Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,001,918	0	A	C	33.9%	87.1 / 26.0	57	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 (0/19);  total (34/23)
Fisher's exact test for biased strand distribution p-value = 3.63e-12
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00
Rejected as consensus: Frequency below/above cutoff threshold.

AATTCACGATAAACAGCCCTGCGTTATATGAGTTATCGGCATGATTATCCGTTTCTGCAGGGTTTTTAATCGGACGATTAGTGGGTGAAATGAGGGGTTATTTGGGGGTTACAGGTAAATT‑CCAGG‑CAGAAAAAAACCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATAAATTGCAATTCAACTTGTAGGCCTGAT  >  NC_000913/2001783‑2002048                                                                                                                                          |                                                                                                                                   aaTTCACGATAAACAGCCCTGCGTTATATGAGTTATCGGCATGATTATCCGTTTCTGCAGGGTTTTTAATCGGACGATTAGTGGGTGAAATGAGGGGTTATTTGGGGGTTACAGGT‑AATT‑CCAGG‑CAGAAAAAAACCccg                                                                                                                               >  1:1195398/1‑140 (MQ=255)  aTTCACGATAAACAGCCCTGCGTTATATGAGTTATCGGCATGATTATCCGTTTCTGCAGGGTTTTTAATCGGACGATTAGTGGGTGAAATGAGGGGTTATTTGGGGGTTACAGGTAAATT‑CCAGG‑CAGAAAAAAACCccg                                                                                                                               >  1:590602/1‑140 (MQ=255)   ttCACGAAAAACAGCCCTGCTTTATATGAGTTATCGGCATGTTTATCCGTTTCTGCGGGTTTTTTAATCGGACGATTAGTGGGTAAAATGAGGGTTTATTGGGGGGTTAAAGGTAATTT‑CCAGG‑CAAAAAAAACCCccgc                                                                                                                              <  2:590602/140‑1 (MQ=255)           aaaCAGCCCTGCGTTATATGAGTTATCGGCATGATTATCCGTTTCTGCAGGGTTTTTAATCGGACGATTAGTGGGTGAAATGAGGGGTTATTTGGGGGTTACAGGTAAATT‑CCAGG‑CAGAAAAAAACCCCGCCGGTGGCg                                                                                                                      >  1:1178058/1‑140 (MQ=255)                  ccTGCTTTATATGAGTTATCGGCATGATTATCCGTTTCTGCAGGTTTTTTAATCGGACGATTAGTGGGTAAAATGAGGGTTTATTGGGGGGTTACAGGTAAATC‑CCAGG‑CAAAAAAAACCCCCGCCGGTGGCGGGGAAGc                                                                                                               <  1:683037/140‑1 (MQ=255)                                gTTATCGGCATGATTATCCGTTTCTGCAGGGTTTTTAATCGGACGATTAGTGGGTGAAATGAGGGGTTATTTGGGGGTTACAGGTAAATT‑CCAGG‑CAGAAAAAAACCCCGCCGGTGGCGGGGAAGCACGTTGCTGACaaa                                                                                                 >  2:532969/1‑140 (MQ=255)                                gTTATCGGCATGATTATCCGTTTCTGCAGGGTTTTTAATCGGACGATTAGTGGGTGAAATGAGGGGTTATTTGGGGGTTACAGGTAAATT‑CCAGG‑CAGAAAAAAACCCCGCCGGTGGCGGGGAAGCACGTTGCTGACaaa                                                                                                 >  1:568029/1‑140 (MQ=255)                                  tATCGGCATGATTATCCGTTTCTGGAGGTTTTTTAATCGGACGATTAGGGGGTAAAAGGAGGGGTTATTGGGGGTTTACAGGTAAATT‑CCAGG‑AAAAAAAAACCCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAAtt                                                                                               <  2:476477/140‑1 (MQ=255)                                   aTCGGCATGATTATCCGTTTCTGCAGGGTTTTTAATCGGACGATTAGTGGGTGAAATGAGGGGTTATTTGGGGGTTACAGGTAAATT‑CCAGG‑CAGAAAAAAACCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTg                                                                                              >  2:1265544/1‑140 (MQ=255)                                   aTCGGCATGATTATCCGTTTCTGCAGGGTTTTTAATCGGACGATTAGTGGGTGAAATGAGGGGTTATTTGGGGGTTACAGGTAAATT‑CCAGG‑CAGAAAAAAACCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTg                                                                                              >  2:927118/1‑140 (MQ=255)                                     cGGCATGATTATCCGTTTCTGCAGGGTTTTTAATCGGACGATTAGTGGGTGAAATGAGGGGTTATTTGGGGGTTACAGGTAAATT‑CCAGG‑CAGAAAAAAACCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTgcg                                                                                            >  2:711038/1‑140 (MQ=255)                                     cGGCATGATTATCCGTTTCTGCAGGGTTTTTAATCGGACGATTAGTGGGTGAAATGAGGGGTTATTTGGGGGTTACAGGTAAATT‑CCAGG‑CAGAAAAAAACCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTgcg                                                                                            >  1:415461/1‑140 (MQ=255)                                     cGGCATGATTATCCGTTTCTGCAGGGTTTTTAATCGGACGATTAGTGGGTGAAATGAGGGGTTATTTGGGGGTTACAGGTAAATT‑CCAGG‑CAGAAAAAAACCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTacg                                                                                            >  2:948941/1‑140 (MQ=255)                                          tGATTATCCGTTTCTGCAGGGTTTTTAATCGGACGATTAGTGGGTGAAATGAGGGGTTATTTGGGGGTTACAGGTAAATT‑CCAGG‑CAGAAAAAAACCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTa                                                                                       >  1:476477/1‑140 (MQ=255)                                           gATTATCCGTTTCTGCAGGGTTTTTAATCGGACGATTAGTGGGTGAAATGAGGGGTTATTTGGGGGTTACAGGTAAATT‑CCAGG‑CAGAAAAAAACCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTAt                                                                                      >  2:1263934/1‑140 (MQ=255)                                                tCCGTTTCTGCAGGGTTTTTAATCGGACGATTAGTGGGTGAAATGAGGGGTTATTTGGGGGTTACAGGTAAATT‑CCAGG‑CAGAAAAAAACCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGc                                                                                 >  1:1379545/1‑140 (MQ=255)                                                 ccGTTTCTGCAGGGTTTTTAATCGGACGATTAGCGGGTGAAATGAGGGGTTATTTGGGGGTTACAGGTAAATT‑CCAGG‑CAGAAAAAAACCCCGCCGGTGGCGGGGCAGCACGTTGCTGACAAATTGCGCTTTATGTTGcc                                                                                >  1:420903/1‑140 (MQ=255)                                                     ttCTGCAGGGTTTTTAATCGGACGATTAGTGGGTGAAATGAGGGGTTATTTGGGGGTTACAGGTAAATT‑CCAGG‑CAGAAAAAAACCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGAt                                                                            >  2:392012/1‑140 (MQ=255)                                                      tCTGCAGGGTTTTTAATCGGACGATTAGTGGGTGAAATGAGGGGTTATTTGGGGGTTACAGGTAAATT‑CCAGG‑CAGAAAAAAACCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATg                                                                           >  1:679091/1‑140 (MQ=255)                                                        tGCAGGGTTTTTAATCGGACGATTAGTGGGTGAAATGAGGGGTTATTTGGGGGTTACAGGTAAATT‑CCAGG‑CAGAAAAAAACCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATgcg                                                                         >  1:700549/1‑140 (MQ=255)                                                          cAGGGTTTTTAATCGGACGATTAGTGGGTGAAATGAGGGGTTATTTGGGGGTTACAGGTAAATT‑CCAGG‑CAGAAAAAAACCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATgcggc                                                                       >  1:492611/1‑140 (MQ=255)                                                             ggTTTTTAATCGGACGATTAGTGGGTGAAATGAGGGGTTATTTGGGGGTTACAGGT‑AATT‑CCAGG‑CAGAAAAAAACCCCGCCGGTTGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTaa                                                                   <  2:1195398/140‑1 (MQ=255)                                                             ggTTTTAAATCGGGCGATTAGTGGGTAAAATGGGGATTTATTGGGGGTTCACAGGAAATTT‑CCAGG‑CAGAAAAAACCCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTa                                                                    <  2:700549/140‑1 (MQ=255)                                                              gTTTTTAATCGGACGATTAGTGGGTGAAATGAGGGGTTATTTGGGGGTTACAGGTAAATT‑CCAGG‑CAGAAAAAAACCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTaa                                                                   >  1:13830/1‑140 (MQ=255)                                                               tttttAATCGGACGATTGGGGGGTAAAAGGGGGGGTTATTTGGGGGTTACAGGTAAATT‑CCAGG‑CAAAAAAAACCCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTaaa                                                                  <  1:503748/140‑1 (MQ=255)                                                                         gACGATTAGTGGGTGAAATGAGGGGTTATTTGGGGGTTACAGGTAAATT‑CCAGG‑CAGAAAAAAACCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATcc                                                        >  1:819320/1‑140 (MQ=255)                                                                         gACGATTAGTGGGTGAAATGAGGGGTTATTTGGGGGTTACAGGTAAATT‑CCAGG‑CAGAAAAAAACCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATcc                                                        >  2:853976/1‑140 (MQ=255)                                                                         gACGATTAGTGGGTGAAATGAGGGGTTATTTGGGGGTTACAGGTAAATT‑CCAGG‑CAGAAAAAAACCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATcc                                                        >  1:409585/1‑140 (MQ=255)                                                                         gACGATTAGTGGGTGAAATGAGGGGTTATTTGGGGGTTACAGGTAAATT‑CCAGG‑CAGAAAAAAACCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACACCTTATcc                                                        >  2:166071/1‑140 (MQ=255)                                                                          accaTTAGGGGGTGAAATGGGGGGTTATTGGGGGATTAGAGATAAATC‑CCAGG‑CAGAAAAAACCCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCg                                                       <  2:130962/137‑1 (MQ=38)                                                                          acaaTTAGTGGGTAAAATGGGGGGTTATTTGGGGGTTAAAGG‑AAATT‑CCAGGACAGAAAAAACCCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCg                                                       <  2:744813/137‑1 (MQ=38)                                                                          aCGATTGGTGGGTAAAATGAGGGTTTTTTGGGGGTTTACAGGTAAATC‑CCAGG‑AAAAAAAAACCCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCg                                                       <  2:679091/140‑1 (MQ=37)                                                                          aCGATTAGTGGGTGAAATGAGGGGTTATTTGGGGGTTACAGGTAAATT‑CCAGG‑AAAAAAAAACCCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCg                                                       <  1:1347380/140‑1 (MQ=255)                                                                          aCGATTAGTGGGTAAAATGGGGGTTTTTTTGGGGTTTACAGGAAAATC‑CCAGG‑AAAAAAAAACCCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCg                                                       <  1:245332/140‑1 (MQ=37)                                                                                        aaaTGAGGGGTTATTTGGGGGTTACAGGTAAATT‑CCAGG‑CAGAAAAAAACCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAAtgt                                         >  2:571414/1‑140 (MQ=255)                                                                                                  ttATTTGGGGGTTACAGGTAAATT‑CCAGG‑CAGAAAAAAACCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCaa                               >  1:1295075/1‑140 (MQ=255)                                                                                                   tATTTGGGGGTTACAGGTAAATT‑CCAGG‑CAGAAAAAAACCCCGACGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAAt                              >  2:1101068/1‑140 (MQ=255)                                                                                                    tttggggggTTACGGGAAAATC‑CCAGG‑CAAAAAAAACCCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATa                             <  1:948941/136‑1 (MQ=37)                                                                                                    aTTTGGGGGTTACAGGTAAATT‑CCAGG‑CAGAAAAAAACCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATa                             >  2:893049/1‑140 (MQ=255)                                                                                                    aTTTGGGGGTTACAGGTAAATT‑CCAGG‑CAGAAAAAAACCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATa                             >  1:507827/1‑140 (MQ=255)                                                                                                    aTTTGGGGGTTACAGGTAAATT‑CCAGG‑CAGAAAAAAACCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATa                             >  2:517732/1‑140 (MQ=255)                                                                                                       ggggggTTACAGGAAATTC‑CCAGG‑CAAAAAAAAGCCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATAAAt                          <  2:420903/139‑1 (MQ=37)                                                                                                        gggggTTAAAGGTAAATC‑CCAGG‑AAGAAAAAACCCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATAAAtt                         <  2:568029/140‑1 (MQ=255)                                                                                                          gggTTACAGGTAAATT‑CCAGG‑AAAAAAAAACCCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATAAATTGc                       <  1:711038/140‑1 (MQ=255)                                                                                                           ggTTACAGGTAAATT‑CCAGG‑CAGAAAAAAACCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGGGCAACTTCAATAAATTGCa                      >  2:111071/1‑140 (MQ=255)                                                                                                           ggTTAAAAGGAAATTCCCAGG‑AAAAAAAAACCCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATAAATTGc                       <  2:507827/140‑1 (MQ=25)                                                                                                               aCAGGTAAATT‑CCAGG‑CAGAAAAAAACCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATAAATTGCAATTc                  >  2:406007/1‑140 (MQ=255)                                                                                                               aCAGGTAAATT‑CCAGG‑CAGAAAAAAACCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATAAATTGCAATTc                  >  1:1025532/1‑140 (MQ=255)                                                                                                                cAGGTAAATT‑CCAGG‑CAGAAAAAAACCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATAAATTGCAATTCa                 <  2:913262/140‑1 (MQ=255)                                                                                                                aaGGTAAATT‑CCGGG‑AAAAAAAAACCCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATAAATTGCAATTCa                 <  1:1098498/139‑1 (MQ=255)                                                                                                                aaGGAAAATT‑CCAGG‑AAAAAAAAACCCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATAAATTGCAATTCa                 <  2:1153089/139‑1 (MQ=255)                                                                                                                     aaaTT‑CCAGG‑CAGAAAAAACCCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATAAATTGCAATTCAACTTg            <  1:392012/140‑1 (MQ=255)                                                                                                                      aaTT‑CCAGG‑CAGAAAAAAACCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATAAATTGCAATTCAACTTGt           >  1:1099670/1‑140 (MQ=255)                                                                                                                       aTT‑CCAGG‑CAAAAAAAACCCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATAAATTGCAATTCAACTTGTa          <  1:1374879/140‑1 (MQ=255)                                                                                                                           ccAGG‑AAAAAAAAACCCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATAAATTGCAATTCAACTTGTAGGc       <  2:409585/140‑1 (MQ=255)                                                                                                                           ccAGG‑AAAAAAAAACCCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATAAATTGCAATTCAACTTGTAGGc       <  2:1099670/140‑1 (MQ=255)                                                                                                                            cAGG‑CAGAAAAAAACCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATAAATTGCAATTCAACTTGTAGGcc      >  2:873940/1‑140 (MQ=255)                                                                                                                                 cAGAAAAAAACCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATAAATTGCAATTCAACTTGTAGGCCTGAt  <  2:1379545/140‑1 (MQ=255)                                                                                                                                          |                                                                                                                                   AATTCACGATAAACAGCCCTGCGTTATATGAGTTATCGGCATGATTATCCGTTTCTGCAGGGTTTTTAATCGGACGATTAGTGGGTGAAATGAGGGGTTATTTGGGGGTTACAGGTAAATT‑CCAGG‑CAGAAAAAAACCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATAAATTGCAATTCAACTTGTAGGCCTGAT  >  NC_000913/2001783‑2002048

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑