Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,604,344	0	C	T	51.0%	28.8 / 73.8	52	S62F (TCT→TTT)	bglJ	bgl operon transcriptional activator
Reads supporting (aligned to +/- strand):  ref base C (6/19);  new base T (26/0);  total (33/19)
Fisher's exact test for biased strand distribution p-value = 3.65e-09
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.25e-08

ATAGAAAAATGCGTCATGAGTAGTATCGGTATTGAGAGTTTATTCAGAAAGTTTGCGGGTAACCCTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTAAGTTTCCGCGTACCCGGCGTTTAGTTATTGCGGATGATGATATTGAAGCTCGGCTGATTGGTTCATTGTCGCCATCACC  >  NC_000913/4604199‑4604485                                                                                                                                                  |                                                                                                                                              aTAGAAAAATGCGTCATGAGTAGTATCGGTATTGAGAGTTTATTCAGAAAGTTTGCGGGTAACCCTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATtttttcttttt                                                                                                                                          <  1:913127/151‑1 (MQ=255)       aaaTGCGTCATGAGTAGTATCGGTATTGAGAGTTTATTCAGAAAGTTTGCGGGTAACCCTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTTAttttttttttttactac                                                                                                                                     >  1:5018/1‑145 (MQ=255)            cGTCATGAGTAGTATCGGTATTGAGAGTTTATTCAGAAAGTTTGCGGGTAACCCTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATgaga                                                                                                                               <  1:435480/151‑1 (MQ=255)               cATGAGTAGTATCGGTATTGAGAGTTTATTCAGAAAGTTTGCGGGTAACCCTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAg                                                                                                                             <  2:1668/150‑1 (MQ=255)               cATGAGTAGTATCGGTATTGAGAGTTTATTCAGAAAGTTTGCGGGTAACCCTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAg                                                                                                                             <  2:633450/150‑1 (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)                                                                                                                                                  |                                                                                                                                              ATAGAAAAATGCGTCATGAGTAGTATCGGTATTGAGAGTTTATTCAGAAAGTTTGCGGGTAACCCTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTAAGTTTCCGCGTACCCGGCGTTTAGTTATTGCGGATGATGATATTGAAGCTCGGCTGATTGGTTCATTGTCGCCATCACC  >  NC_000913/4604199‑4604485

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: ‑