Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_000913357,8900CA58.3% ‑1.1 / 35.4 36L267F (TTG→TTT) cynRtranscriptional activator of cyn operon; autorepressor
Reads supporting (aligned to +/- strand):  ref base C (10/5);  new base A (0/21);  total (10/26)
Fisher's exact test for biased strand distribution p-value = 1.18e-05
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.80e-03

ATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAA‑TGCCT‑TCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGC‑TTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCGCCTC  >  NC_000913/357743‑358033
                                                                                                                                                      |                                                                                                                                                 
aTAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAA‑TGCCT‑TCGCGGCGGCTGTCTGCCGGCTATTTTT‑CCGCCGcaacaa                                                                                                                                                 <  2:814195/150‑1 (MQ=255)
     cGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAA‑TGCCT‑TCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAAccgc                                                                                                                                           >  1:1009120/1‑151 (MQ=255)
      gTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAA‑TGCCT‑TCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAAccgcc                                                                                                                                          <  2:168112/151‑1 (MQ=255)
        aGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAA‑TGCCT‑TCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGt                                                                                                                                        >  2:226140/1‑151 (MQ=255)
            cATCGGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTCCCGCCAACACCCGCGCATTTATCCAACGCCATGTGCAAAAA‑GGCCT‑TCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAAccgccg                                                                                                                                         <  2:150198/146‑1 (MQ=255)
                    attcccAGCCGAAGCCTTGTGTCGGCGGCTCCCGTGTTTCATTCCCCCCAACACCCGCGCTTTTACCCACCCCCATGTGAAAAAA‑GCCCT‑CCGCGGCGGCTTTCTCCCAGTTTTTTTC‑CCGCCGCAAAAAAACCGCCGTTCTCTCCagta                                                                                                                             <  2:478763/146‑1 (MQ=255)
                    aaTTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAA‑TGCCT‑TCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCagt                                                                                                                              >  1:92199/1‑149 (MQ=255)
                       tCCAGCCGCAGACCTGTGTCAGCGGCTCCAGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAA‑TGCCT‑TCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGACGTTCTCTCCagtag                                                                                                                            >  1:1049213/1‑148 (MQ=255)
                       cccggCCCCAGCCCTGTGCCGGCGGCTCCGGTTATTCATCCCCCCCAACACCCGCCCATTTACCAACCGCCATTCAAAAAAA‑GGCCT‑CCGGGGCGGCTCTCGGCCATTTTTTTTC‑CCGCCGAAAAAAAACCGCCGTTCTCTCCagtagt                                                                                                                           <  1:254438/145‑1 (MQ=255)
                          aGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCCCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAA‑TGCCT‑TCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGC‑gg                                                                                                                     >  1:736617/1‑151 (MQ=255)
                           gCCGCAGACTTGTGTCGGCGGCTACCGTGTTTCATTCCCGCCAACACCCGCGCTTTTATCCACCGCCTTGTGAAAAAA‑TGCCT‑TCGCGGCGGCTGTCTGCCAGTTTTTTTC‑CCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGC‑ggg                                                                                                                    <  2:946317/151‑1 (MQ=255)
                               cAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAA‑TGCCT‑TCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGC‑gg                                                                                                                     >  1:491814/1‑146 (MQ=255)
                                 gACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAA‑TGCCT‑TCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGC‑gggg                                                                                                                   >  1:1039360/1‑146 (MQ=255)
                                           aGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAA‑TGCCT‑TCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGCAAGAGAACTaagt                                                                                                     >  1:714642/1‑148 (MQ=255)
                                            gCGGCTCCCGTGTTTCTTTCCCCCAAACACCCGCGCTTTTACCCAACCCCTTGTGAAAAAA‑TGCCT‑TCGGGGCGGCTGTCGGCCAGTTTTTTTC‑CCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGC‑ttt                                                                                                  <  2:1019753/151‑1 (MQ=255)
                                              ggctccgtcaaTTCTTTCCCGCCACCACCCGCCCTTTTACCCAGCCCCATGGAAAAAAG‑TGCCG‑CCGCGGCGGTTGTCGGCCATTTTTTTTC‑CCGCGGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGC‑t                                                                                                    <  1:525196/137‑1 (MQ=255)
                                              ggCTCCCGTGATTCTTTCCCGCAAACACCCGCGCATTTACCCACCGCCATGGGAAAAAA‑TCCCT‑TCGCGGCGGCTGTCTGCCACTTTTTTTC‑CCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGC‑TTTaa                                                                                                <  2:552642/151‑1 (MQ=255)
                                              gcctcccttGATTCTTTCCCCCAAACACCCGCGAATTTACCCACCGCCTTGTGAAAAAA‑GGCCT‑TCGCGGCGGCTGTCTGCAAGCTTTTTTC‑CCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAaga                                                                                                              <  2:1017708/130‑1 (MQ=255)
                                                ctcccttGATTCATTCCCCCCAACACCCGCACTTTTACCCACCCCCATGTACAAAAT‑TGCTT‑TCGGGGCGTCTGTCTGCAATATTTTTTT‑CCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGC‑TTTAAg                                                                                               <  1:901104/144‑1 (MQ=255)
                                                             ttccccccAACACCCGCGCATTTACCCAACGCAATGTGAAAAAA‑TCCCT‑CCGCGGCGGCTGTCTGCCAGCTTTTTTC‑CCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGC‑TTTAAGCCCGTCAtgttgt                                                                                  <  2:350993/144‑1 (MQ=255)
                                                             ttccccccAACACCCGCGAATTTACCCACCCCCATG‑GCAAAAAGGGCTT‑TCGGGGCGGCTGTCTGCCAGTTATTTTC‑CCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGC‑TTTAAGc                                                                                              <  2:144483/132‑1 (MQ=255)
                                                             ttcccccaaacaccCGCGCATTTACCCACCGCAATGTGAAAAAA‑TCCTT‑TCGGGGCGGCTGTCTGCCTGTTTTTTTC‑CCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGC‑TTTAAGCCCGTCAtgttgt                                                                                  <  2:536495/142‑1 (MQ=255)
                                                               cccGCAACCACCCGCGCATTTACCCACCGCCATGTGCAAAAA‑TGCCT‑TCGCGGCGGCTGTCGGCCATTTTTTTTC‑CCGCCGCAAAAAATCCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGC‑TTTAAGCCCGTCATGTtgtg                                                                                 <  1:997673/148‑1 (MQ=37)
                                                                      acaccCGCGCTTTTACCAAACCCCATGGGAAAAAA‑TGCCT‑CCGCGGGGGCTGTCGGCCAGTTTTTTTC‑CCGCCAAAAAAAATCCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGC‑TTTAAGCCCGTCATGTTGTGTGGCAATc                                                                         <  1:226076/150‑1 (MQ=255)
                                                                                 tttACCCACCGCCTTGTGAAAAAA‑TGCCT‑CCGGGGCGGCTGCCTGCATTTTTTTTTC‑CCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGC‑TTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTaa                                                              <  1:513382/150‑1 (MQ=255)
                                                                                 tttACCCACCGCCATGTGCAAAAT‑TCTTT‑TCGGGGGGGCGGTCTGCCTTTTTTTTTC‑CCGCCAAAAAAAATCCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGC‑TTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTa                                                               <  2:155124/149‑1 (MQ=255)
                                                                                   tATCCAACGCCATGTGCAAAAA‑TGCCT‑TCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGGGAGAGAAAAAACATTTAAACCC‑CCCTGTTTTGTGGGGATAGCTGCTgg                                                                 >  2:724348/1‑145 (MQ=25)
                                                                                     cccACCGCCATGTGAAAAAA‑TGCTT‑TCGCGGCGCCTGTCTGCCGGTTTTTTTC‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGC‑TTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAAt                                                          <  2:894008/149‑1 (MQ=255)
                                                                                        accGCCATGTGAAAAAA‑GGCCT‑CCGGGGGGGCTGTCCCCCAGTTTTTTTC‑CCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGC‑TTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACaa                                                           <  2:260193/144‑1 (MQ=255)
                                                                                          ccccgtgtgCAAAAA‑TTCTG‑GCGGGGCGGTTGTCGGCCAGCTTTTTTC‑CCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGC‑TTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAAtgtg                                                       <  1:617588/143‑1 (MQ=255)
                                                                                          cGCCATGTACAAAAT‑GGCTT‑CCGCGGGTTCTGTCCGCCAGTTTTTTTC‑CCGCCAAAAAAAACCCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGC‑TTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGa                                                     <  1:883731/150‑1 (MQ=255)
                                                                                          cGCCATGT‑CAAAAA‑ACCCTCTCGGGGGGGCTGTCGCCCACCTTTTTTC‑CCGCGGAAACAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGC‑TTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGaa                                                    <  2:285669/151‑1 (MQ=255)
                                                                                                    aaaaa‑TCCCT‑TCGCGGCGCCGGTCT‑CCAGGTATTTTTCCCGCCACAACAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGC‑TTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGt                                            <  1:832533/149‑1 (MQ=255)
                                                                                                                    ggcggcTGTCTGCCATCTTTTTTC‑CCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGC‑TTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAg                                <  2:94984/147‑1 (MQ=255)
                                                                                                                    ggcggcTGTCTCCCGGCTTTTTTC‑CCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGC‑TTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTcc                            <  2:983871/151‑1 (MQ=255)
                                                                                                                      cggcTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGGGAGAGAAAAAAC‑ATTTACCCCCCCCCGTTGTGTGGGGATCGCTGCTGGGGAAAAAGTGGGAAGGGGAgagggggg                                      >  1:553290/1‑132 (MQ=255)
                                                                                                                                     ttttttc‑CCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGC‑TTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTg            <  2:92208/148‑1 (MQ=255)
                                                                                                                                                   caacaaAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGGCAGAGAAAAAAC‑TTTTAACCCCCCCTGTTTTGTGGGGATCGCCGCTGGGGACAAAATGGGAAGGGGAGGGGGGGGGAACAACCCCCGAAAAGCGCCAATTTAGTTTGcccc  >  2:588988/1‑145 (MQ=255)
                                                                                                                                                      |                                                                                                                                                 
ATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAA‑TGCCT‑TCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGC‑TTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCGCCTC  >  NC_000913/357743‑358033

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: ‑