Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	357,880	0	T	C	47.9%	55.3 / 15.5	48	K271E (AAA→GAA)	cynR	transcriptional activator of cyn operon; autorepressor
Reads supporting (aligned to +/- strand):  ref base T (18/7);  new base C (0/23);  total (18/30)
Fisher's exact test for biased strand distribution p-value = 7.04e-08
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

ACTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAAT‑GCCTT‑CGCGGCGG‑CTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGA‑AATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGT  >  NC_000913/357730‑358026                                                                                                                                                          |                                                                                                                                                    aCTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAAT‑GCCTT‑CGCGGCGG‑CTGTCTGCCAGCTAttttt                                                                                                                                                     <  1:114114/151‑1 (MQ=255)   tCGTAGGCCTGATAAGCGTAGCGCATCAGGAAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAAT‑GCCTT‑CGCGGCGG‑CTGTCTGCCAGCTATTTTTcc                                                                                                                                                   >  2:924010/1‑151 (MQ=255)    cGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAAT‑GCCTT‑CGCGGCGG‑CTGTCTGCCAGCTATTTTTccg                                                                                                                                                  >  2:682999/1‑151 (MQ=255)      tAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAAT‑GCCTT‑CGCGGCGG‑CTGTCTGCCAGCTATTTTTccgcc                                                                                                                                                >  1:837733/1‑151 (MQ=255)            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)                                                                                                                                               ccggtttttttcCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGA‑AATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACcgc             <  2:466942/140‑1 (MQ=255)                                                                                                                                               ccAGTTTTTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGA‑AATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACcgc             <  2:1091735/147‑1 (MQ=255)                                                                                                                                                       tttcCCGCCCCAAAAAACCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGA‑AATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGt  <  1:678474/150‑1 (MQ=255)                                                                                                                                                          |                                                                                                                                                    ACTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAAT‑GCCTT‑CGCGGCGG‑CTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGA‑AATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGT  >  NC_000913/357730‑358026

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: ‑