Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	357,890	0	C	A	48.9%	31.2 / 26.2	47	L267F (TTG→TTT)	cynR	transcriptional activator of cyn operon; autorepressor
Reads supporting (aligned to +/- strand):  ref base C (18/6);  new base A (0/23);  total (18/29)
Fisher's exact test for biased strand distribution p-value = 3.68e-08
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.60e-01

CTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAA‑TG‑CCTTC‑GCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGC‑TGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCGCCTCAATGA  >  NC_000913/357740‑358038                                                                                                                                                          |                                                                                                                                                        cTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAA‑TG‑CCTTC‑GCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGcaac                                                                                                                                                         >  1:763457/1‑151 (MQ=255)    aTAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAA‑TG‑CCTTC‑GCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGcaaca                                                                                                                                                        >  2:563015/1‑149 (MQ=255)      aaGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAA‑TG‑CCTTC‑GCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAAc                                                                                                                                                    >  1:326544/1‑151 (MQ=255)       aGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAA‑TG‑CCTTC‑GCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAAcc                                                                                                                                                   <  2:993498/151‑1 (MQ=255)         cGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAA‑TG‑CCTTC‑GCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAAccgc                                                                                                                                                 >  1:939199/1‑151 (MQ=255)                   cAGCCAATTCCACCCGCAGCCCTGTGTCAGCGGCTACCGTGATTCATTCCCGCCAACACCCGCGCATTTACCCACCCCCATGTGCAAAAA‑TG‑CCTTC‑GCGGCGGCTTTCGCCCACTTTTTTTCCCGCCGCAACAAAACCGCCGTTCTCTcc                                                                                                                                       <  2:702634/151‑1 (MQ=18)                        aaTTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAA‑TG‑CCTTC‑GCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCagt                                                                                                                                    >  1:803851/1‑149 (MQ=255)                        aaTTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAA‑TG‑CCTTC‑GCGGCGGCCGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCa                                                                                                                                      >  1:77563/1‑147 (MQ=255)                            ccccccgccgtcttgtgTCGGCGGTTACCGTAATTCTTTCCCGCCAACACCCGCCCTTTAACCCATCGCCATGTACAAAAA‑TC‑CCTGC‑GCGGCGCCTTTCTCCCAGCTTTTTTTCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGc                                                                                                                              <  2:282624/138‑1 (MQ=255)                            ccAGCCGCAGCCTGGTGTCAGCGGCTCCCGTGTTTCTTTCCCCCCAACACCCGCGCTTTTACCCACCGCCTTGTCAAAAAA‑GG‑CTTTG‑GGGGCGGCTGTCTGCCAGCTTTTTTCCCGCCGCAACAAAACCGCCGTTCTCTCCagta                                                                                                                                   <  2:223333/146‑1 (MQ=255)                               gCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAA‑TG‑CCTTC‑GCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGC‑ggg                                                                                                                          >  1:110773/1‑151 (MQ=255)                                ccGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAA‑TG‑CCTTC‑GCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGC‑gg                                                                                                                           >  1:1108322/1‑149 (MQ=255)                                   cAGCCCTGTGTCAGCGCCTCCCTTGTTTCTTCCCCCCCACCACCCCCGCATTTCCCAACCCCCTTGTCAAAAAA‑GC‑CCTTC‑GCGCCGGCTGTCTCCCAGTTTTTTTCCCGCCCAAAAAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCa                                                                                                                       <  1:999413/150‑1 (MQ=255)                                   cAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAA‑TG‑CCTTC‑GCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGC‑ggtg                                                                                                                         >  1:195653/1‑146 (MQ=255)                                    agcccTGTGTCAGCGGCTCCGGTATTTCTTTCCCCCAAACACCCGCCCATTTACCCAACGCCAGGTAAAAAAA‑T‑‑CCTTCGGCGGCGGCTGTCTCCCAGTTATTTTCCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCa                                                                                                                       <  2:995915/146‑1 (MQ=255)                                         tgtgTCAGCGCCTCCCGTTATTCATTCCCCCCAACACCCGCGTTTTTATCCACCGCCATTTGAAAAAA‑TG‑CCTTC‑GGGGCGGCTGTCTCCCAGTTTTTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAgag‑a                                                                                                                 <  2:288146/149‑1 (MQ=255)                                          gtgcaaGCGGCTACCGTGTTTCATTCCCGCAAACACCCGCGCATTTCCCCAACGCCATGTGAAAAAA‑TG‑CTTTC‑GGGGCGGCTGTCTGCCAGTTTTTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAG‑aa                                                                                                                <  2:425476/144‑1 (MQ=255)                                             tCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAA‑TG‑CCTTC‑GCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGGGAGAG‑aa                                                                                                                >  1:830618/1‑146 (MQ=255)                                                 cGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAA‑TG‑CCTTC‑GCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGGGAGAG‑aaaaaacatt                                                                                                        >  2:799937/1‑143 (MQ=255)                                                  ggcacccgtatttCTTTCCCCCCACCACCCCCGCATTTACCCACCGCCATGTGCAAAAA‑TC‑CTTCC‑GGGGGGGCGGTCGCCCAGTTTTTTTCCCGCCAAAAAAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAG‑AAATAGCt                                                                                                          <  1:978377/136‑1 (MQ=255)                                                  ggCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAA‑TG‑CCTTC‑GCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGGAAGAG‑aaaaaaactt                                                                                                        >  2:246535/1‑142 (MQ=255)                                                  ggCTACCGTGATTCATTCCCGCAAACCCCCGCACATTTACCCACCCCAATTTGAAAAAA‑TC‑CCTCC‑GGGGCGCCTGTCTCCCAGCTATTTTCCCCCCCCAAAAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAG‑AAATAGCt                                                                                                          <  2:840700/147‑1 (MQ=255)                                                   gCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAA‑TG‑CCTTC‑GCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGACGTTCTCTCCAGTAGTGGC‑GGGGCCAGGG‑AAAAAACATTaa                                                                                                      >  1:704758/1‑150 (MQ=25)                                                      cccttatttCATTCCCCCCAACACCCGCGCATTTACCCAACCCCAGGTGAAAAAA‑TC‑CCGTC‑GGGGCGGTTTGCTCCCAGCTTTTTTCCCGCCAAAAAAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAG‑AAATAGCTTTAAGcc                                                                                                   <  1:716068/143‑1 (MQ=255)                                                          ttatccatccccGCAAACACCCGCGCATTTCCCCACCGCCATGTACAAAAA‑TG‑CTTCC‑GCGGCGGCTTTCTGCCAGTTATTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAG‑AAATAg                                                                                                            <  1:979305/127‑1 (MQ=255)                                                                 ttcccGCAAACACCCGCGTTTTTCTCCCCCGCCATGT‑AAAAAA‑TGCCCTCC‑GCGGCGGTTTTCGGCCATCTTTTTTCCCGCCAAAAAAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAG‑AAATAGCTTTAAGCCCGTCAtgttg                                                                                         <  1:672539/146‑1 (MQ=255)                                                                     cccaaccccccGCGCTTTTACCCACCCCCAT‑TGAAAAAATTG‑CCTCC‑GGGGCGGCTGTCTGCCAGTTTTTTTCCCGCCAAAAAAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGc                                                                                   <  1:731578/142‑1 (MQ=255)                                                                     cGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAA‑TG‑CCTTC‑GCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGCAAGAG‑AAAAAACATCAAGccgctactttttgggg                                                                                     >  1:949000/1‑136 (MQ=25)                                                                              ccGCGCTTTAACCCACCCCCTTGTGAAAAAA‑TG‑CCTCC‑GGGGCGGCTGTTTCCCAGCTATTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCgc‑t                                                                           <  2:716879/149‑1 (MQ=255)                                                                              ccGCCCTTTTACCCACCGCCCTTTGAAAAAA‑TC‑CCTGG‑GCGGCGGTTGTCGGCCGTCTTTTTTTCGCCCACAAAAAAGCCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCgc‑tg                                                                          <  1:280338/150‑1 (MQ=255)                                                                                     tttATCCAACGCCATGTGCAAAAA‑TG‑CCTTC‑GCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGGAAGAG‑AAAAAACTTTTAATCCCTCCTGTTGTGTGGGGATCGC‑TGCTgg                                                                      >  2:754043/1‑147 (MQ=37)                                                                                         tCCAACGCCATGTGCAAAAA‑TG‑CCTTC‑GCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGGCCGGG‑AAAAAACATTTAACCCCTCCTGTTGTGTGGGGATCGC‑GGCTggggaaaa                                                                >  1:199130/1‑143 (MQ=25)                                                                                            aaCGCCATGTGCAAAAA‑TG‑CCTTC‑GCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGGGAGAG‑AAAAAAATTTTAACCCCCCCTGTTTTGTGGGGAACGCTTCCTGGTAAAAAttgg                                                            >  2:787896/1‑148 (MQ=21)                                                                                              cGCCATGTAAAAAAA‑TG‑CTTGC‑GCGGGCGTTGGTTCCGAGATTTTTTCCCGCCTAAACAACCCCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGC‑TGCTGGTAAc                                                                  <  1:692731/142‑1 (MQ=255)                                                                                                        aaaat‑TG‑CCTTC‑GGGGCGTTTGTCGGCCAGTTTTTTTCCCGCCACAAAAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGC‑TGCTGGTAACAATGTGGAAAGGGAAGTg                                                <  1:308419/150‑1 (MQ=255)                                                                                                         aaaa‑TG‑CTTTG‑GGGGGGCCTGCCGGCAAGCTATTTTTCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGC‑TGCTGGTAACAATGTGGAAAGGGAAGTgcg                                              <  2:49146/151‑1 (MQ=255)                                                                                                         aaaa‑TG‑CCTTC‑GCGGCGGTTGTCGCCCAGCTTTTTTCCCCCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGC‑TGCTGGTAACAATGTGGAAAGGGAAGTgcg                                              <  2:489569/151‑1 (MQ=255)                                                                                                             agggctttC‑GGGGCGCCTGTCTGCCAGTTTTTTTCCCGCCAAAAAAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGC‑TGCTGGTAACAATGTGGAAAGGGAAGTgcggc                                            <  2:326551/145‑1 (MQ=255)                                                                                                                 ctttC‑GCGGGGCCTGTCTGCCAGTTTTTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGC‑TGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGa                                          <  2:48216/147‑1 (MQ=255)                                                                                                                 ccTCC‑GCGGCGGCTGTCTGCCAGTTTTTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGC‑TGCTGGTAACAATGTGGAAAGGGAAGTgcggcg                                           <  2:100236/148‑1 (MQ=255)                                                                                                                       ggggcggcTGTCTCCCGGTTATTTTCCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGC‑TGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGa                                          <  2:488350/142‑1 (MQ=255)                                                                                                                                   tGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGGAAGAG‑AAATAACTTTTTACCCCGCCTCTTGTGTGGTGAACCC‑TGCTGGTTACAAAGTGGGAAAGGGAGGGGGGCGGATCACCTccccaaacgc                         >  2:457006/1‑141 (MQ=255)                                                                                                                                     ccattttttttcCCGCCAAAAAAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGC‑TGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCa                                <  1:97543/133‑1 (MQ=255)                                                                                                                                     ccAGTTTTTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGC‑TGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCgcgc                       <  2:1028557/149‑1 (MQ=255)                                                                                                                                     ccAGTTATTTTTCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGC‑TGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCt                      <  2:41166/150‑1 (MQ=255)                                                                                                                                       agtttttttcCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGC‑TGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTaa                    <  1:322696/145‑1 (MQ=255)                                                                                                                                         cTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGGGAGAG‑AAAAAGCTTTTAAGCCGTCCCGTTTTTTGGGCATCGC‑GGCTGGGGAGAAAATGGGAAAGGAAGGGGGGGGGATAAACTCCCGAACCgcgcccatt                  >  2:602884/1‑145 (MQ=255)                                                                                                                                              ttcccgccgAAAAAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGC‑TGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGtt             <  1:494125/147‑1 (MQ=255)                                                                                                                                                     cgcAACAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGGAAGAG‑AAAAAAAATTAAAACCCCCCTTTTTTGTGGGGGACGC‑TGCCGGGAACAAAGGGGGAAGGGGAGGGGGGGGGAGCAACTCCAGAAACCCGCCCACTGAGGTTGCCTcc      >  1:930611/1‑149 (MQ=255)                                                                                                                                                         acaaAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGGGAGAGAAAAAAAATTTAAACCC‑TCATGTTTTGTGGGAAACGC‑TGCTGGGTAAAAAATGGGAAGGGGAGGGGGGCGGATCAACTCCCCAACCACGCCAATTTAGTTTGCCCCAAtta  >  2:377105/1‑148 (MQ=255)                                                                                                                                                          |                                                                                                                                                        CTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAA‑TG‑CCTTC‑GCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGC‑TGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCGCCTCAATGA  >  NC_000913/357740‑358038

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 26 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑