Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,604,344	0	C	T	42.3%	48.9 / 26.1	52	S62F (TCT→TTT)	bglJ	bgl operon transcriptional activator
Reads supporting (aligned to +/- strand):  ref base C (13/17);  new base T (22/0);  total (35/17)
Fisher's exact test for biased strand distribution p-value = 8.94e-06
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

AAAAATGCGTCATGAGTAGTATCGGTATTGAGAGTTTATTCAGAAAGTTTGCGGGTAACCCTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTAAGTTTCCGCGTACCCGGCGTTTAGTTATTGCGGATGATGATATTGAAGCTCGGCTGATTGGTTCATTGTCGCCATCACCGCTGG  >  NC_000913/4604203‑4604490                                                                                                                                              |                                                                                                                                                   aaaaaTGCGTCATGAGTAGTATCGGTATTGAGAGTTTATTCAGAAAGTTTGCGGGTAACCCTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTttttttttttct                                                                                                                                             >  2:993432/1‑149 (MQ=255)  aaaaTGCGTCATGAGTAGTATCGGTATTGAGAGTTTATTCAGAAAGTTTGCGGGTAACCCTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTAAATTTTTTTTTTTTTggc                                                                                                                                          >  2:833411/1‑149 (MQ=255)    aaTGCGTCATGAGTAGTATCGGTATTGAGAGTTTATTCAGAAAGTTTGCGGGTAACCCTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCAt                                                                                                                                        <  1:910583/151‑1 (MQ=255)             tGAGTAGTATCGGTATTGAGGGTTTATTCAGAAAGTTTGCGGGTAACCCTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGGCATTTTTTCTTTTTTTGCCCAGAGAAg                                                                                                                                  >  1:330974/1‑148 (MQ=255)             tGAGTAGTATCGGTATTGAGAGTTTATTCAGAAAGTTTGCGGGTAACCCTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGCGATTTTTTTTTTTTTTGccgttagcacgg                                                                                                                                >  1:398906/1‑140 (MQ=255)              gAGTAGTATCGGTATTGAGAGTTTATTCAGAAAGTTTGCGGGTAACCCTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTTTGCCATgaggaggg                                                                                                                                >  2:534078/1‑147 (MQ=255)                  agtaTCGGTATTGAGAGTTTATTCAGAAAGTTTGCGGGTAACCCTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTGCCATGAGAAGTGAgcg                                                                                                                            >  1:368891/1‑149 (MQ=255)                   gtaTCGGTATTGAGAGTTTATTCAGAAAGTTTGCGGGTAACCCTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCag                                                                                                                         <  1:52200/151‑1 (MQ=255)                     aTCGGTATTGAGAGTTTATTCAGAAAGTTTGCGGGTAACCCTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCaga                                                                                                                        <  1:276147/150‑1 (MQ=255)                          tATTGAGAGTTTATTCAGAAAGTTTGCGGGTAACCCTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTGGCCTGAGAAGTGAGGGCagggaggg                                                                                                                   >  1:123508/1‑150 (MQ=255)                           aTTGAGAGTTTATTCAGAAAGTTTGCGGGTAACCCTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTGCCATGAGAAGTGAGGGCAGAGAggg                                                                                                                   >  1:471589/1‑149 (MQ=255)                             tGAGAGTTTATTCAGAAAGTTTGCGGGTAACCCTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGAtt                                                                                                                <  1:313584/150‑1 (MQ=255)                              gagaGTTTATTCAGAAAGTTTGCGGGTAACCCTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTGCCATGAGAAGGGAGCGCAGGGAGGGGTTAt                                                                                                              >  2:963971/1‑151 (MQ=255)                               agagTTTATTCAGAAAGTTTGCGGGTAACCCTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATc                                                                                                             <  1:858141/151‑1 (MQ=255)                                gagTTTATTCAGAAAGTTTGCGGGTAACCCTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCCTTTTTTTTTTTTTTGCCCTGAGAAGTGAGCGCCGAGGGGGGtttttt                                                                                                            >  1:410440/1‑147 (MQ=255)                                gagTTTATTCAGAAAGTTTGCGGGTAACCCTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTTTCATGAGAAGGGAGCGCGGGGAGGGGATATCt                                                                                                            >  1:241146/1‑151 (MQ=255)                                 agTTTATTCAGAAAGTTTGCGGGTAACCCTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTGCCATGAGAAGTGAGCGCAGAGAGGGGTTAtttt                                                                                                           >  2:517946/1‑151 (MQ=255)                                    ttATTCAGAAAGTTTGCGGGTAACCCTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCCTTTTTTTTTTTTTTTCCATGAGAAGGGAGCGCAGAGAGGGGTTATCTTTcc                                                                                                        >  1:965071/1‑151 (MQ=255)                                        tCAGAAAGTTTGCGGGTAACCCTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTAATTTTTTTTTTTTTTGTCATGAGAAGAGAGCGCAGAGAGGGGTTATATTGc                                                                                                         >  1:606339/1‑146 (MQ=255)                                           gAAAGTTTGCGGGTAACCCTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCCTGAGAAGGGAGCGCAGAGAGGGATTATCTTGCctgactg                                                                                                  >  2:255337/1‑150 (MQ=255)                                             aaGTTTGCGGGTAACCCTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCCTGAGAAGTGAAGGCAGGGCGGGATTATCCTGCCTGGCTTaa                                                                                                >  2:860301/1‑150 (MQ=255)                                               gTTTGCGGGTAACCCTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTg                                                                                             <  1:872441/151‑1 (MQ=255)                                                  tGCGGGTAACCCTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCCTTTTTTTTTTTTCTTCCCTGGGAAGGGAGGGCAGAGAGGGATTATCTTTCCTGACTGAACTGGCg                                                                                          >  2:558095/1‑151 (MQ=255)                                                          tcccTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCAATTTTTCTTTTTTTGCCCCGTAAAAGGAGGGCAGAGCGGGGTTATTTTTGCTTACTGAAGTggggcatga                                                                                     >  1:445860/2‑141 (MQ=255)                                                            ccTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTATTCCCTCAGAAGAGAGAGCAGAAGGGGGTTATCCTGGCTGACTCAACTGGAGATTTAAttt                                                                                 >  1:287603/1‑150 (MQ=255)                                                                ataAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTAAGTTTCcgc                                                                             <  2:823095/150‑1 (MQ=255)                                                                   aGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTGCCCTGAGGAAGGAGCGCAGGGAGGGATTATCTTTCCTGACTGAACTGGGGATTAAGTTTCCGGGt                                                                           >  2:824537/1‑149 (MQ=255)                                                                       ccATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTAAGTTTCCGCGTACCCg                                                                      <  1:474365/150‑1 (MQ=255)                                                                        cATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTAAGTTTCCGCGTACCCGGc                                                                    <  2:318058/151‑1 (MQ=255)                                                                                  ccAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGGTTATCTTGCCTGACTGAAATGGCGATTAAGTTTTCGCGGACCCGGCGGTTAGttt                                                           >  1:906899/1‑149 (MQ=255)                                                                                    aGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTGCCATGAGAAGGGAGCGCCGAGAGGGATTATCTTTCCTGACCTAACTGGCGGTTTAGTTTTCGCGGACCCGGCGgtttggtttt                                                         >  1:939553/1‑143 (MQ=255)                                                                                       cAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTAAGTTTCCGCGTACCCGGCGTTTAGTTATTGCgg                                                     >  2:457385/1‑151 (MQ=255)                                                                                            gTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGAGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACGGGCGATTAAGTTTCCGCGTACCCGGCGTTTAGTTATTGCGgatgat                                                <  1:970142/151‑1 (MQ=255)                                                                                                 ttCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGAGATTAAGTTTCCGCGTACCCGGCGTTTAGTTATTGCGGATGATGata                                            <  1:217833/150‑1 (MQ=255)                                                                                                   cAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTGATTTTTTTTTTTTTTTCCACTTGAAGTGGGCGCAGAGAGGGGTTATCTTGCCTGACCGAACTGGCGATTAAGATTCCGCGTACCCGGCGTTTTGTTTTTGCGGATGGTGTTAtt                                          >  2:476272/1‑150 (MQ=255)                                                                                                   cAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTAAGTTTCCGCGTACCCGGCGTTTAGTTATTGCGGGTGATGATAtt                                          >  1:448013/1‑150 (MQ=255)                                                                                                     ggATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTAAGTTTCCGCGTACCCGGCGTTTAGTTATTGCGGATGATGATATTGaa                                       <  2:368670/151‑1 (MQ=255)                                                                                                       aTGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTAAGTTTCCGCGTACCCGGCGTTTAGTTATTGCGGATGATGATATTGAAg                                      <  2:1008777/150‑1 (MQ=255)                                                                                                           cATGTCGCGGATCTCGTTTGCGGCGGTCCTTTTTTTTTTTTTTGCCCTGGGAAGTGAGCGCAGGGAGGGATTAACTTGCCTGAATGAAATGGGGTTTAAATTTTCCCGTACCCGGCGTTTTGTTATTTCGGATGATGATATTTAAggccgg                                 >  2:814592/1‑146 (MQ=255)                                                                                                                 gcgGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGGGAGCGCCGAGAGGGGTTATCTTTCCTGACTGAACTGGCGATTAAGTTTCCGCGTACCCGGCGTTTAGTTATTGCGGATGATGATATTGAAGCTCGGCTGAtt                           >  2:811894/1‑151 (MQ=255)                                                                                                                   ggATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTGCCATGAGAAGGGAGCGCAGGGGGGGGTTTTCTTGCCTGACTGAACTGGGGATTAAGTTTTCGCGTAACCGGCGGTTAGTTTTTGCGGGTGGTGATATTTAAGCTCGGCTGATTgg                         >  1:731246/1‑151 (MQ=255)                                                                                                                   ggATCTCGTTTGCGGCGGTCATTTTTTCTTTTTTTTCCATGTGAAGGGAGCGCCGAGAGGGGTTATCTTGCCTGACTGAACTGGCGATTAAATTTCCGCGTACCCCGCGTTTAGTTATTTCGGATGGTGATATTTAAGCTCGGCTGAtttg                         >  2:429788/1‑149 (MQ=255)                                                                                                                         cGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTAAGTTTCCGCGTACCCGGCGTTTAGTTATTGCGGATGATGATATTGAAGCTCGGCTGATTGGtt                       <  1:932076/147‑1 (MQ=255)                                                                                                                         cGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTAAGTTTCCGCGTACCCGGCGTTTAGTTATTGCGGATGATGATATTGAAGCTCGGCTGATTGGtt                       <  1:770209/147‑1 (MQ=255)                                                                                                                          gTTTGCGGCGGTCCTTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGGTTTTCTTGCCTGACTGAAATGGCGATTAAGTTTTCGCGTACCCGGGGTTTTGTTATTGCGGGTGGTGATATTGAAACTCGGCTGATTTGTTCAtt                   >  1:1481/1‑150 (MQ=255)                                                                                                                          gTTTGCGGCGGTCATTTTTTTTTTTTCTGCCCTGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTAAGGTTTCGCGTACCCGGCGTTTTGTTATTTCGGATGATGATATTGAAGCTCGGCTGATTGGTTCAtt                   >  2:857761/1‑150 (MQ=255)                                                                                                                          gTTTGCGGCGGTCATTTTTTTTTTTTCTGCCATGAGAAGAGAGCGCAGAGAGGGATTATTTTTCCTGACTTAACTGGCGATTTAGTTTCCGCGGAACCGGCGTTTAGTTATTTCGGATGAAGATATTGAAGCTCGGCTGGTTTGTTCCtt                   >  1:877729/1‑150 (MQ=255)                                                                                                                              gcggcgGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTAAGTTTCCGCGTACCCGGCGTTTAGTTATTGCGGATGATGATATTGAAGCTCGGCTGATTGGTTCATTGTCg               <  1:584820/150‑1 (MQ=255)                                                                                                                                   ggTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTAAGTTTCCGCGTACCCGGCGTTTAGTTATTGCGGATGATGATATTGAAGCTCGGCTGATTGGTTCATTGTCGCCATc          >  2:935442/1‑150 (MQ=255)                                                                                                                                    gTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTAAGTTTCCGCGTACCCGGCGTTTAGTTATTGCGGATGATGATATTGAAGCTCGGCTGATTGGTTCATTGTCGCCATCAc        >  2:794472/1‑151 (MQ=255)                                                                                                                                      cATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTAAGTTTCCGCGTACCCGGCGTTTAGTTATTGCGGATGATGATATTGAAGCTCGGCTGATTGGTTCATTGTCGCCATCAcc       <  2:276034/150‑1 (MQ=255)                                                                                                                                        ttttttCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTAAGTTTCCGCGTACCCGGCGTTTAGTTATTGCGGATGATGATATTGAAGCTCGGCTGATTGGTTCATTGTCGCCATCACCg      >  1:345318/1‑149 (MQ=255)                                                                                                                                        ttttttCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTAAGTTTCCGCGTACCCGGCGTTTAGTTATTGCGGATGATGATATTGAAGCTCGGCTGATTGGTTCATTGTCGCCATCACCGCt    >  1:697362/1‑151 (MQ=255)                                                                                                                                           tttctttttctGCCATGAGAAGTGAGCGCAGCGAGGGATTATCTTGCCTGACTGAACTGGCGATTAAGTTTCCGCGTACCCGGCGTTTAGTTATTGCGGATGATGATATTGAAGCTCGGCTGATTGGTTCATTGTCGCCATCACCGCTgg  >  2:695948/1‑150 (MQ=255)                                                                                                                                              |                                                                                                                                                   AAAAATGCGTCATGAGTAGTATCGGTATTGAGAGTTTATTCAGAAAGTTTGCGGGTAACCCTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTAAGTTTCCGCGTACCCGGCGTTTAGTTATTGCGGATGATGATATTGAAGCTCGGCTGATTGGTTCATTGTCGCCATCACCGCTGG  >  NC_000913/4604203‑4604490

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑