Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,349,145	0	A	C	49.1%	72.6 / 20.2	55	F110V (TTC→GTC)	inaA	acid‑inducible Kdo/WaaP family putative kinase
Reads supporting (aligned to +/- strand):  ref base A (25/3);  new base C (0/27);  total (25/30)
Fisher's exact test for biased strand distribution p-value = 1.18e-12
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CGAACATAACAACAGCCATGCTGACGATTAATGCTATGCATTTTCTTAAACGCCAGCGCCACTGCTTTCAACATGGCTTGCCGTACTTCGTCAGAATAAGG‑CGATACTGCATGCTGGGCATACCAGTCAGCAATGCTGATGAACCCCGCCATATCTTCAGTCACCAGCAACGCTCGCCATTCACCCTCAATTTTCACCGCTTCACCAAAAACGATCTTCGGCACGATGACACCGGCCCGTTCCAGTTCTTTAATTACCGCAACCTCACGGACAATCGTTGGTCGGCC  >  NC_000913/2349003‑2349289                                                                                                                                                |                                                                                                                                                 cGAACATAACAACAGCCATGCTGACGATTAATGCTATGCATTTTCTTAAACGCCAGCGCCACTGCTTTCAACATGGCTTGCCGTACTTCGTCAGAATAAGG‑CGATACTGCATGCTGGGCATACCAGTCAGCAATGCTGATGAACCCCGcc                                                                                                                                           >  2:575167/1‑150 (MQ=255)     cATAACAACAGCCATGCTGACGATTAATGCTATGCATTTTCTTAAACGCCAGCGCCACTGCTTTCAACATGGCTTGCCGTACTTCGTCAGAATAAGG‑CGATACTGCATGCTGGGCATACCAGTCAGCAATGCTGATGAACCCCGCCATATc                                                                                                                                      >  2:791198/1‑151 (MQ=255)          caacaGCCATGCTGACGATTAATGCTATGCATTTTCTTAAACGCCAGCGCCACTGCTTTCAACATGGCTTGCCGTACTTCGTCAGAATAAGG‑CGATACTGCATGCTGGGCATACCAGTCAGCAATGCTGATGAACCCCGCCATATCTTc                                                                                                                                   >  1:651958/1‑149 (MQ=255)                ccATGCTGATAATAAATGCTTTGCTTTTTCTAAAACGCCACCGCCACTGTTTTCAACATGGTTTGCCTTACTTCGTCAAAAAAAGG‑CGATCCTCCATGCTGGGCATACCAGTCAGCAATGCTAATAACCCCCGCCATATCTTCAGTCACCa                                                                                                                           <  2:569966/151‑1 (MQ=255)                ccATGCTGACGATTAATGCTATGCTTTTTCTAAAACGCCAGCGCCACTGCTTTCAACATGGTTTGCCGTACTTCGTAAGAATAGGG‑CGATACTGCATGCTGGGCATACCAGTCAGAAATGCTGATGACCCCCGCCATATCTTCAGTCACCa                                                                                                                           <  1:258934/151‑1 (MQ=255)                   tGCTGACGATTAATGCTTTGCTTTTTTTAAAACCCCAGCGCCCCTGCTTTCAACATGGCTTGCCGTCTTTCGTAAAAATAAGG‑CGATCCTGCATGCTGGGCATACCAGTCAGCAATGCTGATAACCCCCGCCATATCTTCAGTCACCAg                                                                                                                          <  2:29417/149‑1 (MQ=255)                    gCTGACGATTAATGCTATGCATTTTCTTAAACGCCAGCGCCACTGCTTTCAACATGGCTTGCCGTCCTTCGTCAAAATAAGG‑CGATACTGCATGCTGGGCATACCAGTCAGCAATGCTGATGAACCCCGCCATATCTTCAGTCACCAGCa                                                                                                                        <  1:562555/150‑1 (MQ=255)                    gCTGACGATTAAGGTTATGCTTTTTCTAAACCCCCAGCCCCCCTGCTTTCAACATGGTTTGCCGTCCTTCGTAAAAATAAGG‑CGATACTGCATGCGGGGCATCCCAGTCAGCAATGCTGATAACCCCCGCCATATCTTCAGTCACCAGCa                                                                                                                        <  2:541946/150‑1 (MQ=255)                        actaTTAATGCTATGTTTTTTCTAAACCGCCGGCGCCACTTCTTTAAACTGGGCTTGCCTTCCTTCGAAAAAAAAGGG‑CGATCCTACATGCTGGGCATCCCAGCCAGCAATGCTGATGAACCCCGCCATATCTTCAGTCACCAGCAACGCt                                                                                                                   <  2:222159/148‑1 (MQ=255)                        acaaTTAATGTTATGCATTTTTTAAAACCCCAGCGCCCCTGTTTTAAACAGGGTTTGCCGTCCTTCTAAAAAAGAAGG‑CGATACTGAATGCGGGGCATCCCAGTCAGAAATGCTGATGACCCCCGCCATATCTTCAGTCACCAGCAACg                                                                                                                     <  2:739133/146‑1 (MQ=255)                        aCGATTAATGCTATGCATTTTCTTAAACGCCAGCGCCACTGCTTTCAACATGGCTTGCCGTACTTCGTCAGAATAAGG‑CGATACTGCATGCTGGGCATACCAGTCAGCAATGCTGATGAACCCCGCCATATCTTCAGTCACCAGCAACGCt                                                                                                                   >  2:371027/1‑151 (MQ=255)                         cGATTAATGCTATGCTTTTTCTTAAACCCCAGCCCCCCTGTTTTAAACATGGCTTGCCGTCTTTCGTAAAAATAAGG‑CGATACTGCATGCTGGGCATACCAGTCAGAAATGCTGATGACCCCCGCCATATCTTCAGTCACCAGCAACg                                                                                                                     <  1:854102/148‑1 (MQ=255)                         cGATTAATGCTATGCTTTTTCTAAACCGCCAGCGCCCCTGTTTTAAACAGGGCTTGCCTTACTTCGTAAAAAAAAGG‑CGATACTGCATGCTGGGCATCCCAGCCAGCAATGCTGATGACCCCCGCCATATCTTCAGTCACCAGCAACGCt                                                                                                                   <  1:754040/150‑1 (MQ=255)                              aaTGCTATGCATTTTCTTAAACGCCAGCGCCACTGCTTTCAACATGGCTTGCCGTACTTCGTCAGAATAAGG‑CGATACTGCATGCTGGGCATACCAGTCAGCAATGCTGATGAACCCCGCCATATCTTCAGTCACCAGCAACGCTCGCCAt                                                                                                             >  1:863516/1‑151 (MQ=255)                               aTGCTATGTTTTTTTTAAAACCCCCGCGCCACTGCTTTAAACTTGGCTGGCCGTTCTTCGTAAAAAAAGGG‑CGATACTGCATGCTGGCCATACCAGTCAGCAAGGCTGATGACCCCCGCCATATCTTCAGTCACCAGCAACGCTCGcc                                                                                                               <  2:769152/148‑1 (MQ=255)                                 gCTATGCTTTTTCTAAAACGCCAGCGCCCCTGTTTTCAACAGGGCTTGCCGTACTTCGTCAGAAAAAGG‑CGATACTGCATGCGGGGCATCCCAGCCAGAAATGCTGATGACCCCCGCCATATCTTCAGTCACCAGCAACGCTCGCCATTc                                                                                                           <  1:44339/150‑1 (MQ=255)                                      gCATTTTCTTAAACGCCAGCGCCACTGCTTTCAACATGGCTTGCCGTACTTCGTCAGAATAAGG‑CGATACTGCATGCTGGGCATACCAGTCAGCAATGCTGATGAACCCCGCCATATCTTCAGTCACCAGCAACGCTCGCCATTCACCCTc                                                                                                     >  1:338037/1‑151 (MQ=255)                                               tAAACGCCAGCGCCACTGCTTTCAACATGGCTTGCCGTACTTTGTCAGAATAAGG‑CGATACTGCATGCTGGGCATACCAGTCAGCAATGCTGATGAACCCCGCCATATCTTCAGTCACCAGCAACGCTCGCCATTCACCCTCAATTTTCAc                                                                                            >  1:51147/1‑151 (MQ=255)                                                aaccGCCGGCGCCACTGCTTTCAACATGGCTTGCCGTCCTTCGTCAAAATAAGG‑CGATACTGCATGCTGGGCATACCAGTCAGCAATGCTGATAACCCCCGCCATATCTTCAGTCACCAGCAACGCTCGCCATTCACCCTCAAttt                                                                                                <  1:43470/143‑1 (MQ=255)                                                  accccAGCCCCACTTCTTTAAACATGCTTTGCTATGCTTCTAGAAAAAAAGG‑CGTTCCTGCGTGCGGGGCATCCCAACCAACAATGGTGATGACCCCCGCCATATCTTCAGTCACCAGCAACGCTCGCCATTCACCCTCAATTTTCACCGc                                                                                         <  1:782565/148‑1 (MQ=255)                                                    gCCAGCGCCACTGCTTTCAACATGGCTTGCCGTACTTCGTCAGAATAAGG‑CGATACTGCATGCTGGGCATACCAGTCAGCAATGCTGATGAACCCCGCCATATCTTCAGTCACCAGCAACGCTCGCCATTCACCCTCAATTTTCACCGCtt                                                                                       >  1:571034/1‑151 (MQ=255)                                                     ccAGCCCCCCTGCTTTCAACATGGCTTCCCTTCCTTCGTCAGAATAAGG‑CGATACTGCATGCGGGGCATCCCAGTCAGAAATGCTGATGACCCCCGCCATATCTTCAGTCACCAGCAACGCTCGCCATTCACCCTCAATTTTCACCGCTTc                                                                                      <  1:579378/151‑1 (MQ=255)                                                                gCTTTCAACATGGCTTGCCGTACTTCGTCAGAATAAGG‑CGATACTGCATGCTGGGCATACCAGTCAGCAATGCTGATGAACCCCGCCATATCTTCAGTCACCAGCAACGCTCGCCATTCACCCTCAATTTTCACCGCTTCACCAAAAACg                                                                            >  1:467303/1‑150 (MQ=255)                                                                gCTTTCAACATGGCTTGCCGTACTTCGTCAGAATAAGG‑CGATACTGCATGCTGGGCATACCAGTCAGCAATGCTGATGAACCCCGCCATATCTTCAGTCACCAGCAACGCTCGCCATTCACCCTCAATTTTCACCGCTTCACCAAAAACg                                                                            >  1:103802/1‑150 (MQ=255)                                                                  tcacAACGTTGCTTGCCGTGTTTCG‑CAAAAAAAGGCCAATCCTGCAGGCGGGGAACCCCACCCAACAAGCCTGATAACCCCCGCCATATCTTCAGTCACCAGCAACGCTCGCCATTCACCCTCAATTTTCACCGCTTCACCAAAAACg                                                                            <  2:368295/145‑1 (MQ=255)                                                                    tCAACATGGCTTGCCGTACTTCGTCAGAATAAGG‑CGATACTGCATGCTGGGCATACCAGTCAGCAATGCTGATGAACCCCGCCATATCTTCAGTCACCAGCAACGCTCGCCATTCACCCTCAATTTTCACCGCTTCACCAAAAACGATCtt                                                                       >  2:651854/1‑151 (MQ=255)                                                                      aaCATGGCTTGCCTTACTTCGTCAAAATAAGG‑CAATACTGCATGCTGGGCATACCAGCCAGCAATTCTGATGACCCCCGCCATATCTTCAGTCACCAGCAACGCTCGCCATTCACCCTCAATTTTCACCGCTTCACCAAAAACGATCtt                                                                       <  2:771900/149‑1 (MQ=255)                                                                       aCATGGCTTGCCGTACTTCGTCAGAATAAGG‑CGATACTGCATGCTGGGCATACCAGTCAGCAATGCTGATGAACCCCGCCATATCTTCAGTCACCAGCAACGCTCGCCATTCACCCTCAATTTTCACCGCTTCACCAAAAACGATCTTCgg                                                                    >  2:347816/1‑151 (MQ=255)                                                                        cATGGTTGGCCTTACTTCTTAAAAAAAAGC‑CGATACTCCATGCGGGGCATCCCAGCCAGCAATTCTGAGAACCCCCGCCATATCTTCAGTCACCAGCAACGCTCGCCATTCACCCTCAATTTTCACCGCTTCACCAAAAACGATCTTCGGc                                                                   <  2:211929/151‑1 (MQ=255)                                                                              ttGCCGTACTTCGTCAGAATAAGG‑CGATACTGCATGCTGGGCATACCAGTCAGCAATGCTGATGAACCCCGCCATATCTTCAGTCACCAGCAACGCTCGCCATTCACCCTCAATTTTCACCGCTTCACCAAAAACGATCTTCGGCACGATg                                                             >  2:379620/1‑151 (MQ=255)                                                                                     aCTTCGTCAGAATAAGG‑CGATACTGCATGCTGGGCATACCAGTCAGCAATGCTGATGAACCCCGCCATATCTTCAGTCACCAGCAACGCTCGCCATTCACCCTCAATTTTCACCGCTTCACCAAAAACGATCTTCGGCACGATGACACCgg                                                      >  1:836062/1‑151 (MQ=255)                                                                                           tCAGAATAAGG‑CGATACTGCATGCTGGGCATACCAGTCAGCAATGCTGATGAACCCCGCCATATCTTCAGTCACCAGCAACGCTCGCCATTCACCCTCAATTTTCACCGCTTCACCAAAAACGATCTTCGGCACGATGACACCGGCCCGt                                                 >  1:296033/1‑150 (MQ=255)                                                                                           tCAGAAAAAGG‑CAATCCTGCATGCTGGGCATCCCAGTCAGAAATCCTGATGACCCCCGCCATATCTTCAGTCACCAGCAACGCTCGCCATTCACCCTCAATTTTCACCGCTTCACCAAAAACGATCTTCGGCACGATGACACCGGccc                                                   <  1:440428/148‑1 (MQ=255)                                                                                             aaaaaaggg‑CGATCCTGCATGCTGGGCATCCCAGTCAGCAATGCAGATGACCCCCGCCATATCTTCAGTCACCAGCAACGCTCGCCATTCACCCTCAATTTTCACCGCTTCACCAAAAACGATCTTCGGCACGATGACACCGGCCCGtt                                                <  2:171928/142‑1 (MQ=255)                                                                                                  aaGG‑CGATACTGCATGCTGGGCATACCAGTCAGCAATGCTGATGAACCCCGCCATATCTTCAGTCACCAGCAACGCTCGCCATTCACCCTCAATTTTCACCGCTTCACCAAAAACGATCTTCGGCACGATGACACCGGCCCGTTCCAGTTc                                         >  1:416436/1‑151 (MQ=255)                                                                                                    gg‑CGATACTGCATGCTGGGCATACCAGTCAGCAATGCTGATGAACCCCGCCATATCTTCAGTCACCAGCAACGCTCGCCATTCACCCTCAATTTTCACCGCTTCACCAAAAACGATCTTCGGCACGATGACACCGGCCCGTTCCAGTTCtt                                       <  1:224237/151‑1 (MQ=255)                                                                                                           ccTGAATGCGGGCCACCCCAGCCAGCAATCTTGATGACCCCCGCCATATCTTCAGTCACCAGCAACGCTCGCCATTCACCCTCAATTTTCACCGCTTCACCAAAAACGATCTTCGGCACGATGACACCGGCCCGTTCCAGTTCTTTAAtt                                  <  2:150148/149‑1 (MQ=255)                                                                                                             tccATGCGGGCCATCCCACTCAGAAATGCTGATACCCCCCGCCATATCTTCAGTCACCAGCAACGCTCGCCATTCACCCTCAATTTTCACCGCTTCACCAAAAACGATCTTCGGCACGATGACACCGGCCCGTTCCAGTTCTTTaa                                    <  2:462792/144‑1 (MQ=255)                                                                                                             tGCATGCTGGGCATACCAGTCAGCAATGCTGATGAACCCCGCCATATCTTCAGTCACCAGCAACGCTCGCCATTCACCCTCAATTTTCACCGCTTCACCAAAAACGATCTTCGGCACGATGACACCGGCCCGTTCCAGTTCTTTAATTAcc                               >  1:424285/1‑151 (MQ=255)                                                                                                               caggcggggCATCCCAGTCAGAAATGCTGATGACCCCCGCCATATCTTCAGTCACCAGCAACGCTCGCCATTCACCCTCAATTTTCACCGCTTCACCAAAAACGATCTTCGGCACGATGACACCGGCCCGTTCCAGTTCTTTAATTAcc                               <  1:575232/143‑1 (MQ=255)                                                                                                               cATGCTGGGCATCCCAGCCAGCAATGCTGATGACCCCCGCCATATCTTCAGTCACCAGCAACGCTCGCCATTCACCCTCAATTTTCACCGCTTCACCAAAAACGATCTTCGGCACGATGACACCGGCCCGTTCCAGTTCTTTAATTACCGc                             <  1:237515/151‑1 (MQ=255)                                                                                                               cATGCTGGGCATACCAGTCAGCAATGCTGATGAACCCCGCCATATCTTCAGTCACCAGCAACGCTCGCCATTCACCCTCAATTTTCACCGCTTCACCAAAAACGATCTTCGGCACGATGACACCGGCCCGTTCCAGTTCTTTAATTACCGc                             >  2:118390/1‑151 (MQ=255)                                                                                                                    tGGGCATACCAGTCAGCAATGCTGATGAACCCCGCCATATCTTCAGTCACCAGCAACGCTCGCCATTCACCCTCAATTTTCACCGCTTCACCAAAAACGATCTTCGGCACGATGACACCGGCCCGTTCCAGTTCTTTAATTACCGCAACCt                        >  1:680738/1‑151 (MQ=255)                                                                                                                    tGGGCACCCCAGCCAGCAATGCTGATGACCCCCGCCATATCTTCAGTCACCAGCAACGCTCGCCATTCACCCTCAATTTTCACCGCTTCACCAAAAACGATCTTCGGCACGATGACACCGGCCCGTTCCAGTTCTTTAATTACCGCaa                           <  1:489042/148‑1 (MQ=255)                                                                                                                          tACCAGTCAGCAATGCTGATGAACCCCGCCATATCTTCAGTCACCAGCAACGCTCGCCATTCACCCTCAATTTTCACCGCTTCACCAAAAACGATCTTCGGCACGATGACACCGGCCCGTTCCAGTTCTTTAATTACCGCAACCTCACgg                   >  2:351142/1‑150 (MQ=255)                                                                                                                            ccagccagAAATGCTGATGACCCCCGCCATATCTTCAGTCACCAGCAACGCTCGCCATTCACCCTCAATTTTCACCGCTTCACCAAAAACGATCTTCGGCACGATGACACCGGCCCGTTCCAGTTCTTTAATTACCGCAACCTCAc                     <  1:736978/146‑1 (MQ=255)                                                                                                                            ccAGTCAGCAATGCTGATGAACCCCGCCATATCTTCAGTCACCAGCAACGCTCGCCATTCACCCTCAATTTTCACCGCTTCACCAAAAACGATCTTCGGCACGATGACACCGGCCCGTTCCAGTTCTTTAATTACCGCAACCTCACGGAc                 >  2:91276/1‑150 (MQ=255)                                                                                                                            ccAGTCAGCAATGCTAAGCACCCCCGCCATATCTTCAGTCACCAGCAACGCTCGCCATTCACCCTCAATTTTCACCGCTTCACCAAAAACGATCTTCGGCACGATGACACCGGCCCGTTCCAGTTCTTTAATTACCGCAACCTCACg                    <  2:161681/147‑1 (MQ=255)                                                                                                                               accAGTAATGTTAATCACCCCCGCCATATCTTCAGTCACCAGCAACGCTCGCCATTCACCCTCAATTTTCGCCGCTTCACCAAAAACGATCTTCGGCACGATGACACCGGCCCGTTCCAGTTCTTTAATTACCGCAACCTCACGGACa                <  2:228358/146‑1 (MQ=255)                                                                                                                                 cAGCATTCCTAATAACCCCCGCCATATCTTCAGTCACCAGCAACGCTCGCCATTCACCCTCAATTTTCACCGCTTCACCAAAAACGATCTTCGGCACGATGACACCGGCCCGTTCCAGTTCTTTAATTACCGCAACCTCACGGACAATc             <  2:165629/149‑1 (MQ=255)                                                                                                                                   gCAATGCTGATGAACCCCGCCATATCTTCAGTCACCAGCAACGCTCGCCATTCACCCTCAATTTTCACCGCTTCACCAAAAACGATCTTCGGCACGATGACACCGGCCCGTTCCAGTTCTTTAATTACCGCAACCTCACGGACAATCGTTg         >  1:891/1‑151 (MQ=255)                                                                                                                                     attgtgaataaaCCCCGCCATATCTTCAGTCACCAGCAACGCTCGCCATTCACCCTCAATTTTCACCGCTTCACCAAAAACGATCTTCGGCACGATGACACCGGCCCGTTCCAGTTCTTTAATTACCGCAACCTCACGGACAATc             <  1:822105/135‑1 (MQ=255)                                                                                                                                      aTGCTGATGAACCCCGCCATATCTTCAGTCACCAGCAACGCTCGCCATTCACCCTCAATTTTCACCGCTTCACCAAAAACGATCTTCGGCACGATGACACCGGCCCGTTCCAGTTCTTTAATTACCGCAACCTCACGGACAATCGTTGGTc      >  2:736284/1‑151 (MQ=255)                                                                                                                                       tGCTGATGAACCCCGCCATATCTTCAGTCACCAGCAACGCTCGCCATTCACCCTCAATTTTCACCGCTTCACCAAAAACGATCTTCGGCACGATGACACCGGCCCGTTCCAGTTCTTTAATTACCGCAACCTCACGGACAATCGTTGGTCg     >  1:455751/1‑151 (MQ=255)                                                                                                                                         cTGATAACCCCCGCCATATCTTCAGTCACCAGCAACGCTCGCCATTCACCCTCAATTTTCACCGCTTCACCAAAAACGATCTTCGGCACGATGACACCGGCCCGTTCCAGTTCTTTAATTACCGCAACCTCACGGACAATCGtt          <  2:295999/144‑1 (MQ=255)                                                                                                                                          tgatgaACCCCGCCATATCTTCAGTCACCAGCAACGCTCGCCATTCACCCTCAATTTTCACCGCTTCACCAAAAACGATCTTCGGCACGATGACACCGGCCCGTTCCAGTTCTTTAATTACCGCAACCTCACGGACAATCGTTGGTCGGcc  >  2:277289/1‑151 (MQ=255)                                                                                                                                                |                                                                                                                                                 CGAACATAACAACAGCCATGCTGACGATTAATGCTATGCATTTTCTTAAACGCCAGCGCCACTGCTTTCAACATGGCTTGCCGTACTTCGTCAGAATAAGG‑CGATACTGCATGCTGGGCATACCAGTCAGCAATGCTGATGAACCCCGCCATATCTTCAGTCACCAGCAACGCTCGCCATTCACCCTCAATTTTCACCGCTTCACCAAAAACGATCTTCGGCACGATGACACCGGCCCGTTCCAGTTCTTTAATTACCGCAACCTCACGGACAATCGTTGGTCGGCC  >  NC_000913/2349003‑2349289

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑