Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	357,875	0	A	T	43.1%	70.3 / 17.9	51	N272K (AAT→AAA)	cynR	transcriptional activator of cyn operon; autorepressor
Reads supporting (aligned to +/- strand):  ref base A (21/8);  new base T (0/22);  total (21/30)
Fisher's exact test for biased strand distribution p-value = 4.30e-08
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GAACTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAAT‑GCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACC  >  NC_000913/357728‑358013                                                                                                                                                     |                                                                                                                                             gAACTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAAT‑GCCTTCGCGGCGGCTGTCTGCCAGCTAttt                                                                                                                                           <  1:943365/151‑1 (MQ=255)        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)                                                                                                                                                     |                                                                                                                                             GAACTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAAT‑GCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACC  >  NC_000913/357728‑358013

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: ‑