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
A5 F91 I0 R1 918 53.4 2573728 94.2% 2424451 136.5

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_002947 1,070,265 G→C 10.3% intergenic (+62/+82) aroP‑I → / ← PP_0928 aromatic amino acid transport protein/K+‑dependent Na+/Ca+ exchanger‑like protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0029471,070,2650GC10.3% 140.2 / 6.1 46intergenic (+62/+82)aroP‑I/PP_0928aromatic amino acid transport protein/K+‑dependent Na+/Ca+ exchanger‑like protein
Reads supporting (aligned to +/- strand):  ref base G (23/18);  new base C (3/2);  total (26/20)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CGCATCTCGGTAATGCTGATCCCGGCATGGATCGCTGTGCTGTGGGTGGCTTTCAAGCTGAAGAAGGCTCGCCAGGCCAAGGGCTGATCGGGTTTGTTCGTAAGGGGTATGCCGTTAGGTTTTCGGCGCCTGTGAGATCGAGCGCCGCGCGGGCGGCGCTCGATCTCACAGGCGATGAAAGCCTAAAGGCATGCGTCTGGCGGCCCTGACGCGTTCCCCTTCCATGCCCCTCAATGCTGCCTCCGCCAAGCACGCACAGTGGTGTACAGCAACACCGTAGCGAGCACCGGCAGTACA  >  NC_002947/1070117‑1070413
                                                                                                                                                    |                                                                                                                                                    
cGCATCTCGGTAATGCTGATCCCGTCATAGATCGCTGTGCTGTGGGTGGCTTTCAAGCTGAAGAAGCCTCGCCAGTCCAAGGGCTGATCGGGTTTGTTCGTAAGGGGTATGCCGTTAGGTTTTCGGCGCCTGTGAGATCGAGCGCcgcgc                                                                                                                                                     <  2:459104/150‑1 (MQ=255)
 gCATCTCGGTAATGCTGATCCCGGCATGGATCGCTGTGCTGTGGGTGGCTTTCAAGCTGAAGAAGGCTCGCCAGGCCAAGGGCTGATCGGGTTTGTTCGTAAGGGGTATGCCGTTAGGTTTTCGGCGCCTGTGAGATCGAGCGCcgcgcg                                                                                                                                                    >  2:1061955/1‑150 (MQ=255)
    tctcGGTAATGCTGATCCCGGCATGGATCGCTGTGCTGTGGGTGGCTTTCAAGCTGAAGAAGGCTCGCCAGGCCAAGGGCTGATCGGGTTTGTTCGTAAGGGGTATGCCGTTAGGTTTTCGGCGCCTGTGAGATCGAGCGCCGCgcgggc                                                                                                                                                 >  1:686707/1‑150 (MQ=255)
               cTGATCCCGGCATGGATCGCTGTGCTGTGGGTGGCTTTCAAGCTGAAGAAGGCTCGCCAGGCCAAGGGCTGATCGGGTTTGTTCGTAAGGGGTATGCCGTTAGGTTTTCGGCGCCTGTGAGATCGAGCGCCGCGCGGGCGGCGCTCGAtc                                                                                                                                      >  1:1243614/1‑150 (MQ=255)
                      cGGCATGGATCGCTGTGCTGTGGGTGGCTTTCAAGCTGAAGAAGGCTCGCCAGGCCAAGGGCTGATCGGGTTTGTTCGTAAGGGGTATGCCGTTAGGTTTTCGGCGCCTGTGAGGTCGAGCGCCGCGCGGGCGGCGCTCGATCTCACAgg                                                                                                                               >  1:852666/1‑150 (MQ=255)
                              aTCGCTGTGCTGTGGGTGGCTTTCAAGCTGAAGAAGGCTCGCCAGGCCAAGGGCTGATCGGGTTTGTTCGTAAGGGGTATGCCGTTAGGTTTTCGGCTCCTTGTTTATCGAGCGCCGCGCGGGCGGCGCTCGATCTCACAGGAGATGaaa                                                                                                                       <  1:553979/150‑1 (MQ=39)
                                    gtgctgtgGGTGGCTTTCAAGCTGAAGAAGGCTCGCCAGGCCAAGGGCTGATCGGGTTTGTTCGTAAGGGGTATGCCGTTAGGTTTTCGGCGCCTGTGAGATCGAGCGCCGCGCGGGCGGCGCTCGATCTAACAGGCGATGAAAGCCTaa                                                                                                                 <  2:356344/150‑1 (MQ=255)
                                      gctgtgGGTGGCTTTCAAGCTGAAGAAGGCTCGCCAGGCCAAGGGCTGATCGGGTTTGTTCGTAAGGGGTATGCCGTTAGGTTTTCGGCGCCTGTGAGATCGAGCGCCGCGCGGGCGGCGCTCGATCTCACAGGCGATGAAAGCCTAAAg                                                                                                               >  2:259216/1‑150 (MQ=255)
                                      gctgtgGGTGGCTTTCAAGCTGAAGAAGGCTCGCCAGGCCAAGGGCTGATCGGGTTTGTTCGTAAGGGGTATGCCGTTAGGTTTTCGGCGCCTGTGAGATCGAGCGCCGCGCGGGCGGCGCTCGATCTCACAGGCGATGAAAGCCTAAAg                                                                                                               <  1:259216/150‑1 (MQ=255)
                                          tgggtggCTTTCAAGCTGAAGAAGGCTCGCCAGGCCAAGGGCTGATCGGGTTTGTTCGTAAGGGGTATGCCGTTAGGTTTTCGGCGCCTGTGAGATCGAGCGCCGCGCGGGCGGCGCTCGATCTCACAGGCGATGAAAGCCTaaa                                                                                                                >  2:205629/1‑145 (MQ=255)
                                          tgggtggCTTTCAAGCTGAAGAAGGCTCGCCAGGCCAAGGGCTGATCGGGTTTGTTCGTAAGGGGTATGCCGTTAGGTTTTCGGCGCCTGTGAGATCGAGCGCCGCGCGGGCGGCGCTCGATCTCACAGGCGATGAAAGCCTaaa                                                                                                                <  1:205629/145‑1 (MQ=255)
                                              tggCTTTCAAGCTGAAGAAGGCTCGCCAGGCCAAGGGCTGATCGGGTTTGTTCGTAAGGGGTATGCCGTTAGGTTTTCGGCGCCTGTGAGATCGAGCGCCGCGCGGGCGGCGCTCGATCTCACAGGCGATGAAAGCCTAAAGGCATGCGt                                                                                                       >  2:792146/1‑150 (MQ=255)
                                                  tttCAAGCTGAAGAAGGCTCGCCAGGCCAAGGGCTGATCGGGTTTGTTCGTAAGGGGTATGCCGTTAGGTTTTCGGCGCCTGTGAGATCGAGCGCCGCGCGGGCGGCGCTCGATCTCACAGGCGATGAAAGCCTAAAGGCATGCGTCTgg                                                                                                   >  1:1267218/1‑150 (MQ=255)
                                                      aaGCTGAAGAAGGCTCGCCAGGCCAAGGGCTGATCGGGTTTGTTCGTAAGGGGTATGCCGTTAGGTTTTCGGCGCCTGTGAGATCGAGCGCCGCGCGGGCGGCGCTCGATCTCACAGGCGATGAAAGCCTAAAGGCATACGACTggcggc                                                                                               >  1:903914/1‑150 (MQ=255)
                                                       aGCTGAAGAAGGCTCGCCAGGCCAAGGGCTGATCGGGTTTGTTCGTAAGGGGTATGCCGTTAGGTTTTCGGCGCCTGTGAGATCGAGCGCCGCGCGGGCGGCGCTCGAt                                                                                                                                       <  2:1007374/109‑1 (MQ=255)
                                                       aGCTGAAGAAGGCTCGCCAGGCCAAGGGCTGATCGGGTTTGTTCGTAAGGGGTATGCCGTTAGGTTTTCGGCGCCTGTGAGATCGAGCGCCGCGCGGGCGGCGCTCGAt                                                                                                                                       >  1:1007374/1‑109 (MQ=255)
                                                       aGCTGAAGAAGGCTCGCCAGGCCAAGGGCTGATCGGGTTTGTTCGTAAGGGGTATGCCGTTAGGTTTTCGGCGCCTGTGAGATCGAGCGCCGCGCGGGCGGCGCTCGATCTCACAGGCGATGAAAGCCTAAAGGCATGCGTCTGGCGGcc                                                                                              >  2:161435/1‑150 (MQ=255)
                                                       aGCTGAAGAAGGCTCGCCAGGCCAAGGGCTGATCGGGTTTGTTCGTAAGGGGTATGCCGTTAGGTTTTCGGCGCCTGTGAGATCGAGCGCCGCGCGGGCGGCGCTCGATCTCACAGGCGATGAAAGCCTAAAGGCATGCGTCTGGCGGcc                                                                                              <  1:161435/150‑1 (MQ=255)
                                                        gCTGAAGAAGGCTCGCCAGGCCAAGGGCTGATCGGGTTTGTTCGTAAGGGGTATGCCGTTAGGTTTTCGGCGCCTGTGAGATCGAGCGCCGCGCGGGCGGCGCTCGATCTCACAGGCGATGAAAGCCTAAAGGCATGCGTCTGGCGGccc                                                                                             >  2:481634/1‑150 (MQ=255)
                                                        gCTGAAGAAGGCTCGCCAGGCCAAGGGCTGATCGGGTTTGTTCGTAAGGGGTATGCCGTTAGGTTTTCGGCGCCTGTGAGATCGAGCGCCGCGCGGGCGGCGCTCGATCTCACAGGCGATGAAAGCCTAAAGGCATGCGTCTGGCGGccc                                                                                             >  2:230076/1‑150 (MQ=255)
                                                            aagaagGCTCGCCAGGCCAAGGGCTGATCGGGTTTGTTCGTAAGGGGTATGCCGTTAGGTTTTCGGCGCCTGTGAGATCGAGCGCCGCGCGGGCGGCGCTCGATCTCACAgg                                                                                                                               >  2:229798/1‑112 (MQ=255)
                                                            aagaagGCTCGCCAGGCCAAGGGCTGATCGGGTTTGTTCGTAAGGGGTATGCCGTTAGGTTTTCGGCGCCTGTGAGATCGAGCGCCGCGCGGGCGGCGCTCGATCTCACAgg                                                                                                                               <  1:229798/112‑1 (MQ=255)
                                                            aagaagGCTCGCCAGGCCAAGGGCTGATCGGGTTTGTTCGTAAGGGGTATGCCGTTAGGTTTTCGGCGCCTGTGAGATCGAGCGCCGCGCGGGCGGCGCTCGATCTCACAGGCGATGAAAGCCTAAAGGCATGCGTCTGGCGGCCCTGAc                                                                                         >  2:697942/1‑150 (MQ=255)
                                                                 ggCTCGCCAGGCCAAGGGCTGATCGGGTTTGTTCGTAAGGGGTATGCCGTTAGGTTTTCGGCGCCTGTGAGATCGAGCGCCGCGCGGGCGGCGCTCGATCTCGCAgg                                                                                                                               <  2:939690/107‑1 (MQ=255)
                                                                 ggCTCGCCAGGCCAAGGGCTGATCGGGTTTGTTCGTAAGGGGTATGCCGTTAGGTTTTCGGCGCCTGTGAGATCGAGCGCCGCGCGGGCGGCGCTCGATCTCGCAgg                                                                                                                               >  1:939690/1‑107 (MQ=255)
                                                                 ggCTCGCCAGGCCAAGGGCTGATCGGGTTTGTTCGTAAGGGGTATGCCGTTAGGTTTTCGGCGCCTGTGAGATCGAGCGCCGCCCGCGCGGCGCt                                                                                                                                           <  2:1012631/95‑1 (MQ=255)
                                                                 ggCTCGCCAGGCCAAGGGCTGATCGGGTTTGTTCGTAAGGGGTATGCCGTTAGGTTTTCGGCGCCTGTGAGATCGAGCGCCGCCCGCGCGGCGCt                                                                                                                                           >  1:1012631/1‑95 (MQ=255)
                                                                    tCGCCAGGCCAAGGGCTGATCGGGTTTGTTCGTAAGGGGTATGCCGTTAGGTTTTCGGCGCCTGTGAGATCGAGCGCCGCGCGGGCGGCGCTCGATCTCACAGGCGATGAAAGCCTAAAGGCATGCGTCTGGCGGCCCTGACGCGTTccc                                                                                 >  2:258344/1‑150 (MQ=255)
                                                                           gCCAAGGGCTGATCGGGTTTGTTCGTAAGGGGTATGCCGTTAGGTTTTCGGCGCCTGTGAGATCGAGCGCCGCGCGGGCGGCGCTCGATCTCACAGGCGATGAAAGCCTAAAGGCATGCGTCTGGCGGCCCTGACGCGTTCCCCTTCCAt                                                                          >  1:232754/1‑150 (MQ=255)
                                                                                 ggCTGATCGGGTTTGTTCGTAAGGGGTATGCCGTTAGGTTTTCGGCGCCTGTGAGATCGAGCGCCGCGCGGGCGGCGCTCGATCTCACAGGCGATGAAAGCCTAAAGGCATGCGTCTGGCGGCCCTGACGCGTTCCCCTTCCATGCCCCt                                                                    <  2:187750/150‑1 (MQ=255)
                                                                                        cGGGTTTGTTCGTAAGGGGTATGCCGTTACGTTTTCGGCGCCTGTGAGATCGAGCGCCGCGCGGGCGGCGCTCGATCTCACAGGCGATGAAAGCCTAAAGGCATGCGTCTGGCGGCCCTGACGCGTTCCCCTTCCATGCCCCTCAAtgct                                                             <  1:75766/150‑1 (MQ=255)
                                                                                                ttCGTAAGGGGTATGCCGTTAGGTTTTCGGCGCCTGTGAGATCGAGCGCCGCGCGGGCGGCGCTCGATCTCACAGGCGCTGAAAGCCTAAAGGCAGGTGTCTTTCGGCCCGGACGCGTTCCCCTTCCATGCCCCTCAATGCTGCCTCCGc                                                     >  2:1108747/1‑150 (MQ=38)
                                                                                                ttCGTAAGGGGTATGCCGTTAGGTTTTCGGCGCCTGTAAGATCGAGCGCCGCGCGGGAGGCGCTCGATCTCACAGGCGATGAAAGCCTAAAGGCATGCGTCTGGCGGCCCTGACGCGTTCACCTTCCATGCCCCTCAATGCTGACTCCGc                                                     >  1:411953/1‑150 (MQ=255)
                                                                                                   gTAAGGGGTATGCCGTTAGGTTTTCGGCGCCTGTGAGATCGAGCGCCGCGCGGGCGGCGCTCGATCTCACAGGCGATGAAAGCCTAAAGGCATGCGTCTGGCGGCCCTGACGCGTTCCCCTTCCATGCCCCTCAATGCTGCCTCCGCCaa                                                  <  1:697942/150‑1 (MQ=255)
                                                                                                   gTAAGGGGTATGCCGTTAGGTTTTCGGCGCCTGTGAGATCGAGCGCCGCGCGGGCGGCGCTCGATCTCACAGGCGATGAAAGCCTAAAGGCATGCGTCTGGCGGCCCTGACGCGTTCCCCTTCCATGCCCCTCAATGCTGCCTCCGCCaa                                                  <  1:481634/150‑1 (MQ=255)
                                                                                                   gTAAGGGGTATGCCGTTAGGTTTTCGGCGCCTGTGAGATCGAGCGCCGCGCGGGCGGCGCTCGATCTCACAGGCGATGAAAGCCTAAAGGCATGCGTCTGGCGGCCCTGACGCGTTCCCCTTCCATGCCCCTCAATGCTGCCTCCGCCaa                                                  <  1:1061955/150‑1 (MQ=255)
                                                                                                          gTATGCCGTTAGGTTTTCGGCGCCTGTGAGATCGAGCGCCGCGCGGGCGGCGCTCGATCTCACAGGCGATGAAAGCCTAAAGGCATGCGTCTGGCGGCCCTGACGCGTTCCCCTTCCATGCCCCTCAATGCTGCCTCCGCCAAgcacgca                                           <  2:686707/150‑1 (MQ=255)
                                                                                                          gTATGCCGTTAGGTTTTCGGCGCCTGTGAGATCGAGCGCCGCGCGGGCGGCGCTCGATCTCACAGGCGATGAAAGCCTAAAGGCATGCGTCTGGCGGCCCTGACGCGTTCCCCTTCCATGCCCCTCAATGCTGCCTCCGCCAAgcacgca                                           <  2:852666/150‑1 (MQ=255)
                                                                                                             tGCCGTTAGGTTTTCGGCGCCTGTGAGATCGAGCGCCGCGCGGGCGGCGCTCGATCTCACAGGCGATGAAAGCCTAAAGGCATGCGTCTGGCGGCCCTGACGCGTTCCCCTTCCATGCCCCTCAATGCTGCCTCCGCCAAGCACGCACAg                                        >  2:958462/1‑150 (MQ=255)
                                                                                                               ccGTTAGGTTTTCGGCGCCTGTGAGATCGAGCGCCGCGCGGGCGGCGCTCGATCTCACAGGCGATGAAAGCCTAAAGGCATGCGTCTGGCGGCCCTGACGCGTTCCCCTTCCATGCCCCTCAATGCTGCCTCCGCCAAGCACGCACAgtg                                      <  1:935437/150‑1 (MQ=255)
                                                                                                               ccGTTAGGTTTTCGGCGCCTGTGAGATCGAGCGCCGCGCGGGCGGCGCTCGATCTCACAGGCGATGAAAGCCTAAAGGCATGCGTCTGGCGGCCCTGACGCGTTCCCCTTCCATGCCCCTCAATGCTGCCTCCGCCAAGCACGCACAgtg                                      <  1:230076/150‑1 (MQ=255)
                                                                                                               ccGTTAGGTTTTCGGCGCCTGTGAGATCGAGCGCCGCGCGGGCGGCGCTCGATCTCACAGGCGATGAAAGCCTAAAGGCATGCGTCTGGCGGCCCTGACGCGTTCCCCTTCCATGCCCCTCAATGCTGCCTCCGCCAAGCACGCACAgtg                                      >  2:935437/1‑150 (MQ=255)
                                                                                                                cGTTAGGTTTTCGGCGCCTGTGAGATCGAGCGCCGCGCGGGCGGCGCTCGATCTCACAGGCGATGAAAGCCTAAAGGCATGCGTCTGGCGGCCCTGACGCGTTCCCCTTCCATGccc                                                                      >  2:168112/1‑117 (MQ=255)
                                                                                                                cGTTAGGTTTTCGGCGCCTGTGAGATCGAGCGCCGCGCGGGCGGCGCTCGATCTCACAGGCGATGAAAGCCTAAAGGCATGCGTCTGGCGGCCCTGACGCGTTCCCCTTCCATGccc                                                                      <  1:168112/117‑1 (MQ=255)
                                                                                                                  ttAGGTTTTCGGCGCCTGTGAGATCGAGCGCCGCGCGGGCGGCGCTCGATCTCACAGGCGATGAAAGCCTAAAGGCATGCGTCTGGCGGCCCTGACGCGTTCCCCTTCCATGCCCCTCAATGCTGCCTCCGCCAAGCACGCACAgtggtg                                   >  1:913902/1‑150 (MQ=255)
                                                                                                                                        aTCGAGCGCCGCCCGCGCGGCGCTCGATCTCACAGGCGATGAAAGCCTAAAGGCATGCGTCTGGCGGCCCTGACGCGTTCCCCTTCCATGCCCCTCAATGCTGCCTCCGCCAAGCACGCACAGTGGTGTACAGCAACACCGTAGCGAGCa             >  2:847573/1‑150 (MQ=255)
                                                                                                                                           gAGCGCCGCGCGGGCGGCGCTCGATCTCACAGGCGATGAAAGCCTAAAGGCATGCGTCTGGCGGCCCTGACGCGTTCCCCTTCCATGCCCCTCAATGCTGCCTCCGCCAAGCACGCACAGTGGTGTACAGCAACACCGTAGCGAGCACCg          >  1:913946/1‑150 (MQ=255)
                                                                                                                                           gAGCGCCGCCCGCGCGGCGCTCGATCTCACAGGCGATGAAAGCCTAAAGGCATGCGTCTGGCGGCCCTGACGCGTTCCCCTTCCATGCCCCTCAATGCTGCCTCCGCCAAGCACGCACAGTGGTGTACAGCaa                           >  2:515674/1‑133 (MQ=255)
                                                                                                                                           gAGCGCCGCCCGCGCGGCGCTCGATCTCACAGGCGATGAAAGCCTAAAGGCATGCGTCTGGCGGCCCTGACGCGTTCCCCTTCCATGCCCCTCAATGCTGCCTCCGCCAAGCACGCACAGTGGTGTACAGCaa                           <  1:515674/133‑1 (MQ=255)
                                                                                                                                                 cgcgcgGGCGGCGCTCGATCTCACAGGCGATGAAAGCCTAAAGGCATGCGTCTGGCGGCCCTGACGCGTTCCCCTTCCATGCCCCTCAATGCTGCCTCCACCAAGCACGCACAGTGGTGTACAGCAACACCGTAGCGAGCACCGGCAGTa    <  1:258344/150‑1 (MQ=255)
                                                                                                                                                   cgcgGGCGGCGCTCGATCTCACAGGCGATGAAAGCCTAAAGGCATGCGTCTGGCGGCCCTGACGCGTTCCCCTTCCATGCCCCTCAATGCTGCCTCCGCCAAGCACGCACAGTGGTGTACAGCAACACCGTAGCGAGCACCGGCAGTACa  >  1:215328/1‑150 (MQ=255)
                                                                                                                                                    |                                                                                                                                                    
CGCATCTCGGTAATGCTGATCCCGGCATGGATCGCTGTGCTGTGGGTGGCTTTCAAGCTGAAGAAGGCTCGCCAGGCCAAGGGCTGATCGGGTTTGTTCGTAAGGGGTATGCCGTTAGGTTTTCGGCGCCTGTGAGATCGAGCGCCGCGCGGGCGGCGCTCGATCTCACAGGCGATGAAAGCCTAAAGGCATGCGTCTGGCGGCCCTGACGCGTTCCCCTTCCATGCCCCTCAATGCTGCCTCCGCCAAGCACGCACAGTGGTGTACAGCAACACCGTAGCGAGCACCGGCAGTACA  >  NC_002947/1070117‑1070413

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A