Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_000913357,8750AT45.7% 34.9 / 20.1 35N272K (AAT→AAAcynRtranscriptional activator of cyn operon; autorepressor
Reads supporting (aligned to +/- strand):  ref base A (17/2);  new base T (0/16);  total (17/18)
Fisher's exact test for biased strand distribution p-value = 4.19e-08
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GAACTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTA  >  NC_000913/357728‑358019
                                                                                                                                                      |                                                                                                                                                
gAACTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCACACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTAt                                                                                                                                                 <  1:549066/149‑1 (MQ=255)
  aCTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTAttttt                                                                                                                                             >  1:728186/1‑151 (MQ=255)
   cTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTAttttt                                                                                                                                             <  2:679799/150‑1 (MQ=255)
   cTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTc                                                                                                                                            >  2:938777/1‑151 (MQ=255)
    tCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTcc                                                                                                                                           >  1:710858/1‑151 (MQ=255)
       tAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTccgcc                                                                                                                                        >  1:206926/1‑151 (MQ=255)
       tAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTccgcc                                                                                                                                        >  1:359736/1‑151 (MQ=255)
                   gCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAAccg                                                                                                                            >  2:8227/1‑151 (MQ=255)
                   gCGTAGCGCATCAGCCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCCCGCATTTATCCAACGCCATGCGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCCCCGCAACAAAAcc                                                                                                                             >  1:233872/1‑150 (MQ=255)
                     gTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAAccgcc                                                                                                                          >  1:780471/1‑151 (MQ=255)
                                ggCATTTCCAGCCGCAGCCCTGTTTCGGGGGCTCCCGTGTTTCTTTCCCCCCAACACCCGCCCTTTTACCCACCCCCTTGTGAAAAAATGCCTTGGCGGCGGTTTTCTCCCATTTTTTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCag                                                                                                               <  2:648146/151‑1 (MQ=255)
                                           ccGCAGCCTTGTGTCAGCGGCTCCGGTGTTTCTTTCCCCCCAACACCCGCGCATTTACCCACCGCCATGTGAAAAAATGCCTTCGGGGGGGCTGTCTCCCAGTTTTTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCagtagt                                                                                                           <  2:145602/144‑1 (MQ=255)
                                           ccGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCgggg                                                                                                    >  2:404092/1‑151 (MQ=255)
                                              tctcccgatctcggCGGCTCCGGTGATTATTTCCCGCAAACACCCCCTCATTTATCCACCGCCAGGTGAAAAAATGCCTTCGCGGCGGCTGTCGGCCAGTTTTTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTg                                                                                                          <  2:291020/129‑1 (MQ=255)
                                                   cTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCagg                                                                                                >  2:722709/1‑145 (MQ=255)
                                                    tgtgTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCgggg                                                                                                    >  2:406207/1‑142 (MQ=255)
                                                      tgtCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAGGAGaaa                                                                                           >  2:582323/1‑149 (MQ=255)
                                                         cAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTg                                                                                                          >  1:291000/1‑131 (MQ=255)
                                                          aGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAACAGaaaaaaactt                                                                                    >  2:920843/1‑144 (MQ=255)
                                                             ggCTCCGGTGTTTCTTTCCCCCCAACACCCGCGCATTTACCCACCGCAATGTGAAAAAATCCCTTCGCGGCGGCTGTCGGCCAGCTTTTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGc                                                                                       <  2:383537/146‑1 (MQ=255)
                                                                  ctttgtttCTTTCCCGCCAACACCCGCGCTTTTACCCACCCCCAGGTGAAAAAATCCCTCGGGGGGGGCTGTCTCCCATCTTTTTTCCCGCCACAAAAAATCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCtt                                                                                     <  1:82146/137‑1 (MQ=255)
                                                                   cGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGAAGGGAAAAAGGTTTAAAccc                                                                              >  2:958366/1‑149 (MQ=255)
                                                                    gTGATTCTTTCCCCCCAAACCCCGCGCTTTTACCCACCCCAATGTGAAAAAATCCCTCCGGGGCGCCTTTCTCCCAGTTTTTTTCCCGCCAAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGt                                                                            <  2:872343/150‑1 (MQ=255)
                                                                        ttCTTTCCCGCCAACACCCGCGCTTTTACCCACCGCCTTGTCAAAAATTCCTTCCGCGGCGGTTGTCTGCCAGTTTTTTTCCCGCCGAAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGt                                                                            <  2:116817/146‑1 (MQ=255)
                                                                        ttCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGGAGAGaaaaaaactttaaacc                                                                              >  2:606923/1‑131 (MQ=25)
                                                                                    accacccGCGCATTTACCCACCCCCATGTGAAAAAATGCCTCCGCGGCGGCTGTCTGCCAGCTTTTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAAt                                                            <  2:809971/145‑1 (MQ=255)
                                                                                        acCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAAAAATAAATTTTAAACCGCACTTTTGTGTGGCGATCgc                                                         >  1:95770/1‑149 (MQ=25)
                                                                                                    cccAACGCCATGAAAAAAAATGCCTCCGGGGCGTCTGTCGCCCAGTTTTCTTCCCGCCGAAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAAt                                            <  1:832176/149‑1 (MQ=255)
                                                                                                     cccaccccaatgtcAAAAATGCCCTCCGGGGCGGCTTCCGCCAAGTTTTTTTCCCCCCAAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACaa                                             <  1:375821/136‑1 (MQ=255)
                                                                                                     ccacccccttttcaaaaaaTCCTTCCGCGGCGTCTTTCTCCCCGTTTTTTTCCCGCCACAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAAc                                               <  1:410443/132‑1 (MQ=255)
                                                                                                      cacccccttgtaaaaaaaTCCCTCCGGGGCGGTTGTGTCCCGGTTTTTTTCCCGCAGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAAtg                                           <  1:603782/136‑1 (MQ=255)
                                                                                                         cccctggaaaaaaaaTCCTTCCGGGGCGGCTGTCCGCCAGTTTTTTTCCCGCCCAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAAtgtg                                         <  1:717219/138‑1 (MQ=255)
                                                                                                           cctggtgAAAAATTCCCTCCGCGGCGGTTGTCCCCCACTTTTTTTCCCGCCGAAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGaa                                      <  1:158096/145‑1 (MQ=255)
                                                                                                                                         tGTCTCCCAGTTTTTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATc                    <  2:79190/139‑1 (MQ=255)
                                                                                                                                               ccAGTTTTTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTa  <  1:688169/151‑1 (MQ=255)
                                                                                                                                                      |                                                                                                                                                
GAACTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTA  >  NC_000913/357728‑358019

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap:     Deleted base: