Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,412,898	0	C	T	47.3%	36.1 / 43.0	56	A190T (GCC→ACC)	acrS	acrAB operon transcriptional repressor
Reads supporting (aligned to +/- strand):  ref base C (24/5);  new base T (0/26);  total (24/32)
Fisher's exact test for biased strand distribution p-value = 7.81e-11
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CCACTAAAACTGGTTAACTGTGACGAACTGAATTTTCAGGACAGAATGTGAATTTACATGACACTTAATTCATTCGTTTGATGAATTAATTTCGTTATGTTTTCATCTGGCATGAACATTCTTAATACGTTATCGACCAGAGCGGGGGCTTGTTTATAAAGATCATAACCCGCCATATTCATTAACCAGTTTTGAACAATTCCGCTGAAGGCACCATCAATAATAATCATCACAACATCTAAATCGAGGTTATTTGCTACACAACCTTGTTGCTGACACGCCTGCAATACTTCGCGG  >  NC_000913/3412750‑3413046                                                                                                                                                     |                                                                                                                                                     ccACTAAAACTGGTTAACTGTGACGAACTGAATTTTCAGGACAGAATGTGAATTTACATGACACTTAATTCATTCGTTTGATGAATTAATTTCGTTATGTTTTCATCTGGCATGAACATTCTTAATACGTTATCGACCAGAGCGGGGGCtt                                                                                                                                                    >  1:422340/1‑151 (MQ=255)  cACTAAAACTGGTTAACTGTGACGAACTGAATTTTCAGGACAGAATGTGAATTTACATGACACTTAATTCATTCGTTTGATGAATTAATTTCGTTATGTTTTCATCTGGCATGAACATTCTTAATACGTTATCGACCAGAGCGGGGGCTTg                                                                                                                                                   >  1:312294/1‑151 (MQ=255)     tAAAACTGGTTAACTGTGACGAACTGAATTTTCAGGACAGAATGTGAATTTACATGACACTTAATTCATTCGTTTGATGAATTAATTTCGTTATGTTTTCATCTGGCATGAACATTCTTAATACGTTATCGACCAGAGCGGGGGCTTGttt                                                                                                                                                >  2:147463/1‑151 (MQ=255)      aaaaCTGGTTAACTGTGACGAACTGAATTTTCAGGACAGAATGTGAATTTACATGACACTTAATTCATTCGTTTGATGAATTAATTTCGTTATGTTTTCATCTGGCATGAACATTCTTAATACGTTATCGACCAGAGCGGGGGCTTGttt                                                                                                                                                >  1:522138/1‑150 (MQ=255)        aaCTGGTTAACTGTGACGAACTGAATTTTCAGGACAGAATGTGAATTTACATGACACTTAATTCATTCGTTTGATGAATTAATTTCGTTATGTTTTCATCTGGCATGAACATTCTTAATACGTTATCGACCAGAGCGGGGGCTTGTTtat                                                                                                                                              >  1:127916/1‑150 (MQ=255)             gTTAACTGTGACGAACTGAATTTTCAGGACAGAATGTGAATTTACATGACACTTAATTCATTCGTTTGATGAATTAATTTCGTTATGTTTTCATCTGGCATGAACATTCTTAATACGTTATCGACCAGAGCGGGGGCTTGTTTATaa                                                                                                                                            >  2:64/1‑147 (MQ=255)               tAACTGTGACGAACTGAATTTTCAGGACAGAATGTGAATTTACATGACACTTAATTCATTCGTTTGATGAATTAATTTCGTTATGTTTTCATCTGGCATGAACATTCTTAATACGTTATCGACCAGAGCGGGGGCTTGTTTATAAAGATc                                                                                                                                       >  1:74972/1‑150 (MQ=255)                aaCTGTGACGAACTGAATTTTCAGGACAGAATGTGAATTTACATGACACTTAATTCATTCGTTTGATGAATTAATTTCGTTATGTTTTCATCTGGCATGAACATTCTTAATACGTTATCGACCAGAGCGGGGGCTTGTTTATAAAGATCa                                                                                                                                      <  2:29408/150‑1 (MQ=255)                             tGAATTTTCAGGACAGAATGTGAATTTACATGACACTTAATTCATTCGTTTGATGAATTAATTTCGTTATGTTTTCATCTGGCATGAACATTCTTAATACGTTATCGACCAGAGCGGGGGCTTGTTTATAAAGATCATAACCCGCCATAtt                                                                                                                        >  2:604420/1‑151 (MQ=255)                               aaTTTTCAGGACAGAATGTGAATTTACATGACACTTAATTCATTCGTTTGATGAATTAATTTCGTTATGTTTTCATCTGGCATGAACATTCTTAATACGTTATCGACCAGAGCGGGGGCTTGTTTATAAAGATCATAACCCGCCatat                                                                                                                         <  1:302552/148‑1 (MQ=255)                               aaTTTTCAGGACAGAATGTGAATTTACATGACACTTAATTCATTCGTTTGATGAATTAATTTCGTTATGTTTTCATCTGGCATGAACATTCTTAATACGTTATCGACCAGAGCGGGGGCTTGTTTATAAAGATCATAACCCGCCATATTc                                                                                                                       >  1:255425/1‑150 (MQ=255)                                 ttttCAGGAAAGAATTTGATTTTACATGACATTTAATTCTTTCGTTTGATGAATTATTTTCTTTATTTTTTCATCTGGCATAAACATTCTTAATACTTTATCAACCAGAGCGGGGGCTTGTTTATAAAGATCATACCCCGCCATATTCAt                                                                                                                     <  1:592507/150‑1 (MQ=255)                                             aaTGTGAATTTACATGACATTTATTTCTTTCGTTTGATAAATTATTTTCGTTATTTTTTCATCGGGCATAAACATTTTTAATACGTTATCGACCAGGGGGGGGGTTTTTTTATAAAGATCATAACCCGCCATATTCATTAACCAGttt                                                                                                           <  2:127925/148‑1 (MQ=255)                                                   aaTTTACATGACACTTAATTCATTCGTTTGATGAATTAATTTCGTTATTTTTTCATCTGGCATGAACATTTTTAATACGTTATCGCCCAGAGCGGGGGTTTTTTTATAAAGATCATAACCCGCCATATTCATTAACCAGTTTTGAACAAt                                                                                                   <  2:184218/150‑1 (MQ=255)                                                    aTTTACATGACACTTAATTCATTCGTTTGATGAATTAATTTCGTTATGTTTTCATCTGGCATGAACATTCTTAATACGTTATCGACCAGAGCGGGGGCTTGTTTATAAAGATCATAACCCGCCATATTCATTAACCAGTTTTGAACAATTc                                                                                                 >  2:141854/1‑151 (MQ=255)                                                     tttACATGACTTTTATTTTTTTTTTTTGATAAATTATTTTCGTTTTTTTTTCATCTGCCATGAACATTTTTAATCCTTTATCGACCAGAGGGGGGTTTTTTTTAAAAAATTCATAACCCGCCATATTCATTAACCAGTTTTg                                                                                                         <  1:5770/142‑1 (MQ=255)                                                     tttACATGACATTTAATTCATTCTTTTGATGAATTAATTTCGTTATTTTTTCATCTGGCATGAACATTCTTAATACTTTATCGACCAGAGCGGGGGTTTTTTTAAAAAGATCATACCCCGCCATATTCATTAACCAGTTTTGAACAATTc                                                                                                 <  2:627394/150‑1 (MQ=255)                                                        aCATGACACTTAATTCATTCGTTTGATGAATTAATTTCGTTATGTTTTCATCTGGCATGAACATTCTTAATACGTTATCGACCAGAGCGGGGGCTTGTTTATAAAGATCATAACCCGCCATATTCATTAACCAGTTTTGAACAATTCCGCt                                                                                             >  2:45679/1‑151 (MQ=255)                                                        aCATGACACTTAATTCATTCGTTTGATGAATTAATTTCGTTATGTTTTCATCTGGCATGAACATTCTTAATACGTTATCGACCAGAGCGGGGGCTTGTTTATAAAGATCATAACCCGCCATATTCATTAACCAGTTTTGAACAATTCCGCt                                                                                             >  2:685944/1‑151 (MQ=255)                                                          aTGAAATTTAATTCATTTTTTTGATAAATTAATTTCTTTTTTTTTTCTTTTGGAATAAACATTTTTAATCCTTTATCGCCCAGAGGGGGGGTTTTTTTAAAAAGACCATAACCCGCCATATTCATTAACCAGTTTTGAACAATTCCGCt                                                                                             <  1:147450/149‑1 (MQ=255)                                                              catttAATTCATTCGTTTGATAAATTAATTTCTTTATTTTTTCTTCTGGCATAAACTTTCTTAATACGTTATCGACCAGGGCGGGGGTTTTTTTAAAAAGATCAAACCCCGCCATATTCATTAACCAGTTTTGAACAATTCCGCTGAAgg                                                                                        <  2:139978/147‑1 (MQ=255)                                                                 ttatttttttcTTTTGATAAATTTTTTTCGTTTTGTTTTCATCGGGAATAAACATTCTTAACACTTTATCGACCAGAGCGGGGGTTTGTTTAAAAAGATCAACACCCGCCATATTCATTAACCAGTTTTGAACAATTCCGCTGAAGGc                                                                                       <  1:468070/140‑1 (MQ=255)                                                                 ttAATTCATTGTTTTGATAAATAATTTTCTTTTTTTTTTCATCTGGAATGAACATTCTAAATCTTTTACCGCCCAGGGGGGGGGTTTTTTTATAAAAATAATACCCCGCCATATTCATTAACCAGTTTTGAACAATTCCGCTGAAGGc                                                                                       <  2:882886/148‑1 (MQ=255)                                                                  tAATTCATTTGTTTGATGAATTAATTTCTTTATTTTTTCATCTGGCATGAACATTCTTAATCCTTTATCGACAAGAGGGGGTTTTTGTTTATAAAGATCATAGCCCGCCATATTCATTAACCAGTTTTGAACAATTCCGCTGAAgg                                                                                        <  1:371002/146‑1 (MQ=255)                                                                     ttcattcTTTTGATAAATTATTTTCTTTTTTTTTTCTTCTGGAATAAACTTTTTTAATACTTTACCGACCAGAGCGGGGGTTTTTTAAAAAAGATCATAACCCGCCATATTCATTAACCAGTTTTGAACAATTCCGCTGAAGGCACCAt                                                                                  <  1:549894/149‑1 (MQ=255)                                                                      tcattcGTTTGATGAATTAATTTCGTTATGTTTTCATCTGGCATGAACATTCTTAATACGTTATCGACCAGAGCGGGGGCTTGTTTATAAAGATCATAACCCGCCATATTCATTAACCAGTTTTGAACAATTCCGCTGAAGGCACCATCa                                                                                >  1:454477/1‑150 (MQ=255)                                                                       cattcGTTTGATGAATTAATTTCGTTATGTTTTCATCTGGCATGAACATTCTTAATACGTTATCGACCAGAGCGGGGGCTTGTTTATAAAGATCATAACCCGCCATATTCATTAACCAGTTTTGAACAATTCCGCTGAAGGCACCATCaat                                                                              >  2:172318/1‑151 (MQ=255)                                                                         ttcGTTTAATAAATTAATTTCTTTTTTTTTTCATCTGGCATAAACTTTCTTAATCCTTTATCGACCAGGGGGGGGGTTTTTTTAAAAAGATCATAACCCGCCATATTCATTAACCAGTTTTGAACAATTCCGCTGAAGGCACCATCaata                                                                             <  2:422241/150‑1 (MQ=255)                                                                          tcttttGATAAATTAATTTCGTTTTTTTTCTATCTGGCAAGAACATTCTTAATACTTTATCGACAAGGGCGGGGCGTTTTTTAAAAAGATCAAAACCCGCCATATTCATTAACCAGTTTTGAACAATTCCGCTGAAGGCACCATCaataa                                                                            <  2:446934/147‑1 (MQ=255)                                                                             tttGATGAATTAATTTCGTTATGTTTTCATCTGGCATGAACATTCTTAATACGTTATCGACCAGAGCGGGGGCTTGTTTATAAAGATCATAACCCGCCATATTCATTAACCAGTTTTGAACAATTCCGCTGAAGGCACCATCaataataat                                                                        >  1:704686/1‑151 (MQ=255)                                                                              ttGATGAATTAATTTCGTTATGTTTTCATCTGGCATGAACATTCTTAATACGTTATCGACCAGAGCGGGGGCTTGTTTATAAAGATCATAACCCGCCATATTCATTAACCAGTTTTGAACAATTCCGCTGAAGGCACCATCAATAATAatc                                                                       >  1:67854/1‑151 (MQ=255)                                                                                      ttatttTCTTTTTGTTTTCATCTGGCATAAACATTTTTAATACGTTATCGACCAGAGCGGGGGTTTTTTTAAAAAAATCATACCCCGCCATATTCATTAACCAGTTTTGAACAATTCCGCTGAAGGCACCATCAATAATAATCATCacaa                                                                <  2:104340/150‑1 (MQ=255)                                                                                      ttaattTCGTTATGTTTTCATCTGGCATGAACATTCTTAATACGTTATCGACCAGAGCGGGGGCTTGTTTATAAAGATCATAACCCGCCATATTCATTAACCAGTTTTGAACAATTCCGCTGAAGGCACCATCAATAATAATCATCacaac                                                               >  2:131992/1‑151 (MQ=255)                                                                                       taattTCGTTATGTTTTCATCTGGCATGAACATTCTTAATACGTTATTGACCAGAGCGGGGGCTTGTTTATAAAGATCATAACCCGCCATATTCATTAACCAGTTTTGAACAATTCCGCTGAAGGCACCATCAATAATAATCATCacaac                                                               >  2:256286/1‑150 (MQ=255)                                                                                            tctttATTTTTTCTTCTGGCATGAACATTTTTAATCCTTTACCGACCAGAGGGGGGGTTTGTTTATAAAGATCATAACCCGCCATATTCATTAACCAGTTTTGAACAATTCCGCTGAAGGCACCATCAATAATAATCATCACAACATCTa                                                          <  2:602346/147‑1 (MQ=255)                                                                                               tttttttttCATCTGGCATGAACATTCTTAATACTTTATCGACCAGAGCGGGGGTTTTTTTATAAAGATCATACCCCGCCATATTCATTAACCAGTTTTGAACAATTCCGCTGAAGGCACCATCAATAATAATCATCACAACATCTaaa                                                        <  2:132697/144‑1 (MQ=255)                                                                                               ttATTTTTTCATCTGGCATGAACATTCTTAATACGTTATCGACCAGAGCGGGGGCTTTTTTAAAAAAATCATAACCCGCCATATTCATTAACCAGTTTTGAACAATTCCGCTGAAGGCACCATCAATAATAATCATCACAACATCTAAAt                                                       <  2:18886/150‑1 (MQ=255)                                                                                                   tttttAATCTGACAGAAACTTTCTTAATTTTTTACCAACAAGGGGGGGGGTTTGTTTAAAAATATCATACCCCGCCATATTCATTAACCAGTTTTGAACAATTCCGCTGAAGGCACCATCAATAATAATCATCACAACATCTAAATCGAg                                                   <  2:463601/149‑1 (MQ=255)                                                                                                    ttttCATCTGGCATAAACATTCTTAATACGTTATCGACCAGAGGGGGGGTTTTTTTAAAAAGATCAAAACCCGCCATATTCATTAACCAGTTTTGAACAATTCCGCTGAAGGCACCATCAATAATAATCATCACAACATCTAAATCGAgg                                                  <  2:353960/150‑1 (MQ=255)                                                                                                    ttttCATCTGGCATAAACATTCTTAATACGTTATCGACCAGAGCGGGGGTTTGTTTAAAAAAATCAAACCCCGCCATATTCATTAACCAGTTTTGAACAATTCCGCTGAAGGCACCATCAATAATAATCATCACAACATCTAAATCGAg                                                   <  2:739618/149‑1 (MQ=255)                                                                                                     tttCTTCTGGTATAAACATTTTTAATCCTTTATCGACAAGCGCGGGGCTTTTTTTAAAAAGACCATAGCCCGCCATATTCATTAACCAGTTTTGAACAATTCCGCTGAAGGCACCATCAATAATAATCATCACAACATCTAAATCGAGGt                                                 <  1:256605/150‑1 (MQ=255)                                                                                                        cATCTGGCATGAACATTCTTAATACGTTATCGACCAGAGCGGGGGCTTGTTTATAAAGATCATAACCCGCCATATTCATTAACCAGTTTTGAACAATTCCGCTGAAGGCACCATCAATAATAATCATCACAACATCTAAATCGAGGTTAtt                                             >  1:674136/1‑151 (MQ=255)                                                                                                             ggCATGAACATTTTTAATACGTTATCGACCAGGGCGGGGTCTTTTTTATAAAAATCATAACCCGCCATATTCATTAACCAGTTTTGAACAATTCCGCTGAAGGCACCATCAATAATAATCATCACAACATCTAAATCGAGGTTATTTg                                           <  2:262883/148‑1 (MQ=255)                                                                                                                ataaaCTTTCTTAATCCGTTATCGACCAGAGGGGGGGTTTTTTTAAAAAGATAATACCCCGCCATATTCATTAACCAGTTTTGAACAATTCCGCTGAAGGCACCATCAATAATAATCATCACAACATCTAAATCGAGGTTATTTGCTaca                                      <  2:642180/147‑1 (MQ=255)                                                                                                                   aaCATTTTTAATACTTTATCGCCCAGGGGGGGGTTTTTTTTATAAAAATAATACCCCGCCATATTCATTAACCAGTTTTGAACAATTCCGCTGAAGGCACCATCAATAATAATCATCACAACATCTAAATCGAGGTTATTTGCTACACaa                                   <  2:265637/150‑1 (MQ=255)                                                                                                                   aaCATTTTTAATACGTTACCGCCAAGAGGGGGGTTTTTTTTAAAAAGATCATACCCCGCCATATTCATTAACCAGTTTTGAACAATTCCGCTGAAGGCACCATCAATAATAATCATCACAACATCTAAATCGAGGTTATTTGCTAcaca                                    <  2:275533/149‑1 (MQ=255)                                                                                                                      aTTCTTAATACGTTATCGACCAGAGCGGGGGCTTGTTTATAAAGATCATAACCCGCCATATTCATTAACCAGTTTTGAACAATTCCGCTGAAGGCACCATCAATAATAATCATCACAACATCTAAATCGAGGTTATTTGCTACACAACCtt                               >  2:122949/1‑151 (MQ=255)                                                                                                                       tttttAATACTTTACCGACCAGAGGGGGGGTTTGTTTATAAAGATCATACCCCGCCATATTCATTAACCAGTTTTGAACAATTCCGCTGAAGGCACCATCAATAATAATCATCACAACATCTAAATCGAGGTTATTTGCTACACAACCtt                               <  2:367003/147‑1 (MQ=255)                                                                                                                             aTACGTTATCGACCAGAGCGGGGGCTTGTTTATAAAGATCATAACCCGCCATATTCATTAACCAGTTTTGAACAATTCCGCTGAAGGCACCATCAATAATAATCATCACAACATCTAAATCGAGGTTATTTGCTACACAACCTTGTTGCTg                        >  1:216563/1‑151 (MQ=255)                                                                                                                                      caaCCAGGGCGGGGGTTTATTTATAAAAATCATAACCCGCCATATTCATTAACCAGTTTTGAACAATTCCGCTGAAGGCACCATCAATAATAATCATCACAACATCTAAATCGAGGTTATTTGCTACACAACCTTGTTGCTGACACGCCTg               <  2:743771/149‑1 (MQ=255)                                                                                                                                      cGACCAGAGCGGGGTTTTTTTTAAAAAGATCAAACCCCGCCATATTCATTAACCAGTTTTGAACAATTCCGCTGAAGGCACCATCAATAATAATCATCACAACATCTAAATCGAGGTTATTTGCTACACAACCTTGTTGCTGACACGc                  <  1:774861/148‑1 (MQ=255)                                                                                                                                           agagGGGGGATTTGTTTAAAAGGATAAAAACCCGCCATATTCATTAACCAGTTTTGAACAATTCCGCTGAAGGCACCATCAATAATAATCATCACAACATCTAAATCGAGGTTATTTGCTACACAACCTTGTTGCTGACACGCCTGCaa            <  1:4633/149‑1 (MQ=255)                                                                                                                                           agagCGGGGGCTTGTTTATAAAGATCATAACCCGCCATATTCATTAACCAGTTTTGAACAATTCCGCTGAAGGCACCATCAATAATAATCATCACAACATCTAAATCGAGGTTATTTGCTACACAACCTTGTTGCTGACACGCCTGCAAt           >  1:376419/1‑150 (MQ=255)                                                                                                                                                gggggTTTTTTTATAAAGATCATAACCCGCCATATTCATTAACCAGTTTTGAACAATTCCGCTGAAGGCACCATCAATAATAATCATCACAACATCTAAATCGAGGTTATTTGCTACACAACCTTGTTGCTGACACGCCTGCAATACTTc      <  2:422406/150‑1 (MQ=255)                                                                                                                                                gggggCTTGTTTATAAAGATCATAACCCGCCATATTCATTAACCAGTTTTGAACAATTCCGCTGAAGGCACCATCAATAATAATCATCACAACATCTAAATCGAGGTTATTTGCTACACAACCTTGTTGCTGACACGCCTGCAATACTTcg     >  2:292714/1‑151 (MQ=255)                                                                                                                                                    gCTTGTTTATAAAGATCATAACCCGCCATATTCATTAACCAGTTTTGAACAATTCCGCTGAAGGCACCATCAATAATAATCATCACAACATCTAAATCGAGGTTATTTGCTACACAACCTTGTTGCTGACACGCCTGCAATACTTCGCgg  >  2:361131/1‑150 (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 < 33 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑