Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_000913357,8900CA52.8% 15.3 / 57.4 36L267F (TTG→TTTcynRtranscriptional activator of cyn operon; autorepressor
Reads supporting (aligned to +/- strand):  ref base C (13/4);  new base A (0/19);  total (13/23)
Fisher's exact test for biased strand distribution p-value = 1.03e-06
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.54e-05

ATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCGCCTCA  >  NC_000913/357743‑358034
                                                                                                                                                       |                                                                                                                                                  
aTAAGCGTAGCGCATCAGCCAATTCCAGCCGCAGACCTGTGTCAGCGGGTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGTTATTTTTCCGCCGcaacaa                                                                                                                                                  <  1:1198493/150‑1 (MQ=255)
      gTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAAccgcc                                                                                                                                          <  2:672552/151‑1 (MQ=255)
             aTCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTtctct                                                                                                                                   >  1:823140/1‑151 (MQ=255)
               cAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTcc                                                                                                                                 >  2:201264/1‑151 (MQ=255)
                 ggCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTcc                                                                                                                                 >  1:532118/1‑149 (MQ=255)
                      ttCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTg                                                                                                                          >  2:822166/1‑151 (MQ=255)
                            ccGCAGCCCTGTGTCGGCGCCTCCCGTGTTTCATTCCCCCAAACACCCGCGCTTTTACCCACCGCCATGTGAAAAAATGCCTCCGCGGCGGCTGTCTGCCAGTTATTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCgggg                                                                                                                    <  2:268130/151‑1 (MQ=255)
                              gCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCgggg                                                                                                                    >  2:985575/1‑149 (MQ=255)
                               cAGACCTGTTTCAGCGGCTCCCGTTTTTCTTTCCCCCCAACACCCCCGCTTTTATCCACCCCCTTGTGAAAAAATGCCTTCGGGGCGGCTGTCTGCCAGTTTTTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGc                                                                                                                   <  2:571533/149‑1 (MQ=255)
                                  aCCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCggggggaggg                                                                                                              >  1:153783/1‑145 (MQ=255)
                                     tgtgTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGCAGAGaa                                                                                                           >  2:870932/1‑150 (MQ=255)
                                         tcggCGGCTCCCGTGATTCTTTCCCGCCACCACCCGCGCTTTTACCCAACGCCTTGTGAAAAAATGCCTCGGGGGCGGCTGTCTGCCATTTTTTTTCCCGCCCAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATa                                                                                                        <  2:708748/146‑1 (MQ=255)
                                           aGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGAAGAGaaaaa                                                                                                        >  2:737081/1‑145 (MQ=255)
                                              gccccccGTTATTCTTTCCCCCCAACACCCGCCCATTTACCCACCGCCATGGCAAAAAAGCCCTCCGCGGCGGCTGTCGCCCAGTTTTTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATa                                                                                                        <  1:1199398/139‑1 (MQ=255)
                                                 tACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGGAGGGaaaaaaaatttaaac                                                                                              >  2:99090/1‑139 (MQ=25)
                                                   cgttatttaaTTCCCGCCAACACCCGCGCTTTTCCCCACCTCTTTGTAAAAAATCGCTTTGGGGCCGGTTTTCCCCCGGCTTTTTTCCCCCGAAAAAAAATCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTa                                                                                                  <  1:1145831/136‑1 (MQ=255)
                                                   ccGTAATTCATTCCCCCCAACACCCGCGCATTTACCCAACGCCATGTGAAAAAATCCCTCCGGGGCGGCTGTCTGCCAGTTTTTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCg                                                                                            <  2:292263/151‑1 (MQ=255)
                                                     gTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCGCGACGAAAAAGCTTTAAAccacc                                                                                           >  2:951018/1‑148 (MQ=25)
                                                         ttCTTTCCCCCCAACACCCCCGCATTTACCCACCGCCTTGTAAAAAAATGCCTTCGCGGCGGTTGTCTGCCAGTTTTTTTCCCGCCAAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGcc                                                                                              <  1:1117506/143‑1 (MQ=255)
                                                           cATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCGAGAGAAAAAAATTTAAAcccccccccgt                                                                                     >  1:754086/1‑142 (MQ=25)
                                                             ttcccccaaacaccCGCGATTTTCGCCACCCCCATGTCAAAAATGGCCTCGGCGGCGGCTTTCGCCGAGTTTTTTTCCCGCCGAAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCAtgtt                                                                                     <  2:728455/140‑1 (MQ=255)
                                                               cccccaaacaccCGCGCTTTTATCCAACCCCTTGGCAAAAAAGCCCTTCGCGGCGGCTGTCTCCCAGTTTTTTTCCCCCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTtgtgtg                                                                                <  2:410661/145‑1 (MQ=255)
                                                               cccGCCAACACCCGCCCTTTCCCCCACCCCCATGTAAAAAACCCCCTTCGGGGCGGCTGTCCGCAAGTTTTTTTTCCGCAGAAAAAAACCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGccc                                                                                             <  1:56813/137‑1 (MQ=255)
                                                                     acaacccGCCCTTTTACCCACCCCCATGTAAAAAAATCCCTCCGGGGCGGTTGTCTCCCAGTTTTTTTCCCGCCCCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATc                                                                          <  2:131576/146‑1 (MQ=255)
                                                                        acccccgcTTTTACCCACCGCCTTTTGAAAAATTGCCTCCGGGGCGGCTGTCTGCCAGTTTTTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCg                                                                         <  2:1035824/144‑1 (MQ=255)
                                                                         cccgctctttcccccACCGCAATGTAAAAAAAGGCCTGCGCGGGGGTTGTCGGCGAGTTTTTTTCCCGCCGAAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCgct                                                                       <  1:397720/137‑1 (MQ=255)
                                                                               cATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGCAAAGAAAAAAAGTTTAACCCCCCATGTTTTGTggggataggt                                                                       >  1:820411/1‑136 (MQ=25)
                                                                                         aCGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGGAGAGAAAAAACTTTTAAACCGCCCTTTTTTGGGGGAATCGCTGCCGGGTAAAATGTgg                                                       >  2:1145543/1‑150 (MQ=25)
                                                                                            ccttgtgAAAAATTGCCTCCGGGGGGGTTGTCTCCAAGTTTTTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAg                                                   <  1:805939/148‑1 (MQ=255)
                                                                                             aaggtcaaaaatTGCCTCGGGGGCGTCTTTCGGCCGTCTTTTTTCCCCCCGCAAAAAAGCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAgg                                                  <  2:972581/144‑1 (MQ=255)
                                                                                                   aaaaatTGCTTTCGGGGCGGCTGTCTCCCAGTTTTTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGt                                             <  2:1024505/149‑1 (MQ=255)
                                                                                                    aaaaaTCCCTGCGGGGGGGTTTTCGCCAGTTTTTTTTCCCGCCACAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGa                                                <  1:915469/146‑1 (MQ=255)
                                                                                                    aaaaaTCCTTCGGCGGGGGCTGTCGCCCAGTTTTTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGaa                                               <  2:591194/147‑1 (MQ=255)
                                                                                                    aaaaaGCCCTCCGGGGCGGCTGTCGCCCAGTTTTTTTCCCGCCCAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTg                                            <  2:1203386/150‑1 (MQ=255)
                                                                                                               ttCGCGGCGGCTGTCTGCCAGTTTTTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAAt                                    <  2:50346/149‑1 (MQ=255)
                                                                                                                                            tcgcccccaaccaaAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTc        <  2:205088/139‑1 (MQ=255)
                                                                                                                                               cgccgaAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTc        <  2:153785/147‑1 (MQ=255)
                                                                                                                                                 ccccaaaaaAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCGCCTCa  <  2:1078424/148‑1 (MQ=255)
                                                                                                                                                  cgcAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCGCCTCa  <  1:201261/150‑1 (MQ=255)
                                                                                                                                                       |                                                                                                                                                  
ATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCGCCTCA  >  NC_000913/357743‑358034

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap:     Deleted base: