Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,604,344	0	C	T	46.3%	30.5 / 18.7	42	S62F (TCT→TTT)	bglJ	bgl operon transcriptional activator
Reads supporting (aligned to +/- strand):  ref base C (4/18);  new base T (19/0);  total (24/18)
Fisher's exact test for biased strand distribution p-value = 5.49e-08
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CACTCATAGAAAAATGCGTCATGAGTAGTATCGGTATTGAGAGTTTATTCAGAAAGTTTGCGGGTAACCCTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCG‑ATTAAGTTTCCGCGTACCCGGCGTTTAGTTATTGCGGATGATGATATTGAAGCTCGGCTGATTGGTTCATTGTCGCCATCACCGCTGGAC  >  NC_000913/4604194‑4604492                                                                                                                                                       |                                                                                                                                                      cACTCATAGAAAAATGCGTCATGAGTAGTATCGGTATTGAGAGTTTATTCAGAAAGTTTGCGGGTAACCCTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATtttttc                                                                                                                                                       <  1:251759/151‑1 (MQ=255)  aCTCATAGAAAAATGCGTCATGAGTAGTATCGGTATTGAGAGTTTATTCAGAAAGTTTGCGGGTAACCCTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATtttttct                                                                                                                                                      <  1:83183/151‑1 (MQ=255)   cTCATAGAAAAATGCGTCATGAGTAGTATCGGTATTGAGAGTTTATTCAGAAAGTTTGCGGGTAACCCTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATtttttttt                                                                                                                                                     >  1:526504/1‑151 (MQ=255)        aGAAAAATGCGTCATGAGTAGTATCGGTATTGAGAGTTTATTCAGAAAGTTTGCGGGTAACCCTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTttttctttttct                                                                                                                                                <  2:574587/151‑1 (MQ=255)        aGAAAAATGCGTCATGAGTAGTATCGGTATTGAGAGTTTATTCAGAAAGTTTGCGGGTAACCCTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTAATtttttcttttttt                                                                                                                                                >  1:16863/1‑149 (MQ=255)         gAAAAATGCGTCATGAGTAGTATCGGTATTGAGAGTTTATTCAGAAAGTTTGCGGGTAACCCTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTg                                                                                                                                               <  2:570178/151‑1 (MQ=255)          aaaaaTGCGTCATGAGTAGTATCGGTATTGAGAGTTTATTCAGAAAGTTTGCGGGTAACCCTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGc                                                                                                                                              <  2:793877/151‑1 (MQ=255)           aaaaTGCGTCATGAGTAGTATCGGTATTGAGAGTTTATTCAGAAAGTTTGCGGGTAACCCTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGcc                                                                                                                                             <  1:139950/151‑1 (MQ=255)            aaaTGCGTCATGAGTAGTATCGGTATTGAGAGTTTATTCAGAAAGTTTGCGGGTAACCCTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTCTTcc                                                                                                                                             >  1:177100/1‑150 (MQ=255)                gCGTCATGAGTAGTATCGGTATTGAGAGTTTATTCAGAAAGTTTGCGGGTAACCCTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTGccct                                                                                                                                           >  1:679842/1‑146 (MQ=255)                    cATGAGTAGTATCGGTATTGAGAGTTTATTCAGAAAGTTTGCGGGTAACCCTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGt                                                                                                                                    <  2:112421/151‑1 (MQ=255)                     aTGAGTAGTATCGGTATTGAGAGTTTATTCAGAAAGTTTGCGGGTAACCCTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTTGCATGAGAAGTg                                                                                                                                   >  2:55191/1‑151 (MQ=255)                      tGAGTAGTATCGGTATTGAGAGTTTATTCAGAAAGTTTGCGGGTAACCCTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGGCTCTTTTTATTTTTTTGccttaatg                                                                                                                                       >  2:524521/1‑140 (MQ=255)                        agtagtATCGGTATTGAGAGTTTATTCAGAAAGTTTGCGGGTAACCCTTATAAGCTCCATACCTATACCAGTCAGGCGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAgc                                                                                                                                <  2:669252/151‑1 (MQ=255)                        agtagtATCGGTATTGAGAGTTTATTCAGAAAGTTTGCGGGTAACCCTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTg                                                                                                                                   >  1:106240/1‑148 (MQ=255)                                cGGTATTGAGAGTTTATTCAGAAAGTTTGCGGGTAACCCTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCTGCTTTTCTTTTTATTTCATTAGAAGTGGGAGCagcg                                                                                                                          >  2:415984/1‑147 (MQ=255)                                cGGTATTGAGAGTTTATTCAGAAAGTTTGCGGGTAACCCTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCagaga                                                                                                                         <  1:522599/150‑1 (MQ=255)                                  gTATTGAGAGTTTATTCAGAAAGTTTGCGGGTAACCCTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAggg                                                                                                                      <  2:40414/151‑1 (MQ=255)                                   tATTGAGAGTTTATTCAGAAAGTTTGCGGGTAACCCTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTCTGCCCATAGAAGCGGGGGCAGAGAggg                                                                                                                      >  2:766559/1‑150 (MQ=255)                                    aTTGAGAGTTTATTCAGAAAGTTTGCGGGTAACCCTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGa                                                                                                                     <  2:305516/150‑1 (MQ=255)                                    aTTGAGAGTTTATTCAGAAAGTTTGCGGGTAACCCTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTACTTTTTTTTTTTTTTGCCCTGAGGAGGGAGGGCAGAGAggg                                                                                                                      >  2:77726/1‑149 (MQ=255)                                                   aGAAAGTTTGCGGGTAACCCTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCTTTTTTTTTTTTTTTTCCATGAGAAGTGAGCGCAGAGAGGGGTTATCTTGCctgact                                                                                                      >  2:734062/1‑150 (MQ=255)                                                       aGTTTGCGGGTAACCCTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTTCCATGAGAAGTGAGCGCAGGGAGGGGTTTTCTTTCCTGGCTGAACt                                                                                                 >  1:433506/1‑151 (MQ=255)                                                           tGCGGGTAACCCTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGc                                                                                              <  1:382226/150‑1 (MQ=255)                                                             cGGGTAACCCTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTTCCATGAGAAGTGAGGGCAGAGAGGGGTTATCTTTCCTGACTGAACTGGCggt                                                                                           >  2:407715/1‑149 (MQ=255)                                                                    cccTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTGCCATTAGAAGTGAGCGCAGGGAGGGATTATCTTTTCTGACTGAACTGGCG‑GTTTAGttt                                                                                   >  1:323840/1‑151 (MQ=255)                                                                       ttATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTGCCCTGGGAAGGGAGGGGAGAGAGGGGTTATTTTGCCTGACTGAACTGGCG‑ATTTAGTTTTcg                                                                                >  2:514294/1‑151 (MQ=255)                                                                         ataAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTGCCATGAGAAGTGAGCGCAGAGAGGGGTTATTTTGCCTGACTGAAATGGCG‑ATTAAAttttc                                                                                 >  1:277253/1‑146 (MQ=255)                                                                           aaGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCG‑ATTAAGTTTCCGCGt                                                                             <  2:569465/150‑1 (MQ=255)                                                                            aGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCG‑ATTAAGTTTCCGCGTAc                                                                           <  1:47022/151‑1 (MQ=255)                                                                             gCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTTCCCTGAGAAGTGAGCGCAGAGAGGGGTTATCTTGCCTTACTGAACTGGCG‑ATTAAGTTTTCGCGTAcc                                                                          >  2:462991/1‑151 (MQ=255)                                                                                   tACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTAATTTTTTTTTTTTTTTCCTTTAGAAGTGAGGGCAGGGAGGGGTTATTTTTCCTTACTGCACTGGAGCATTAAATTTCCCGGTCCCCgcgt                                                                     >  1:296154/1‑148 (MQ=255)                                                                                    aCCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTTCCATTAGAAGTGAGCGCAGGGAGGGGTTTTCTTTCCTGACTTAAATGGCG‑ATTAAGGTTTCCCGTACCCGGCggt                                                                   >  1:730180/1‑149 (MQ=255)                                                                                        ataCCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCTTTTTTTTTTTTTCTGCCATGAGAAGTGAGCGCCGAGAGGGGTTATCTTGCCTGACTGAAATGGCG‑ATTAAGTTTTCGCGTACCCGGCGttt                                                                  >  2:171848/1‑148 (MQ=255)                                                                                           ccAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATATTGCCTGACTGAACTGGCG‑ATTAAGTTTCCGCGTACCCGGCGTTTAGTTAt                                                            <  1:707613/151‑1 (MQ=255)                                                                                            cAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTTTGCCCTGAGAAGTGAGCGCAGAGGGGGATTATCTTGCCTGACTGAACTTGCG‑ATTAAGTTTTCGCGTACCCGGCGTTTTGTTAtt                                                           >  1:305848/1‑151 (MQ=255)                                                                                                          ttCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTTCCCTGAGGAGTGAGCGCAGAGAGGGGTTATCTTGCCTTACTGAACTGGCG‑GTTAAGTTTTCGCGTACCCGGCGTTTAGTTATTGCGggtgat                                                  >  1:313290/1‑146 (MQ=255)                                                                                                           tCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCG‑ATTAAGTTTCCGCGTACCCGGCGTTTAGTTATTGCGGATGATGatat                                             <  1:570921/150‑1 (MQ=255)                                                                                                              ggATGCCATGTCGCGGATCTCGTTTGCGGCGGTCCTTTTTTTTTTTTCTGCCATGAGAAGTGAGCGCCGAGAGGGGTTATCTTGCCTGACTGAACTGGCG‑ATTAAGTTTCCGCGTACCCGGCGGTTAGTTATTGCGGGTGATGATAtt                                            >  2:645736/1‑148 (MQ=255)                                                                                                               gATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCG‑ATTAAGTTTCCGCGTACCCGGCGTTTAGTTATTGCGGATGATGATATTGAAg                                        <  2:156703/151‑1 (MQ=255)                                                                                                                   ccATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTGCCCCGAGAAGGGAGGGCCGGGAGGGGTTATTTTGTCTTTCTCAACTGGGG‑CTTAAGTTTTCGCGTACCCGGGGTTTTGGTATTGGGGGTTATGATATTTAAggccg                                    >  2:473376/1‑147 (MQ=255)                                                                                                                     aTGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCG‑ATTAAGTTTCCGCGTACCCGGCGTTTAGTTATTGCGGATGATGATATTGAAGCTCGGc                                  <  2:318273/151‑1 (MQ=255)                                                                                                                       gTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCG‑ATTAAGTTTCCGCGTACCCGGCGTTTAGTTATTGCGGATGATGATATTGAAGCTCGGCt                                 <  1:829353/150‑1 (MQ=255)                                                                                                                            ggATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCG‑ATTAAGTTTCCGCGTACCCGGCGTTTAGTTATTGCGGATGATGATATTGAAGCTCGGCTGATTgg                           <  1:366210/151‑1 (MQ=255)                                                                                                                               tctcGTTTGCGGCGGTCATTTTTTTTTTTTTTGTCCTGGGAGGTGAGCGCCAAGAGGGATTATCTTGCCTACGTGAACTGGCG‑GTTAAGATTTCGCGTTACCGGCGTGTTGATTTTGAGGATAATGATAATTAAGCTAAACTGATTGGt                          >  2:302274/1‑149 (MQ=255)                                                                                                                                  cGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCG‑ATTAAGTTTCCGCGTACCCGGCGTTTAGTTATTGCGGATGATGATATTGAAGCTCGGCTGATTGGTTc                        <  2:604478/148‑1 (MQ=255)                                                                                                                                          gcggTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCG‑ATTAAGTTTCCGCGTACCCGGCGTTTAGTTATTGCGGATGATGATATTGAAGCTCGGCTGATTGGTTCATTGTCGCCAt             >  2:133448/1‑151 (MQ=255)                                                                                                                                                    tttctttttctGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCG‑ATTAAGTTTCCGCGTACCCGGCGTTTAGTTATTGCGGATGATGATATTGAAGCTCGGCTGATTGGTTCATTGTCGCCATCACCGCTgg    <  2:127671/150‑1 (MQ=255)                                                                                                                                                      tctttttctGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCG‑ATTAAGTTTCCGCGTACCCGGCGTTTAGTTATTGCGGATGATGATATTGAAGCTCGGCTGATTGGTTCATTGTCGCCATCACCGCTGGAc  <  1:26606/150‑1 (MQ=255)                                                                                                                                                       |                                                                                                                                                      CACTCATAGAAAAATGCGTCATGAGTAGTATCGGTATTGAGAGTTTATTCAGAAAGTTTGCGGGTAACCCTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCG‑ATTAAGTTTCCGCGTACCCGGCGTTTAGTTATTGCGGATGATGATATTGAAGCTCGGCTGATTGGTTCATTGTCGCCATCACCGCTGGAC  >  NC_000913/4604194‑4604492

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑