Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,604,350	0	C	T	43.5%	48.1 / 20.6	46	S64F (TCT→TTT)	bglJ	bgl operon transcriptional activator
Reads supporting (aligned to +/- strand):  ref base C (6/20);  new base T (20/0);  total (26/20)
Fisher's exact test for biased strand distribution p-value = 5.22e-08
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GCGTCATGAGTAGTATCGGTATTGAGAGTTTATTCAGAAAGTTTGCGGGTAACCCTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTAAGTTTCCGCGTACCCGGCGTTTAGTTATTGCGGATGATGATATTGAAGCTCGGCTGATTGGTTCATTGTCGCCATCACCGCTGGACGGTGTAT  >  NC_000913/4604209‑4604499                                                                                                                                              |                                                                                                                                                      gCGTCATGAGTAGTATCGGTATTGAGAGTTTATTCAGAAAGTTTGCGGGTAACCCTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTTTGCCATggg                                                                                                                                              >  1:188719/1‑149 (MQ=255)    tCATGAGTAGTATCGGTATTGATAGTTTATTCAGAAAGTTTGCGGGTAAACCTTATAAGCTCCCTACCTATACCAGTCAGGAGTCATTTCAGTATGCCATGTCGCGGATCTCGTTTGCGGCGGTCTTTTTTTCTTTTTTTTCCATGAGaa                                                                                                                                            >  1:160427/1‑150 (MQ=255)     cATGAGTAGTATCGGTATTGAGAGTTTATTCAGAAAGTTTGCGGGTAACCCTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGt                                                                                                                                          <  1:45821/151‑1 (MQ=255)        gAGTAGTATCGGTATTGAGAGTTTATTCAGAAAGTTTGCGGGTAACCCTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAg                                                                                                                                       <  2:573032/151‑1 (MQ=255)            attaTCGGTATTGAGAGTTTATTCAGAAAGTTTGCGGGTAACCCTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGGCATTTTTTTTTTTTTTTCCATGTGAAGTGAgcgc                                                                                                                                    >  2:804402/3‑150 (MQ=255)                   gTATTGAGAGTTTATTCAGAAAGTTTGCGGGTAACCCTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTGTGCGGCGGTCATGTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAggg                                                                                                                            <  1:412725/151‑1 (MQ=255)                     aTTGAGAGTTTATTCAGAAAGTTTGCGGGTAACCCTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGAt                                                                                                                          <  1:751563/151‑1 (MQ=255)                         agagTTTATTCAGAAAGTTTGCGGGTAACCCTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCA‑TTTTTCTTTTTTTGCCATGAGAAGTGAGGGCAGAGAGGGGTTTTCt                                                                                                                     >  2:122247/1‑151 (MQ=255)                               tATTCAGAAAGTTTGCGGGTAACCCTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTGCCCTGAGAAGTGAGCGCAGAGAGGGGttttttt                                                                                                                    >  1:405746/1‑142 (MQ=255)                                 ttCAGAAAGTTTGCGGGTAACCCTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGCTGCCATGTCGCGGCTCTCGTTTGCGGCGGTCCTTTTTTATTTTTTTTTCCCGGGAAATGAGAGCCGAGGGGGGTTCTCTTTCct                                                                                                                >  1:697586/1‑149 (MQ=255)                                 ttCAGAAAGTTTGCGGGTAACCCTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTGCCCTGGGGAAGGAGCGCAGGGAGGGGtttttttttctt                                                                                                               >  1:589317/1‑140 (MQ=255)                                   cAGAAAGTTTGCGGGTAACCCTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCCTTTTTTTTTTTTTTGCCATGAGAAGTGAGCGCAGAGGGGGATTATCTTTTctgact                                                                                                            >  1:658948/1‑151 (MQ=255)                                   cAGAAAGTTTGCGGGTAACCCTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCctgact                                                                                                            <  1:472269/151‑1 (MQ=255)                                       aaGTTTGCGGGTAACCCTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGGTTATCTTGCCTGACTGaa                                                                                                         >  2:169181/1‑150 (MQ=255)                                               gggTAACCCTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTGCCATGAGAAGGGAGGGCAGAGAGGGGTTATTTTGCCTGACTGAACTgggg                                                                                                   >  2:547523/1‑146 (MQ=255)                                                 gTAACCCTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTaa                                                                                              <  1:553428/151‑1 (MQ=255)                                                    aCCCTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTCTGCCCTGAGAAGGGAGCGCAGAGAGGGGTTATCTTGCCTGTCTGAAATGGCGATTaa                                                                                              >  2:169876/1‑148 (MQ=255)                                                     cccTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGGTTAAGttt                                                                                          >  2:217621/1‑151 (MQ=255)                                                      ccTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTAAGTTTc                                                                                         <  1:210020/151‑1 (MQ=255)                                                          ataAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTAAGTTTCcgc                                                                                      <  1:887209/150‑1 (MQ=255)                                                            aaGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCCTTTTTTTTTTTTCTGCCATTGGGAGTGGGGGCCGGGAGGGATTATCTTTCCTGACTTAACTGGCGGTTAAGTTTCCGCGt                                                                                    >  2:835811/1‑150 (MQ=255)                                                             aGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTAAGTTTCCGCGTAc                                                                                  <  2:396404/151‑1 (MQ=255)                                                                 ccATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGCCTTTTTTTTTTTTTTTTCCATTCGTAGTTGATGCAGAGGGGGAGTGTGTTGGCTGAATGAACTAGCGGGTAAGttttagcg                                                                                     >  1:315110/1‑139 (MQ=255)                                                                  cATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTAAGTTTCCGCGTACCCGGc                                                                             <  2:896142/151‑1 (MQ=255)                                                                   aTACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTTCCCTGAGGAGTGAGCGCAGAGAGGGGTTATCTTTCCTGACTGAACTGGCGATTAAGTTTTCGCGTAcc                                                                                 >  1:729785/1‑146 (MQ=255)                                                                   aTACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTTCCCTGAGAAGGGAGCGCAGAGAGGGGTTATCTTTCCTGACTGAACTGGCGATTAAGTTTTCGCGGACCCcgcg                                                                            >  2:672584/1‑151 (MQ=255)                                                                      ccTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTAAGTTTCCGCGTACCCGGCGttt                                                                         <  1:645220/151‑1 (MQ=255)                                                                       cTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGGCATTTTTTTTTTTTTTTCCATGAGGAGTGGGCGCAGAGGGGGATTATTTTGCCTGATTGAACTGGGGATTAAGTTTCCGCGTCCCCGGCggt                                                                          >  1:669792/1‑147 (MQ=255)                                                                         ataCCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTCCCTTGAGAGAGAAGGGGCGAGGGGGGTTTTTTTTCCTGCATGAATTGGCGATTAAGTTTCCGAGGACCCGGCGttt                                                                         >  1:104885/1‑148 (MQ=255)                                                                            ccAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTTCCATGGGAAGAGAGCGGCGAGGGGGATTATCTTGCCCTACTGTACTGGCGATTAAGTTTTCGCCTACCCCGCGTTTTTTTAt                                                                   >  2:211421/1‑151 (MQ=255)                                                                              aGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGGTTATCTTGCCTGACTGAACTGGCGATTAAGTTTCCGCGTACCCGGCGTTTAGTTAtt                                                                  >  2:555105/1‑150 (MQ=255)                                                                               gTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTAAGTTTCCGCGTACCCGGCGTTTAGTTATTGc                                                                <  2:453883/151‑1 (MQ=255)                                                                                tCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTTATTTTTTCTTTTTTTTCCCTGAGAAGAGAGCGCCGAGAGGGATTATCTTGCCTGACTGAACCGGGGATTTAGTTTCCGCGTACCCGGCGTTTTGTTATTGCg                                                               >  2:395171/1‑151 (MQ=255)                                                                                 cAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTAAGTTTCCGCGTACCCGGCGTTTAGTTATTGCg                                                               <  2:730215/150‑1 (MQ=255)                                                                                       tCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTTTGCCATGAGAAGTGAGCGCAGAGAGGGGTTATCTTTCCTGACTGAACTGGCGATTAAGTTTCCGCGTACCCGGCGTTTTGTTATTTCGggtg                                                           >  2:300281/1‑148 (MQ=255)                                                                                        cATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTAAGTTTCCGCGTACCCGGCGTTTAGTTATTGCGgatgatga                                                       <  2:315516/151‑1 (MQ=255)                                                                                         aTTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCTGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTAAGTTTCCGCGTACCCGGCGTTTAGTTATTGCGgatgatgat                                                      <  2:21641/151‑1 (MQ=255)                                                                                               ggATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTGCCATGGGAAGTGGGCGCAGAGAGGGGTTATCTTGCCTGACTGAACTGGCGGTTAAGGTTTCGCGTACCCCGCGTTTTGTTTTTTGGGGTGGTGATAtt                                                   >  2:428527/1‑148 (MQ=255)                                                                                               ggATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTAAGTTTCCGCGTACCCGGCGTTTAGTTATTGCGGATGATGATATTGaa                                                <  2:727698/151‑1 (MQ=255)                                                                                                 aTGCCATGTCGCGGATCTCGTTTGCGGCGGGCCTTTTTTTTTTTTTTGCCATGAGAAGGGAGCGCCGAGAGGGGGTATCTTTCCTTACCTAACTGGCGATTAAGTTTTCGCGTACCCCGCGTTTAGTTTTTGCGGGTGATGATATTTaa                                                >  1:737283/1‑149 (MQ=255)                                                                                                          cgcgGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTAAGTTTCCGCGTACCCGGCGTTTAGTTATTGCGGATGATGATATTGAAGCTCGGCTGa                                      <  2:842162/150‑1 (MQ=255)                                                                                                            cgGATCTCGTTTGCGGCGGTCCTTTTTTTTTTTTTTGCCATGAGAAGTGAGGGCAGAGAGGGGTTATTTTTCCTGACTGAACTGGCGATTTAGTTTCCGCGTACCCGGCGTTTTGTTATTGCGGGTGATGATATTTAAGCTCGGCTGAtt                                    >  2:342073/1‑150 (MQ=255)                                                                                                                   cGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTAAGTTTCCGCGTACCCGGCGTTTAGTTATTGCGGATGATGATATTGAAGCTCGGCTGATTGGt                                 <  2:250036/146‑1 (MQ=255)                                                                                                                        gcggcgGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTAAGTTTCCGCGTACCCGGCGTTTAGTTATTGCGGATGATGATATTGAAGCTCGGCTGATTGGTTCATTGTCg                        <  2:378422/150‑1 (MQ=255)                                                                                                                        gcggcgGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTAAGTTTCCGCGTACCCGGCGTTTAGTTATTGCGGATGATGATATTGAAGCTCGGCTGATTGGTGCATTGTCg                        <  1:804189/150‑1 (MQ=255)                                                                                                                          ggcggTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTAAGTTTCCGCGTACCCGGCGTTTAGTTATTGCGGATGATGATATTGAAGCTCGGCTGATTGGTTCATTGTCGcc                      >  1:14622/1‑150 (MQ=255)                                                                                                                                         tttttctGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTAAGTTTCCGCGTACCCGGCGTTTAGTTATTGCGGATGATGATATTGAAGCTCGGCTGATTGGTTCATTGTCGCCATCACCGCTGGACGgt      >  2:266099/1‑151 (MQ=255)                                                                                                                                             tctGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTAAGTTTCCGCGTACCCGGCGTTTAGTTATTGCGGATGATGATATTGAAGCTCGGCTGATTGGTTCATTGTCGCCATCACCGCTGGACGGTGTa   <  1:4590/150‑1 (MQ=255)                                                                                                                                             tctGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTAAGTTTCCGCGTACCCGGCGTTTAGTTATTGCGGATGATGATATTGAAGCTCGGCTGATTGGTTCATTGTCGCCATCACCGCTGGACGGTGTAt  >  2:407261/1‑151 (MQ=255)                                                                                                                                             tctGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTAAGTTTCCGCGTACCCGGCGTTTAGTTATTGCGGATGATGATATTGAAGCTCGGCTGATTGGTTCATTGTCGCCATCACCGCTGGACGGTGTAt  >  2:311441/1‑151 (MQ=255)                                                                                                                                              |                                                                                                                                                      GCGTCATGAGTAGTATCGGTATTGAGAGTTTATTCAGAAAGTTTGCGGGTAACCCTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTAAGTTTCCGCGTACCCGGCGTTTAGTTATTGCGGATGATGATATTGAAGCTCGGCTGATTGGTTCATTGTCGCCATCACCGCTGGACGGTGTAT  >  NC_000913/4604209‑4604499

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: ‑