Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*CP0007301,440,0850GT60.3% 36.1 / 60.3 59intergenic (‑45/‑891)cspA/xpaCcold shock protein CspA/5‑bromo‑4‑chloroindolyl phosphate hydrolysis protein XpaC
Reads supporting (aligned to +/- strand):  ref base G (5/18);  new base T (23/12);  total (28/31)
Fisher's exact test for biased strand distribution p-value = 1.34e-03
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.95e-01
Rejected as consensus: Frequency below/above cutoff threshold.

TGGTTAATTGCTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAATTGCAATACAATAATAAAAAATATTCATTTAATCAATTATTGGTAGTTT  >  CP000730/1439937‑1440231
                                                                                                                                                    |                                                                                                                                                  
tGGTTAATTGCTGAAAAAGGGACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGTTTATTCg                                                                                                                                                    <  2:92734/149‑1 (MQ=255)
    tAATTGCTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCata                                                                                                                                                <  2:533121/149‑1 (MQ=255)
    tAATTGCTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCata                                                                                                                                                <  2:188183/149‑1 (MQ=255)
            gAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATACTTATTCTCat                                                                                                                                                 >  1:666108/1‑140 (MQ=255)
                aaggTACTAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACAAAAAATa                                                                                                                                    <  2:444914/146‑1 (MQ=255)
                aaTGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTTTTTCATAATCTGAAACCTCCAAAACTAAAATTCATTCAATATGCTTATTCGCATATTACAAAAAATa                                                                                                                                    <  2:182747/149‑1 (MQ=255)
                aaTGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTa                                                                                                                                             <  1:791704/140‑1 (MQ=255)
                   gTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTTCac                                                                                                                                          >  1:900633/1‑139 (MQ=255)
                   gTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACaa                                                                                                                                          >  1:874589/1‑140 (MQ=255)
                   gTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACaa                                                                                                                                          >  1:900853/1‑140 (MQ=255)
                      cGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACaaaaa                                                                                                                                       <  1:324013/140‑1 (MQ=255)
                            cGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACAt                                                                                                                                 <  1:956075/140‑1 (MQ=255)
                               cATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCa                                                                                                                              >  1:54857/1‑140 (MQ=255)
                                aTTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCaa                                                                                                                             >  1:597659/1‑140 (MQ=255)
                                   ttCTCCTTCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAAtt                                                                                                                          <  1:108487/140‑1 (MQ=255)
                                     ctcCTTCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACAAAAAATACATGCAAATTTCACTCAAata                                                                                                               <  2:133398/149‑1 (MQ=255)
                                         ttCAGCTTCTATAAAGGCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATACGCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCt                                                                                                           <  2:206336/149‑1 (MQ=255)
                                         ttCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCt                                                                                                           >  2:77515/1‑149 (MQ=255)
                                         ttCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCt                                                                                                           <  2:521144/149‑1 (MQ=255)
                                         ttCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATAAAAAAAAAAAAAAAAATACATGCAAATTTCACTCAAATATTCt                                                                                                           <  2:506691/149‑1 (MQ=255)
                                                 cGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTc                                                                                                            >  1:831572/1‑140 (MQ=255)
                                                 cGATAAAGCCGAATCCTTTTTCAGCGTTAAAACATTTAACAGGACAATATGTCATAATCTGAAACCTCCAGGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAATAACACGCAAATTTCACTCAAATATTc                                                                                                            >  1:594757/1‑140 (MQ=255)
                                                       aGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCa                                                                                                      <  1:978333/140‑1 (MQ=255)
                                                        gCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCACGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTATTTGCaa                                                                                                     >  1:16483/1‑140 (MQ=255)
                                                        gCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGaata                                                                                            >  2:155989/1‑149 (MQ=255)
                                                                  ttttCAGCGTTAAACCTTTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGaataa                                                                                           >  1:503621/1‑140 (MQ=255)
                                                                  ttttCAGCGTTAAACCCTTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGaataa                                                                                           <  1:377306/140‑1 (MQ=255)
                                                                    ttCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTCCAAAAAATACATGCAAATTTCACTCAAATATTCTTTACAATATGGAATAatc                                                                                         >  1:493741/1‑140 (MQ=255)
                                                                     tCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAatca                                                                                        >  1:6112/1‑140 (MQ=255)
                                                                     tCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTaa                                                                               <  2:314661/149‑1 (MQ=255)
                                                                         cGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTg                                                                           <  2:253990/149‑1 (MQ=255)
                                                                          gTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATACTCATCTGc                                                                                   >  1:773518/1‑140 (MQ=255)
                                                                             aaaCCTTTAAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTAtatt                                                                       <  2:417858/149‑1 (MQ=255)
                                                                             aaaCCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGtatt                                                                       <  2:263095/149‑1 (MQ=255)
                                                                              aaCCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTTAAATATGGAATAATCATCTACTTTCCTTGaatta                                                                      >  2:56691/1‑149 (MQ=255)
                                                                               aCCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGAATAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTacc                                                                              >  1:194799/1‑138 (MQ=255)
                                                                                 cATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACtt                                                                            >  1:33179/1‑140 (MQ=255)
                                                                                   tttAACTGTATCTTGTTTCATAATCTGAAATCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACAAAAACTACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTg                                                                 <  2:379699/149‑1 (MQ=255)
                                                                                   tttAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAATTTGt                                                                          <  1:687676/140‑1 (MQ=255)
                                                                                       aCTGTACCTTGTTTCATAATCTGAAACCTCCAATACTAAAATTCATTCAATATGCTTATTCGCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGt                                                             <  2:179455/149‑1 (MQ=255)
                                                                                       aCTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGt                                                             >  2:302053/1‑149 (MQ=255)
                                                                                       aCTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGt                                                             <  2:490681/149‑1 (MQ=255)
                                                                                        cTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGtt                                                            <  2:441625/149‑1 (MQ=255)
                                                                                         tGTACCTTGTTTCATTATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATtata                                                                    <  1:813674/140‑1 (MQ=255)
                                                                                               ttGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAg                                                              >  1:883214/1‑140 (MQ=255)
                                                                                                   ttCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTTCGTTGTATTTTAGTGCTGttat                                                          >  1:98015/1‑140 (MQ=255)
                                                                                                          tCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACAAAAAATACATGCAAATTTAATTAAAATATTCTTTGCAATATGTAATAATCATCTGCTTAAATTGTATTATAGTCCAGTTATTACAAAATTAcaaaca                                          >  2:181935/1‑146 (MQ=255)
                                                                                                           cTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAAt                                                  >  1:803457/1‑140 (MQ=255)
                                                                                                              aaaCCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAATTGc                                               >  1:543161/1‑140 (MQ=255)
                                                                                                              aaaCCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAATTGc                                               >  1:693500/1‑140 (MQ=255)
                                                                                                                      aaGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAATTGcaatacaat                                       <  1:491109/140‑1 (MQ=255)
                                                                                                                              aaTTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAATTGCAATACAATAATaaaaa                               >  1:136248/1‑140 (MQ=255)
                                                                                                                                 tcattcaATATGCTTATTCTCATATTACAAAAAATATAGGTAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAACTTGCAATACAATAATAAAAAata                            >  1:997501/1‑140 (MQ=255)
                                                                                                                                   attcaATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAATTGCAATACAATAATAAAAAATAtt                          <  1:714975/140‑1 (MQ=255)
                                                                                                                                    ttcaATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAATTGAAATACAATAATAAAAAATATTc                         >  1:891270/1‑140 (MQ=255)
                                                                                                                                         tatGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAATTGCAATACAATAATAAAAAATATTCATTTa                    <  1:511450/140‑1 (MQ=255)
                                                                                                                                         aatGCTTATTCGCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAATTGCAATACAATAATAAAAAATATTCATTTAATCAattat           <  2:193990/148‑1 (MQ=255)
                                                                                                                                             cTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCACCATCGCCCAAGCAGCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAATTGCAATACAATAATAAAAAATATTCATTTAATCa                <  1:734987/140‑1 (MQ=255)
                                                                                                                                              ttATTCGCATATTACAAAAAATACATGCCAATTTCCCTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAATTGCAATACAATAATAAAAAATATTCATTTAATCaa               <  1:418453/140‑1 (MQ=255)
                                                                                                                                                  tCGCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAATTGCAATACAATAATAAAAAATATTCATTTCATCAATTATTGGTAGttt  <  2:507187/149‑1 (MQ=255)
                                                                                                                                                    |                                                                                                                                                  
TGGTTAATTGCTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAATTGCAATACAATAATAAAAAATATTCATTTAATCAATTATTGGTAGTTT  >  CP000730/1439937‑1440231

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑