Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,604,344	0	C	T	47.6%	29.7 / 22.7	42	S62F (TCT→TTT)	bglJ	bgl operon transcriptional activator
Reads supporting (aligned to +/- strand):  ref base C (5/17);  new base T (20/0);  total (25/17)
Fisher's exact test for biased strand distribution p-value = 1.08e-07
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

ATAGAAAAATGCGTCATGAGTAGTATCGGTATTGAGAGTTTATTCAGAAAGTTTGCGGGTAACCCTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTAAGTTTCCGCGTACCCGGCG‑TTTAGTTATTGCGGATGATGATATTGAAGCTCGGCTGATTGGTTCATTGTCGCCATCA  >  NC_000913/4604199‑4604483                                                                                                                                                  |                                                                                                                                             aTAGAAAAATGCGTCATGAGTAGTATCGGTATTGAGAGTTTATTCAGAAAGTTTGCGGGTAACCCTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCAtttttttttttt                                                                                                                                         >  1:262691/1‑151 (MQ=255) aTAGAAAAATGCGTCATGAGTAGTATCGGTATTGAGAGTTTATTCAGAAAGTTTGCGGGTAACCCTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATtttttcttttt                                                                                                                                         <  1:82522/151‑1 (MQ=255)   aGAAAAATGCGTCATGAGTAGTATCGGTATTGAGAGTTTATTCAGAAAGTTTGCGGGTAACCCTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATtttttctttttc                                                                                                                                        <  2:432522/150‑1 (MQ=255)   aGAAAAATGCGTCATGAGTAGTATCGGTATTGAGAGTTTATTCAGAAAGTTTGCGGGTAACCCTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATtttttctttttc                                                                                                                                        <  1:905758/150‑1 (MQ=255)          tGCGTCATGAGTAGTATCGGTATTGAGAGTTTATTCAGAAAGTTTGCGGGTAACCCTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCCTTTTTTTTTTTTTTGCCATg                                                                                                                                 >  2:62648/1‑150 (MQ=255)          tGCGTCATGAGTAGTATCGGTATTGAGAGTTTATTCAGAAAGTTTGCGGGTAACCCTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTGcc                                                                                                                                    >  2:134899/1‑147 (MQ=255)                 tGAGTAGTATCGGTATTGAGAGTTTATTCAGAAAGTTTGCGGGTAACCCTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTTCCATGAGAAGt                                                                                                                           >  2:108821/1‑149 (MQ=255)                 tGAGTAGTATCGGTATTGAGAGTTTATTCAGAAAGTTTGCGGGTAACCCTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGGGaa                                                                                                                             >  1:672059/1‑147 (MQ=255)                      agtaTCGGTATTGAGAGTTTATTCAGAAAGTTTGCGGGTAACCCTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTGCCATGAGAAgg                                                                                                                           >  2:285261/1‑143 (MQ=255)                       gtaTCGGTATTGAGAGTTTATTCAGAAAGTTTGCGGGTAACCCTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTGCCATGAGAAGTGAgcg                                                                                                                      >  1:864439/1‑148 (MQ=255)                       gtaTCGGTATTGAGAGTTTATTCAGAAAGTTTGCGGGTAACCCTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCAATTTTTTATTTTTTGTCATTGGAAATGAgcag                                                                                                                     >  1:971327/1‑147 (MQ=255)                         aTCGGTATTGAGAGTTTATTCAGAAAGTTTGCGGGTAACCCTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCagag                                                                                                                 <  1:843099/151‑1 (MQ=255)                         aTCGGTATTGAGAGTTTATTCAGAAAGTTTGCGGGTAACCCTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCaga                                                                                                                  <  1:400546/150‑1 (MQ=255)                             gTATTGAGAGTTTATTCAGAAAGTTTGCGGGTAACCCTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTGCCCTGAGAAGTGGGCGCCGAGAggg                                                                                                             >  1:145364/1‑151 (MQ=255)                               aTTGAGAGTTTATTCAGAAAATTTGCGGGTAACCCTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGa                                                                                                            <  2:78833/150‑1 (MQ=255)                                    gagTTTATTCAGAAAGTTTGCGGGTAACCCTTATAAGCTCCATACCTATACCAGTCTGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCt                                                                                                      <  2:277523/151‑1 (MQ=255)                                         tATTCAGAAAGTTTGCGGGTAACCCTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTGCCCTGAGAAGTGAGCGCAGAGGGGGGTTATCTTGcc                                                                                                  >  2:20836/1‑150 (MQ=255)                                          aTTCAGAAAGTTTGCGGGTAACCCTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCctg                                                                                                <  2:911393/151‑1 (MQ=255)                                          aTTCAGAAAGTTTGCGGGTAACCCTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCct                                                                                                 <  1:81929/150‑1 (MQ=255)                                            tCAGAAAGTTTGCGGGTAACCCTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCctga                                                                                               <  2:80429/150‑1 (MQ=255)                                              aGAAAGTTTGCGGGTAACCCTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCCTTTTTTTTTTTTCTGCCATGAGAAGGGAGGGCAGAGAGGGGGTATCTTTCctgact                                                                                             >  2:795665/1‑150 (MQ=255)                                               gAAAGTTTGCGGGTAACCCTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTTCCCTTAGAAGGGAGCGCAGAGAGGGGTTATCTTGCctgtct                                                                                             >  2:274405/1‑149 (MQ=255)                                                       gCGGGTAACCCTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCg                                                                                    <  1:167953/150‑1 (MQ=255)                                                                   tataAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTGCCCTGAGAAGGGAGCGCAGGGGGGGATTATTTTTCCTGACTGAACTGGCGATTAAATTTcc                                                                         >  1:815230/1‑149 (MQ=255)                                                                    ataAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTGCCATGAGAAGTGAGCGCAGAGAGGGGTTATTTTGCCTGACTGAACTGGCGGTTAAGttttc                                                                         >  2:13384/1‑146 (MQ=255)                                                                      aaGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTAAGTTTCCGCGTa                                                                    <  1:411286/151‑1 (MQ=255)                                                                           ccATACCTATACCAGTCATGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTAAGTTTCCGCGTAccc                                                                 <  1:304155/149‑1 (MQ=255)                                                                               aCCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTAAGTTTCCGCGTACCCGGCG‑t                                                           <  1:647948/150‑1 (MQ=255)                                                                                   ataCCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTGCCCTGAGAAGGGAGGGCGGAGGGGGGTTATTTTTCCTGGCTGAACTGGGGGTTAAGTTTTCGCGTACCCcgcg                                                             >  2:596150/1‑145 (MQ=255)                                                                                       cAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTAAGTTTCCGCGTACCCGGCG‑TTTAGTTAtt                                                  <  1:299520/151‑1 (MQ=255)                                                                                        aGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTTCCCTGAGAAGTGAGCGCAGAGAGGGGTTATCTTTCCTGACTGAACTGGAGGTTAAGTTTTCGCGTACCCCGCG‑GTTTGTTAtt                                                  >  1:678607/1‑150 (MQ=255)                                                                                         gTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTAAGTTTCCGCGTACCCGGCG‑TTTAGTTATTGc                                                <  2:496040/151‑1 (MQ=255)                                                                                             ggAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTAAGTTTCCGCGTACCCGGCG‑TTTAGTTATTGCGgat                                            <  2:493850/151‑1 (MQ=255)                                                                                                     ttCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTGCCATGAGAAGTGAGCGCAGAGAGGGGTTATTTTGCCTGACTGAACTGGCGGTTTAGTTTTCGCGGACCCCGCG‑GTTTGTTATTGCGggtg                                           >  2:486177/1‑144 (MQ=255)                                                                                                     ttCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTCTTCCATGAGAAGGGAGGGCAGAGGGGGGTTATTTTGCCTTACTGAACTGGCGGTTTAGGTTTCGCGGACCCCGCG‑GTTTGTTTTTGCGggtggt                                         >  2:8117/1‑144 (MQ=255)                                                                                                        aGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCCTGAGAAGTGAGCGCAGAGGGGGGTTATCTTGCCTGACTGAACTGGCGATTAAGTTTTCGCGTACCCGGCG‑TTTTGGTTTTTCGGATGATGATAtt                                   >  1:908546/1‑149 (MQ=255)                                                                                                                aTGTCGCGGATCTCGTTTGCGGCGGTCACTTTTTTTTTTTTTGTCCTAAGGAGTGAGGGCGCAGAGGGGGTTTTTTTCCTCACTGAAACGGGGGTTAAGGTTTCGCGGTGCCGGCGCTTTAG‑TATTGTGGGTGAAGGTATTGaa                                >  2:488106/1‑144 (MQ=255)                                                                                                                    cgcgGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTAAGTTTCCGCGTACCCGGCG‑TTTTGTTATTGCGGATGATGATATTGAAGCTCGGCTGAt                     >  2:553173/1‑151 (MQ=255)                                                                                                                        gATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTTGCATGAGAAGTGAGCGCAGGGAGGGATTATCTTGCCTGACTGAAATGGCGGTTAAGGTTTCGCGGACCCGGCG‑GTTTGTTTTTTCGGGTGGTGGTATTGAAGCTCGGCt                        >  2:62759/1‑144 (MQ=255)                                                                                                                        gATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTAAGTTTCCGCGTACCCGGCG‑TTTAGTTATTGCGGATGATGATATTGAAGCTCGGCTGATTg                   <  2:328933/149‑1 (MQ=255)                                                                                                                              gTTTGCGGCGGTCATTTTTTTTTTTTCTGCCATGAGAAGTGAGGGCAGGGAGGGATTATCTTTCCTGACTGTAATGGCGATTAAGTTTCCGCGGACCCGGCG‑TTTTGTTATTGCGGGTGATGGTATTGAAGCTCGGCTGGTTTGTTCAtt            >  2:821204/1‑150 (MQ=255)                                                                                                                              gTTTGCGGCGGTCATTTTTTTTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTTCCTGACTGAACTGGCGATTAAGTTTCCGCGTACCCGGCG‑TTTAGTTATTGCGGATGATGATATTGAAGCTCGGCTGATTGGTTCAtt            >  1:526217/1‑150 (MQ=255)                                                                                                                                      cggTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTAAGTTTCCGCGTACCCGGCG‑TTTAGTTATTGCGGATGATGATATTGAAGCTCGGCTGATTGGTTCATTGTCGCCATc   <  1:888015/151‑1 (MQ=255)                                                                                                                                      cggTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTAAGTTTCCGCGTACCCGGCG‑TTTAGTTATTGCGGATGATGATATTGAAGCTCGGCTGATTGGTTCATTGTCGCCATc   >  2:378956/1‑151 (MQ=255)                                                                                                                                       ggTCATTTTTTCTTTTTCTGCCATGAGAAGAGAGCGCAGTGAGGGATTATCTTGCCTGTCTGAACTGGCGATTAAGTTTCCGCGTACCCGGCG‑TTTAGTTATTGAGGATGATGATATTGAAGCTCGGCTGATTGGTTCATTGTCGCCAt    >  1:471358/1‑149 (MQ=255)                                                                                                                                        gTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTAAGTTTCCGCGTACCCGGCG‑TTTAGTTATTGCGGATGATGATATTGAAGCTCGGCTGATTGGTTCATTGTCGCCATCa  <  1:141313/150‑1 (MQ=255)                                                                                                                                                  |                                                                                                                                             ATAGAAAAATGCGTCATGAGTAGTATCGGTATTGAGAGTTTATTCAGAAAGTTTGCGGGTAACCCTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTAAGTTTCCGCGTACCCGGCG‑TTTAGTTATTGCGGATGATGATATTGAAGCTCGGCTGATTGGTTCATTGTCGCCATCA  >  NC_000913/4604199‑4604483

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: ‑