Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,285,853	0	G	T	43.4%	66.6 / 27.7	53	A126S (GCC→TCC)	agaD	N‑acetylgalactosamine‑specific enzyme IID component of PTS
Reads supporting (aligned to +/- strand):  ref base G (3/27);  new base T (23/0);  total (26/27)
Fisher's exact test for biased strand distribution p-value = 4.17e-12
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TTAATTTCGATGGAAGAAAAAGGAGAAAACCGCGACACCATTAAAGGCCTCAAAGTGGCACTGTTTGGCCCAATCGCCGGGATTGGCGATGCGATTTTCTGGTTTACTTTGTTGCCGATTATGGC‑GGGAATTTGCTCATCATTTGCCAGCCAGGGAAACCTGCTGGGGCCGATTCTATTTTTCGCCGTTTACCTGCTTATCTTTTTCCTGCGCGTCGGCTGGACCCACGTCGGTTATTCAGTCGGCGTGAAGGCGATCGATAAAGTGCGAGAGAACTCGCAGATGATTGCCC  >  NC_000913/3285709‑3286000                                                                                                                                                  |                                                                                                                                                    ttaATTTCGATGGAAGAAAAAGGAGAAAACCGCGACACCATTAAAGGCCTCAAAGTGGCACTGTTTGGCCCAATCGCCGGGATTGGCGATGCGATTTTCTGGTTTACTTTGTTGCCGATTATGGC‑GGGAATTTGCTCATCATTTgccagc                                                                                                                                                <  2:462166/150‑1 (MQ=255)   aaTTTCGATGGAAGAAAAAGGAGAAAACCGCGACACCATTAAAGGCCTCAAAGTGGCACTGTTTGGCCCAATCGCCGGGATTGGCGATGCGATTTTCTGGTTTACTTTGTTGCCGATTATGGC‑GGGAATTTGCTCATCATTTgccagcca                                                                                                                                              <  2:762861/150‑1 (MQ=255)    aTTTCGATGGAAGAAAAATGAGAAAACCGCGACACCATTAAAGGCCTCAAAGTGGCACTGTTTGGCCCAATCGCCGGGATTGGCGATGCGATTTTCTGGTTTACTTTGTTGCCGATTATGGC‑GGGAATTTGCTCATCATTTGCCAGCCAgg                                                                                                                                            <  2:666323/151‑1 (MQ=255)       tCGATGGAAGAAAAAGGAGAAAACCGCGACACCATTAAAGGCCTCAAAGTGGCACTGTTTGGCCCAATCGCCGGGATTGGCGATGCGATTTTCTGGTTTACTTTGTTGCCGATTATGGC‑GGGGATTTTTTTCTTATTTTCCAGCCAggg                                                                                                                                           >  1:654715/1‑149 (MQ=255)             gaagaaAACGGAGAAAACCGCGACACCATTAAAGGCCTCAAAGTGGCACTGTTTGGCCCAATCGCCGGGATTGGCGATGCGCTTTTCTGGTTTACTTTGTTGCCGATTATGGC‑GGGAATTTTTTCCTCCTTTTCCCGCCAggg                                                                                                                                           >  1:542051/1‑143 (MQ=255)              aagaaAAAGGAGAAAACCGCGACACCATTAAAGGCCTCAAAGTGGCACTGTTTGGCCCAATCGCCGGGATTGGCGATGCGATTTTCTGGTTTACTTTGTTGCCGATTATGGC‑GGGGATTTTTTCATCATTTTCCCGCCAGGGgaa                                                                                                                                        >  1:563598/1‑145 (MQ=255)                   aaaGGAGAAAACCGCGACACCATTAAAGGCCTCAAAGTGGCACTGTTTGGCCCAATCGCCGGGATTGGCGATGCGATTTTCTGGTTTACTTTGTTGCCGATTATGGC‑GGGAATTTGCTCATCATTTGCCAGCCAGGGAAACCTGCTGGGGc                                                                                                                             <  1:779349/151‑1 (MQ=255)                    aaGGAGAAAACCGCGACACCATTAAAGGCCTCAAAGTGGCACTGTTTGGCCCAATCGCCGGGATTGGCGATGCGATTTTCTGGTTTACTTTGTTGCCGATTATGGC‑GGGGAATTTCTCATTCTTTTTCCGCCAGGGGAACCTTCTgggg                                                                                                                              >  1:815375/1‑149 (MQ=255)                    aaGGAGAAAACCGCGACACCATTAAAGGCCTCAAAGTGGCACTGTTTGGCCCAATCGCCGGGATTGGCGATGCGATTTTCTGGTTTACTTTGTTGCCGATTATGGC‑GGGAATTTGCTCATCATTTGCCAGCCAGGGAAACCTGCTGGGGcc                                                                                                                            <  2:918883/151‑1 (MQ=255)                          aaaaCCGCGACACCATTAAAGGCCTCAAAGTGGCACTGTTTGGCCCAATCGCCGGGATTGGCGATGCGATTTTCTGGTTTACTTTGTTGCCGATTATGGC‑GGGGAATTTCTCATTATTTTTCAGCCAGGGGAAACTGCTGGGGGCggt                                                                                                                         >  1:725990/1‑146 (MQ=255)                           aaaCCGCGACACCATTAAAGGCCTCAAAGTGGCACTGTTTGGCCCAATCGCCGGGATTGGCGATGCGATTTTCTGGTTTACTTTGTTGCCGATTATGGC‑GGGAATTTGCTCATCATTTGCCAGCCAGGGAAACCTGCTGGGGCCGATTCTa                                                                                                                     <  1:283280/151‑1 (MQ=255)                               cgcgACACCATTAAAGGCCTCAAAGTGGCACTGTTTGGCCCAATCGCCGGGATTGGCGATGCGATTTTCTGGTTTACTTTGTTGCCGATTATGGC‑GGGGATTTTCTCATCATTTTCCAGCCAGGGGAACCTGCTGGGGGCGGTTCtttttt                                                                                                                 >  2:715676/1‑151 (MQ=255)                               cgcgACACCATTAAAGGCCTCAAAGTGGCACTGTTTGGCCCAATCGCCGGGATTGGCGATGCGATTTTCTGGTTTACTTTGTTGCCGATTATGGC‑GGGAATTTGCTCATCATTTGCCAGCCAGGGAAACCTGCTGGGGCCGATTCTAtttt                                                                                                                 <  1:540072/151‑1 (MQ=255)                                 cgACACCATTAAAGGCCTCAAAGTGGCACTGTTTGGCCCAATCGCCGGGATTGGCGATGCGATTTTCTGGTTTACTTTGTTGCCGATTATGGC‑GGGAATTTGCTCATCATTTGCCAGCCAGGGAAACCTGCTGGGGCCGATTCTATTTTTc                                                                                                               <  2:620834/151‑1 (MQ=255)                                   acacCATTAAAGGCCTCAAAGTGGCACTGTTTGGCCCAATCGCCGGGATTGGCGATGCGATTTTCTGGTTTACTTTGTTGCCGATTATGGC‑GGGGATTTTCTCATCATTTTTCAACCCGGGAAACCTGCTGGGGCCGGTTCTAttttt                                                                                                                >  1:576390/1‑148 (MQ=255)                                      ccATTAAAGGCCTCAAAGTGGCACTGTTTGGCCCAATCGCCGGGATTGGCGATGCGATTTTCTGGTTTACTTTGTTGCCGATTATGGC‑GGGGATTTGTTTCTTAATTTTCAGCCAAGGGAACCCCCTTGGGGCGCttttttttttttcc                                                                                                            >  1:910728/1‑145 (MQ=255)                                        aTTAAAGGCCTCAAAGTGGCACTGTTTGGCCCAATCGCCGGGATTGGCGATGCGATTTTCTGGTTTACTTTGTTGCCGATTATGGCGGGGAATTTG‑TCATCATTTTGCACCCCGGGGAACCCGCCGGGGGCGGTTCTtttttt                                                                                                                >  2:156638/1‑143 (MQ=255)                                        aTTAAAGGCCTCAAAGTGGCACTGTTTGGCCCAATCGCCGGGATTGGCGATGCGATTTTCTGGTTTACTTTGTTGCCGATTATGGC‑GGGAATTTTCTCATCATTTTTCCGCCCGGGAAAACCGCTGGGGGCGGTTTTAtttttttcccttt                                                                                                        >  1:782118/1‑143 (MQ=255)                                         ttAAAGGCCTCAAAGTGGCACTGTTTGGCCCAATCGCCGGGATTGGCGATGCGATTTTCTGGTTTACTTTGTTGCCGATTATGGC‑GGGGATTTTTTCTTCTTTTTTCCGCCAGGGGAAACTGCTGGGGCCGGGTCTATTTTTTGCCGttt                                                                                                        >  2:168830/1‑150 (MQ=255)                                         ttAAAGGCCTCAAAGTGGCACTGTTTGGCCCAATCGCCGGGATTGGCGATGCGATTTTCTGGTTTACTTTGTTGCCGATTATGGC‑GGGAATTTTTTCCTCATTTTTCAGCCAGGGGAAACTGCTGGGGGCGGTTCTTTTTTTTGCCGttt                                                                                                        >  2:310481/1‑150 (MQ=255)                                          tAAAGGCCTCAAAGTGGCACTGTTTGGCCCAATCGCCGGGATTGGCGATGCGATTTTCTGGTTTACTTTGTTGCCGATTATGGC‑GGGGATTTTCTCCTCATTTTTCAGCCCCGGGAACCCGCTGGGGGCGGGTCTATTTTTTGCCGgtt                                                                                                        >  1:522586/1‑149 (MQ=255)                                          tAAAGGCCTCAAAGTGGCACTGTTTGGCCCAATCGCCGGGATTGGCGATGCGATTTTCTGGTTTACTTTGTTGCCGATTATGGC‑GGGGAGTTGGTCATCATTTTCCCACCCAGGAAAACTGCTGGGGGCGAGTCTttttttttttcttt                                                                                                        >  2:295161/1‑141 (MQ=255)                                           aaaGGCCTCAAAGTGGCACTGTTTGGCCCAATCGCCGGGATTGGCGATGCGATTTTCTGGTTTACTTTGTTGCCGATTATGGC‑GGGAATTTGCTCATCATTTGCCAGCCAGGGAAACCTGCTGGGGCCGATTCTATTTTTCGCCGTTTAc                                                                                                      <  1:515379/150‑1 (MQ=255)                                                ccTCAAAGTGGCACTGTTTGGCCCAATCGCCGGGATTGGCGATGCGATTTTCTGGTTTACTTTGTTGCCGATTATGGC‑GGGGAATTTCTCATCATTTTCCAGCCCGGGGAAACCGCTGGGGCCGCTTCTTTTTTTTTCCGTTTTccccctt                                                                                                >  1:103507/1‑146 (MQ=255)                                                  tCAAAGTGGCACTGTTTGGCCCAATCGCCGGGATTGGCGATGCGATTTTCTGGTTTACTTTGTTGCCGATTATGGC‑GGGGATTTGCTCCTCATTTGCCCGCCCGGGGAACCTGCTTGGGGCGGTTCTTTTTTTTTCCCGTTACCTGCtttt                                                                                              >  2:505612/1‑149 (MQ=255)                                                       gTGGCACTGTTTGGCCCAATCGCCGGGATTGGCGATGCGATTTTCTGGTTTACTTTGTTGCCGATTATGGC‑GGGAATTTGCTCCTCATTTGCCAACCCGGGGAACCTGCTGGGGGCGACTTTATTTTTCGCCGGTTTACTActtttctttt                                                                                         >  1:330355/1‑151 (MQ=255)                                                         ggCACTGTTTGGCCCAATCGCCGGGATTGGCGATGCGATTTTCTGGTTTACTTTGTTGCCGATTATGGC‑GGGGAATTTTTCATCATTTTTCAGCCCGGGGAAACTGCTGGGGGCGCTTCTTTTTTTTTCCGTTTTCCTGCttttttttttt                                                                                       >  2:878707/1‑150 (MQ=255)                                                               gTTTGGCCCAATCGCCGGGATTGGCGATGCGATTTTCTGGTTTACTTTGTTGCCGATTATGGC‑GGGAATTTGCTCATCATTTGCCAGCCAGGGAAACCTGCTGGGGCCGATTCTATTTTTCGCCGTTTACCTGCTTATCTTTTTCCTgcgc                                                                                 <  2:844231/151‑1 (MQ=255)                                                               gTTTGGCCCAATCGCCGGGATTGGCGATGCGATTTTCTGGTTTACTTTGTTGCCGATTATGGC‑GGGAATTTGCTCATCATTTGCCAGCCAGGGAAACCTGCTGGGGCCGATTCTATTTTTCGCCGTTTACCTGCTTATCTTTTTCCTgcgc                                                                                 <  2:454477/151‑1 (MQ=255)                                                                      ccAATCGCCGGGATTGGCGATGCGATTTTCTGGTTTACTTTGTTGCCGATTATGGC‑GGGGATTTGCTCATCATTTTCCAACCCGGGAAAACTGCTGGGGGCGGTTCTTTTTTTTTCCGGTTTCCTTCTTATCttttt                                                                                        >  1:658784/1‑137 (MQ=255)                                                                      ccAATCGCCGGGATTGGCGATGCGATTTTCTGGTTTACTTTGTTGCCGATTATGGC‑GGGAATTTGCTCATCATTTGCCAGCCAGGGAAACCTGCTGGGGCCGATTCTATTTTTCGCCGTTTACCTGCTTATCTTTTTCCTGCGCGTCGGCt                                                                          <  1:248655/151‑1 (MQ=255)                                                                             ccGGGATTGGCGATGCGATTTTCTGGTTTACTTTGTTGCCGATTATGGC‑GGGGATTTTTTCATCATTTTCCAGCCAGGGGAACCTGCTGGGGGCGACTTTTTTTTTTTCCGCTTTTCTGCTTATTTTTTTTCTTCGCGTCGGCTGGGccc                                                                    >  2:309876/1‑150 (MQ=255)                                                                                ggATTGGCGATGCGATTTTCTGGTTTACTTTGTTGCCGATTATGGC‑GGGGATTTTCTCATCATTTTCCAGCCCGGGAAACCCGCTGGGGCCGGTTCTATTTTTTGCCGTTTTCCTGCTTTTCTTTTTTCTGCGCGTCGGCTGGACCCAc                                                                  >  1:886075/1‑149 (MQ=255)                                                                                 gATTGGCGATGCGATTTTCTGGTTTACTTTGTTGCCGATTATGGC‑GGGAATTTTCTCATCATTTTTCAGCCCGGGAAAACTGCTGGGGGCGGTTCTTTTTTTTGCCGTTTTCCTGCTTTTCTTTTTTCTGCGCGTCGGCTGGACCCa                                                                   >  1:169834/1‑147 (MQ=255)                                                                                 gATTGGCGATGCGATTTTCTGGTTTACTTTGTTGCCGATTATGGC‑GGGAATTTGCTCATCATTTGCCAGCCAGGGAAACCTGCTGGGGCCGATTCTATTTTTCGCCGTTTACCTGCTTATCTTTTTCCTGCGCGTCGGCTGGACCCACGTc                                                               <  2:699681/151‑1 (MQ=255)                                                                                        gatgcgatTTTCTGGTTTACTTTGTTGCCGATTATGGC‑GGGAATTTTCTCATCATTTTCCAGCCCGGGGAAACCGCTGGGGGCGGTTTTATTTTTTGCCGTTTTACTGCTTATTTTTTTTCTGCGCGGCGGGTGGGCCCACGTCGGTtttt                                                        >  1:385056/1‑151 (MQ=255)                                                                                        gatgcgatTTTCTGGTTTACTTTGTTGCCGATTATGGC‑GGGAATTTGCTCATCATTTGCCAGCCAGGGAAACCTGCTGGGGCCGATTCTATTTTTCGCCGTTTACCTGCTTATCTTTTTCCTGCGCGTCGGCTGGACCCACGTCGGTTAtt                                                        <  2:563521/151‑1 (MQ=255)                                                                                             gatTTTCTGGTTTACTTTGTTGCCGATTATGGC‑GGGGATTTTTTTATCATTTTTCAGCCA‑GGAAAACTGCTGGGGGCGGTTTTTTTTTTTTCCGCTTACCCGCCTATTTTTTTTCTTCGCGTCGGCCGGGccccccgcgggttttt                                                       >  2:624613/1‑133 (MQ=255)                                                                                              atTTTCTGGTTTACTTTGTTGCCGATTATGGC‑GGGAATTTGCTCATCATTTGCCAGCCAGGGAAACCTGCTGGGGCCGATTCTATTTTTCGCCGTTTACCTGCTTATCTTTTTCCTGCGCGTCGGCTGGACCCACGTCGGTTATTCAGTCg                                                  <  2:236172/151‑1 (MQ=255)                                                                                               ttttCTGGTTTACTTTGTTGCCGATTATGGC‑GGGAATTTGCTCATCATTTGCCAGCCAGGGAAACCTGCTGGGGCCGATTCTATTTTTCGCCGTTTACCTGCTTATCTTTTTCCTGCGCGTCGGCTGGACCCACGTCGGTTATTCAGTCg                                                  <  2:265204/150‑1 (MQ=255)                                                                                                 ttCTGGTTTACTTTGTTGCCGATTATGGC‑GGGAATTTGCTCATCATTTGCCAGCCAGGGAAACCTGCTGGGGCCGATTCTATTTTTCGCCGTTTACCTGCTTATCTTTTTCCTGCGCGTCGGCTGGACCCACGTCGGTTATTCAGTCGGc                                                <  2:532906/150‑1 (MQ=255)                                                                                                 ttCTGGTTTACTTTGTTGCCGATTATGGC‑GGGAATTTGCTCATCATTTGCCAGCCAGGGAAACCTGCTGGGGCCGATTCTATTTTTCGCCGTTTACCTGCTTATCTTTTTCCTGCGCGTCGGCTGGACCCACGTCGGTTATTCAGTCGGc                                                <  2:143496/150‑1 (MQ=255)                                                                                                  tCTGGTTTACTTTGTTGCCGATTATGGC‑GGGAATTTGCTCATCATTTGCCAGCCAGGGAAACCTGCTGGGGCCGATTCTATTTTTCGCCGTTTACCTGCTTATCTTTTTCCTGCGCGTCGGCTGGACCCACGTCGGTTATTCAGTCGGCg                                               <  2:556193/150‑1 (MQ=255)                                                                                                    tGGTTTACTTTGTTGCCGATTATGGC‑GGGAATTTGGTCATCATTTTTCAGCCCGGGGAACCTGCTGGGGGCGGTTCTATTTTTTTCCGTTTTCCTGCTTTTCTTTTTTCTTCGCGTCGGCTGGACCCCCCTCGGGTATTTTGTCGGCGTg                                             >  2:555225/1‑150 (MQ=255)                                                                                                                           ggC‑GGGAATTTGCTCATCATTTGCCAGCCAGGGAAACCTGCTGGGGCCGATTCTATTTTTCGCCGTTTACCTGCTTATCTTTTTCCTGCGCGTCGGCTGGACCCACGTCGGTTATTCAGTCGGCGTGAAGGCGATCGATAAAGTGCgagag                     <  1:622462/151‑1 (MQ=255)                                                                                                                             c‑GGGAATTTGCTCATCATTTGCCAGCCAGGGAAACCTGCTGGGGCCGATTCTATTTTTCGCCGTTTACCTGCTTATCTTTTTCCTGCGCGTCGGCTGGACCCACGTCGGTTATTCAGTCGGCGTGAAGGCGATCGATAAAGTGCGAGAGaa                   <  1:705305/151‑1 (MQ=255)                                                                                                                               gggAATTTGCTCATCATTTGCCAGCCAGGGAAACCTGCTGGGGCCGATTCTATTTTTCGCCGTTTACCTGCTTATCTTTTTCCTGCGCGTCGGCTGGACCCACGTCGGTTATTCAGTCGGCGTGAAGGCGATCGATAAAGTGCGAGAGAAc                  <  1:884056/151‑1 (MQ=255)                                                                                                                                 gAATTTGCTCATCATTTGCCAGCCAGGGAAACCTGCTGGGGCCGATTCTATTTTTCGCCGTTTACCTGCTTATCTTTTTCCTGCGCGTCGGCTGGACCCACGTCGGTTATTCAGTCGGCGTGAAGGCGATCGATAAAGTGCGAGAGAACTc                <  1:52746/151‑1 (MQ=255)                                                                                                                                 gAATTTGCTCATCATTTGCCAGCCAGGGAAACCTGCTGGGGCCGATTCTATTTTTCGCCGTTTACCTGCTTATCTTTTTCCTGCGCGTCGGCTGGACCCACGTCGGTTATTCAGTCGGCGTGAAGGCGATCGATAAAGTGCGAGAGAACTc                <  2:794422/151‑1 (MQ=255)                                                                                                                                       gCTCATCATTTGCCAGCCAGGGAAACCTGCTGGGGCCGATTCTATTTTTCGCCGTTTACCTGCTTATCTTTTTCCTGCGCGTCGGCTGGACCCACGTCGGTTATTCAGTCGGCGTGAAGGCGATCGATAAAGTGCGAGAGAACTCGCAga           <  2:157661/150‑1 (MQ=255)                                                                                                                                          catcatTTGCCAGCCAGGGAAACCTGCTGGGGCCGATTCTATTTTTCGCCGTTTACCTGCTTATCTTTTTCCTGCGCGTCGGCTGGACCCACGTCGGTTATTCAGTCGGCGTGAAGGCGATCGATAAAGTGCGAGAGAACTCGCAgatgat       <  2:576312/151‑1 (MQ=255)                                                                                                                                          catcatTTGCCAGCCAGGGAAACCTGCTGGGGCCGATTCTATTTTTCGCCGTTTACCTGCTTATCTTTTTCCTGCGCGTCGGCTGGACCCACGTCGGTTATTCAGTCGGCGTGAAGGCGATCGATAAAGTGCGAGAGAACTCGCAgatga        <  2:815272/150‑1 (MQ=255)                                                                                                                                           atcatTTGCCAGCCAGGGAAACCTGCTGGGGCCGATTCTATTTTTCGCCGTTTACCTGCTTATCTTTTTCCTGCGCGTCGGCTGGACCCACGTCGGTTATTCAGTCGGCGTGAAGGCGATCGATAAAGTGCGAGAGAACTCGCAGATGAtt      <  1:878827/151‑1 (MQ=255)                                                                                                                                           atcatTTGCCAGCCAGGGAAACCTGCTGGGGCCGATTCTATTTTTCGCCGTTTACCTGCTTATCTTTTTCCTGCGCGTCGGCTGGACCCACGTCGGTTATTCAGTCGGCGTGAAGGCGATCGATAAAGTGCGAGAGAACTCGCAGATGAtt      <  2:910603/151‑1 (MQ=255)                                                                                                                                               tttGCCAGCCAGGGAAACCTGCTGGGGCCGATTCTATTTTTCGCCGTTTACCTGCTTATCTTTTTCCTGCGCGTCGGCTGGACCCACGTCGGTTATTCAGTCGGCGTGAAGGCGATCGATAAAGTGCGAGAGAACTCGCAGATGATTGccc  >  1:874718/1‑151 (MQ=255)                                                                                                                                                  |                                                                                                                                                    TTAATTTCGATGGAAGAAAAAGGAGAAAACCGCGACACCATTAAAGGCCTCAAAGTGGCACTGTTTGGCCCAATCGCCGGGATTGGCGATGCGATTTTCTGGTTTACTTTGTTGCCGATTATGGC‑GGGAATTTGCTCATCATTTGCCAGCCAGGGAAACCTGCTGGGGCCGATTCTATTTTTCGCCGTTTACCTGCTTATCTTTTTCCTGCGCGTCGGCTGGACCCACGTCGGTTATTCAGTCGGCGTGAAGGCGATCGATAAAGTGCGAGAGAACTCGCAGATGATTGCCC  >  NC_000913/3285709‑3286000

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑