Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	357,890	0	C	A	49.0%	32.6 / 32.3	51	L267F (TTG→TTT)	cynR	transcriptional activator of cyn operon; autorepressor
Reads supporting (aligned to +/- strand):  ref base C (14/12);  new base A (0/25);  total (14/37)
Fisher's exact test for biased strand distribution p-value = 1.09e-05
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

ATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGGC‑TGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTG‑TGTGGCAATCGCTGCT‑GGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCGCC  >  NC_000913/357743‑358031                                                                                                                                                      |                                                                                                                                                 aTAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGGC‑TGTCTGCCAGCTATTTTTCCGCCGCAACaaa                                                                                                                                               <  1:780144/151‑1 (MQ=255)   aaGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCACCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGGC‑TGTCTGCCAGCTATTTTTCCGCCGCAACAAAAc                                                                                                                                             <  1:292312/151‑1 (MQ=255)    aGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGGC‑TGTCTGCCAGCTATTTTTCCGCCGCAACAAAAcc                                                                                                                                            <  2:873304/151‑1 (MQ=255)    aGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGGC‑TGTCTGCCAGCTATTTTTCCGCCGCAACAAAAcc                                                                                                                                            <  2:586773/151‑1 (MQ=255)     gCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGGC‑TGTCTGCCAGCTATTTTTCCGCCGCAACAAAAcc                                                                                                                                            >  1:259895/1‑150 (MQ=255)       gTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGGC‑TGTCTGCCAGCTATTTTTCCGCCGCAACAAAAccgcc                                                                                                                                         <  1:4934/151‑1 (MQ=255)          gcgcTTCAGGCAATTCCACCCGCAGCCCTGTGTCAGCGGCTCCCGTGATTCATTCCCGCCAACACCCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGGC‑TGTCTGCCAGCTATTTTTCCGCCGCAACAAAAccgccg                                                                                                                                        <  2:303111/149‑1 (MQ=18)            gcATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGGC‑TGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTtc                                                                                                                                     >  1:25094/1‑150 (MQ=255)             cATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGGC‑TGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTtctc                                                                                                                                   >  1:384520/1‑151 (MQ=255)                    cattcccAGCCGCACACCTGTTTCGGCGGCTCCCGTGTTTATTCCCCGCCAACACCCGCGCTTTTACCCAACGCCAGGTGAAAAAATGCCTC‑CGCGGCGGC‑TGTCGCCCAGCTTTTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCag                                                                                                                              <  1:218428/144‑1 (MQ=255)                       tcccAGCCGCAGCCCTGTGTCAGCGGCTCCCGTGATTCTTTCCCGCCAACACCCGCGCTTTTACCCACCGCCATGTGCAAAAATGCCTT‑CGCGGGGGC‑TGTCTGCCAGCTATTTTCCCGCCGCAACAAAACCGCCGTTCTCTCCagtag                                                                                                                           <  2:775153/147‑1 (MQ=21)                         ccAGCCGAAGACCTGTGTCAGCGGTTCCCGTGATTCATTCCCGCCAAACCCCGCGCTTTTACCCAACCCCATGCACAAAAATCCCTC‑CGCGGCGCC‑TGCCTGCCGGTTTTTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCagtagt                                                                                                                          <  2:213606/148‑1 (MQ=255)                         ccACCCGCAGACCTGTGTCAGCGCCTACCGTGTTTCATTCCCGCCAACACCCGCGCATTTACCCACCGCCATGTGCAAAAATGCCTC‑CGCGGCGGC‑TGTCTGCCAGTTATTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTgg                                                                                                                        <  2:553548/150‑1 (MQ=21)                               gCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGGC‑TGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGC‑gggggg                                                                                                                >  1:821485/1‑149 (MQ=255)                                    cttgtgTCAGCGGCTCCCGTGATTCATTCCCGCCAACACCCGTGCATTTACCCAACGCCATGTGAAAAAATGCTTC‑CGCGGCGGC‑TGTCTGCCAGCTATTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAag                                                                                                              <  2:610437/146‑1 (MQ=21)                                     cTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGGC‑TGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCaacaaa                                                                                                           >  1:901596/1‑146 (MQ=255)                                      tgtgTCAGGGCCTCCCGTGATTCTTTCCCCCCAACACCCGCGCTTTTATCCACCCCCATGCGAAAAAAGCCCTG‑CGCGGCGCC‑TTTCTGCCACTTTTTTTCCCGCCGAACAAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAagag                                                                                                            <  2:280186/148‑1 (MQ=255)                                      tgtgTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGGC‑TGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGC‑ggg                                                                                                                   >  1:809230/1‑141 (MQ=255)                                        tgccggCGGCTACCGTGTTTCATTCCCCCCAACACCCGCGCATTTACCAAACCCATTGTGCAAAAAGGCCTC‑CGGGGCGGT‑TTTCTCCCATCTTTTTTCCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGaaa                                                                                                         <  1:952074/144‑1 (MQ=255)                                             gCGGCTACGGTGTTTCTTTCCCGCCAACACCCGCGAATTTAACCAACGCCATGTGAAAAATTGCCTC‑CGCGGCGGC‑TGTCGGCCAGTTATTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGCttt                                                                                                  <  2:641045/151‑1 (MQ=255)                                             gCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGGC‑TGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGGGAGAGAAAAAACttt                                                                                                  >  2:268660/1‑151 (MQ=255)                                              cGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGGC‑TGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGGAGGAGgaaaaaaatt                                                                                                  >  1:767493/1‑143 (MQ=25)                                               gcctcccGTGTTTAATTCCCCCAAACAACCGCCCTTTTACCCACCCCCTTGTGAAAAAAGGCCTC‑CGCGGCGGC‑TGTCTGCAGGTTTTTTTCCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGaa                                                                                                          <  1:726127/136‑1 (MQ=255)                                                 ctcccGTGATTCATTCCCCCCAACACCCGCGCTTTTACCCACCGCCTTGTGCAAAAATCCCTC‑CGCGGCGGC‑TTTCTCCCAGCTTTTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGCtt                                                                                                   <  2:280016/143‑1 (MQ=255)                                                    ccGTAATTTATTCCCCCCACCACCCGCCCTTTTCCCAAACCCCATGTCAAAAAATCCTTC‑CGGGGGGGT‑TGTCTCCAATTTTTTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGCTTTaa                                                                                                <  1:880043/146‑1 (MQ=255)                                                        gATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGGC‑TGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGGGAGAGaaaaaacatttagacc                                                                                            >  2:231084/1‑133 (MQ=25)                                                         aTTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGGC‑TGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGGACGAGaaaaaagatttagacc                                                                                            >  2:737051/1‑132 (MQ=25)                                                          ttCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGGC‑TGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGCAACGGAAAAAAATTTAAGCCCG‑CAtgt                                                                                     >  2:744037/1‑151 (MQ=25)                                                             aTTCCCGCAAACAACCGCGCTTTTACCCAACGCCATGTGAAAAAATGCCTT‑CGCGGGGGC‑TGTCGGCCAGTTATTTTCCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGCTTTAAGCCCGTCAtg                                                                                      <  2:728432/147‑1 (MQ=255)                                                               tccccccAAAACCCGCATATTTACCAACCCCCATGT‑CAAAAATGCCTTCCGGGGCGGC‑TGTCTCCCAGTTTTTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTtg‑tg                                                                                <  2:562760/145‑1 (MQ=255)                                                                 ccGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGGC‑TGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGGCAGAAAAAAAACATTAAACCACTCCTGTTG‑TGTgg                                                                             >  2:162713/1‑151 (MQ=25)                                                                         acccccgcTTTTACCCACCCCCATGCAAAAAAATGCCTC‑GGGGGCGGG‑TGTCTCCCATTTTTTTTCCCGCCGCAAAAAATCCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTG‑TGTGGCAATCg                                                                       <  1:39028/144‑1 (MQ=255)                                                                         acccGCGCTTTTACCCACCGCCATGTGAAAAAAGGCCTT‑CGGGGCGGC‑TGTCTGCCAGCTATTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTG‑TGTGGCAATCg                                                                       <  2:737081/147‑1 (MQ=255)                                                                                   ttACCCACCCCCATGTCAAAAAATCCTTT‑CGCGGGGGC‑TTTCTGCCAGTTTTTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTG‑TGTGGCAATCGCTGCT‑GGTAAc                                                           <  2:549148/150‑1 (MQ=255)                                                                                           cGCCATGTCAAAAAATCCCTT‑CGCGGCGGC‑TGTCGGCCAGTTTTTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTG‑TGTGGCAATCGCTGCT‑GGTAACAATGTgg                                                    <  2:979188/149‑1 (MQ=255)                                                                                             ccATGTGCAAAAAGCCCTC‑CGGGGCGGC‑TGTCGGCCAGTTTTTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTG‑TGTGGCAATCGCTGCT‑GGTAACAATGTGGAAAg                                                <  2:370733/151‑1 (MQ=255)                                                                                                 gtgAAAAAATGCCTC‑CGCGGCGGC‑TGTCTGCCAGCTTTTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTG‑TGTGGCAATCGCTGCT‑GGTAACAATGTGGAAAGGGa                                             <  2:627080/150‑1 (MQ=255)                                                                                                     aaaatTGCCTC‑CGCGGCGGC‑TGTCTGCCAGTTTTTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTG‑TGTGGCAATCGCTGCT‑GGTAACAATGTGGAAAGGGAAGt                                          <  2:1557/149‑1 (MQ=255)                                                                                                     aaaaaTCCTTC‑CGCGGGGGC‑TTTCTGCCAGTTTTTTTCCCGCCGCAAAAAAGCCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTG‑TGTGGCAATCGCTGCT‑GGTAACAATGTGGAAAGGGAAGTg                                         <  1:191628/150‑1 (MQ=255)                                                                                                        aattccttccggggcgcc‑TGTCCGCCGCTTTTTTTTCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTG‑TGTGGCAATCGCTGCT‑GGTAACAATGTGGAAAGGGAAGTgcgg                                      <  2:62910/139‑1 (MQ=255)                                                                                                           gCCTT‑CGCGGCGGC‑TGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGGGAGAGAAAAAAATTTTAAACCCCCCTGTTT‑TGTGGGGAAAGCTGCT‑GGGTACAAAGTGGGAAGGGGAgggggg                                      >  2:763457/1‑142 (MQ=255)                                                                                                                    ggggggtgttCTGCCGGTTTTTTTCCCGCCACAAAAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTG‑TGTGGCAATCGCTGCT‑GGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTc                           <  1:39004/142‑1 (MQ=255)                                                                                                                    ggcggc‑TGTCTCCCATTTTTTTTCCCCCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTG‑TGTGGCAATCGCTGCT‑GGTAACAATGTGGAAAGGGAAGTGCGGCGaa                                  <  1:530518/143‑1 (MQ=255)                                                                                                                     gcggctTGTCTCCCAGTTTTTTTCCCGCCACAAAAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTG‑TGTGGCAATCGCTGCT‑GGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTc                           <  1:77259/150‑1 (MQ=255)                                                                                                                       ggc‑TGTCTGCCAGTTTTTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTG‑TGTGGCAATCGCTGCT‑GGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGa                       <  2:727389/151‑1 (MQ=255)                                                                                                                                     tttttttcCCCCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTG‑TGTGGCAATCGCTGCT‑GGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAAc                     <  1:436883/137‑1 (MQ=255)                                                                                                                                      ttttttcCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTG‑TGTGGCAATCGCTGCT‑GGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAAtt           <  2:581259/147‑1 (MQ=255)                                                                                                                                        ttttccccccaaaacaaAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTG‑TGTGGCAATCGCTGCT‑GGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTg          <  1:456190/136‑1 (MQ=255)                                                                                                                                        ttttcCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTG‑TGTGGCAATCGCTGCT‑GGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAg        <  2:313559/150‑1 (MQ=255)                                                                                                                                            ccccccgcAAAAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTG‑TGTGGCAATCGCTGCT‑GGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGtt      <  1:874191/144‑1 (MQ=255)                                                                                                                                             ccgccgCAAAAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTG‑TGTGGCAATCGCTGCT‑GGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCg    <  2:205623/149‑1 (MQ=255)                                                                                                                                                 cgcAACAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGGCAGAGGAAAAACTTTAAAACCCCCCTGGTG‑TGTGGGAATCGCTGCTGGGGAAAAATG‑GGGGAGGGAAGGGGGGGGGAACAGCTCCAGAACCCCGCCAAATTAGTTTGcc  >  2:237983/1‑147 (MQ=255)                                                                                                                                                   caacaaAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGGAATAAAAAAAAGTCTTAGCGCCTTACTTTGTTGTGG‑GATCGCTGCT‑GGTGACAATCTGGGAAGGGGAGTGAGGGGAAGCAAGTCCACAAAAGCACTGATTTAGttttcc  >  2:763022/1‑141 (MQ=255)                                                                                                                                                      |                                                                                                                                                 ATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGGC‑TGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTG‑TGTGGCAATCGCTGCT‑GGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCGCC  >  NC_000913/357743‑358031

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: ‑