Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	357,880	0	T	C	50.0%	45.0 / 15.3	48	K271E (AAA→GAA)	cynR	transcriptional activator of cyn operon; autorepressor
Reads supporting (aligned to +/- strand):  ref base T (16/8);  new base C (0/24);  total (16/32)
Fisher's exact test for biased strand distribution p-value = 6.52e-07
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGGC‑TGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAG  >  NC_000913/357731‑358025                                                                                                                                                        |                                                                                                                                                   cTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGGC‑TGTCTGCCAGCTATTTTTc                                                                                                                                                   >  2:84697/1‑151 (MQ=255) cTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGGC‑TGTCTGCCAGCTATTTTTc                                                                                                                                                   >  2:429387/1‑151 (MQ=255)       ggCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGGC‑TGTCTGCCAGCTATTTTTccgccg                                                                                                                                              >  1:61326/1‑150 (MQ=255)             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‑GGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTtgtg                                                                         <  2:562760/145‑1 (MQ=255)                                                                             ccGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGGC‑TGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGGCAGAAAAAAAACATTAAACCACTCCTGTTGTGTgg                                                                      >  2:162713/1‑151 (MQ=25)                                                                                     acccccgcTTTTACCCACCCCCATGCAAAAAAATGCCTC‑GGGGGCGGG‑TGTCTCCCATTTTTTTTCCCGCCGCAAAAAATCCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCg                                                                <  1:39028/144‑1 (MQ=255)                                                                                     acccGCGCTTTTACCCACCGCCATGTGAAAAAAGGCCTT‑CGGGGCGGC‑TGTCTGCCAGCTATTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCg                                                                <  2:737081/147‑1 (MQ=255)                                                                                               ttACCCACCCCCATGTCAAAAAATCCTTT‑CGCGGGGGC‑TTTCTGCCAGTTTTTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAAc                                                     <  2:549148/150‑1 (MQ=255)                                                                                                       cGCCATGTCAAAAAATCCCTT‑CGCGGCGGC‑TGTCGGCCAGTTTTTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTgg                                              <  2:979188/149‑1 (MQ=255)                                                                                                         ccATGTGCAAAAAGCCCTC‑CGGGGCGGC‑TGTCGGCCAGTTTTTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAg                                          <  2:370733/151‑1 (MQ=255)                                                                                                             gtgAAAAAATGCCTC‑CGCGGCGGC‑TGTCTGCCAGCTTTTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGa                                       <  2:627080/150‑1 (MQ=255)                                                                                                                 aaaatTGCCTC‑CGCGGCGGC‑TGTCTGCCAGTTTTTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGt                                    <  2:1557/149‑1 (MQ=255)                                                                                                                 aaaaaTCCTTC‑CGCGGGGGC‑TTTCTGCCAGTTTTTTTCCCGCCGCAAAAAAGCCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTg                                   <  1:191628/150‑1 (MQ=255)                                                                                                                    aattccttccggggcgcc‑TGTCCGCCGCTTTTTTTTCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTgcgg                                <  2:62910/139‑1 (MQ=255)                                                                                                                       gCCTT‑CGCGGCGGC‑TGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGGGAGAGAAAAAAATTTTAAACCCCCCTGTTTTGTGGGGAAAGCTGCTGGGTACAAAGTGGGAAGGGGAgggggg                                >  2:763457/1‑142 (MQ=255)                                                                                                                                ggggggtgttCTGCCGGTTTTTTTCCCGCCACAAAAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTc                     <  1:39004/142‑1 (MQ=255)                                                                                                                                ggcggc‑TGTCTCCCATTTTTTTTCCCCCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGaa                            <  1:530518/143‑1 (MQ=255)                                                                                                                                 gcggctTGTCTCCCAGTTTTTTTCCCGCCACAAAAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTc                     <  1:77259/150‑1 (MQ=255)                                                                                                                                   ggc‑TGTCTGCCAGTTTTTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGa                 <  2:727389/151‑1 (MQ=255)                                                                                                                                                 tttttttcCCCCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAAc               <  1:436883/137‑1 (MQ=255)                                                                                                                                                  ttttttcCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAAtt     <  2:581259/147‑1 (MQ=255)                                                                                                                                                    ttttcCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAg  <  2:313559/150‑1 (MQ=255)                                                                                                                                                        |                                                                                                                                                   CTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGGC‑TGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAG  >  NC_000913/357731‑358025

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑