Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_000913357,8900CA50.0% 33.8 / 26.1 46L267F (TTG→TTTcynRtranscriptional activator of cyn operon; autorepressor
Reads supporting (aligned to +/- strand):  ref base C (15/8);  new base A (0/23);  total (15/31)
Fisher's exact test for biased strand distribution p-value = 1.92e-06
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.57e-01

ATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTC  >  NC_000913/357743‑358028
                                                                                                                                                          |                                                                                                                                             
aTAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGcaacaa                                                                                                                                             <  2:1144613/150‑1 (MQ=255)
aTAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACaaa                                                                                                                                            <  2:1054938/151‑1 (MQ=255)
aTAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACaaa                                                                                                                                            <  1:646499/151‑1 (MQ=255)
 tAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACaaa                                                                                                                                            >  2:192340/1‑150 (MQ=255)
     cGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAAccgc                                                                                                                                       >  1:1171240/1‑151 (MQ=255)
     cGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAAccg                                                                                                                                        <  2:1078427/150‑1 (MQ=255)
        aGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGt                                                                                                                                    >  1:1037005/1‑151 (MQ=255)
         gcgcATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAAccgccg                                                                                                                                     <  1:768133/149‑1 (MQ=255)
               cAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTcc                                                                                                                             >  2:408317/1‑151 (MQ=255)
                 ggCATTTCCGGCCCCAGCCCTTTGTCGGCGGCTCCCGTTTTTCTTTCCCCCAAACACCCGCGCTTTTATCCACCCCCATGTCCAAAAATCCCTTCGGGGCGGCTGTCTCCCAGCTTTTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCag                                                                                                                           <  1:1198153/151‑1 (MQ=255)
                   cattcccAGCCGCAGCGTTGTGTCAGCGGCTACCGTGTTTCTTCCCCGCCAACAACCGCGCATTTATCCACCGCCATGTGCAAAAATGCCGTCGGGGCGGCTGTCTGCCATTTTTTTTTCCCCCGCAACAAAACCGCCGTtctctc                                                                                                                              <  2:1276174/141‑1 (MQ=255)
                     aTTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCGGTCTGCCAGCTATTTTTCCACCGCAACAAAACCGCCGTTCTCTCCagta                                                                                                                         >  2:77627/1‑149 (MQ=255)
                        ccccccGCAGCCTTGTGTCAGCGGCTCCCGTTTTTCATTCCCCCCACCACCCCCCCTTTTCCCCACCCCCATGTAAAAAAATCCCTCCGCGGCGGCTGCCTGCAAGTTTTTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCagta                                                                                                                         <  2:31752/142‑1 (MQ=255)
                          aGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCgg                                                                                                                  >  1:768704/1‑151 (MQ=255)
                            ccGAAGCCCTGTGACAGCGGCTCCGGTATTTATTTCCCCCCAACACCCGCCCTTTTACCCACCCCCTTGTGAAAAAATGCTTTCGGGGGGGCTGTCTGCCAGTTTTTTTCCCCCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCgg                                                                                                                  <  1:52819/149‑1 (MQ=255)
                               ctgccttgtgTCGGCGGCTTCGGTGATTCATTTCCGCCAACACCCGCTCTTTTAACCACCGCTATTTAAAAAACTGCCTCGGCGGCGCCTCTCTGCGATCTATTTTCCCCCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCa                                                                                                              <  1:311717/144‑1 (MQ=255)
                                   cttgtgCCAGCGGCCCCCCTGATTCTTTCCCCCCAACACCCGCGCATTTACCCACCGCCATGTGAAAAAATGCTTCGGGGGGGCTGTTCGGCCAGTTTTTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCaa                                                                                                             <  2:1081003/145‑1 (MQ=255)
                                   ccTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCggg                                                                                                                 >  1:991877/1‑143 (MQ=255)
                                      gtgtCGGCGCCTCCCGTGATTCTTTCCCCCAAACACCCGCGTTTTTACCCACCCCCTTGTAAAAAAAGCCCTCCGCGGGGGCTGTCGGCCAGTTTTTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAgaga                                                                                                        <  2:113503/148‑1 (MQ=255)
                                      gtgtCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCgggggacgtaga                                                                                                        >  2:327771/1‑141 (MQ=255)
                                        gccAGCGGTTCCCGTGATTCTTTCCCCCCAAAACCCGCCCTTTTACCCACCCCCTTGTGAAAAAAGGCTTCCGGGGGGGCTTTCTGCCAGTTTTTTTCCCCCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAgaga                                                                                                        <  1:1242738/144‑1 (MQ=255)
                                               ggctcccgtttttaTTTCCCCCAAACACCCGCGAATTTTCCAACCGCCAGGTAAAAAAATCCTTCCGGGGCGCTTGTCTCCCATTTTTTTTCCCCCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAagag                                                                                                          <  1:377618/126‑1 (MQ=255)
                                                ctcccgtttttCTTTCCCCCCACCACCCGCCCTTTTACCCACCCCCTTTTCAAAAAATCCTTCCGCGGCGGCTTTCTCCAAGTTTTTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGcggg                                                                                               <  1:408735/138‑4 (MQ=255)
                                                cTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGCAGAGaaaaaaa                                                                                                  >  1:300445/1‑140 (MQ=255)
                                                 tACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGTGGAaggaaaaaaacattta                                                                                              >  1:632960/1‑134 (MQ=25)
                                                   ccttatttCATTCCCGCCACCACCCGCGTTTTTATCCACCCCAATGTGAAAAAAGGCCTGCGGGGCGGCTTTCGGCCAGCTTTTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGccc                                                                                        <  1:1034467/144‑1 (MQ=255)
                                                      tttttCTTTCCCCCCACCACCCGCTCTTTTACCAAACCCTTTGTAAAAAAATGCCTCCGCGGGGGTTGTCTCCAGGTTTTTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTc                                                                                     <  2:803179/147‑1 (MQ=255)
                                                      tGATTCTTTCCCCCAAACACCCCCGATTTTACCCACCGCATTGTCAAAAATTCCCTCGGCGGGGGCTGTCGGCAAGTTTTTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGt                                                                                      <  2:1226909/149‑1 (MQ=255)
                                                                  ccccaaacaccCGCGCTTTTACCCACCCCCTTGTAAAAAAATGCCTTCGCGGCGGTTGTCTGCCAGTTTTTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTtgtgtg                                                                           <  1:102361/145‑1 (MQ=255)
                                                                      caaacaccccctaTTTAACCAACCGCCATTTAAAAAATTCCCTCCGGGGCGGCTTTCTGCCAGTTTTTTTCCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCaa                                                                       <  1:562494/139‑1 (MQ=255)
                                                                       accacccGCGCTTTTACCAACCCCATTGTAAAAAAATCCTTCGGGGGCGGTTGTCTGCCGGTTTTTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCaa                                                                       <  2:1279175/144‑1 (MQ=255)
                                                                              gcgcATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGGAAAGAAAAAACATTAAAACCCTCCAGTTGTggggggaaag                                                                    >  1:133189/1‑139 (MQ=25)
                                                                               cccttttACCCACCCCCATGGAAAAAAATCCTTCCGGGGCGGCTGTCTCCCAGTTTTTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTgg                                                             <  1:992909/147‑1 (MQ=255)
                                                                                         cccaccgcctttagaaaaaaTCCCTTCGCGGCGGCTGTCCGCCACTTTTTTTCCCGCCGCAAAAAAGCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAAt                                                     <  1:1711/135‑1 (MQ=255)
                                                                                                        aaaaaTGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGGAGAGAAAAAACTTTTAACCCCTCACGTTTTGTTGGTCTCGCTCCTCGTGAACAAGTGGGAAGGGGAgag                                      >  2:167779/1‑148 (MQ=255)
                                                                                                         aaaaTGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCGCGAGAAAAAAATTTTAAACCCCCCAGTTGTGTGGGGAACGCCGCTGGGGAAAAAGTGGGAAGGGGAgaggg                                    >  1:240995/1‑147 (MQ=255)
                                                                                                          aaaTGCCTCGGGGGGGGTTTTCGGCCAGTTTTTTTCCCCCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTgcgg                                   <  1:745586/151‑1 (MQ=255)
                                                                                                                     gggggggcTGTCGGCCGTTTTTTTTCCCGCCAAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCa                            <  2:1186843/143‑1 (MQ=255)
                                                                                                                     ggggcggcTGTCTGCCGTCTTTTTTCCCGCCAAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAg                           <  2:376923/147‑1 (MQ=255)
                                                                                                                       ggcggcTTTCTGCCACTTTTTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATc                             <  1:1227983/145‑1 (MQ=255)
                                                                                                                          ggcTGTCGCCCAGTTATTTTCCCGCCGAAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAg                     <  1:364959/150‑1 (MQ=255)
                                                                                                                             tGTCTGCCATTTTTTTTCCCGCCCCAAAAAATCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGa                    <  2:509482/148‑1 (MQ=255)
                                                                                                                                 cTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGCAGAGAAAAAACTTTTAACCCCGCCTGTTGTGTGGGAAACGCCGCTGGGAAAAAAGTGGGAAGGGGAGGGGGGGGGATCAACTCCCCAAcccc               >  1:812105/1‑148 (MQ=255)
                                                                                                                                      attttttttcCCCCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTaa          <  1:1080179/145‑1 (MQ=255)
                                                                                                                                              ttCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGCAGAGAAAAAACATTTAACCCCGCACGTTTTGTGGGAAACGCCGCTGGTAACAAAGTGGGAAGGGGAGGGGGGGGGAAAAACCCCCGAACCGCGCCAAATGAggt   >  1:413138/1‑147 (MQ=255)
                                                                                                                                                 ccgccgCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTc  <  1:57540/148‑1 (MQ=255)
                                                                                                                                                  ccccgcAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTc  <  1:60673/145‑1 (MQ=255)
                                                                                                                                                          |                                                                                                                                             
ATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTC  >  NC_000913/357743‑358028

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 25 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap:     Deleted base: