Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_000913_3_KO_pgi1,169,3820CG20.0% 126.3 / 32.0 56intergenic (+52/+30)bhsA/ldtCbiofilm, cell surface and signaling protein/L,D‑transpeptidase linking Lpp to murein
Reads supporting (aligned to +/- strand):  ref base C (23/21);  new base G (5/6);  total (28/28)
Fisher's exact test for biased strand distribution p-value = 7.46e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 3.33e-01
Rejected as consensus: Frequency below/above cutoff threshold.

TGGCGCAAAAAGCGGATGAGATGGGCGCAAAATCTTTCCGTATTACTTCTGTAACCGGTCCGAATACCCTCCATGGAACAGCAGTAATTTATAAATAAGCATTAACCCTCATTAATGCCTGCTACTGCTGATTTTTTCCCCGCGACATGCCGTGTCGCGGGGATTTTTTTATCCGGGCTTTACAGCGTTTGTGGGCTCACTTGATGACGGCGGACATCCACCGGCATCCCGGAACGGACATCCATCACATGTTGCATCACTTCAGCGTCAGTTTGTGCTGCATCTTTAAATGATTGCAT  >  NC_000913_3_KO_pgi/1169233‑1169531
                                                                                                                                                     |                                                                                                                                                     
tGGCGCAAAAAGCGGATGAGATGGGCGCAAAATCTTTCCGTATTACTTCTGTAACCGGTCCGAATACCCTCCATGGAACGGCAGTACTTTATAAATAAGCATTAACCCTCATTCATGCCTGATACTGCTGATTTTTTCCCGGCGACATGc                                                                                                                                                       >  2:106814/1‑150 (MQ=255)
          aGCGGATGAGATGGGCGCAAAATCTTTCCGTATTATTTCTGTATCCGGTCCGAATACCCTCCATGGAACAGCAGTAATTTATAAATAAGCATTAACCCTCATTAGTGCCTGCTACTGCTGATTTTTTCCCCGCGACATGCCGTGTCGCgg                                                                                                                                             <  2:471491/150‑1 (MQ=255)
          aGCGGATGAGATGGGCGCAAAATCTTTCCGTATTACTTCTGTAACCGGTCCGAATACCCTCCATGGAACAGCAGTAATTTATAAATAAGCATTAACCCTCATTAATGCCTGCTACTGCTGATTTTTTCCCCGCGACACGGCATGTCGCgg                                                                                                                                             <  2:638010/150‑1 (MQ=255)
                 gagaTGGGCGCAAAATCTTTCCGTATTACTTCTGTAACCGGTCCGAATACCCTCCATGGAACAGCAGTAATTTATAAATAAGCATTAACCCTCATTAATGCCTGCTACTGCTGATTTTTTCCCCGCGACATGCCGTGTCGCGGGGAtttt                                                                                                                                      >  4:104986/1‑150 (MQ=255)
                                   ttCCGTATTACTTCTGTAACCGGTCCGAATACCCTCCATGGAACAGCAGTAATTTATAAATAAGCATTAACCCTCATTAATGCCTGCTACTGCTGATTTTTTCCCCGCGACATGCCGTGTCGCGGGGATTTTTTTATCCGGGCTTTACAg                                                                                                                    >  4:338074/1‑150 (MQ=255)
                                       gTATTACTTCTGTAACCGGTCCGAATACCCTCCATGGAACAGCAGTAATTTATAAATAAGCATTAACCCTCATTAATGCCTGCTACTGCTGATTTTTTCCCCGCGACACGGCATGTcgcg                                                                                                                                              <  1:693828/120‑1 (MQ=255)
                                       gTATTACTTCTGTAACCGGTCCGAATACCCTCCATGGAACAGCAGTAATTTATAAATAAGCATTAACCCTCATTAATGCCTGCTACTGCTGATTTTTTCCCCGCGACACGGCATGTcgcg                                                                                                                                              >  2:693828/1‑120 (MQ=255)
                                             cTTCTGTAACCGGTCCGAATACCCTCCATGGAACAGCAGTAATTTATAAATAAGCATTAACCCTCATTAATGCCTGCTACTGCTGATTTTTTCCCCGCGACATGCCGTGTCGCGGGGATTTTTTTATCCGGGCTTTACAGCGTTTGTggg                                                                                                          >  2:623484/1‑150 (MQ=255)
                                              ttCTGTAACCGGTCCGAATATCCTCCATGGAACAGCAGTAATTTATAAATAAGCATTAACCCTCATTAATGCCTGCTACTGCTGATTTTTTCCCCGCGACATGCCGTGTCGCGGGGATTTTTTTATTTGGGCTTTTCAGCGTTTGTgggt                                                                                                         >  2:388097/1‑149 (MQ=255)
                                               tCTGTAACCGGTCCGAATACCCTCCATGGAACAGCAGTAATTTATAAATAAGCATTAACCCTCATTAATGCCTGCTACTGCTGATTTTTTCCCCGCGACACGGCATGTCGCgg                                                                                                                                             <  2:651206/113‑1 (MQ=255)
                                               tCTGTAACCGGTCCGAATACCCTCCATGGAACAGCAGTAATTTATAAATAAGCATTAACCCTCATTAATGCCTGCTACTGCTGATTTTTTCCCCGCGACACGGCATGTCGCgg                                                                                                                                             >  1:651206/1‑113 (MQ=255)
                                                      ccGGTCCGAATACCCTCCATGGAACAGCAGTAATTTATACATACGCATTACCCCACACTAATGCGCATTCTTGCAGTGTATTTCCCCGCGACATGCCGTGTCGCGGGGATTTTTTTATCCGGGCTTTACAGCGTTTGTGGGCTCACTtga                                                                                                 <  1:347537/150‑1 (MQ=255)
                                                            cGAATACCCTCCATGGAACAGCAGTAATTTATAAATAAGCATTAACCCTCATTAATGCCTGCTACTGCTGATTTTTTCCCCGCGACATGCCGTGTCGCGGGGATTTTTTTATCCGGGCTTTACAGCGTTTGTGGGCTCACTTGATGAcgg                                                                                           >  3:424585/1‑150 (MQ=255)
                                                            cGAATACCCCCCATGGAACAGCAGTAATTTATAAATAAGCATTAACCCTCATTAATGCCTGCTACTGCTGATTTTTTCCCCGCGACATGCCGTGTCGCGGGGGTTTTTTTCTCCGGGCTCTACAGCGCTTGTGGGCTCACTTGATGAcgg                                                                                           >  2:510159/1‑150 (MQ=255)
                                                             gAATACCCTCCATGGAACAGCAGTAATTTATAAATAAGCATTAACCCTCATTAAGGCCTGCTACTGCTGATTTTTTCCCCGCGACATGCCGTGTCGCGGGGATTTTTTTATCCGGGCTTTACAGCGTTTGTGGGCTCACTTGATggcggc                                                                                          >  3:415497/1‑150 (MQ=255)
                                                               aTACCCTCCATGGAACAGCAGTAATTTATAAATAAGCATTAACCCTCAATAATGCCTGCTACTGCTGATTTTTACCCCGCGACAAAACGTGTCGCGGGGATTTTTTTATCCGGGCTTTACAGCGTTTGTGGGCTCACTTGATGAcggcgg                                                                                        <  1:623484/150‑1 (MQ=255)
                                                                accccTCCATGGAACAGCAGTAATTTATAAATAAGCATTAACCCTCATTAATGCCTGCTACTGCTGATTTTTTCCCCCCGACATGCCGTGTCGCTTGGATTTTTTTATCCGGTCTTTACAGCGTTTGTGGGCTCACTTGATGACGGCGGa                                                                                       <  1:106814/148‑1 (MQ=255)
                                                                       cATGGAACAGCAGTAATTTATAAATAAGCATTAACCCTCATTAATGCCTGCTACTGCTGATTTTTTCCCCGCGACATGCCGTGTCGCGGGGATTTTTTTATCCGGGCTTTACAGCGTTTGTGTTCTCACTTGATGACGGCGGACATCCAc                                                                                <  4:424585/150‑1 (MQ=255)
                                                                         tGGAACAGCAGTAATTTATAAATAAGCATTAACCCTCATTAATGCCTGCTACTGCTGATTTTTTCCCCGCGACATGCCGTGTCGCGGGGATTTTTTTATCCGGGCTTTACAGCGTTTGTGGGCTCACTTGATGACGGCGGACATCCACCg                                                                              <  2:362672/150‑1 (MQ=255)
                                                                           gAACAGCAGTAATTTATAAATAAGCATTAACCCTCATTAATGCCTGCTACTGCTGATTTTTTCCCCGCGACATGCCGTGTCGCGGGGATTTTTTTATCCGGGCTTTACAGCGTTTGTGGGCTCACTTGATGACGGCGGACATCCACCGGc                                                                            <  1:568737/150‑1 (MQ=255)
                                                                              cagcagTAATTTATAAATAAGCATTAACCCTCATTAATGCCTGCTACTGCTGATTTTTTCCCCGCGACATGCCGTGTCGCGGGGATTTTTTTATCCGGGCTTTACAGCGTTTGTGGGCTCACTTGATGACGGCGGACATCCACCGGCATc                                                                         >  1:24724/1‑150 (MQ=255)
                                                                                    tAATTTATAAATAAGCATTAACCCTCATTAATGCCTGCTACTGCTGATTTTTTCCCCGCGACATGCCGTGTCGCGGGGATTTTTTTATCCGGGCTTTACAGCGTTTGTGGGCTCACTTGATGATGGCGGACATCCACCGGCATCCCGGaa                                                                   >  1:163077/1‑150 (MQ=255)
                                                                                    tAATTTATAAATAAGCATTAACCCTCATTAATGCCTGCTACTGCTGATTTTTTCCCCGCGACATGCCGTGTCGCGGGGATTTTTTTATCCGGGCTTTACAGCGTTTGTGGGCTCACTTGATGATGGCGGACATCCACCGGCATCCCGGaa                                                                   >  1:162867/1‑150 (MQ=255)
                                                                                    tAATTTATAAATAAGCATTAACCCTCATTAATGCCTGCTACTGCTGATTTTTTCCCCGCGACATGCCGTGTCGCGGGGATTTTTTTATCCGGGCTTTACAGCGTTTGTGGGCTCACTTGATGACGGCGGACATCCAc                                                                                <  1:203648/137‑1 (MQ=255)
                                                                                    tAATTTATAAATAAGCATTAACCCTCATTAATGCCTGCTACTGCTGATTTTTTCCCCGCGACATGCCGTGTCGCGGGGATTTTTTTATCCGGGCTTTACAGCGTTTGTGGGCTCACTTGATGACGGCGGACATCCAc                                                                                >  2:203648/1‑137 (MQ=255)
                                                                                    tAATTTATAAATAAGCATTAACCCTCATTAATGCCTGCTACTGCTGATTTTTTCCCCGCGACATGCCGTGTCGCGGGGATTTTTTTATCCGGGCTTTACAGCGTTTGTGGGCTCACTTGATGACGGCGGACATCCACCGGCATCCCGGaa                                                                   <  3:104986/150‑1 (MQ=255)
                                                                                          ataaataaGCATTAACCCTCATTAATGCCTGCTACTGCTGATTTTTTCCCCGCGACATGCCGTGTCGCGGGGAtttt                                                                                                                                      <  1:646044/77‑1 (MQ=255)
                                                                                          ataaataaGCATTAACCCTCATTAATGCCTGCTACTGCTGATTTTTTCCCCGCGACATGCCGTGTCGCGGGGAtttt                                                                                                                                      >  2:646044/1‑77 (MQ=255)
                                                                                            aaataaGCATTAACCCTCATTAATGCCTGCTACTGCTGATTTTTTTTTTTTTTTATTCTTTGTCTCTGGGTTTTTTTTATCCTGGCTTTACAGCGTTTGTTGGCTCACTTGTTGTCGGCGGTCATCCACCGGCATCCCGGAACGGAcatc                                                           >  4:268355/1‑150 (MQ=255)
                                                                                               taaGCATTAACCCTCATTAATGCCTGCTACTGCTGATTTTTTCCCCGCGACATGCCGTGTCGCGGGGATTTTTTTATCCGGGCTTTACAGCGTTTGTGGGCTCACTTGATGACGGCGGACATCCACCGGCATCCCGGAACGGAcatccat                                                        <  2:24724/150‑1 (MQ=255)
                                                                                                    aTTAACCCTCATTAATGCCTGCTACTGCTGATTTTTTCCCCGCGACATGCCGTGTCGCGGGGATTTTTTTATCCGGGCTTTACAGCGTTTGTGGGCTCACTTGATGACGGCGGACATCCACCGGCATCCCg                                                                      >  3:411524/1‑131 (MQ=255)
                                                                                                    aTTAACCCTCATTAATGCCTGCTACTGCTGATTTTTTCCCCGCGACATGCCGTGTCGCGGGGATTTTTTTATCCGGGCTTTACAGCGTTTGTGGGCTCACTTGATGACGGCGGACATCCACCGGCATCCCg                                                                      <  4:411524/131‑1 (MQ=255)
                                                                                                         cccTCATTAATGCCTGCTACTGCTGATTTTTTCCCCGCGACATGCCGTGTCGCGGGGATTTTTTTATCCGGGCTTTACAGCGTTtgt                                                                                                             >  2:61734/1‑87 (MQ=255)
                                                                                                         cccTCATTAATGCCTGCTACTGCTGATTTTTTCCCCGCGACATGCCGTGTCGCGGGGATTTTTTTATCCGGGCTTTACAGCGTTtgt                                                                                                             <  1:61734/87‑1 (MQ=255)
                                                                                                           cTCATTAATGCCTGCTACTGCTGATTTTTTCCCCGCGACATGCCGTGTCGCGGGGATTTTTTTATCCGGGCTTTACAGCGTTTGTGGGCTCACTTGATGATGGCGGACATCCACCGGCATCCCGGAACGGACATCCATCACATGTTGCAt                                            <  2:163077/150‑1 (MQ=255)
                                                                                                           cTCATTAATGCCTGCTACTGCTGATTTTTTCCCCGCGACATGCCGTGTCGCGGGGATTTTTTTATCCGGGCTTTACAGCGTTTGTGGGCTCACTTGATGATGGCGGACATCCACCGGCATCCCGGAACGGACATCCATCACATGTTGCAt                                            <  2:162867/150‑1 (MQ=255)
                                                                                                              aTTAATGCCTGCTACTGCTGATTTTTTCCCCGCGACATGCCGTGTCGCGGGGATTTTTTTCTCCGGGCTTTACAGCGTTTGTGGGCTCACTTGATGACGGCGGACATCCACCGGCATCCCGGAACGGACATCCATCACATGTTGCATCAc                                         >  1:406688/1‑150 (MQ=255)
                                                                                                                tAATGCCTGCTACTGCTGATTTTTTCCCCGCGACATGCCGTGTCGCGGGGATTTTTTTATCCGGGCTTTACAGCGTTTGTGGGCTCACTTGATGACGGCGGACATCCACCGGCATCCCGGAACGGAc                                                              >  2:53057/1‑127 (MQ=255)
                                                                                                                tAATGCCTGCTACTGCTGATTTTTTCCCCGCGACATGCCGTGTCGCGGGGATTTTTTTATCCGGGCTTTACAGCGTTTGTGGGCTCACTTGATGACGGCGGACATCCACCGGCATCCCGGAACGGAc                                                              <  1:53057/127‑1 (MQ=255)
                                                                                                                        gCTACTGCTGATTTTTTCCCCGCGACATGCCGTGTCGCGGGGATTTTTTTATCCGGGCTTTACAGCGTTTGTGGGCTCACTTGATGACGGCGGACATCCAGCGGCATCCCGGAACGGACATCCATCACATGTTGCATCACTTCAGCGTCa                               <  2:406688/150‑1 (MQ=255)
                                                                                                                          tACTGCTGATTTTTTCCCCGCGACATGCCGTGTCGCgg                                                                                                                                             >  1:41509/1‑38 (MQ=255)
                                                                                                                          tACTGCTGATTTTTTCCCCGCGACATGCCGTGTCGCgg                                                                                                                                             <  2:41509/38‑1 (MQ=255)
                                                                                                                            ctgctgATTTTTTCCCCGCGACATGCCGTGTCGCGGGGATTTTTTTATCCGGGCTTTACAGCGTTTGTGGGCTCACTTGATGACGGCGGACATCCACCGGCATCCCGGAACGGACATCCATCACATGTTGCATCACTTCAGCGTCAGttt                           <  3:338074/150‑1 (MQ=255)
                                                                                                                               ctgATTTTTTCCCCGCGACATGCCGTGTCGCGGGGATTTTTTTATCCGGGCTTTACAGCGTTTGTGGGCTCACTTGATGACGGCGGACATCCACCGGCATCCCGGAACGGAcatcc                                                          >  4:160565/1‑116 (MQ=255)
                                                                                                                               ctgATTTTTTCCCCGCGACATGCCGTGTCGCGGGGATTTTTTTATCCGGGCTTTACAGCGTTTGTGGGCTCACTTGATGACGGCGGACATCCACCGGCATCCCGGAACGGAcatcc                                                          <  3:160565/116‑1 (MQ=255)
                                                                                                                                tgATTTTTTCCCCGCGACATGCCGTGTCGCGGGGATTTTTTTATCCGGGCTTTACAGCGTTtg                                                                                                              >  1:142038/1‑63 (MQ=255)
                                                                                                                                tgATTTTTTCCCCGCGACATGCCGTGTCGCGGGGATTTTTTTATCCGGGCTTTACAGCGTTtg                                                                                                              <  2:142038/63‑1 (MQ=255)
                                                                                                                                  aTTTTTTCCCCGCGACATGCCGTGTCGCGGGGATTTTTTTATCCGGGCTTTACAGCGTTTGTGGGCTCACTTGATGACGGCGGACATCCACCGGCATCCCGGAACGGACATCCATCACATGTTGCATCACTTCAGCGTCAGTTTGtgctg                     >  1:621172/1‑150 (MQ=255)
                                                                                                                                          cccGCGACATGCCGTGTCGCGGGGATTTTTTTTTTTTTTTTTTACAGCGTTTGTGGGCTCACTTGATGACGGCGGACGTCCACCGGCATCCCGGAACGGCCCTCCATCACCTGTTCCCTCACTTCAGCGTCCGTTTGTGCTGCTTCtttt             >  4:152880/1‑149 (MQ=255)
                                                                                                                                          cccGCGACACGGCATGTCGCGGGGATTTTTTTATCCGGGCTTTACAGCGTTTGTGGGCTCACTTGATGACGGCGGACATCCAcc                                                                               >  3:170692/1‑84 (MQ=38)
                                                                                                                                          cccGCGACACGGCATGTCGCGGGGATTTTTTTATCCGGGCTTTACAGCGTTTGTGGGCTCACTTGATGACGGCGGACATCCAcc                                                                               <  4:170692/84‑1 (MQ=38)
                                                                                                                                          cccGCGACACGGCATGTCGCGGGGATTTTTTTATCCGGGCTTTACAGCGTTTGTGGGCTCACTTGATGACGGCGGACATCCACCGGCATCCCGGAACGGACATCCATCACAt                                                   >  3:344275/1‑112 (MQ=255)
                                                                                                                                          cccGCGACACGGCATGTCGCGGGGATTTTTTTATCCGGGCTTTACAGCGTTTGTGGGCTCACTTGATGACGGCGGACATCCACCGGCATCCCGGAACGGACATCCATCACAt                                                   <  4:344275/112‑1 (MQ=255)
                                                                                                                                           ccGCGACATGCCGTGTCGCGGGGATTTTTTTATCCGGGCTTTACAGCGTTTGTGGGCTCACTTGATGACGGCGGACATCCACCGGCATCCCGGAACGGACATCCATCACATGTTGCATCACTTCAGCGTCAGTTTGTGCTGCATCTTTaa            >  3:207776/1‑150 (MQ=255)
                                                                                                                                           ccGCGACACGGCATGTCGCGGGGATTTTTTTATCCGGGCTTTACAGCGTTTGTGGGCTCACTTGATGACGGCGGACATCCACCGGCATCCCGGAACGGACATCCATCACATGTTGCATCACTTCAGCGTCAGTTTGTGCTGCATCttt              <  1:144005/148‑1 (MQ=255)
                                                                                                                                           ccGCGACACGGCATGTCGCGGGGATTTTTTTATCCGGGCTTTACAGCGTTTGTGGGCTCACTTGATGACGGCGGACATCCACCGGCATCCCGGAACGGACATCCATCACATGTTGCATCACTTCAGCGTCAGTTTGTGCTGCATCttt              >  2:144005/1‑148 (MQ=255)
                                                                                                                                                aCATGCCGTGTCGCGGGGATTTTTTTATCCGGGCTTTACAGCGTTTGTGGGCTCACTTGATGACGGCGGACATCCACCGGCATCCCGGAACGGACATCCATCACATGTTGCATCACTTCAGCGTCAGTTTGTGCTGCATCTTTAAATGat       <  3:152880/150‑1 (MQ=255)
                                                                                                                                                     ccGTGTCGCGGGGATTTTTTTATCCGGGCTTTACAGCGTTTGTGGGCTCACTTGATGACGGCGGACATCCACCGGCATCCCGGAACGGACATCCATCACATGTTGCATCACTTCAGCGTCAGTTTGTGCTGCATCTTTAAATGattgcat  >  3:176674/1‑150 (MQ=255)
                                                                                                                                                     |                                                                                                                                                     
TGGCGCAAAAAGCGGATGAGATGGGCGCAAAATCTTTCCGTATTACTTCTGTAACCGGTCCGAATACCCTCCATGGAACAGCAGTAATTTATAAATAAGCATTAACCCTCATTAATGCCTGCTACTGCTGATTTTTTCCCCGCGACATGCCGTGTCGCGGGGATTTTTTTATCCGGGCTTTACAGCGTTTGTGGGCTCACTTGATGACGGCGGACATCCACCGGCATCCCGGAACGGACATCCATCACATGTTGCATCACTTCAGCGTCAGTTTGTGCTGCATCTTTAAATGATTGCAT  >  NC_000913_3_KO_pgi/1169233‑1169531

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap:     Deleted base: