Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,578,287	0	T	C	40.8%	71.5 / 13.3	49	E147G (GAA→GGA)	gntR	d‑gluconate inducible gluconate regulon transcriptional repressor
Reads supporting (aligned to +/- strand):  ref base T (27/2);  new base C (0/20);  total (27/22)
Fisher's exact test for biased strand distribution p-value = 8.17e-12
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

ACGTTCGTCGAGACGTGCGCCGAGATAGGCAATGTGGCGATGCCCGCGAGCAATAATGGCAGTGG‑TCATCTGGCGTGCTGCTTCAAAGTTATCAAAA‑CC‑GACGGCGATATCAAGGCATGGCGACTTGCTGTCCATCAGTTCCACCACGGGAATACCCGCCACTTCAATCATCTTTAAGGTGCGCGGCGTGTGGGTACGTTCGGTGAGGATCAGGCCGTCGATATTCCAGGAGAGCATGGATTCGAGGCGTTCTTGCTCCATTTCCGGTTTATAACCGTAGTGCGCCAGC  >  NC_000913/3578148‑3578436                                                                                                                                               |                                                                                                                                                      aCGTTCGTCGAGACGTGCGCCGAGATAGGCAATGTGGCGATGCCCGCGAGCAATAATGGCAGTGG‑TCATCTGGCGTGCTGCTTCAAAGTTATCAAAA‑CC‑GACGGCGATATCAAGGCATGGCGACTTGCTGTCCATCAGTTCCACCACggg                                                                                                                                             >  1:734349/1‑150 (MQ=255)     tcgtcgAGACGTGCGCCGAGATAGGCAATGTGGCGATGCCCGCGAGCAATAATGGCAGTGG‑TCATCTGGCGTGCTGCTTCAAAGTTATCAAAA‑CC‑GACGGCGATATCAAGGCATGGCGACTTGCTGTCCATCAGTTCCACCACGGGAATAc                                                                                                                                        >  1:886885/1‑151 (MQ=255)               gcgcgcCGAGATAGGCAATGCGGCGATGCCCGCGAGCAATAATGGCAGTGG‑TCATCTGGCGTGCTGCTTCAAAGTTATCAAAA‑CC‑GACGGCGATATCAAGGCATGGCGACTTGCTGTCCATCAGTTCCACCACGGGAATACCCGCCACTTc                                                                                                                              >  2:872908/3‑151 (MQ=255)                  cgcCGAGATAGGCAATGTGGCGATGCCCGCGAGCAATAATGGCAGTGG‑TCATCTGGCGTGCTGCTTCAAAGTTATCAAAA‑CC‑GACGGCGATATCAAGGCATGGCGACTTGCTGTCCATCAGTTCCACCACGGGAATACCCGCCACTTCAat                                                                                                                           >  2:541411/1‑151 (MQ=255)                   gcCGAGATAGGCAATGTGGCGATGCCCGCGAGCAATAATGGCAGTGG‑TCATCTGGCGTGCTGCTTCAAAGTTATCAAAA‑CC‑GACGGCGATATCAAGGCATGGCGACTTGCTGTCCATCAGTTCCACCACGGGAATACCCGCCACTTCAatc                                                                                                                          >  2:767945/1‑151 (MQ=255)                          tAGGCAATGTGGCGATGCCCGCGAGCAATAATGGCAGTGG‑TCATCTGGCGTGCTGCTTCAAAGTTATCAAAA‑CC‑GACGGCGATATCAAGGCATGGCGACTTGCTGTCCATCAGTTCCACCACGGGAATACCCGCCACTTCAATCATCttt                                                                                                                    >  2:181761/1‑150 (MQ=255)                                 tgtgGCGATGCCCGCGAGCAATAATGGCAGTGG‑TCATCTGGCGTGCTGCTTCAAAGTTATCAAAA‑CC‑GACGGCGATATCAAGGCATGGCGACTTGCTGTCCATCAGTTCCACCACGGGAATACCCGCCACTTCAATCATCTTTAAGGTgcg                                                                                                            >  1:207376/1‑151 (MQ=255)                                  gtgGCGATGCCCGCGAGCAATAATGGCAGTGG‑TCATCTGGCGTGCTGCTTCAAAGTTATCAAAA‑CC‑GACGGCGATATCAAGGCATGGCGACTTGCTGTCCATCAGTTCCACCACGGGAATACCCGCCACTTCAATCATCTTTAAGGTgcgc                                                                                                           >  2:58839/1‑151 (MQ=255)                                  ggggCGATGCCCGGGAAAAATAATGGCAGTGG‑TCATCGGGCGTGCTGCTAAAAAGTTACCAAAC‑CC‑GGCGGCGATATAAAGGCAGGGCGCCTTGTTGCCCATCAGTCCCCCCACGGAAATCCCCGCCACTTCAATCATCTTTAAGGTgcg                                                                                                            <  1:352722/148‑1 (MQ=255)                                   gggcgtcgCCCGGGAAAAAAAATGGC‑GTGGTTCATCGGGGGTGCTCTTAAAAATTTAAAAAAC‑CC‑GACGGCGATATCAAGCGGTGGGTTCTTGCTCTCCATCATTCCCACCAGGGAAATCCCCGCCACTTCAATCATCTTTAAGGTGcgcg                                                                                                          <  2:579318/144‑1 (MQ=255)                                          gCCCGCGAGCAATAATGGCAGTGG‑TCATCTGGCGTGCTGCTTCAAAGTTATCAAAA‑CC‑GACGGCGATATCAAGGCATGGCGACTTGCTGTCCATCAGTTCCACCACGGGAATACCCGCCACTTCAATCATCTTTAAGGTGCGCGGCGggtg                                                                                                   >  2:561612/1‑151 (MQ=255)                                           cccGCGAGAAATAAGGGCAGGGT‑TCTTGGGGCGTGCTGCTTAAAATTTAAAAAAC‑CC‑GGCGGGGATATAAAGGCAGGGCGATTTGCTGCCCATCAGTCCCCCCACGGAAATCCCCGCCACTTCAATCATCTTTAAGGTGCGCGGCgtgt                                                                                                    <  1:401049/149‑1 (MQ=255)                                            ccGCGAGCAATAATGGCAGTGG‑TCATCTGGCGTGCTGCTTCAAAGTTATCAAAA‑CC‑GACGGCGATATCAAGGCATGGCGACTTGCTGTCCATCAGTTCCACCACGGGAATACCCGCCACTTCAATCATCTTTAAGGTGCGCGGCGTGTggg                                                                                                 >  1:965511/1‑151 (MQ=255)                                            ccGCGAGCAATAATGGCAGTGG‑TCATCTGGCGTGCTGCTTCAAAGTTATCAAAA‑CC‑GACGGCGATATCAAGGCATGGCGACTTGCTGTCCATCAGTTCCACCACGGGAATACCCGCCACTTCAATCATCTTTAAGGTGCGCGGCGTGTggg                                                                                                 >  2:659666/1‑151 (MQ=255)                                              gcgAGCAATAATGGCAGTGG‑TCATCTGGCGTGCTGCTTCAAAGTTATCAAAA‑CC‑GACGGCGATATCAAGGCATGGCGACTTGCTGTCCATCAGTTCCACCACGGGAATACCCGCCACTTCAATCATCTTTAAGGTGCGCGGCGTGTGGGt                                                                                                >  2:879091/1‑150 (MQ=255)                                                 agaaaaaagggaggTGG‑TCATCGGGCGTGCTGCTTAAAATTTATAAAAC‑CC‑GCCGGCGATATAAAGGCAGGGCGATTTGCTGTCCATCAGTCCCCCCCGGGAAATCCCCGCCACTTCAATCATCTTTAAGGTGCGCGGCGTGTGGGTAc                                                                                              <  1:181524/136‑1 (MQ=255)                                                 aacAAAAATGCCAGTGT‑TCAGCGGGCGGGCCGCTTC‑AAGTTAAAAAAACCC‑GAGGGCGATAAAAAGGCATGGAGCCTTGCTGCCCAGCAGTCCCCCCGCGGAAAGCCCCGCCACTTCAATCATCTTTAAGGTGCGCGGCGTGTggg                                                                                                 <  2:524795/144‑1 (MQ=255)                                                  gCAATAATGGCAGTGG‑TCATCTGGCGTGCTGCTTCAAAGTTATCAAAA‑CC‑GACGGCGATATCAAGGCATGGCGACTTGCTGTCCATCAGTTCCACCACGGGAATACCCGCCACTTCAATCATCTTTAAGGTGCGCGGCGTGTGGGTACGtt                                                                                           >  1:831037/1‑151 (MQ=255)                                                    aaaagtGGCAGTGG‑TCATCTGGCGTGCTGCTAAAAATTTAAAAAAC‑CC‑GCCGGCGATATCAAGGCAGGGCGTTTTGCTGCCCATCAGTCCCCCCAGGGGAATACCCGCCACTTCAATCATCTTTAAGGTGCGCGGCGTGTGGGTACGTTCg                                                                                         <  2:627291/146‑1 (MQ=255)                                                           gCAGTGG‑TCATCTGGCGTGCTGCTTCAAAGTTATCAAAA‑CC‑GACGGCGATATCAAGGCATGGCGACTTGCTGTCCATCAGTTCCACCACGGGAATACCCGCCACTTCAATCATCTTTAAGGTGCGCGGCGTGTGGGTACGTTCGGTGAgg                                                                                   >  1:473318/1‑150 (MQ=255)                                                             aGTGG‑TCATCTGGCGTGCTGCTTCAAAGTTATCAAAA‑CC‑GACGGCGATATCAAGGCATGGCGACTTGCTGTCCATCAGTTCCACCACGGGAATACCCGCCACTTCAATCATCTTTAAGGTGCGCGGCGTGTGGGTACGTTCGGTGAGGATc                                                                                >  1:249062/1‑151 (MQ=255)                                                              gTGG‑TCATCTGGGGTGCTTTTTAAAATTTAAAAAAC‑CC‑GACGGCAATATAAGGGCAGGGCGTTTTGCTGCCCATCAGTCCCCCCACGGGAATCCCCGCCACTTCAATCATCTTTAAGGTGCGCGGCGTGTGGGTACGTTCGGTGAGGATc                                                                                <  1:1062472/150‑1 (MQ=255)                                                              gTGG‑TAGTCGGGCGCGCTCCTAAAAATTTA‑CAAAA‑CCGGAGGGGGATACCAGGGCGGGGCGTTTTGCTGCCCATCATTCCCCCCACGGGAATCCCCGCCACTTCAATCATCTTTAAGGTGCGCGGCGTGTGGGTACGTTCGGTGAGGATCa                                                                               <  2:661351/151‑1 (MQ=255)                                                                gg‑TCATCGGGCGTGCTGCTAAAAATTTAAAAAAA‑CC‑GGCGGCAATAAAAAGGCAGGGCGATTTGTTCTCCATCAGTTCCCCCACGGGAATACCCGCCACTTCAATCATCTTTAAGGTGCGCGGCGTGTGGGTACGTTCGGTGAGGATc                                                                                <  1:108776/148‑1 (MQ=255)                                                                        gggCGTGCTGCTTAAGATTTACAAAAC‑CC‑GCGGGAAATATCAAGGCATGGCGTCTTGCTGTCCATCAGTCCCCCCACGGAAATCCCCGCCACTTCAATCATCTTTAAGGTGCGCGGCGTGTGGGTACGTTCGGTGAGGATCAGGCCg                                                                          <  1:251035/146‑1 (MQ=255)                                                                         ggCGTGCTTCTTAAAATTTATAAAAC‑CC‑GACGGCAATACAAAGGCATGGCTTTTTGCTCTCCATCATTCCCCCCAGGGGAATCCCCGCCACTTCAATCATCTTTAAGGTGCGCGGCGTGTGGGTACGTTCGGTGAGGATCAGGcc                                                                           <  1:565352/145‑1 (MQ=255)                                                                               cttctTAAAATTTACCAAAG‑CC‑GACGGCAATACAAGGGCAGGCCGTCTTGCTTCCAATCATTCCCCCAAGGGGAATCCCCGCCACTTCAATCATCTTTAAGGTGCGCGGCGTGTGGGTACGTTCGGTGAGGATCAGGCCGTCGATATTcc                                                                <  2:765270/147‑1 (MQ=255)                                                                               ctgctTCAAAGTTATCAAAA‑CC‑GACGGCGATATCAAGGCATGGCGACTTGCTGTCCATCAGTTCCACCACGGGAATACCCGCCACTTCAATCATCTTTAAGGTGCGCGGCGTGTGGGTACGTTCGGTGAGGATCAGGCCGTCGATATTcc                                                                >  1:984303/1‑150 (MQ=255)                                                                                 gctTCAAAGTTATCAAAA‑CC‑GACGGCGATATCAAGGCATGGCGACTTGCTGTCCATCAGTTCCACCACGGGAATACCCGCCACTTCAATCATCTTTAAGGTGCGCGGCGTGTGGGTACGTTCGGTGAGGATCAGGCCGTCGATATTCCAgg                                                             >  2:997169/1‑151 (MQ=255)                                                                                   ttCAAAGTTATCAAAA‑CC‑GACGGCGATATCAAGGCATGGCGACTTGCTGTCCATCAGTTCCACCACGGGAATACCCGCCACTTCAATCATCTTTAAGGTGCGCGGCGTGTGGGTACGTTCGGTGAGGATCAGGCCGTCGATATTCCAgg                                                             >  1:748196/1‑149 (MQ=255)                                                                                     cAAAGTTATCAAAA‑CC‑GACGGCGATATCAAGGCATGGCGACTTGCTGTCCATCAGTTCCACCACGGGAATACCCGCCACTTCAATCATCTTTAAGGTGCGCGGCGTGTGGGTACGTTCGGTGAGGATCAGGCCGTCGATATTCCAGgag                                                           >  2:328859/1‑149 (MQ=255)                                                                                      aaaTTTAACAACA‑CG‑GACGGAGATATAAGGCCAGGGGGGTTTGCTGCCACTCTGTTCCCCGACGGAATTCCCCGCCACTTCAATCATCTTTAAGGTGCGCGGCGTGTGGGTACGTTCGGTGAGGATCAGGCCGTCGATATTCCAg                                                              <  2:602593/145‑1 (MQ=255)                                                                                            ataaaac‑CC‑GCCGGCAATACCAAGGCATGGCGCTTTGCTGCCCATCATTCCCCCCGCGGAAACCCCCGCCACTTCAATCATCTTTAAGGTGCGCGGCGTGTGGGTACGTTCGGTGAGGATCAGGCCGTCGATATTCCAGGAGAGCATGGa                                                   <  2:21459/147‑1 (MQ=255)                                                                                            aacAAAC‑CC‑GACGGCGATATCAAGGCATGGCGATTTGCTGTCCATCAGTCCCCCCACGGGAATCCCCGCCACTTCAATCATCTTTAAGGTGCGCGGCGTGTGGGTACGTTCGGTGAGGATCAGGCCGTCGATATTCCAGGAGAGCATg                                                     <  1:323976/146‑1 (MQ=255)                                                                                                   ccc‑GACGGCGATAACGAGCCAGGGCGTCTTGTTTTCCTCCAGTCCCCCCAGGGGATTCCCCGCCACTTCAATCATCTTTAAGGTGCGCGGCGTGTGGGTACGTTCGGTGAGGATCAGGCCGTCGATATTCCAGGAGAGCATGGATTCGa                                              <  2:455663/148‑1 (MQ=255)                                                                                                           gCGATATCAAGGCATGGCGACTTGCTGTCCATCAGTTCCACCACGGGAATACCCGCCACTTCAATCATCTTTAAGGTGCGCGGCGTGTGGGTACGTTCGGTGAGGATCAGGCCGTCGATATTCCAGGAGAGCATGGATTCGAGGCGTTCtt                                     >  2:763485/1‑151 (MQ=255)                                                                                                             gATATCAAGGCATGGCGACTTGCTGTCCATCAGTTCCACCACGGGAATACCCGCCACTTCAATCATCTTTAAGGTGCGCGGCGTGTGGGTACGTTCGGTGAGGATCAGGCCGTCGATATTCCAGGAGAGCATGGATTCGAGGCGTTCTTGc                                   >  1:35552/1‑151 (MQ=255)                                                                                                              atatCAAGGCATGGCGACTTGCTGTCCATCAGTTCCACCACGGGAATACCCGCCACTTCAATCATCTTTAAGGTGCGCGGCGTGTGGGTACGTTCGGTGAGGATCAGGCCGTCGATATTCCAGGAGAGCATGGATTCGAGGCGTTCTTGCt                                  >  2:746137/1‑151 (MQ=255)                                                                                                                atCAAGGCATGGCGACTTGCTGTCCATCAGTTCCACCACGGGAATACCCGCCACTTCAATCATCTTTAAGGTGCGCGGCGTGTGGGTACGTTCGGTGAGGATCAGGCCGTCGATATTCCAGGAGAGCATGGATTCGAGGCGTTCTTGCTcc                                >  1:635245/1‑151 (MQ=255)                                                                                                                    aGGCATGGCGACTTGCTGTCCATCAGTTCCACCACGGGAATACCCGCCACTTCAATCATCTTTAAGGTGCGCGGCGTGTGGGTACGTTCGGTGAGGATCAGGCCGTCGATATTCCAGGAGAGCATGGATTCGAGGCGTTCTTGCTCCAttt                            >  2:70255/1‑151 (MQ=255)                                                                                                                     ggCATGGCGTCTTNCTCTCCNTCAGTCCCCCCGGNNNNNNCCCCGCCACTTCAATCATCTTTAAGGTGCGCGGCGTGTGGGt                                                                                                <  2:152058/82‑1 (MQ=255)                                                                                                                      gCAGGGCGATTTTCTGCCCACCAGTCCCACCACGAGAATACCCGCCACTTCAATCATCTTTAAGGTGCGCGGCGTGTGGGTACGTTCGGTGAGGATCAGGCCGTCGATATTCCAGGAGAGCATGGATTCGAGGCGTTCTTGCTCCATTTcc                          <  2:898064/151‑1 (MQ=255)                                                                                                                       cATGGCGTTTTCCTGCCCATCATTCCCCCCCGGGGAATCCCCGCCACTTCAATCATCTTTAAGGTGCGCGGCGTGTGGGTACGTTCGGTGAGGATCAGGCCGTCGATATTCCAGGAGAGCATGGATTCGAGGCGTTCTTGCTCCATTTcc                          <  1:205657/150‑1 (MQ=255)                                                                                                                        ttggcgttttcttttCCATCTGTCCCACCGGGGAAATACCCGCCACTTCAATCATCTTTAAGGTGCGCGGCGTGTGGGTACGTTCGGTGAGGATCAGGCCGTCGATATTCCAGGAGAGCATGGATTCGAGGCGTTCTTGCTCCATTTCCg                         <  1:83909/136‑1 (MQ=255)                                                                                                                          ggggtcTTGCTGTCCATCAGTCCCCCCCGGGAAATCCCCGCCACTTCAATCATCTTTAAGGTGCGCGGCGTGTGGGTACGTTCGGTGAGGATCAGGCCGTCGATATTCCAGGAGAGCATGGATTCGAGGCGTTCTTGCTCCATTTcc                          <  1:663305/142‑1 (MQ=255)                                                                                                                             gACTTGCTGTCCATCAGTTCCACCACGGGAATACCCGCCACTTCAATCATCTTTAAGGTGCGCGGCGTGTGGGTACGTTCGGTGAGGATCAGGCCGTCGATATTCCAGGAGAGCATGGATTCGAGGCGTTCTTGCTCCATTTCCGGTTtat                   >  2:861475/1‑151 (MQ=255)                                                                                                                             gACTTGCTGTCCATCAGTTCCACCACGGGAATACCCGCCACTTCAATCATCTTTAAGGTGCGCGGCGTGTGGGTACGTTCGGTGAGGATCAGGCCGTCGATATTCCAGGAGAGCATGGATTCGAGGCGTTCTTGCTCCATTTCCGGTTtat                   >  1:228007/1‑151 (MQ=255)                                                                                                                                ttGCTGTCCATCAGTTCCACCACGGGAATACCCGCCACTTCAATCATCTTTAAGGTGCGCGGCGTGTGGGTACGTTCGGTGAGGATCAGGCCGTCGATATTCCAGGAGAGCATGGATTCGAGGCGTTCTTGCTCCATTTCCGGTTTATAAc                >  1:93283/1‑151 (MQ=255)                                                                                                                                           cAGTCCCCCCACGGGAACACCCGCCACTTCAATCATCTTTAAGGTGCGCGGCGTGTGGGTACGTTCGGTGAGGATCAGGCCGTCGATATTCCAGGAGAGCATGGATTCGAGGCGTTCTTGCTCCATTTCCGGTTTATAACCGTAGTGCGcc     <  2:886752/151‑1 (MQ=255)                                                                                                                                              ttCCACCACGGGAATACCCGCCACTTCAATCATCTTTAAGGTGCGCGGCGTGTGGGTACGTTCGGTGAGGATCAGGCCGTCGATATTCCAGGAGAGCATGGATTCGAGGCGTTCTTGCTCCATTTCCGGTTTATAACCGTAGTGCGCCAGc  >  2:455710/1‑151 (MQ=255)                                                                                                                                               |                                                                                                                                                      ACGTTCGTCGAGACGTGCGCCGAGATAGGCAATGTGGCGATGCCCGCGAGCAATAATGGCAGTGG‑TCATCTGGCGTGCTGCTTCAAAGTTATCAAAA‑CC‑GACGGCGATATCAAGGCATGGCGACTTGCTGTCCATCAGTTCCACCACGGGAATACCCGCCACTTCAATCATCTTTAAGGTGCGCGGCGTGTGGGTACGTTCGGTGAGGATCAGGCCGTCGATATTCCAGGAGAGCATGGATTCGAGGCGTTCTTGCTCCATTTCCGGTTTATAACCGTAGTGCGCCAGC  >  NC_000913/3578148‑3578436

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑