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
A1 F1 I1 R1 773 79.9 4112934 92.2% 3792125 104.5

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 2,576,407 T→C E657E (GAA→GAG)  maeB ← malic enzyme: putative oxidoreductase/phosphotransacetylase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009132,576,4070TC100.0% 238.3 / NA 66E657E (GAA→GAG) maeBmalic enzyme: putative oxidoreductase/phosphotransacetylase
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (39/27);  total (39/27)

CCATGTTCGGCATCACCAGAATATTGGCGGAACCTTTCAAAGAGCTGTCCGGCATACGGTCGTTGCGAATCGCTTCCACCAGCGCTGCATCGCCGTGCATTTCACCATCAATCATCAGTTCTGGTGCACGTTCCCTGACCAGTTCCAGCGCCTGACGCATTTTGCTCGACGACGGGCAGTCAGAAGAACCAAAGTTGGAGTGCGACAACAAAGCAACGCGCGGCTCAATACCAAAACGACGGACAGTTTCTGCCGCCATCAA  >  NC_000913/2576277‑2576538
                                                                                                                                  |                                                                                                                                   
ccATGTTCGGCATCACCAGAATATTGGCGGAACCTTTCAAAGAGCTGTCCGGCATACGGTCGTTGCGAATCGCTTCCACCAGCGCTGCATCGCCGTGCATTTCACCATCAATCATCAGTTCTGGTGCACGCTCCCTGAc                                                                                                                             <  2:1630782/139‑1 (MQ=255)
       cGGCATCACCAGAATATTGGCTGAACCTTTCAAAGAGCTGTCCGGCATACGGTCGTTGCGAATCGCTTCCACCAGCGCTGCATCGCCGTGCATTTCACCATCAATCATCAGTTCTGGTGCACGCTCCCTGACCAGTTcc                                                                                                                      >  1:1433660/1‑139 (MQ=255)
       cGGCATCACCAGAATATTGGCGGAACCTTTCAAAGAGCTGTCCGGCATACGGTCGTTGCGAATCGCTTCCACCAGCGCTGCATCGCCGTGCATTTCACCATCAATCATCAGTTCTGGTGCACGCTCCCTGACCAGTTcc                                                                                                                      >  1:393290/1‑139 (MQ=255)
       cGGCATCACCAGAATATTGGCGGAACCTTTCAAAGAGCTGTCCGGCATACGGTCGTTGCGAATCGCTTCCACCAGCGCTGCATCGCCGTGCATTTCACCATCAATCATCAGTTCTGGTGCACGCTCCCTGACCAGTTcc                                                                                                                      >  1:735018/1‑139 (MQ=255)
       cGGCATCACCAGAATATTGGCGGAACCTTTCAAAGAGCTGTCCGGCATACGGTCGTTGCGAATCGCTTCCACCAGCGCTGCATCGCCGTGCATTTCACCATCAATCATCAGTTCTGGTGCACGCTCCCTGACCAGTTcc                                                                                                                      >  2:170441/1‑139 (MQ=255)
               ccAGAATATTGGCGGAACCTTTCAAAGAGCTGTCCGGCATACGGTCGTTGCGAATCGCTTCCACCAGCGCTGCATCGCCGTCCATTTCACCATCAATCATCAGTTCTGGTGCACGCTCCCTGACCAGTTCCAGCGCCTg                                                                                                              >  2:2012728/1‑139 (MQ=255)
                        tGGCGGAACCTTTCAAAGAGCTGTCCGGCATACGGTCGTTGCGAATCGCTTCCACCAGCGCTGCATCGCCGTGCATTTCACCATCAATCATCAGTTCTGGTGCACGCTCCCTGACCAGTTCCAGCGCCTGACGCAtttt                                                                                                     >  1:844414/1‑139 (MQ=255)
                          gCGGAACCTTTCAAAGAGCTGTCCGGCATACGGTCGTTGCGAATCGCTTCCACCAGCGCTGCATCGCCGTGCATTTCACCATCAATCATCAGTTCTGGTGCACGCTCCCTGACCAGTTCCAGCGCCTGACGCATTTTGc                                                                                                   >  1:2038570/1‑139 (MQ=255)
                           cGGAACCTTTCAAAGAGCTGTCCGGCATACGGTCGTTGCGAATCGCTTCCACCAGCGCTGCATCGCCGTGCATTTCACCATCAATCATCAGTTCTGGTGCACGCTCCCTGACCAGTTCCAGCGCCTGACGCATTTTGCt                                                                                                  <  2:1735216/139‑1 (MQ=255)
                             gAACCTTTCAAAGAGCTGTCCGGCATACGGTCGTTGCGAATCGCTTCCACCAGCGCTGCATCGCCGTGCATTTCACCATCAATCATCAGTTCTGGTGCACGCTCCCTGAc                                                                                                                             >  2:1322192/1‑110 (MQ=255)
                             gAACCTTTCAAAGAGCTGTCCGGCATACGGTCGTTGCGAATCGCTTCCACCAGCGCTGCATCGCCGTGCATTTCACCATCAATCATCAGTTCTGGTGCACGCTCCCTGAc                                                                                                                             <  1:1322192/110‑1 (MQ=255)
                             gAACCTTTCAAAGAGCTGTCCGGCATACGGTCGTTGCGAATCGCTTCCACCAGCGCTGCATCGCCGTGCATTTCACCATCAATCATCAGTTCTGGTGCACGCTCCCTGACCAGTTCCAGCGCCTGACGCATTTTGCTcg                                                                                                >  2:10539/1‑139 (MQ=255)
                             gAACCTTTCAAAGAGCTGTCCGGCATACGGTCGTTGCGAATCGCTTCCACCAGCGCTGCATCGCCGTGCATTTCACCATCAATCATCAGTTCTGGTGCACGCTCCCTGACCAGTTCCAGCGCCTGACGCATTTTGCTcg                                                                                                >  2:346902/1‑139 (MQ=255)
                                   ttCAAAGAGCTGTCCGGCATACGGTCGTTGCGAATCGCTTCCACCAGCGCTGCATCGCCGTGCATTTCACCATCAATCATCAGTTCTGGTGCACGCTCCCTGACCAGTTCCAGCGCCTGACGCATTTTGCTCGacgacg                                                                                          <  2:1433660/139‑1 (MQ=255)
                                    tCAAAGAGCTGTCCGGCATACGGTCGTTGCGAATCGCTTCCACCAGCGCTGCATCGCCGTGCATTTCACCATCAATCATCAGTTCTGGTGCACGCTCCCTGACCAGTTCCAGCGCCTGACGCATTTTGCTCGACGACgg                                                                                         >  2:317727/1‑139 (MQ=255)
                                     cAAAGAGCTGTCCGGCATACGGTCGTTGCGAATCGCTTCCACCAGCGCTGCATCGCCGTGCATTTCACCATCAATCATCAGTTCTGGTGCACGCTCCCTGACCAGTTCCAGCGCCTGACGCATTTTGCTCGACGACggg                                                                                        <  1:10539/139‑1 (MQ=255)
                                     cAAAGAGCTGTCCGGCATACGGTCGTTGCGAATCGCTTCCACCAGCGCTGCATCGCCGTGCATTTCACCATCAATCATCAGTTCTGGTGCACGCTCCCTGACCAGTTCCAGCGCCTGACGCATTTTGCTCGACGACggg                                                                                        <  2:1123573/139‑1 (MQ=255)
                                            cTGTCCGGCATACGGTCGTTGCGAATCGCTTCCACCAGCGCTGCATCGCCGTGCATTTCACCATCAATCATCAGTTCTGGTGCACGCTCCCTGACCAGTTCCAGCGCCTGACGCATTTTGCTCGACGACGGGCAGTCag                                                                                 <  2:735018/139‑1 (MQ=255)
                                               tCCGGCATACGGTCGTTGCGAATCGCTTCCACCAGCGCTGCATCGCCGTGCATTTCACCATCAATCATCAGTTCTGGTGCACGCTCCCTGACCAGTTCCAGCGCCTGAc                                                                                                            >  2:1425692/1‑109 (MQ=255)
                                               tCCGGCATACGGTCGTTGCGAATCGCTTCCACCAGCGCTGCATCGCCGTGCATTTCACCATCAATCATCAGTTCTGGTGCACGCTCCCTGACCAGTTCCAGCGCCTGAc                                                                                                            <  1:1425692/109‑1 (MQ=255)
                                               tCCGGCATACGGTCGTTGCGAATCGCTTCCACCAGCGCTGCATCGCCGTGCATTTCACCATCAATCATCAGTTCTGGTGCACGCTCCCTGACCAGTTCCAGCGCCTGACGCATTTTGCTCGACGACGGGCAGTCagaag                                                                              >  2:114201/1‑139 (MQ=255)
                                               tCCGGCATACGGTCGTTGCGAATCGCTTCCACCAGCGCTGCATCGCCGTGCATTTCACCATCAATCATCAGTTCTGGTGCACGCTCCCTGACCAGTTCCAGCGCCTGACGCATTTTGCTCGACGACGGGCAGTCagaag                                                                              >  1:184379/1‑139 (MQ=255)
                                                  ggCATACGGTCGTTGCGAATCGCTTCCACCAGCGCTGCATCGCCGTGCATTTCACCATCAATCATCAGTTCTGGTGCACGCTCCCTGACCAGTTCCAGCGCCTGACGCATTTTGCTCGACGACGGGCAGTCAGAAGAAc                                                                           <  2:2038570/139‑1 (MQ=255)
                                                   gCATACGGTCGTTGCGAATCGCTTCCACCAGCGCTGCATCGCCGTGCATTTCACCATCAATCATCAGTTCTGGTGCACGCTCCCTGACCAGTTCCAGCGCCTGACGCATTTTGCTCGACGACGGGCAGTCAGAAGAAcc                                                                          <  1:170441/139‑1 (MQ=255)
                                                              ttGCGAATCGCTTCCACCAGCGCTGCATCGCCGTGCATTTCACCATCAATCATCAGTTCTGGTGCACGCTCCCTGAc                                                                                                                             <  2:1730059/77‑1 (MQ=255)
                                                              ttGCGAATCGCTTCCACCAGCGCTGCATCGCCGTGCATTTCACCATCAATCATCAGTTCTGGTGCACGCTCCCTGAc                                                                                                                             >  1:1730059/1‑77 (MQ=255)
                                                              ttGCGAATCGCTTCCACCAGCGCTGCATCGCCGTGCATTTCACCATCAATCATCAGTTCTGGTGCACGCTCCCTGACCAGTTCCAGCGCCTGACGCATTTTGCTCGACGACGGGCAGTCAGAAGAACCAAAGTTGGAGt                                                               >  2:653143/1‑139 (MQ=255)
                                                                  gAATCGCTTCCACCAGCGCTGCATCGCCGTGCATTTCACCATCAATCATCAGTTCTGGTGCACGCTCCCTGACCAGTTCCAGCGCCTGACGCATTTTGCTCGACGACGGGCAGTCAGAAGAACCAAAGTTGGAGTGCGa                                                           <  1:346902/139‑1 (MQ=255)
                                                                   aaTCGCTTCCACCAGCGCTGCATCGCCGTGCATTTCACCATCAATCATCAGTTCTGGTGCACGCTCCCTGACCAGTTCCAGCGCCTGACGCATTTTGCTCGACGACGGGCAGTCAGAAGAACCAAAGTTGGAGTGCGac                                                          >  2:1782145/1‑139 (MQ=255)
                                                                     tCGCTTCCACCAGCGCTGCATCGCCGTGCATTTCACCATCAATCATCAGTTCTGGTGCACGCTCCCTGACCAGTTCCAGCGCCTGACGCATTTTGCTCGACGACGGGCAGTCAGAAGAACCAAAGTTGGAGTGCGacaa                                                        >  1:1737045/1‑139 (MQ=255)
                                                                        cTTCCACCAGCGCTGCATCGCCGTGCATTTCACCATCAATCATCAGTTCTGGTGCACGCTCCCTGACCAGTTCCAGCGCCTGACGCATTTTGCTCGACGACGGGCAGTCAGAAGAACCAAAGTTGGAGTGCGAcaacaa                                                     >  2:845960/1‑139 (MQ=255)
                                                                         ttCCACCAGCGCTGCATCGCCGTGCATTTCACCATCAATCATCAGTTCTGGTGCACGCTCCCTGACCAGTTCCAGCGCCTGACGCATTTTGCTCGACGACGGGCAGTCAGAAGAACCAAAGTTGGAGTGCGa                                                           <  2:1023744/132‑1 (MQ=255)
                                                                         ttCCACCAGCGCTGCATCGCCGTGCATTTCACCATCAATCATCAGTTCTGGTGCACGCTCCCTGACCAGTTCCAGCGCCTGACGCATTTTGCTCGACGACGGGCAGTCAGAAGAACCAAAGTTGGAGTGCGa                                                           >  1:1023744/1‑132 (MQ=255)
                                                                            caccaGCGCTGCATCGCCGTGCATTTCACCATCAATCATCAGTTCTGGTGCACGCTCCCTGACCAGTTCCAGCGCCTGACGCATTTTGCTCGACGACGGGCAGTCAGAAGAACCAAAGTTGGAGTGCGACAACAAAGCa                                                 <  1:114201/139‑1 (MQ=255)
                                                                                       cATCGCCGTGCATTTCACCATCAATCATCAGTTCTGGTGCACGCTCCCTGAc                                                                                                                             <  1:50714/52‑1 (MQ=255)
                                                                                       cATCGCCGTGCATTTCACCATCAATCATCAGTTCTGGTGCACGCTCCCTGAc                                                                                                                             >  2:50714/1‑52 (MQ=255)
                                                                                       cATCGCCGTGCATTTCACCATCAATCATCAGTTCTGGTGCACGCTCCCTGACCAGTTCCAGCGCCTGACGCATTTTGCTCGACGACGGGCAGTCAGAAGAACCAAAGTTGGAGTGCGACAACAAAGCAACGCGCGGCTc                                      <  1:653143/139‑1 (MQ=255)
                                                                                       cATCGCCGTGCATTTCACCATCAATCATCAGTTCTGGTGCACGCTCCCTGACCAGTTCCAGCGCCTGACGCATTTTGCTCGACGACGGGCAGTCAGAAGAACCAAAGTTGGAGTGCGACAACAAAGCAACGCGCGGCTc                                      >  1:1649064/1‑139 (MQ=255)
                                                                                                 cATTTCACCATCAATCATCAGTTCTGGTGCACGCTCCCTGACCAGTTCCAGCGCCTGACGCATTTTGCTCGACGACGGGCAGTCag                                                                                 <  1:1021419/86‑1 (MQ=255)
                                                                                                 cATTTCACCATCAATCATCAGTTCTGGTGCACGCTCCCTGACCAGTTCCAGCGCCTGACGCATTTTGCTCGACGACGGGCAGTCag                                                                                 >  2:1021419/1‑86 (MQ=255)
                                                                                                    ttCACCATCAATCATCAGTTCTGGTGCACGCTCCCTGACCAGTTCCAGCGCCTGACGCATTTTGCTCGACGACGGGCAGTCAGAAGAACCAAAGTTGGAGTGCGACAACAAAGCAACGCGCGGCTCAATACCAAAacga                         >  1:813309/1‑139 (MQ=255)
                                                                                                           tcaatcaTCAGTTCTGGTGCACGCTCCCTGACCAGTTCCAGCGCCTGACGCATTTTGCt                                                                                                  <  2:895467/59‑1 (MQ=255)
                                                                                                           tcaatcaTCAGTTCTGGTGCACGCTCCCTGACCAGTTCCAGCGCCTGACGCATTTTGCt                                                                                                  >  1:895467/1‑59 (MQ=255)
                                                                                                           tcaatcaTCAGTTCTGGTGCACGCTCCCTGACCAGTTCCAGCGCCTGACGCATTTTGCTCGACGACGGGCAGTCAGAAGAACCAAAGTTGGAGTGCGACAACAAAGCAACGCGCGGCTCAATACCAAAACGACGGACAg                  >  2:555571/1‑139 (MQ=255)
                                                                                                           tcaatcaTCAGTTCTGGTGCACGCTCCCTGACCAGTTCCAGCGCCTGACGCATTTTGCTCGACGACGGGCAGTCAGAAGAACCAAAGTTGGAGTGCGACAACAAAGCAACGCGCGGCTCAATACCAAAACGACGGACAg                  >  2:335887/1‑139 (MQ=255)
                                                                                                              atcatcAGTTCTGGTGCACGCTCCCTGACCAGTTCCAGCGCCTGACGCATTTTGCTCGACGACGGGCAGTCAGAAGAACCAAAGTTGGAGTGCGACAACAAAGCAACGCGCGGCTCAATACCAAAACGACGGACAGttt               >  2:851661/1‑139 (MQ=255)
                                                                                                              atcatcAGTTCTGGTGCACGCTCCCTGACCAGTTCCAGCGCCTGACGCATTTTGCTCGACGACGGGCAGTCAGAAGAACCAAAGTTGGAGTGCGACAACAAAGCAACGCGCGGCTCAATACCAAAACGACGGACAGttt               >  1:1026365/1‑139 (MQ=255)
                                                                                                              atcatcAGTTCTGGTGCACGCTCCCTGACCAGTTCCAGCGCCTGACGCATTTTGCTCGACGACGGGCAGTCAGAAGAACCAAAGTTGGAGTGCGACAACAAAGCAACGCGCGGCTCAATACCAAAACGACGGACAGttt               >  2:2020088/1‑139 (MQ=255)
                                                                                                                catcaGTTCTGGTGCACGCTCCCTGACCAGTTCCAGCGCCTGACGCATTTTGCTCGACGACggg                                                                                        >  1:280527/1‑64 (MQ=255)
                                                                                                                catcaGTTCTGGTGCACGCTCCCTGACCAGTTCCAGCGCCTGACGCATTTTGCTCGACGACggg                                                                                        <  2:280527/64‑1 (MQ=255)
                                                                                                                  tcaGTTCTGGTGCACGCTCCCTGACCAGTTCCAGCGCCTGACGCATTTTGCTCGACGACGGGCAGTCAGAAGAACCAAAGTTGGAGTGCGACAACAAAGCAACGCGCGGCTCAATACCAAAACGACGGACAGTTTCTgc           <  2:393290/139‑1 (MQ=255)
                                                                                                                      ttCTGGTGCACGCTCCCTGACCAGTTCCAGCGCCTGACGCATTTTGCTCGACGACGGGc                                                                                       >  1:491716/1‑59 (MQ=255)
                                                                                                                      ttCTGGTGCACGCTCCCTGACCAGTTCCAGCGCCTGACGCATTTTGCTCGACGACGGGc                                                                                       <  2:491716/59‑1 (MQ=255)
                                                                                                                      ttCTGGTGCACGCTCCCTGACCAGTTCCAGCGCCTGACGCATTTTGCTCGACGACGGGCAGTCAGAAGAACCAAAGTTGGAGTGCGACAACAAAGCAACGCGCGGCTCAATACCAAAACGACGGACAGTTTCTgccgcc       >  1:208584/1‑139 (MQ=255)
                                                                                                                       tCTGGTGCACGCTCCCTGACCAGTTCCAGCGCCTGACGCATTTTGCTCGACGACGGGCAGTCAGAAGAACCAAAGTTGGAGTGCGACAACAAAGCAACGCGCGGCTCAATACCAAAACGACGGACAGTTTCTGCCGCCa      <  1:2020088/139‑1 (MQ=255)
                                                                                                                       tCTGGTGCACGCTCCCTGACCAGTTCCAGCGCCTGACGCATTTTGCTCGACGACGGGCAGTCAGAAGAACCAAAGTTGGAGTGCGACAACAAAGCAACGCGCGGCTCAATACCAAAACGACGGACAGTTTCTGCCGCCa      >  2:1057256/1‑139 (MQ=255)
                                                                                                                       tCTGGTGCACGCTCCCTGACCAGTTCCAGCGCCTGACGCATTTTGCTCGACGACGGGCAGTCAGAAGAACCAAAGTTGGAGTGCGACAACAAAGCAACGCGCGGCTCAATACCAAAACGACGGACAGTTTCTGCCGCCa      <  1:1782145/139‑1 (MQ=255)
                                                                                                                           gTGCACGCTCCCTGACCAGTTCCAGCGCCTGACGCATTTTGCTCGACGACGGGCAGTCAGAAGAACCAAAGt                                                                     >  2:2038112/1‑72 (MQ=255)
                                                                                                                           gTGCACGCTCCCTGACCAGTTCCAGCGCCTGACGCATTTTGCTCGACGACGGGCAGTCAGAAGAACCAAAGTTGGAg                                                                >  1:1012542/1‑77 (MQ=255)
                                                                                                                           gTGCACGCTCCCTGACCAGTTCCAGCGCCTGACGCATTTTGCTCGACGACGGGCAGTCAGAAGAACCAAAGTTGGAg                                                                <  2:1012542/77‑1 (MQ=255)
                                                                                                                           gTGCACGCTCCCTGACCAGTTCCAGCGCCTGACGCATTTTGCTCGACGACGGGCAGTCAGAAGAACCAAAGTTGGAGTGc                                                             >  1:146136/1‑80 (MQ=255)
                                                                                                                           gTGCACGCTCCCTGACCAGTTCCAGCGCCTGACGCATTTTGCTCGACGACGGGCAGTCAGAAGAACCAAAGTTGGAGTGCGACAACAAAGCAAcgcg                                            >  2:1541333/1‑97 (MQ=255)
                                                                                                                           gTGCACGCTCCCTGACCAGTTCCAGCGCCTGACGCATTTTGCTCGACGACGGGCAGTCAGAAGAACCAAAGTTGGAGTGCGACAACAAAGCAAcgcg                                            <  1:1541333/97‑1 (MQ=255)
                                                                                                                           gTGCACGCTCCCTGACCAGTTCCAGCGCCTGACGCATTTTGCTCGACGACGGGCAGTCAGAAGAACCAAAGTTGGAGTGCGACAACAAAGCAACGCGCGGCTCAATACCAAAACGACGGACAGTTTCTGCCGCCATCaa  >  1:59738/1‑139 (MQ=255)
                                                                                                                           gTGCACGCTCCCTGACCAGTTCCAGCGCCTGACGCATGTTGCTCGACGACGGGCAGTCAGAAGAACCAAAGt                                                                     <  1:2038112/72‑1 (MQ=255)
                                                                                                                           gTGCACGCGCCCTGACCAGTTCCAGCGCCTGACGCATTTTGCTCGACGACGGGCAGTCAGAAGAACCAAAGTTGGAGTGc                                                             <  2:146136/80‑1 (MQ=255)
                                                                                                                                  |                                                                                                                                   
CCATGTTCGGCATCACCAGAATATTGGCGGAACCTTTCAAAGAGCTGTCCGGCATACGGTCGTTGCGAATCGCTTCCACCAGCGCTGCATCGCCGTGCATTTCACCATCAATCATCAGTTCTGGTGCACGTTCCCTGACCAGTTCCAGCGCCTGACGCATTTTGCTCGACGACGGGCAGTCAGAAGAACCAAAGTTGGAGTGCGACAACAAAGCAACGCGCGGCTCAATACCAAAACGACGGACAGTTTCTGCCGCCATCAA  >  NC_000913/2576277‑2576538

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A