Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	357,880	0	T	C	44.0%	61.8 / 14.8	50	K271E (AAA→GAA)	cynR	transcriptional activator of cyn operon; autorepressor
Reads supporting (aligned to +/- strand):  ref base T (21/7);  new base C (0/22);  total (21/29)
Fisher's exact test for biased strand distribution p-value = 2.63e-08
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAAT‑GCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTG  >  NC_000913/357735‑358023                                                                                                                                                   |                                                                                                                                                  tAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAAT‑GCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTccgcc                                                                                                                                              >  2:668400/1‑151 (MQ=255) tAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAAT‑GCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTccgc                                                                                                                                               >  2:185842/1‑150 (MQ=255)  aGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAAT‑GCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTccgcc                                                                                                                                              <  1:740037/150‑1 (MQ=255)     ccTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAAT‑GCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGca                                                                                                                                           >  2:55470/1‑150 (MQ=255)            aGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAAT‑GCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAA‑cc                                                                                                                                  <  1:1071556/151‑1 (MQ=255)             gCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAAT‑GCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAA‑ccg                                                                                                                                 <  1:326658/151‑1 (MQ=255)                  gcgcATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAAT‑GCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAA‑CCGCCGtt                                                                                                                            >  2:656120/1‑151 (MQ=255)                   cgcATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACACCCGCGCATTTATCCAACGCCATGTGCAAAAAT‑GCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAA‑ccgccg                                                                                                                              <  1:902048/148‑1 (MQ=255)                   cgcATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTCCCGCCAACACCCGCGCATTTATCCAACGCCACGTGCAAAAAT‑GCTTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAA‑ccgccg                                                                                                                              <  2:191938/148‑1 (MQ=255)                              aTTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAAT‑GCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAA‑CCGCCGTTCTCTCCagtag                                                                                                                 >  1:762804/1‑150 (MQ=255)                                       gCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAAT‑GCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAA‑CCGCCGTTCTCTCCAGTAGTGGCgggg                                                                                                         >  1:559615/1‑149 (MQ=255)                                        cAGACCTGTGTCAGCGGCTACCGTGATTCCTTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAAT‑GCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAA‑CCGCCGTTCTCTCCAGTAGTGGCtgggtg                                                                                                       >  1:160806/1‑148 (MQ=255)                                         aGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCCTTTATCCAACGCCATGTGCTAAAAT‑GCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAA‑CCGCCGTTCTCTCCAGTAGTGGCgggg                                                                                                         >  2:651744/1‑147 (MQ=255)                                         aGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAAT‑GCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAA‑CCGCCGTTCTCTCCAGTAGTGGCggggg                                                                                                        >  1:36967/1‑147 (MQ=255)                                            ccTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAAT‑GCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAA‑CCGCCGTTCTCTCCAGTAGTGGCgggg                                                                                                         >  1:664113/1‑144 (MQ=255)                                            ccTGTGTCAGCGGCTACCGTGATTCATTCCCCCCAACACCCGCGCTTTTACCCAACGCCATGTGAAAAAAT‑GCCTTCGCGGCGGCTGTCTGCCAGCTTTTTTCCCGCCGCAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAga‑ga                                                                                                 <  1:934100/151‑1 (MQ=21)                                               gtgtCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAAT‑GCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGGAAGA‑Gaaa                                                                                               >  2:179581/1‑150 (MQ=255)                                                tgtCGGCGGCTCCCGTGTTTCTTTCCCCCCAACACCCGCGATTTTACCCACCGCCTTGTGAAAAAGT‑GCCTTCGGGGGGGCTTTCTCCCAGTTTTTTTCCCCCCGAAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAAt                                                                                              <  1:646027/150‑1 (MQ=255)                                                 gtCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAAT‑GCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGGAAGG‑Gaaaaa                                                                                             >  1:368806/1‑148 (MQ=255)                                                 ggctgggcttccggtgtTTCTTTTCCGCAAAAACCCGCGATTTTACCAAACCCTTTGT‑CAAAAATGGCCTGCGGGGCGGCTGCCTCCAAGTTTTTTTCCCGCCCAAACAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATa                                                                                             <  1:588702/137‑1 (MQ=255)                                                     gCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAAT‑GCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGGGAGA‑Ggaaaaacatt                                                                                        >  1:684269/1‑144 (MQ=255)                                                      cGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAAT‑GCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAA‑CCGCCGTTCTCTCCAGTAGTGGCggggggaggggaa                                                                                                >  1:155204/1‑134 (MQ=255)                                                       ggCTACCGTGATTCATTCCCGCCAACACCCGCGCATTTACCCAACGCCATGTGAAAAAAT‑GCCTCCGCGGCGGCTGTCTGCCAGCTATTTTCCCGCCGCAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGCttt                                                                                        <  1:109962/149‑1 (MQ=25)                                                            ccGTGTTTCTTTCCCCCAAACACCCGCGCTTTTACCCACCCCCTGGTGAAAAAAG‑CCCTCCGGGGCGGCTGTCGGCCAGTTTTTTTCCCGCCGCAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGCTTTAAg                                                                                     <  1:361824/147‑1 (MQ=255)                                                            ccGTGTTTCATTCCCGCAAACACCCGCGCATTTACCCAACGCCATGTGCAAAAAT‑CCCTTCGCGGCGGCTGTCTCCCATTTTTTTTCCCGCCGCAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGCtt                                                                                         <  1:978662/143‑1 (MQ=255)                                                              gTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAAT‑GCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCGAGA‑Gaaaaaaactttaaac                                                                                   >  1:429261/1‑135 (MQ=255)                                                               tgtttCATTCCCCCCAACCCCCGCGCTTTTATCCACCCCCATGTCAAAAAAT‑GCCTTCGCGGCGTCTTTCTCCCATTTTTTTTCCCGCCAAAACAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGCTTTAAGccc                                                                                  <  2:656791/144‑1 (MQ=255)                                                               tGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAAT‑GCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGGCAGA‑Gaaaaaaattttaa                                                                                     >  1:272494/1‑134 (MQ=25)                                                                      ttccccccAACAACCGCGCTTTTACCCACCCCCTTGTGAAAAAAG‑GCCTCCGCGGCGGCTGTCTGCCAGTTTTTTTCCCGCCGCAACAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGCTTTAAGCCCGt                                                                                <  1:884471/136‑1 (MQ=255)                                                                      ttcccGCCAACACCCGCGCTTTTACCCACCGCCATGTGAAAAAAT‑GCCTTCGCGGGGGCTGTCGCCCAGTTTTTTTCCCGCCGAAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGCTTTAAGCCCGTCAtgtt                                                                          <  1:464731/145‑1 (MQ=255)                                                                              aacaacCGCGCATTTAACAAACGCAATTTAAAAAAAC‑CCCTTGGCGGGGGCTGCCGGCCAGCTTTTTTCCCGCCGCAAAAAAC‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAAt                                                                <  1:592215/150‑1 (MQ=255)                                                                                  ccccccctttttcccAACCCCATGTGAAAAACC‑CCCTTCGCGGCGCGTGTCCGCCACCATTTTTCCCCCCGAAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCgct                                                            <  1:283877/137‑1 (MQ=255)                                                                                      cgcTTTTACCCAACCCCATGTGAAAAAAT‑GCCTTCGCGGCGGCTGTCTCCCAGCTTTTTTCCCGCCGCAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGctgctg                                                        <  1:685844/150‑1 (MQ=255)                                                                                         aTTTATCCAACGCCATGTGCAAAAAT‑GCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAAA‑GAAAAAAATTTTAAACCCTCCTTTTGTTTGGGGATCgctgc                                                          >  1:1050610/1‑145 (MQ=25)                                                                                          tttaccaaccGCCAGGTCAAAAAAG‑CCCTCCGGGGCGCCGTTCTGCCAGTTTTTTTCCCGCCGCAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCgctgct                                                         <  1:836948/136‑1 (MQ=255)                                                                                            tATCCAACGCCATGTGCAAAAAT‑GCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCGAGA‑GAAAAAACTTTTAGCACCTCCAGTTGTGTgggggacgccg                                                           >  2:298851/1‑132 (MQ=25)                                                                                                cAACGCCATGTGCAAAAAT‑GCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGGGAGAGGAAAAAAATTTAA‑ACCGCCACGGTGTGTGGGGATCGCTGCTGGGTACaaaat                                              >  1:766672/1‑147 (MQ=21)                                                                                                 aacccattgtgCAAAAAT‑GCTTCCGGGGCGGCTTTCTCCCAGTTTTTTTCCCGCCGCAACAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACa                                                  <  1:258165/138‑1 (MQ=255)                                                                                                   cgcctgttgCAAAAAT‑CCCTTCGCGGCGGCTGTCTCCCAG‑TTTTTTTCCCCCCCAAAAAAACCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGaa                                          <  1:503908/144‑1 (MQ=255)                                                                                                     ccttgtaaaaaatT‑CCCTTCGGGGCGGCTGTCCGCCAGCTTTTTTCCCGCCGAAACAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAg                                        <  1:419157/143‑1 (MQ=255)                                                                                                              aaaaTGGCCTTCGGGGCGGCTTTCGCCCAGTTTTTTTCCCGCCACAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGaaa                                         <  2:677525/142‑1 (MQ=255)                                                                                                              aaaaT‑GCCTCCGCGGCGGCGGTCCGCCAGTTTTTTTCCCGCCGCAAAAAAC‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTgcg                               <  2:1016606/151‑1 (MQ=255)                                                                                                                aaT‑GCCTTCGCGGCGGGTTTCTGCCACCTTTTTTTCCCCCGAAACAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTgcggc                             <  1:840926/151‑1 (MQ=255)                                                                                                                aaT‑GCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGGGAGA‑GGAAAAACTTTAAAACCCTCATGTTGTGTGGGGATTGCTGCTGGTGACAAAGTGGGAAGGGGAgggggg                              >  1:682057/1‑145 (MQ=255)                                                                                                                     ccTCCGGGGCGCCTTTCTGCAATTTATTTTCCCGCCCCAACAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGa                           <  1:474364/149‑1 (MQ=255)                                                                                                                     ccTCCGCGGCGGCTTTCTGCCAGCTTTTTTCCCCCCGCAACAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGaa                          <  1:179945/150‑1 (MQ=255)                                                                                                                            ggcggcTGTCTGCCATTTTTTTTCCCGCCGCAACAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCt                    <  1:679222/149‑1 (MQ=255)                                                                                                                            ggcggcTGTCTGCCAGCTATTTTTCCGCCGCAACAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGGCAGA‑GGAATAACTTTTAGACCCTCATTTTTTGTGTGAAAAAGGGCTTGTGACAATGGGGGGAGGGAGGTgcgggggaacatcac                   >  2:230825/1‑139 (MQ=255)                                                                                                                                   gtcgcccAGCTTTTTTCCCGCCGCAACAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAAcc            <  1:33307/145‑1 (MQ=255)                                                                                                                                    tctcCCAGCTTTTTTCCCGCCGCAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGaa              <  1:445165/147‑1 (MQ=255)                                                                                                                                             ttttttcCCGCCGAAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTg  <  1:22311/148‑1 (MQ=255)                                                                                                                                                   |                                                                                                                                                  TAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAAT‑GCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTG  >  NC_000913/357735‑358023

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑