Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,604,344	0	C	T	50.0%	25.0 / 33.2	50	S62F (TCT→TTT)	bglJ	bgl operon transcriptional activator
Reads supporting (aligned to +/- strand):  ref base C (5/20);  new base T (25/0);  total (30/20)
Fisher's exact test for biased strand distribution p-value = 2.25e-09
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CTCATAGAAAAATGCGTCATGAGTAGTATCGGTATTGAGAGTTTATTCAGAAAGTTTGCGGGTAACCCTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGC‑GCAGAGAGGGATTATCTTGCCTGACT‑GAACTGGCGA‑TTAAGTTTCCGCGTACCCGGCGTTTAGTTATTGCGGATGATGATATTGAAGCTCGGCTGATTGGTTCATTGTCGCCATCACCGCTGGAC  >  NC_000913/4604196‑4604492                                                                                                                                                     |                                                                                                                                                        cTCATAGAAAAATGCGTCATGAGTAGTATCGGTATTGAGAGTTTATTCAGAAAGTTTGCGGGTAACCCTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATtttttttt                                                                                                                                                       >  1:90529/1‑151 (MQ=255) cTCATAGAAAAATGCGTCATGAGTAGTATCGGTATTGAGAGTTTATTCAGAAAGTTTGCGGGTAACCCTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGGCCTtttttttt                                                                                                                                                       >  1:289666/1‑151 (MQ=255)                     gAGTAGTATCGGTATTGAGAGTTTATTCAGAAAGTTTGCGGGTAACCCTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTTCCCTGGGGAGTGAg                                                                                                                                   >  1:180606/1‑151 (MQ=255)                     gAGTAGTATCGGTATTGAGAGTTTATTCAGAAAGTTTGCGGGTAACCCTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTTCCATTAGAAGGGAg                                                                                                                                   >  1:611961/1‑151 (MQ=255)                          gtaTCGGTATTGAGAGTTTATTCAGAAAGTTTGCGGGTAACCCTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGGCATTTTTTTTTTTTTTGCCCTGAGAAGGGAgg‑gcgg                                                                                                                             >  1:63571/1‑149 (MQ=255)                           taTCGGTATTGAGAGTTTATTCAGAAAGTTTGCGGGTAACCCTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGC‑GCag                                                                                                                             <  1:587129/150‑1 (MQ=255)                            aTCGGTATTGAGAGTTTATTCAGAAAGTTTGCGGGTAACCCTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGC‑GCagag                                                                                                                           <  1:298491/151‑1 (MQ=255)                             tCGGTATTGAGAGTTTATTCAGAAAGTTTGCGGGTAACCCTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTTTCCTGAGAAGGGAGG‑GCggagg                                                                                                                          >  2:107058/1‑150 (MQ=255)                               ggTATTGAGAGTTTATTCAGAAAGTTTGCGGGTAACCCTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTTCCATGAGAAGGGAGG‑GCAGAGAgg                                                                                                                        >  1:408982/1‑151 (MQ=255)                                       gagTTTATTCAGAAAGTTTGCGGGTAACCCTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTCTTCCCTGGGAAGGGGGG‑GCAGAGAgggggtat                                                                                                                  >  2:510490/1‑144 (MQ=255)                                            tATTCAGAGAGTTTGCGGGTTACCCATAGAAGCTCCACTGCTATACCAGTCAGGACTCATTTCAGGATGCCACGTCGCGGATCTCGTTTGCGCCGGTCATTTTTTCTTTTTCTGCCATCAGAAGTGAGC‑GCAGAGAGGGATTGTCTTGcc                                                                                                            <  1:393121/150‑1 (MQ=255)                                                       tttGCGGGTAACCCTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGC‑GCAGAGAGGGATTATCTTGCCTGACT‑GAACTgg                                                                                               <  1:211009/151‑1 (MQ=255)                                                             ggTAACCCTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTTCCCTGAGGAGTGAGC‑GCAGAGAGGGGTTATCTTGCCTGTCT‑TAACTggggtgta                                                                                         >  1:25030/1‑145 (MQ=255)                                                               tAACCCTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGC‑GCAGAGAGGGATTATCTTGCCTGACT‑GAACTGGCGA‑TTAAg                                                                                      <  1:9953/151‑1 (MQ=255)                                                               tAACCCTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGC‑GCAGAGAGGGATTATCTTGCCTGACT‑GAACTGGCGA‑TTAAg                                                                                      <  1:350255/151‑1 (MQ=255)                                                                  cccTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCCTTTTTTCTTTTTTTGCCCTGAGAAGTGAGC‑GCAGAGAGGGAGTATCTTGCCTGACT‑GAAATGGCGA‑TTTAGttt                                                                                   >  1:556199/1‑151 (MQ=255)                                                                  cccTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTGTCATGAGAAGTGGGC‑GCAGAGAGGGGTTATTTTTCCTGATT‑GAACTGGGGA‑TTTAGttt                                                                                   >  1:306526/1‑151 (MQ=255)                                                                  cccTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTCTGCCATGAGAAGGGAGC‑GCAGAGAGGGATTATCTTGCCTGACT‑GAACTGGCGA‑TTAAGgtt                                                                                   >  1:132679/1‑151 (MQ=255)                                                                   ccTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGC‑GCAGAGAGGGATTATCTTGCCTGACT‑GAACTGGCGA‑TTAAGTTTc                                                                                  <  1:319590/151‑1 (MQ=255)                                                                   ccTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGC‑GCAGAGAGGGATTATCTTGCCTGACT‑GAACTGGCGA‑TTAAGTTTc                                                                                  <  2:163023/151‑1 (MQ=255)                                                                      tataAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTTTCCTGAGAAGTGGGA‑GCCGAGAGGGGTTTTTTTTCCTGTCT‑GAAATGGTGA‑TTAAGtttt                                                                                  >  1:8996/1‑147 (MQ=255)                                                                           gCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGGCATTTTTTCTTTTTTTGCCATGAGAAGTGAGC‑GCAGCGAGGGGGTATCTTGCCTTGAT‑GAACTGGCGC‑TTATGATTCCGCGTAc                                                                           >  1:362260/1‑150 (MQ=255)                                                                            cTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGC‑GCAGAGAGGGATTATCTTGCCTGACT‑GAACTGGCGA‑TTAAGTTTCCGCGTAccc                                                                         <  1:146862/151‑1 (MQ=255)                                                                                aTACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTTCCATGAGAAGTGAGC‑GCAGAGGGGGGTTATTTTGCCTGACT‑GAACTTGCGA‑TTAAATTTCCGCGTACCCGGCg                                                                     >  1:350430/1‑151 (MQ=255)                                                                                 tACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCCTTTTTTTTTTTTCTTCCATGAGAAGGGGGG‑GCCGAGAGGGGGTTTTTTGCCTGACT‑TAACTTGCGA‑TTAAATTTTCGCGGAACCGGCgg                                                                    >  2:587683/1‑150 (MQ=255)                                                                                 tACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCCTTTTTTCTTTTTCTTGCCTGAGAAGTCAGG‑GCCGGGGGGGGTTTTCTTTCCTGGCT‑TAACCGGCGATTTAAGTTCCCG‑GTAACCCGCGt                                                                    >  2:558360/1‑151 (MQ=255)                                                                                 tACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTGGCCTGAGAAGGGAGC‑GCAGGGGGGGGTTATTTTTCCTTTCT‑GGAATGGGGATTTAAGTTTcccggaccccgggg                                                                     >  2:296392/1‑139 (MQ=255)                                                                                 tACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGGCATTTTTTTTTTTTTTTCCCTGGGAAGTGAGG‑GCCGAGAGGGGATATTTTTCCTGTCT‑GAACCTGGGG‑TTAAGTTTTCGCGTACCCcgcgg                                                                    >  1:284500/1‑150 (MQ=255)                                                                                  aCCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTTATTTTTTTTTTTTCTGCCATGGGAAGGGGGC‑GGAGAGAGGGGTTTTCTTTCCTTTTT‑GAACTTGGGG‑TTAAGTTTCCGCGGAGCCGGGGtt                                                                   >  2:305867/1‑151 (MQ=255)                                                                                      ataCCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCCTTTTTTCTTTTTTTGCCCTGGGAAGGGAGC‑GCAGAGAGGGGTTATCTTTCTTCACT‑GAACTGGGGG‑TTTAGATTCCGCGGACCCCGAGTTTAGt                                                               >  1:370748/1‑151 (MQ=255)                                                                                        aCCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGC‑GCAGAGAGGGATTATCTTGCCTGACT‑GAACTGGCGA‑TTAAGTTTCCGCGTACCCGGCGTTTAGTTa                                                             <  1:614750/151‑1 (MQ=255)                                                                                            gTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTTCCATGAGGAGGGAGG‑GCCGAGAGGGGTTTTCTTTTCTTGCTGGAATTGCGGA‑TTAAGTTTCCGGGCACCGGGGGtttgttttttg                                                          >  1:477972/1‑143 (MQ=255)                                                                                                   gTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTGGCCTGAGAAATGAGG‑GGAGAGAGGGGGTTTTTTTTCTGACT‑TAACTGGGGA‑GTAAGTTTTCGCGTACCCGGCGTTTTGTTATTGCGgatgat                                                  >  1:464153/1‑151 (MQ=255)                                                                                                   gTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCAATTTTTTTTTTTTTGCCATGGGAAGTGGGC‑GCAGAGGGGGGTTTTTTTTCCTGACT‑GAACTGGCGA‑TTAAGTTTTCGCGGACCCGGCGGTTTGTTTTTGTGggtggt                                                  >  2:6501/1‑149 (MQ=255)                                                                                                     cATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTTCCCTGAGAAGTGAGC‑GCCGAGGGGGGTTATCTTTCCTGACT‑GAACTGGCGA‑TTTAGTTTCCGCGTTCCCCGCGGTTTGTTTTTTCGggtgatgg                                                >  1:115957/1‑150 (MQ=255)                                                                                                         tCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCCTTTTTTTTTTTTTTGCCCTGGGAAGTGAGC‑GCAGGGAGGGGTTTTTTTTCCTTTCT‑GAACTGGCGA‑TTTAGTTTCCGCGTACCCGGCGGTTTGTTTTTGCGGGTGATGATAtt                                            >  2:221096/1‑151 (MQ=255)                                                                                                          cAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTCTGTCATGAGAAATGAGG‑GGAGGGAGGGGTTATCTTTCCTTACT‑GTAATGGCGA‑TTTAGGTTCCGCGTGCCCGGCGTTTTGTTATTTCGGATGATGATAttt                                           >  1:188746/1‑150 (MQ=255)                                                                                                             gATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGC‑GCAGAGAGGGATTATCTTGCCTGACT‑GAACTGGCGA‑TTAAGTTTCCGCGTACCCGGCGTTTAGTTATTGCGGATGATGATATTg                                           <  2:478129/148‑1 (MQ=255)                                                                                                             gATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGC‑GCAGAGAGGGATTATCTTGCCTGACT‑GAACTGGCGA‑TTAAGTTTCCGCGTACCCGGCGTTTAGTTATTGCGGATGATGATATTg                                           <  2:461772/148‑1 (MQ=255)                                                                                                              aTGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGC‑GCAGAGAGGGATTATCTTGCCTGACT‑GAACTGGCGA‑TTAAGTTTCCGCGTACCCGGCGTTTAGTTATTGCGGATGATGATATTGAAGc                                       <  2:208275/151‑1 (MQ=255)                                                                                                               tGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGC‑GCAGAGAGGGATTATCTTGCCTGACT‑GAACTGGCGA‑TTAAGTTTCCGCGTACCCGGCGTTTAGTTATTGCGGATGATGATATTGAAGCt                                      <  2:381184/151‑1 (MQ=255)                                                                                                               tGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGC‑GCAGAGAGGGATTATCTTGCCTGACT‑GAACTGGCGA‑TTAAGTTTCCGCGTACCCGGCGTTTAGTTATTGCGGATGATGATATTGAAGCt                                      <  2:476262/151‑1 (MQ=255)                                                                                                                gCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTGCCATGAGAAGGGGGG‑GCAGAGAGGGATTATCTTGCCTGACT‑GAACTGGCGA‑TTAAGTTTTCGCGTACCCGGGGGTTAGTTTTTGCGGGTGATGAGATTGTAGcc                                      >  1:165525/1‑149 (MQ=255)                                                                                                                  cATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTTCCCTTAGGAGTGAGC‑GCCGAGGGGGGTTATTTTGTCTTACT‑TAATTGGCGA‑TTTAGTTTTCGCGTACCCCGCGGTTATTTTTTTTGGGTGATGATATTTAAGCGCgg                                   >  2:518795/1‑151 (MQ=255)                                                                                                                     gTCGCGGATCTCGTTTGCGGCGGGCATTTTTTTTTTTTTTGCCCTGAGAAGTGGGG‑GCAGAGAGGGGTTTTTTTTCCTGACT‑GAACTGGCGG‑TTTAGTTTTCGCGGACCCGGCGTTTTGTTATTTGGGATGGTGATATTTAAACCCgggtt                                >  2:180059/1‑148 (MQ=255)                                                                                                                       cgcgGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTGCCATGAGAAGGGAGCGGCGGGGGGGGATT‑TTTTGCCTGACT‑GGAATGGGGA‑TTAAGGTTTCGCGGACCCGGCGTTTAGTTATTTCGGATGATGATATTGAAGCTCGGGTGAt                              >  1:574333/1‑151 (MQ=255)                                                                                                                         cgGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGC‑GCAGAGAGGGATTATCTTGCCTGACT‑GAACTGGCGA‑TTAAGTTTCCGCGTACCCGGCGTTTAGTTATTGCGGATGATGATATTGAAGCTCGGCTGATTg                            <  2:350564/151‑1 (MQ=255)                                                                                                                            aTCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGC‑GCAGAGAGGGATTATCTTGCCTGACT‑GAACTGGCGA‑TTAAGTTTCCGCGTACCCGGCGTTTAGTTATTGCGGATGATGATATTGAAGCTCGGCTGATTGGt                          <  1:345997/150‑1 (MQ=255)                                                                                                                                cGTTTGCGGCGGTCATTTTTTCTTTTTTTGCCCTGAGAAGGGAGC‑GCAGAGAGGGGTTTTCTTGCCTTACT‑GAACTGGGGG‑TTAAGTTTCCGGGTACCCGGCGGTTAGTTTTTGCGGGTGATGGAATTGAAGCCCGGCTGGTTGGTTCAtt                     >  2:610009/1‑151 (MQ=255)                                                                                                                                  tttGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGC‑GCAGAGAGGGATTATCTTGCCTGACT‑GAACTGGCGA‑TTAAGTTTCCGCGTACCCGGCGTTTAGTTATTGCGGATGATGATATTGAAGCTCGGCTGATTGGTTCATTGt                   <  2:180654/151‑1 (MQ=255)                                                                                                                                    tGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGC‑GCAGAGAGGGATTATCTTGCCTGACT‑GAACTGGCGA‑TTAAGTTTCCGCGTACCCGGCGTTTAGTTATTGCGGATGATGATATTGAAGCTCGGCTGATTGGTTCATTGTCg                 <  2:132705/151‑1 (MQ=255)                                                                                                                                              aTTTTTTCTTTTTCTGCCATGAGAAGTGAGC‑GCAGAGAGGGATTATCTTGCCTGACT‑GAACTGGCGA‑TTAAGTTTCCGCGTACCCGGCGTTTAGTTATTGCGGATGATGATATTGAAGCTCGGCTGATTGGTTCATTGTCGCCATCACCGc       <  2:574511/151‑1 (MQ=255)                                                                                                                                                   ttctttttctGCCATGAGAAGTGAGC‑GCAGAGAGGGATTATCTTGCCTGACT‑GAACTGGCGA‑TTAAGTTTCCGCGTACCCGGCGTTTAGTTATTGCGGATGATGATATTGAAGCTCGGCTGATTGGTTCATTGTCGCCATCACCGCTGGAc  <  2:23103/151‑1 (MQ=255)                                                                                                                                                     |                                                                                                                                                        CTCATAGAAAAATGCGTCATGAGTAGTATCGGTATTGAGAGTTTATTCAGAAAGTTTGCGGGTAACCCTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGC‑GCAGAGAGGGATTATCTTGCCTGACT‑GAACTGGCGA‑TTAAGTTTCCGCGTACCCGGCGTTTAGTTATTGCGGATGATGATATTGAAGCTCGGCTGATTGGTTCATTGTCGCCATCACCGCTGGAC  >  NC_000913/4604196‑4604492

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑