Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	357,880	0	T	C	44.0%	61.1 / 13.9	50	K271E (AAA→GAA)	cynR	transcriptional activator of cyn operon; autorepressor
Reads supporting (aligned to +/- strand):  ref base T (18/10);  new base C (0/22);  total (18/32)
Fisher's exact test for biased strand distribution p-value = 7.68e-07
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTAT‑CCAA‑CGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCT‑GCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCG‑CTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTA  >  NC_000913/357733‑358019                                                                                                                                                        |                                                                                                                                             cGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTAT‑CCAA‑CGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCT‑GCCAGCTATTTTTccg                                                                                                                                           <  1:468495/151‑1 (MQ=255)  gTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTAT‑CCAA‑CGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCT‑GCCAGCTATTTTTccgc                                                                                                                                          >  2:935467/1‑151 (MQ=255)     ggCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTAT‑CCAA‑CGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCT‑GCCAGCTATTTTTCcgccgc                                                                                                                                       >  1:792963/1‑151 (MQ=255)       ccTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTAT‑CCAA‑CGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCT‑GCCAGCTATTTTTCCGCCGcaa                                                                                                                                     <  1:914161/151‑1 (MQ=255)       ccTGATAACCGTAACGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTAT‑CCAA‑CGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCT‑GCCAGCTATTTTTCCGCCGca                                                                                                                                      <  2:836180/150‑1 (MQ=255)          gATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTAT‑CCAA‑CGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCT‑GCCAGCTATTTTTCCGCCGcaacaa                                                                                                                                  <  1:602581/151‑1 (MQ=255)           aTAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTAT‑CCAA‑CGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCT‑GCCAGCTATTTTTCCGCCGcaacaa                                                                                                                                  >  2:135003/1‑150 (MQ=255)                   aGCGAATCGGTCATTCCCAGCCACACACATGTCTCGGCGGCTACCTTGATTCATTCCCGCCAACACCCGCGCATTTTC‑CCAA‑CGCCATGTGCAAAAATGCTTT‑CGCGGCGGCTGTCT‑GCCAGCTATTTTCCCGCCGCAAAAAAAccgccg                                                                                                                          <  2:196032/150‑1 (MQ=17)                    gcgcATCAGGAAATTCCAGCCGCAGACCTGTGTCAGCGGCTCCCGTGATTCATTCCCGCCAACAACCGCGCATTTAC‑CCAA‑CGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCT‑GCCAGTTATTTTTCCGCCGCAACAAAAccgccg                                                                                                                          <  1:842782/149‑1 (MQ=255)                     cgcATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACTGTGATTCATTTCCGCCAACAACCGCGCATTTAT‑CCAA‑CGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCT‑GCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTtc                                                                                                                       >  1:196317/1‑151 (MQ=255)                     cgcATCAGGAAATTCCAGCCGCAGACCTGTGTCAGCGGCTCCCGTGATTCATTCCCGCCAACAACCGCGCATTTAT‑CCAA‑CGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCT‑GCCAGCTATTTTTCCGCCGCAACAAAAccgccg                                                                                                                          <  1:209318/148‑1 (MQ=255)                      gcATCAGGCATTTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTCCCGCCAACAACCGCGCATTTAC‑CCAA‑CGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCT‑GCCAGCTATTTTTCCGCCGCAAC‑AAACCGCCGTtct                                                                                                                      <  1:978990/150‑1 (MQ=255)                               aaTTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTAT‑CCAA‑CGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCT‑GCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCagt                                                                                                               >  2:213567/1‑149 (MQ=255)                               aaTTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTAT‑CCAA‑CGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCT‑GCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCagt                                                                                                               >  1:978624/1‑149 (MQ=255)                               aaTTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTAT‑CCAA‑CGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCT‑GCCAGCGATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCag                                                                                                                >  2:506247/1‑148 (MQ=255)                                aTTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTAT‑CCAA‑CGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCT‑GCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCagtagt                                                                                                            >  2:743260/1‑151 (MQ=255)                                aTTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTAT‑CCAA‑CGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCT‑GCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCagtag                                                                                                             >  1:22861/1‑150 (MQ=255)                                 ttCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTAT‑CCAA‑CGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCT‑GCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTg                                                                                                           >  2:849391/1‑151 (MQ=255)                                     aGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTAT‑CCAA‑CGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCT‑GCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCgg                                                                                                       >  2:588693/1‑151 (MQ=255)                                       ccgcggttttgtgTCGGCGGCTCCCGTGATTCATCCCCCCCAACACCCGCGCATTCCC‑CCAC‑CGCCATGTGAAAAAATGCCTC‑CGCGGGGGCTGTCT‑GCCAGTTATTTTTCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCggg                                                                                                      <  1:427178/141‑1 (MQ=255)                                          cAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTAT‑CCAA‑CGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCT‑GCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCgggg                                                                                                     >  2:870887/1‑148 (MQ=255)                                           aGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTAT‑CCAA‑CGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCT‑GCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCCGTAGTGGCggtgg                                                                                                    >  2:153824/1‑145 (MQ=255)                                            gccttgtaacgggggCTCCGGTGATACATTCCCGCCAACACCCGCGTTTTTAT‑CCAA‑CGCTGTGTGAAAAATTGCCTT‑CGGGGGGGGTTTCT‑GCCAGTTATTTTCCCCCCGCAAAAAAGCCGCCGTTCTCTCCAGTAGTGGCGGGGCAag                                                                                                 <  1:315808/137‑1 (MQ=255)                                              cttgtgCCGGCGCCTCCGGTGATTCTTTCCCCCCAACACCCGCGCTTTTAC‑CCAC‑CGCCTTGTGAAAAATCCCCTT‑CGGGGCGGTTGTCG‑GCCCGTTTTTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAagag                                                                                               <  2:738165/148‑1 (MQ=255)                                                   gtCGGCGGCTCCCGTGATTCTTTCCCCCCAACACCCGCCCTTTTAC‑CCAC‑CCCCATGTGCAAAAATGCCTT‑CGGGGCGGCTGTCT‑GCCAGTTTTTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATa                                                                                          <  1:846329/150‑1 (MQ=255)                                                       ggggCTCCCGTGTTTCTTTCCCCCAAACACCCGCGCATTTAC‑CCAC‑CGCCATGTGAAAAAATGCTTC‑CGGGGCGGCTGTCG‑GCCAGCTTTTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAgaga                                                                                              <  1:730675/140‑1 (MQ=255)                                                       gCGGCTCCCGTGTTTCTTTCCCGCCAACACCCGCGCTTTTAC‑CCAC‑CCCCATGTGAAAAAATCCCTC‑CGCGGCGGCTGTCT‑GCCAGCTTTTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAg                                                                                         <  1:979285/147‑1 (MQ=255)                                                         ggCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTAT‑CCAA‑CGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCT‑GCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCgggggcatggaaaaaa                                                                                         >  2:709588/1‑133 (MQ=255)                                                            tACCGTGATTCATTTCCGCCAACAACCGCGCATTTAT‑CCAA‑CGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCT‑GCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGAATAGAAATaaaatttaagc                                                                                >  1:822339/1‑141 (MQ=255)                                                              ccGTGTTTCATTCCCCCCAAAACCCGCGCTTTTCC‑CAAC‑CCCCATGTCAAAAAATCCCTC‑CGGGGGGGCTGTCT‑GCCAGTTTTTTTCCCGCCAAAAAAAACCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCt                                                                                       <  2:874362/142‑1 (MQ=255)                                                                          cccGCCAACACCCGCGTATTTAT‑CCAC‑CGCCATGTGCAAAAATGCTTT‑CGGGGCGGCTGTCG‑GCCAGCTTTTTTCCCGCCGCAACAAAGCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTtgtgtg                                                                  <  1:329218/150‑1 (MQ=255)                                                                           ccGCAAACACCCGCCCTTTTAT‑CCAC‑CCCAGTGTAAAAAATTCCCTG‑CGGGGCGGCTGTCT‑CCCGGTTTTTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTtgtgtg                                                                  <  1:71023/150‑1 (MQ=255)                                                                             ccccaaaaaaccgcATTTTTACCAACCGCCATGTCAAAAATTCCCTT‑CGGGGCGGCTTTCT‑CCCAGTTTTTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTtgtgt                                                                   <  1:555876/138‑1 (MQ=255)                                                                                            tttAC‑CCAC‑CGCCATGTGAAAAAATCCCTC‑CGCGGCGGCTGTCT‑GCCAGTTTTTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCG‑CTGCTGGt                                                  <  1:173426/148‑1 (MQ=255)                                                                                             ttAT‑CCAA‑CGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCT‑GCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCGAGAGAAAAAAATTTAAAACCGTCCTGTTGTGTgggga                                                              >  1:26017/1‑133 (MQ=37)                                                                                                  ccAC‑CGCCATGTGAAAAAATGCCTC‑CGCGGCGGCTGTCT‑GCCAGCTATTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCG‑CTGCTGGTAACa                                              <  1:83898/147‑1 (MQ=255)                                                                                                             gccaaaaaaGCCCTC‑CGCGGGGGCTGGCT‑GCCGGTTTTTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCG‑CTGCTGGTAACAATGTGGAAAGGGa                                 <  2:850671/146‑1 (MQ=255)                                                                                                             ataaaaaaaTCCTTC‑CGCGCCTGCTCCCT‑CCCATTTATTTTTCCCCCGAAAAAAACCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCG‑CTGCTGGTAACAATGTGGaaa                                     <  2:36207/142‑1 (MQ=255)                                                                                                                aaaaaaGGCCTC‑CGGGGCGGCTGCCT‑GCCAGTTTTTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCG‑CTGCTGGTAACAATGTGGAAAGGGAAg                               <  1:538701/148‑1 (MQ=255)                                                                                                                  aaaaTGCCTT‑CGCGGCGGCTGTCT‑GCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGCGCCAGGGAAAAAGAATTAAAACCCTTCTGTTTTTTGGGGATAGCCTCCGGGGAACAAGGGGGAAAGGGaaaggg                            >  2:531136/1‑147 (MQ=255)                                                                                                                  aaaaTCCCTT‑CGGGGCGGCTGTCT‑GCCCGTTTTTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCG‑CTGCTGGTAACAATGTGGAAAGGGAAGTgcg                           <  1:816946/151‑1 (MQ=255)                                                                                                                  aaaaAGCCTTCCGGGGCGGCTGTCG‑GCCAGTTTTTTTCCCCCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCG‑CTGCTGGTAACAATGTGGAAAGGGAAg                               <  2:814374/148‑1 (MQ=255)                                                                                                                           tccgcgGCGGCGTTCT‑CCAAGCTATTTTCCCGCCGAAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCG‑CTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAAt                     <  1:298639/147‑1 (MQ=255)                                                                                                                                ggcggcTGTCG‑CCCAGTTTTTTTCCCGCCGAAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCG‑CTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGaa                      <  2:914391/143‑1 (MQ=255)                                                                                                                                 ggggcTGTCCGGCCTGCTTTTTGTCACCCGAAACAAAGCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCG‑CTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAAt                     <  2:151971/142‑1 (MQ=255)                                                                                                                                  cggcTGTCT‑GCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCGAGAGGAAAAAAATTAAACCCGCCACACTGGGTGGTAATCG‑CCGGTGGGTACAAAATGGGAAAGGGAGGGCGGGGGATCAGCTcc              >  1:186039/1‑149 (MQ=255)                                                                                                                                      tGTCG‑GCCAGTTTTTTTCCCCCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCG‑CTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGaa          <  1:865924/149‑1 (MQ=255)                                                                                                                                             ccAGTTTTTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCG‑CTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACcgcg     <  1:564484/148‑1 (MQ=255)                                                                                                                                             ccAGTTTTTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCG‑CTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTa  <  2:77676/151‑1 (MQ=255)                                                                                                                                             ccAGTTATTTTCCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCG‑CTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCt   <  1:204538/150‑1 (MQ=255)                                                                                                                                                        |                                                                                                                                             CGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTAT‑CCAA‑CGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCT‑GCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCG‑CTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTA  >  NC_000913/357733‑358019

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑