Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	357,880	0	T	C	43.8%	56.0 / 17.9	48	K271E (AAA→GAA)	cynR	transcriptional activator of cyn operon; autorepressor
Reads supporting (aligned to +/- strand):  ref base T (20/7);  new base C (0/21);  total (20/28)
Fisher's exact test for biased strand distribution p-value = 8.13e-08
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAA‑TG‑CCTTC‑GCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGC‑TGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATT  >  NC_000913/357733‑358022                                                                                                                                                       |                                                                                                                                                 cGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAA‑TG‑CCTTC‑GCGGCGGCTGTCTGCCAGCTATTTTTccg                                                                                                                                               >  1:126578/1‑151 (MQ=255) cGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAA‑TG‑CCTTC‑GCGGCGGCTGTCTGCCAGCTATTTTTcc                                                                                                                                                <  2:793563/150‑1 (MQ=255)  gTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAA‑TG‑CCTTC‑GCGGCGGCTGTCTGCCAGCTATTTTTccgc                                                                                                                                              <  2:863071/151‑1 (MQ=255)        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‑GGGGCAAgaga                                                                                                 <  2:288146/149‑1 (MQ=255)                                                 gtgcaaGCGGCTACCGTGTTTCATTCCCGCAAACACCCGCGCATTTCCCCAACGCCATGTGAAAAAA‑TG‑CTTTC‑GGGGCGGCTGTCTGCCAGTTTTTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGaa                                                                                                <  2:425476/144‑1 (MQ=255)                                                    tCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAA‑TG‑CCTTC‑GCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGGGAGAGaa                                                                                                >  1:830618/1‑146 (MQ=255)                                                        cGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAA‑TG‑CCTTC‑GCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGGGAGAGaaaaaacatt                                                                                        >  2:799937/1‑143 (MQ=255)                                                         ggcacccgtatttCTTTCCCCCCACCACCCCCGCATTTACCCACCGCCATGTGCAAAAA‑TC‑CTTCC‑GGGGGGGCGGTCGCCCAGTTTTTTTCCCGCCAAAAAAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGCt                                                                                          <  1:978377/136‑1 (MQ=255)                                                         ggCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAA‑TG‑CCTTC‑GCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGGAAGAGaaaaaaactt                                                                                        >  2:246535/1‑142 (MQ=255)                                                         ggCTACCGTGATTCATTCCCGCAAACCCCCGCACATTTACCCACCCCAATTTGAAAAAA‑TC‑CCTCC‑GGGGCGCCTGTCTCCCAGCTATTTTCCCCCCCCAAAAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGCt                                                                                          <  2:840700/147‑1 (MQ=255)                                                          gCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAA‑TG‑CCTTC‑GCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGACGTTCTCTCCAGTAGTGGC‑GGGGCCAGGGAAAAAACATTaa                                                                                      >  1:704758/1‑150 (MQ=25)                                                             cccttatttCATTCCCCCCAACACCCGCGCATTTACCCAACCCCAGGTGAAAAAA‑TC‑CCGTC‑GGGGCGGTTTGCTCCCAGCTTTTTTCCCGCCAAAAAAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGCTTTAAGcc                                                                                   <  1:716068/143‑1 (MQ=255)                                                                 ttatccatccccGCAAACACCCGCGCATTTCCCCACCGCCATGTACAAAAA‑TG‑CTTCC‑GCGGCGGCTTTCTGCCAGTTATTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAg                                                                                            <  1:979305/127‑1 (MQ=255)                                                                        ttcccGCAAACACCCGCGTTTTTCTCCCCCGCCATGT‑AAAAAA‑TGCCCTCC‑GCGGCGGTTTTCGGCCATCTTTTTTCCCGCCAAAAAAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGCTTTAAGCCCGTCAtgttg                                                                         <  1:672539/146‑1 (MQ=255)                                                                            cccaaccccccGCGCTTTTACCCACCCCCAT‑TGAAAAAATTG‑CCTCC‑GGGGCGGCTGTCTGCCAGTTTTTTTCCCGCCAAAAAAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGc                                                                   <  1:731578/142‑1 (MQ=255)                                                                            cGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAA‑TG‑CCTTC‑GCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGCAAGAGAAAAAACATCAAGccgctactttttgggg                                                                     >  1:949000/1‑136 (MQ=25)                                                                                     ccGCGCTTTAACCCACCCCCTTGTGAAAAAA‑TG‑CCTCC‑GGGGCGGCTGTTTCCCAGCTATTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCgc‑t                                                           <  2:716879/149‑1 (MQ=255)                                                                                     ccGCCCTTTTACCCACCGCCCTTTGAAAAAA‑TC‑CCTGG‑GCGGCGGTTGTCGGCCGTCTTTTTTTCGCCCACAAAAAAGCCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCgc‑tg                                                          <  1:280338/150‑1 (MQ=255)                                                                                            tttATCCAACGCCATGTGCAAAAA‑TG‑CCTTC‑GCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGGAAGAGAAAAAACTTTTAATCCCTCCTGTTGTGTGGGGATCGC‑TGCTgg                                                      >  2:754043/1‑147 (MQ=37)                                                                                                tCCAACGCCATGTGCAAAAA‑TG‑CCTTC‑GCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGGCCGGGAAAAAACATTTAACCCCTCCTGTTGTGTGGGGATCGC‑GGCTggggaaaa                                                >  1:199130/1‑143 (MQ=25)                                                                                                   aaCGCCATGTGCAAAAA‑TG‑CCTTC‑GCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGGGAGAGAAAAAAATTTTAACCCCCCCTGTTTTGTGGGGAACGCTTCCTGGTAAAAAttgg                                            >  2:787896/1‑148 (MQ=21)                                                                                                     cGCCATGTAAAAAAA‑TG‑CTTGC‑GCGGGCGTTGGTTCCGAGATTTTTTCCCGCCTAAACAACCCCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGC‑TGCTGGTAAc                                                  <  1:692731/142‑1 (MQ=255)                                                                                                               aaaat‑TG‑CCTTC‑GGGGCGTTTGTCGGCCAGTTTTTTTCCCGCCACAAAAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGC‑TGCTGGTAACAATGTGGAAAGGGAAGTg                                <  1:308419/150‑1 (MQ=255)                                                                                                                aaaa‑TG‑CTTTG‑GGGGGGCCTGCCGGCAAGCTATTTTTCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGC‑TGCTGGTAACAATGTGGAAAGGGAAGTgcg                              <  2:49146/151‑1 (MQ=255)                                                                                                                aaaa‑TG‑CCTTC‑GCGGCGGTTGTCGCCCAGCTTTTTTCCCCCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGC‑TGCTGGTAACAATGTGGAAAGGGAAGTgcg                              <  2:489569/151‑1 (MQ=255)                                                                                                                    agggctttC‑GGGGCGCCTGTCTGCCAGTTTTTTTCCCGCCAAAAAAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGC‑TGCTGGTAACAATGTGGAAAGGGAAGTgcggc                            <  2:326551/145‑1 (MQ=255)                                                                                                                        ctttC‑GCGGGGCCTGTCTGCCAGTTTTTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGC‑TGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGa                          <  2:48216/147‑1 (MQ=255)                                                                                                                        ccTCC‑GCGGCGGCTGTCTGCCAGTTTTTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGC‑TGCTGGTAACAATGTGGAAAGGGAAGTgcggcg                           <  2:100236/148‑1 (MQ=255)                                                                                                                              ggggcggcTGTCTCCCGGTTATTTTCCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGC‑TGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGa                          <  2:488350/142‑1 (MQ=255)                                                                                                                                          tGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGGAAGAGAAATAACTTTTTACCCCGCCTCTTGTGTGGTGAACCC‑TGCTGGTTACAAAGTGGGAAAGGGAGGGGGGCGGATCACCTccccaaacgc         >  2:457006/1‑141 (MQ=255)                                                                                                                                            ccattttttttcCCGCCAAAAAAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGC‑TGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCa                <  1:97543/133‑1 (MQ=255)                                                                                                                                            ccAGTTTTTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGC‑TGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCgcgc       <  2:1028557/149‑1 (MQ=255)                                                                                                                                            ccAGTTATTTTTCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGC‑TGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCt      <  2:41166/150‑1 (MQ=255)                                                                                                                                              agtttttttcCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGC‑TGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTaa    <  1:322696/145‑1 (MQ=255)                                                                                                                                                cTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGGGAGAGAAAAAGCTTTTAAGCCGTCCCGTTTTTTGGGCATCGC‑GGCTGGGGAGAAAATGGGAAAGGAAGGGGGGGGGATAAACTCCCGAACCgcgcccatt  >  2:602884/1‑145 (MQ=255)                                                                                                                                                       |                                                                                                                                                 CGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAA‑TG‑CCTTC‑GCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGC‑TGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATT  >  NC_000913/357733‑358022

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: ‑