Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	357,875	0	A	T	44.4%	54.2 / 20.6	45	N272K (AAT→AAA)	cynR	transcriptional activator of cyn operon; autorepressor
Reads supporting (aligned to +/- strand):  ref base A (17/8);  new base T (0/20);  total (17/28)
Fisher's exact test for biased strand distribution p-value = 1.09e-06
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

ACTGAACTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAAT‑GCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACC  >  NC_000913/357725‑358013                                                                                                                                                         |                                                                                                                                            aCTGAACTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAAT‑GCCTT‑CGCGGCGGCTGTCTGCCAGCTa                                                                                                                                             <  1:1102366/151‑1 (MQ=255)   tGAACTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAAT‑GCCTT‑CGCGGCGGCTGTCTGCCAGCTAtt                                                                                                                                           >  1:218293/1‑151 (MQ=255)     aaCTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAAT‑GCCTT‑CGCGGCGGCTGTCTGCCAGCTAtttt                                                                                                                                         >  2:214906/1‑151 (MQ=255)      aCTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAAT‑GCCTT‑CGCGGCGGCTGTCTGCCAGCTAttttt                                                                                                                                        <  2:724624/151‑1 (MQ=255)      aCTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAAT‑GCCTT‑CGCGGCGGCTGTCTGCCAGCTAtttt                                                                                                                                         <  2:430130/150‑1 (MQ=255)       cTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTGTCCAACGCCATGTGCAAAAAT‑GCCTT‑CGCGGCGGCTGTCTGCCAGCTAttttt                                                                                                                                        >  1:523831/1‑150 (MQ=255)        tCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAAT‑GCCTT‑CGCGGCGGCCGTCTGCCAGCTATTTTT‑cc                                                                                                                                     >  2:1025236/1‑151 (MQ=255)         cGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAAT‑GCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTT‑cc                                                                                                                                     <  1:812663/150‑1 (MQ=255)            aGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAAT‑GCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTT‑ccgccg                                                                                                                                 <  1:811251/151‑1 (MQ=255)              gCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAAT‑GCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGca                                                                                                                               <  2:498226/151‑1 (MQ=255)                   aTAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAAT‑GCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACaaa                                                                                                                          <  1:922235/151‑1 (MQ=255)                    tAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAAT‑GCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACaaa                                                                                                                          >  1:974599/1‑150 (MQ=255)                      aGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAAT‑GCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAAcc                                                                                                                       >  1:796146/1‑151 (MQ=255)                          tAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAAT‑GCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAAccgccg                                                                                                                   >  1:1356179/1‑151 (MQ=255)                               cATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAAT‑GCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTtctc                                                                                                              >  1:419240/1‑151 (MQ=255)                                  cAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAAT‑GCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTcc                                                                                                           >  1:546520/1‑151 (MQ=255)                                     gCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAAT‑GCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCagt                                                                                                        >  2:1008182/1‑151 (MQ=255)                                       aaTTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAAT‑GCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCag                                                                                                         >  1:235204/1‑148 (MQ=255)                                         ttCCAGCCGCAGACCTGTGCCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAAT‑GCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTg                                                                                                    >  2:1318795/1‑151 (MQ=255)                                              gCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAAT‑GCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCggg                                                                                               >  2:1236678/1‑151 (MQ=255)                                                   accccgtcgccAGCGCCTCCCTTGGTTCATTCCCCCCAACACCCGC‑CTTTTTTCCCACCCCA‑GTGGGAAAATGGACTTCCGGGTCGGCGGCCGGCCGGTTTTTTTC‑CCGCCCAAAAAAATCCGCCGTTCTCTCCAGTAGTGGCGGGGCa                                                                                            <  2:212643/139‑1 (MQ=255)                                                      ctggggtaggCGGCTACTGTTATTCATTCCCGCAAACACCCGCGTTTTTTCCCAACGCTATGTGAAAAAAT‑GCCTT‑GGGGGCGGCTGTCTGCCGGTTTTTTTC‑CCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGc                                                                                             <  1:544232/136‑1 (MQ=255)                                                             cAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAAT‑GCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCgggggagcaggaaaaaa                                                                                 >  1:946977/1‑137 (MQ=255)                                                               gCGGCTACGGTGTTTCATTCCCGCCAACACCCGCGCATTTACCCAACGCAATGTGCAAAAAT‑GCCTT‑CGGGGCGGTTGTCTGCCAGTTTTTTTC‑CCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCtt                                                                               <  1:1257470/150‑1 (MQ=255)                                                                 gcctccggTGATTATTTCCCGCCAACACCCGCGCTTTTACCCACCGCCATGTGAAAAAAG‑GCCTC‑CGGGGCGCTTGTCTCCCAGTTTTTTTC‑CCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCttt                                                                              <  1:444086/142‑1 (MQ=255)                                                                        gTGATTCTTCCCCGCAAACACCCGCGCTTTAACCCACCGCCTTTTCAAAAAAT‑GCCGC‑CGGGGGGCCTGCCGGCCAGTTTTTTTC‑CCGCCAAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTaa                                                                            <  2:590918/144‑1 (MQ=255)                                                                            ttCTTTCCCCCCAACACCCGCGCTTTTATCAACCCCCATGTAAAAAATT‑CCCTT‑CGGGGCGGCTGTCTGCCAGTTTTTTTC‑CCCCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCa                                                                    <  1:463071/148‑1 (MQ=255)                                                                                  tCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAAT‑GCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGGAGAGAAAAAACATTaaaacccccacgt                                                                 >  1:389867/1‑134 (MQ=25)                                                                                         acccccGCGCTTTTACCCACCCCCGGGTGAAAAAAT‑CCTTT‑GGCGGGGGCTTTCTGCCATTTTTTTTC‑CCGCCCAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCg                                                    <  2:735499/147‑1 (MQ=255)                                                                                         acaacCGCGCATTTATCCAACGCCATGTGCAAAAAT‑GCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCGAGAGAAAAAAATTTTAACCCCGCCTGTTTTGTgggga                                                       >  1:584722/1‑145 (MQ=25)                                                                                           acccGCGATTTTACCAACCGCCTTGTAAAAAAAG‑CCCTT‑GGGGGCGGCTTTCTGCCAGTTTTTTTC‑CCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCg                                                    <  2:433373/147‑1 (MQ=255)                                                                                            cccGCGTTTTTACCCACCGCTATGTGAAAAAAT‑GCCTC‑CGCGGCGGTTTTCTGCATGTTATTTTC‑CCCCCAAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCg                                                    <  2:893212/147‑1 (MQ=255)                                                                                                         caaccccattgtaaaaaatT‑CCCTT‑CGGGGCGGCTGTCGGCCAGTTTTTTTC‑CCCCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAAtg                                     <  1:591114/136‑1 (MQ=255)                                                                                                                      aaaaaaT‑GCCGT‑CGGGGGGGTTGGGT‑CCAGGTAATTGTCCCGCCACAAAAAAGCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAg                         <  2:1291585/148‑1 (MQ=255)                                                                                                                       aaaaaT‑CCCTT‑GGCGGGGCCTGTCGGCGAGCTTTTTTC‑CCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGt                        <  1:225521/149‑1 (MQ=255)                                                                                                                       aaaaaT‑CCCTT‑CGGGGCGGTTTTCTCCCAGCTTTTTTC‑CCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAg                              <  2:299949/143‑1 (MQ=255)                                                                                                                       aaaaaT‑CCCTC‑CGCGGCGGCTTTCTGCCATTTTTTTTC‑CCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAg                         <  1:373852/148‑1 (MQ=255)                                                                                                                       aaaaaT‑CCCTC‑CGCGGCGGCTGTCTGCCAGTTTTTTTC‑CCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTgc                      <  1:936711/151‑1 (MQ=255)                                                                                                                           aT‑GCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGCAGAGAAAAAGATTTTAACCCCCCCTGTTTTGTGGGGGTCGCCGGTGGTGAAAAAACGggaagggaagggggggg                  >  2:720528/1‑144 (MQ=255)                                                                                                                                  tccgggggggcTGTCTGCCAGTTTTTTTC‑CCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTgcggcg                  <  1:614854/138‑1 (MQ=255)                                                                                                                                     gggggggttttcggCCAGTTTTTTTC‑CCCCCCAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAg            <  1:288669/136‑1 (MQ=255)                                                                                                                                     gcggcgTCTGTCTGCAATCTTTTTTC‑CCGCCCCAAAAAACCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCa             <  2:147/148‑1 (MQ=255)                                                                                                                                       ggcggcTGTCGCCCAGTTTTTTTC‑CCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCa             <  1:1228773/146‑1 (MQ=255)                                                                                                                                           gttGTCTGCCAGGTTTTGCT‑CCCCCGAAAAAACACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCt          <  1:150900/143‑1 (MQ=255)                                                                                                                                             tttCTGCCATTTTTTTTC‑CCGCCGAAAAAAACCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAg            <  2:1145847/139‑1 (MQ=255)                                                                                                                                              gTCTGCCAGCTTTTTTC‑CCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAAcc  <  1:413733/150‑1 (MQ=255)                                                                                                                                                         |                                                                                                                                            ACTGAACTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAAT‑GCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACC  >  NC_000913/357725‑358013

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑