Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,412,898	0	C	T	42.1%	56.6 / 43.4	58	A190T (GCC→ACC)	acrS	acrAB operon transcriptional repressor
Reads supporting (aligned to +/- strand):  ref base C (32/1);  new base T (0/24);  total (32/26)
Fisher's exact test for biased strand distribution p-value = 3.32e-15
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CCACTAAAACTGGTTAACTGTGACGAACTGAATTTTCAGGACAGAATGTGAATTTACATGACACTTAATTCATTCGTTTGATGAATTAATTTCGTTATGTTTTCATCTGGCATGAACATTCTTAATACGTTATCGACCAGAGCGGGGGCTTGTTTATAAAGATCATAACCCGCCATATTCATTAACCAGTTTTGAACAATTCCGCTGAAGGCACCATCAATAATAATCATCACAACATCTAAATCGAGGTTATTTGCTACACAACCTTGTTGCTGACACGCCTGCAATACTTCGCGG  >  NC_000913/3412750‑3413046                                                                                                                                                     |                                                                                                                                                     ccACTAAAACTGGTTAACTGTGACGAACTGAATTTTCAGGACAGAATGTGAATTTACATGACACTTAATTCATTCGTTTGATGAATTAATTTCGTTATGTTTTCATCTGGCATGAACATTCTTAATACGTTATCGACCAGAGCGGGGGCtt                                                                                                                                                    >  2:306935/1‑151 (MQ=255)       aaaCTGGTTAACTGTGACGAACTGAATTTTCAGGACAGAATGTGAATTTACATGACACTTAATTCATTCGTTTGATGAATTAATTTCGTTATGTTTTCATCTGGCATGAACATTCTTAATACGTTATCGACCAGAGCGGGGGCTTGTTtat                                                                                                                                              <  1:804734/151‑1 (MQ=255)          cTGGTTAACTGTGACGAACTGAATTTTCAGGACAGAATGTGAATTTACATGACACTTAATTCATTCGTTTGATGAATTAATTTCGTTATGTTTTCATCTGGCATGAACATTCTTAATACGTTATCGACCAGAGCGGGGGCTTGTTTATaa                                                                                                                                            >  2:240470/1‑150 (MQ=255)              ttAACTGTGACGAACTGAATTTTCAGGACAGAATGTGAATTTACATGACACTTAATTCATTCGTTTGATGAATTAATTTCGTTATGTTTTCATCTGGCATGAACATTCTTAATACGTTATCGACCAGAGCGGGGGCTTGTTTATaa                                                                                                                                            >  1:215864/1‑146 (MQ=255)               tAACTGTGACGAACTGAATTTTCAGGACAGAATGTGAATTTACATGACACTTAATTCATTCGTTTGATGAATTAATTTCGTTATGTTTTCATCTGGCATGAACATTCTTAATACGTTATCGACCAGAGCGGGGGCTTGTTTATAAAGATc                                                                                                                                       >  1:290628/1‑150 (MQ=255)                  cTGTGACGAACTGAATTTTCAGGACAGAATGTGAATTTACATGACACTTAATTCATTCGTTTGATGAATTAATTTCGTTATGTTTTCATCTGGCATGAACATTCTTAATACGTTATCGACCAGAGCGGGGGCTTGTTTATAAAGATCATa                                                                                                                                    >  2:687430/1‑150 (MQ=255)                          aaCTGAATTTTAAGGATAGAATGTGAATTTACATGACTCTTAATTCTTTCGTTTGATAAATTAATTTCTTTTTGTTTTCATCTGGCATGAACATTCTTAATACTTTACCGCCCAGAGCGGGGGTTTGTTTATAAAAATCATACCCCGCCat                                                                                                                           <  2:215701/151‑1 (MQ=255)                              gAATTTTCAGGACAGAATGTGAATTTACATGACACTTAATTCATTCGTTTGATGAATTAATTTCGTTATGTTTTCATCTGGCATGAACATTCTTAATACGTTATCGACCAGAGCGGGGGCTTGTTTATAAAGATCATAACCCGCCATATTc                                                                                                                       >  2:153225/1‑151 (MQ=255)                                      agaaCAAAATGTTAATTTACATGCCATTTAATTCTTTTTTTTGATAAATTATTTTCGTTATTTTTTCATCTGGCATAAACTTTTTTAATCCGTTACCGACCAGAGCGGGGTTTTTTTTATAAAAATCATAACCCGCCATATTCATTaa                                                                                                                  <  2:971606/145‑1 (MQ=255)                                             aaTGTGAATTTACATGACACTTAATTCATTCGTTTGATGAATTAATTTCGTTATGTTTTCATCTGGCATGAACATTCTTAATACGTTATCGACCAGAGCGGGGGCTTGTTTATAAAGATCATAACCCGCCATATTCATTAACCAGTTTTg                                                                                                         >  2:456365/1‑150 (MQ=255)                                              aTGTGAATTTACATGACACTTAATTCATTCGTTTGATGAATTAATTTCGTTATGTTTTCATCTGGCATGAACATTCTTAATACGTTATCGACCAGAGCGGGGGCTTGTTTATAAAGATCATAACCCGCCATATTCATTAACCAGTTTTGa                                                                                                        >  2:201133/1‑150 (MQ=255)                                               tgtgAATTTACATGACTTTTAATTCATTCTTTTGATGAATTAATTTTTTTATTTTTTCATCTGGCATGAACATTTTTAATACGTTATCGCCCAGAGGGGGGGTTTGTTTAAAAAGATCAAACCCCGCCATATTCATTAACCAGTTTTGaa                                                                                                       <  1:744053/150‑1 (MQ=255)                                                   aaTTTACATGACACTTAATTCATTCGTTTGATGAATTAATTTCGTTATGTTTTCATCTGGCATGAACATTCTTAATACGTTATCGACCAGAGCGGGGGCTTGTTTATAAAGATCATAACCCGCCATATTCATTAACCAGTTTTGAACAAtt                                                                                                  >  2:673177/1‑151 (MQ=255)                                                      ttACATGACATTTAATTCATTCTTTTGATGAATTAATTTCGTTTTTTTTTCATCTGGAATGAACATTTTTAATACGTTATCGACCAGGGGGGGGGTTTGTTTATAAAGATCATAACCCGCCATATTCATTAACCAGTTTTGAACAATTcc                                                                                                <  1:30294/150‑1 (MQ=255)                                                       tACATGACACTTAATTCATTCGTTTGATGAATTAATTTCGTTATGTTTTCATCTGGCATGAACATTCTTAATACGTTATCGACCAGAGCGGGGGCTTGTTTAT‑AAGATCATAAACCGCCCTATTCATTAACCAGGTTTGAACAAATCCGc                                                                                              >  2:800157/1‑150 (MQ=255)                                                        aCATGACACTTAATTCATTCGTTTGATGAATTAATTTCGTTATGTTTTCATCTGGCATGAACATTCTTAATACGTTATCGACCAGAGCGGGGGCTTGTTTATAAAGATCATAACCCGCCATATTCATTAACCAGTTTTGAACAATTCCGCt                                                                                             >  1:209980/1‑151 (MQ=255)                                                        aCATGACACTTAATTCATTCGTTTGATGAATTAATTTCGTTATGTTTTCATCTGGCATGAACATTCTTAATACGTTATCGACCAGAGCGGGGGCTTGTTTATAAAGATCATAACCCGCCATATTCATTAACCAGTTTTGAACAATTCCGCt                                                                                             >  1:170127/1‑151 (MQ=255)                                                             acatTTATTTCTTTCGTTTGATAATTTATTTTCTTTTTTTTTTCATCGGGCATGAACTTTTTTAATACTTTATCGCCCAGAGGGGGGTTTTTTTTAAAAAGATCATACCCCGCCATATTCATTAACCAGTTTTGAACAATTCCGCTGAAg                                                                                         <  1:861462/150‑1 (MQ=255)                                                             acacTTAATTCATTCGTTTGATGAATTAATTTCGTTATGTTTTCATCTGGCATGAACATTCTTAATACGTTATCGACCAGAGCGGGGGCTTGTTTATAAAGATCATAACCCGCCATATTCATTAACCAGTTTTGAACAATTCCGCTGAAgg                                                                                        >  2:316940/1‑151 (MQ=255)                                                                 ttatttttttcTTTTGATAAATTATTTTCTTTTTTTTTTCATCTGGCATAAACATTCTTAATCCTTTACCGCCCAGGGGGGGGGTTTTTTTAAAAAGATCATACCCCGCCATATTCATTAACCAGTTTTGAACAATTCCGCTGAAgg                                                                                        <  1:162870/139‑1 (MQ=255)                                                                 ttAATTCTTTCTTTTGATAAATTATTTTCGTTATTTTTTCATCTGGCATAAACATTCTAAATACGTTACCAACCAGAGCGGGGTTTTTTTTAAAAAAACCATAACCCGCCATATTCATTAACCAGTTTTGAACAATTCCGCTGAAGGc                                                                                       <  2:91465/148‑1 (MQ=255)                                                                        attcGTTTGATGAATTAATTTCGTTATGTTTTCATCTGGCATGAACATTCTTAATACGTTATCGACCAGAGCGGGGGCTTGTTTATAAAGATCATAACCCGCCATATTCATTAACCAGTTTTGAACAATTCCGCTGAAGGCACCATCaat                                                                              >  1:308272/1‑150 (MQ=255)                                                                             tttGATAAATTAATTTCTTTATTTTTTCATCTGGCATAAACATTCTTAATACGTTATCGACCAGAGCGGGGGTTTTTTTAAAAAGATCATACCCCGCCATATTCATTAACCAGTTTTGAACAATTCCGCTGAAGGCACCATCaataataa                                                                         <  1:762307/150‑1 (MQ=255)                                                                               tgatgaATTAATTTCGTTATGTTTTCATCTGGCATGAACATTCTTAATACGTTATCGACCAGAGCGGGGGCTTGTTTATAAAGATCATAACCCGCCATATTCATTAACCAGTTTTGAACAATTCCGCTGAAGGCACCATCAATAATAatc                                                                       >  2:870781/1‑150 (MQ=255)                                                                                    aattatttTCTTTTTTTTTTCATCTGGCATGAACATTCTTAATCCTTTACCGCCCAGAGCGGGGGTTTGTTTATAAAGATCATAACCCGCCATATTCATTAACCAGTTTTGAACAATTCCGCTGAAGGCACCATCAATAATAatc                                                                       <  1:345810/145‑1 (MQ=255)                                                                                    aataaattTTTTTTTTTTTTCATCTGGCATAAACATTTTTATTCCTTTACCGCCAAGAGGGGGGGTTTTTTTATAAAGATCAAACCCCGCCATATTCATTAACCAGTTTTGAACAATTCCGCTGAAGGCACCATCAATAATAatcat                                                                     <  1:45287/147‑1 (MQ=255)                                                                                      ttaattTCGTTATGTTTTCATCTGGCATGAACATTCTTAATACGTTATCGACCAGAGCGGGGGCTTGTTTATAAAGATCATAACCCGCCATATTCATTAACCAGTTTTGAACAATTCCGCTGAAGGCACCATCAATAATAATCATCacaac                                                               >  2:716563/1‑151 (MQ=255)                                                                                        attttCTTTTTTTTTTCATCTGGCATAAACATTTTTAATACTTTATCGACCAGAGCGGGGTTTTTTTAAAAAAGATCATAACCCGCCATATTCATTAACCAGTTTTGAACAATTCCGCTGAAGGCACCATCAATAATAAtcatca                                                                   <  2:225567/143‑1 (MQ=255)                                                                                          tttCTTTTTTTTTTCCTCTTGCATAATTTTTTTTAATTCTTTACCGACCAGGGGGGGTTTTTTTTTATAAAATTAATACCCCGCCATATTCATTAACCAGTTTTGAACAATTCCGCTGAAGGCACCATCAATAATAATCATCacaaca                                                              <  2:597429/148‑1 (MQ=255)                                                                                          tttCGTTATGTTTTCATCTGGCATGAACATTCTTAATACGTTATCGACCAGAGCGGGGGCTTGTTTATAAAGATCATAACCCGCCATATTCATTAACCAGTTTTGAACAATTCCGCTGAAGGCACCATCAATAATAATCATCACAACATCt                                                           >  1:930502/1‑151 (MQ=255)                                                                                          tttCGTTATGTTTTCATCTGGCATGAACATTCTTAATACGTTATCGACCAGAGCGGGGGCTTGTTTATAAAGATCATAACCCGCCATATTCATTAACCAGTTTTGAACAATTCCGCTGAAGGCACCATCAATAATAATCATCACAACATCt                                                           >  2:202725/1‑151 (MQ=255)                                                                                           ttttttATTTTTTCATCTGGTATAAACATTCTAAATACTTTACCCACCAGAGGGGGGGTTTTTTAAAAAAGATAATACCCCGCCATATTCATTAACCAGTTTTGAACAATTCCGCTGAAGGCACCATCAATAATAATCATCACAACATCt                                                           <  2:868899/146‑1 (MQ=255)                                                                                           ttCGTTATTTTTTCATCTGGCATAAACATTCTTAATACTTTATCGACCAGGGCGGGGGTTTTTTTATAAAGATCATAACCCGCCATATTCATTAACCAGTTTTGAACAATTCCGCTGAAGGCACCATCAATAATAATCATCACAACATCt                                                           <  1:762376/150‑1 (MQ=255)                                                                                             cGTTATGTTTTCATCTGGCATGAACATTCTTAATACGTTATCGACCAGAGCGGGGGCTTGTTTATAAAGATCATAACCCGCCATATTCATTAACCAGTTTTGAACAATTCCGCTGAAGGCACCATCAATAATAATCATCACAACATCTaa                                                         >  2:878163/1‑150 (MQ=255)                                                                                              gTTATGTTTTCATCTGGCATGAACATTCTTAATACGTTATCGACCAGAGCGGGGGCTTGTTTATAAAGATCATAACCCGCCATATTCATTAACCAGTTTTGAACAATTCCGCTGAAGGCACCATCAATAATAATCATCACAACATCTAAAt                                                       >  2:472787/1‑151 (MQ=255)                                                                                               tttttttttCTTCTGACATGAACTTTTTTAATCCTTAATCGCCGAGAGGGGGGGTTTTTTTAAAAAGATCATACCCCGCCATATTCATTAACCAGTTTTGAACAATTCCGCTGAAGGCACCATCAATAATAATCATCACAACATCTaa                                                         <  1:289993/143‑1 (MQ=255)                                                                                                     tttCATCTGGTATGAACATTCTTAATACGTTATCGCCCAGAGCGGGGTTTTGTTTATAAAGATCATACCCCGCCATATTCATTAACCAGTTTTGAACAATTCCGCTGAAGGCACCATCAATAATAATCATCACAACATCTAAATCGAGGt                                                 <  1:147167/150‑1 (MQ=255)                                                                                                     tttCATCTGGCATGAACATTCTTAATACGTTATCGACCAGAGCGGGGGCTTGTTTATAAAGATCATAACCCGCCATATTCATTAACCAGTTTTGAACAATTCCGCTGAAGGCACCATCAATAATAATCATCACAACATCTAAATCGAGGtt                                                >  2:508039/1‑151 (MQ=255)                                                                                                     tttCATCTGGCATGAACATTCTTAATACGTTATCGACCAGAGCGGGGGCTTGTTTATAAAGATCATAACCCGCCATATTCATTAACCAGTTTTGAACAATTCCGCTGAAGGCACCATCAATAATAATCATCACAACATCTAAATCGAGGtt                                                >  2:798712/1‑151 (MQ=255)                                                                                                          tCTGGCATCAACCTTCTTGATACGTTATATACCAGAGCGCGGGCGTGTTTATAAAGATCATAACCCGCCATATTAATTAACCAGGTTTGGACAATTCAGCTGAAGGCACCATCAATAATAATCATCACAACATCTAAATCGCGGTTATTTg                                           >  2:560133/1‑151 (MQ=255)                                                                                                          tCTGGAATAAACATTTTTAATACGTTACCGACCAGGGGGGGGGTTTTTTTATAAAGATAATAACCCGCCATATTCATTAACCAGTTTTGAACAATTCCGCTGAAGGCACCATCAATAATAATCATCACAACATCTAAATCGAGGTTAt                                              <  2:563489/148‑1 (MQ=255)                                                                                                             ggCATGAACATTCTTAATACTTTATCGACCAGAGCGGGGGTTTTTTTATAAAAATCATAACCCGCCATATTCATTAACCAGTTTTGAACAATTCCGCTGAAGGCACCATCAATAATAATCATCACAACATCTAAATCGAGGTTAttt                                            <  1:648515/147‑1 (MQ=255)                                                                                                                     cATTCTTAATACGTTATCGACCAGAGCGGGGGCTTGTTTATAAAGATCATAACCCGCCATATTCATTAACCAGTTTTGAACAATTCCGCTGAAGGCACCATCAATAATAATCATCACAACATCTAAATCGAGGTTATTTGCTACACAACCt                                >  2:12677/1‑151 (MQ=255)                                                                                                                     cATTCTTAATACGTTATCGACCAGAGCGGGGGCTTGTTTATAAAGATCATAACCCGCCATATTCATTAACCAGTTTTGAACAATTCCGCTGAAGGCACCATCAATAATAATCATCACAACATCTAAATCGAGGTTATTTGCTACACAACCt                                >  2:240662/1‑151 (MQ=255)                                                                                                                       ttCTTAATACTTTATCGACCAGGGGGGGGTTTTTTTTAAAAAGATCAAAACCCGCCATATTCATTAACCAGTTTTGAACAATTCCGCTGAAGGCACCATCAATAATAATCATCACAACATCTAAATCGAGGTTATTTGCTACACAAcc                                 <  2:594405/148‑1 (MQ=255)                                                                                                                            aaTACTTTATCGACCAGAGCGGGTGTTTTTTAATAAAGATCATAACCCGCCATATTCATTAACCAGTTTTGAACAATTCCGCTGAAGGCACCATCAATAATAATCATCACAACATCTAAATCGAGGTTATTTGCTACACAACCTTGTTGCt                         <  2:412682/151‑1 (MQ=255)                                                                                                                             attcgttttcaacgggagCGGTGTTTTTTTTAAAAAGCCCATACCCCGCCATATTCATTAACCAGTTTTGAACAATTCCGCTGAAGGCACCATCAATAATAATCATCACAACATCTAAATCGAGGTTATTTGCTACACAACCTTGTTGCTg                        <  2:779788/136‑1 (MQ=255)                                                                                                                             aTACTTTACCGACCAGAGGGGGGGTTTTTTTAAAAAGATCAAAACCCGCCATATTCATTAACCAGTTTTGAACAATTCCGCTGAAGGCACCATCAATAATAATCATCACAACATCTAAATCGAGGTTATTTGCTACACAACCTTGTTGCTg                        <  1:316975/151‑1 (MQ=255)                                                                                                                             aTACGTTATCGACCAGAGCGGGGGCTTGTTTATAAAGATCATAACCCGCCATATTCATTAACCAGTTTTGAACAATTCCGCTGAAGGCACCATCAATAATAATCATCACAACATCTAAATCGAGGTTATTTGCTACACAACCTTGTTGCTg                        >  1:488422/1‑151 (MQ=255)                                                                                                                               actttATCGACCAGAGCGGGGGTTTTTTTAAAAAGATCAAAACCCGCCATATTCATTAACCAGTTTTGAACAATTCCGCTGAAGGCACCATCAATAATAATCATCACAACATCTAAATCGAGGTTATTTGCTACACAACCTTGTTGCt                         <  2:33014/145‑1 (MQ=255)                                                                                                                                       gACCAGAGCGGGGGCTTGTTTATAAAGATCATAACCCGCCATATTCATTAACCAGTTTTGAACAATTCCGCTGAAGGCACCATCAATAATAATCATCACAACATCTAAATCGAGGTTATTTGCTACACAACCTTGTTGCTGACACGCCTGc              >  2:75825/1‑151 (MQ=255)                                                                                                                                       gACCAGAGCGGGGGCTTGTTTATAAAGATCATAACCCGCCATATTCATTAACCAGTTTTGAACAATTCCGCTGAAGGCACCATCAATAATAATCATCACAACATCTAAATCGAGGTTATTTGCTACACAACCTTGTTGCTGACACGCCTGc              >  1:55590/1‑151 (MQ=255)                                                                                                                                         ccAGAGCGGGGGCTTGTTTATAAAGATCATAACCCGCCATATTCATTAACCAGTTTTGAACAATTCCGCTGAAGGCACCATCAATAATAATCATCACAACATCTAAATCGAGGTTATTTGCTACACAACCTTGTTGCTGACACGCCTGCa             >  2:574161/1‑150 (MQ=255)                                                                                                                                         caaccgCGGGGCGTTTTTTAAAAAGATCACAGTCCGCCATATTCATTAACCAGTTTTGAACAATTCCGCTGAAGGCACCATCAATAATAATCATCACAACATCTAAATCGAGGTTATTTGCTACACAACCTTGTTGCTGACACTCCt                <  2:641464/142‑1 (MQ=255)                                                                                                                                             agCGGGGGCTTGTTTATAAAGATCATAACCCGCCATATTCATTAACCAGTTTTGAACAATTCCGCTGAAGGCACCATCAATAATAATCATCACAACATCTAAATCGAGGTTATTTGCTACACAACCTTGTTGCTGACACGCCTGCAATACt        >  1:248391/1‑151 (MQ=255)                                                                                                                                              gCGGGGGCTTGTTTATAAAGATCATAACCCGCCATATTCATTAACCAGTTTTGAACAATTCCGCTGAAGGCACCATCAATAATAATCATCACAACATCTAAATCGAGGTTATTTGCTACACAACCTTGTTGCTGACACGCCTGCAATACtt       >  2:953983/1‑151 (MQ=255)                                                                                                                                                 ggggTTTTTTTATAAATATAATAACCCGCCATATTCATTAACCAGTTTTGAACAATTCCGCTGAAGGCACCATCAATAATAATCATCACAACATCTAAATCGAGGTTATTTGCTACACAACCTTGTTGCTGACACGCCTGCAATACTTcgc    <  1:673253/151‑1 (MQ=255)                                                                                                                                                    gCTTGTTTATAAAGATCATAACCCGCCATATTCATTAACCAGTTTTGAACAATTCCGCTGAAGGCACCATCAATAATAATCATCACAACATCTAAATCGAGGTTATTTGCTACACAACCTTGTTGCTGACACGCCTGCAATACTTCGCgg  >  2:714096/1‑150 (MQ=255)                                                                                                                                                     |                                                                                                                                                     CCACTAAAACTGGTTAACTGTGACGAACTGAATTTTCAGGACAGAATGTGAATTTACATGACACTTAATTCATTCGTTTGATGAATTAATTTCGTTATGTTTTCATCTGGCATGAACATTCTTAATACGTTATCGACCAGAGCGGGGGCTTGTTTATAAAGATCATAACCCGCCATATTCATTAACCAGTTTTGAACAATTCCGCTGAAGGCACCATCAATAATAATCATCACAACATCTAAATCGAGGTTATTTGCTACACAACCTTGTTGCTGACACGCCTGCAATACTTCGCGG  >  NC_000913/3412750‑3413046

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑