAGTTCAATTGTCGTCAGCCTGCGGAATTTGCGGTGTGGCATTCGCGGGCAAGCCCGCTCCCACAG‑GGTTTCATGCAACCTCTGTggg                                                                                                                                >  2:631519/1‑149 (MQ=255)
                      tACGGCCATAACCGTTGAGTGCAACTTTGTAGGGACGGTGGGGAATTCGGGGCTCACGAGACAGTTCAATTGTCGTCAGCCTGCGGAATTTGTGGTGTGGCATTCGCGGGCAAGCCCGCTCGCACAG‑CGTTTCATGCAACCTCTGTGGGa                                                                                                                               <  2:523722/150‑1 (MQ=255)
                        cGGCCATAACCGTTGAGTGCAACTTTGTAGGGACGGTGGGGCATTCGGGGCTCACGAGACAGTTCAATTGTCGTCAGCCTGCGGAATTTGCGGTGTGGCATTCGCGGGCAAGCCCGCTCCCACAGAGGTTGCATGAAACC‑CTGTGGGAGc                                                                                                                             <  1:742805/150‑1 (MQ=37)
                         ggCCATAACCGTTGAGTGCAACTTTGTAGGGACGGTGGGGCATTCGGGGCTCACGAGACAGTTCAATTGTCGTCAGCCTGCGGAATTTGCGGTGTGGCATTCGCGGGCAAGCCCGCTCCCACAG‑GGTTTCATGCAACCTCTGTGGGAGCg                                                                                                                            >  2:1459691/1‑150 (MQ=255)
                          gCCATAACCGTTGAGTGCAACTTTGTAGGGACGGTGGGGCATTCGGGGCTCACGAGACAGTTCAATTGTCGTCAGCCTGCGGAATTTGCGGTGTGGCATTCGCGGGCAAGCCCGCTCCCACAG‑GGTTTCATGCAACCTCTGTgggcgagg                                                                                                                           <  2:1096492/150‑6 (MQ=255)
                          gCCATAACCGTTGAGTGCAACTTTGTAGGGACGGTGGGGCATTCGGGGCTCACGAGACAGTTCAATTGTCGTCAGCCTGCGGAATTTGCGGTGTGGCATTCGCGGGCAAGCCCGCTCCCACAG‑GGTTTCATGCAACCTCTGCGGGAGCgg                                                                                                                           <  2:1292585/150‑1 (MQ=255)
                           ccATAACCGTTGAGTGCAACTTTGTAGGGACGGTGGGGCATTCGGGGCTCACGAGACAGTTCAATTGTCGTCAGCCTGCGGAATTTGCGGTGTGGCATTCGCGGGCAAGCCCGCTCCCACAG‑GGTTTCATGCAACCTCTGTGGGAGCggg                                                                                                                          <  1:481369/150‑1 (MQ=255)
                             aTAACCGTTGAGTGCAACTTTGTAGGGACGGTGGGGCATTCGGGGCTCACGAGACAGTTCAATTGTCGTCAGCCTGCGGAATTTGCGGTGTGGCATTCGCGGGCAAGCCCGCTCCCACAg                                                                                                                                                       <  2:1601031/120‑1 (MQ=255)
                             aTAACCGTTGAGTGCAACTTTGTAGGGACGGTGGGGCATTCGGGGCTCACGAGACAGTTCAATTGTCGTCAGCCTGCGGAATTTGCGGTGTGGCATTCGCGGGCAAGCCCGCTCCCACAg                                                                                                                                                       >  1:1601031/1‑120 (MQ=255)
                              tAACCGTTGAGTGCAACTTTGTAGGGACGGTGGGGCATTCGGGGCTCACGAGACAGTTCAATTGTCGTCAGCCTGCGGAATTTGCGGTGTGGCATTCGCGGGCAAGCCCGCTCCCACAG‑GGTTTCATGCAACCTCTGTGGGAGCGGGCtt                                                                                                                       <  1:491371/150‑1 (MQ=255)
                                              cTTTGTAGGGACGGTGGGGCATTCGGGGCTCACGAGACAGTTCAATTGTCGTCAGCCTGCGGAATTTGCGGTGTGGCATTCGCGGGCAAGCCCGCTCCCACAG‑GGTTTCATGCAACCTCTGTGGGAGCGGGCTTGCCCGCGAATGAAGGc                                                                                                       <  1:384329/150‑1 (MQ=255)
                                                ttGTAGGGACGGTGGGGCATTCGGGGCTCACGAGACAGTTCAATTGTCGTCAGCCTGCGGAATTTGCGGTGTGGCATTCGCGGGCAAGCCCGCTCCCACAG‑GGTTTCATGCAACCTCTGTGGGAGCGGGCTTGCCCGCGAATGAAGGCGa                                                                                                     <  1:1480079/150‑1 (MQ=255)
                                                      ggACGGTGGGGCATTCGGGGCTCACGAGACAGTTCAATTGTCGTCAGCCTGCGGAATTTGCGGTGTGGCATTCGCGGGCAAGCCCGCTCCCACAG‑GGTTTc                                                                                                                                                <  1:390656/101‑1 (MQ=255)
                                                      ggACGGTGGGGCATTCGGGGCTCACGAGACAGTTCAATTGTCGTCAGCCTGCGGAATTTGCGGTGTGGCATTCGCGGGCAAGCCCGCTCCCACAG‑GGTTTc                                                                                                                                                >  2:390656/1‑101 (MQ=255)
                                                      ggACGGTGGGGCATTCGGGGCTCACGAGACAGTTCAATTGTCGTCAGCCTGCGGAATTTGCGGTGTGGCATTCGCGGGCAAGCCCGCTCCCACAG‑GGTTTCATGCAACCTCtgt                                                                                                                                   >  2:1588608/1‑114 (MQ=255)
                                                      ggACGGTGGGGCATTCGGGGCTCACGAGACAGTTCAATTGTCGTCAGCCTGCGGAATTTGCGGTGTGGCATTCGCGGGCAAGCCCGCTCCCACAG‑GGTTTCATGCAACCTCtgt                                                                                                                                   <  1:1588608/114‑1 (MQ=255)
                                                                   ttCGGGGCTCACGAGACAGTTCAATTGTCGTCAGCCTGCGGAATTTGCGGTGTGGCATTCGCGGGCAAGCCCGCTCCCACAG‑GGTTTCATGCAACCTCTGTGGGAGCGGGCTTGCCCGCGAATGAAGGCGACACCGCCCGCAGATCTTTa                                                                                  >  2:195989/1‑150 (MQ=255)
                                                                           tCACGAGACAGTTCAATTGTCGTCAGCCTGCGGAATTTGCGGTGTGGCATTCGCGGGCAAGCCCGCTCCCACAG‑GCTATCAAGAAACCTCTGTTGGAGCGGGCTTGCCCGCCAATGAAGGAGCCACTTCCCGCAGGTCATTAAATCAGTc                                                                          >  1:282767/1‑150 (MQ=37)
                                                                                    aGTTCAATTGTCGTCAGCCTGCGGAATTTGCGGTGTGGCATTCGCGGGCAAGCCCGCTCCCACAg‑g                                                                                                                                                     <  1:1447335/66‑1 (MQ=255)
                                                                                    aGTTCAATTGTCGTCAGCCTGCGGAATTTGCGGTGTGGCATTCGCGGGCAAGCCCGCTCCCACAg‑g                                                                                                                                                     >  2:1447335/1‑66 (MQ=255)
                                                                                      ttCAATTGTCGTCAGCCTGCGGAATTTGCGGTGTGGCATTCGCGGGCAAGCCCGCTCCCACAG‑GGTTTCATGCAACCTCTGTGGGAGCGGGCTTGCCCGCGAATGAAGGCGACACCGCCCGCAGATCTTTAAATCAGTCTTCCAGCAGct                                                               >  2:435706/1‑150 (MQ=255)
                                                                                         aaTTGTCGTCAGCCTGCGGAATTTGCGGTGTGGCATTCGCGGGCAAGCCCGCTCCCACAGAGGTTGCATGAAACC‑CTGTGGGAGCGGGc                                                                                                                         <  1:718216/89‑1 (MQ=17)
                                                                                         aaTTGTCGTCAGCCTGCGGAATTTGCGGTGTGGCATTCGCGGGCAAGCCCGCTCCCACAGAGGTTGCATGAAACC‑CTGTGGGAGCGGGc                                                                                                                         >  2:718216/1‑89 (MQ=17)
                                                                                         aaTTGTCGTCAGCCTGCGGAATTTGCGGTGTGGCATTCGCGGGCAAGCCCGCTCCCACAG‑GGTTTCATGCAACCTCtgt                                                                                                                                   >  1:1496829/1‑79 (MQ=255)
                                                                                         aaTTGTCGTCAGCCTGCGGAATTTGCGGTGTGGCATTCGCGGGCAAGCCCGCTCCCACAG‑GGTTTCATGCAACCTCtgt                                                                                                                                   >  1:1496807/1‑79 (MQ=255)
                                                                                         aaTTGTCGTCAGCCTGCGGAATTTGCGGTGTGGCATTCGCGGGCAAGCCCGCTCCCACAG‑GGTTTCATGCAACCTCtgt                                                                                                                                   <  2:1496829/79‑1 (MQ=255)
                                                                                         aaTTGTCGTCAGCCTGCGGAATTTGCGGTGTGGCATTCGCGGGCAAGCCCGCTCCCACAG‑GGTTTCATGCAACCTCtgt                                                                                                                                   <  2:1496807/79‑1 (MQ=255)
                                                                                         aaTTGTCGTCAGCCTGCGGAATTTGCGGTGTGGCATTCGCGGGCAAGCCCGCTCCCACAG‑AGTTTCATGCAACTTCTGGGGGAGCGGGCTTGCCCGCGAATGAAGGCGACACCGCCCGCAGATCTTTAAATCAGTCTTCCAGCAGCTCtt                                                            >  1:608678/1‑150 (MQ=255)
                                                                                           ttGTCGTCAGCCTGCGGAATTTGCGGTGTGGCATTCGCGGGCAAGCCGGCTCCCACAG‑GGTTTCATGCCACCTCTGTGGGAGCGTGATTGCCCGCGAATGAAGGCGACACCGCCCGCAGATCTTTAAATACGTCTTCCAGCAGCCCTTCg                                                          >  2:93144/1‑150 (MQ=255)
                                                                                                   aGCCTGCGGAATTTGCGGTGTGGCATTCGCGGGCAAGCCCGCTCCCACAG‑GGTTTCATGCAACCTCTGTGGGAGCGGGCTTGCCCGCGAATGAAGGCGACACCGCCCGCAGATCTTTAAATCAGTCTTCCAGCAGCTCTTCGGCAGTAcc                                                  <  1:195989/150‑1 (MQ=255)
                                                                                                            aaTTTGCGGTGTGGCATTCGCGGGCAAGCCCGCTCCCACAG‑GGTTTCATGCAACCTCTGTGGGAGCGGGCTTGCCCGCGAATGAAGGCGACACCGCCCGCAGATCTTTAAATCAGTCTTCCAGCAGCTCTTCGGCAGTACCGAGGATGtt                                         >  1:1425908/1‑150 (MQ=255)
                                                                                                                    gtgtGGCATTCGCGGGCAAGCCCGCTCCCACAG‑GGTTTCATGCAACCTCTGTGGGAGCGGGCTTGCCCGCGAATGAAGGCGACACCGCCCGCAGATCTTTAAATCAGTCTTCCAGCAGCTCTTCGGCAGTACCGAGGATGTTCTCCAggg                                 <  2:282767/150‑1 (MQ=255)
                                                                                                                                cgGGCAAGCCCGCTCCCACAG‑GGTTTCATGCAACCTCTGTGGGAGCGGGCTGGCCCGCGAATGAAGGCGACACCGCCCGCAGATCTTTAAATCAGTCTTCCAGCAGCTCTTCGGCAGTACCGAGGATGTTCTCCAGGGTGAAGCCAAAct                     <  1:1593345/150‑1 (MQ=255)
                                                                                                                                     aaGCCCGCTCCCACAG‑GGTTTCATGCAACCTCTGTGGGAGCGGGCTTGCCCGCGAATGAAGGCGACACCGCCCGCAGATCTTTAAATCAGTCTTCCAGCAGCTCTTCGGCAGTACCGAGGATg                                           <  2:349924/123‑1 (MQ=255)
                                                                                                                                     aaGCCCGCTCCCACAG‑GGTTTCATGCAACCTCTGTGGGAGCGGGCTTGCCCGCGAATGAAGGCGACACCGCCCGCAGATCTTTAAATCAGTCTTCCAGCAGCTCTTCGGCAGTACCGAGGATg                                           >  1:349924/1‑123 (MQ=255)
                                                                                                                                         ccGCTCCCACAG‑GGTTTCATGCAACCTCTGTGGGAGCGGGCTTGCCCGCGAATGAAGGCGACACCGCCCGCAGATCTTTAAATCAGTCTTCCAGCAGCTCTTCGGCAGTACCGAGGATGTTCTCCAGGGTGAAGCCAAACTCTTCGAACa            >  2:1282517/1‑150 (MQ=255)
                                                                                                                                           gCTCCCACAG‑GTTTTCATGCAACCTCTGTGGGAGCGGGCTTGCCCGCGAATGAAGGCGACACCGCCCGCAGATCTTTAAATCAGTCTTCCAGCAGCTCTTCGGCAGTACCGAGGATGTTCTCCAGGGTGAAGCCAAACTCTTCGAACAAt          >  1:1372304/1‑150 (MQ=255)
                                                                                                                                             tCCCACAG‑GGTTTCATGCAACCTCTGTGGGAGCGGGCTTGCCCGCGAATGAAGGCGACACCGCCCGCAGATCTTTAAATCAGTCTTCCAGCAGCTCTTCGGCAGTACCGAGGATGTTCTCCGGGGTGAAGCCAAACTCTTCGAACAATGc        >  2:99916/1‑150 (MQ=255)
                                                                                                                                               ccACAGAGGTTGCATGAAACC‑CTGTGGGAGCGGGCTTGCCCGCGAATGCAGGCGACACCGCCCGCAGATCTTTAAATCAGTCTTCCAGCAGCTCTTCGGCAGTACCGAGGATGTTCTCCAGGGTGAAGCCAAACTCTTCGAACAATGCCg      >  1:1611478/1‑150 (MQ=37)
                                                                                                                                               ccACAGAGGTTGCATGAAACC‑CTGTGGGAGCGGGCTTGCCCGCGAATGAAGGCGACACCGCCCGCAGATCTTTAAATc                                                                              >  2:1556743/1‑78 (MQ=17)
                                                                                                                                               ccACAGAGGTTGCATGAAACC‑CTGTGGGAGCGGGCTTGCCCGCGAATGAAGGCGACACCGCCCGCAGATCTTTAAATc                                                                              <  1:1556743/78‑1 (MQ=14)
                                                                                                                                               ccACAG‑GGTTTCATGCAACCTCTGTGGGAGCGGGCTTGCCCGCGAATGAAGGCGACACCGCCCGCAGATCTTTAAATCAGTCTTcc                                                                      <  2:1410835/86‑1 (MQ=255)
                                                                                                                                               ccACAG‑GGTTTCATGCAACCTCTGTGGGAGCGGGCTTGCCCGCGAATGAAGGCGACACCGCCCGCAGATCTTTAAATCAGTCTTcc                                                                      >  1:1410835/1‑86 (MQ=255)
                                                                                                                                                cacaG‑GGTTTCATGCAACCTCTGTGGGAGCGGGCTTGCCCGCGAATGAAGGCGACACCGCCCGCAGATCTTTAAATCAGTCTTCCAGCAGCTCTTCGGCAGTACCGAGGATGTTCTCCAGGGTGAAGCCAAACTCTTCGAACAATGCCGa     >  1:789340/1‑150 (MQ=255)
                                                                                                                                                 acaG‑GGTTTCATGCAACCTCTGTGGGAGCGGGCTTGCCCGCGAATGAAGGCGACACCGCCCGCAGATCTTTAAATCAGTCTTCCAGCAGCTCTTCGGCAGTACCGAGGATg                                           >  2:1025864/1‑111 (MQ=255)
                                                                                                                                                 acaG‑GGTTTCATGCAACCTCTGTGGGAGCGGGCTTGCCCGCGAATGAAGGCGACACCGCCCGCAGATCTTTAAATCAGTCTTCCAGCAGCTCTTCGGCAGTACCGAGGATGTTCTCCAGGGTGAAGCCAAACTCTTCGAACAATGCCGaa    >  1:352591/1‑150 (MQ=255)
                                                                                                                                                 acaG‑GGTTTCATGCAACCTCTGTGGGAGCGGGCTTGCCCGCGAATGAAGGCGACACCGCCCGCAGATCTTTAAATCAGTCTTCCAGCAGCTCTTCGGCAGTACCGAGGATGTTCTCCAGGGTGAAGCCAAACTCTTCGAACAATGCCGaa    >  2:6528/1‑150 (MQ=255)
                                                                                                                                                 acaG‑GGTTTCATGCAACCTCTGTGGGAGCGGGCTTGCCCGCGAATGAAGGCGACACCGCCCGCAGATATTTAAATCAGTCTTCCAGCAGCTCTTCGGCAGTACCGAGGATg                                           <  1:1025864/111‑1 (MQ=255)
                                                                                                                                                   aG‑GGTTTCATGCAACCTCTGTGGGAGCGGGCTTGCCCGCGAATGAAGGCGACACCGCCCGCAGATCTTTAAATCAGTCTTCCAGCAGCTCTTCGGCAGTACCGAGGATGTTCTCCAGGGTGAAGCCAAACTCTTCGAACAATGCCGAAGc  <  2:608678/150‑1 (MQ=255)
                                                                                                                                                     |                                                                                                                                                    
GCGCGCAGGACACAGCGGCCGATACGGCCATAACCGTTGAGTGCAACTTTGTAGGGACGGTGGGGCATTCGGGGCTCACGAGACAGTTCAATTGTCGTCAGCCTGCGGAATTTGCGGTGTGGCATTCGCGGGCAAGCCCGCTCCCACAG‑GGTTTCATGCAACCTCTGTGGGAGCGGGCTTGCCCGCGAATGAAGGCGACACCGCCCGCAGATCTTTAAATCAGTCTTCCAGCAGCTCTTCGGCAGTACCGAGGATGTTCTCCAGGGTGAAGCCAAACTCTTCGAACAATGCCGAAGC  >  NC_002947/5655529‑5655825

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A