Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,628,649	0	A	C	31.1%	71.1 / 15.6	45	intergenic (+102/+206)	nadR/ettA	DNA‑binding transcriptional repressor/NMN adenylyltransferase NadR/energy‑dependent translational throttle protein EttA
Reads supporting (aligned to +/- strand):  ref base A (28/3);  new base C (0/14);  total (28/17)
Fisher's exact test for biased strand distribution p-value = 4.07e-09
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00
Rejected as consensus: Frequency below/above cutoff threshold.

TGGAACTGGTGCGGGAGATGATGGGGGAGCAGAGATAACCGTGATGAAACTGCTCAAAGGCGAGGTATAAAATGAGTTTTTTTGATGAGTTGAAAACCTCTCTGGAAGAGGCTGTCGAGATTAAACAAGGTTTGAAAAAA‑CCTGCACGGGT‑GACCCGCCACGAAATTGAGGATGCTAAGGCTGTTGTAGACCGGAAACGGTGTTCACGCCGCATCCGGCATTCGGTGCTCAATGCCTGA‑‑‑TGCGACGCTTACCGCGTCTTATCAGGCCTACAGTTTTACA  >  NC_000913/4628510‑4628788                                                                                                                                            |                                                                                                                                                 tGGAACTGGTGCGGGAGATGATGGGGGAGCAGAGATAACCGTGATGAAACTGCTCAAATGCGAGGTATAAAATGAGTTTTTTTGATGAGTTGAAAACCTCTCTGGAAGAGGCTGTCGAGATTAAACAAGGTTTGaaaaaa                                                                                                                                                  >  1:1117710/1‑140 (MQ=255)         gTGCGGGAGATGATGGGGGAGCAGAGATAACCGTGATGAAACTGCTCAAAGGCGAGGTATAAAATGAGTTTTTTTGATGAGTTGAAAACCTCTCTGGAAGAGGCTGTCGAGATTAAACAAGGTTTGAAAAAA‑CCTGCACg                                                                                                                                         >  2:542349/1‑140 (MQ=255)         gTGCGGGAGATGATGGGGGAGCAGAGATAACCGTGATGAAACTGCTCAAAGGCGAGGTATAAAATGAGTTTTTTTGATGAGTTGAAAACCTCTCTGGAAGAGGCTGTCGAGATTAAACAAGGTTTGAAAAAA‑CCTGCACg                                                                                                                                         >  1:6321/1‑140 (MQ=255)          tGCGGGAGATGATGGGGGAGCAGAGATAACCGTGATGAAACTGCTCAAAGGCGAGGTATAAAATGAGTTTTTTTGATGAGTTGAAAACCTCTCTGGAAGAGGCTGTCGAGATTAAACAAGGTTTGAAAAAA‑CCTGCACgg                                                                                                                                        >  1:807718/1‑140 (MQ=255)              ggAGATGATGGGGGAGCAGAGATAACCGTGATGAAACTGCTCAAAGGCGAGGTATAAAATGAGTTTTTTTGATGAGTTGAAAACCTCTCTGGAAGAGGCTGTCGAGATTAAACAAGGTTTGAAAAAA‑CCTGCACGGGT‑Ga                                                                                                                                   >  2:35427/1‑140 (MQ=255)                 gatgatGGGGGAGCAGAGATAACCGTGATGAAACTGCTCAAAGGCGAGGTATAAAATGAGTTTTTTTGATGAGTTGAAAACCTCTCTGGAAGAGGCTGTCGAGATTAAACAAGGTTTGAAAAAA‑CCTg                                                                                                                                             <  1:117594/128‑1 (MQ=255)                 gatgatGGGGGAGCAGAGATAACCGTGATGAAACTGCTCAAAGGCGAGGTATAAAATGAGTTTTTTTGATGAGTTGAAAACCTCTCTGGAAGAGGCTGTCGAGATTAAACAAGGTTTGAAAAAA‑CCTg                                                                                                                                             >  2:117594/1‑128 (MQ=255)                          ggAGCAGAGATAACCGTGATGAAACTGCTCAAAGGCGAGGTATAAAATGAGTTTTTTTGATGAGTTGAAAACCTCTCTGGAAGAGGCTGTCGAGATTAAACAAGGTTTGAAAAAA‑CCTGCACGGGT‑GACCCGCCACGaaa                                                                                                                       >  1:642737/1‑140 (MQ=255)                          ggAGAAGAGATAACCGTAATGAAACTGCTCAAAGGGGGGATAAAAAATGAGTTTTTTTGATGGGTTGAAACCCTCTCGGGAAGGGGCTGTGGAAATAAAAAAAGTTTTGAAAAAC‑CCTGCAGGGGT‑GCCCCGCCACGaaa                                                                                                                       <  2:929550/140‑1 (MQ=255)                              cAGAGATAACCGTGATGAAACTGCTCAAAGGCGAGGTATAAAATGAGTTTTTTTGATGAGTTGAAAACCTCTCTGGAAGAGGCTGTCGAGATTAAACAAGGTTTGAAAAAA‑CCTGCACGGGT‑GACCCGCCACGAAATTGa                                                                                                                   >  2:425887/1‑140 (MQ=255)                               agagATAACCGTGATGAAACTGCTCAAAGGCGAGGTATAAAATGAGTTTTTTTGATGAGTTGAAAACCTCTCTGGAAGAGGCTGTCGAGATTAAACAAGGTTTGAAAAAC‑CCTGCACGGGT‑GACCCGCCACGAAATTGAg                                                                                                                  <  1:35427/140‑1 (MQ=255)                               agagATAACCGTGATGAAACTGCTCAAAGGCGAGGTATAAAATGAGTTTTTTTGATGAGTTGAAAACCTCTCTGGAAGAGGCTGTCGAGATTAAACAAGGTTTGAAAAAA‑CCTGCACGGGT‑GACCCGCCACGAAATTGAg                                                                                                                  >  1:330411/1‑140 (MQ=255)                               agagATAACCGTGATGAAACTGCTCAAAGGCGAGGTATAAAATGAGTTTTTTTGATGAGTTAAAACCCTCTCTGGAAGAGGCTGTCGAGATAAAACAAGGTTTAAAAAAC‑CCTGCAGGGGT‑GACCCGCCACGAAATTGAg                                                                                                                  <  2:12/140‑1 (MQ=255)                               agaaATAACCGTGAAAAAACTGCTCAAAGGCGAGGTATAAAATGAGTTTTTTTGATGAGTTAAAAACCTCTCTGGAAGAGGCTGTCGAGATTAAACAAGGTTTGAAAAAA‑CCTGCACGGGT‑GACCCGCCACGAAATTGAg                                                                                                                  <  1:111200/140‑1 (MQ=255)                                     acccGTGATAAAACTGCTAAAATGCGAGGTATAAAATGATTTTTTTTGATGAGTTAAAACCCTCTCTGGAAGAGGCTGTCGAGATTAAACAAGGTTTGAAAAAA‑CCTGCACGGGT‑GACCCGCCACGAAATTGAGGATGCt                                                                                                            <  2:1117710/138‑1 (MQ=255)                                     aaCCGTGATGAAACTGCTCAAAGGCGAGGTATAAAATGAGTTTTTTTGATGAGTTGAAACCCTCTCTGGAAGAGGCTGTCGAGATTAAACAAGGTTTGAAAAAC‑CCTGCACGGGT‑GACCCGCCACGAAATTGAGGATGCt                                                                                                            <  2:1037501/140‑1 (MQ=255)                                     aaCCGTGATGAAACTGCTCAAAGGCGAGGTATAAAATGAGTTTTTTTGATGAGTTGAAACCCTCTCTGGAAGAGGCTGTCGAGATAAAACAAGTTTTGAAAAAC‑CCTGCACGGGT‑GACCCGCCACGAAATTGAGGATGCt                                                                                                            <  2:296618/140‑1 (MQ=255)                                     aaCCGTGATGAAACTGCTCAAAGGCGAGGTATAAAATGAGTTTTTTTGATGAGTTGAAACCCTCTCTGGAAGAGGCTGTCGAGATAAAACAAGGTTTGAAAAAC‑CCTGCACGGGT‑GACCCGCCACGAAATTGAGGATGCt                                                                                                            <  2:655259/140‑1 (MQ=255)                                         gTGATGAACCTGCTCAAAGGCGAGTTAAAAAATGAGTTTTTTTGATGAGTTGAAACCCTCTCTGGAAGAGGCTGACGAAATAAAACAAGGTTTAAAAAAA‑CCTGCGCGGGG‑GCCCCGCCACGAAATTGAGGATGCTAAgg                                                                                                        <  2:330411/140‑1 (MQ=255)                                          tgatgaAACTGCTCAAAGGCGAGGTATAAAATGATTTTTTTTGATGAGTTGAAACCCTCTCTGGAAGAGGCTGTCGAGATAAAACAAGGTTTAAAAAAC‑CCTGCACGGGT‑GACCCGCCACGAAATTGAGGATGCTAAGGc                                                                                                       <  1:574316/140‑1 (MQ=255)                                           gatgaAACTGCTCAAAGGCGAGGTATAAAATGAGTTTTTTTGATGAGTTGAAAACCTCTCTGGAAGAGGCTGTCGAGATTAAACAAGGTTTGAAAAAA‑CCTGCACGGGT‑GACCCGCCACGAAATTGAGGATGCTAAGGCt                                                                                                      >  2:353767/1‑140 (MQ=255)                                             tgaAACTGCTCAAAGGCGAGGTATAAAATGAGTTTTTTTGATGAGTTGAAAACCTCTCTGGAAGAGGCTGTCGAGATTAAACAAGGTTTGAAAAAA‑CCTGCACGGGT‑GACCCGCCACGAAATTGAGGATGCTAAGGCtgt                                                                                                    >  2:615992/1‑140 (MQ=255)                                                 aCTGCTCAAAGGCGAGGTATAAAATGAGTTTTTTTGATGAGTTGAAAACCTCTCTGGAAGAGGCTGTCGAGATTAAACAAGGTTTGAAAAAA‑CCTGCACGGGT‑GACCCGCCACGAAATTGAGGATGCTAAGGCTGTTGTa                                                                                                >  2:217605/1‑140 (MQ=255)                                                     cTCAAAGGCGAGGTATAAAATGAGTTTTTTTGATGAGTTGAAAACCTCTCTGGAAGAGGCTGTCGAGATTAAACAAGGTTTGAAAAAA‑CCTGCACGGGT‑GACCCGCCACGAAATTGAGGATGCTAAGGCTGTTGTAGAcc                                                                                            >  1:1153847/1‑140 (MQ=255)                                                               aGGTATAAAATGAGTTTTTTTGATGAGTTGAAAACCTCTCTGGAAGAGGCTGTCGAGATTAAACAAGGTTTGAAAAAA‑CCTGCACGGGT‑GACCCGCCACGAAATTGAGGATGCTAAGGCTGTTGTAGACCGGAAACGgtg                                                                                  >  1:910195/1‑140 (MQ=255)                                                                    taAAATGAGTTTTTTTGATGAGTTGAAAACCTCTCTGGAAGAGGCTGTCGAGATTAAACAAGGTTTGAAAAAA‑CCTGCACGGGT‑GACCCGCCACGAAATTGAGGATGCTAAGGCTGTTGTAGACCGGAAACGGTGTTCAc                                                                             >  2:629391/1‑140 (MQ=255)                                                                    aaaaaTGAGTTTTTTTGATGAGTTGAAAACCTCTCTGGAAGAGGCTGTCGAGATTAAACAAGGTTTGAAAAAA‑CCTGCACGGGT‑GACCCGCCACGAAATTGAGGATGCTAAGGCTGTTGTAGACCGGAAACGGTGTTCAc                                                                             >  1:529326/2‑140 (MQ=255)                                                                     aaaaTGAGTTTTTTTGAGGATTTAAAAACCTCTCTGGAAGAGGCTGCGGAGATTAAACAGGGTTTAAAAAAC‑CCTGCGGGGGT‑GCCCCGCCACGAAATTGAGGATGCTAAGGCTGTTGTAGACCGGAAACGGTGTTCAcg                                                                            <  2:7065/140‑1 (MQ=255)                                                                      aaaGGATTTTTTTTGAGGAGTGAAAAACCTCTGGGGAAGGGGCTGTCGAGATAAAAAAAGTTTTAAAAAAC‑CCTGCAGGGGT‑GACCCGCCACGAAATTGAGGATGCTAAGGCTGTTGTAGACCGGAAACGGTGTTCAcgc                                                                           <  2:807718/140‑1 (MQ=255)                                                                           aGTTTTTTTGATGAGTTGAAAACCTCTCTGGAAGAGGCTGTCGAGATTAAACAAGGTTTGAAAAAA‑CCTGCACGGGT‑GACCCGCCACGAAATTGAGGATGCTAAGGCTGTTGTAGACCGGAAACGGTGTTCACGCCGCAt                                                                      >  1:552987/1‑140 (MQ=255)                                                                                 tttGATGAGTTGAAAACCTCTCTGGAAGAGGCTGTCGAGATTAAACAAGGTTTGAAAAAA‑CCTGCACGGGT‑GACCCGCCACGAAATTGAGGATGCTAAGGCTGTTGTAGACCGGAAACGGTGTTCACGCCGCATCCGGCa                                                                >  1:246587/1‑140 (MQ=255)                                                                                     atgaGTTGAAAACCTCTCTGGAAGAGGCTGTCGAGATTAAACAAGGTTTGAAAAAA‑CCTGCACGGGT‑GACCCGCCACGAAATTGAGGATGCTAAGGCTGTTGTAGACCGGAAACGGTGTTCACGCCGCATCCGGCATTCg                                                            >  1:878132/1‑140 (MQ=255)                                                                                          ttGAAAACCTCTCTGGAAGAGGCTGTCGAGATTAAACAAGGTTTGAAAAAA‑CCTGCACGGGT‑GACCCGCCACGAAATTGAGGATGCTAAGGCTGTTGTAGACCGGAAACGGTGTTCACGCCGCATCCGGCATTCGGTGCt                                                       >  2:1142173/1‑140 (MQ=255)                                                                                           taaaacCCTCTCGGGAAGAGGCTGTCGAGATAAAACAAGGTTTAAAAAAC‑CCTGCAGGGGT‑GCCCCGCCACGAAATTGAGGATGCTAAGGCTGTTGTAGACCGGAAACGGTGTTCACGCCGCATCCGGCATTCGGTGCTc                                                      <  1:353767/138‑1 (MQ=255)                                                                                                    ctctGGAAGAGGCTGTCGAGATTAAACAAGGTTTGAAAAAA‑CCTGCACGGGT‑GACCCGCCACGAAATTGAGGATGCTAAGGCTGTTGTAGACCGGAAACGGTGTTCACGCCGCATCCGGCATTCGGTGCTCAATGCCTGa                                             >  2:732185/1‑140 (MQ=255)                                                                                                    ctctGGAAGAGGCTGTCGAGATTAAACAAGGTTTGAAAAAA‑CCTGCACGGGT‑GACCCGCCACGAAATTGAGGATGCTAAGGCTGTTGTAGACCGGAAACGGTGTTCACGCCGCATCCGGCATTCGGTGCTCAATGCCTGa                                             >  1:157765/1‑140 (MQ=255)                                                                                                       tGGAAGAGGCTGTCGAGATTAAACAAGGTTTGAAAAAA‑CCTGCACGGGT‑GACCCGCCACGAAATTGAGGATGCTAAGGCTGTTGTAGACCGGAAACGGTGTTCACGCCGCATCCGGCATTCGGTGCTCAATGCCTGA‑‑‑TGc                                       >  2:60321/1‑140 (MQ=255)                                                                                                          agggggCTGTAGAAATAAAACAGGGTTTAAAAAAC‑CCTGCGGGGGT‑GCCCCGCCACGAAATTGAGGATGCTAAGGCTGTTGTAGACCGGAAACGGTGTTCACGCCGCATCCGGCATTCGGTGCTCAATGCCTGA‑‑‑TGCGAc                                    <  2:6321/136‑1 (MQ=37)                                                                                                               gCTGTGGAGATAAAACAGGTTTTGAAAAAC‑CCTGCGCGGGT‑GCCCCGCCACGAAATTGAGGATGCTAAGGCTGTTGTAGACCGGAAACGGTGTTCACGCCGCATCCGGCATTCGGTGCTCAATGCCTGA‑‑‑TGCGACGCTTa                               <  1:542349/140‑1 (MQ=38)                                                                                                               gCTGTCGAGATTAAACAAGGTTTGAAAAAA‑CCTGCACGGGT‑GACCCGCCACGAAATTGAGGATGCTAAGGCTGTTGTAGACCGGAAACGGTGTTCACGCCGCATCCGGCATTCGGTGCTCAATGCCTGA‑‑‑TGCGACGCTTa                               >  1:1161658/1‑140 (MQ=255)                                                                                                                cTGTCGAGATAAAACAAGGTTTAAAAAAC‑CCTGCCCGGGT‑GCCCCGCCACGAAATTGAGGATGCTAAGGCTGTTGTAGACCGGAAACGGTGTTCACGCCGCATCCGGCATTCGGTGCTCAATGCCTGA‑‑‑TGCGACGCTTAc                              <  1:446271/140‑1 (MQ=38)                                                                                                                cTGTAGAGATAAAACAAGGTTAAAAAAAC‑CCTGCGGGGGT‑GCCCCGCCACGAAATTGAGGATGCTAAGGCTGTTGTAGACCGGAAACGGTGTTCACGCCGCATCCGGCATTCGGTGCTCAATGCCTGA‑‑‑TGCGACGCTTAc                              <  2:1153847/140‑1 (MQ=38)                                                                                                                   tCGAGATTAAACAAGGTTTGAAAAAA‑CCTGCACGGGT‑GACCCGCCACGAAATTGAGGATGCTAAGGCTGTTGTAGACCGGAAACGGTGTTCACGCCGCATCCGGCATTCGGTGCTCAATGCCTGA‑‑‑TGCGACGCTTACcgc                           >  2:235632/1‑140 (MQ=255)                                                                                                                          aaaaaaaGGTTTAAAAAAC‑CCTGCGGGGGT‑GCCCCGCCACGAAATTGAGGATGCTAAGGCTGTTGTAGACCGGAAACGGTGTTCACGCCGCATCCGGCATTCGGTGCTCAATGCCTGA‑‑‑TGCGACGCTTACCGCGTCTTAt                    <  2:910195/139‑1 (MQ=37)                                                                                                                          aaaaCAGGGTTTAAAAAAC‑CCTGCGGGGGT‑GACCCGCCACGAAATTGAGGATGCTAAGGCTGTTGTAGACCGGAAACGGTGTTCACGCCGCATCCGGCATTCGGTGCTCAATGCCTGA‑‑‑TGCGACGCTTACCGCGTCTTAt                    <  2:157765/139‑1 (MQ=38)                                                                                                                          aaaaCAGGGTTAAAAAAAC‑CCGGCAGGGGT‑GCCCCGCCACGAAATTGAGGATGCTAAGGCTGTTGTAGACCGGAAACGGTGTTCACGCCGCATCCGGCATTCGGTGCTCAATGCCTGA‑‑‑TGCGACGCTTACCGCGTCTTAt                    <  2:183566/139‑1 (MQ=37)                                                                                                                           aaaaaaAGTTTAAAAAAACCCTGCAGGGGT‑GACCCGCCACGAAATTGAGGATGCTAAGGCTGTTGTAGACCGGAAACGGTGTTCACGCCGCATCCGGCATTCGGTGCTCAATGCCTGA‑‑‑TGCGACGCTTACCGCGTCTTAt                    <  2:1161658/140‑1 (MQ=38)                                                                                                                            aaaaaGGTGTGAAAAAG‑CCGGCAGGTGT‑GCCCCGCCACGAAATTGAGGATGCTAAGGCTGTTGTAGAC‑‑‑‑‑‑CGGTGTTCACGCCGCATCCGGCATTCGGTGCTCAATGCCTGA‑‑‑TGCGACGCTTACCGCGTCTTATCAGGCCTa            <  2:526569/137‑1 (MQ=21)                                                                                                                                 ggTTTGAAAAAA‑CCTGCACGGGT‑GACCCGCCACGAAATTGAGGATGCTAAGGCTGTTGTAGACCGGAAACGGTGTTCACGCCGCATCCGGCATTCGGTGCTCAATGCCTGA‑‑‑TGCGACGCTTACCGCGTCTTATCAGGCCt             >  2:106289/1‑140 (MQ=255)                                                                                                                                 ggTTTGAAAAAA‑CCTGCACGGGT‑GACCCGCCACGAAATTGAGGATGCTAAGGCTGTTGTAGACCGGAAACGGTGTTCACGCCGCATCCGGCATTCGGTGCTCAATGCCTGA‑‑‑TGCGACGCTTACCGCGTCTTATCAGGCCt             >  1:884629/1‑140 (MQ=255)                                                                                                                                 ggTTTGAAAAAA‑CCTGCACGGGT‑GACCCGCCACGAAATTGAGGATGCTAAGGCTGTTGTAGAC‑‑‑‑‑‑CGGTGTTCACGCCGCATCCGGCATTCGGTGCTCAATGCCTGA‑‑‑TGCGACGCTTACCGCGTCTTATCAGGCCTACAGtt       >  1:526569/1‑140 (MQ=37)                                                                                                                                  gTTTAAAAAAC‑CCTGCAGGGGT‑GCCCCGCCACGAAATTGAGGATGCTAAGGCTGTTGTAGACCGGAAACGGTGTTCACGCCGCATCCGGCATTCGGTGCTCAATGCCTGA‑‑‑TGCGACGCTTACCGCGTCTTATCAGGCCTa            <  1:406198/140‑1 (MQ=255)                                                                                                                                   tttGAAAAAA‑CCTGCACGGGT‑GACCCGCCACGAAATTGAGGATGCTAAGGCTGTTGTAGACCGGAAACGGTGTTCACGCCGCATCCGGCATTCGGTGCTCAATGCCTGATGCTGCGACGCTTACCGCGTCTTATCAGGcc              >  2:114568/1‑140 (MQ=38)                                                                                                                                   tttAAAAAAA‑CCCGGAAGGGTAGGCCCGCCACGAAATTGAGGATGCTAAGGCTGTTGTAGACCGGAAACGGTGTTCACGCCGCATCCGGCATTCGGTGCTCAATGCCTGA‑‑‑TGCGACGCTTACCGCGTCTTATCAGGCCTa            <  2:642737/140‑1 (MQ=37)                                                                                                                                    ttGAAAAAC‑CCTGCACGGGT‑GCCCCGCCACGAAATTGAGGATGCTAAGGCTGTTGTAGACCGGAAACGGTGTTCACGCCGCATCCGGCATTCGGTGCTCAATGCCTGA‑‑‑TGCGACGCTTACCGCGTCTTATCAGGCCTACa          <  1:235632/140‑1 (MQ=255)                                                                                                                                            a‑CCTGCACGGGT‑GACCCGCCACGAAATTGAGGATGCTAAGGCTGTTGTAGACCGGAAACGGTGTTCACGCCGCATCCGGCATTCGGTGCTCAATGCCTGA‑‑‑TGCGACGCTTACCGCGTCTTATCAGGCCTACAGTTTTACa  >  2:397361/1‑140 (MQ=255)                                                                                                                                            |                                                                                                                                                 TGGAACTGGTGCGGGAGATGATGGGGGAGCAGAGATAACCGTGATGAAACTGCTCAAAGGCGAGGTATAAAATGAGTTTTTTTGATGAGTTGAAAACCTCTCTGGAAGAGGCTGTCGAGATTAAACAAGGTTTGAAAAAA‑CCTGCACGGGT‑GACCCGCCACGAAATTGAGGATGCTAAGGCTGTTGTAGACCGGAAACGGTGTTCACGCCGCATCCGGCATTCGGTGCTCAATGCCTGA‑‑‑TGCGACGCTTACCGCGTCTTATCAGGCCTACAGTTTTACA  >  NC_000913/4628510‑4628788

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑