Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_000913357,8900CA43.6% 51.9 / 19.0 40L267F (TTG→TTTcynRtranscriptional activator of cyn operon; autorepressor
Reads supporting (aligned to +/- strand):  ref base C (16/6);  new base A (0/17);  total (16/24)
Fisher's exact test for biased strand distribution p-value = 2.06e-06
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

ATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCGCCTCA  >  NC_000913/357743‑358034
                                                                                                                                                       |                                                                                                                                                
aTAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACaaa                                                                                                                                               <  2:711974/151‑1 (MQ=255)
       tAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTTCCAGCTATTTTTCCGCCGCAACAAAAccgccg                                                                                                                                        >  1:309877/1‑151 (MQ=255)
           gcATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTtct                                                                                                                                    >  2:141516/1‑151 (MQ=255)
            cATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTtctc                                                                                                                                   >  1:377765/1‑151 (MQ=255)
             aTCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTtctct                                                                                                                                  >  2:480804/1‑151 (MQ=255)
               cAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTcc                                                                                                                                >  2:92828/1‑151 (MQ=255)
               cAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTcc                                                                                                                                >  2:642902/1‑151 (MQ=255)
                   cattcccACCCGCAGCCCTTTTTCGCCGGCTCCGGTGATTCTTTCCCGCCACCACCCGCCCTTTTCCCCACCCCCTTGTCCAAAATTGCTTTCGCGGCGCCTTTCTGCCCCTTTTTTTCCCCCCGCAAAAAAACCGCCGTTCTCTCCag                                                                                                                              <  2:119585/144‑1 (MQ=255)
                     aTTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCagtagt                                                                                                                          >  2:55331/1‑151 (MQ=255)
                       tCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTgg                                                                                                                        >  2:87425/1‑151 (MQ=255)
                        ccAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGc                                                                                                                       >  1:487165/1‑151 (MQ=255)
                            ccGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCgggg                                                                                                                   >  2:603249/1‑151 (MQ=255)
                             cccAGCCCTGTGTCAGCGCCTCCCGTGATTCATTCCCCCCACCAACCGCGTTTTTACCCACCCCCATGTGAAAAAATCCCTGCGGGGGGGTTGTCGGCCATTTTTTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGc                                                                                                                  <  1:727708/149‑1 (MQ=255)
                             cGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCgggg                                                                                                                   >  2:38519/1‑150 (MQ=255)
                                aGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCggggg                                                                                                                  >  1:312360/1‑147 (MQ=255)
                                 gccttgtgTCAGCGCCACCCGTGTTTCATTCCCCCAAACACCCGCGCTTTTACCCACCGCCTTGTGAAAAAAGGCCTTCGGGGCGGTTGTCTCCCATTTTTTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCaa                                                                                                                <  1:396986/145‑1 (MQ=255)
                                     tgtggatggggttACTGTGATTAATTCCCGCAACAACCCGGGCTTTTATCCACCGCCTTGCAAAAAAACGCCTTCGGGGCGCCTTTCTGCCAGTTATTTTCCCGCCAAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCaa                                                                                                                <  2:840692/133‑1 (MQ=255)
                                       tgccggCGGCCACCGTTTTTCATTCCCCCCACCACCCGCGCTTTTACCAACCCCCTTTTAAAAAAATCCCTGCGGGGCGGCTGTCTCCCAGTTTTTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGaa                                                                                                           <  1:244935/143‑1 (MQ=255)
                                           aGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCGAGAGgaaaa                                                                                                        >  2:524840/1‑145 (MQ=255)
                                              ggCTCCCGTTATTCTTTCCCCCCACCACCCGCCCTTTTACCCAACCCCATGGCAAAAATTGCTTCCGGGGGGGCTGTCTGCAGGTTTTTTTCCCGCCAAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCttt                                                                                                   <  1:597632/149‑1 (MQ=255)
                                               gcctccggtatttctttCCCCCAAACACCCGCCCTTTTACCCACCGCCATGTGAAAAAACGCCTGCGCGGGGGCTGTCTCCCAGCTTTTTTCCCGCGAAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGaaa                                                                                                          <  1:55322/128‑1 (MQ=255)
                                                   ccGTGTTTCATTCCCCCCACCACCCGCGCTTTTATCCACCCCCATGTGAAAAAATCCCTCCGCGGGGGCTGTCTGCCATTTTTTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGcc                                                                                              <  2:378963/149‑1 (MQ=255)
                                                         ttCTTTCCCCCCACCACCCGCGCTTTTACCCACCCCCTTGGGAAAAAATCCCTCCGGGGCGGTTTTCTCCCAGTTTTTTTCCCGCCACAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCtt                                                                                                    <  1:541758/137‑1 (MQ=255)
                                                               tCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGGAGAGAAAAAACTTTTTGCCCGTCAtgt                                                                                      >  2:195146/1‑145 (MQ=37)
                                                               ccccccAACACCCGCGCTTTTACCCACCCCCATGGAAAAAAATCCCTTCGCGGCGGCTGTCTGCCAGTTTTTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTtgtgt                                                                                 <  2:862511/146‑1 (MQ=255)
                                                                      aacaccCGCGCTTTTTCCCACCCCAATGTGAAAAAATCCCTCCGCGGCGTCTTTCTCCCAGTTTTTTTCCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAAt                                                                           <  2:321177/150‑1 (MQ=255)
                                                                           cccGCACATTTACCCACCCCCTTGAAAAAAAACCCTTCCGGGGCGTCTGTCTGCCAGTTTTTTTCCCGCCAAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATc                                                                          <  1:65109/146‑1 (MQ=255)
                                                                            ccGCGCTTTTCCCCACCCCCATGTGAAAAAATGCCTTCGCGGCGGTTGTCTCCCAGCTTTTTTCCCGCCGAACAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCa                                                                             <  1:641477/143‑1 (MQ=255)
                                                                            ccGCGCTTTTACCCACCGCCTTGTGAAAAATTGCCTTCGCGGCGGCTGTCTGCCACTTTTTTTCCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCgc                                                                        <  2:155336/148‑1 (MQ=255)
                                                                             cgcgCATTTACCCAACCCCATGTAAAAAAATGCCTCCGCGGCGGCTGTCTGCCAGTTATTTTCCCGCCGAAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCgctgct                                                                    <  2:316885/151‑1 (MQ=255)
                                                                                           acgctgtatgtaaaaaTACCTACGCGGCGGCTAGTGCCTATCTATTTTTCCGCCAAAGGAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAAtgt                                                         <  2:745263/137‑1 (MQ=255)
                                                                                                   tgCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCGAGAGAAAAAAATTTAAACCCCCCAAGGTGTGTGGGGATCTCCGCTGGGGACAAAGTGGGAAgg                                                  >  2:167454/1‑147 (MQ=255)
                                                                                                     aaaaaaTGCCTTCGGGGCGGCTGTCTGCCAGTTATTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTg                                            <  2:893929/150‑1 (MQ=255)
                                                                                                      aaaaaTGCCCCCGCGGCGGCTTCCTGCCAGTTTTTTTCCCGCAGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGt                                             <  1:281193/149‑1 (MQ=255)
                                                                                                      aaaaaTCCTTCCGGGGCGGTTGTCTGCCAGTTTTTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAg                                              <  2:6437/148‑1 (MQ=255)
                                                                                                         aaTCCCTTCGGGGGGGCTTTCTCCCAGTTTTTTTCCCGCCCCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTgcggc                                        <  2:626853/151‑1 (MQ=255)
                                                                                                                                       ttttttcCCGCCCAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCgcgc                   <  1:105931/142‑1 (MQ=255)
                                                                                                                                          ttttCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGAAGGGAAAAAAATTTTAAACCCCCATGTTTTGTGGGGAACGCTGCTGGTAACAATTTGGGAAGGGAAGGGGGGGGGATACGCTCCAGAAACGCGCCAATTGAg           >  2:259385/1‑149 (MQ=255)
                                                                                                                                              cccccgcAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCGcc     <  2:502447/148‑1 (MQ=255)
                                                                                                                                                 ccgcAACAAAACCACCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCGCCTCa  <  1:605430/151‑1 (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: