Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	357,890	0	C	A	50.0%	29.0 / 28.4	44	L267F (TTG→TTT)	cynR	transcriptional activator of cyn operon; autorepressor
Reads supporting (aligned to +/- strand):  ref base C (17/5);  new base A (0/22);  total (17/27)
Fisher's exact test for biased strand distribution p-value = 7.67e-08
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.56e-01

GATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAA‑TGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTT‑TCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAA‑GA‑G‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCGCCT  >  NC_000913/357742‑358032                                                                                                                                                        |                                                                                                                                                  gATAAGCGTAGGGCATCAGGAAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAA‑TGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTT‑TCCGCCGcaacaa                                                                                                                                                 <  2:998617/151‑1 (MQ=255) gATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAA‑TGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTT‑TCCGCCGcaac                                                                                                                                                   <  2:365079/149‑1 (MQ=255) gATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAA‑TGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTT‑TCCGCCGcaac                                                                                                                                                   <  1:269316/149‑1 (MQ=255)    aaGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAA‑TGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTT‑TCCGCCGCAACaaaa                                                                                                                                               <  2:246712/150‑1 (MQ=255)      gCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAA‑TGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTT‑TCCGCCGCAACAAAAccg                                                                                                                                            >  1:69609/1‑151 (MQ=255)        gTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAA‑TGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTT‑TCCGCCGCAACAAAAccgcc                                                                                                                                          <  2:119031/151‑1 (MQ=255)                   ggCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAA‑TGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTT‑TCCGCCGCAACAAAACCGCCGTTCTCTcc                                                                                                                                 >  2:581645/1‑149 (MQ=255)                      attcccACCCGCAGCCTTGTGCCAGCGCTTCCGGTGATTCATCCCCGCCACCACCCGCGCTTTTACCCACCCCCATTTGAAAAAA‑TCCCTC‑CGCGGCGGTTTTCTCCCAGTTTTTTT‑CCCGCCGCAAAAAAACCGCCGTTCTCTCCagt                                                                                                                              <  2:294242/145‑1 (MQ=255)                      aaTCCCAGCCGCAGCCCTGTGCCAGCGGCTCCCGTGATTCATTCCCGCCAACACCCGCGCATTTCTCCAACGCAATGTGCAAAAA‑TGCCTT‑CGCGGGGGCTGTCGCCCAGCTATTTT‑TCCGCCGAAAAAAAACCGCCGTTCTCTCCagta                                                                                                                             <  1:184268/150‑1 (MQ=18)                          ccAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAA‑TGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTT‑TCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGc                                                                                                                        >  2:1003516/1‑151 (MQ=255)                          ccAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTCCCGCCAACACCCGCGCATTTACCCAACGCCATGTGCAAAAA‑TGCCTT‑CGCGGCGGCTGTCTGCCAGCTTTTTT‑CCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGc                                                                                                                        <  1:718091/151‑1 (MQ=18)                               cGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAA‑TGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTT‑TCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCgggg                                                                                                                    >  1:116144/1‑150 (MQ=255)                                   gccgtgtgTCGGCGCCTACCGTGATTCTTTCCCGCCAACAACCGCGCTTTTACCAACCGCATTGTCAAAAAA‑TGCCTC‑CGGGGCGGCTGTCTCCCATTTTTTTT‑CCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAa‑g                                                                                                               <  2:677522/146‑1 (MQ=255)                                   gACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAA‑TGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTT‑TCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCgggg                                                                                                                    >  1:75829/1‑146 (MQ=255)                                       tgtgTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAA‑TGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTT‑TCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGGA‑GA‑G‑aa                                                                                                         >  1:817799/1‑150 (MQ=255)                                       tgtgTCAGCGGCTACCGTGATTCACTTCCGCCAACAACCGCGCATTTATCCAGCGCCATGTGCAAAAA‑TGCCTT‑CGCGGCGGCTGTCTGCCAGTTATTTT‑TCCGCCGCAACAAAACCGCCGGTCTCTCCAGTAGTGGCggcggcg                                                                                                                 >  2:57986/1‑140 (MQ=21)                                         tgtCAGCGGCTCCCGTGTTTCATTCCCCCCACCACCCGCGCTTTTCCCAAACCCCTTGTGAAAAAA‑TCCTTC‑CGGGGCGGCTGTCTCCCAGTTTTTTT‑CCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAA‑GA‑G‑aaa                                                                                                        <  2:997511/149‑1 (MQ=255)                                            cAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAA‑TGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTT‑TCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGGA‑GA‑G‑gaaaaa                                                                                                     >  1:366742/1‑146 (MQ=255)                                              ggggCAACGGTGATTCTTTTCCCCCAACACCCGGGCATTTACCCACCGCC‑TTTGCAAAAATTCCCTT‑GGCGCGGGCTGTCTGCCAGCTATTTT‑TCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAA‑GA‑G‑AAATAGCttt                                                                                                 <  1:495690/149‑1 (MQ=255)                                              gCGGCTACCGTGATTCTTTCCCGCCAACACCCGCGCTTTTACCAACCGCCATGTGAAAAAA‑TGCCTG‑CGCGGGGGCTGTCTGCCAGTTTTTTT‑CCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAA‑GA‑G‑AAATAGCttt                                                                                                 <  1:881171/151‑1 (MQ=255)                                               cGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAA‑TGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTT‑TCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGAAGGA‑G‑aaaaaattt                                                                                                  >  1:973989/1‑144 (MQ=255)                                                ggCTACCTTGATCCATTCCCGCAAACACCCGCCCTTTTATCCACCCCCATTTACAAAAA‑TGCCTT‑CGCGGGGGCTTTTTCCCGGTTTTTTT‑CCCCCCACAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAA‑GA‑G‑AAATAGCTTTaa                                                                                               <  1:258914/151‑1 (MQ=255)                                                   ccccGTGATCCATTCCCGCCAACACCCGCCCTTTTACCCAACCCCTTGTCAAAAAA‑TGCCTC‑GGGGGCGGCTGTCGCCCAGTTTTTTT‑CCCGCCGCAAAAAACCCGCCGTTCTCTCCAGTAGTGGCGGGGCAA‑GA‑G‑AAATAGCTTTaa                                                                                               <  2:147000/146‑1 (MQ=255)                                                      cGTGATTCATTCCCGCCAACACCCGGTTTTTTACCAAACCCCGTGT‑AAAAAA‑GGCCTT‑TGGGGGGGCTGTTTTGCAGTTTTTTTCCCCGCGAAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAA‑GA‑G‑AAATAGCTTTAAGccc                                                                                           <  2:87346/149‑1 (MQ=255)                                                           ttCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAA‑TGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTT‑TCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGAA‑GG‑G‑AAAAAACttttaaacccccctgt                                                                                    >  1:473067/1‑138 (MQ=25)                                                              aTTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAA‑TGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTT‑TCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGTGGAA‑GAGG‑AAAAAATTTTAAACCCgcctgt                                                                                     >  1:891548/1‑143 (MQ=25)                                                               ttcccccaaacaccCGCCCTTTTCCCCACCGCCTTGTGAAAAAA‑TCCCTT‑CGGGGCGGCTGTCTGCCAGTTTTTTT‑CCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAA‑GA‑G‑AAATAGCTTTAAGCCCGTCAtgt                                                                                    <  2:953701/139‑1 (MQ=255)                                                                  ccGCCACCACCCGCGCTTTTACCCAACGCATTGTCAAAAAA‑TGCCTT‑CGCGGCGGTTGTCTGCCAGTTTTTTT‑CCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAA‑GA‑G‑AAATAGCTTTAAGCCCGTCATGTtgtgtg                                                                              <  2:375936/150‑1 (MQ=255)                                                                           cccGCGCATTTACCAAACCCAATG‑GGAAAAA‑AGCCTTCCGGGGGGGCTGTCTGCCACTTTTTTT‑CCCGCCGAAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAA‑GA‑G‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCa                                                                           <  2:740990/143‑1 (MQ=255)                                                                                 cATTTATCCAACGCCATGTGCAAAAA‑TGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTT‑TCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGGA‑GA‑G‑AAAAAAGATTAAACCCCTCCTGTTTTGTGGGGGTCGCCGCTGGtg                                                              >  2:273531/1‑150 (MQ=25)                                                                                      acccACCGCAATGTAAAAAAA‑GGCTTT‑CGGGGCGGCTGTCTCCCAGTTTTTTT‑CCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAA‑GA‑G‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACaa                                                          <  1:953373/148‑1 (MQ=255)                                                                                          acccccttgtgAAAAAA‑TCCCTC‑CGCGGCGCTTGTCTCCCTGTTTTTTT‑CCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAA‑GA‑G‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAAt                                                         <  2:535721/140‑1 (MQ=255)                                                                                          accccctggaaaaaaaa‑TGCCTT‑CGGGGCGGTTGTCGGCCATTTTTTTT‑CCCGCCGAAAAAAATCCGCCGTTCTCTCCAGTAGTGGCGGGGCAA‑GA‑G‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTgg                                                     <  2:443320/139‑1 (MQ=255)                                                                                            cccgttgtgCAAAAA‑GCCATC‑CGGGGCGGCGGTCGGCCAGTTATTTT‑CCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAA‑GA‑G‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTgg                                                     <  1:658630/144‑1 (MQ=255)                                                                                                aTGTGCAAAAA‑TGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTT‑TCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGAA‑GA‑GAAAAAAACTTTAAACCCG‑CCTGTTTTGTGGGGAACGCTGCTGGGAACAAAATGGGAAggg                                               >  1:454856/1‑151 (MQ=255)                                                                                                  gtgCAAAAA‑TGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTT‑TCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGGA‑GA‑G‑AAAAAAATTTTAACCCCGCCTGTTGTGTGGGGGTAGCTGCTGGGGACAAAGTGGAAAagg                                               >  1:586914/1‑149 (MQ=255)                                                                                                      aaaaa‑TGCCTC‑CGCGGCGGCTGTCTGCCAGTTTTTTT‑CCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAA‑GA‑G‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTg                                          <  1:751995/150‑1 (MQ=255)                                                                                                      aaaaa‑GCCCTG‑CGCGGCGGCTCTCTGCCAGCTATTTT‑CCCCCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAA‑GA‑G‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGaa                                             <  2:463603/147‑1 (MQ=255)                                                                                                                   cgcgGCGGCTGTCTGCCAGCTATTTT‑TCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAA‑GA‑G‑AAAAAAAATTTAACCCTCCTTGGTTTGTGGCGAGAGCGGCTGGGAACCAATTGggaagggaagggagggg                                     >  2:294084/1‑137 (MQ=255)                                                                                                                      ggcggcTGTCTGCCAGCTATTTT‑TCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCGA‑GA‑G‑AAAAAAAATTAAAACCCCCCTGGTTTGTGGGGATCGCTGCTGGTGAAAATGTGGGAAGGGGAGGGGGGCGGGTCAGCTcc                           >  2:19472/1‑151 (MQ=255)                                                                                                                      ggcggcTGTCGGCCAGTTATTTT‑CCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAA‑GA‑G‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCt                             <  1:80270/149‑1 (MQ=255)                                                                                                                         ggcTGTCTGCCAGCTATTTT‑TCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGGA‑CA‑GAAAAAAAATTTAACACCCCCCT‑TTTTGTGGGGACCGCGGCTGGGAAAAATCTGGGAAGGGGGGGGCGGCGGAGCAGCTcc                           >  2:983215/1‑148 (MQ=255)                                                                                                                                     gttttttt‑cCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAA‑GA‑G‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAAtt            <  1:786366/147‑1 (MQ=255)                                                                                                                                       tttttt‑cCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAA‑GA‑G‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTg           <  1:232253/148‑1 (MQ=255)                                                                                                                                         tttt‑cCCGCCACAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAA‑GA‑G‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAg         <  1:518936/150‑1 (MQ=255)                                                                                                                                               ccgccgAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAA‑GA‑G‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTc      <  1:816508/148‑1 (MQ=255)                                                                                                                                                  ccgaAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAA‑GA‑G‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCGCCt  <  1:673574/149‑1 (MQ=255)                                                                                                                                                        |                                                                                                                                                  GATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAA‑TGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTT‑TCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAA‑GA‑G‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCGCCT  >  NC_000913/357742‑358032

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑