Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,604,237	0	C	T	43.4%	52.7 / 24.0	53	S64L (TCG→TTG)	lsrD	autoinducer 2 import system permease protein
Reads supporting (aligned to +/- strand):  ref base C (7/23);  new base T (23/0);  total (30/23)
Fisher's exact test for biased strand distribution p-value = 3.44e-09
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.91e-01

GTTATTGAGATTGTCGCATTTGGTGCAATTAACCCGCGAATGTTAGATCTCAATATGTTGCTGTTCAGCACCAGTGACTTTATCTGCATTGGCATTGTCGCCCTACCGCTAACGATGGTGATTGTCAGTGGCGGGATCGATATTTCGTTTGGTTCGACCATCGGCCTCTGCGCCATTGCATTGGGCGTACTGTTTCAAAGTGGTGTGCCGATGCCGCTGGCGATACTCCTGACCTTACTGCTCGGCGCATTGTGCGGGCTGATCAACGCCGGATTAATTATCTATACCAA  >  NC_000913/1604092‑1604381                                                                                                                                                  |                                                                                                                                                 gTTATTGAGATTGTCGCATTTGGTGCAATTAACCCGCGAATGTTAGATCTCAATATGTTGCTGTTCAGCACCAGTGACTTTATCTGCATTGGCATTGTCGCCCTACCGCTAACGATGGAGATTGTCAGTGGCGGGACAGATAATTTTTTTg                                                                                                                                             >  1:491058/1‑151 (MQ=255)   tATTGAGATTGTCGCATTTGGTGCAATTAACCCGCGAATGTTAGATCTCAATATGTTGCTGTTCAGCACCAGTGACTTTATCTGCATTGGCATTGTCGCCCTACCGCTAACGATGGTGATTGTCAGTGGCGGGATCGGTATTTTGTTTGGt                                                                                                                                           >  1:416099/1‑151 (MQ=255)       gagaTTGTCGCATTTGGTGCAATTAACCCGCGAATGTTAGATCTCAATATGTTGCTGTTCAGCACCAGTGACTTTATCTGCATTGGCATTGTCGCCCTACCGCTAACGATGGTGATTGTCAGTGGCGGGATCGATATTTCGTTTGGTTCGa                                                                                                                                       <  1:912196/151‑1 (MQ=255)        agaTTGTCGCATTTGGTGCAATTAACCCGCGAATGTTAGATCTCAATATGTTGCTGTTCAGCACCAGTGACTTTATCTGCATTGGCATTGTCGCCCTACCGCTAACGATGGTGATTGTCAGTGGCGGGATCGATATTTCGTTTGGTTCGAc                                                                                                                                      <  1:275009/151‑1 (MQ=255)         gaTTGTCGCATTTGGTGCAATTAACCCGCGAATGTTAGATCTCAATATGTTGCTGTTCAGCACCAGTGACTTTATCTGCATTGGCATTGTCGCCCTACCGCTAACGATGGTGATTGTCAGTGGCGGGATCGATATTTCGTTTGGTTCGAcc                                                                                                                                     <  1:63945/151‑1 (MQ=255)           ttGTCGCATTTGGTGCAATTAACCCGCGAATGTTAGATCTCAATATGTTGCTGTTCAGCACCAGTGACTTTATCTGCATTGGCATTGTCGCCCTACCGCTAACGATGGTGATTGTCAGTGGCGGGATCGATATTTTGTTTGGTTCTAcc                                                                                                                                     >  1:233819/1‑149 (MQ=255)             gTCGCATTTGGTGCAATTAACCCGCGAATGTTAGATCTCAATATGTTGCTGTTCAGCACCAGTGACTTTATCTGCATTGGCATTGTCGCCCTACCGCTAACGATGGTGATTGTCAGTGGCGGGATCGATATTTCGTTTGGTTCGACCATCg                                                                                                                                 <  2:837765/151‑1 (MQ=255)                gCATTTGGTGCAATTAACCCGCGAATGTTAGATCTCAATATGTTGCTGTTCAGCACCAGTGACTTTATCTGCATTGGCATTGTCGCCCTACCGCTAACGATGGTGATTGTCAGTGGCGGGATCGATATTTCGTTTTGTTTGACCATCGGcc                                                                                                                              >  1:63415/1‑151 (MQ=255)                 cATTTGGTGCAATTAACCCGCGAATGTTAGATCTCAATATGTTGCTGTTCAGCACCAGTGACTTTATCTGCATTGGCATTGTCGCCCTACCGCTAACGATGGTGATTGTCAGTGGCGGGATCGATATTTTGTTTTGTTTGACCATCGGcc                                                                                                                              >  1:554484/1‑150 (MQ=255)                  aTTTGGTGCAATTAACCCGCGAATGTTAGATCTCAATATGTTGCTGTTCAGCACCAGTGACTTTATCTGCATTGGCATTGTCGCCCTACCGCTAACGATGGTGATTGTCAGTGGCGGGATCGATATTTTGTTTTGTTCGACCATCGGCct                                                                                                                             >  1:720303/1‑150 (MQ=255)                    ttGGTGCAATTAACCCGCGAATGTTAGATCTCAATATGTTGCTGTTCAGCACCAGTGACTTTATCTGCATTGGCATTGTCGCCCTACCGCTAACGATGGTGATTGTCAGTGGCGGGATCGATATTTTGTTTTGTTTGACCATCGGCctct                                                                                                                           >  1:668054/1‑150 (MQ=255)                      ggTGCAATTAACCCGCGAATGTTAGATCTCAATATGTTGCTGTTCAGCACCAGTGACTTTATCTGCATTGGCATTGTCGCCCTACCGCTAACGATGGTGATTGTCAGTGGCGGGATCGATATTTCGTTTGGTTCGACCATCGGCCTCTgc                                                                                                                         <  1:773308/150‑1 (MQ=255)                        tGCAATTAACCCGCGAATGTTAGATCTCAATATGTTGCTGTTCAGCACCAGTGACTTTATCTGCATTGGCATTGTCGCCCTACCGCTAACGATGGTGATTGTCAGTGGCGGGATCGATATTTTGTTTTGTTCGACCCTCCGCCTCTGCGcc                                                                                                                      >  1:535623/1‑151 (MQ=255)                               aaCCCGCGAATGTTAGATCTCAATATGTTGCTGTTCAGCACCAGTGACTTTATCTGCATTGGCATTGTCGCCCTACCGCTAACGATGGTGATTGTCAGTGGCGGGATCGATATTTCGTTTGGTTCGACCATCGGCCTCTGCGCcattgcat                                                                                                               <  1:888635/151‑1 (MQ=255)                               aaCCCGCGAATGTTAGATCTCAATATGTTGCTGTTCAGCACCAGTGACTTTATCTGCATTGGCATTGTCGCCCTACCGCTAACGATGGTGATTGTCAGTGGCGGGATCGATATTTCGTTTGGTTCGACCATCGGCCTCTGCGCcattgca                                                                                                                <  1:302872/150‑1 (MQ=255)                                  ccGCGAATGTTAGATCTCAATATGTTGCTGTTCAGCACCAGTGACTTTATCTGCATTGGCATTGTCGCCCTACCGCTAACGATGGTGATTGTCAGTGGCGGGATCGATATTTTGTTTGGTTCTACCATCGGCCTCTTCGCcactgcatttg                                                                                                            >  2:602930/1‑149 (MQ=255)                                   cgcgAATGTTAGATCTCAATATGTTGCTGTTCAGCACCAGTGACTTTATCTGCATTGGCATTGTCGCCCTACCGCTAACGATGGTGATTGTCAGTGGCGGGCTCGCAATTTCCTTTTTTTCGATCATATGCCCCTGCGCcatttcat                                                                                                               >  1:533120/1‑147 (MQ=255)                                      gAATGTTAGATCTCAATATGTTGCTGTTCAGCGCCAGTGACTTTATCTGCATTGGCATTGTCGCCCTACCGCTAACGATGGTGATTGTCAGTGGCGGGGTTGATATTTTGTTTTGTTCGACCATCCGCCTCCGTGCcctttcctttgggg                                                                                                         >  1:442103/1‑140 (MQ=255)                                        aTGTTAGATCTCAATATGTTGCTGTTCAGCACCAGTGACTTTATCTGCATTGGCATTGTCGCCCTACCGCTAACGATGGTGATTGTCAGTGGCGGGGTCGTTATTTCGTTTTGGTTGACCAACCGCCTCCCCGcccctttcttgggcg                                                                                                         >  2:334821/1‑135 (MQ=255)                                           ttAGATCTCAATATGTTGCTGTTCAGCACCAGTGACTTTATCTGCATTGGCATTGTCGCCCTACCGCTAACGATGGTGATTGTCAGTGGCGGGGTCGATATTTTGTTTTGGTCGACCATCGACCTCTCCGCCATTTCATTGGGCGGACt                                                                                                     >  2:667608/1‑149 (MQ=255)                                                 ctcAATATGTTGCTGTTCAGCACCAGTGACTTTATCTGCATTGGCATTGTCGCCCTACCGCTAACGATGGTGATTGTCAGTGGCGGGGTCGATATTTTGTTTGGTTTGGCCATCGGCCTCTTCGCCCTTGCATTGGGGGGACTGTTTTaa                                                                                              >  1:118115/1‑150 (MQ=255)                                                   cAATATGTTGCTGTTCAGCACCAGTGACTTTATCTGCATTGGCATTGTCGCCCTACCGCTAACGATGGTGATTGTCAGTGGCGGGATCGATATTTCTTTTGGTTCGACCATCGGCCTCTGCGCCCTTGCATTGGGCGGACTGTTTTaaa                                                                                             >  2:594228/1‑149 (MQ=255)                                                     atatGTTGCTGTTCAGCACCAGTGACTTTATCTGCATTGGCATTGTCGCCCTACCGCTAACGATGGTGATTGTCAGTGGCGGGATCGATATTTCGTTTGGTTCGACCATCGGCCTCTGCGCCATTGCATTGGGCGTACTGTTTCAAAgtgg                                                                                         <  1:976694/151‑1 (MQ=255)                                                     atatGTTGCTGTTCAGCACCAGTGACTTTATCTGCAGTGGCATTGTCGCCCTACCGCTAACGATGGTGAGTGTCAGTGGCGGGATCGATATTTCGTTTGGTTCGACCATCGGCCTCTGCGCCATTGCATTGGGCGTACTGTTTCAAAgtgg                                                                                         <  2:516476/151‑1 (MQ=255)                                                      tatGTTGCTGTTCAGCACCAGTGACTTTATCTGCATTGGCATTGTCGCCCTACCGCTAACGATGGTGATTGTCAGTGGCGGGGTCGATATTTTGTTTTGTTCGACCATCGGCCTCTGCGCCCTTTCATTGGGCGTACTGTTTTAAAgggg                                                                                         >  2:189401/1‑150 (MQ=255)                                                               gTTCAGCACCAGTGACTTTATCTGCATTGGCATTGTCGCCCTACCGCTAACGATGGTGATTGTCAGTGGCGGGGTCGGTATTTTCTTTTGTTTGACCATCGGCCTCTGCGGCCCTGCATTTGGGGGACTGTTTCTAAGTGGGGTGcccgt                                                                                >  1:476560/1‑147 (MQ=255)                                                               gTTCAGCACCAGTGACTTTATCTGCATTGGCATTGTCGCCCTACCGCTAACGATGGTGATTGTCAGTGGCGGGATCGATTTTTTGTTTGGTTTGACCATCGGCCTCTTCGCCATTGCATTTGGGGGACTGTTTTAAAGTGGGGGGCCGAt                                                                                >  2:860285/1‑150 (MQ=255)                                                               gTTCAGCACCAGTGACTTTATCTGCATTGGCATTGTCGCCCTACCGCTAACGATGGTGATTGTCAGTGGCGGGATCGATATTTTGTTTTGTTCGACCCTCGGCCCCTGCGCCCCTTCATTGGGCGTACTGTTTTAAAGGGGtgtggc                                                                                   >  2:886780/1‑145 (MQ=255)                                                                       ccAGTGACTTTATCTGCATTGGCATTGTCGCCCTACCGCTAACGATGGTGATTGTCAGTGGCGGGATCGATATTTCGTTTTGTTCGACCCTCCGCCTCTGCGCCCTTTCATTGGGCGGACTGTTTTTAAGGGGTGTGCCGGTGCCGCCgg                                                                        >  2:480064/1‑150 (MQ=255)                                                                        cAGTGACTTTATCTGCATTGGCATTGTCGCCCTACCGCTAACGATGGTGATTGTCAGTGGCGGGATCGATATTTTGTTTTGTTCGACCATCGGCCCCTGCGCCATTGCATTGGGCGGACTGGTTCTAAGAGGGGTGCCGATGCCGCCGGCg                                                                      >  1:133409/1‑151 (MQ=255)                                                                        cAGTGACTTTATCTGCATTGGCATTGTCGCCCTACCGCTAACGATGGTGATTGTCAGTGGCGGGATCGATATTTCGTTTGGTTCGACCATCGGCCTCTGCGCCATTGCATTGGGCGTACTGTTTCAAAGTGGTGTGCCGATGCCGCTGGCg                                                                      <  2:960643/151‑1 (MQ=255)                                                                        cAGTGACTTTATCTGCATTGGCATTGTCGCCCTACCGCTAACGATGGTGATTGTCAGTGGCGGGATCGATATTTCGTTTGGTTCGACCATCGGCCTCTGCGCCATTGCATTGGGCGTACTGTTTCAAAGTGGTGTGCCGATGCCGCTGGCg                                                                      <  1:87184/151‑1 (MQ=255)                                                                                 tATCTGCATTGGCATTGTCGCCCTACCGCTAACGATGGTGATTGTCAGTGGCGGGATCGATATTTCGTTTGGTTCGACCATCGGCCTCTGCGCCATTGCATTGGGCGTACTGTTTCAAAGTGGTGTGCCGATGCCGCTGGCGATACTCCt                                                              <  2:769366/150‑1 (MQ=255)                                                                                      gcattggcattgTCGCCCTACCGCTAACGATGGTGATTGTCAGTGGCGGGATCGATATTTCGTTTGGTTCGACCATCGGCCTCTGCGCCATTGCATTGGGCGTACTGTTTCAAAGTGGTGTGCCGATGCCGCTGGCGATACTCCTGACCtt                                                        <  2:597833/151‑1 (MQ=255)                                                                                              attgTCGCCCTACCGCTAACGATGGTGATTGTCAGTGGCGGGATCGATATTTCGTTTGGTTCGACCATCGGCCTCTGCGCCATTGCATTGGGCGTACTGTTTCAAAGTGGTGTGCCGATGCCGCTGGCGATACTCCTGACCTTACTGCTCg                                                <  1:572986/151‑1 (MQ=255)                                                                                                tgTCGCCCTACCGCTAACGATGGTGATTGTCAGTGGCGGGATCGATATTTTGTTTGGTTCGGCCATCGGCCTCTGCGCCCTTGCATTGGGCGGACTGTTTTAAAGAGGTGTGCCGATGCCGCTGGGGGTACTCCTGACCTTACTGCTCgg                                               >  1:117443/1‑150 (MQ=255)                                                                                                   cGCCCTACCGCTAACGATGGTGATTGTCAGTGGCGGGATCGATATTTCGTTTGGTTCGACCATCGGCCTCTGCGCCATTGCATTGGGCGTACTGTTTCAAAGTGGTGTGCCGATGCCGCTGGCGATACTCCTGACCTTACTGCTCGGCGCa                                           <  2:576142/151‑1 (MQ=255)                                                                                                       cTACCGCTAACGATGGTGATTGTCAGTGGCGGGATCGATATTTTGTTTTGTTCGACCATCGGCCTCTGCGCCATTGCATTTGGGGTACTGTTTTAAAATGGGGTGCCGCTGCCGCCGGGGGTACTCCCGACCTTACTGCTCCGCGCCtt                                         >  1:45164/1‑149 (MQ=255)                                                                                                         aCCGCTAACGATGGTGATTGTCAGTGGCGGGATCGATATTTTGTTTTGTTCGACCATCGGCCCCTGCGCCCTTTCCTTTGGGGTACTGTTTTAAAGTGGGGTGCCGCTGCCGCCGGCGGGATTCCCGGCCTTACTTCCCGGCGGCTtgtg                                      >  2:65423/1‑150 (MQ=255)                                                                                                          ccGCTAACGATGGTGATTGTCAGTGGCGGGATCGATATTTTGTTTTGTTCGACCATCGGCCTCTGCGCCATTGCCTTGGGCGGACTGTTTCAAAATGGGGTGGCGCGGCCCCTGGCGATACTCCTGACCTTACTGCTCGGCGCATtgtg                                      >  1:612981/1‑149 (MQ=255)                                                                                                          ccGCTAACGATGGTGATTGTCAGTGGCGGGATCGATATTTCGTTTGGTTCGACCATCGGCCTCTGCGCCATTGCATTGGGCGTACTGTTTCAAAGTGGTGTGCCGATGCCGCTGGCGATACTCCTGACCTTACTGCTCGGCGCATTGTGc                                     <  2:68674/150‑1 (MQ=255)                                                                                                          ccGCTAACGATGGTGATTGTCAGTGGCGGGATCGATATTTCGTTTGGTTCGACCATCGGCCTCTGCGCCATTGCATTGGGCGTACTGTTTCAAAGTGGTGTGCCGATGCCGCTGGCGATACTCCTGACCTTACTGCTCGGCGCATTGTGCg                                    <  2:730590/151‑1 (MQ=255)                                                                                                            gCTAACGATGGTGATTGTCAGTGGCGGGATCGATATTTTGTTTGGTTCGACCAACGGCCTCTGCGCCATTGCATTTGGCGGACTGTTTTAAAGTGGGGTGCCGATGCCGCTGGCGGAACTCCTTACCTTTCTGCTCGGCGCCTTTTGCggg                                  >  1:947718/1‑151 (MQ=255)                                                                                                              tAACGATGGTGATTGTCAGTGGCGGGATCGGAATTTTGTTTTGTTCGACCATCGGCCTCTGCGGCACTGCATTGGGCGCACTGTTTTCAAGTGGGGTGCCGATGCCGCTGGCGGTACTCCCGACCCTTCTGCTCGGCGCATTGTGgggg                                  >  2:526034/1‑149 (MQ=255)                                                                                                               aaCGATGGTGATTGTCAGTGGCGGGGTCGATATTTTGTTTTGTTCGGCCAACCGCCTCTGCGCCCTTGCCTTTGGGGGTCTGTTTTTAAGTGGGGTGCCGATGCCGCTGGCGGTACCCCTGACCTTACTGCTCCGCGCATTGTGCggg                                  >  2:543149/1‑148 (MQ=255)                                                                                                                      gTGATTGTCAGTGGCGGGATCGATATTTCGTTTGGTTCGACCATCGGCCTCTGCGCCATTGCATTGGGCGTACTGTTTCAAAGTGGTGTGCCGATGCCGCTGGCGATACTCCTGACCTTACTGCTCGGCGCATTGTGCGGGCTGATCAACg                        <  2:135915/151‑1 (MQ=255)                                                                                                                            gTCAGTGGCGGGATCGATATTTCGTTTGGTTCGACCATCGGCCTCTGCGCCATTGCATTGGGCGTACTGTTTCAAAGTGGTGTGCCGATGCCGCTGGCGATACTCCTGACCTTACTGCTCGGCGCATTGTGCGGGCTGATCAACGCCGGat                  <  1:860290/151‑1 (MQ=255)                                                                                                                                    cGGGATCGATATTTCGTTTGGTTCGACCATCGGCCTCTGCGCCATTGCATTGGGCGTACTGTTTCAAAGTGGTGTGCCGATGCCGCTGGCGATACTCCTGACCTTACTGCTCGGCGCATTGTGCGGGCTGATCAACGCCGGATTAATTATc          <  2:214442/151‑1 (MQ=255)                                                                                                                                        aTCGATATTTCGTTTGGTTCGACCATCGTCCTCTGCGCCATTGCATTGGGCGTACTGTTTCAAAGTGGTGTGCCGATGCCGCTGGCGATACTCCTGACCTTACTGCTCGGCGCATTGTGCGGGCTGATCAACGCCGGATTAATTATCtat       <  2:565360/150‑1 (MQ=255)                                                                                                                                        aTCGATATTTCGTTTGGTTCGACCATCGGCCTCTGCGCCATTGCATTGGGCGTACTGTTTCAAAGTGGTGTGCCGATGCCGCTGGCGATACTCCTGACCTTACTGCTCGGCGCATTGTGCGGGCTGATCAACGCCGGATTAATTATCtat       >  2:781877/1‑150 (MQ=255)                                                                                                                                          cGATATTTCGTTTGGTTCGACCATCGGCCTCTGCGCCATTGCATTGGGCGTACTGTTTCAAAGTGGTGTGCCGATGCCGCTGGCGATACTCCTGACCTTACTGCTCGGCGCATTGTGCGGGCTGATCAACGCCGGATTAATTATCTATAcc    >  2:580236/1‑151 (MQ=255)                                                                                                                                            atatTTCGTTTGGTTCGACCATCGGCCTCTGCGCCATTGCATTGGGCGTACTGTTTCAAAGTGGTGTGCCGATGCCGCTGGCGATACTCCTGACCTTACTGCTCGGCGCATTGTGCGGGCTGATCAACGCCGGATTAATTATCTATACCaa  <  2:185258/151‑1 (MQ=255)                                                                                                                                             tatTTCGTTTGGTTCGACCATCGGCCTCTGCGCCATTGCATTGGGCGTACTGTTTCAAAGTGGTGTGCCGATGCCGCTGGCGATACTCCTGACCTTACTGCTCGGCGCATTGTGCGGGCTGATCAACGCCGGATTAATTATCTATACCaa  <  2:395534/150‑1 (MQ=255)                                                                                                                                                  |                                                                                                                                                 GTTATTGAGATTGTCGCATTTGGTGCAATTAACCCGCGAATGTTAGATCTCAATATGTTGCTGTTCAGCACCAGTGACTTTATCTGCATTGGCATTGTCGCCCTACCGCTAACGATGGTGATTGTCAGTGGCGGGATCGATATTTCGTTTGGTTCGACCATCGGCCTCTGCGCCATTGCATTGGGCGTACTGTTTCAAAGTGGTGTGCCGATGCCGCTGGCGATACTCCTGACCTTACTGCTCGGCGCATTGTGCGGGCTGATCAACGCCGGATTAATTATCTATACCAA  >  NC_000913/1604092‑1604381

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: ‑