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 F1 I2 R1 94 59.5 3027142 91.9% 2781943 108.1

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 4,242,259 A→G intergenic (‑5/+367) xylE ← / ← malG D‑xylose transporter/maltose transporter subunit

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009134,242,2590AG100.0% 257.3 / NA 69intergenic (‑5/+367)xylE/malGD‑xylose transporter/maltose transporter subunit
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base G (35/34);  total (35/34)

ACAAAGACGGTATTGAGTGACTCAACAGTACCGGAAATAACGGCGGTGTCGTAGCCAAATAATAAACCACCTAATGTAGCGACTAAGGTAATCGAAAATATATAACTGGAATTATACTGGGTATTCATTCAGACCTGCCTTAGACCATTCTGATCTTTTATCAGTGCATTGATGTTGGAATTGTCAGGCAGTTAAGGCAATTATCATTTTTTACAATGCGTTTACGTAATGTCTTTTCTGTGATCTTAATTGTGATAATTATCCA  >  NC_000913/4242127‑4242391
                                                                                                                                    |                                                                                                                                    
acaaAGACGGTATTGAGTGACTCAACAGTACCGGAAATAACGGCGGTGTCGTAGCCAAATAATAAACCACCTAATGTAGCGACTAAGGTAATCGAAAATATATAACTGGAATTATACTGGGTATTCATTCAGGCCTGcc                                                                                                                                <  2:1149198/139‑1 (MQ=255)
   aaGACGGTATTGAGTGACTCAACAGTACCGGAAATAACGGCGGTGTCGTAGCCAAATATTAAACCACCTAATGTAGCGACTAAGGTAATCGAAAATATATAACTGGAATTATACTGGGTATTCATTCAGGCCTGCCTTa                                                                                                                             <  2:66195/139‑1 (MQ=255)
           aTTGAGTGACTCAACAGTACCGGAAATAACGGCGGTGTCGTAGCCAAATAATAAACCACCTAATGTAGCGACTAAGGTAATCGAAAATAGATAACTGGAATTATACTGGGTATTCATTCAGGCCTGCCTTAGACCATTc                                                                                                                     >  2:906381/1‑139 (MQ=255)
            ttGAGTGACTCAACAGTACCGGAAATAACGGCGGTGTCGTAGCCAAATAATAAACCACCTAATGTAGCGACTAAGGTAATCGAAAATATATAACTGGAATTATACTGGGTATTCATTCAGGCCTGCCTTAGACCATTCt                                                                                                                    <  1:707214/139‑1 (MQ=255)
            ttGAGTGACTCAACAGTACCGGAAATAACGGCGGTGTCGTAGCCAAATAATAAACCACCTAATGTAGCGACTAAGGTAATCGAAAATATATAACTGGAATTATACTGGGTATTCATTCAGGCCTGCCTTAGACCATTCt                                                                                                                    <  1:906381/139‑1 (MQ=255)
                    cTCAACAGTACCGGAAATAACGGCGGTGTCGTAGCCAAATAATAAACCACCTAATGTAGCGACTAAGGTAATCGAAAATATATAACTGGAATTATACTGGGTATTCATTCAGGCCTGCCTTAGACCATTCt                                                                                                                    >  1:636079/1‑131 (MQ=255)
                    cTCAACAGTACCGGAAATAACGGCGGTGTCGTAGCCAAATAATAAACCACCTAATGTAGCGACTAAGGTAATCGAAAATATATAACTGGAATTATACTGGGTATTCATTCAGGCCTGCCTTAGACCATTCt                                                                                                                    <  2:636079/131‑1 (MQ=255)
                      cAACAGTACCGGAAATAACGGCGGTGTCGTAGCCAAATAATAAACCACCTAATGTAGCGACTAAGGTAATCGAAAATATATAACTGGAATTATACTGGGTATTCATTCAGGCCTGCCTTAGACCATTCTGATCTTTTAt                                                                                                          <  1:1408201/139‑1 (MQ=255)
                      cAACAGTACCGGAAATAACGGCGGTGTCGTAGCCAAATAATAAACCACCTAATGTAGCGACTAAGGTAATCGAAAATATATAACTGGAATTATACTGGGTATTCATTCAGGCCTGCCTTAGACCATTCTGATCTTTTAt                                                                                                          >  1:168635/1‑139 (MQ=255)
                        aCAGTACCGGAAATAACGGCGGTGTCGTAGCCAAATAATAAACCACCTAATGTAGCGACTAAGGTAATCGAAAATATATAACTGGAATTATACTGGGTATTCATTCAGGCCTGCCTTAGACCATTCTGATCTTTTATCa                                                                                                        <  1:197023/139‑1 (MQ=255)
                            tACCGGAAATAACGGCGGTGTCGTAGCCAAATAATAAACCACCTAATGTAGCGACTAAGGTAATCGAAAATATATAACTGGAATTATACTGGGTATTCATTCAGGCCTGCCTTAGACCATTCt                                                                                                                    >  1:1432179/1‑123 (MQ=255)
                            tACCGGAAATAACGGCGGTGTCGTAGCCAAATAATAAACCACCTAATGTAGCGACTAAGGTAATCGAAAATATATAACTGGAATTATACTGGGTATTCATTCAGGCCTGCCTTAGACCATTCt                                                                                                                    <  2:1432179/123‑1 (MQ=255)
                              ccGGAAATAACGGCGGTGTCGTAGCCAAATAATAAACCACCTAATGTAGCGACTAAGGTAATCGAAAATATATAACTGGAATTATACTGGGTATTCATTCAGGCCTGCCTTAGACCATTCTGATCTTTTATCAGTGCAt                                                                                                  <  1:28999/139‑1 (MQ=255)
                              ccGGAAATAACGGCGGTGTCGTAGCCAAATAATAAACCACCTAATGTAGCGACTAAGGTAATCGAAAATATATAACTGGAATTATACTGGGTATTCATTCAGGCCTGCCTTAGACCATTCTGATCTTTTATCAGTGCAt                                                                                                  >  2:538124/1‑139 (MQ=255)
                                 gAAATAACGGCGGTGTCGTAGCCAAATAATAAACCACCTAATGTAGCGACTAAGGTAATCGAAAATATATAACTGGAATTATACTGGGTATTCATTCAGGCCTGCCTTAGACCATTCTGATCTTTTATCAGTGCATTGa                                                                                               >  1:1511693/1‑139 (MQ=255)
                                      aaCGGCGGTGTCGTAGCTAAATAATAAACCACCTAATGTAGCGACTAAGGTAATCGAAAATATATAACTGGAATTATACTGGGTATTCATTCAGGCCTGCCTTAGACCATTCTGATCTTTTATCa                                                                                                        <  2:6850/125‑1 (MQ=255)
                                      aaCGGCGGTGTCGTAGCCAAATAATAAACCACCTAATGTAGCGACTAAGGTAATCGAAAATATATAACTGGAATTATACTGGGTATTCATTCAGGCCTGCCTTAGACCATTCTGATCTTTTATCa                                                                                                        >  1:6850/1‑125 (MQ=255)
                                                          ataataAACCACCTAATGTAGCGACTAAGGTAATCGAAAATATATAACTGGAATTATACTGGGTATTCATTCAGGcc                                                                                                                                    >  1:772799/1‑77 (MQ=255)
                                                          ataataAACCACCTAATGTAGCGACTAAGGTAATCGAAAATATATAACTGGAATTATACTGGGTATTCATTCAGGCCTGCCTTAGACCATTCTGATCTTTTAt                                                                                                          <  2:1337713/103‑1 (MQ=255)
                                                          ataataAACCACCTAATGTAGCGACTAAGGTAATCGAAAATATATAACTGGAATTATACTGGGTATTCATTCAGGCCTGCCTTAGACCATTCTGATCTTTTAt                                                                                                          >  1:1337713/1‑103 (MQ=255)
                                                          ataataAACCACCTAATGTAGCGACTAAGGTAATCGAAAATATATAACTGGAATTATACTGGGTATTCATTCAGGCCTGCCTTAGACCATTCTGATCTTTTATCAGTGCATTGATGTTGGAATTGTCa                                                                                 >  2:828289/1‑128 (MQ=255)
                                                          ataataAACCACCTAATGTAGCGACTAAGGTAATCGAAAATATATAACTGGAATTATACTGGGTATTCATTCAGGCCTGCCTTAGACCATTCTGATCTTTTATCAGTGCATTGATGTTGGAATTGTCa                                                                                 <  1:828289/128‑1 (MQ=255)
                                                             ataaACCACCTAATGTAGCGACTAAGGTAATCGAAAATATATAACTGGAATTATACTGGGTATTCATTCAGGCCTGCCTTAGACCATTCTGATCttt                                                                                                             <  2:1322680/97‑1 (MQ=255)
                                                             ataaACCACCTAATGTAGCGACTAAGGTAATCGAAAATATATAACTGGAATTATACTGGGTATTCATTCAGGCCTGCCTTAGACCATTCTGATCttt                                                                                                             >  1:1322680/1‑97 (MQ=255)
                                                                aaCCACCTAATGTAGCGACTAAGGTAATCGAAAATATATAACTGGAATTATACTGGGTATTCATTCAGGCCTGCCTTAGACCATTCt                                                                                                                    <  1:341306/87‑1 (MQ=255)
                                                                aaCCACCTAATGTAGCGACTAAGGTAATCGAAAATATATAACTGGAATTATACTGGGTATTCATTCAGGCCTGCCTTAGACCATTCt                                                                                                                    >  2:341306/1‑87 (MQ=255)
                                                                aaCCACCTAATGTAGCGACTAAGGTAATCGAAAATATATAACTGGAATTATACTGGGTATTCATTCAGGCCTGCCTTAGACCATTCTGATCTTTTATCAGTGCATTGATGTTGGAATTGTCAGGCAGTTAAGGCAATTa                                                                <  2:1511693/139‑1 (MQ=255)
                                                                             aGCGACTAAGGTAATCGAAAATATATAACTGGAATTATACTGGGTATTCATTCAGGCCTGCCTTAGACCATTCTGATCTTTTATCAGTGCATTGATGTTGGAATTGTCAGGCAGTTAAGGCAATTATCATTTTTTACaa                                                   >  1:410938/1‑139 (MQ=255)
                                                                              gCGACTAAGGTAATCGAAAATATATAACTGGAATTATACTGGGTATTCATTCAGGCCTGCCTTAGACCATTCt                                                                                                                    >  1:375135/1‑73 (MQ=255)
                                                                              gCGACTAAGGTAATCGAAAATATATAACTGGAATTATACTGGGTATTCATTCAGGCCTGCCTTAGACCATTCt                                                                                                                    <  2:375135/73‑1 (MQ=255)
                                                                              gCGACTAAGGTAATCGAAAATATATAACTGGAATTATACTGGGTATTCATTCAGGCCTGCCTTAGACCATTCTGATCTTTTATCAGTGCATTGATGTTGGAATTGTCAGGCAGTTAAGGCAATTATCATTTTTTACAAt                                                  >  2:312263/1‑139 (MQ=255)
                                                                               cGACTAAGGTAATCGAAAATATATAACTGGAATTATACTGGGTATTCATTCAGGCCTGCCTTAGACCATTCTGATCTTTTAt                                                                                                          >  2:1117051/1‑82 (MQ=255)
                                                                               cGACTAAGGTAATCGAAAATATATAACTGGAATTATACTGGGTATTCATTCAGGCCTGCCTTAGACCATTCTGATCTTTTAt                                                                                                          <  1:1117051/82‑1 (MQ=255)
                                                                               cGACTAAGGTAATCGAAAATATATAACTGGAATTATACTGGGTATTCATTCAGGCCTGCCTTAGACCATTCTGATCTTTTATCAGTGCAt                                                                                                  >  2:1130044/1‑90 (MQ=255)
                                                                               cGACTAAGGTAATCGAAAATATATAACTGGAATTATACTGGGTATTCATTCAGGCCTGCCTTAGACCATTCTGATCTTTTATCAGTGCAt                                                                                                  <  1:1130044/90‑1 (MQ=255)
                                                                                gACTAAGGTAATCGAAAATATATAACTGGAATTATACTGGGTATTCATTCAGGCCTGCCTTAGACCATTCTGATCTTTTATCAGTGCATTGATGTTGGAATTGTCAGGCAGTTAAGGCAATTATCATTTTTTACAATGc                                                >  1:287418/1‑139 (MQ=255)
                                                                                     aGGTAATCGAAAATATATAACTGGAATTATACTGGGTATTCATTCAGGCCTGCCTTAGACCATTCTGATCTTTTATCAGTGCATTGATGTTGGAATTGTCAGGCAGTTAAGGCAATTATCATTTTTTACAATGCGTTTa                                           >  1:446762/1‑139 (MQ=255)
                                                                                          aTCGAAAATATATAACTGGAATTATACTGGGTATTCATTCAGGCCTGCCTTAGACCATTCTGATCTTTTATCAGTGCATTGATGTTGGAATTGTCAGGCAGTTAAGGCAATTATCATTTTTTACAATGCGTTTACGTaa                                      <  2:465775/139‑1 (MQ=255)
                                                                                          aTCGAAAATATATAACTGGAATTATACTGGGTATTCATTCAGGCCTGCCTTAGACCATTCTGATCTTTTATCAGTGCATTGATGTTGGAATTGTCAGGCAGTTAAGGCAATTATCATTTTTTACAATGCGTTTACGTaa                                      >  1:154924/1‑139 (MQ=255)
                                                                                          aTCGAAAATATATAACTGGAATTATACTGGGTATTCATTCAGGCCTGCCTTAGACCATTCTGATCTTTTATCAGTGCATTGATGTTGGAATTGTCAGGCAGTTAAGGCAATTATCATTTTTTACAATGCGTTTACGTaa                                      <  1:1029557/139‑1 (MQ=255)
                                                                                          aTCGAAAATATATAACTGGAATTATACTGGGTATTCATTCAGGCCTGCCTTAGACCATTCTGATCTTTTATCAGTGCATTGATGTTGGAATTGTCAGGCAGTTAAGGCAATTATCATTTTTTACAATGCGTTTACGTaa                                      <  2:410938/139‑1 (MQ=255)
                                                                                             gAAAATATATAACTGGAATTATACTGGGTATTCATTCAGGCCTGCCTTAGACCATTCTGATCTTTTATCAGTGCATTGATGTTGGAATTGTCAGGc                                                                              <  2:637968/96‑1 (MQ=255)
                                                                                             gAAAATATATAACTGGAATTATACTGGGTATTCATTCAGGCCTGCCTTAGACCATTCTGATCTTTTATCAGTGCATTGATGTTGGAATTGTCAGGc                                                                              >  1:637968/1‑96 (MQ=255)
                                                                                               aaaTATATAACTGGAATTATACTGGGTATTCATTCAGGCCTGCCTTAGACCATTCTGATCTTTTATCAGTGCATTGATGTTGGAATTGTCAGGCAGTTAAGGCAATTATCATTTTTTACAATGCGTTTACGTAATGTCt                                 <  2:168635/139‑1 (MQ=255)
                                                                                                     ataACTGGAATTATACTGGGTATTCATTCAGGCCTGCCTTAGACCATTCTGATCTTTTATCAGTGCATTGATGTTGGAATTGTCAGGCAGTTAAGGCAATTATCATTTTTTACaa                                                   <  2:1387975/115‑1 (MQ=255)
                                                                                                     ataACTGGAATTATACTGGGTATTCATTCAGGCCTGCCTTAGACCATTCTGATCTTTTATCAGTGCATTGATGTTGGAATTGTCAGGCAGTTAAGGCAATTATCATTTTTTACaa                                                   >  1:1387975/1‑115 (MQ=255)
                                                                                                            gAATTATACTGGGTATTCATTCAGGCCTGCCTTAGACCATTCTGATCTTTTATCAGTGCATTGATGTTGGAATTGTCAGGCAGTTAAGGCAATTATCATTTTTTACAATGCGTTTACGTAATGTCTTTTCTGTGATCtt                    >  2:74255/1‑139 (MQ=255)
                                                                                                             aaTTATACTGGGTATTCATTCAGGCCTGCCTTAGACCATTCTGATCTTTTATCAGTGCATTGATGTTGGAATTGTCAGGCAGTTAAGGCAATTATCATTTTTTACAATGCGTTTACGTAATGTCTTTTCtgt                          <  1:699100/132‑1 (MQ=255)
                                                                                                             aaTTATACTGGGTATTCATTCAGGCCTGCCTTAGACCATTCTGATCTTTTATCAGTGCATTGATGTTGGAATTGTCAGGCAGTTAAGGCAATTATCATTTTTTACAATGCGTTTACGTAATGTCTTTTCtgt                          >  2:699100/1‑132 (MQ=255)
                                                                                                              aTTATACTGGGTATTCATTCAGGCCTGCCTTAGACCATTCTGATCTTTTATCAGTGCa                                                                                                   <  2:955250/58‑1 (MQ=255)
                                                                                                              aTTATACTGGGTATTCATTCAGGCCTGCCTTAGACCATTCTGATCTTTTATCAGTGCa                                                                                                   >  1:955250/1‑58 (MQ=255)
                                                                                                              aTTATACTGGGTATTCATTCAGGCCTGCCTTAGACCATTCTGATCTTTTATCAGTGCATTGATGTTGGAATTGTCAGGCAGTTAAGGCAATTATCATTTTTTACAAt                                                  <  1:559334/107‑1 (MQ=255)
                                                                                                              aTTATACTGGGTATTCATTCAGGCCTGCCTTAGACCATTCTGATCTTTTATCAGTGCATTGATGTTGGAATTGTCAGGCAGTTAAGGCAATTATCATTTTTTACAAt                                                  >  2:559334/1‑107 (MQ=255)
                                                                                                              aTTATACTGGGTATTCATTCAGGCCTGCCTTAGACCATTCTGATCTTTTATCAGTGCATTGATGTTGGAATTGTCAGGCAGTTAAGGCAATTATCATTTTTTACAATGCGTTTACGTAATGTCTTTTCTGTGATCTTaa                  <  2:154924/139‑1 (MQ=255)
                                                                                                              aTTATACTGGGTATTCATTCAGGCCTGCCTTAGACCATTCTGATCTTTTATCAGTGCATTGATGTTGGAATTGTCAGGCAGTTAAGGCAATTATCATTTTTTACAATGCGTTTACGTAATGTCTTTTCTGTGATCTTaa                  <  2:446762/139‑1 (MQ=255)
                                                                                                                  taCTGGGTATTCATTCAGGCCTGCCTTAGACCATTCTGATCTTTTATCAGTGCATTGATGTTGGAATTGTCAGGCAGTTAAGGCAATTATCATTTTTTACAATGCGTTTACGTAATGTCTTTTCTGTGATCTTAATtgt              <  1:538124/139‑1 (MQ=255)
                                                                                                                       ggTATTCATTCAGGCCTGCCTTAGACCATTCTGATCTTTTa                                                                                                           <  2:901354/41‑1 (MQ=255)
                                                                                                                       ggTATTCATTCAGGCCTGCCTTAGACCATTCTGATCTTTTa                                                                                                           >  1:901354/1‑41 (MQ=255)
                                                                                                                       ggTATTCATTCAGGCCTGCCTTAGACCATTCTGATCTTTTATCAGTGCa                                                                                                   >  2:188058/1‑49 (MQ=255)
                                                                                                                       ggTATTCATTCAGGCCTGCCTTAGACCATTCTGATCTTTTATCAGTGCa                                                                                                   <  1:188058/49‑1 (MQ=255)
                                                                                                                       ggTATTCATTCAGGCCTGCCTTAGACCATTCTGATCTTTTATCAGTGCAtt                                                                                                 <  1:248272/51‑1 (MQ=255)
                                                                                                                       ggTATTCATTCAGGCCTGCCTTAGACCATTCTGATCTTTTATCAGTGCAtt                                                                                                 >  2:248272/1‑51 (MQ=255)
                                                                                                                       ggTATTCATTCAGGCCTGCCTTAGACCATTCTGATCTTTTATCAGTGCATTGATGTTGGAATTGTCAgg                                                                               <  2:1322170/69‑1 (MQ=255)
                                                                                                                       ggTATTCATTCAGGCCTGCCTTAGACCATTCTGATCTTTTATCAGTGCATTGATGTTGGAATTGTCAgg                                                                               >  1:1322170/1‑69 (MQ=255)
                                                                                                                       ggTATTCATTCAGGCCTGCCTTAGACCATTCTGATCTTTTATCAGTGCATTGATGTTGGAATTGTCAGGCAGTTAAGGCAATTATCATTTTTTACAATGCGTTTACGTAATGTCTTTTCTGTGATCTTAATTGTGATaa         >  2:519435/1‑139 (MQ=255)
                                                                                                                       ggTATTCATTCAGGCCTGCCTTAGACCATTCTGATCTTTTATCAGTGCATTGATGTTGGAATTGTCAGGCAGTTAAGGCAATTATCATTTTTTACAATGCGTTTACGTAATGTCTTTTCTGTGATCTTAATTGTGATaa         >  2:843982/1‑139 (MQ=255)
                                                                                                                       ggTATTCATTCAGGCCTGCCTTAGACCATTCTGATCTTTTATCAGTGCATTGATGTTGGAATTGTCAGGCAGTTAAGGCAATTATCATTTTTTACAATGCGTTTACGTAATGTCTTTTCTGTGATCTTAATTGTGATaa         >  1:1216497/1‑139 (MQ=255)
                                                                                                                       ggTATTCATTCAGGCCTGCCTTAGACCATTCTGATCTTTTATCAGTGCATTGATGTTGGAATTGTCAGGCAGTTAAGGCAATTATCATTTTTTACAATGCGTTTACGTAATGTCTTTTCTGTGATCTTAATTGTGATaa         >  1:115383/1‑139 (MQ=255)
                                                                                                                              attcaGGCCTGCCTTGGACCATTCTGATCTTTTATCAGTGCATTGATGTTGGAATTGTCAGGCAGTTAAGGCAATTATCATTTTTTAAAATGCGTTTACGTAATGTCTTTTCTGTGATCTTAATTGTGATAATTATCCa  >  2:1006796/1‑139 (MQ=255)
                                                                                                                                    |                                                                                                                                    
ACAAAGACGGTATTGAGTGACTCAACAGTACCGGAAATAACGGCGGTGTCGTAGCCAAATAATAAACCACCTAATGTAGCGACTAAGGTAATCGAAAATATATAACTGGAATTATACTGGGTATTCATTCAGACCTGCCTTAGACCATTCTGATCTTTTATCAGTGCATTGATGTTGGAATTGTCAGGCAGTTAAGGCAATTATCATTTTTTACAATGCGTTTACGTAATGTCTTTTCTGTGATCTTAATTGTGATAATTATCCA  >  NC_000913/4242127‑4242391

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A