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
A6 F1 I1 R1 750 51.0 2595496 93.6% 2429384 106.4

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 3,457,616 G→A A414T (GCC→ACC)  gspD → general secretory pathway component, cryptic

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009133,457,6160GA100.0% 198.0 / NA 61A414T (GCC→ACC) gspDgeneral secretory pathway component, cryptic
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (28/33);  total (28/33)

GGCGAATAAAAACGTTGGCGCACAGCAATTTACCAATACCGGATTACCGATTTTTAACGCTGCGCAAGGTGTGGCTGATTATAAAAAGAATGGTGGGATCACCAGCGCGAATCCTGCCTGGGATATGTTTAGCGCCTACAATGGCATGGCCGCAGGCTTCTTCAATGGCGACTGGGGAGTACTGCTTACCGCGCTGGCCAGTAACAATAAAAATGACATCCTCGCCACCCCAAGCATCGTAACGCTGGATAATAAACTCGCGTCCTTCA  >  NC_000913/3457483‑3457751
                                                                                                                                     |                                                                                                                                       
ggCGAATAAAAACGTTGGCGCACAGCAATTTACCAATACCGGATTACCGATTTTTAACGCTGCGCAAGGTGTGGCTGATTATAAAAAGAATGGTGGGATCACCAGCGCGAATCCTGCCTGGGATATGTTTAGCACCTAc                                                                                                                                    <  2:113850/139‑1 (MQ=255)
                            tttACCAATACCGGATTACCGATTTTTAACGCTGCGCAAGGTGTGGCTGATTATAAAAAGAATGGTGGGATCACCAGCGCGAATCCTGCCTGGGATATGTTTAGCACCTACAATGGCATGGCCg                                                                                                                       >  1:114975/1‑124 (MQ=255)
                            tttACCAATACCGGATTACCGATTTTTAACGCTGCGCAAGGTGTGGCTGATTATAAAAAGAATGGTGGGATCACCAGCGCGAATCCTGCCTGGGATATGTTTAGCACCTACAATGGCATGGCCg                                                                                                                       <  2:114975/124‑1 (MQ=255)
                                ccAATACCGGATTACCGATTTTTAACGCTGCGCAAGGTGTGGCTGATTATAAAAAGAATGGTGGGATCACCAGCGCGAATCCTGCCTGGGATATGTTTAGCACCTACAATGGCATGGCCGCAGGCTTCTTCAATGGCGa                                                                                                    <  2:760102/139‑1 (MQ=255)
                                   aTACCGGATTACCGATTTTTAACGCTGCGCAAGGTGTGGCTGATTATAAAAAGAATGGTGGGATCACCAGCGCGAATCCTGCCTGGGATATGTTTAGCACCTACAATGGCATGGCCGCAGGc                                                                                                                  <  2:631348/122‑1 (MQ=255)
                                   aTACCGGATTACCGATTTTTAACGCTGCGCAAGGTGTGGCTGATTATAAAAAGAATGGTGGGATCACCAGCGCGAATCCTGCCTGGGATATGTTTAGCACCTACAATGGCATGGCCGCAGGc                                                                                                                  >  1:631348/1‑122 (MQ=255)
                                   aTACCGGATTACCGATTTTTAACGCTGCGCAAGGTGTGGCTGATTATAAAAAGAATGGTGGGATCACCAGCGCGAATCCTGCCTGGGATATGTTTAGCACCTACAATGGCATGGCCGCAGGCTTCTTCAATGGCGACTg                                                                                                 >  1:408373/1‑139 (MQ=255)
                                        ggATTACCGATTTTTAACGCTGCGCAAGGTGTGGCTGATTATAAAAAGAATGGTGGGATCACCAGCGCGAATCCTGCCTGGGATATGTTTAGCACCTACAATGGCATGGCCGCAGGCTTCTTCAATGGCGACTGGGGAg                                                                                            <  2:408373/139‑1 (MQ=255)
                                         gATTACCGATTTTTAACGCTGCGCAAGGTGTGGCTGATTATAAAAAGAATGGTGGGATCACCAGCGCGAATCCTGCCTGGGATATGTTTAGCACCTACAATGGCATGGCCGCAGGc                                                                                                                  >  2:794089/1‑116 (MQ=255)
                                         gATTACCGATTTTTAACGCTGCGCAAGGTGTGGCTGATTATAAAAAGAATGGTGGGATCACCAGCGCGAATCCTGCCTGGGATATGTTTAGCACCTACAATGGCATGGCCGCAGGc                                                                                                                  <  1:794089/116‑1 (MQ=255)
                                              ccGATTTTTAACGCTGCGCAAGGTGTGGCTGATTATAAAAAGAATGGTGGGATCACCAGCGCGAATCCTGCCTGGGATATGTTTAGCACCTACAATGGCATGGCCGCAGGCTTCTTCAATGGCGACTGGGGAGTACTGc                                                                                      >  1:1086645/1‑139 (MQ=255)
                                               cGATTTTTAACGCTGCGCAAGGTGTGGCTGATTATAAAAAGAATGGTGGGATCACCAGCGCGAATCCTGCCTGGGATATGTTTAGCACCTACAATGGCATGGCCGCAGGCTTCTTCAATGGCGACTGGGGAGTACTGCt                                                                                     >  2:761519/1‑139 (MQ=255)
                                                 aTTTTTAACGCTGCGCAAGGTGTGGCTGATTATAAAAAGAATGGTGGGATCACCAGCGCGAATCCTGCCTGGGATATGTTTAGCACCTACAATGGCATGGCCGCAGGCTTCTTCAATGGCGACTGGGGAGTACTGCTTa                                                                                   <  1:1025368/139‑1 (MQ=255)
                                                           cTGCGCAAGGTGTGGCTGATTATAAAAAGAATGGTGGGATCACCAGCGCGAATCCTGCCTGGGATATGTTTAGCACCTACAATGGCATGGCCGCAGGCTTCTTCAATgg                                                                                                       >  2:983056/1‑109 (MQ=255)
                                                           cTGCGCAAGGTGTGGCTGATTATAAAAAGAATGGTGGGATCACCAGCGCGAATCCTGCCTGGGATATGTTTAGCACCTACAATGGCATGGCCGCAGGCTTCTTCAATgg                                                                                                       <  1:983056/109‑1 (MQ=255)
                                                              cgcAAGGTGTGGCTGATTATAAAAAGAATGGTGGGATCACCAGCGCGAATCCTGCCTGGGATATGTTTAGCACCTACAATGGCATGGCCGCAGGCTTCTTCAATGGCGACTGGGGAGTACTGCTTACCGCGCTGGCCAg                                                                      >  2:248539/1‑139 (MQ=255)
                                                               gcAAGGTGTGGCTGATTATAAAAAGAATGGTGGGATCACCAGCGCGAATCCTGCCTGGGATATGTTTAGCACCTACAATGGCATGGCCGCAGGCTTCTTCAATGGCGACTGGGGAGTACTGCTTACCGCGCTGGCCAGt                                                                     <  1:761519/139‑1 (MQ=255)
                                                               gcAAGGTGTGGCTGATTATAAAAAGAATGGTGGGATCACCAGCGCGAATCCTGCCTGGGATATGTTTAGCACCTACAATGGCATGGCCGCAGGCTTCTTCAATGGCGACTGGGGAGTACTGCTTACCGCGCTGGCCAGt                                                                     <  2:1086645/139‑1 (MQ=255)
                                                                   ggTGTGGCTGATTATAAAAAGAATGGTGGGATCACCAGCGCGAATCCTGCCAGGGATATGTTTAGCACCTACAATGGCATGGCCGCAGGCTTCTTCAATGGCGACTg                                                                                                 >  2:796232/1‑107 (MQ=255)
                                                                   ggTGTGGCTGATTATAAAAAGAATGGTGGCATCACCAGCGCGAATCCTGCCTGGGATATGTTTAGCACCTACAATGGCATGGCCGCAGGCTTCTTCAATGGCGACta                                                                                                 <  1:796232/107‑2 (MQ=255)
                                                                      gtgGCTGATTATAAAAAGAATGGTGGGATCACCAGCGCGATTCCTGCCTGGGATATGTTTAGCACCTACAATGGCATGGCCGCAGGCTTCTTCAAGGGCGATTGGGGAGTACTGCTTACCGCGCTGGCCAGTAACAATa                                                              <  1:865929/139‑1 (MQ=255)
                                                                      gtgGCTGATTATAAAAAGAATGGTGGGATCACCAGCGCGAATCCTGCCTGGGATATGTTTAGCACCTACAATGGCATGGCCGCAGGCTTCTTCAATGGCGACTGGGGAGTACTGCTTACCGCGCTGGCCAGTAACAATa                                                              <  1:796615/139‑1 (MQ=255)
                                                                             aTTATAAAAAGAATGGTGGGATCACCAGCGCGAATCCTGCCTGGGATATGTTTAGCACCTACAatggc                                                                                                                              <  2:150412/68‑1 (MQ=255)
                                                                             aTTATAAAAAGAATGGTGGGATCACCAGCGCGAATCCTGCCTGGGATATGTTTAGCACCTACAatggc                                                                                                                              >  1:150412/1‑68 (MQ=255)
                                                                             aTTATAAAAAGAATGGTGGGATCACCAGCGCGAATCCTGCCTGGGATATGTTTAGCACCTACAATGGCATGGCCGCAGGCTTCTTCAATGGCGACTGGGGAGTACTGCTTACCGCGCTGGCCAGTAACAATAAAAATGa                                                       >  2:418516/1‑139 (MQ=255)
                                                                               tataAAAAGAATGGTGGGATCACCAGCGCGAATCCTGCCTGGGATATGTTTAGCACCTACAATGGCATGGCCGCAGGCTTCTTCAATGGCGACTGGGGAGTACTGCTTACcgcg                                                                              <  2:1219522/114‑1 (MQ=255)
                                                                               tataAAAAGAATGGTGGGATCACCAGCGCGAATCCTGCCTGGGATATGTTTAGCACCTACAATGGCATGGCCGCAGGCTTCTTCAATGGCGACTGGGGAGTACTGCTTACcgcg                                                                              >  1:1219522/1‑114 (MQ=255)
                                                                               tataAAAAGAATGGTGGGATCACCAGCGCGAATCCTGCCTGGGATATGTTTAGCACCTACAATGGCATGGCCGCAGGCTTCTTCAATGGCGACTGGGGAGTACTGCTTACCGCGCTGGCCAGTAACAATAAAAATGACa                                                     >  1:1264458/1‑139 (MQ=255)
                                                                                     aaGAATGGTGGGATCACCAGCGCGAATCCTGCCTGGGATATGTTTAGCACCTACAATGGCATGGCCGCAGGCTTCTTCAATGGCGACTGGGGAGTACTGCTTACCGCGCTGGCCAGTAACAATAAAAATGACATCCTCg                                               <  2:653523/139‑1 (MQ=255)
                                                                                         aTGGTGGGATCACCAGCGCGAATCCTGCCTGGGATATGTTTAGCACCTACAATGGCATGGCCGCAGGCTTCTTCAATGGCGACTGGGGAGTACTGCTTACCGCGCTGGCCAGTAACaa                                                                >  1:34148/1‑118 (MQ=255)
                                                                                         aTGGTGGGATCACCAGCGCGAATCCTGCCTGGGATATGTTTAGCACCTACAATGGCATGGCCGCAGGCTTCTTCAATGGCGACTGGGGAGTACTGCTTACCGCGCTGGCCAGTAACaa                                                                <  2:34148/118‑1 (MQ=255)
                                                                                         aTGGTGGGATCACCAGCGCGAATCCTGCCTGGGATATGTTTAGCACCTACAATGGCATGGCCGCAGGCTTCTTCAATGGCGACTGGGGAGTACTGCTTACCGCGCTGGCCAGTAACAATaa                                                             <  2:703804/121‑1 (MQ=255)
                                                                                         aTGGTGGGATCACCAGCGCGAATCCTGCCTGGGATATGTTTAGCACCTACAATGGCATGGCCGCAGGCTTCTTCAATGGCGACTGGGGAGTACTGCTTACCGCGCTGGCCAGTAACAATaa                                                             >  1:703804/1‑121 (MQ=255)
                                                                                         aTGGTGGGATCACCAGCGCGAATCCTGCCTGGGATATGTTTAGCACCTACAATGGCATGGCCGCAGGCTTCTTCAATGGCGACTGGGGAGTACTGCTTACCGCGCTGGCCAGTAACAATAAAAATGACATCCTCGc                                              <  1:126283/136‑1 (MQ=255)
                                                                                         aTGGTGGGATCACCAGCGCGAATCCTGCCTGGGATATGTTTAGCACCTACAATGGCATGGCCGCAGGCTTCTTCAATGGCGACTGGGGAGTACTGCTTACCGCGCTGGCCAGTAACAATAAAAATGACATCCTCGc                                              >  2:126283/1‑136 (MQ=255)
                                                                                                gATCACCAGCGCGAATCCTGCCTGGGATATGTTTAGCACCTACAATGGCATGGCCGCAGGCTTCTTCAATGGCGACTGGGGAGTACTGCTTACcgcg                                                                              <  2:1101956/97‑1 (MQ=255)
                                                                                                gATCACCAGCGCGAATCCTGCCTGGGATATGTTTAGCACCTACAATGGCATGGCCGCAGGCTTCTTCAATGGCGACTGGGGAGTACTGCTTACcgcg                                                                              >  1:1101956/1‑97 (MQ=255)
                                                                                                 aTCACCAGCGCGAATCCTGCCTGGGATATGTTTAGCACCTACAATGGCATGGCCGCAGGCTTCTTCAATGGCGACTGGGGAGTACTGCTTACCGCGCTGGCCAGTAACAATAAAAATGACATCCTCGCCACCCCAAGCa                                   <  1:248539/139‑1 (MQ=255)
                                                                                                  tCACCAGCGCGAATCCTGCCTGGGATATGTTTAGCACCTACAATGGCATGGCCGCAGGCTTCTTCAAt                                                                                                         <  2:567587/68‑1 (MQ=255)
                                                                                                  tCACCAGCGCGAATCCTGCCTGGGATATGTTTAGCACCTACAATGGCATGGCCGCAGGCTTCTTCAAt                                                                                                         >  1:567587/1‑68 (MQ=255)
                                                                                                     ccAGCGCGAATCCTGCCTGGGATATGTTTAGCACCTACAATGGCATGGCCGCAGGCTTCTTCAATGGCGACTGGGGAGTACCGCTTACCGCGCTGGCCAGTAACAATAAAAATGACATCCTCGCCACCCCAAGCATCGt                               >  1:430215/1‑139 (MQ=255)
                                                                                                       aGCGCGAATCCTGCCTGGGATATGTTTAGCACCTACAATGGCATGGCCGCAGGCTTCTTCAATGGCGACTGGGGAGTACTGCTTACcgcg                                                                              <  1:148065/90‑1 (MQ=255)
                                                                                                       aGCGCGAATCCTGCCTGGGATATGTTTAGCACCTACAATGGCATGGCCGCAGGCTTCTTCAATGGCGACTGGGGAGTACTGCTTACcgcg                                                                              >  2:148065/1‑90 (MQ=255)
                                                                                                         cgcgAATCCTGCCTGGGATATGTTTAGCACCTACAATGGCATGGCCGCAGGCTTCTTCAATGGCGACTGGGGAGTACTGCTTACCGCGCTGGCCAGTAACAATAAAAATGACATCCTCGCCACCCCAAGCATCGTAACg                           <  1:25879/139‑1 (MQ=255)
                                                                                                           cgAATCCTGCCTGGGATATGTTTAGCACCTACAATGGCATGGCCGCAGGCTTCTTCAATGGCGACTGGGGAGTACTGCTTACCGCGCTGGCCAGTAACAATAAAAATGACATCCTCGCCACCCCAAGCATCg                                >  2:806713/1‑132 (MQ=255)
                                                                                                           cgAATCCTGCCTGGGATATGTTTAGCACCTACAATGGCATGGCCGCAGGCTTCTTCAATGGCGACTGGGGAGTACTGCTTACCGCGCTGGCCAGTAACAATAAAAATGACATCCTCGCCACCCCAAGCATCg                                <  1:806713/132‑1 (MQ=255)
                                                                                                              aTCCTGCCTGGGATATGTTTAGCACCTACAATGGCATGGCCGCAGGCTTCTTCAATGGCGACTGGGGAGTACTGCTTACCGCGCTGGCCAGTAACAATAAAAATGACATCCTCGCCACCCCAAg                                     <  1:1268547/124‑1 (MQ=255)
                                                                                                              aTCCTGCCTGGGATATGTTTAGCACCTACAATGGCATGGCCGCAGGCTTCTTCAATGGCGACTGGGGAGTACTGCTTACCGCGCTGGCCAGTAACAATAAAAATGACATCCTCGCCACCCCAAg                                     >  2:1268547/1‑124 (MQ=255)
                                                                                                              aTCCTGCCTGGGATATGTTTAGCACCTACAATGGCATGGCCGCAGGCTTCTTCAATGGCGACTGGGGAGTACTGCTTACCGCGCTGGCCAGTAACAATAAAAATGACATCCTCGCCACCCCAAGCATCGTAACGCTGGa                      >  1:1275899/1‑139 (MQ=255)
                                                                                                                    cctgGGATATGTTTAGCACCTACAATGGCATGGCCGCAGGCTTCTTCAATGGCGACTGGGGa                                                                                             <  2:140959/62‑1 (MQ=255)
                                                                                                                    cctgGGATATGTTTAGCACCTACAATGGCATGGCCGCAGGCTTCTTCAATGGCGACTGGGGa                                                                                             >  1:140959/1‑62 (MQ=255)
                                                                                                                        ggATATGTTTAGCACCTACAATGGCATGGCCGCAGGCTTCTTCAATGGCGACTGGGGAGTACTGCTTACCGCGCTGGCCAGTAACAATAAAAATGACATCCTCGCCACCCCAAGCATCGTa                              >  2:94544/1‑121 (MQ=255)
                                                                                                                        ggATATGTTTAGCACCTACAATGGCATGGCCGCAGGCTTCTTCAATGGCGACTGGGGAGTACTGCTTACCGCGCTGGCCAGTAACAATAAAAATGACATCCTCGCCACCCCAAGCATCGTa                              <  1:94544/121‑1 (MQ=255)
                                                                                                                           tatGTTTAGCACCTACAATGGCATGGCCGCAGGCTTCTTCAATGGCGACTggg                                                                                               >  1:1124068/1‑53 (MQ=255)
                                                                                                                           tatGTTTAGCACCTACAATGGCATGGCCGCAGGCTTCTTCAATGGCGACTggg                                                                                               <  2:1124068/53‑1 (MQ=255)
                                                                                                                           tatGTTTAGCACCTACAATGGCATGGCCGCAGGCTTCTTCAATGGCGACTGGGGAGTACTGCTTACCGCGCTGGCCAGTAACAATAAAAATGACATCCTCGCCACCCCAAGCATCGTAACGCTGGATAATAAACTcgcg         <  1:418516/139‑1 (MQ=255)
                                                                                                                           tatGTTTAGCACCTACAATGGCATGGCCGCAGGCTTCTTCAATGGCGACTGGGGAGTACTGCTTACCGCGCTGGCCAGTAACAATAAAAATGACATCCTCGCCACCCCAAGCATCGTAACGCTGGATAATAAACTcgcg         <  2:1264458/139‑1 (MQ=255)
                                                                                                                              gTTTAGCACCTACAATGGCATGGCCGCAGGCTTCTTCAATGGCGACTGGGGAGTACTGCTTACCGCGCTGGCCAGTAACAATAAAAATGACATCCTCGCCACCCCAAGCATCGTAACGCTGGATAATAAACTCGCGTcc      >  2:148710/1‑139 (MQ=255)
                                                                                                                                ttAGCACCTACAATGGCATGGCCGCAGGCTTCTTCAATGGCGACTGGGGAGTACCGCTTACCGCGCTGGCCAGTAACAATAAAAATGACATCCTCGCCACCCCAAGCATCGTAACGCTGGATAATAAACTCGCGTCCtt    <  2:430215/139‑1 (MQ=255)
                                                                                                                                  aGCACCTACAATGGCATGGCCGCAGGCTTCTTCAATGGCGACTGGGGAGTACTGCTTACCGCGCTGGCCAGTAACAATa                                                              <  2:449539/79‑1 (MQ=255)
                                                                                                                                  aGCACCTACAATGGCATGGCCGCAGGCTTCTTCAATGGCGACTGGGGAGTACTGCTTACCGCGCTGGCCAGTAACAATAAAAATGACATCCTCGCCACCCCAAGCATCGTAACGCTGGATAATAAACTCGCGTCCTTCa  >  2:310127/1‑139 (MQ=255)
                                                                                                                                     |                                                                                                                                       
GGCGAATAAAAACGTTGGCGCACAGCAATTTACCAATACCGGATTACCGATTTTTAACGCTGCGCAAGGTGTGGCTGATTATAAAAAGAATGGTGGGATCACCAGCGCGAATCCTGCCTGGGATATGTTTAGCGCCTACAATGGCATGGCCGCAGGCTTCTTCAATGGCGACTGGGGAGTACTGCTTACCGCGCTGGCCAGTAACAATAAAAATGACATCCTCGCCACCCCAAGCATCGTAACGCTGGATAATAAACTCGCGTCCTTCA  >  NC_000913/3457483‑3457751

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A