Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,604,350	0	C	T	44.2%	47.3 / 24.9	52	S64F (TCT→TTT)	bglJ	bgl operon transcriptional activator
Reads supporting (aligned to +/- strand):  ref base C (10/19);  new base T (23/0);  total (33/19)
Fisher's exact test for biased strand distribution p-value = 2.75e-07
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CGTCATGAGTAGTATCGGTATTGAGAGTTTATTCAGAAAGTTTGCGGGTAACCCTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTAAGTTTCCGCGTACCCGGCGTTTAGTTATTGCGGATGATGATATTGAAGCTCGGCTGATTGGTTCATTGTCGCCATCACCGCTGGACGGTGTATT  >  NC_000913/4604210‑4604500                                                                                                                                             |                                                                                                                                                       cGTCATGAGTAGTATCGGTATTGAGAGTTTATTCAGAAAGTTTGCGGGTAACCCTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATgaga                                                                                                                                              <  1:435480/151‑1 (MQ=255)    cATGAGTAGTATCGGTATTGAGAGTTTATTCAGAAAGTTTGCGGGTAACCCTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAg                                                                                                                                            <  2:633450/150‑1 (MQ=255)    cATGAGTAGTATCGGTATTGAGAGTTTATTCAGAAAGTTTGCGGGTAACCCTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAg                                                                                                                                            <  2:1668/150‑1 (MQ=255)    cATGAGTAGTATCGGTATTGAGAGTTTATTCAGAAAGTTTGCGGGTAACCCTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGt                                                                                                                                           <  2:673316/151‑1 (MQ=255)     aTGAGTAGTATCGGTATTGAGAGTTTATTCAGAAAGTTTGCGGGTAACCCTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCCTTTTTTTTTTTTTTGCCATGAGaa                                                                                                                                             >  1:412157/1‑148 (MQ=255)     aTGAGTAGTATCGGTATTGAGAGTTTATTCAGAAAGTTTGCGGGTAACCCTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTg                                                                                                                                          <  2:988637/151‑1 (MQ=255)     aTGAGTAGTATCGGTATTGAGAGTTTATTCAGAAAGTTTGCGGGTAACCCTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTg                                                                                                                                          <  2:831566/151‑1 (MQ=255)     aTGAGTAGTATCGGTATTGAGAGTTTATTCAGAAAGTTTGCGGGTAACCCTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTg                                                                                                                                          >  2:699763/1‑151 (MQ=255)       gAGTAGTATCGGTATTGAGAGTTTATTCAGAAAGTTTGCGGGTAACCCTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTTCCATTAGaa                                                                                                                                             >  1:491138/1‑146 (MQ=255)              aTCGGTATTGAGAGTTTATTCAGAAAGTTTGCGGGTAACCCTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCCTTTTTTTTTTTTCTGCCATGAGAAGTGAgcg                                                                                                                                      >  1:426567/1‑146 (MQ=255)              aTCGGTATTGAGAGTTTATTCAGAAAGTTTGCGGGTAACCCTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCagag                                                                                                                                 <  2:960806/151‑1 (MQ=255)               tCGGTATTGAGAGTTTATTCAGAAAGTTTGCGGGTAACCCTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTGCCCTGAGAAGTGAGCGCagag                                                                                                                                 >  2:752099/1‑150 (MQ=255)                   tATTGAGAGTTTATTCAGAAAGTTTGCGGGTAACCCTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTTCCATGAGAAGGGAGCGCAGAGAggg                                                                                                                             >  2:382164/1‑150 (MQ=255)                      tGAGAGTTTATTCAGAAAGTTTGCGGGTAACCCTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGAtt                                                                                                                          <  2:1009879/150‑1 (MQ=255)                           gTTTATTCAGAAAGTTTGCGGGTAACCCTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTTCCCTGGGAAGGGAGCGCAGAGAGGGGTTTTCtt                                                                                                                     >  1:84906/1‑150 (MQ=255)                              tATTCAGAAAGTTTGCGGGTAACCCTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTCTTCCATGAGAAGGGAGCGCAGAGAGGGGTTATTTTTCct                                                                                                                 >  1:68631/1‑151 (MQ=255)                                     aaaGTTTGCGGGTAACCCTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCCTTTTTTTTTTTTTTTCCCTGAGAAGTGAGAGCGGAGAGGGAATATCTTGCctgact                                                                                                             >  1:837483/1‑148 (MQ=255)                                        gTTTGCGGGTAACCCTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCCTTTTTTTTTTTTTTGCCATGGGAAGGGGGGGGAGCGGGGGGTTATCTTGCctggc                                                                                                              >  1:1032451/1‑142 (MQ=255)                                        gTTTGCGGGTAACCCTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTg                                                                                                       <  2:437672/151‑1 (MQ=255)                                          ttGCGGGTAACCCTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTTCCATTAGAAGGGAGGGCAGGGAGGGGGTATCTTTCCTGACTGaa                                                                                                          >  2:271888/1‑146 (MQ=255)                                            gCGGGTAACCCTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCg                                                                                                    <  2:747348/150‑1 (MQ=255)                                              gggTAACCCTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTCTGCCCTGAGAAGTGAGCGCCGAGAGGGATTTTTTTGCCTGACTGAAATGGGGAtt                                                                                                 >  1:134089/1‑151 (MQ=255)                                                      cTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTTTGTCACGAGAAGTGAGCGCCGCGGGGGGTTATCTTGGCCGACTGTACTGGCGGTTAAGtttt                                                                                          >  2:493054/1‑149 (MQ=255)                                                       ttATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTCTGCCATGAGAAGTGGGCGCAGAGAGGGATTATCTTTCCTGACTGAAATGGCGATTTAGttttc                                                                                         >  2:769283/1‑148 (MQ=255)                                                        tataAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTTCCCTGAGAAGAGAGGGCCGGGAGGGGTTTTTTTTCCTTACTGAACTGGCGATTAAGatt                                                                                           >  1:4709/1‑147 (MQ=255)                                                              cTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTCTGCCATGAGAAGGGGGGGCAGAGAGGGGTTTTCTTTCCTGACCGAAATGGGGATTTAGTTTCCGCGGAccc                                                                                 >  2:929272/1‑151 (MQ=255)                                                               tCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTGCCCTGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTAAGTTTTCGCGTAccc                                                                                 >  2:776627/1‑150 (MQ=255)                                                                 cATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTAAGTTTCCGCGTACCCGGc                                                                              <  1:972601/151‑1 (MQ=255)                                                                 cATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGGCCTTTTTTTTTTTTTTTCCCTTAGGAGTGGGGGCCGGGGGGGGTTTTTTTTCCTTGCTTTACTGGCGGTTTAGGTTTcgccgggccgg                                                                               >  1:389677/1‑142 (MQ=255)                                                                   tACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTAATTTTTTTTTTTTTTTCCCTCCGAAGGGAGGCGAGAGGGGGGTTTTTTTGTCCGACTGAAATTGCGAGTTAGttttctggtgccc                                                                                 >  1:631053/1‑136 (MQ=255)                                                                   tACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGGCCTTTTTTTTTTTTTTTCCCTGAGAAGTGCGCGCAGAGAGGGGTTTTCTTTTCTGACTGAAATGGCGATTAAGGTTTCGGGTACCCcgcg                                                                             >  1:14795/1‑150 (MQ=255)                                                                      cTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTGCCCTGAGGAGTGAGCGCAGGGGGGGGTTATTTTTCCTGACTGGACTGGCGATTAAGTTTTCGCGGACCCGGCGgttt                                                                         >  1:872441/1‑150 (MQ=255)                                                                       tataCCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTGCCCTGAGAAGGGAGCGCAGAGGGGGGTTATTTTGCCTGACTGAACTGGCGATTAAGTTTTCGCGGACCCGGCGgtt                                                                          >  1:291846/1‑149 (MQ=255)                                                                        ataCCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGGCATTTTTT‑TTTTTCTGCCATGGGAAGTGAGCGGCGAGAGGGATTATCTTGCCTGGCTGAACTGGCGATTTAGTTTTCGCGGACCCCGCGGTTAGtt                                                                      >  1:723551/1‑151 (MQ=255)                                                                          aCCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTAAGTTTCCGCGTACCCGGCGTTTAGtt                                                                      <  2:23187/150‑1 (MQ=255)                                                                           ccAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTTCCCTGAGAAGTGAGGGCAGAGAGGGGTTATTTTGCCTGACTGAACTGGCGGTTAAGTTTTCGCGTACCCGGCGGTTAGTTAt                                                                    >  2:740027/1‑151 (MQ=255)                                                                            cAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTGCCCTGAGAAGGGAGGGCAGGGGGGGGTTATCTTTGCTGTCTGAAATGGCGATTTAGATTTCGCGGAACCCGCGttttggtttt                                                                   >  1:589589/1‑144 (MQ=255)                                                                             aGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCCTTTTTTTTTTTTTTGCCATTAAAAGTGAGCGGAGGAGGGGATTTTCTTGTCTGGTTGGAATTGGGATTAAGTTTCCGCGCAATCGGCGCCTAGGTAtt                                                                   >  2:552396/1‑150 (MQ=255)                                                                                cAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTTGTTTTTTTTTTTTTTGGCAGAAAAAATGCGAGGAGAGAGGGGGTATCTTGCCAGACTGAACATGCGGTTAAGTTTCCCCGGCCCCGGCGtttttgtatttgtg                                                               >  2:30162/1‑140 (MQ=255)                                                                                    aGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTTTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTAAGTTTCCGCGTACCCGGCGTTTTGTTATTGCGgatg                                                            >  2:685311/1‑150 (MQ=255)                                                                                         tttCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTTTTCCATGAGAAGTGAGCGCAGAGGGGGGTTATCTTGCCTGACTGAACTGGCGGTTAAGTTTCCGCGTACCCGGCGTTTTGTTATTGCGggtgatgat                                                       >  2:250911/1‑150 (MQ=255)                                                                                                    cATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTTCCATGAGAAGGGGGCGCCGGGGGGGGTTATCTTTCCTTACTGAACTGGGGATTTAATTTTCGCGTACCCGGGGGTTTGTTATTTCGGGTGGTGATATTTAAGCTCgg                                           >  1:589796/1‑151 (MQ=255)                                                                                                       gTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTAAGTTTCCGCGTACCCGGCGTTTAGTTATTGCGGATGATGATATTGAAGCTCGGCTg                                        <  2:148384/151‑1 (MQ=255)                                                                                                         cgcgGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTAAGTTTCCGCGTACCCGGCGTTTAGTTATTGCGGATGATGATATTGAAGCTCGGCTGa                                       <  2:610469/150‑1 (MQ=255)                                                                                                           cgGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTAAGTTTCCGCGTACCCGGCGTTTAGTTATTGCGGATGATGATATTGAAGCTCGGCTGATTg                                    <  2:360723/151‑1 (MQ=255)                                                                                                            ggATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTAAGTTTCCGCGTACCCGGCGTTTAGTTATTGCGGATGATGATATTGAAGCTCGGCTGATTgg                                   <  2:887607/151‑1 (MQ=255)                                                                                                                  cGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTAAGTTTCCGCGTACCCGGCGTTTAGTTATTGCGGATGATGATATTGAAGCTCGGCTGATTGGTTCa                               <  2:632392/149‑1 (MQ=255)                                                                                                                   gTTTGCGGCGGTCATTTTTTTTTTTTCTTCCCTGAGAAGTGAGGGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGGTTAAATTTCCGCGTACCCGGCGGTTTGTTATTGCGGATGATGATATTGAAGCTCGGCTGATTGGTTCAtt                             >  2:139455/1‑150 (MQ=255)                                                                                                                      tGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTAAGTTTCCGCGTACCCGTCGTTTAGTTATTGCGGATGATGATATTGAAGCTCGGCTGATTGGTTCAgtgt                           <  1:35412/149‑1 (MQ=255)                                                                                                                        cggcggTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTAAGTTTCCGCGTACCCGGCGTTTAGTTATTGCGGATGATGATATTGAAGCTCGGCTGATTGGTTCATTGTCGcc                       <  1:829634/151‑1 (MQ=255)                                                                                                                            ggTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCGGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTAAGTTTCCGCGTACCCGGCGTTTAGTTATTGCGGATGATGATATTGAAGCTCGGCTGATTGGTTCATTGTCGCCATc                    >  2:431121/1‑150 (MQ=255)                                                                                                                              tCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTAAGTTTCCGCGTACCCGGCGTTTAGTTATTGCGGATGATGATATTGAAGCTCGGCTGATTGGTTCATTGTCGCCATCAcc                 >  2:191394/1‑151 (MQ=255)                                                                                                                                         ttttctGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTAAGTTTCCGCGTACCCGGCGTTTAGTTATTGCGGATGATGATATTGAAGCTCGGCTGATTGGTTCATTGTCGCCATCACCGCTGGACGgtg      >  1:13376/1‑151 (MQ=255)                                                                                                                                             ctGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTAAGTTTCCGCGTACCCGGCGTTTAGTTATTGCGGATGATGATATTGAAGCTCGGCTGATTGGTTCATTGTCGCCATCACCGCTGGACGGTGTAtt  >  2:15298/1‑151 (MQ=255)                                                                                                                                             |                                                                                                                                                       CGTCATGAGTAGTATCGGTATTGAGAGTTTATTCAGAAAGTTTGCGGGTAACCCTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTAAGTTTCCGCGTACCCGGCGTTTAGTTATTGCGGATGATGATATTGAAGCTCGGCTGATTGGTTCATTGTCGCCATCACCGCTGGACGGTGTATT  >  NC_000913/4604210‑4604500

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑