Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 3,078,852 T→C N3S (AAC→AGC)  cmtA ← putative mannitol‑specific PTS IIB and IIC components

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009133,078,8520TC98.5% 237.4 / NA 67N3S (AAC→AGC) cmtAputative mannitol‑specific PTS IIB and IIC components
Reads supporting (aligned to +/- strand):  ref base T (0/0);  major base C (31/35);  minor base A (0/1);  total (31/36)
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

GTTCGTTAGGCAGCCAACCGGTGGGAATAAATAACGCAGTAATAAAACCCCAGGCAATAAAAGCACCAATATTGGGGATGACCATTGCAGTCAAAAAGCCCCCAAAAGCCTGGACCTTTGCACGAGCAGACTTGTTTTCCATAATATTATCCTGTAGAGGAGAGAGTAATTATCCGCGGCTGATAATGTCCGCTAATTGTTTTTCTGATGATGCTGTTAAGAGTTGTTCGAGTATTTCTTCTTCGCACAGTAATTCACTTAACGCC  >  NC_000913/3078718‑3078983
                                                                                                                                      |                                                                                                                                   
gTTCGTTAGGCAGCCAACCGGTGGGAATAAATAACGCAGTAATAAAACCCCAGGCAATAAAAGCACCAATATTGGGGATGACCATTGCAGTCAAAAAGCCCCCAAAAGCCTGGACCTTTGCACGAGCAGACTTGCTTTc                                                                                                                                 <  2:394237/139‑1 (MQ=255)
  tCGTTAGGCAGCCAACCGGTGGGAATAAATAACGCAGTAATAAAACCCCAGGCAATAAAAGCACCAATATTGGGGGTGACCATTGCAGTCAAAAAGCCCCCAAAAGCCTGGACCTTTGCACGAGCAGACTTGCTTTCCa                                                                                                                               <  2:694088/139‑1 (MQ=255)
  tCGTTAGGCAGCCAACCGGTGGGAATAAATAACGCAGTAATAAAACCCCAGGCAATAAAAGCACCAATATTGGGGATGACCATTGCAGTCAAAAAGCCCCCAAAAGCCTGTACCTTTGCACGAGCAGACTTGCTTTCCa                                                                                                                               <  2:847209/139‑1 (MQ=255)
     ttAGGCAGCCAACCGGTGGGAATAAATAACGCAGTAATAAAACCCCAGGCAATAAAAGCACCAATATTGGGGATGACCATTGCAGTCAAAAAGCCCCCAAAAGCCTGGACCTTTGCACGAGCAGACTTGCTTTCCataa                                                                                                                            <  1:409612/139‑1 (MQ=255)
             ccAACCGGTGGGAATAAATAACGCAGTAATAAAACCCCAGGCAATAAAAGCACCAATATTGGGGATGACCATTGCAGTCAAAAAGCCCCCAAAAGCCTGGACCTTTGCACGAGCAGACTTGCTTTCCATAATATTATcc                                                                                                                    >  1:33147/1‑139 (MQ=255)
              cAACCGGTGGGAATAAATAACGCAGTAATAAAACCCCAGGCAATAAAAGCACCAATATTGGGGATGACCATTGCAGTCAAAAAGCCCCCAAAAGCCTGGACCTTTGCACGAGCAGACTTGCTTTCCATAATATTATCCt                                                                                                                   <  2:98083/139‑1 (MQ=255)
                 ccGGTGGGAATAAATAACGCAGTAATAAAACCCCAGGCAATAAAAGCACCAATATTGGGGATGACCATTGCAGTCAAAAAGCCCCCAAAAGCCTGGACCTTTGCACGAGCAGACTTGCTTTCCATAATATTATCCTGTa                                                                                                                <  2:113643/139‑1 (MQ=255)
                       ggAATAAATAACGCAGTAATAAAACCCCAGGCAATAAAAGCACCAATATTGGGGATGACCATTGCAGTCAAAAAGCCCCCAAAAGCCTGGACCTTTGCACGAGCAGACTTGCTTTCCATAATATTATCCTGTAgaggag                                                                                                          >  2:1366304/1‑139 (MQ=255)
                                       taataaAACCCCAGGCAATAAAAGCACCAATATTGGGGATGACCATTGCAGTCAAAAAGCCCCCAAAAGCCTGGACCTTTGCACGAGCAGACTTGCTTTCCa                                                                                                                               <  2:606189/102‑1 (MQ=255)
                                       taataaAACCCCAGGCAATAAAAGCACCAATATTGGGGATGACCATTGCAGTCAAAAAGCCCCCAAAAGCCTGGACCTTTGCACGAGCAGACTTGCTTTCCa                                                                                                                               >  1:606189/1‑102 (MQ=255)
                                               ccccAGGCAATAAAAGCACCAATATTGGGGATGACCATTGCAGTCAAAAAGCCCCCAAAAGCCTGGACCTTTGCACGAGCAGACTTGCTTTCCATAATATTATCCTGTAGAGgaga                                                                                                         >  2:657730/1‑116 (MQ=255)
                                               ccccAGGCAATAAAAGCACCAATATTGGGGATGACCATTGCAGTCAAAAAGCCCCCAAAAGCCTGGACCTTTGCACGAGCAGACTTGCTTTCCATAATATTATCCTGTAGAGgaga                                                                                                         <  1:657730/116‑1 (MQ=255)
                                                 ccAGGCAATAAAAGCACCAATATTGGGGATGACCATTGCAGTCAAAAAGCCCCCAAAAGCCTGGACCTTTGCACGAGCAGACTTGCTTTCCATAATATTATCCTGTaga                                                                                                              >  1:1370946/1‑109 (MQ=255)
                                                 ccAGGCAATAAAAGCACCAATATTGGGGATGACCATTGCAGTCAAAAAGCCCCCAAAAGCCTGGACCTTTGCACGAGCAGACTTGCTTTCCATAATATTATCCTGTaga                                                                                                              <  2:1370946/109‑1 (MQ=255)
                                                 ccAGGCAATAAAAGCACCAATATTGGGGATGACCATTGCAGTCAAAAAGCCCCCAAAAGCCTGGACCTTTGCACGAGCAGACTTGCTTTCCATAATATTATCCTGTAGAGGAGAGAGTAATTATCCGCGGCTGATAATg                                                                                >  1:902999/1‑139 (MQ=255)
                                                 ccAGGCAATAAAAGCACCAATATTGGGGA‑GACCATTGCAGTCAAAAAGCCCCCAAAAGCCTGGACCTTTGCACGAGCAGACTTGCTTTCCataata                                                                                                                          <  1:307451/96‑1 (MQ=255)
                                                 ccAGGCAATAAAAGCACCAATATTGGGGA‑GACCATTGCAGTCAAAAAGCCCCCAAAAGCCTGGACCTTTGCACGAGCAGACTTGCTTTCCataata                                                                                                                          >  2:307451/1‑96 (MQ=255)
                                                   aGGCAATAAAAGCACCAATATTGGGGATGACCATTGCAGTCAAAAAGCCCCCAAAAGCCTGGACCTTTGCACGAGCAGACTTGCTTTCCATAATATTATc                                                                                                                     <  2:712757/100‑1 (MQ=255)
                                                   aGGCAATAAAAGCACCAATATTGGGGATGACCATTGCAGTCAAAAAGCCCCCAAAAGCCTGGACCTTTGCACGAGCAGACTTGCTTTCCATAATATTATc                                                                                                                     >  1:712757/1‑100 (MQ=255)
                                                    ggCAATAAAAGCACCAATATTGGGGATGACCATTGCAGTCAAAAAGCCCCCAAAAGCCTGGACCTTTGCACGAGCAGACTTGCTTTCCa                                                                                                                               >  1:1280286/1‑89 (MQ=255)
                                                    ggCAATAAAAGCACCAATATTGGGGATGACCATTGCAGTCAAAAAGCCCCCAAAAGCCTGGACCTTTGCACGAGCAGACTTGCTTTCCa                                                                                                                               <  2:1280286/89‑1 (MQ=255)
                                                                         ggggATGACCATTGCAGTCAAAAAGCCCCCAAAAGCCTGGACCTTTGCACGAGCAGACTTGCTTTCCa                                                                                                                               >  1:1351900/1‑68 (MQ=255)
                                                                         ggggATGACCATTGCAGTCAAAAAGCCCCCAAAAGCCTGGACCTTTGCACGAGCAGACTTGCTTTCCa                                                                                                                               <  2:1351900/68‑1 (MQ=255)
                                                                          gggATGACCATTGCAGTCAAAAAGCCCCCAAAAGCCTGGACCTTTGCACGAGCAGACTTGCTTTCCa                                                                                                                               >  2:1010906/1‑67 (MQ=255)
                                                                          gggATGACCATTGCAGTCAAAAAGCCCCCAAAAGCCTGGACCTTTGCACGAGCAGACTTGCTTTCCa                                                                                                                               <  1:1010906/67‑1 (MQ=255)
                                                                          gggATGACCATTGCAGTCAAAAAGCCCCCAAAAGCCTGGACCTTTGCACGAGCAGACTTGCTTTCCATAATATTATCCTGTAGAGGAGAGAGTAATTATCCGCGGc                                                                                        >  2:996549/1‑106 (MQ=255)
                                                                          gggATGACCATTGCAGTCAAAAAGCCCCCAAAAGCCTGGACCTTTGCACGAGCAGACTTGCTTTCCATAATATTATCCTGTAGAGGAGAGAGTAATTATCCGCGGc                                                                                        <  1:996549/106‑1 (MQ=255)
                                                                          gggATGACCATTGCAGTCAAAAAGCCCCCAAAAGCCTGGACCTTTGCACGAGCAGACTTGCTTTCCATAATATTATCCTGTAGAGGAGAGAGTAATTATCCGCGGCTGATAATGTCCGCTAATTGTTTTTCTGatgatg                                                       <  1:1179094/139‑1 (MQ=255)
                                                                          gggATGACCATTGCAGTCAAAAAGCCCCCAAAAGCCTGGACCTTTGCACGAGCAGACTTGCTTTCCATAATATTATCCTGTAGAGGAGAGAGTAATTATCCGCGGCTGATAATGTCCGCTAATTGTTTTTCTGatgatg                                                       >  1:409144/1‑139 (MQ=255)
                                                                          gagATGACCAGTGCAGCCACTAATCCCTCAAAAGTCATGATCTTTGCACGAATCGAATTGATTTCAATAATAAAGTCGTGTAGTGGAGAGAGTAATGATCCGCGGCTGATACTGTCCGATAATTGTTTTTCTGatgatg                                                       <  1:1103461/137‑1 (MQ=255)
                                                                            gATGACCATTGCAGTCAAAAAGCCCCCAAAAGCCTGGACCTTTGCACGAGCAGACTTGCTTTCCata                                                                                                                             <  2:186850/67‑1 (MQ=255)
                                                                            gATGACCATTGCAGTCAAAAAGCCCCCAAAAGCCTGGACCTTTGCACGAGCAGACTTGCTTTCCata                                                                                                                             >  1:186850/1‑67 (MQ=255)
                                                                              tGACCATTGCAGTCAAAAAGCCCCCAAAAGCCTGGACCTTTGCACGAGCAGACTTGCTTTCCATAATATTATCCTGTAGAGGAGAGAGTAATTATCCGCGGCTGATAATGTCCGCTAATTGTTTTTCTgatgat                                                        >  2:525947/1‑134 (MQ=255)
                                                                              tGACCATTGCAGTCAAAAAGCCCCCAAAAGCCTGGACCTTTGCACGAGCAGACTTGCTTTCCATAATATTATCCTGTAGAGGAGAGAGTAATTATCCGCGGCTGATAATGTCCGCTAATTGTTTTTCTgatgat                                                        <  1:525947/134‑1 (MQ=255)
                                                                              tGACCATTGCAGTCAAAAAGCCCCCAAAAGCCTGGACCTTTGCACGAGCAGACTTGCTTTCCATAATATTATCCTGTAGAGGAGAGAGTAATTATCCGCGGCTGATAATGTCCGCTAATTGTTTTTCTGATGATGCTGt                                                   <  2:409144/139‑1 (MQ=255)
                                                                               gACCATTGCAGTCAAAAAGCCCCCAAAAGCCTGGACCTTTGCACGAGCAGACTTGCTTTCCATAATATTATc                                                                                                                     >  2:517483/1‑72 (MQ=255)
                                                                               gACCATTGCAGTCAAAAAGCCCCCAAAAGCCTGGACCTTTGCACGAGCAGACTTGCTTTCCATAATATTATc                                                                                                                     <  1:517483/72‑1 (MQ=255)
                                                                               gACCATTGCAGTCAAAAAGCCCCCAAAAGCCTGGACCTTTGCACGAGCAGACTTGCTTTCCATAATATTATCCTGTAGAGGAGAGAGTAATTATCCGCGGCTGATAATGTCCGCTAATTGTTTTTCTGatgatg                                                       <  2:131461/134‑1 (MQ=255)
                                                                               gACCATTGCAGTCAAAAAGCCCCCAAAAGCCTGGACCTTTGCACGAGCAGACTTGCTTTCCATAATATTATCCTGTAGAGGAGAGAGTAATTATCCGCGGCTGATAATGTCCGCTAATTGTTTTTCTGatgatg                                                       >  1:131461/1‑134 (MQ=255)
                                                                                    ttGCAGTCAAAAAGCCCCCAAAAGCCTGGACCTTTGCACGAGCAGACTTGCTTTCCATAATATTATc                                                                                                                     <  2:1263723/67‑1 (MQ=255)
                                                                                    ttGCAGTCAAAAAGCCCCCAAAAGCCTGGACCTTTGCACGAGCAGACTTGCTTTCCATAATATTATc                                                                                                                     >  1:1263723/1‑67 (MQ=255)
                                                                                    ttGCAGTCAAAAAGCCCCCAAAAGCCTGGACCTTTGCACGAGCAGACTTGCTTTCCATAATATTATCCTGTAGAGGAGAGAGTAATTATCCGCGGCTGATAATGTCCGCTAATTGTTTTTCTGATGATGCTGTTAagag                                             <  2:483264/139‑1 (MQ=255)
                                                                                     tGCAGTCAAAAAGCCCCCAAAAGCCTGGACCTTTGCACGAGCAGACTTGCTTTCCa                                                                                                                               <  2:1275450/56‑1 (MQ=255)
                                                                                     tGCAGTCAAAAAGCCCCCAAAAGCCTGGACCTTTGCACGAGCAGACTTGCTTTCCa                                                                                                                               >  1:1275450/1‑56 (MQ=255)
                                                                                           cAAAAAGCCCCCAAAAGCCTGGACCTTTGCACGAGCAGACTTGCTTTCCATAATATTATCCTGTAGAGGAGAGAGTAATTATCCGCGGCTGATAATGTCCGCTAATTGTTTTTCTGATGATGCTGTTAAGAGTTGTTCg                                      >  2:400720/1‑139 (MQ=255)
                                                                                            aaaaaGCCCCCAAAAGCCTGGACCTTTGCACGAGCAGACTTGCTTTCCATAATATTATCCTGTAGAGGAGAGAGTAATTATCCGCGGCTGATAATGTCCGCTAATTGTTTTTCTGATGATGCTGTTAAGAGTTGTTCGa                                     >  1:661244/1‑139 (MQ=255)
                                                                                             aaaaGCCCCCAAAAGCCTGGACCTTTGCACGAGCAGACTTGCTTTCCATAATATTATCCTGTAGAGGAGAGAGTAATTATCCGCGGCTGATAATGTCCGCTAATTGTTTTTCTGATGATGCTGTTAAGAGTTGTTCGAg                                    <  2:902999/139‑1 (MQ=255)
                                                                                                    cccAAAAGCCTGGACCTTTGCACGAGCAGACTTGCTTTCCATAATATTATCCTGTAGAGGAGAGAGTAATTATCCGCGGCTGATAATGTcc                                                                             <  1:81593/91‑1 (MQ=255)
                                                                                                    cccAAAAGCCTGGACCTTTGCACGAGCAGACTTGCTTTCCATAATATTATCCTGTAGAGGAGAGAGTAATTATCCGCGGCTGATAATGTcc                                                                             >  2:81593/1‑91 (MQ=255)
                                                                                                    cccAAAAGCCTGGACCTTTGCACGAGCAGACTTGCTTTCCATAATATTATCCTGTAGAGGAGAGAGTAATTATCCGCGGCTGATAATGTCCGCTAATTGTTTTTCtga                                                            <  2:653748/108‑1 (MQ=255)
                                                                                                    cccAAAAGCCTGGACCTTTGCACGAGCAGACTTGCTTTCCATAATATTATCCTGTAGAGGAGAGAGTAATTATCCGCGGCTGATAATGTCCGCTAATTGTTTTTCtga                                                            >  1:653748/1‑108 (MQ=255)
                                                                                                       aaaaGCCTGGACCTTTGCACGAGCAGACTTGCTTTCCATAATATTATCCTGTAGAGGAGAGAGTAATTATCCGCGGCTGATAATGTCCGCTAATTGTTTTTCTGATGATGCTGTTAAGAGTTGTTCGAGTATttcttct                          <  2:33147/139‑1 (MQ=255)
                                                                                                            ccTGGACCTTTGCACGAGCAGACTTGCTTTCCATAATATTATCCTGTAGAGGAGAGAGTAATTATCCGCGGCTGATAATGTCCGCTCATTGTTTTTCTGATGATGCTGTTAAGAGTTGTTCGAGTATTTCTTCTTCGca                     >  2:905461/1‑139 (MQ=255)
                                                                                                               ggACCTTTGCACGAGCAGACTTGCTTTCCATAATATTATCCTGTAGAGGAGAGAGTAATTATCCGCGGCTGATAATGTCCGCt                                                                          >  2:145418/1‑83 (MQ=255)
                                                                                                               ggACCTTTGCACGAGCAGACTTGCTTTCCATAATATTATCCTGTAGAGGAGAGAGTAATTATCCGCGGCTGATAATGTCCGCt                                                                          <  1:145418/83‑1 (MQ=255)
                                                                                                                gACCTTTGCACGAGCAGACTTGCTTTCCATAATATTATCCTGTAGAGGAGAGAGTAATTATCCGCGGCTGATAATGTCCGCTAATTGTTTTTCTGATGATGCTGTTAAGAGTTGTTCGAGTATTTCTTCTTCGCACAGt                 >  2:997134/1‑139 (MQ=255)
                                                                                                                    tttGCACGAGCAGACTTGCTTTCCATAATATTATCCTGTAGAGGAGAGAGTAATTATCCGCGGCTGATAATGTCCGCTAATTGTTTTTCTGATGATGCTGTTAAGAGTTGTTCGAGTATTTCTTCTTCGCACAGTAAtt             <  2:661244/139‑1 (MQ=255)
                                                                                                                      tGCACGAGCAGACTTGCTTTCCATAATATTATCCTGTAGAGGAGCGAGTAATTATCCGCGGCTGATAATGTCCGCTAATTGTTTTTCTGatgatg                                                       >  1:968631/1‑95 (MQ=255)
                                                                                                                      tGCACGAGCAGACTTGCTTTCCATAATATTATCCTGTAGAGGAGAGAGTAATTATCcgc                                                                                           <  1:641469/59‑1 (MQ=255)
                                                                                                                      tGCACGAGCAGACTTGCTTTCCATAATATTATCCTGTAGAGGAGAGAGTAATTATCcgc                                                                                           >  2:641469/1‑59 (MQ=255)
                                                                                                                      tGCACGAGCAGACTTGCTTTCCATAATATTATCCTGTAGAGGAGAGAGTAATTATCCGCGGCTGATAATGTCCGCTAATTGTTTTTCTGatgatg                                                       <  2:968631/95‑1 (MQ=255)
                                                                                                                      tGCACGAGCAGACTTGCTTTCCATAATATTATCCTGTAGAGGAGAGAGTAATTATCCGCGGCTGATAATGTCCGCTAATTGTTTTTCTGATGATGCTGTTAAGAGTTGTTCGAGTATTTCTTCTTCGCACAGTAATTCa           >  2:58419/1‑139 (MQ=255)
                                                                                                                      tGCACGAGCAGACTTGCTTTCCATAATATTATCCTGTAGAGGAGAGAGTAATTATCCGCGGCTGATAATGTCCGCTAATTGTTTTTCTGATGATGCTGTTAAGAGTTGTTCGAGTATTTCTTCTTCGCACAGTAATTCa           >  2:50137/1‑139 (MQ=255)
                                                                                                                         aCGAGCAGACTTGCTTTCCATAATATTATCCTGTAGAGGAGAGAGTAATTATCCGCGGCTGATAATGTCCGCTAATTGTTTTTCTGATGATGCTGTTAAGAGTTGTTCGAGTATTTCTTCTTCGCACAGTAATTCACtt        <  1:50137/139‑1 (MQ=255)
                                                                                                                         aCGAGCAGACTTGCTTTCCATAATATTATCCTGTAGAGGAGAGAGTAATTATCCGCGGCTGATAATGTCCGCTAATTGTTTTTCTGATGATGCTGTTAAGAGTTGTTCGAGTATTTCTTCTTCGCACAGTAATTCACtt        <  1:1366304/139‑1 (MQ=255)
                                                                                                                                gACTTGCTTTCCATAATATTATCCTGTAGAGGAGAGAGTAATTATCCGCGGCTGATAATGTCCGCTAATTGTTTTTCTGATGATGCTGTTAAGAGTTGTTCGAGTATTTCTTCTTCGCACAGTAATTCACTTAACGcc  <  2:974066/138‑1 (MQ=255)
                                                                                                                                gACTTGCTTTCCATAATATTATCCTGTAGAGGAGAGAGTAATTATCCGCGGCTGATAATGTCCGCTAATTGTTTTTCTGATGATGCTGTTAAGAGTTGTTCGAGTATTTCTTCTTCGCACAGTAATTCACTTAACGcc  >  1:974066/1‑138 (MQ=255)
                                                                                                                                      |                                                                                                                                   
GTTCGTTAGGCAGCCAACCGGTGGGAATAAATAACGCAGTAATAAAACCCCAGGCAATAAAAGCACCAATATTGGGGATGACCATTGCAGTCAAAAAGCCCCCAAAAGCCTGGACCTTTGCACGAGCAGACTTGTTTTCCATAATATTATCCTGTAGAGGAGAGAGTAATTATCCGCGGCTGATAATGTCCGCTAATTGTTTTTCTGATGATGCTGTTAAGAGTTGTTCGAGTATTTCTTCTTCGCACAGTAATTCACTTAACGCC  >  NC_000913/3078718‑3078983

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑