Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	357,890	0	C	A	40.0%	41.0 / 20.1	40	L267F (TTG→TTT)	cynR	transcriptional activator of cyn operon; autorepressor
Reads supporting (aligned to +/- strand):  ref base C (16/8);  new base A (0/16);  total (16/24)
Fisher's exact test for biased strand distribution p-value = 1.22e-05
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCA‑TGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGCTTTAAGCCCGTCATGTTGT‑GTGGCAATCGCT‑G‑CTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCGCC  >  NC_000913/357740‑358031                                                                                                                                                         |                                                                                                                                                   cTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCA‑TGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGcaac                                                                                                                                                    >  2:824259/1‑151 (MQ=255)  tGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCA‑TGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGcaac                                                                                                                                                    >  2:861452/1‑150 (MQ=255)    aTAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCA‑TGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGcaacaa                                                                                                                                                  >  2:398199/1‑150 (MQ=255)    aTAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCA‑TGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGcaacaa                                                                                                                                                  >  2:707535/1‑150 (MQ=255)    aTAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCA‑TGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACaaa                                                                                                                                                 <  2:893521/151‑1 (MQ=255)      aaGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCA‑TGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAA‑c                                                                                                                                              <  2:498382/151‑1 (MQ=255)      aaGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCA‑TGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAA‑c                                                                                                                                              >  1:654664/1‑151 (MQ=255)      aaGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCA‑TGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAA‑c                                                                                                                                              >  2:637613/1‑151 (MQ=255)               gcATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCA‑TGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAA‑CCGCCGTtct                                                                                                                                     >  1:205400/1‑151 (MQ=255)                            ccAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCA‑TGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAA‑CCGCCGTTCTCTCCAGTAGTGGc                                                                                                                        >  2:741005/1‑151 (MQ=255)                             cAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCA‑TGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAA‑CCGCCGTTCTCTCCAGTAGTGGCg                                                                                                                       >  2:686184/1‑151 (MQ=255)                               gCCGCAGACCTGTGTCAGCGGCTACCGCGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCA‑TGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAA‑CCGCCGTTCTCTCCAGTAGTGGCgg                                                                                                                      >  2:891424/1‑150 (MQ=255)                                ccGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCA‑TGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAA‑CCGCCGTTCTCTCCAGTAGTGGCggg                                                                                                                     >  1:125471/1‑150 (MQ=255)                                ccGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCA‑TGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAA‑CCGCCGTTCTCTCCAGTAGTGGCggcg                                                                                                                    >  2:790163/1‑149 (MQ=255)                                       ccTGTCTCCGCGCCTCCCTGGTTTCATTCCCCCCAACACCCGCGCTTTTCCCCAACGCCA‑TGTGCAAAAAGCCCTCCGCGGCGGCTTTCTGCCAGCTTTTTTC‑CCGCCGCAACGAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAaga‑g                                                                                                             <  1:777378/150‑1 (MQ=255)                                                gCGGCTCCCGTGATTCATTCCCCCCAACACCCGCGCATTTACCCAACGCCA‑TGTGAAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTTTTTTC‑CCGCCGCAACAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑Gaaa                                                                                                          <  2:723951/144‑1 (MQ=255)                                                    ctcccGTGATTCTTTCCCGCAAACACCCGCGCTTTTACCCAACGCCA‑TGGGCAAAATTGCTTCCGCGGGGGTTGCCTCCAATCTATTTTC‑CGGCCTCAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGCTTTa                                                                                                  <  2:316673/145‑1 (MQ=255)                                                    cTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCA‑TGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGGAAGA‑Gaaaaaaaattta                                                                                                 >  2:548917/1‑140 (MQ=255)                                                    cTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCA‑TGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCGAGG‑GAAAAAGCatt                                                                                                   >  1:560326/1‑147 (MQ=255)                                                           gATTCTTTCCCCCCAACACCCGCGCATTTACCCACCGCCA‑TGTGAAAAAATGCCTCCGCGGCGGCTTTCGGCCAGTTTTTTTC‑CCGCCGAAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGCTTTAAGCCCGt                                                                                           <  2:722835/148‑1 (MQ=255)                                                             ttCATTCCCGCCAACACCCGCGCATTTATCCAACGCCA‑TGTGAAAAAATGCCTTCGCGGCGGCTGTCTGCAAGTTTTTTTC‑CCGCCGCAACAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGCTTTAAGCCCGTCAtg                                                                                       <  2:493311/150‑1 (MQ=255)                                                                 tccccGCCACCACCCGCCCTTTTACCCACCCCCG‑TGTGAAAAAATCCCTCCGCGGCGGTTGTCTGCCGGTTTTTTTT‑CCGCCACAAAAAAC‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGCTTTAAGCCCGTCAtgtt                                                                                     <  1:856421/145‑1 (MQ=255)                                                                         aacaacCGCGCATTTATCCAACGCCA‑TGTGCAAACATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCGGGC‑GAAAAAGGTTTTAGACCGTCaccatgt                                                                                   >  1:1856/1‑136 (MQ=255)                                                                             accccgtcttttTCCCACCCCATTGTGAAAAAAGCCCTCGGCGGCGCCTTTCGCCCGGTTTTTTTC‑CCGCCGAAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGCTTTAAGCCCGTCATGTTGT‑GTGGCAATCgc                                                                       <  1:950685/142‑1 (MQ=255)                                                                                     tttACCCACCGCCA‑GTTAAAAAAATCCCTCCCCGGCGCCTGTCGGCCGGTTATTTTC‑CCGCCGAAAAAAAG‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGCTTTAAGCCCGTCATGTTGT‑GTGGCAATCGCT‑G‑CTGGTaa                                                            <  1:63580/150‑1 (MQ=255)                                                                                     tttACCCACCGCAT‑TGTGCAAAAATGCCTCCGCGGCGGTTGTCGCCCAGCTTTTTTC‑CCCCCGAAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGCTTTAAGCCCGTCATGTTGT‑GTGGCAATCgct‑g‑c                                                                  <  2:715078/144‑1 (MQ=255)                                                                                     tttACCCAACGCCA‑TGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGCTTTAAGCCCGTCATGTTGT‑GTGGCAATCGCT‑G‑CTGGTaa                                                            <  1:1001652/150‑1 (MQ=255)                                                                                      ttATCCAACGCCA‑TGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGGGGAA‑GGAATAAAGTTAAACACCTCCTGTTTT‑GTGGGAAGCGCC‑G‑CTggggac                                                           >  1:1077012/1‑146 (MQ=21)                                                                                            accGCCA‑TGTGAAAAAAGCCCTTCGGGGCGGCTGTCTGCCAGTTATTTTC‑CCGCCGCAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGCTTTAAGCCCGTCATGTTGT‑GTGGCAATCGCT‑G‑CTGGTAACAATGTgg                                                    <  2:384170/149‑1 (MQ=255)                                                                                              cGCCA‑TGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGGAAGAGGAAAAACTTTTAAACCCG‑CATTTTGTGGGGGAAATCgct‑gtggggaaaaagtg                                                       >  2:3107/1‑135 (MQ=21)                                                                                                   tggtcaaaaagTGCCTGCGGGGCGTCTGT‑TGGCAGGTTTTTTTCCCGCCAAAAAAAAG‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGCTTTAAGCCCGTCATGTTGT‑GTGGCAATCGCT‑G‑CTGGTAACAATGTGGaaa                                                 <  1:271803/142‑1 (MQ=255)                                                                                                     gggCAAAAAGCCCTGCCCGGGGGCGGCCTGCCGTTTATTTTT‑CCGCCACAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGCTTTAAGCCCGTCATGTTGT‑GTGGCAATCGCT‑G‑CTGGTAACAATGTGGAAAGGGa                                             <  1:947367/148‑1 (MQ=255)                                                                                                         aaaaaTGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGGGAGA‑GAAAAAAATTTTAACCCCCCATGTTTT‑GTGGGGAACGCTGG‑CTGGGAAAAAGTGGGAAAGGGaggg                                          >  2:1015588/1‑147 (MQ=255)                                                                                                                ccTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GGAAAAAATTTAAACCCCCCCTGTTGT‑GTGGGAATCGCT‑GCCTGGAAAAAATGGGGAAAGGGaggggggg                                      >  2:634899/1‑140 (MQ=255)                                                                                                                   tcggggcggggtccTGCAAGGTTTTTTC‑CCGCCGCAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGCTTTAAGCCCGTCATGTTGT‑GTGGCAATCGCT‑G‑CTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCa                               <  1:619656/137‑1 (MQ=255)                                                                                                                    cgcggcgttttgtgcccAGTTATTTGC‑CCG‑CGAAACAAAACCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGCTTTAAGCCCGTCATGTTGT‑GTGGCAATCGCT‑G‑CTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGc                             <  2:198893/136‑1 (MQ=255)                                                                                                                                cgccaagtttttttc‑CCGCCACAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGCTTTAAGCCCGTCATGTTGT‑GTGGCAATCGCT‑G‑CTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAAc                     <  1:917502/137‑1 (MQ=255)                                                                                                                                  tgccgtctttttgcccgccaCAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGCTTTAAGCCCGTCATGTTGT‑GTGGCAATCGCT‑G‑CTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGaa                      <  1:438318/131‑1 (MQ=255)                                                                                                                                   ccAGTTTTTTTC‑CCGCCGCAAAAAAC‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGCTTTAAGCCCGTCATGTTGT‑GTGGCAATCGCT‑G‑CTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACcgc                  <  1:174679/147‑1 (MQ=255)                                                                                                                                   ccAGTTTTTTTC‑CCGCCAAAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGCTTTAAGCCCGTCATGTTGT‑GTGGCAATCGCT‑G‑CTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACcgc                  <  1:930058/147‑1 (MQ=255)                                                                                                                                    cccgctttttgccccccgaAACAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGCTTTAAGCCCGTCATGTTGT‑GTGGCAATCGCT‑G‑CTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTa              <  1:58921/136‑1 (MQ=255)                                                                                                                                    cattttttttc‑CCGCCGAAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGCTTTAAGCCCGTCATGTTGT‑GTGGCAATCGCT‑G‑CTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGa                       <  1:959654/135‑1 (MQ=255)                                                                                                                                               cccgcccCAAAAAAC‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGCTTTAAGCCCGTCATGTTGT‑GTGGCAATCGCT‑G‑CTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCg    <  1:529124/149‑1 (MQ=255)                                                                                                                                                 cgccgcAACAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGGCAGA‑GAAAAAACATTTAAACCGTCCTGTTTT‑GTGGGAATCGCT‑G‑CTGGGAAAAAAATGGGAAGGGGAGGGGGGGGGAACAGCCCCCGAACCGCGCCAATTGAGGTTGcc  >  2:802678/1‑150 (MQ=255)                                                                                                                                                         |                                                                                                                                                   CTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCA‑TGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGCTTTAAGCCCGTCATGTTGT‑GTGGCAATCGCT‑G‑CTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCGCC  >  NC_000913/357740‑358031

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑