Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_000913357,8900CA48.4% 27.9 / 17.9 31L267F (TTG→TTT) cynRtranscriptional activator of cyn operon; autorepressor
Reads supporting (aligned to +/- strand):  ref base C (15/1);  new base A (0/15);  total (15/16)
Fisher's exact test for biased strand distribution p-value = 5.66e-08
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.41e-01

TAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAA‑CAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAG  >  NC_000913/357744‑358009
                                                                                                                                                   |                                                                                                                       
tAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAA‑CAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACaaa                                                                                                                      >  1:218776/1‑150 (MQ=255)
 aaGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAA‑CAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACaaaa                                                                                                                     <  1:443971/150‑1 (MQ=255)
     gTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAA‑CAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAAccgcc                                                                                                                >  2:587543/1‑151 (MQ=255)
     gTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAA‑CAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAAccgcc                                                                                                                >  1:197860/1‑151 (MQ=255)
      tAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAA‑CAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAAccgccg                                                                                                               >  1:919527/1‑151 (MQ=255)
        gcgcATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAA‑CAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGtt                                                                                                             >  2:286551/1‑151 (MQ=255)
        gcgcATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAA‑CAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGtt                                                                                                             >  2:171478/1‑151 (MQ=255)
           cATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAA‑CAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTtctc                                                                                                          >  2:1148003/1‑151 (MQ=255)
            aTCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAA‑CAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTtctct                                                                                                         >  1:1181424/1‑151 (MQ=255)
               aGGCAATACCAGCCGCAGACCTGCGTCAGCGGCTAACGTGATTCATTTACGCCAC‑CAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTcc                                                                                                       >  1:996805/1‑150 (MQ=255)
                    ttcccccccGCAGTCGTTTGCCAGCGGCTCCGGTTTTTCATTCCCGCAAA‑CACCCGCGCTTTTATCCACCGCCATGTGAAAAAAGCCCTCCGGGGGGGCTGTCTGCCAGTTTTTTTCCCGCCACAAAAAAACCGCCGTTCTCTCCagtag                                                                                                  <  2:1107850/143‑1 (MQ=255)
                      tCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAA‑CAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTgg                                                                                               >  1:109625/1‑151 (MQ=255)
                          gCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAA‑CAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCggg                                                                                           >  2:285933/1‑151 (MQ=255)
                           ccGCAGCCTTGTGCCGGCGCCTCCCGTGTTTCTTTCCCCCCAA‑CACCCGCGCTTTTACCCAACGCCATTTGAAAAAATGCCTCCGGGGCGGCTGTCGGCCAGTTTTTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCgggg                                                                                          <  2:672496/151‑1 (MQ=255)
                           ccGCAGCCCTTTGTAAGCGGCTCCGGTGTTTCTTTTCCGCCAA‑CACCCGCCCTTTTACCCAACCCCGTTTGAAAAAATGCTTTCGCGGGGGCTTTCTGCCAGTTTTTTTCCCGCCCAAAAAAAACCGCCGTTCTCTCCAGTAGCGGCggg                                                                                           <  2:241043/150‑1 (MQ=255)
                           ccGCAGACCTATGTCAGCGGCTACCGTGATTCATTTTCGCTAA‑CAACCGCGCATTTCTCCAACGCCATTTGCAAAAATGCCTTCGCGGCGGTTGTCTGCCAGCTATTTTTCCGCCGCAACCAAACCGCAGTTCTCTCCagcagt                                                                                                 >  1:123906/1‑144 (MQ=18)
                            cGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAA‑CAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGcaacaa                                                                                                                       <  2:1026053/121‑1 (MQ=255)
                            cGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAA‑CAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGcaacaa                                                                                                                       >  1:1026015/1‑121 (MQ=255)
                            cGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAA‑CAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCggggg                                                                                         >  2:839074/1‑150 (MQ=255)
                                 aCCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAA‑CAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCggggg                                                                                         >  1:555298/1‑145 (MQ=255)
                                              gctcctgTGATTC‑TTTCCCCCAACCACCCGCCCTTTTACCCAACGCCTGGGGAAAAACTCCCGCCGCGGCGGCTGTCGGCAAGCTTTTTTCCCGCCAAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAAt                                                                                <  1:624463/136‑1 (MQ=255)
                                                   cGTGTTTCATTCCCGCCAA‑CACCCGCGCTTTTACCCACCGCCTTGTGAAAAAATGCCTCCGCGGCGGCTGTCGGCCAGTTTTTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCg                                                                   <  2:1020308/150‑1 (MQ=255)
                                                      gtttCATTCCCCCCAC‑CACCCGCGCTTTTACCCAGCGCCTTGTGAAAAAGTCCCTGGGGGGGGGCTTTCTCCCCGTTTTTTTCCCCCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCAt                                                               <  2:849717/149‑1 (MQ=255)
                                                            ttcccccaaa‑caacCGCCCTTTTTCCCAACCCTTGGTAAAAAAATCCCTGCGCGGCGGCTGTCCCCCGGTTATTTTCCCCCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTc                                                                 <  2:175270/135‑1 (MQ=255)
                                                              ccccccAA‑CACCCGCCCTTTTCCCCACCCCCTTGTGAAAAAATCCCTCCGGGGCGGCTGTCGCCCAGTTTTTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTtgtgtg                                                       <  2:946263/147‑1 (MQ=255)
                                                               cccccAA‑CACCCGCTCATTTACCCACCCCCTGGTAAAAAAAGCCCTCGGCGGCGGCTGTCTGCCAGTTATTTTCCCCCCAAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCAtgttgt                                                          <  2:920299/144‑1 (MQ=255)
                                                                                 tttACCCACCCCCATGTGAAAAAATGCTTCCGGGGCGGCTGTCGCCGAGTTTTTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGt                                        <  2:1068350/148‑1 (MQ=255)
                                                                                      ccACCGCCATGTGAAAAAATGCCTCCGGGGCGGCTGTCTCCCAGTTTTTTTCCCCCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACaa                                   <  2:385215/148‑1 (MQ=255)
                                                                                               tgtgCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGCAGGGAAAAAAATTTTAGACCCCCATGTTTTGTGGGGATCCCCGCTGGGGAAAATGTGGGGAggg                        >  2:711895/1‑150 (MQ=255)
                                                                                                    aaaagTCCCTCCGCGGCGGCTGTCTGCCAGTTTTTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTgc                  <  1:187565/151‑1 (MQ=255)
                                                                                                             ttCGGGGGGGCTGTCTCCAAGCTTTTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGaa            <  2:779713/148‑1 (MQ=255)
                                                                                                                  gggggctgccgcccAGTTTTTTTCCCGCCCAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTcc    <  2:815587/139‑1 (MQ=255)
                                                                                                                              ccAGTTTTTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAg  <  2:36304/141‑1 (MQ=255)
                                                                                                                                                   |                                                                                                                       
TAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAA‑CAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAG  >  NC_000913/357744‑358009

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑