Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,101,514	0	G	T	23.2%	152.6 / 18.3	56	intergenic (+84/‑176)	sodA/kdgT	superoxide dismutase (Mn)/2‑dehydro‑3‑deoxy‑D‑gluconate:H(+) symporter
Reads supporting (aligned to +/- strand):  ref base G (7/36);  new base T (13/0);  total (20/36)
Fisher's exact test for biased strand distribution p-value = 4.10e-08
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00
Rejected as consensus: Frequency below/above cutoff threshold.

TGGTGAACTGGGACGAAGCAGCGGCACGTTTTGCGGCGAAAAAATAATCATTTGCCGCCTGCTGCAATGAGGCGTATAGGCCGCATATCAGCTTAAAAAATGAACCATCGCCAACGGCGGTGGTTTTTTTGTGATCAATTTCAAAATAAAAACAATGATCCGATAAAAATAAAACAGCGTTTCAATTGATGTGGTTTTGATCACTTTTATTGATTAAATGAATGTCTATCTTCGTTTCCATCAACACTGATGCTCCATTGAGG  >  NC_000913/4101384‑4101646                                                                                                                                   |                                                                                                                                     tggtgAACTGGGACGAAGCAGCGGCACGTTTTGCGGCGAAAAAATAATCATTTGCCGCCTGCTGCAATGAGGCGTATAGGCCGCATATCAGCTTAAAAAATGAACCATCGCCAACGGCGGTGGTTTTTTTGTGATCAAtt                                                                                                                             >  1:1015620/1‑140 (MQ=255) tggtgAACTGGGACGAAGCAGCGGCACGTTTTGCGGCGAAAAAATAATCATTTGCCGCCTGCTGCAATGAGGCGTATAGGCCGCATATCAGCTTAAAAAATGAACCATCGCCAACGGCGGTGGTTTTTTTGTGATCAAtt                                                                                                                             >  1:804134/1‑140 (MQ=255) tggtgAACTGGGACGAAGCAGCGGCACGTTTTGCGGCGAAAAAATAATCATTTGCCGCCTGCTGCAATGAGGCGTATAGGCCGCATATCAGCTTAAAAAATGAACCATCGCCAACGGCGGTGGGTTTTTTTTGGTTAAtt                                                                                                                             >  2:82933/1‑140 (MQ=255) tggtgAACTGGGACGAAGCAGCGGCACGTTTTGCGGCGAAAAAATAATCATTTGCCGCCTGCTGCAATGAGGCGTATAGGCCGCATATCAGCTTAAAAAATGAACCATCGCCAACGGCGGTGGGTTTTTTTTGGTCAAtt                                                                                                                             >  2:464868/1‑140 (MQ=255)   gtgAACTGGGACGAAGCAGCGGCACGTTTTGCGGCGAAAAAATAATCATTTGCCGCCTGCTGCAATGAGGCGTATAGGCCGCATATCAGCTTAAAAAATGAACCATCGCCAACGGCGGTGGTTTTTTTGTGATCAATTTc                                                                                                                           <  2:35235/140‑1 (MQ=255)      aaCTGGGACGAAGCAGCGGCACGTTTTGCGGCGAAAAAATAATCATTTGCCGCCTGCTGCAATGAGGCGTATAGGCCGCATATCAGCTTAAAAAATGAACCATCGCCAACGGCGGTGGTTTTTTTGTGATCAATTTCaaa                                                                                                                        >  1:1418425/1‑140 (MQ=255)      aaCTGGGACGAAGCAGCGGCACGTTTTGCGGCGAAAAAATAATCATTTGCCGCCTGCTGCAATGAGGCGTATAGGCCGCATATCAGCTTAAAAAATGAACCATCGCCAACGGCGGCGGGTTTTTTTTGATCAAATTTaaa                                                                                                                        >  2:765100/1‑140 (MQ=255)          gggACGAAGCAGCGGCACGTTTTGCGGCGAAAAAATAATCATTTGCCGCCTGCTGCAATGAGGCGTATAGGCCGCATATCAGCTTAAAAAATGAACCATCGCCAACGGCGGTGGTTTTTTTGTGATCAATTTCAAAATaa                                                                                                                    <  1:784964/140‑1 (MQ=255)            gACGAAGCAGCGGCACGTTTTGCGGCGAAAAAATAATCATTTGCCGCCTGCTGCAATGAGGCGTATAGGCCGCATATCAGCTTAAAAAATGAACCATCGCCAACGGCGGTGGGTTTTTTTTGATCAATTTtaaaataaaa                                                                                                                  >  2:1333720/1‑140 (MQ=255)             aCGAAGCAGCGGCACGTTTTGCGGCGAAAAAATAATCATTTGCCGCCTGCTGCAATGAGGCGTATAGGCCGCATATCAGCTTAAAAAATGAACCATCGCCAACGGCGGTGGGTTTTTTTTGATCAATTTTAAAATaaaaa                                                                                                                 >  2:467299/1‑140 (MQ=255)              cGAAGCAGCGGCACGTTTTGCGGCGAAAAAATAATCATTTGCCGCCTGCTGCAATGAGGCGTATAGGCCGCATATCAGCTTAAAAAATGAACCATCGCCAACGGCGGTGGTTTTTTTGTGATCAATTTCAAAATAAAAAc                                                                                                                <  2:481512/140‑1 (MQ=255)                    agcGGCACGTTTTGCGGCGAAAAAATAATCATTTGCCGCCTGCTGCAATGAGGCGTATAGGCCGCATATCAGCTTAAAAAATGAATCATCGCCAACGGCGGTGGTTTTTTTGTGATCAATTTCAAAATAAAAACAATGAt                                                                                                          <  2:644114/140‑1 (MQ=255)                     gctgCACGTTTTGCGGCGAAAAAATAATCATTTGCCGCCTGCTGCAATGAGGCGTATAGGCCGCATATCAGCTTAAAAAATGAACCATCGCCAACGACGGTGGGTTTTTTGTGATCAATTTCAAAAAAAAAAAAATGATc                                                                                                         >  1:1106209/4‑140 (MQ=255)                     gcGGCACGTTTTGCGGCGAAAAAATAATCATTTGCCGCCTGCTGCAATGAGGCGTATAGGCCGCATATCAGCTTAAAAAATGAACCATCGCCAACGGCGGTGGGTTTTTTTTGATCAAATTTAAAATaaaaaaaaaaatc                                                                                                         >  2:979774/1‑135 (MQ=255)                      cGGCACGTTTTGCGGCGAAAAAATAATCATTTGCCGCCTGCTGCAATGAGGCGTATAGGCCGCATATCAGCTTAAAAAATGAACCATCGCCAACGGCGGCGGGTTTTTTGTTATCAACTTTAaaaaaaaaaaaaaaatgc                                                                                                        >  2:638071/1‑134 (MQ=255)                                    gcgAAAAAATAATCATTTGCCGCCTGCTGCAATGAGGCGTATAGGCCGCATATCAGCTTAAAAAATGAACCATCGCCAACGGCGGTGGTTTTTTTGTGATCAATTTCAAAATAAAAACAATGATCCGATAAAAATAAAAc                                                                                          <  2:804134/140‑1 (MQ=255)                                         aaaaTAATCATTTGCCGCCTGCTGCAATGAGGCGTATAGGCCGCATATCAGCTTAAAAAATGAACCATCGCCAACGGCGGTGGTTTTTTTGTGATCAATTTCAAAATAAAAACAATGATCCGATAAAAATAAAACAGCGt                                                                                     <  1:467299/140‑1 (MQ=255)                                         aaaaTAATCATTTGCCGCCTGCTGCAATGAGGCGTATAGGCCGCATATCAGCTTAAAAAATGAACCATCGCCAACGGCGGTGGTTTTTTTGTGATCAATTTCAAAATAAAAACAATGATCCGATAAAAATAAAACAGCGt                                                                                     <  1:765100/140‑1 (MQ=255)                                            ataatCATTTGCCGCCTGCTGCAATGAGGCGTATAGGCCGCATATCAGCTTAAAAAATGAACCATCGCCAACGGCGGTGGTTTTTTTGTGATCAATTTCAAAATAAAAACAATGATCCGATAAAAATAAAACAGCGTTTc                                                                                  <  1:1227954/140‑1 (MQ=255)                                               atCATTTGCCGCCTGCTGCAATGAGGCGTATAGGCCGCATATCAGCTTAAAAAATGAACCATCGCCAACGGCGGTGGTTTTTTTGTGATCAATTTCAAAATAAAAACAATGATCCGATAAAAATAAAACAGCGTTTCAAt                                                                               <  1:82933/140‑1 (MQ=255)                                                   tttGCCGCCTGCTGCAATGAGGCGTATAGGCCGCATATCAGCTTAAAAAATGAACCATCGCCAACGGCGGTGGTTTTTTTGTGATCAATTTCAAAATAAAAACAATGATCCGATAAAAATAAAACAGCGTTTCAATTGAt                                                                           <  2:846183/140‑1 (MQ=255)                                                   tttGCCGCCTGCTGCAATGAGGCGTATAGGCCGCATATCAGCTTAAAAAATGAACCATCGCCAACGGCGGTGGTTTTTTTGTGATCAATTTCAAAATAAAAACAATGATCCGATAAAAATAAAACAGCGTTTCAATTGAt                                                                           <  2:1089847/140‑1 (MQ=255)                                                    ttGCCGCCTGCTGCAATGAGGCGTATAGGCCGCATATCAGCTTAAAAAATGAACCATCGCCAACGGCGGTGGTTTTTTTTTGGTCAATTTTAAAAAAAAAAAAAAAATCCGATAAAAA‑AAAAAAACGTTTTAATTTAtgt                                                                         >  2:1172748/1‑140 (MQ=255)                                                    ttGCCGCCTGCTGCAATGAGGCGTATAGGCCGCATATCAGCTTAAAAAATGAACCATCGCCAACGGCGGTGGTTTTTTTGTGATCAATTTCAAAATAAAAACAATGATCCGATAAAAATAAAACAGCGTTTCAATTGAtg                                                                          <  2:621847/140‑1 (MQ=255)                                                    ttGCCGCCTGCTGCAATGAGGCGTATAGGCCGCATATCAGCTTAAAAAATGAACCATCGCCAACGGCGGTGGTTTTTTTGTGATCAATTTCAAAATAAAAACAATGATCCGATAAAAATAAAACAGCGTTTCAATTGAtg                                                                          <  1:597323/140‑1 (MQ=255)                                                    ttGCCGCCTGCTGCAATGAGGCGTATAGGCCGCATATCAGCTTAAAAAATGAACCATCGCCAACGGCGGTGGTTTTTTTGTGATCAATTTCAAAATAAAAACAATGATCCGATAAAAATAAAACAGCGTTTCAATTGAtg                                                                          <  2:1608163/140‑1 (MQ=255)                                                    ttGCCGCCTGCTGCAATGAGGCGTATAGGCCGCATATCAGCTTAAAAAATGAACCATCGCCAACGGCGGTGGTTTTTTTGTGATCAATTTCAAAATAAAAACAATGATCCGATAAAAATAAAACAGCGTTTCAATTGAtg                                                                          <  1:920514/140‑1 (MQ=255)                                                    ttGCCGCCTGCTGCAATGAGGCGTATAGGCCGCATATCAGCTTAAAAAATGAACCATCGCCAACGGCGGTGGGTTTTTTTTGGTCAATTTCAAAAAAAAAAAAAAAATCCCATAAAAAAAAAAAAACGTTTTAATTTAtg                                                                          >  2:515539/1‑140 (MQ=255)                                                    ttGCCGCCTGCTGCAATGAGGCGTATAGGCCGCATATCAGCTTAAAAAATGAACCATCGCCAACGGCGGTGGGTTTTTTTTGATCAATTTTAAAATAAAAAAAAAGATCCGATAAAAAAAAAAAAACGGTTCAATTTAtg                                                                          >  2:1072934/1‑140 (MQ=255)                                                            tgctgcAATGAGGCGTATAGGCCGCATATCAGCTTAAAAAATGAACCATCGCCAACGGCGGTGGGTTTTTTTTGATCAATTTTAAAATAAAAACAATGATCCGATAAAAATAAAAAAGCGTTTCAATTTATGTGGttttt                                                                  >  2:131892/1‑139 (MQ=255)                                                              ctgcAATGAGGCGTATAGGCCGCATATCAGCTTAAAAAATGAACCATCGCCAACGGCGGTGGTTTTTTTGTGATCAATTTCAAAATAAAAACAATGATCCGATAAAAATAAAACAGCGTTTCAATTGATGTGGTTTTGAt                                                                <  2:563185/140‑1 (MQ=255)                                                              ctgcAATGAGGCGTATAGGCCGCATATCAGCTTAAAAAATGAACCATCGCCAACGGCGGTGGTTTTTTTGTGATCAATTTCAAAATAAAAACAATGATCCGATAAAAATAAAACAGCGTTTCAATTGATGTGGTTTTGAt                                                                <  2:1418425/140‑1 (MQ=255)                                                               tgcAATGAGGCGTATAGGCCGCATATCAGCTTAAAAAATGAACCATCGCCAACGGCGGTGGTTTTTTTGTGATCAATTTCAAAATAAAAACAATGATCCGATAAAAATAAAACAGCGTTTCAATTGATGTGGTTTTGATc                                                               <  1:638071/140‑1 (MQ=255)                                                                      aGGCGTATAGGCCGCATATCAGCTTAAAAAATGAACCATCGCCAACGGCGGTGGTTTTTTTGTGATCAATTTCAAAATAAAAACAATGATCCGATAAAAATAAAACAGCGTTTCAATTGATGTGGTTTTGATCACTTTTa                                                        <  1:453788/140‑1 (MQ=255)                                                                          gTATAGGCCGCATATCAGCTTAAAAAATGAACCATCGCCAACGGCGGTGGTTTTTTTGTGATCAATTTCAAAATAAAAACAATGATCCGATAAAAATAAAACAGCGTTTCAATTGATGTGGTTTTGATCACTTTTATTGa                                                    <  1:1458207/140‑1 (MQ=255)                                                                           tataGGCCGCATATCAGCTTAAAAAATGAACCATCGCCAACGGCGGAGGGTTTTTTTTGATCCAATTTAAAATAAAAAAAAATATCCGCTAAAAATAAAAAAGCGGTTCAATTGATGTGGGTTTTGTCACTTTTATTGAt                                                   >  2:1149823/1‑140 (MQ=255)                                                                             taGGCCGCATATCAGCTTAAAAAATGAACCATCGCCAACGGCGGTGGTTTTTTTTTTTTCAATTTCAAAATAAAAACAATGATCCGATAAAAATAAAAAAACGTTTCAATTGATGTGGTTTTGATCACTTTTATTGATTa                                                 >  1:594174/1‑140 (MQ=255)                                                                             taGGCCGCATATCAGCTTAAAAAATGAACCATCGCCAACGGCGGTGGGTTTTTTTTGATCAATTTTAAAATAAAAAAAAAGATCCGATAAAAAAAAAAAAACGGTTCAATTGATGTGGGTTTTATCACTTTTTTTGATTa                                                 >  1:811107/1‑140 (MQ=255)                                                                                gCCGCATATCAGCTTAAAAAATGAACCATCGCCAACGGCGGTGGTTTTTTTTTGATCAATTTCAAAATAAAAACAATGATCCGATAAAAATAAAAAAGCGTTTCAATTGATGTGGTTTTGATCACTTTTATTGATTAaat                                              >  1:934027/1‑140 (MQ=255)                                                                                gCCGCATATCAGCTTAAAAAATGAACCATCGCCAACGGCGGTGGTTTTTTTGTGATCAATTTCAAAATAAAAACAATGATCCGATAAAAATAAAACAGCGTTTCAATTGATGTGGTTTTGATCACTTTTATTGATTAaat                                              <  2:1015620/140‑1 (MQ=255)                                                                                 ccGCATATCAGCTTAAAAAATGAACCATCGCCAACGGCGGTGGTTTTTTTGTGATCAATTTCAAAATAAAAACAATGATCCGATAAAAATAAAACAGCGTTTCAATTGATGTGGTTTTGATCACTTTTATTGATTAaatg                                             <  1:131892/140‑1 (MQ=255)                                                                                  cGCATATCAGCTTAAAAAATGAACCATCGCCAACGGCGGTGGTTTTTTTGTGATCAATTTCAAAATAAAAACAATGATCCGATAAAAATAAAACAGCGTTTCAATTGATGTGGTTTTGATCACTTTTATTGATTAaatga                                            <  1:590644/140‑1 (MQ=255)                                                                                   gCATATCAGCTTAAAAAATGAACCATCGCCAACGGCGGTGGGTTTTTTGTGATCAATTTTAAAATAAAAAAAATAATCCGATAAAAAAAAAAAAGCGTTTTAATTGATGTGGGTTTGATCACTTTTTTTGTTTAaatgaa                                           >  2:679247/1‑140 (MQ=255)                                                                                     atatCAGCTTAAAAAATGAACCATCGCCAACGGCGGTGGTTTTTTTTTGATCAATTTTAAAATAAAAACAAAGATCCGATAAAAATAAAAAAGCGTTTCAATTGATGTGGTTTTGATCACTTTTTTTTATTAaatgaatg                                         >  2:93615/1‑140 (MQ=255)                                                                                          aGCTTAAAAAATGAACCATCGCCAACGGCGGTGGGTTTTTTGTGATCAATTTCAAAAAAAAAACAATGATCCGATAAAAATAAAACAGCGTTTCAATTGATGTGGTTTTGATCACTTTTATTGATTAAATGAATGTCTAt                                    >  1:730491/1‑140 (MQ=255)                                                                                            cTTAAAAAATGAACCATCGCCAACGGCGGTGGTTTTTTTGTGATCAATTTCAAAATAAAAACAATGATCCGATAAAAATAAAACAGCGTTTCAATTGATGTGGTTTTGATCACTTTTATTGATTAAATGAATGTCTATCt                                  <  1:464868/140‑1 (MQ=255)                                                                                                 aaaaTGAACCATCGCCAACGGCGGTGGTTTTTTTGTGATCAATTTCAAAATAAAAACAATGATCCGATAAAAATAAAACAGCGTTTCAATTGATGTGGTTTTGATCACTTTTATTGATTAAATGAATGTCTATCTTCGtt                             <  2:1251827/140‑1 (MQ=255)                                                                                                       aaCCATCGCCAACGGCGGTGGTTTTTTTGTGATCAATTTCAAAATAAAAACAATGATCCGATAAAAATAAAACAGCGTTTCAATTGATGTGGTTTTGATCACTTTTATTGATTAAATGAATGTCTATCTTCGTTTCCATc                       <  2:811107/140‑1 (MQ=255)                                                                                                           aTCGCCAACGGCGGTGGGTTTTTTTTGATCAATTTCAAAATAAAAAAAAAGATCCGATAAAAATAAAAAAACGGTTTAATTGATGTGGGTTTTATCACTTTTATTGATTAAAAGAATGTCTATCTTCGTTTTCATCAaca                   >  2:1236931/1‑140 (MQ=255)                                                                                                            tCGCCAACGGCGGTGGTTTTTTTGTGATCAATTTCAAAATAAAAACAATGATCCGATAAAAATAAAACAGCGTTTCAATTGATGTGGTTTTGATCACTTTTATTGATTAAATGAATGTCTATCTTCGTTTCCATCAacac                  <  2:12750/140‑1 (MQ=255)                                                                                                            tCGCCAACGGCGGTGGTTTTTTTGTGATCAATTTCAAAATAAAAACAATGATCCGATAAAAATAAAACAGCGTTTCAATTGATGTGGTTTTGATCACTTTTATTGATTAAATGAATGTCTATCTTCGTTTCCATCAacac                  <  1:515539/140‑1 (MQ=255)                                                                                                             cGCCAACGGCGGTGGTTTTTTTGTGATCAATTTCAAAATAAAAACAATGATCCGATAAAAATAAAACAGCGTTTCAATTGATGTGGTTTTGATCACTTTTATTGATTAAATGAATGTCTATCTTCGTTTCCATCAACACt                 >  1:1247613/1‑140 (MQ=255)                                                                                                             cGCCAACGGCGGTGGGTTTTTTTTGGTCAATTTTAAAATAAAAAAAATGATCCGATAAAAATAAAAAAGCGTTTCAATTTATGTGGTTTTTATCACTTTTTTTTATTAAATGAATGTCTATCTTCGTTTCCATCAacacc                 >  2:11035/1‑139 (MQ=255)                                                                                                             cGCCAACGGCGGTGGGTTTTTTTTGATCAATTTTAAAATAAAAAAAAAGATCCGGTAAAAATAAAACAGCGGTTCAATTGATGTGGGTTTTATCACTTTTATTTATTAAATGAATGTCTATCTTTGTTTTCATCAacacc                 >  2:463383/1‑139 (MQ=255)                                                                                                                 aaCGGCGGTGGTTTTTTTGTGATCAATTTCAAAATAAAAACAATGATCCGATAAAAATAAAACAGCGTTTCAATTGATGTGGTTTTGATCACTTTTATTGATTAAATGAATGTCTATCTTCGTTTCCATCAACACTGATg             <  2:1106209/140‑1 (MQ=255)                                                                                                                  aCGGCGGTGGTTTTTTTGTGATCAATTTCAAAATAAAAACAATGATCCGAT‑AAAATAAAACAGCGTTTCAATTGATGTGGTTTTGATCACTTTTATTGATTAAATGAATGTCTATCTTCGTTTCCATCAACACTGATGCt           <  1:1172748/140‑1 (MQ=255)                                                                                                                   cggcggTGGTTTTTTTGTGATCAATTTCAAAATAAAAACAATGATCCGATAAAAATAAAACAGCGTTTCAATTGATGTGGTTTTGATCACTTTTATTGATTAAATGAATGTCTATCTTCGTTTCCATCAACACTGATGCt           <  1:1072934/140‑1 (MQ=255)                                                                                                                    ggcggTGGTTTTTTTGTGATCAATTTCAAAATAAAAACAATGATCCGATAAAAATAAAACAGCGTTTCAATTGATGTGGTTTTGATCACTTTTATTGATTAAATGAATGTCTATCTTCGTTTCCATCAACACTGATGCTc          <  1:1149823/140‑1 (MQ=255)                                                                                                                         tggtTTTTTTGTGATCAATTTCAAAATAAAAACAATGATCCGATAAAAATAAAACAGCGTTTCAATTGATGTGGTTTTGATCACTTTTATTGATTAAATGAATGTCTATCTTCGTTTCCATCAACACTGATGCTCCATTg     <  1:88556/140‑1 (MQ=255)                                                                                                                           gtTTTTTTGTGATCAATTTCAAAATAAAAACAATGATCCGATAAAAATAAAACAGCGTTTCAATTGATGTGGTTTTGATCACTTTTATTGATTAAATGAATGTCTATCTTCGTTTCCATCAACACTGATGCTCCATTGAg   <  1:556950/140‑1 (MQ=255)                                                                                                                            tttttttGTGATCAATTTCAAAATAAAAACAATGATCCGATAAAAATAAAACAGCGTTTCAATTGATGTGGTTTTGATCACTTTTATTGATTAAATGAATGTCTATCTTCGTTTCCATCAACACTGATGCTCCATTGAgg  <  1:1333720/140‑1 (MQ=255)                                                                                                                            tttttttGTGATCAATTTCAAAATAAAAACAATGATCCGATAAAAATAAAACAGCGTTTCAATTGATGTGGTTTTGATCACTTTTATTGATTAAATGAATGTCTATCTTCGTTTCCATCAACACTGATGCTCCATTGAgg  <  1:679247/140‑1 (MQ=255)                                                                                                                                   |                                                                                                                                     TGGTGAACTGGGACGAAGCAGCGGCACGTTTTGCGGCGAAAAAATAATCATTTGCCGCCTGCTGCAATGAGGCGTATAGGCCGCATATCAGCTTAAAAAATGAACCATCGCCAACGGCGGTGGTTTTTTTGTGATCAATTTCAAAATAAAAACAATGATCCGATAAAAATAAAACAGCGTTTCAATTGATGTGGTTTTGATCACTTTTATTGATTAAATGAATGTCTATCTTCGTTTCCATCAACACTGATGCTCCATTGAGG  >  NC_000913/4101384‑4101646

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑