Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009131,622,8160GA42.6% 46.7 / 49.4 54intergenic (+75/+144)yneM/dgcZinner membrane‑associated protein/diguanylate cyclase, zinc‑sensing
Reads supporting (aligned to +/- strand):  ref base G (29/2);  new base A (0/23);  total (29/25)
Fisher's exact test for biased strand distribution p-value = 2.76e-13
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TATGGCCGTACTGGGAATAATTTTATTTTCTGGTTTTCTGGCCGCGTATTTCAGCCACAAATGGGATGACTAATGAACGGAGATAATCCCTCACCTAACCGGCCCCTTGTTACAGTTGTGTACAAGGGGCCTGATTTTTATGACGGCGAAAAAAAACCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGATTTGTGTTTTGCTTTTACGCTAACAGGCATTTTCCTGCACTGATAACGAATCGTTGACACAGTAGCATCAGTTTTCTCAATGAATGTTAAACGGAGCTTAAA  >  NC_000913/1622669‑1622964
                                                                                                                                                          |                                                                                                                                                    
tATGGCCGTACTGGGAATAATTTTATTTTCTGGTTTTCTGGCCGCGTATTTCAGCCACAAATGGGATGACTAATGAACGGAGATAATCCCTCACCTAACCGGCCCCTTGTTACAGTTGTGTACAAGGGGCCTGATTTTTATGACGGCGaa                                                                                                                                                    <  2:275474/150‑1 (MQ=255)
 aTGGCCGTACTGGGAATAATTTTATTTTCTGGTTTTCTGGCCGCGTATTTCAGCCACAAATGGGATGACTAATGAACGGAGATAATCCCTCACCTAACCGGCCCCTTGTTACAGTTGTGTACAAGGGGCCTGATTTTTATGACGGCGaaa                                                                                                                                                   >  2:22230/1‑150 (MQ=255)
   ggCCGTACTGGGAATAATTTTATTTTCTGGTTTTCTGGCCGCGTATTTCAGCCACAAATGGGATGACTAATGAACGGAGATAATCCCTCACCTAACCGGCCCCTTGTTACAGTTGTGTACAAGGGGCCTGATTTTTATGACGGCGaaaaa                                                                                                                                                 <  1:866732/150‑1 (MQ=255)
         aCTGGGAATAATTTTATTTTCTGGTTTTCTGGCCGCGTATTTCAGCCACAAATGGGATGACTAATGAACGGAGATAATCCCTCACCTAACCGGCCCCTTGTTACAGTTGTGTACAAGGGGCCTGATTTTTATGACGGCGAAAAAAAACCGc                                                                                                                                          >  1:805640/1‑151 (MQ=255)
          cTGGGAATAATTTTATTTTCTGGTTTTCTGGCCGCGTATTTCAGCCACAAATGGGATGACTAATGAACGGAGATAATCCCTCACCTAACCGGCCCCTTGTTACAGTTGTGTACAAGGGGCCTGATTTTTATGACGGCGAAAAAAAACCGcc                                                                                                                                         >  2:835710/1‑151 (MQ=255)
                   attttattttCTGGTTTTCTGGCCGCGTATTTCAGCCACAAATGGGATGACTAATGAACGGAGATAATCCCTCACCTAACCGGCCCCTTGTTACAGTTGTGTACAAGGGGCCTGATTTTTATGACGGCGAAAAAAAACCGCCAGTAAACcg                                                                                                                                >  1:146585/1‑151 (MQ=255)
                     tttattttCTGGTTTTCTGGCCGCGTATTTCAGCCACAAATGGGATGACTAATGAACGGAGATAATCCCTCACCTAACCGGCCCCTTGTTACAGTTGTGTACAAGGGGCCTGATTTTTATGACGGCGAAAAAAAACCGCCAGTAAACcggc                                                                                                                              >  2:228348/1‑151 (MQ=255)
                     tttattttCTGGTTTTCTGGCCGCGTATTTCAGCCACAAATGGGATGACTAATGAACGGAGATAATCCCTCACCTAACCGGCCCCTTGTTACAGTTGTGTACAAGGGGCCTGATTTTTATGACGGCGAAAAAAAACCGCCAGTAAACcggc                                                                                                                              >  2:1034479/1‑151 (MQ=255)
                      ttattttCTGGTTTTCTGGCCGCGTATTTCAGCCACAAATGGGATGACTAATGAACGGAGATAATCCCTCACCTAACCGGCCCCTTGTTACAGTTGTGTACAAGGGGCCTGATTTTTATGACGGCGAAAAAAAACCGCCAGTAAACcggcg                                                                                                                             >  1:787990/1‑151 (MQ=255)
                       ttttttttggttttcggcCCGCTTTTTCCACCAAAAAAGGGGATGATAAAAGAACGGAAATAACCCCTCCCCTACCGGCCCCTTTGTTACTTTTGTGTACAGGGGCCTTGTTTTTTAGGACGGAAAAAAAAAACCGCCAGTAAACcggc                                                                                                                              <  1:798560/147‑1 (MQ=255)
                        attttCTGGTTTTCTGGCCGCGTATTTCAGCCACAAATGGGATGACTAATGAACGGAGATAATCCCTCACCTAACCGGCCCCTTGTTACAGTTGTGTACAAGGGGCCTGATTTTTATGACGGCGAAAAAAAACCGCCAGTAAACcggcgg                                                                                                                            >  1:208419/1‑150 (MQ=255)
                         ttttctggttttctggCCGCGTATTTCAGCCACAAATGGGATGACTAATGAACGGAGATAATCCCTCACCTAACCGGCCCCTTGTTACAGTTGTGTACAAGGGGCCTGATTTTTATGACGGCGAAAAAAAACCGCCAGTAAACCGGCGGTg                                                                                                                          >  1:744967/1‑151 (MQ=255)
                              tgtttttctggCCGCTTTTTTCACCCAAAAATGGGATGACTAATGAAGGGAGATAACCCCTCCCCTACCCGCCCCTTTTTTCAAGTTGTGTAAAGGGGGCTTGTTTTTTATGACGGAAAAAAAAAACCGCCAGTAAACCGGCGGTGaa                                                                                                                        <  2:797527/145‑1 (MQ=255)
                                  tttcttgCCGGTTTTTTCAGCCCAAAAGGGGGATGATAAAGGAAGGGAAATAACCCCCCCCCAACCCGCCCCCTTTTAAATGTTGTTAAAAGGGGGCGGTTTTTTAAGAGCGGAAAAAAAAACCCGCCAGTAAACCGGCGGTGaa                                                                                                                        <  1:551104/145‑1 (MQ=255)
                                     ctggCCGCGTATTTCAGCCACAAATGGGATGACTAATGAACGGAGATAATCCCTCACCTAACCGGCCCCTTGTTACAGTTGTGTACAAGGGGCCTGATTTTTATGACGGCGAAAAAAAACCGCCAGTAAACCGGCGGTGAATGCTTGCATg                                                                                                              >  2:1034220/1‑151 (MQ=255)
                                      tggCCGCGTATTTCAGCCACAAATGGGATGACTAATGAACGGTGATAATCCCTCACCTAACCGGCCCCTTGTTACAGTTGTGTACAAGGGGCCTGATTTTTATGACGGCGAAAAAAAACCGCCAGTAAACCGGCGGTGAATGCTTGCATgg                                                                                                             >  1:101193/1‑151 (MQ=255)
                                      tggCCGCGTATTTCAGCCACAAATGGGATGACTAATGAACGGAGACAATCCCTCACCTAACCGGCCCCTTGTTACAGTTGTGTACAAGGGGCCTGATTTTTATGACGGCGAAAAAAAACCGCCAGTAAACCGGCGGTGAATGCTTGCATgg                                                                                                             >  2:544114/1‑151 (MQ=255)
                                         ccGCTTATTACACCCACAAGTGGGAGAAATAATGAGCGGAAAAACCCCCCCACCAACCCGCCCCCTTGTAACAGTGGGAAAAAGGGGCCTTTTTTTTTATGACGGAAAAAAAAAACCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATa                                                                                                          <  1:800189/151‑1 (MQ=255)
                                           gtgTATTCCACCCACAAAGGGGATGACTAATAAACGGAGATAACCCCTCACCTACCCGCCCCTTTTTTACAGTTGTGTACAGGGGGCCTAATTTTTATGACGGAAAAAAAAAACCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAg                                                                                                         <  2:48904/148‑1 (MQ=255)
                                           gcgTATTTCAGCCACAAATGGGATGACTAATGAACGGAGATAATCCCTCACCTAACCGGCCCCTTGTTACAGTTGTGTACAAGGGGCCTGATTTTTATGACGGCGAAAAAAAACCGCCAGTAAACCGGCGGTGAATGCTTGCATGGa                                                                                                            >  1:194960/1‑147 (MQ=255)
                                            cgTATTTCAGCCACAAATGGGATGACTAATGAACGGAGATAATCCCTCACCTAACCGGCCCCTTGTTACAGTTGTGTACAAGGGGCCTGATTTTTATGACGGCGAAAAAAAACCGCCAGTAAACCGGCGGTGAATGCTTGCATgg                                                                                                             >  1:731440/1‑145 (MQ=255)
                                                tttCAGCCACAAATGGGATGACTAATGAACGGAGATAATCCCTCACCTAACCGGCCCCTTGTTACAGTTGTGTACAAGGGGCCTGATTTTTATGACGGCGAAAAAAAACCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGATTtgt                                                                                                   >  2:326498/1‑151 (MQ=255)
                                                         aaaaaGGGGATGATTAAAAAAGGGAGATACCCCCCCCCCTACCCGCCCCTTTGTTACGTTTGTGTACAGGGGGCTTGTTTTTTAGGCGGGAAAAAAAAAACCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGATTTgtgt                                                                                                 <  2:417979/143‑1 (MQ=255)
                                                           aaaGGGGATGAAAAAAGAAGGGAAATAACCCCCCCCCAACCCGGCCCCTTGTTAAATTTGTGTAAAAGGGGCCTGTTTTTTATGGGGGAAAAAAAAAACCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGATTTGTGTTTTGc                                                                                            <  2:1012314/148‑1 (MQ=255)
                                                               gggATAAATAATGAAGTGAAATACTCCCCCACCAACCCGCCCCTTTGTTACAGTGGTGGAAAGGGGCCCTGTTTTTTATGCCGGAAAAAAAAAACCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGATTTGTGTTTTGCTTTTa                                                                                       <  2:879193/149‑1 (MQ=255)
                                                                     aaaaaTGAAGGGAAATACCCCCTCCCCAACCGGCCCCTTTTTAACTGTTGTTTAAAGGGGCCTTATTTTTAAGGCCGGAAAAAAAAAACCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGATTTGTGTTTTGCTTTTACGCTAACa                                                                               <  2:141265/148‑1 (MQ=255)
                                                                      cTAATGAACGGAGATAATCCCTCACCTAACCGGCCCCTTGTTACAGTTGTGTACAAGGGGCCTGATTTTTATGACGGCGAAAAAAAACCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGATTTGTGTTTTGCTTTTACGCTAAc                                                                                >  2:350082/1‑149 (MQ=255)
                                                                        aagaaaCGGAAATAACCCCCCCCCAACCCGCCCCTTTGTTACATTTTTTCAAAGGGGCCTTTTTTTTTATGCGGGCAAAAAAAAACCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGATTTGTGTTTTGCTTTTACGCTAAc                                                                                <  2:797181/143‑1 (MQ=255)
                                                                            aaCGGAGATAATCCCTCACCTAACCGGCCCCTTGTTACAGTTGTGTACAAGGGGCCTGATTTTTATGACGGCGAAAAAAAACCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGATTTGTGTTTTGCTTTTACGCTAACAGGCAttt                                                                        >  2:756484/1‑151 (MQ=255)
                                                                               ggAGATAATCCCTCACCTAACCGGCCCCTTGTTACAGTTGTGTACAAGGGGCCTGATTTTTATGACGGCGAAAAAAAACCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGATTTGTGTTTTGCTTTTACGCTAACAGGCATTTTcc                                                                     >  2:215462/1‑151 (MQ=255)
                                                                                     aacccccccccTACCCGCCCCGTGGTAACAGTTTTGTACAGGGGGCTTTTTTTTTAGGAAGAAAAAAAAAAACCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGATTTGTGTTTTGCTTTTACGCTAACAGGCATTTTCCTGCACt                                                               <  1:358427/142‑1 (MQ=255)
                                                                                      accccctccccaaCCCGCCCCTTTTTTAAGTTTGTGAACAGGGGGCTTTTTTTTTATGACGGAAAAAAAAAACCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGATTTGTGTTTTGCTTTTACGCTAACAGGCATTTTCCt                                                                    <  2:147982/135‑1 (MQ=255)
                                                                                        ccccccccaaaCCGGCCCTTTTTTACAGTTTGGAAAAGGGGGCCTTTTTTTTAGGGGGGAAAAAAAAAACCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGATTTGTGTTTTGCTTTTACGCTAACAGGCATTTTCCTGCACTGa                                                             <  1:803861/141‑1 (MQ=255)
                                                                                        ccccCACCTACCCGCCCCTTTTTTACAGTTGTGTAAAGGGGGCTTGTTTTTTATGCCGGAAAAAAAAAACCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGATTTGTGTTTTGCTTTTACGCTAACAGGCATTTTCCTGCACTg                                                              <  1:429497/149‑1 (MQ=255)
                                                                                        cccTCCCCTACCCGCCCCTTTTTTACAGTTTTGTACAGGGGGCTTGTTTTTTAGGACGGCAAAAAAAAACCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGATTTGTGTTTTGCTTTTACGCTAACAGGCATTTTCCTGCACTGAt                                                            <  2:755007/151‑1 (MQ=255)
                                                                                        cccTCACCTAACCGGCCCCTTGTTACAGTTGTGTACAAGGGGCCTGATTTTTATGACGGCGAAAAAAAACCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGATTTGTGTTTTGCTTTTACGCTAACAGGCATTTTCCTGCACTGAt                                                            >  1:524880/1‑151 (MQ=255)
                                                                                              ccTACCCGCCCCTTTTTTACATTTGTTTAAAGGGGGCTTGTTTTTTATGCCGGAAAAAAAAAACCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGATTTGTGTTTTGCTTTTACGCTAACAGGCATTTTCCTGCACTGATAACGaa                                                      <  1:835524/151‑1 (MQ=255)
                                                                                                tAACCGGCCCCTTGTTACAGTTGTGTACAAGGGGCCTGATTTTTATGACGGCGAAAAAAAACCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGATTTGTGTTTTGCTTTTACGCTAACAGGCATTTTCCTGCCCTGATAACGAAt                                                     >  1:747958/1‑150 (MQ=255)
                                                                                                     ggCCCCTTGTTACAGTTGTGTACAAGGGGCCTGATTTTTATGACGGCGAAAAAAAACCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGATTTGTGTTTTGCTTTTACGCTAACAGGCATTTTCCTGCACTGATAACGAATCGTTg                                                >  2:707520/1‑150 (MQ=255)
                                                                                                       ccctTTTTTACAGTTGTGGAAAAGGGGCTTTTTTTTTAGGACGGCAAAAAAAAACCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGATTTGTGTTTTGCTTTTACGCTAACAGGCATTTTCCTGCACTGATAACGAATCGTTGaca                                             <  1:846516/151‑1 (MQ=255)
                                                                                                                tACAGTTGTGTACAAGGGGCCTGATTTTTATGACGGCGAAAAAAAACCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGATTTGTGTTTTGCTTTTACGCTAACAGGCATTTTCCTGCACTGATAACGAATCGTTGACACAGTAGc                                      >  1:372447/1‑150 (MQ=255)
                                                                                                                  aCAGTTGTGTACAAGGGGCCTGATTTTTATGACGGCGAAAAAAAACCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGATTTGTGTTTTGCTTTTACGCTAACAGGCATTTTCCTGCACTGATAACGAATCGTTGACACAGTAGCAt                                    >  1:117000/1‑151 (MQ=255)
                                                                                                                  aCAGTTGTGTAAAGGGGGCTTGTTTTTTAGGAGGGAAAAAAAAAACCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGATTTGTGTTTTGCTTTTACGCTAACAGGCATTTTCCTGCACTGATAACGAATCGTTGACACAGTAGCa                                     <  2:60236/150‑1 (MQ=255)
                                                                                                                   acgtttGTGAAAAGGGGGCTTTTTTTTTATGGGGGAAAAAAAAAACCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGATTTGTGTTTTGCTTTTACGCTAACAGGCATTTTCCTGCACTGATAACGAATCGTTGACACAGTAGCa                                     <  2:672556/146‑1 (MQ=255)
                                                                                                                       gtgtgaaaagggggCCTTTTTTTTAGGACGACAAAAAAAATCCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGATTTGTGTTTTGCTTTTACGCTAACAGGCATTTTCCTGCACTGATAACGAATCGTTGACACAGTAGCa                                     <  2:880922/136‑1 (MQ=255)
                                                                                                                        tgtgTACAAGGGGCCTGATTTTTATGACGGCGAAAAAAAACCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGATTTGTGGTTTGCTTTTACGCTAACAGGCATTTTCCTGCACTGATAACGAATCGTTGACACAGTAGCATCAGtt                               >  1:414956/1‑151 (MQ=255)
                                                                                                                            taaaaGGGGCTGGTTTTTTATGCGGAAAAAAAAAAACCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGATTTGTGTTTTGCTTTTACGCTAACAGGCATTTTCCTGCACTGATAACGAATCATTGACACAGTAGCATCAGtttt                             <  1:185311/146‑1 (MQ=255)
                                                                                                                             aCAGGGGGCTTTTTTTTTTTGCCGGAAAAAAAAAACCGCCAGTAAACCGGCGGTGAATGCTTGTATGGATAGATTTGTGTTTTGCTTTTACGCTAACAGGCATTTTCCTGCACTGATAACGAATCGTTGACACAGTAGCATCAGTTTtctc                          <  1:175473/151‑1 (MQ=255)
                                                                                                                               aaGGGGCCTGATTTTTATGACGGCGAAAAAAAACCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGATTTGTGTTTTGCTTTTACGCTAACAGGCATTTTCCTGCACTGATAACGAATCGTTGACACAGTAGCATCAGTTTTCTCa                         >  2:818916/1‑150 (MQ=255)
                                                                                                                                   gggttttttttttAGGACGAAAAAAAAAAACCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGATTTGTGTTTTGCTTTTACGCTAACAGGCATTTTCCTGCACTGATAACGAATCGTTGACACAGTAGCATCAGTTTTCTCaatga                     <  1:1014550/143‑1 (MQ=255)
                                                                                                                                         gATTTTTATGACGGCGAAAAAAAACCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGATTTGTGTTTTGCTTTTACGCTAACAGGCATTTTCCTGCACTGATAACGAATCGTTGACACAGTAGCATCAGTTTTCTCAATGAATGtt                >  2:398960/1‑150 (MQ=255)
                                                                                                                                           tttttATGACGGCGAAAAAAAACCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGATTTGTGTTTTGCTTTTACGCTAACAGGCATTTTCCTGCACTGATAACGAATCGTTGACACAGTAGCATCAGTTTTCTCAATGAATGTTaa              >  2:484275/1‑150 (MQ=255)
                                                                                                                                            ttttATGACGGCGAAAAAAAACCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGATTTGTGTTTTGCTTTTACGCTAACAGGCATTTTCCTGCACTGATAACGAATCGTTGACACAGTAGCATCAGTTTTCTCAATGAATGTTaaa             >  1:879759/1‑150 (MQ=255)
                                                                                                                                                         cGAAAAAAAACCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGATTTGTGTTTTGCTTTTACGCTAACAGGCATTTTCCTGCACTGATAACGAATCGTTGACACAGTAGCATCAGTTTTCTCAATGAATGTTAAACGGAGCTTaaa  >  2:41838/1‑150 (MQ=255)
                                                                                                                                                          |                                                                                                                                                    
TATGGCCGTACTGGGAATAATTTTATTTTCTGGTTTTCTGGCCGCGTATTTCAGCCACAAATGGGATGACTAATGAACGGAGATAATCCCTCACCTAACCGGCCCCTTGTTACAGTTGTGTACAAGGGGCCTGATTTTTATGACGGCGAAAAAAAACCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGATTTGTGTTTTGCTTTTACGCTAACAGGCATTTTCCTGCACTGATAACGAATCGTTGACACAGTAGCATCAGTTTTCTCAATGAATGTTAAACGGAGCTTAAA  >  NC_000913/1622669‑1622964

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap:     Deleted base: