Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	357,890	0	C	A	54.0%	23.4 / 82.5	50	L267F (TTG→TTT)	cynR	transcriptional activator of cyn operon; autorepressor
Reads supporting (aligned to +/- strand):  ref base C (20/3);  new base A (1/26);  total (21/29)
Fisher's exact test for biased strand distribution p-value = 7.14e-10
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.28e-06

GTAGCGCATCAGGCAATTCCAG‑CCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑C‑GCGGCGGCTGTCTGC‑CAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑G‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCGCCTCAA  >  NC_000913/357749‑358035                                                                                                                                                  |                                                                                                                                                     gtggcgcCTCAGGCACCCCCAG‑CCGCACACTTCTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑C‑GCGGCGGCTGTCTGC‑CAGCTATTTTTCCGCCGCAACAAAAccgc                                                                                                                                              <  2:204757/147‑1 (MQ=18)   aGCGCATCAGGCAATTCCAG‑CCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑C‑GCGGCGGCTGTCTGC‑CAGCTATTTTTCCGCCGCAACAAAACCGCCGt                                                                                                                                           >  1:172929/1‑151 (MQ=255)        aTCAGGCAATTCCAG‑CCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑C‑GCGGCGGCTGTCTGC‑CAGCTATTTTTCCGCCGCAACAAAACCGCCGTtctct                                                                                                                                      >  2:178931/1‑151 (MQ=255)          cAGGCAATTCCAG‑CCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑C‑GCGGCGGCTGTCTGC‑CAGCTATTTTTCCGCCGCAAAAAAACCGCCGTTCTCTcc                                                                                                                                    >  2:878603/1‑151 (MQ=255)              cAATTCCAG‑CCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑C‑GCGGCGGCTGTCTGC‑CAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCagt                                                                                                                                 >  2:600340/1‑150 (MQ=255)                aTTCCAGCCCGCAGCCTTGGGTCGGGGGCTCCCGTATTTCATTCCCGCAAACACCCGCGATTTTACCCACCGCCATGTGAAAAAAGCCCTT‑C‑GCGGCGGTTGTCTGC‑AACTTTTTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCagtag                                                                                                                               <  1:495573/151‑1 (MQ=255)                    cAG‑CCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑C‑GCGGCGGCTGTCTGC‑CAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCagtag                                                                                                                               >  2:1051213/1‑146 (MQ=255)                    cAG‑CCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑C‑GCGGCGGCTGTCTGC‑CAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCg                                                                                                                          >  2:1174604/1‑151 (MQ=255)                     aG‑CCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑C‑GCGGCGGCTGTCTGC‑CAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCgg                                                                                                                         >  1:1059240/1‑151 (MQ=255)                            agcccTGTGTCGGCGGCTCCGGTGATTAATTCCCCCAAACACCCGCGCTTTTACCAACCCCCTTGTGAAAAAATCCCTC‑C‑GGGGCGGCTTTCTGC‑AAGCTTTTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCaa                                                                                                                    <  1:1080758/147‑1 (MQ=255)                             gACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑C‑GCGGCGGCTGTCTGC‑CAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCgggggcgg                                                                                                                   >  1:474873/1‑146 (MQ=255)                               ccgttgcaaGCGCCTCCCGTTTTTCTTTCCCCCCAACACCCGCGTTTTTACCAACCCCCATGTAAAAAAATGCCTC‑C‑GCGGCGGCTGTCCGC‑CAGTTTTTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAga‑g‑a                                                                                                              <  2:536388/143‑1 (MQ=255)                               ccTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑C‑GCGGCGGCTGTCTGC‑CAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCgggg                                                                                                                       >  1:1233706/1‑144 (MQ=255)                               ccTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑C‑GCGGCGGCTGTCTGC‑CAGCCATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCggggg                                                                                                                      >  2:199740/1‑144 (MQ=255)                                   tgtCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑C‑GCGGCGGCTGTCTGC‑CAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCggaggcagggaaaa                                                                                                             >  1:668473/1‑138 (MQ=255)                                      cAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑C‑GCGGCGGCTGTCTGC‑CAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGGAGA‑G‑gaaaaaa                                                                                                        >  2:1073099/1‑146 (MQ=255)                                          ggCTCCCGTGATTATTTCCCCCCAACACCCGCGCTTTTACCCACCCCCATGTGAAAAAATGCCTT‑C‑GGGGCGGCTGTCTGC‑CAGTTTTTTTCCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑G‑AAATAGCTTTa                                                                                                    <  1:717650/150‑1 (MQ=255)                                            cTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑C‑GCGGCGGCTGTCTGC‑CAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGGAGG‑G‑aaaaaaattt                                                                                                     >  1:642731/1‑140 (MQ=25)                                             tACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑C‑GCGGCGGCTGTCTGC‑CAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGAAGA‑G‑AAAAAAGTTTaaaac                                                                                                >  1:135761/1‑148 (MQ=255)                                              aCCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑C‑GCGGCGGCTGTCTGC‑CAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGTGCGAGA‑G‑gaaaaaacttttaacc                                                                                               >  2:720760/1‑138 (MQ=25)                                               cggTGATTATTTCCCGCCAACACCCGCGCTTTTACCAACCGCCTTGTGAAAAATTGCCTC‑C‑GGGGGGTCTGTCTGC‑CAGTTATTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑G‑AAATAGCTTTa                                                                                                    <  1:1037136/143‑1 (MQ=255)                                                     ttttttccctccAACCCCCGCGCTTTTACCCACCGCTAGGTAAAAAAATCCTTT‑C‑GGGGGGTCTTTCTCC‑CAGTTTTTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑G‑AAATAGCTTTAAGCCCGTCAt                                                                                          <  1:749146/139‑1 (MQ=255)                                                     ttCTTTCCCGCCAAAACCCGCGCTTTTACCCACCCCTAGGT‑AAAAAAAGCCTTCC‑GCGGCGGCTGTCGGC‑CAGTTTTTTTCCCCCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑G‑AAATAGCTTTAAGCCCGTc                                                                                            <  2:1085085/147‑1 (MQ=255)                                                      tttttcccGCCACCACCCCCGATTTTACCCACGCCCTTGTGCAAAACACCCCT‑C‑GCGCCGTCT‑TCAGCACAGTTATTTTTCCACCCAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑G‑AAATAGCTTTAAGCCCGTCAtg                                                                                         <  2:1137432/143‑1 (MQ=255)                                                       cATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑C‑GCGGCGGCTGTCTGC‑CAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGG‑G‑AAAAAgaaataaaac                                                                                                >  2:1138033/1‑132 (MQ=255)                                                               ccaccaaccccctttttATCCAACCCAATTTCAAAAAATCCCGC‑C‑GCGCCGGTTGTCGTC‑CGGTTGTTTCCCCGCCGCAAAAAACCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑G‑AAATAGCTTTAAGCCCGTCATGTtgtgtg                                                                                  <  1:714027/133‑1 (MQ=255)                                                                 accaacCGCGATTTTACCAACCCCCATGTCAAAAAATGCCTC‑C‑GGGGCGGCTGTCTCC‑CGGTTTTTTTCCCGCCACAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑G‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATc                                                                            <  1:545532/149‑1 (MQ=255)                                                                 aacaccCGCTCTTTTCTCCACCCCATTGTACAAAAATGCCTC‑C‑GCGGGGGTTGTCTGC‑AAGTTTTTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑G‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATc                                                                            <  2:911538/151‑1 (MQ=255)                                                                 aacaacCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑C‑GCGGCGGCTGTCTGC‑CAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCGAGA‑G‑AAAAAAATTTTAAACCCTCATGTTTTGTgggga                                                                              >  1:171058/1‑146 (MQ=25)                                                                       cgcgtttttccccAACCCCATGGAAAAAAAGCCCTT‑C‑GGGGGGTTTTTCTGC‑CAGTTTTTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑G‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCgctgct                                                                      <  2:1123886/140‑1 (MQ=255)                                                                         cgcATTTACCCACCGCCAGGTGAAAAAATCCCTC‑C‑GCGGGGGCTTTCGGC‑AAGATTTTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑G‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGctgct‑g                                                                    <  1:729211/150‑1 (MQ=255)                                                                             tttACCCACCCCCATGTCAAAAAGTGCCTG‑G‑GGGGGGGCTTTCTCC‑AGGTTATTTTCCCGCCGCAAAAAATCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑G‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGTa                                                                 <  1:1136802/149‑1 (MQ=255)                                                                                 cccacccccAGGTACAAAAACGCCTT‑G‑GCGGGGGTTGTCTCC‑CAGTTTTTTTTCCCCCGCAAAAAATCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑G‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGTAACaa                                                             <  2:1054560/142‑1 (MQ=255)                                                                                  ccAACGCCATGTGCAAAAATGCCTT‑C‑GCGGCGGCTGTCTGC‑CAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGAAGA‑A‑AAAAAAAGTTAAACCCCTCCTGTTGTTGGGGTAACGCTGCT‑ggctaaaa                                                             >  1:653946/1‑142 (MQ=25)                                                                                    accccaaTGTGAAAAAAGCCCTC‑C‑GCGGCGTCTGTCTGC‑CAGTTTTTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑G‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGTAACaa                                                             <  1:325827/140‑1 (MQ=255)                                                                                             tgaaaaaaTCCCTC‑C‑GGGGCGGTTTTCGCC‑CAGTTTTTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑G‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGTAACAATGTGGAAAGGGaa                                                <  1:920653/147‑1 (MQ=255)                                                                                                 aaaaCGCCTTCC‑GCGGGGGCTGTCTCC‑CTGTTTTTTTCCCCCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑G‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGTAACAATGTGGAAAGGGAAg                                               <  2:684354/148‑1 (MQ=255)                                                                                                  aaatacccctccccggcggCTGTCTCC‑CATCTTTTTTCCCCCCAAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑G‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGTAACAATGTGGAAAg                                                    <  2:323169/130‑1 (MQ=255)                                                                                                  aaaTGCCTC‑C‑GGGGGGGCTGTCTGC‑CAGTTTTTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑G‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGTAACAATGTGGAAAGGGAAGTgcgg                                          <  1:184822/151‑1 (MQ=255)                                                                                                  aaaTGCCCT‑CGGGGGCGGTTGTGGGC‑CATTTTTTTTCCCCCCAAAAAAAACCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑G‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGTAACAATGTGGAAAGGGAAGTgcg                                           <  2:821221/151‑1 (MQ=255)                                                                                                   aaTGCCTT‑C‑GCGGCGGCTGTCTGC‑CAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGAAGA‑GAAAAAAAATTTAAACCC‑CCCTGTTTTTTGGGGATCGCCGCTGGGTAAAAATTGGGAAAGGGaggggggg                                          >  1:1172857/1‑144 (MQ=255)                                                                                                       ccTT‑C‑GCGGCGGCTGTCTGC‑CAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGGAGAGG‑AAAAAATTTTAAACCC‑TCCTGTTTTGTGGGGATCGCCGCT‑GGGGACAAAGTGGGGAggggggggggg                                          >  1:665922/1‑138 (MQ=255)                                                                                                                      tGTCTGC‑CAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCGAGA‑G‑AAAAAAGTTTTATCCCCTCCTTTTTTGGGGGGAACGCTGCT‑GGGTACAAAATGGGAAGGGGAGGGGGGGGGATCaagcccccaa                          >  1:223522/1‑140 (MQ=255)                                                                                                                         cTGC‑CAGTTTTTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑G‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGa                           <  2:1176720/145‑1 (MQ=255)                                                                                                                          ctcccggtttttttcCCGCGCCAAAAAACCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑G‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAAcc                        <  1:387675/138‑1 (MQ=255)                                                                                                                               accttttttcCCCCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑G‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAAt                <  1:528454/146‑1 (MQ=255)                                                                                                                                 tttttctgccgcctCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑G‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAAt                <  2:1098967/141‑1 (MQ=255)                                                                                                                                 ttATTTTTCCCCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑G‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGTAACAATGTGGAAAGTGAAGTGCGGCGAATCAGCTCCAGAAcc                        <  2:635103/140‑1 (MQ=255)                                                                                                                                  ttttttcCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑G‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAAt                <  1:253250/146‑1 (MQ=255)                                                                                                                                            ccgcAAAAAATCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑G‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCGCCTCa   <  1:199727/151‑1 (MQ=255)                                                                                                                                                aacaaAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑G‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCGCCTCaa  <  1:600362/148‑1 (MQ=255)                                                                                                                                                  |                                                                                                                                                     GTAGCGCATCAGGCAATTCCAG‑CCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑C‑GCGGCGGCTGTCTGC‑CAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑G‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCGCCTCAA  >  NC_000913/357749‑358035

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑