Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	357,890	0	C	A	55.1%	19.5 / 72.4	49	L267F (TTG→TTT)	cynR	transcriptional activator of cyn operon; autorepressor
Reads supporting (aligned to +/- strand):  ref base C (14/8);  new base A (0/27);  total (14/35)
Fisher's exact test for biased strand distribution p-value = 4.74e-07
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 2.73e-07

TGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAAT‑GCCTT‑CGCGGCGG‑CTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGA‑AATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCGCCTCA  >  NC_000913/357741‑358034                                                                                                                                                         |                                                                                                                                                  tGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAAT‑GCCTT‑CGCGGCGG‑CTGTCTGCCAGCTATTTTTCCGCCGcaac                                                                                                                                                   >  1:319076/1‑150 (MQ=255)   aTAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAAT‑GCCTT‑CGCGGCGG‑CTGTCTGCCAGCTATTTTTCCGCCGCAACaaa                                                                                                                                                <  1:101915/151‑1 (MQ=255)     aaGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAAT‑GCCTT‑CGCGGCGG‑CTGTCTGCCAGCTATTTTTCCGCCGCAACaaaa                                                                                                                                               <  2:421908/150‑1 (MQ=255)     aaGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAAT‑GCCTT‑CGCGGCGG‑CTGTCTGCCAGCTATTTTTCCGCCGCAACAAAAc                                                                                                                                              <  1:1048721/151‑1 (MQ=255)        cGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAAT‑GCCTT‑CGCGGCGG‑CTGTCTGCCAGCTATTTTTCCGCCGCAACAAAAccgc                                                                                                                                           <  2:945008/151‑1 (MQ=255)        cGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAAT‑GCCTT‑CGCGGCGG‑CTGTCTGCCAGCTATTTTTCCGCCGCAACAAAAccgc                                                                                                                                           <  1:919875/151‑1 (MQ=255)         gTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAAT‑GCCTT‑CGCGGCGG‑CTGTCTGCCAGCTATTTTTCCGCCGCAACAAAAccgcc                                                                                                                                          <  1:547515/151‑1 (MQ=255)          tAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAAT‑GCCCT‑CGCGGCGG‑CTGTCTGCCAGCTATTTTTCCGCCGCAACAAAAccgccg                                                                                                                                         >  2:46176/1‑151 (MQ=255)              gcATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAAT‑GCCTT‑CGCGGCGG‑CTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTtct                                                                                                                                     >  2:1196396/1‑151 (MQ=255)                   aGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAAT‑GCCTT‑CGCGGCGG‑CTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTcc                                                                                                                                 >  1:670861/1‑150 (MQ=255)                       aaTTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAAT‑GCCTT‑CGCGGCGG‑CTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCa                                                                                                                                >  2:1188389/1‑147 (MQ=255)                          tCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAAT‑GCCTT‑CGCGGCGG‑CTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTgg                                                                                                                         >  1:539844/1‑151 (MQ=255)                            cAGCCGCAGCCTTGTGTCGGCGGCTCCGGTTTTTCTTCCCCCCCAACACCCGCCTTTTTTCCCACCGCCTTGTCAAAAAAT‑GCTTC‑CGGGGGGG‑CTGTCTGCCAGCTTTTTTCCCGCCGAAACAAAACCGCCGTTCTCTCCAGTAGTGGCg                                                                                                                       <  1:1241281/151‑1 (MQ=255)                              gCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAAT‑GCCTT‑CGCGGCGG‑CTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCggg                                                                                                                     >  2:202984/1‑151 (MQ=255)                               ccGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAAT‑GCCTT‑CGAGGCGG‑CTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTgg                                                                                                                         >  2:147328/1‑146 (MQ=255)                                 gCAGTCGTGTGCCAGCGGCTGCCGTGATTCATTCCCGCCACCAACCGCGCTTTTACCCACCGCAATGTAAAAAATT‑CCCTT‑CGGGGCGG‑TGGTCTGCAAGCTTTTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGc                                                                                                                        <  1:259221/145‑1 (MQ=255)                                  cAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAAT‑GCCTT‑CGCGGCGG‑CTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCggggggg                                                                                                                 >  2:1191316/1‑148 (MQ=255)                                    gACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAAT‑GCCTT‑CGCGGCGG‑CTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCggg                                                                                                                     >  2:122139/1‑145 (MQ=255)                                      cttgtgTCGGCGCCTCCCGTGTTTCTTTCCCCCCAACACCCGCCCTTTTACCCACCGCCATGTAAAAAAAT‑GCTTC‑CGGGGCGG‑TTGTCTCCCAGTTTTTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAag                                                                                                                <  2:765791/146‑1 (MQ=255)                                        tgtgCCAGCGCCTCCCGGGTTTCATTCCCGCCAACACCCGCGCTTTTACCACCCGCTTTGTGAAAAAAT‑CCCTG‑CCGGGCGG‑TTGTTTGCCATTTATTTTTCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAgaga                                                                                                             <  1:1039552/149‑1 (MQ=255)                                         gtgtCGGCGGCTCCGGTGTTTCTTCCCCCCCAACACCCGCCCTTTTACCCACCCCCATGTAAAAAAAT‑CCCTC‑CGCGGCGG‑CTGTCGGCCGGTTTTTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGa‑a                                                                                                           <  2:739909/149‑1 (MQ=255)                                             cAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAAT‑GCCTT‑CGCGGCGG‑CTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCggggggag                                                                                                                >  2:142814/1‑137 (MQ=255)                                              aGCGGCTACCGTGATTCATTCCCGCCACCACCCCCCAATTTACCCAACCCAGTGTCCAAAAAT‑GCCTC‑GGCGGGGG‑GTGTCTCCCAGTTTTTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGA‑AATAGc                                                                                                      <  1:277412/149‑1 (MQ=255)                                                 gcccacgttttttattttCCGCCAAAACCCGCCTATTAACCCACCCCCGTGGGAAAAATT‑GCCTG‑CGCGGCGG‑CTGTCGCCCAGTTTTTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGA‑AATAGCTTTaa                                                                                                 <  1:775220/136‑1 (MQ=255)                                                      cggTGATTCTTTCCCCCAAACACCCGCGCTTTTACCCACCCCCATGTAAAAAAAT‑CCTTC‑CGCGGGGG‑CTGCCGGCCAGTTTTTTTCCCGCCAAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGA‑AATAGCtt                                                                                                    <  2:153537/141‑1 (MQ=255)                                                      ccgactttCTTTCCCCCCAACACCCGCGATTTTACCCACCGCAATGGGAAAAACT‑GCCTC‑CGGGGCGT‑TTGTCCCCCAGTTTTTTTCCCCCCCCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGA‑AATAGCTTTAAGc                                                                                               <  1:841782/142‑1 (MQ=255)                                                        gTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAAT‑GCCTT‑CGCGGCGG‑CTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGGAGAGG‑AAAAACGTTAAAcccc                                                                                            >  1:1034943/1‑148 (MQ=25)                                                              cATTCCCCCCAACACCCGCCATTTTACCCAACGCCAGGTAAAAAAAT‑CCCTG‑CGCGGCGG‑CTGTCGCCCAGTTATTTTCCCGCCCAAAAAAAGCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGA‑AATAGCTTTAAGCCCGTCAt                                                                                        <  1:1119083/147‑1 (MQ=255)                                                                   cccccAACACCCGCGCTTTTACCCAACGCCATGTGAAAAAAT‑GCCTC‑CGCGGGGG‑CTGTCTGCCAGTTTTTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGA‑AATAGCTTTAAGCCCGTCAtgtt                                                                                     <  1:673574/142‑1 (MQ=255)                                                                   ccGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAAT‑GCCTT‑CGCGGCGG‑CTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCCACAGAGAAAAGGTTTAAGccaacacgttt                                                                                     >  1:183861/1‑137 (MQ=25)                                                                    cGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAAT‑GCCTT‑CGCGGCGG‑CTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGAAAGGA‑AAAAAAGTTAAAACCGGCCTGTTGTGTggg                                                                              >  1:1174377/1‑150 (MQ=25)                                                                            cccGCGCTTTTCCCCACCCCCATGT‑AAAAAAT‑TCCTTCCGCGGGGG‑TTGTCGGCCAGTTATTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGA‑AATAGCTTTAAGCCCGTCATGTTGTGTGGCAAt                                                                           <  2:1136590/145‑1 (MQ=255)                                                                             ccGCGCTTTTGTCAATCGCGATGTAAAAAATT‑GTCTT‑GTGGGGGC‑CTTTCTCCCACTTTTTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGA‑AATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCgctgc                                                                     <  1:640974/151‑1 (MQ=255)                                                                              ccgtcATTTACCCACCGCAATGTGAAAAATT‑CCCTT‑CG‑GGCGGTCTGTCTGCCAGCTTTTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGA‑AATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCgctgct                                                                    <  1:721698/147‑1 (MQ=255)                                                                                    tttaccaacccccATGTGAAAAAAT‑GCCTC‑CGCGGCGG‑TTTTCTGCCGGTTTTTTTCCCGCCCCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGA‑AATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTaa                                                               <  1:139909/139‑1 (MQ=255)                                                                                     ttATCCAACGCCATGTGCAAAAAT‑GCCTT‑CGCGGCGG‑CTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGAAAAGA‑AAAAGATTTTTAACCCTCATGTTGTGTggggat                                                                           >  1:134161/1‑133 (MQ=25)                                                                                         ccaccccctttcaaaaaatT‑CCCTC‑CGGGGCGG‑TTGTCGGCCAGTTTTTTTCCCGCCGCAAAAAACCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGA‑AATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACaa                                                            <  2:834130/134‑1 (MQ=255)                                                                                         ccacccccATGTAAAAAAAT‑GCCTC‑CGCGGCGG‑CTGTCTGCCATTTTTTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGA‑AATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACa                                                             <  2:941705/141‑1 (MQ=255)                                                                                                       aaaaaG‑CCCTC‑CGCGGGGG‑CTTTCTGCAATTTTTTTTCCCACCACAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGA‑AATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAg                                              <  2:1062380/148‑1 (MQ=255)                                                                                                        aaaaTGGCCTC‑CGGGGGGG‑CTGTCTGCCACTTTTTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGA‑AATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTg                                            <  2:393482/150‑1 (MQ=255)                                                                                                                cctgggcggcgC‑CTGTCTGCCAGTTATTTTCCCCCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGA‑AATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTgcggcg                                       <  1:182871/143‑1 (MQ=255)                                                                                                                     ggggcgg‑cGGTCTGCCAGTTTTTTTCCCCCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGA‑AATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAAt                                    <  1:1093017/144‑1 (MQ=255)                                                                                                                       ggcgg‑cTGTCGGCCAGTTTTTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGA‑AATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTcc                             <  2:103832/151‑1 (MQ=255)                                                                                                                        ggcgcttgccTGCCAGTTTTTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGA‑AATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAg                                 <  2:343110/138‑1 (MQ=255)                                                                                                                                   ccctgctttttccccgccaCAACAAAGCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGA‑AATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCt                  <  2:1175834/138‑1 (MQ=255)                                                                                                                                    ccggtttttttcCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGA‑AATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACcgc                     <  2:466942/140‑1 (MQ=255)                                                                                                                                    ccAGTTTTTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGA‑AATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACcgc                     <  2:1091735/147‑1 (MQ=255)                                                                                                                                            tttcCCGCCCCAAAAAACCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGA‑AATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGt          <  1:678474/150‑1 (MQ=255)                                                                                                                                             ttccccccgaAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGA‑AATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGtt         <  1:156286/144‑1 (MQ=255)                                                                                                                                                  cccccaaaaaAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGA‑AATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCGCCt    <  1:479338/146‑1 (MQ=255)                                                                                                                                                   ccgaAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGA‑AATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCGCCTCa  <  1:608467/151‑1 (MQ=255)                                                                                                                                                         |                                                                                                                                                  TGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAAT‑GCCTT‑CGCGGCGG‑CTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGA‑AATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCGCCTCA  >  NC_000913/357741‑358034

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑