Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_000913357,8900CA65.5% 0.2 / 24.7 30L267F (TTG→TTT) cynRtranscriptional activator of cyn operon; autorepressor
Reads supporting (aligned to +/- strand):  ref base C (7/3);  new base A (0/19);  total (7/23)
Fisher's exact test for biased strand distribution p-value = 7.69e-05
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.51e-03

ATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCG‑TGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGC‑GGCGGCTGTCTGCCAG‑CTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCGCCTCAA  >  NC_000913/357743‑358035
                                                                                                                                                      |                                                                                                                                                 
aTAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCG‑TGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGC‑GGCGGCTGTCTGCCAG‑CTATTTTTCCGCCGCAACaaa                                                                                                                                                <  1:226592/151‑1 (MQ=255)
                          aGCCGCAGTCTTGTGTAGGCGG‑TACCGTTTATTCATTCCCCCCCCAAACCGCGCTTTTCCCAACCGCTTTTTAAAAAAATCCCTTCGC‑GGCGGCTGTCCCCAAT‑TTTTTTTCCCCCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCg                                                                                                                       <  1:70507/150‑1 (MQ=255)
                              ccagtcctcgctcggCGGCTAGCG‑TGATCCATTCCCCCCACCACCGGCGCTTTTACCAACCGCCTGGTGCAAAAAGGCGTTCGC‑GGCGTCTTTCGGCCGG‑CTTTTTTCCCCCCGAAAGAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCa                                                                                                                  <  2:590597/137‑1 (MQ=255)
                                   cttgtgTCAGGGCCTACCG‑TGATTCTTTCCCGCCAACAACCGCGCATTTACCCAGCGCCAGGTGAAAAAATGCCTTCGC‑GGCGGCTGTCTGCCAG‑TTATTTTCCCGCCGCAAAAAACCCGCCGTTCTCTCCAGTAGTGGCGGGGCAagag                                                                                                              <  1:248212/148‑1 (MQ=21)
                                   ccTGTGTCAGCGGCTACCG‑TGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGC‑GGCGGCTGTCTGCCAG‑CTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCgggggga                                                                                                                 >  1:474448/1‑144 (MQ=255)
                                      gtgtCAGCGGCTACCG‑TGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGC‑GGCGGCTGTCTGCCAG‑CTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCGGGAGaaa                                                                                                           >  2:218934/1‑150 (MQ=255)
                                       tgtCGGCGGCTCCCG‑TGATTCATTCCCCCCACCACCCGCGCTTTTCCCCACCGCCTTGTGAAAAAATGCTTTCGG‑GGGGGCTGTCTGCCAG‑CTATTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAAt                                                                                                          <  1:219062/150‑1 (MQ=255)
                                        gtCAGCGGCTACCG‑TGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGC‑GGCGGCTGTCTGCCAG‑CTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGAAGAGaaaa                                                                                                          >  1:323489/1‑148 (MQ=255)
                                         ccgcggccccccG‑TAATTCATTCCCCCCACCACCCCCCCTTTTACCCACCCCCAGGTCAAAAAATCCCTCGGG‑GGCGGCGGTCTGCAAG‑TTTTTTTCCCGCCCAAAAAAACCCGCCGTTCTCTCCAGTAGTGGCGGGGCAagag                                                                                                              <  2:686003/134‑1 (MQ=255)
                                             cgtctcccG‑TGTTTCTTTCCCCCCAACACCCGCGTGTTTACCCACCCCCTTGTAAAAAAATCCCGCCGC‑GGGGGCTTTCCGCCTG‑TTTTTTTCCCGCCACAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAaga                                                                                                               <  2:92383/133‑1 (MQ=255)
                                                    ccttgtttCATTTCCCCCAACACCCGCCCTTTTACCCACCGCCATGGGAAAAAATCCCTTCGC‑GGCGGCT‑TCCTCCAGTCGATTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGccc                                                                                              <  2:620218/144‑1 (MQ=255)
                                                    ccgtttttCTTTCCCGCAACCACCCGCCCATTTCTCCACCGCTGTGAGAAAAAAT‑CCCTCGCGGGGGGTTGTCTGCAAT‑CTTTTTTCCCGCCGAAAAAAATCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCtt                                                                                                     <  2:678637/137‑1 (MQ=255)
                                                                cccGCCCACACCCGCTCTTTTCCCCACCTCCATGTCCAAAATGGCCTTCGC‑TGCGGCTGCCCGCCGT‑CTATTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCAtgttgt                                                                                    <  1:201934/147‑1 (MQ=255)
                                                                 cccccAACACCCGCGCTTTTACCCAACGCCTTGTGAAAAAATGCTTTCGC‑GGCGGTTGTCTCCCAG‑CTTTTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTgg                                                                                <  1:206357/148‑1 (MQ=255)
                                                                 ccGCCAACACCCGCGCTTTTACCCAACGCCTTGTGAAAAAATGCCTTCGC‑GGCGGCTGTCTGCCAG‑TTTTTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTgg                                                                                <  1:77219/151‑1 (MQ=255)
                                                                  cGCCACCACCCGCGCTTTCACCCACCCCCGTGGGAAAAAATGCCGCCGC‑GGCGGCTGCCTGCCAT‑TTATTTTTCCGCCACAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGc                                                                               <  2:81075/151‑1 (MQ=255)
                                                                                     acccACCGCCATTTGAAAAAATCCCTTCGG‑GGCGGTTGTCTGCAAG‑CTTTTTTCCCGCCAAAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACa                                                              <  2:283478/147‑1 (MQ=255)
                                                                                         accccaaTGTGAAAAAATCCCTTCGC‑GGCGCCTGTCGCCAAG‑CTATTTTCCCGCCAAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTgg                                                        <  1:157019/145‑1 (MQ=255)
                                                                                              cATGTGAAAAAATGCCTCCGC‑GGCGGCTGTCTGCCAG‑CTATTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAgg                                                   <  1:73266/151‑1 (MQ=255)
                                                                                                                    ggcggtTGTCGGCCAG‑TTTTTTTCCCCCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCa                                   <  1:191949/146‑1 (MQ=255)
                                                                                                                     gcggcTGTGTCCGAG‑TTTTTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCa                                   <  2:14563/145‑1 (MQ=255)
                                                                                                                          tGTCTGCCAG‑CTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGCAGAGAAAAAACCTTTAACCCCCCCTGTTTTGTGGGGATCGCCGCTGGTGACAAATTGGGAAAGGGAGGGCGGCGGAACAACTcccaaa                          >  1:516302/1‑145 (MQ=255)
                                                                                                                          tGTCTGCCAG‑CTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCGAGAGAAAAAACTTTTAACCCCCCCTTTTGTGTGGGGATCGCTGCTGGTGACAAAATGGGAAGGGGAGGGGGGGGGATCAACTccccaa                          >  1:207012/1‑145 (MQ=255)
                                                                                                                                ccAG‑CTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCGCGAGAAAAAAAATTAAACCCCCCCCTTTGTGGGGCGCTCGCTGCTGGGAAAAATGTGGGAAGGGAAGGGCGGGGGAGCAGCTCCCGaaaacc                      >  2:40509/1‑143 (MQ=255)
                                                                                                                                      ttttttcCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAAtt               <  1:72917/147‑1 (MQ=255)
                                                                                                                                         tttcCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGt           <  1:542088/150‑1 (MQ=255)
                                                                                                                                             ccgccgCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTc         <  1:498969/148‑1 (MQ=255)
                                                                                                                                                ccgcAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCGCCTc    <  1:415259/150‑1 (MQ=255)
                                                                                                                                                ccgaAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCGCCTc    <  1:480461/150‑1 (MQ=255)
                                                                                                                                                  gcAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGGAAAGAAAAAACTTTTAACCCCCCATGTTGTGTGGGGAATGCTGCTGGGGAAAAAGTGGAAAGGGGAGAGGGGGGGATCAGCTCCAGAAACGCGCCAAATGAGGTTGCCTcca  >  1:31069/1‑148 (MQ=255)
                                                                                                                                                      |                                                                                                                                                 
ATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCG‑TGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGC‑GGCGGCTGTCTGCCAG‑CTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCGCCTCAA  >  NC_000913/357743‑358035

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 24 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑