Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,001,918	0	A	C	28.8%	105.1 / 15.9	52	intergenic (‑129/+192)	fliA/fliC	RNA polymerase, sigma 28 (sigma F) factor/flagellar filament structural protein
Reads supporting (aligned to +/- strand):  ref base A (34/3);  new base C (0/15);  total (34/18)
Fisher's exact test for biased strand distribution p-value = 1.82e-10
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00
Rejected as consensus: Frequency below/above cutoff threshold.

TGAATTCACGATAAACAGCCCTGCGTTATATGAGTTATCGGCATGATTATCCGTTTCTGCAGGGTTTTTAATCGGACGATTAGTGGGTGAAATGAGGGGTTATTTGGGGGTTACAGGTAAATTCCAGGCAGAAAAAAA‑CC‑CCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATAAATTGCAATTCAACTTGTAGGCCTGATAAGCGC  >  NC_000913/2001781‑2002054                                                                                                                                          |                                                                                                                                           tGAATTCACGATAAACAGCCCTGCGTTATATGAGTTATCGGCATGATTATCCGTTTCTGCAGGGTTTTTAATCGGACGATTAGTGGGTGAAATGAGGGGTTATTTGGGGGTTACAGGTAAATTCCAGGCAGAAAAAAA‑cc                                                                                                                                         >  2:1788954/1‑140 (MQ=255)    aTTCACGATAAACAGCCCTGCGTTATATGAGTTATCGGCATGATTATCCGTTTCTGCAGGGTTTTTAATCGGACGATTAGTGGGTGAAATGAGGGGTTATTTGGGGGTTACAGGTAAATTCCAGGCAGAAAAAAA‑CC‑ccg                                                                                                                                     >  1:1534983/1‑140 (MQ=255)               aCAGCCCTGCGTTATATGAGTTATCGGCATGATTATCCGTTTCTGCAGGGTTTTTAATCGGACGATTAGTGGGTGAAATGAGGGGTTATTTGGGGGTTACAGGTAAATTCCAGGCAGAAAAAAA‑CC‑CCGCCGGTGGCggg                                                                                                                          >  1:116453/1‑140 (MQ=255)               aCAGCCCTGCGTTATATGAGTTATCGGCATGATTATCCGTTTCTGCAGGGTTTTTAATCGGACGATTAGTGGGTGAAATGAGGGGTTATTTGGGGGTTACAGGTAAATTCCAGGCAGAAAAAAA‑CC‑CCGCCGGTGGCggg                                                                                                                          >  1:1310217/1‑140 (MQ=255)                    ccTGCGTTATATGAGTTATCGGCATGATTATCCTTTTCGGCAGGTTTTTTAATGGGACGATTAGTGGGTGAAATGAGGGGTTATTGGGGGGTTACAGGAAAATTCCAGGCAAAAAAAAC‑CC‑CCGCCGGTGGCGGGGAAGc                                                                                                                     <  2:823338/140‑1 (MQ=255)                        cGTTATATGAGTTATCGGCATGATTATCCGTTTCTGCAGGGTTTTTAATCGGACGATTAGTGGGTGAAATGAGGGGTTATTTGGGGGTTACAGGTAAATTCCAGGCAGAAAAAAA‑CC‑CCGCCGGTGGCGGGGAAGCACGt                                                                                                                 >  2:464032/1‑140 (MQ=255)                        cGTTATATGAGTTATCGGCATGATTATCCGTTTCTGCAGGGTTTTTAATCGGACGATTAGTGGGTGAAATGAGGGGTTATTTGGGGGTTACAGGTAAATTCCAGGCAGAAAAAAA‑CC‑CCGCCGGTGGCGGGGAAGCACGt                                                                                                                 >  1:1744299/1‑140 (MQ=255)                          ttATATGAGTTATCGGCATGATTATCCTTTTCTGCAGGGTTTTTAATGGGACGATTAGTGGGTGAAATGAGGGGTTATTTGGGGGTTACAGGTAAATTCCAGCCAAAAAAAAA‑CC‑CCGCCGGTGGCGGGGAAGCACGTTg                                                                                                               <  2:1579906/140‑1 (MQ=255)                             tatGAGTTATCGGCATGATTATCCGTTTCTGCAGGGTTTTTAATCGGACGATTAGTGGGTGAAATGAGGGGTTATTTGGGGGTTACAGGTAAATTCCAGGCAGAAAAAAA‑CC‑CCGCCGGTGGCGGGGAAGCACGTTGCTg                                                                                                            >  2:2362670/1‑140 (MQ=255)                                  gTTATCGGCATGATTATCCGTTTCTGCAGGGTTTTTAATCGGACGATTAGTGGGTGAAATGAGGGGTTATTTGGGGGTTACAGGTAAATTCCAGGCAGAAAAAAA‑CC‑CCGCCGGTGGCGGGGAAGCACGTTGCTGACaaa                                                                                                       >  2:1257645/1‑140 (MQ=255)                                  gTTATCGGCATGATTATCCGTTTCTGCAGGGTTTTTAATCGGACGATTAGTGGGTGAAATGAGGGGTTATTTGGGGGTTACAGGTAAATTCCAGGCAGAAAAAAA‑CC‑CCGCCGGTGGCGGGGAAGCACGTTGCTGACaaa                                                                                                       >  2:198846/1‑140 (MQ=255)                                  gTTATCGGCATGATTATCCGTTTCTGCAGGGTTTTTAATCGGACGATTAGTGGGTGAAATGAGGGGTTATTTGGGGGTTACAGGTAAATTCCAGGCAGAAAAAAA‑CC‑CCGCCGGTGGCGGGGAAGCACGTTGCTGACaaa                                                                                                       >  2:2190094/1‑140 (MQ=255)                                   ttATGGGAATGATTATCCTTTTCTGCGGGTTTTTTAAGCGGACGATTAGGGGGTAAAATGGGGGGTTATTTGGGGGTTACAGGTAAATTCCAGGCAAAAAAACC‑CC‑CCGCCGGTGGCGGGGAAGCACGTTGCTGACAAAt                                                                                                      <  2:388576/140‑1 (MQ=255)                                   ttATCGGCATGATTATCCGTTTCTGCAGGGTTTTTAATCGGACGATTAGTGGGTGAAATGAGGGGTTATTTGGGGGTTACAGGTAAATTCCAGGCAGAAAAAAA‑CC‑CCGCCGGTGGCGGGGAAGCACGTTGCTGACAAAt                                                                                                      >  1:105015/1‑140 (MQ=255)                                    tATCGGAATGATTATCCTTTTCTGCGGGGTTTTTAATCGGACGATTAGTGGGTAAAAGGGGGGTTTATTTGGGGGTTACAGGTAAATTCCAGGCAAAAAAAAC‑CC‑CCGCCGGTGGCGGGGAAGCACGTTGCTGACAAAtt                                                                                                     <  2:1534983/140‑1 (MQ=255)                                     aTCGGCATGATTATCCGTTTCTGCAGGGTTTTTAATCGGACGATTAGTGGGTGAAATGAGGGGTTATTTGGGGGTTACAGGTAAATTCCAGGCAGAAAAAAA‑CC‑CCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTg                                                                                                    >  1:2107309/1‑140 (MQ=255)                                     aTCGGCATGATTATCCGTTTCTGCAGGGTTTTTAATCGGACGATTAGTGGGTGAAATGAGGGGTTATTTGGGGGTTACAGGTAAATTCCAGGCAGAAAAAAA‑CC‑CCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTg                                                                                                    >  1:2395399/1‑140 (MQ=255)                                     aTCGGCATGATTATCCGTTTCTGCAGGGTTTTTAATCGGACGATTAGTGGGTGAAATGAGGGGTTATTTGGGGGTTACAGGTAAATTCCAGGCAGAAAAAAA‑CC‑CCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTg                                                                                                    >  1:2420295/1‑140 (MQ=255)                                     aTCGGCATGATTATCCGTTTCTGCAGGGTTTTTAATCGGACGATTAGTGGGTGAAATGAGGGGTTATTTGGGGGTTACAGGTAAATTCCAGGCAGAAAAAAA‑CC‑CCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTg                                                                                                    >  2:922991/1‑140 (MQ=255)                                       ggggaTGATTATCCGTTCCGCGAGGTTTTTAAATCGTATGTTTAGTGGGAAAAATGAGGGTTTTTTTGGGGGATAAAGAAAAACCCCAGGCAAAAAAAAC‑CC‑CCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTgcg                                                                                                  <  2:2395399/136‑1 (MQ=255)                                                  tCCGTTTCTGCAGGGTTTTTAATCGGACGATTAGTGGGTGAAATGAGGGGTTATTTGGGGGTTACAGGTAAATTCCAGGCAGAAAAAAA‑CC‑CCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGc                                                                                       >  1:346760/1‑140 (MQ=255)                                                       ttCTGCAGGGTTTTTAATCGGACGATTAGTGGGTGAAATGAGGGGTTATTTGGGGGTTACAGGTAAATTCCAGGCAGAAAAAAA‑CC‑CCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGAt                                                                                  >  1:960211/1‑140 (MQ=255)                                                        tCTGCAGGGTTTTTAATCGGACGATTAGTGGGTGAAATGAGGGGTTATTTGGGGGTTACAGGTAAATTCCAGGCAGAAAAAAA‑CC‑CCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATg                                                                                 >  1:1851224/1‑140 (MQ=255)                                                                 tttttAATCGGACGATTAGTGGGTGAAATGAGGGGTTATTTGGGGGTTACAGGTAAATTCCAGGCAGAAAAAAA‑CC‑CCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTaaa                                                                        >  2:252489/1‑140 (MQ=255)                                                                   tttAATCGGACGATTGGTGGGTAAAATGGGGGGTTATTGGGGGGTTACAGGTAAATCCAAGGAAAAAAAAAC‑CC‑CCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACg                                                                      <  2:346760/140‑1 (MQ=255)                                                                           gACGATTAGTGGGTGAAATGAGGGGTTATTTGGGGGTTACAGGTAAATTCCAGGCAGAAAAAAA‑CC‑CCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATcc                                                              >  1:1743595/1‑140 (MQ=255)                                                                            aCGTTTAGGGGGTAAAGGGAGGGGTTTTTGGGGGGTTAGAGGTAAATGCCGGGCAGAAAAAAC‑CC‑CCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCg                                                             <  1:1788954/140‑1 (MQ=37)                                                                                      ggTGAAATGAGGGGTTATTTGGGGGTTATAGGTAAATTCCAGGCAGAAAAAAA‑CC‑CCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACaaaa                                                   >  2:1741613/1‑140 (MQ=255)                                                                                      ggTAAAATGGGGGGTTATTGGGGGGTTAGAGGTAAATTCCAGGCAGAAAAAAC‑CC‑CCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACaaaa                                                   <  1:2284088/140‑1 (MQ=38)                                                                                        tGAAATGAGGGGTTATTTGGGGGTTACAGGTAAATTCCAGGCAGAAAAAAA‑CC‑CCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAAt                                                 >  1:1052843/1‑140 (MQ=255)                                                                                                      aTTTGGGGGTTACAGGTAAATTCCAGGCAGAAAAAAA‑CC‑CCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATa                                   >  1:622443/1‑140 (MQ=255)                                                                                                            gggTTACAGGTAAATTCCAGGCAGAAAAAAA‑CC‑CCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATAAATTGc                             <  1:1257645/140‑1 (MQ=255)                                                                                                             ggTTACAGGTAAATTCCAGGAAAAAAAAAC‑CC‑CCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATAAATTGCa                            <  1:2190094/140‑1 (MQ=255)                                                                                                              gTTACAGGTAAATTCCAGGCAGAAAAAAA‑CC‑CCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATAAATTGCaa                           >  1:352001/1‑140 (MQ=255)                                                                                                              gTTACAGGTAAATTCCAGGCAGAAAAAAA‑CC‑CCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATAAATTGCaa                           >  2:2344471/1‑140 (MQ=255)                                                                                                               ttACAGGTAAATTCCAGGAAAAAAAAAC‑CC‑CCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATAAATTGCAAt                          <  2:680681/140‑1 (MQ=255)                                                                                                                tACAGGTAAATTCCAGGCAGAAAAAAA‑CC‑CCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATAAATTGCAAtt                         >  2:2275824/1‑140 (MQ=255)                                                                                                                 aCAGGTAAATTCCAGGCAGAAAAAAA‑CC‑CCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATAAATTGCAATTc                        >  1:1088145/1‑140 (MQ=255)                                                                                                                 aCAGGTAAATTCCAGGCAGAAAAAAA‑CC‑CCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATAAATTGCAATTc                        >  1:2340417/1‑140 (MQ=255)                                                                                                                 aCAGGTAAATTCCAGGCAGAAAAAAA‑CC‑CCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTACAAATTCAATAAATTGCAATTc                        >  2:493451/1‑140 (MQ=255)                                                                                                                  cAGGTAAATTCCAGGAAAAAAAAAC‑CC‑CCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATAAATTGCAATTCa                       <  1:1091787/140‑1 (MQ=255)                                                                                                                   aaggaaaTTCCCAGAAAAAAAAAA‑CCTCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATAAATTGCAATTCa                       <  2:2340417/136‑1 (MQ=25)                                                                                                                       aaaTCCCAGGAAAAAAAAAC‑CC‑CCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATAAATTGCAATTCAACTTg                  <  2:105015/140‑1 (MQ=255)                                                                                                                        aagtCCAAGCAAAAAAAAACCC‑CCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATAAATTGCAATTCAACTTg                  <  2:2107309/137‑1 (MQ=37)                                                                                                                        aaTTCCAGGCAGAAAAAAA‑CC‑CCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATAAATTGCAATTCAACTTGt                 >  2:824331/1‑140 (MQ=255)                                                                                                                            ccAGGAAGAAAAAAC‑CC‑CCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATAAATTGCAATTCAACTTGTAGGc             <  1:2138465/140‑1 (MQ=255)                                                                                                                            ccAGGAAAAAAAAAC‑CC‑CCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATAAATTGCAATTCAACTTGTAGGc             <  2:902790/140‑1 (MQ=255)                                                                                                                             cAGGCAGAAAAAAC‑CC‑CCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATAAATTGCAATTCa                       <  2:1423570/129‑1 (MQ=255)                                                                                                                             cAGGCAGAAAAAAA‑CC‑CCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATAAATTGCAATTCa                       >  1:1423570/1‑129 (MQ=255)                                                                                                                               ggCAGAAAAAAA‑CC‑CCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATAAATTGCAATTCAACTTGTAGGCCTg          >  1:1183347/1‑140 (MQ=255)                                                                                                                               ggCAGAAAAAAA‑CC‑CCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATAAATTGCAATTCAACTTGTAGGCCTg          >  1:81406/1‑140 (MQ=255)                                                                                                                               ggCAGAAAAAAA‑CC‑CCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATAAATTGCAATTCAACTTGTAGGCCTg          >  2:2283479/1‑140 (MQ=255)                                                                                                                                gaaaaaaaacc‑CC‑CCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATAAATTGCAATTCAACTTGTAGGCCTGa         <  2:1029169/136‑1 (MQ=255)                                                                                                                                gCAGAAAAAAC‑CC‑CCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATAAATTGCAATTCAACTTGTAGGCCTGa         <  1:2344471/140‑1 (MQ=255)                                                                                                                                 aaaaaaaaac‑CC‑CCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATAAATTGCAATTCAACTTGTAGGCCTGAt        <  2:81406/137‑1 (MQ=255)                                                                                                                                       aaac‑CC‑CCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATAAATTGCAATTCAACTTGTAGGCCTGATAagcgc  <  2:352001/140‑1 (MQ=255)                                                                                                                                          |                                                                                                                                           TGAATTCACGATAAACAGCCCTGCGTTATATGAGTTATCGGCATGATTATCCGTTTCTGCAGGGTTTTTAATCGGACGATTAGTGGGTGAAATGAGGGGTTATTTGGGGGTTACAGGTAAATTCCAGGCAGAAAAAAA‑CC‑CCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATAAATTGCAATTCAACTTGTAGGCCTGATAAGCGC  >  NC_000913/2001781‑2002054

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑