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% 204.9 / NA 63A414T (GCC→ACC) gspDgeneral secretory pathway component, cryptic
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (30/33);  total (30/33)

GCGAATAAAAACGTTGGCGCACAGCAATTTACCAATACCGGATTACCGATTTTTAACGCTGCGCAAGGTGTGGCTGATTATAAAAAGAATGGTGGGATCACCAGCGCGAATCCTGCCTGGGATATGTTTAGCGCCTACAATGGCATGGCCGCAGGCTTCTTCAATGGCGACTGGGGAGTACTGCTTACCGCGCTGGCCAGTAACAATAAAAATGACATCCTCGCCACCCCAAGCATCGTAACGCTGGATAATAAACTCGCGTCCTTCA  >  NC_000913/3457484‑3457751
                                                                                                                                    |                                                                                                                                       
gCGAATAAAAACGTTGGCGCACAGCAATTTACCAATACCGGATTACCGATTTTTAACGCTGCGCAAGGTGTGGCTGATTATAAAAAGAATGGTGGGATCACCAGCGCGAATCCTGCCTGGGATATGTTTAGCACCTACa                                                                                                                                   >  1:524011/1‑139 (MQ=255)
      aaaaaCGTTGGCGCACAGCAATTTACCAATACCGGATTACCGATTTTTAACGCTGCGCAAGGTGTGGCTGATTATAAAAAGAATGGTGGGATCACCAGCGCGAATCCTGCCTGGGATATGTTTAGCACCTACAatggca                                                                                                                             <  2:423186/139‑1 (MQ=255)
              tGGCGCACAGCAATTTACCAATACCGGATTACCGATTTTTAACGCTGCGCAAGGTGTGGCTGATTATAAAAAGAATGGTGGGATCACCAGCGCGAATCCTGCCTGGGATATGTTTAGCACCTACAATGGCATGGCCGCa                                                                                                                     >  2:959413/1‑139 (MQ=255)
              tGGCGCACAGCAATTTACCAATACCGGATTACCGATTTTTAACGCTGCGCAAGGTGTGGCTGATTATAAAAAGAATGGTGGGATCACCAGCGCGAATCCTGCCTGGGATATGTTTAGCACCTACAATGGCATGGCCGCa                                                                                                                     <  2:1281708/139‑1 (MQ=255)
               ggCGCACAGCAATTTACCAATACCGGATTACCGATTTTTAACACTGCGCAAGGTGTGGCTGATTATAAAAAGAATGGTGGGATCACCAGCGCGAATCCTGCCTGGGATATGTTTAGCACCTACAATGGCATGGCCGCAg                                                                                                                    >  1:1363094/1‑139 (MQ=255)
                 cgcACAGCAATTTACCAATACCGGATTACCGATTTTTAACGCTGCGCAAGGTGTGGCTGATTATAAAAAGAATGGTGGGATCACCAGCGCGAATCCTGCCTGGGATATGTTTAGCACCTACAATGGCATTGCCGCAGGc                                                                                                                  <  1:959413/139‑1 (MQ=255)
                          aTTTACCAATACCGGATTACCGATTTTTAACGCTGCGCAAGGTGTGGCTGATTATAAAAAGAATGGTGGGATCACCAGCGCGAATCCTGCCTGGGATATGTTTAGCACCTACAATGGCATGGCCGCAGGCTTCTTCAAt                                                                                                         <  1:1287150/139‑1 (MQ=255)
                             tACCAATACCGGATTACCGATTTTTAACGCTGCGCAAGGTGTGGCTGATTATAAAAAGAATGGTGGGATCACCAGCGCGAATCCTGCCTGGGATATGTTTAGCACCTACAATGGCATGGCCGCAGGCTTCTTCAATGGc                                                                                                      <  2:524011/139‑1 (MQ=255)
                                  aTACCGGATTACCGATTTTTAACGCTGCGCAAGGTGTGGCTGATTATAAAAAGAATGGTGGGATCACCAGCGCGAATCCTGCCTGGGATATGTTTAGCACCTACAATGGCATGGCCGCa                                                                                                                     <  2:181967/119‑1 (MQ=255)
                                  aTACCGGATTACCGATTTTTAACGCTGCGCAAGGTGTGGCTGATTATAAAAAGAATGGTGGGATCACCAGCGCGAATCCTGCCTGGGATATGTTTAGCACCTACAATGGCATGGCCGCa                                                                                                                     >  1:181967/1‑119 (MQ=255)
                                  aTACCGGATTACCGATTTTTAACGCTGCGCAAGGTGTGGCTGATTATAAAAAGAATGGTGGGATCACCAGCGCGAATCCTGCCTGGGATATGTTTAGCACCTACAATGGCATGGCCGCAGGCTTCTTCAATGGCGACTg                                                                                                 <  1:292569/139‑1 (MQ=255)
                                   tACCGGATTACCGATTTTTAACGCTGCGCAAGGTGTGGCTGATTATAAAAAGAATGGTGGGATCACCAGCGCGAATCCTGCCTGGGATATGTTTAGCACCTACAATGGCATGGCCGCAGGCTTCTTCAATGGCGACTgg                                                                                                >  2:445975/1‑139 (MQ=255)
                                    aCCGGATTACCGATTTTTAACGCTGCGCAAGGTGTGGCTGATTATAAAAAGAATGGTGGGATCACCAGCGCGAATCCTGCCTGGGATATGTTTAGCACCTACAATGGCATGGCCGCAGGCTTCTTCAATGGCGACTggg                                                                                               <  1:445975/139‑1 (MQ=255)
                                             ccGATTTTTAACGCTGCGCAAGGTGTGGCTGATTATAAAAAGAATGGTGGGATCACCAGCGCGAATCCTGCCTGGGATATGTTTAGCACCTACAATGGCATGGCCGCAGGCTTCTTCAATGGCGACTGGGGa                                                                                             >  1:1049423/1‑132 (MQ=255)
                                             ccGATTTTTAACGCTGCGCAAGGTGTGGCTGATTATAAAAAGAATGGTGGGATCACCAGCGCGAATCCTGCCTGGGATATGTTTAGCACCTACAATGGCATGGCCGCAGGCTTCTTCAATGGCGACTGGGGa                                                                                             <  2:1049423/132‑1 (MQ=255)
                                                aTTTTTAACGCTGCGCAAGGTGTGGCTGATTATAAAAAGAATGGTGGGATCACCAGCGCGAATCCTGCCTGGGATATGTTTAGCACCTACAATGGCATGGCCGCAGGCTTCTTCAATGGCGACTGGGGAGTACTGCTTa                                                                                   <  1:702509/139‑1 (MQ=255)
                                                aTTTTTAACGCTGCGCAAGGTGTGGCTGATTATAAAAAGAATGGTGGGATCACCAGCGCGAATCCTGCCTGGGATATGTTTAGCACCTACAATGGCATGGCCGCAGGCTTCTTCAATGGCGACTGGGGAGTACTGCTTa                                                                                   <  1:183222/139‑1 (MQ=255)
                                                             cgcAAGGTGTGGCTGATTATAAAAAGAATGGTGGGATCACCAGCGCGAATCCTGCCTGGGATATGTTTAGCACCTACAATGGCATGGCCGCAGGCTTCTTCAAt                                                                                                         >  2:1141547/1‑104 (MQ=255)
                                                             cgcAAGGTGTGGCTGATTATAAAAAGAATGGTGGGATCACCAGCGCGAATCCTGCCTGGGATATGTTTAGCACCTACAATGGCATGGCCGCAGGCTTCTTCAAt                                                                                                         <  1:1141547/104‑1 (MQ=255)
                                                              gcAAGGTGTGGCTGATTATAAAAAGAATGGTGGGATCACCAGCGCGAATCCTGCCTGGGATATGTTTAGCACCTACAATGGCATGGCCGCAGGCTTCTTCAATGGCGACTGGGGAGTACTGCTTACCGCGCTGGCCAGt                                                                     <  2:1363094/139‑1 (MQ=255)
                                                               cAAGGTGTGGCTGATTATAAAAAGAATGGTGGGATCACCAGCGCGAATCCTGCCTGGGATATGTTTAGCACCTACAATGGCATGGCCGCAGGCTTCTTCAAt                                                                                                         <  1:1014586/102‑1 (MQ=255)
                                                               cAAGGTGTGGCTGATTATAAAAAGAATGGTGGGATCACCAGCGCAAATCCTGCCTGGGATATGTTTAGCACCTACAATGGCATGGCCGCAGGCTTCTTCAAt                                                                                                         >  2:1014586/1‑102 (MQ=255)
                                                                  ggTGTGGCTGATTATAAAAAGAATGGTGGGATCACCAGCGCGAATCCTGCCTGGGATATGTTTAGCACCTACAATGGCATGGCCg                                                                                                                       >  2:1332292/1‑85 (MQ=255)
                                                                  ggTGTGGCTGATTATAAAAAGAATGGTGGGATCACCAGCGCGAATCCTGCCTGGGATATGTTTAGCACCTACAATGGCATGGCCg                                                                                                                       <  1:1332292/85‑1 (MQ=255)
                                                                       ggCTGATTATAAAAAGAATGGTGGGATCACCAGCGCGAATCCTGCCTGGGATATGTTTAGCACCTACAATGGCATGGCCGCAGGCTTCTTCAATGGCGa                                                                                                    <  2:1343646/99‑1 (MQ=255)
                                                                       ggCTGATTATAAAAAGAATGGTGGGATCACCAGCGCGAATCCTGCCTGGGATATGTTTAGCACCTACAATGGCATGGCCGCAGGCTTCTTCAATGGCGa                                                                                                    >  1:1343646/1‑99 (MQ=255)
                                                                       ggCTGATTATAAAAAGAATGGTGGGATCACCAGCGCGAATCCTGCCTGGGATATGTTTAGCACCTACAATGGCATGGCCGCAGGCTTCTTCAATGGCGACTGGGGAGTACTGCTTACCGCGCTGGCCAGTAACAATaaa                                                            >  2:423405/1‑139 (MQ=255)
                                                                         cTGATTATAAAAAGAATGGTGGGATCACCAGCGCGAATCCTGCCTGGGATATGTTTAGCACCTACAATGGCATGGCCg                                                                                                                       <  1:151811/78‑1 (MQ=255)
                                                                         cTGATTATAAAAAGAATGGTGGGATCACCAGCGCGAATCCTGCCTGGGATATGTTTAGCACCTACAATGGCATGGCCg                                                                                                                       >  2:151811/1‑78 (MQ=255)
                                                                                taAAAAGAATGGTGGGATCACCAGCGCGAATCCTGCCTGGGATATGTTTAGCACCTACAatggc                                                                                                                              >  2:509868/1‑64 (MQ=255)
                                                                                taAAAAGAATGGTGGGATCACCAGCGCGAATCCTGCCTGGGATATGTTTAGCACCTACAatggc                                                                                                                              <  1:509868/64‑1 (MQ=255)
                                                                                taAAAAGAATGGTGGGATCACCAGCGCGAATCCTGCCTGGGATATGTTTAGCACCTACAATGGCATGGCCGCAGGCTTCTTCAATGGCGACTGGGGAGTACTGCTTACCGCGCTGGCCAGTAACAATAAAAATGACATc                                                   >  1:53644/1‑139 (MQ=255)
                                                                                     aGAATGGTGGGATCACCAGCGCGAATCCTGCCTGGGATATGTTTAGCACCTACAATGGCATGGCCGCAGGCTTCTTCAATGGCGACTGGGGAGTACTGCTTACCGCGCTGGCCAGTAACAATAAAAATGACATCCTCGc                                              <  2:1398036/139‑1 (MQ=255)
                                                                                       aaTGGTGGGATCACCAGCGCGAATCCTGCCTGGGATATGTTTAGCACCTACAATGGCATGGCCg                                                                                                                       <  2:718342/64‑1 (MQ=255)
                                                                                       aaTGGTGGGATCACCAGCGCGAATCCTGCCTGGGATATGTTTAGCACCTACAATGGCATGGCCg                                                                                                                       >  1:718342/1‑64 (MQ=255)
                                                                                          ggtggGATCACCAGCGCGAATCCTGCCTGGGATATGTTTAGCACCTACAATGGCATGGCCGCAGGCTTCTTCAATGGCGACTGGGGAGTACTGCTTACCGCGCTGGCCAGTAACAATAAAAATGACATCCTCGCCAccc                                         >  2:765726/1‑139 (MQ=255)
                                                                                           gtggGATCACCAGCGCGAATCCTGCCTGGGATATGTTTAGCACCTACAATGGCATGGCCGCAGGCTTCTTCAATGGCGACTGGGGAGTACTGCTTACCGCGCTGGCCAGTAACAATAAAAATGACATCCTCGCCAcccc                                        <  1:765726/139‑1 (MQ=255)
                                                                                           gtggGATCACCAGCGCGAATCCTGCCTGGGATATGTTTAGCACCTACAATGGCATGGCCGCAGGCTTCTTCAATGGCGACTGGGGAGTACTGCTTACCGCGCTGGCCAGTAACAATAAAAATGACATCCTCGCCAcccc                                        >  2:168260/1‑139 (MQ=255)
                                                                                              ggATCACCAGCGCGAATCCTGCCTGGGATATGTTTAGCACCTACAATGGCATGGCCGCAGGCTTCTTCAATGGCGACTGGGGAGTACTGCTTACCGCGCTGGCCAGTAACAATAAAAATGACATCCTCGCCACCCCAAg                                     <  1:168260/139‑1 (MQ=255)
                                                                                                   aCCAGCGCGAATCCTGCCTGGGATATGTTTAGCACCTACAATGGCATGGCCGCAGGCTTCTTCAATGGCGACTg                                                                                                 >  1:1286989/1‑74 (MQ=255)
                                                                                                   aCCAGCGCGAATCCTGCCTGGGATATGTTTAGCACCTACAATGGCATGGCCGCAGGCTTCTTCAATGGCGACTg                                                                                                 <  2:1286989/74‑1 (MQ=255)
                                                                                                   aCCAGCGCGAATCCTGCCTGGGATATGTTTAGCACCTACAATGGCATGGCCGCAGGCTTCTTCAATGGCGACTGGGGAGTACTGCTTa                                                                                   <  2:601798/88‑1 (MQ=255)
                                                                                                   aCCAGCGCGAATCCTGCCTGGGATATGTTTAGCACCTACAATGGCATGGCCGCAGGCTTCTTCAATGGCGACTGGGGAGTACTGCTTa                                                                                   >  1:601798/1‑88 (MQ=255)
                                                                                                   aCCAGCGCGAATCCTGCCTGGGATATGTTTAGCACCTACAATGGCATGGCCGCAGGCTTCTTCAATGGCGACTGGGGAGTACTGCTTACcgcg                                                                              >  2:591748/1‑93 (MQ=255)
                                                                                                   aCCAGCGCGAATCCTGCCTGGGATATGTTTAGCACCTACAATGGCATGGCCGCAGGCTTCTTCAATGGCGACTGGGGAGTACTGCTTACcgcg                                                                              <  1:591748/93‑1 (MQ=255)
                                                                                                   aCCAGCGCGAATCCTGCCTGGGATATGTTTAGCACCTACAATGGCATGGCCGCAGGCTTCTTCAATGGCGACTGGGGAGTACTGCTTACCGCGCTGGCCAGTAACAATAAAAATGACATCCTCGCCACCCCAAGCGTCg                                <  1:423405/139‑1 (MQ=255)
                                                                                                        cgcgAATCCTGCCTGGGATATGTTTAGCACCTACAATGGCATGGCCGCAGGc                                                                                                                  <  1:940311/52‑1 (MQ=255)
                                                                                                        cgcgAATCCTGCCTGGGATATGTTTAGCACCTACAATGGCATGGCCGCAGGc                                                                                                                  >  2:940311/1‑52 (MQ=255)
                                                                                                          cgAATCCTGCCTGGGATATGTTTAGCACCTACAATGGCATGGCCGCAGGCTTCTTCAATGGCGACTGGGGAGTACTGGTTACCGCGCTGACCAGTAACAATGAAAATGACATGCTCGCCACCCCAAGCGTCGTAACg                           >  2:912274/1‑137 (MQ=255)
                                                                                                          cgAATCCTGCCTGGGATATGTTTAGCACCTACAATGGCATGGCCGCAGGCTTCTTCAATGGCGACTGGGGAGTACTGCTTACCgcgc                                                                             <  2:37024/87‑1 (MQ=255)
                                                                                                          cgAATCCTGCCTGGGATATGTTTAGCACCTACAATGGCATGGCCGCAGGCTTCTTCAATGGCGACTGGGGAGTACTGCTTACCgcgc                                                                             >  1:37024/1‑87 (MQ=255)
                                                                                                          cgAATCCTGCCTGGGATATGTTTAGCACCTACAATGGCATGGCCGCAGGCTTCTTCAATGGCGACTGGGGAGTACTGCTTACCGCGCTGGCCAGt                                                                     <  1:112002/95‑1 (MQ=255)
                                                                                                          cgAATCCTGCCTGGGATATGTTTAGCACCTACAATGGCATGGCCGCAGGCTTCTTCAATGGCGACTGGGGAGTACTGCTTACCGCGCTGGCCAGt                                                                     >  2:112002/1‑95 (MQ=255)
                                                                                                          cgAATCCTGCCTGGGATATGTTTAGCACCTACAATGGCATGGCCGCAGGCTTCTTCAATGGCGACTGGGGAGTACTGCTTACCGCGCTGGCCAGTAACAATAAAAATGACATCCTCGCCACCCCAAGCGTCGTAACGCt                         >  2:715460/1‑139 (MQ=255)
                                                                                                          cgAATCCTGCCTGGGATATGTTTAGCACCTACAATGGCATGGCCGCAGGCTTCTTCAATGGCGACTGGGGAGTACTGCTTACCGCGCTGGCCAGTAACAATAAAAATGACATCCTCGCCACCCCAAGCGTCGTAACGCt                         >  1:762808/1‑139 (MQ=255)
                                                                                                          cgAATCCTGCCTGGGATATGTTTAGCACCTACAATGGCATGGCCGCAGGCTTCTTCAATGGCGACTGGGGAGTACTGCTTACCGCGCTGACCAGTAACAATAAAAATGACATCCTCGCCACCCCAAGCGTCGTAACg                           <  1:912274/137‑1 (MQ=255)
                                                                                                             aTCCTGCCTGGGATATGTTTAGCACCTACAATGGCATGGCCGCAGGCTTCTTCAATGGCGACTGGGGAGTACTGCTTACCGCGCTGGCCAGTAACAATAAAAATGACATCCTCGCCACCCCAAGCGTCGTAACg                           >  2:1351678/1‑134 (MQ=255)
                                                                                                             aTCCTGCCTGGGATATGTTTAGCACCTACAATGGCATGGCCGCAGGCTTCTTCAATGGCGACTGGGGAGTACTGCTTACCGCGCTGGCCAGTAACAATAAAAATGACATCCTCGCCACCCCAAGCGTCGTAACg                           <  1:1351678/134‑1 (MQ=255)
                                                                                                                  gcctgGGATATGTTTAGCACCTACAATGGCATGGCCGCAGGCTTCTTCAATGGCGACTGGGGAGTACTGCTTACCGCGCTGGCCAGTAACAATAAAAATGACATCCTCGCCACCCCAAGCGTCGTAACGCTGGataata                 >  2:915289/1‑139 (MQ=255)
                                                                                                                   cctgGGATATGTTTAGCACCTACAATGGCATGGCCGCAGGCTTCTTCAATGGCGACTGGGGAGTACTGCTTACCGCGCTGGCCAGTAACAATAAAAATAACATCCTCGCCACCCCAAGCGTCGTAACGCTg                        <  1:1391163/131‑1 (MQ=255)
                                                                                                                   cctgGGATATGTTTAGCACCTACAATGGCATGGCCGCAGGCTTCTTCAATGGCGACTGGGGAGTACTGCTTACCGCGCTGGCCAGTAACAATAAAAATAACATCCTCGCCACCCCAAGCGTCGTAACGCTg                        >  2:1391163/1‑131 (MQ=255)
                                                                                                                          tatGTTTAGCACCTACAATGGCATGGCCGCAGGCTTCTTCAATGGCGACTGGGGAGTACTGCTTACCGCGCTGGCCAGTAACAATAAAAATGACATCCTCGCCACCCCAAGCGTCGTAACGCTGGATAATAAACTcgcg         <  1:915289/139‑1 (MQ=255)
                                                                                                                                 aGCACCTACAATGGCATGGCCGCAGGCTTCTTCAATGGCGCCTGGGGAGTACTGCTTACCGCGCTGGCCAGTAACAATAAAAATGACATCCTCGCCCCCCCAAGCGTCGTAACGCTGGATAAAAAACTCGCGTCCTTCa  >  2:808921/1‑139 (MQ=255)
                                                                                                                                    |                                                                                                                                       
GCGAATAAAAACGTTGGCGCACAGCAATTTACCAATACCGGATTACCGATTTTTAACGCTGCGCAAGGTGTGGCTGATTATAAAAAGAATGGTGGGATCACCAGCGCGAATCCTGCCTGGGATATGTTTAGCGCCTACAATGGCATGGCCGCAGGCTTCTTCAATGGCGACTGGGGAGTACTGCTTACCGCGCTGGCCAGTAACAATAAAAATGACATCCTCGCCACCCCAAGCATCGTAACGCTGGATAATAAACTCGCGTCCTTCA  >  NC_000913/3457484‑3457751

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: ‑