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
A35 F60 I1 R1 16 64.9 2210988 99.0% 2188878 138.9

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 4,141,224 T→C D333G (GAC→GGC)  ptsA ← putative PTS multiphosphoryl transfer protein PtsA

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009134,141,2240TC98.3% 210.0 / ‑4.4 58D333G (GAC→GGC) ptsAputative PTS multiphosphoryl transfer protein PtsA
Reads supporting (aligned to +/- strand):  ref base T (0/1);  new base C (23/34);  total (23/35)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.03e-01

GTCAGCGGTACGGGCTTGTTGGGTCAGCCAGACACGCTGTTGCTCACGCAGGGCGTCCTGTACGCGGGCTTCTTGCTGATAATAACGAGCTACGGCTTCCCCTGGCTCAACCACAATCGCCCCGGCGTTGCCGTCGATATAAATCGTTTGTTGCTGCCACGGAGTAAGGGCATCAATATCCACACCAACCAGCGTTGGAATGTTGAACGAACGGGCAAGGATCACCGTATGTGAGGTGGTGCCGCCGCTTTTGAGCAACAATCCTTT  >  NC_000913/4141091‑4141357
                                                                                                                                     |                                                                                                                                     
gTCAGCGGTACGGGCTTGTTGGGTCAGCCAGACACGCTGTTGCTCACGCAGGGCGTCCTGTACGCGGGCTTCTTGCTGATAATAACGAGCTACGGCTTCCCCTGGCTCAACCACAATCGCCCCGGCGTTGCCGCCGatat                                                                                                                                 <  1:60536/140‑1 (MQ=255)
  cAGCGGTACGGGCTTGTAGGGTCAGCCAGACACGCAGTTTCTCACGCACGGCGTCCTGTACGCGGGCTTCTTGCTGATAATAACGAGCTACGGCTTCCCCTGGCTCAACCACAATCGCCCCGGCGTTGCCGCCGATATaa                                                                                                                               <  2:300427/140‑1 (MQ=255)
               ttgttgGGTCAGCCAGACACGCTGTTGCTCACGCAGGGCGTCCTGTACGCGGGCTTCTTGCTGATAATAACGAGCTACGGCTTCCCCTGGCTCAACCACAATGGCCCCGGCGTTTCCGCCGATACAAATCGTTTGTtgct                                                                                                                  >  1:442225/1‑140 (MQ=255)
                   tgGGTCAGCCAGACAGGCTGTTACTCACGTAGGGCGTTCTGTACGCGGGCTTCTTGCTGATAATAACGAGCTACGGCTTCCCCTGGCTCAACCACAATCGCCCCGGCGTTGCCGCCGATATAAATCGTTTGTTGCTGCCa                                                                                                              <  1:381542/140‑1 (MQ=255)
                   tgGGTCAGCCAGACACGCTGTTGCTCACGCAGGGCGTCCTGTACGCGGGCTTCTTGCTGATAATAACGAGCTACGGCTTCCCCTGGCTCAACCACAATCGCCCCGGCGTTGCCGCCGATATAAATCGTTTGTTGCTGCCa                                                                                                              <  1:260413/140‑1 (MQ=255)
                   tgGGTCAGCCAGACACGCTGTTGCTCACGCAGGGCGTCCTGTACGCGGGCTTCTTGCTGATAATAACGAGCTACGGCTTCCCCTGGCTCAACCACAATCGCCCCGGCGTTGCCGCCGATATAAATCGTTTGTTGCTGCCa                                                                                                              <  2:80905/140‑1 (MQ=255)
                   tgGGTCAGCCAGACACGCTGTTGCTCACGCAGGGCGTCCTGTACGCGGGCTTCTTGCTGATAATAACGAGCTACGGCTTCCCCTGGCTCAACCACAATCGCCCCGGCGTTGCCGCCGATATAAATCGTTTGTTGCTGCCa                                                                                                              <  2:894244/140‑1 (MQ=255)
                   tgGGTCAGCCAGACACGCTGTTACTCACGCACGGCGTCCTGTACGCGGACTTCTTGCTGATAATAACGAGCTACGGCTTCCCCTGGCTCAACCACAATCGCCCCGGCGTTGCCGCCGATATAAATCGTTTGTTGCTGCCa                                                                                                              <  2:401449/140‑1 (MQ=255)
                       tCAGCCAGACACGCTGTTGCTCACGCAGGGCGTCCTGTACGCGGGCTTCTTGCTGATAATAACGAGCTACGGCTTCCCCTGGCTCAACCACAATCGCCCCGGCGTTGCCGCCGATATAAATCGTTTGTTGCTGCCACGGa                                                                                                          >  2:591950/1‑140 (MQ=255)
                          gCCAGACACGCTGTTGCTCACGCAGGGCGTCCTGTACGCGGGCTTCTTGCTGATAATAACGAGCTACGGCTTCCCCTGGCTCAACCACAATCGCCCCGGCGTTGCCGCCGATATAAATCGTTTGTTGCTGCCACGGAGTa                                                                                                       <  2:151363/140‑1 (MQ=255)
                           ccAGACACGCTGTTGCTCACGCAGGGCGTCCTGTACGCGGGCTTCTTGCTGATAATAACGAGCTACGGCTTCCCCTGGCTCAACCACAATCGCCCCGGCGTTGCCGCCGATATAAATCGTTTGTTGCTGCCACGGAGTaa                                                                                                      >  2:262300/1‑140 (MQ=255)
                             aGACACGCTGTTGCTCACGCAGGGCGTCCTGTACGCGGGCTTCTTGCTGATAATAACGAGCTACGGCTT‑CCCTGGCTCAACCACAATCGCCCCGGCGTTGCCGCCGATATAAATCGTTTGTTGCTGCCACGGAGTAAggg                                                                                                   <  2:809598/140‑1 (MQ=255)
                              gACACGCTGTTGCTCACGCAGGGCGTCCTGTACGCGGGCTTCTTGCTGATAATAACGAGCTACGGCTTCCCCTGGCTCAACCACAATCGCCCCGGCGTTGCCGCCGATATAAATCGTTTGTTGCTGCCACGGAGTAAggg                                                                                                   <  1:262300/140‑1 (MQ=255)
                                  cGCTGTTGCTCACGCAGGGCGTCCTGTACGCGGGCTTCTTGCTGATAATAACGAGCTACGGCTTCCCCTGGCTCAACCACAATCGCCCCGGCGTTGCCGCCGATATAAATCGTTTGTTGCTGCCACGGAGTAAGGGCATc                                                                                               <  1:84223/140‑1 (MQ=255)
                                   gCTGTTGCTCACGCAGGGCGTCCTGTACGCGGGCTTCTTGCTGATAATAACGAGCTACGGCTTCCCCTGGCTCAACCACAATCGCCCCGGCGTTGCCGCCGATATAAATCGTTTGTTGCTGCCACGGAGTAAGGGCATCa                                                                                              >  2:440031/1‑140 (MQ=255)
                                     tGTTGCTCACGCAGGGCGTCCTGTACGCGGGCTTCTTGCTGATAATAACGAGCTACGGCTTCCCCTGGCTCAACCACAATCGCCCCGGCGTTGCCGCCGATATAAATCGTTTGTTGCTGCCACGGAGTAAGGGCATCAat                                                                                            >  2:31486/1‑140 (MQ=255)
                                         gCTCACGCAGGGCGTCCTGTACGCGGGCTTCTTGCTGATAATAACGAGCTACGGCTTCCCCTGGCTCAACCACAATCGCCCCGGCGTTGCCGCCGATATAAATCGTTTGTTGCTGCCACGGAGTAAGGGCATCAATATcc                                                                                        >  1:126263/1‑140 (MQ=255)
                                         gCTCACGCAGGGCGTCCTGTACGCGGGCTTCTTGCTGATAATAACGAGCTACGGCTTCCCCTGGCTCAACCACAATCGCCCCGGCGTTGCCGCCGATATAAATCGTTTGTTGCTGCCACGGAGTAAGGGCATCAATATcc                                                                                        >  2:1095138/1‑140 (MQ=255)
                                             aCGCAGGGCGTCCTGTACGCGGGCTTCTTGCTGATAATAACGAGCTACGGCTTCCCCTGGCTCAACCACAATCGCCCCGGCGTTGCCGCCGATATAAATCGTTTGTTGCTGCCACGGAGTAAGGGCATCa                                                                                              >  2:642783/1‑130 (MQ=255)
                                             aCGCAGGGCGTCCTGTACGCGGGCTTCTTGCTGATAATAACGAGCTACGGCTTCCCCTGGCTCAACCACAATCGCCCCGGCGTTGCCGCCGATATAAATCGTTTGTTGCTGCCACGGAGTAAGGGCATCa                                                                                              <  1:642783/130‑1 (MQ=255)
                                               gCAGGGCGTCCTGTACGCGGGCTTCTTGCTGATAATAACGAGCTACGGCTTCCCCTGGCTCAACCACAATCGCCCCGGCGTTGCCGCCGATATAAATCGTTTGTTGCTGCCACGGAGTAAGGGCAT‑AATATCCACaccaa                                                                                 >  2:613919/1‑140 (MQ=255)
                                                  gggCGTCCTGTACGCGGGCTTCTTGCTGATAATAACGAGCTACGGCTTCCCCTGGCTCAACCACAATCGCCCCGGCGTTGCCGCCGATATAAATCGTTTGTTGCTGCCACGGAGTAAGGGCATCAATATCCACaccaacc                                                                               <  1:1095138/140‑1 (MQ=255)
                                                        ccTGTACGCGGGCTTCTTGCTGATAATAACGAGCTACGGCTTCCCCTGGCTCAACCACAATCGCCCCGGCGTTGCCGCCGATATAAATCGTTTGTTGCTGCCACGGAGTAAGGGCATCAATATCCACACCAACCAGCGtt                                                                         <  1:1052609/140‑1 (MQ=255)
                                                            tACGCGGGCTTCTTGCTGATAATAACGAGCTACGGCTTCCCCTGGCTCAACCACAATCGCCCCGGCGTTGCCGCCGATATAAATCGTTTGTTGCTGCCACGGAGTAAGGGCATCAATATCCACACCAACCAGCGTTGGaa                                                                     <  1:591950/140‑1 (MQ=255)
                                                                  ggCTTCTTGCTGATAATAACGAGCTACGGCTTCCCCTGGCTCAACCACAATCGCCCCGGCGTTGCCGCCGATATAAATCGTTTGTTGCTGCCACGGAGTAAGGGCATCAATATCCACACCAACCAGCGTTGGAATGTTga                                                               >  1:906676/1‑140 (MQ=255)
                                                                  ggCTTCTTGCTGATAATAACGAGCTACGGCTTCCCCTGGCTCAACCACAATCGCCCCGGCGTTGCCGCCGATATAAATCGTTTGTTGCTGCCACGGAGTAAGGGCATCAATATCCACACCAACCAGCGTTGGAATGTTga                                                               >  1:932905/1‑140 (MQ=255)
                                                                   gCTTCTTGCTGATAATAACGAGCTACGGCTTCCCCTGGCTCAACCACAATCGCCCCGGCGTTGCCGCCGATATAAATCGTTTGTTGCTGCCACGGAGTAAGGGCATCAATATCCACACCAACCAGCGTTGGAATGTTgaa                                                              >  1:652195/1‑140 (MQ=255)
                                                                      tcttGCTGATAATAACGAGCTACGGCTTCCCCTGGCTCAACCACAATCGCCCCGGCGTTGCCGCCGATATAAATCGTTTGTTGCTGCCACGGAGTAAGGGCATCAATATCCACACCAACCAGCGTTGGAATGTTgaacga                                                           >  2:913635/1‑140 (MQ=255)
                                                                      tcttGCTGATAATAACGAGCTACGGCTTCCCCTGGCTCAACCACAATCGCCCCGGCGTTGCCGCCGATATAAATCGTTTGTTGCTGCCACGGAGTAAGGGCATCAATATCCACACCAACCAGCGTTGGAATGTTgaacga                                                           >  2:932194/1‑140 (MQ=255)
                                                                         tGCTGATAATAACGAGCTACGGCTTCCCCTGGCTCAACCACAATCGCCCCGGCGTCGCCGCCGATATAAATCGTTTGTTGCTGCCACGGAGTAAGGGCATCAATATCCACACCAACCAGCGTTGGAATGTTGaacgaacg                                                        >  2:708277/1‑140 (MQ=255)
                                                                            tGATAATAACGAGCTACGGCTTCCCCTGGCTCAACCACAATCGCCCCGGCGTTGCCGCCGATATAAATCGTTTGTTGCTGCCACGGAGTAAGGGCATCAATATCCACACCAACCAGCGTTGGAATGTTGAACGAACGGGc                                                     <  2:932905/140‑1 (MQ=255)
                                                                            tGATAATAACGAGCTACGGCTTCCCCTGGCTCAACCACAATCGCCCCGGCGTTGCCGCCGATATAAATCGTTTGTTGCTGCCACGGAGTAAGGGCATCAATATCCACACCAACCAGCGTTGGAATGTTGAACGAACGGGc                                                     <  1:196532/140‑1 (MQ=255)
                                                                             gATAATACCGAGCTACGCCTTCCCCTGGCTCCACCGCAAACGCCCCGGTGTTGCCGCCGATATAAATCGTTTGTTGCTGCCACGGAGTAAGGGCATCAATATCCACACCAACCAGCGTTGGAATGTTGAACGAACGGGCa                                                    <  2:442225/140‑1 (MQ=255)
                                                                             gATAATAACGAGCTATGGCTTCCCCTGGCGCAACCACAATCGCCCCGGCGTTGCCGCCGATATAAATCGTTTGTTGCTGCCACGGAGTAAGGGCATCAATATCCACACCAACCAGCGTTGGAATGTTGAACGAACGGGCa                                                    <  1:440031/140‑1 (MQ=255)
                                                                               taataaCGAGCTACGGCTTCCCCTGGCTCAACCACAATCGCCCCGGCGTTGCCGCCGATATAAATCGTTTGTTGCTGCCACGGAGTAAGGGCAT‑AATATCCACACCAACCAGCGTTGGAATGTTGAACGAACGGGCAAgg                                                 <  1:613919/140‑1 (MQ=255)
                                                                                  taaCGAGCTACGGCTTCCCCTGGCTCAACCACAATCGCCCCGGCGTTGCCGCCGATATAAATCGTTTGTTGCTGCCACGGAGTAAGGGCATCAATATCCACACCAACCAGCGTTGGAATGTTgaacgaac                                                         >  2:695646/1‑130 (MQ=255)
                                                                                  taaCGAGCTACGGCTTCCCCTGGCTCAACCACAATCGCCCCGGCGTTGCCGCCGATATAAATCGTTTGTTGCTGCCACGGAGTAAGGGCATCAATATCCACACCAACCAGCGTTGGAATGTTgaacgaac                                                         <  1:695646/130‑1 (MQ=255)
                                                                                  taaCGAGCTACGGCTTCCCCTGGCTCAACCACAATCGCCCCGGCGTTGCCGCCGATATAAATCGTTTGTTGCTGCCACGGAGTAAGGGCATCAATATCCACACCAACCAGCGTTGGAATGTTGAACGAACGGGCAAGGAt                                               >  2:606062/1‑140 (MQ=255)
                                                                                  taaCGAGCTACGGCTTCCCCTGGCTCAACCACAATCGCCCCGGCGTTGCCGCCGATATAAATCGTTTGTTGCTGCCACGGAGTAAGGGCATCAATATCCACACCAACCAGCGTTGGAATGTTGAACGAACGGGCAAGGAt                                               <  2:652195/140‑1 (MQ=255)
                                                                                  taaCGAGCTACGGCTTCCCCTGGCTCAACCACAATCGCCCCGGCGTTGCCGCCGATATAAATCGTTTGTTGCTGCCACGGAGTAAGGGCATCAATATCCACAACAACCAGCGTTGGATTGTTGACCGAACGGGCAAGGAt                                               >  1:536685/1‑140 (MQ=255)
                                                                                    aCGAGCTACGGCTTCCCCTGGCTCAACCACAATCGCCCCGGCGTTGCCGCCGATATAAATCGTTTGTTGCTGCCACGGAGTAAGGGCATCAATATCCACACCAACCAGCGTTGGAATGTTGAACGAACGGGCAAGGATCa                                             <  2:126263/140‑1 (MQ=255)
                                                                                     cGAGCTACGGCTTCCCCTGGCTCAACCACAATCGCCCCGGCGTCGCCGCCGATATAAATCGTTTGTTGCTGCCACGGAGTAAGGGCATCAATATCCACACCAACCAGCGTTGGAATGTTGAACGAACGGGCAAGGATCAc                                            <  1:708277/140‑1 (MQ=255)
                                                                                        gCTACGGCTTCCCCTGGCTCAACCACAATCGCCCCGGCGTTGCCGCCGATATAAATCGTTTGTTGCTGCCACGGAGTAAGGGCATCAATATCCACACCAACCAGCGTTGGAATGTTGAACGAACGGGCAAGGATCACCGt                                         <  1:984475/140‑1 (MQ=255)
                                                                                        gCTACGGCTTCCCCTGGCTCAACCACAATCGCCCCGGCGTTGCCGCCGATATAAATCGTTTGTTGCTGCCACGGAGTAAGGGCATCAATATCCACACCAACCAGCGTTGGAATGTTGAACGAACGGGCAAGGATCACCGt                                         <  1:932194/140‑1 (MQ=255)
                                                                                            cGGCTTCCCCTGGCTCAACCACAATCGCCCCGGCGTTGCCGCCGATATAAATCGTTTGTTGCTGCCACGGAGTAAGGGCATCAATATCCACACCAACCAGCGTTGGAATGTTGAACGAACGGGCAAGGAt                                               >  1:693042/1‑130 (MQ=255)
                                                                                            cGGCTTCCCCTGGCTCAACCACAATCGCCCCGGCGTTGCCGCCGATATAAATCGTTTGTTGCTGCCACGGAGTAAGGGCATCAATATCCACACCAACCAGCGTTGGAATGTTGAACGAACGGGCAAGGAt                                               <  2:693042/130‑1 (MQ=255)
                                                                                                ttCCCCTGGCTCAACCACAATCGCCCCGGCGTTGCCGCCGATATAAATCGTTTGTTGCTGCCACGGAGTAAGGGCATCAATATCCACACCAACCAGCGTTGGAATGTTGAACGAACGGGCAAGGATCACCGTATGTGAgg                                 <  2:926970/140‑1 (MQ=255)
                                                                                                        gCTCAACCACAATCGCCCCGGCGTTGCCGCCGATATAAATCGTTTGTTGCTGCCACGGAGTAAGGGCATCAATATCCACACCAACCAGCGTTGGAATGTTGAACGAACGGGCAAGGATCACCGTATGTGAGGTGGTgccg                         >  1:244006/1‑140 (MQ=255)
                                                                                                             aCCACAATCGCCCCGGCGTTGCCGCCGATATAAATCGTTTGTTGCTGCCACGGAGTAAGGGCATCAATATCCACACCAACCAGCGTTGGAATGTTGAACGAACGGGCAAGGATCACCGTATGTGAGGTGGTGCCGCCGCt                    >  2:1009571/1‑140 (MQ=255)
                                                                                                             aCCACAATCGCCCCGGCGTTGCCGCCGATATAAATCGTTTGTTGCTGCCACGGAGTAAGGGCATCAATATCCACACCAACCAGCGTTGGAATGTTGAACGAACGGGCAAGGATCACCGTATGTGAGGTGGTGCCGCCGCt                    >  1:782389/1‑140 (MQ=255)
                                                                                                             aCCACAATCGCCCCGGCGTTGCCGCCGATATAAATCGTTTGTTGCTGCCACGGAGTAAGGGCATCAATATCCACACCAACCAGCGTTGGAATGTTGAACGAACGGGCAAGGATCACCGTATGTGAGGTGGTGCCGCCGCt                    >  2:852074/1‑140 (MQ=255)
                                                                                                                 caATCGCCCCGGCGTTGCCGTCGATATAAATCGTTTGTTGCTGCCACGGAGTAAGGGCATCAATATCCACACCAACCAGCGTTGGAATGTTGAACGAACGGGCAAGGATCACCGTATGTGAGGTGGTGCCGCCGCTTTTg                <  1:73366/140‑1 (MQ=255)
                                                                                                                 caATCGCCCCGGCGTTGCCGCCGATATAAATCGTTTGTTGCTGCCACGGAGTAAGGGCATCAATATCCACACCAACCAGCGTTGGAATGTTGAACGAACGGGCAAGGATCACCGTATGTGAGGTGGTGCCGCCGCTTTTg                <  1:822021/140‑1 (MQ=255)
                                                                                                                 caATCGCCCCGGCGTTGCCGCCGATATAAATCGTTTGTTGCTGCCACGGAGTAAGGGCATCAATATCCACACCAACCAGCGTTGGAATGTTGAACGAACGGGCAAGGATCACCGTATGTGAGGTGGTGCCGCCGCTTTTg                <  2:782389/140‑1 (MQ=255)
                                                                                                                 caATCGCCCCGGCGTTGCCGCCGATATAAATCGTTTGTTGCTGCCACGGAGTAAGGGCATCAATATCCACACCAACCAGCGTTGGAATGTTGAACGAACGGGCAAGGATCACCGTATGTGAGGTGGTGCCGCCGCTTTTg                <  1:852074/140‑1 (MQ=255)
                                                                                                                     cGCCCCGGCGTTGCCGCCGATATAAATCGTTTGTTGCTGCCACGGAGTAAGGGCATCAATATCCACACCAACCAGCGTTGGAATGTTGAACGAACGGGCAAGGATCACCGTATGTGAGGTGGTGCCGCCGCTTTTGAGca            <  2:244006/140‑1 (MQ=255)
                                                                                                                        cccGGCGTTGCCGCCGATATAAATCGTTTGTTGCTGCCACGGAGTAAGGGCATCAATATCCACACCAACCAGCGTTGGAATGTTGAACGAACGGGCAAGGATCACCGTATGTGAGGTGGTGCCGCCGCTTTTGAGcaaca         <  1:1009571/140‑1 (MQ=255)
                                                                                                                            gCGTTGCCGCCGATATAAATCGTTTGTTGCTGCCACGGAGTAAGGGCATCAATATCCACACCAACCAGCGTTGGAATGTTGAACGAACGGGCAAGGATCACCGTATGTGAGGTGGTGCCGCCGCtttt                 >  1:619125/1‑128 (MQ=255)
                                                                                                                            gCGTTGCCGCCGATATAAATCGTTTGTTGCTGCCACGGAGTAAGGGCATCAATATCCACACCAACCAGCGTTGGAATGTTGAACGAACGGGCAAGGATCACCGTATGTGAGGTGGTGCCGCCGCtttt                 <  2:619125/128‑1 (MQ=255)
                                                                                                                               ttGCCGCCGATATAAATCGTTTGTTGCTGCCACGGAGTAAGGGCATCAATATCCACACCAACCAGCGTTGGAATGTTGAACGAACGGGCAAGGATCACCGTATGTGAGGTGGTGCCGCCGCTTTTGAGCAACAATCCttt  <  1:606062/140‑1 (MQ=255)
                                                                                                                                     |                                                                                                                                     
GTCAGCGGTACGGGCTTGTTGGGTCAGCCAGACACGCTGTTGCTCACGCAGGGCGTCCTGTACGCGGGCTTCTTGCTGATAATAACGAGCTACGGCTTCCCCTGGCTCAACCACAATCGCCCCGGCGTTGCCGTCGATATAAATCGTTTGTTGCTGCCACGGAGTAAGGGCATCAATATCCACACCAACCAGCGTTGGAATGTTGAACGAACGGGCAAGGATCACCGTATGTGAGGTGGTGCCGCCGCTTTTGAGCAACAATCCTTT  >  NC_000913/4141091‑4141357

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A