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%	34.6 / 16.4	40	K271E (AAA→GAA)	cynR	transcriptional activator of cyn operon; autorepressor
Reads supporting (aligned to +/- strand):  ref base T (14/6);  new base C (0/20);  total (14/26)
Fisher's exact test for biased strand distribution p-value = 3.34e-06
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

ACTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAAT‑GCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAG  >  NC_000913/357730‑358025                                                                                                                                                         |                                                                                                                                                   aCTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAAT‑GCCTT‑CGCGGCGGCTGTCTGCCAGCTAttttt                                                                                                                                                    <  2:724624/151‑1 (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)                                                                                                                                        tttcgccaattttttttc‑CCCCCCCAACAAAGCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCa                   <  1:1217303/133‑1 (MQ=255)                                                                                                                                        tttCTGCCATTTTTTTTC‑CCGCCGAAAAAAACCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAg                        <  2:1145847/139‑1 (MQ=255)                                                                                                                                         gTCTGCCAGCTTTTTTC‑CCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAAcc              <  1:413733/150‑1 (MQ=255)                                                                                                                                               cagtttttttc‑CCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACcgcg           <  1:662798/141‑1 (MQ=255)                                                                                                                                                  tttttttc‑CCGCCCAAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAAt      <  2:523822/146‑1 (MQ=255)                                                                                                                                                     ttttc‑CCCCCGCAAAAAAGCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAg  <  1:1289055/150‑1 (MQ=255)                                                                                                                                                     tttct‑CCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAg  <  2:113715/150‑1 (MQ=255)                                                                                                                                                         |                                                                                                                                                   ACTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAAT‑GCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAG  >  NC_000913/357730‑358025

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: ‑