Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	357,875	0	A	T	40.6%	32.1 / 11.8	32	N272K (AAT→AAA)	cynR	transcriptional activator of cyn operon; autorepressor
Reads supporting (aligned to +/- strand):  ref base A (12/7);  new base T (0/13);  total (12/20)
Fisher's exact test for biased strand distribution p-value = 4.46e-04
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATG‑CCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAAC  >  NC_000913/357733‑358012                                                                                                                                                |                                                                                                                                           cGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATG‑CCTTCGCGGCGGCTGTCTGCCAGCTATTTTTccg                                                                                                                                    >  1:323772/1‑151 (MQ=255)       ccTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATG‑CCTTCGCGGCGGCTGTCTGCCAGCTATTTTTccgcc                                                                                                                                  >  1:33041/1‑147 (MQ=255)       ccTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATG‑CCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGca                                                                                                                               >  2:681491/1‑150 (MQ=255)             aaGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATG‑CCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACaaaa                                                                                                                         <  2:711508/150‑1 (MQ=255)             aaGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATG‑CCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAAc                                                                                                                        <  1:691605/151‑1 (MQ=255)                 gTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATG‑CCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAAccgcc                                                                                                                    <  2:178882/151‑1 (MQ=255)                     cgcATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTCCCGTGATTCATTTCCCCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATG‑CCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAAccgccg                                                                                                                   <  2:108882/148‑1 (MQ=255)                          cAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATG‑CCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTcc                                                                                                           >  1:606954/1‑151 (MQ=255)                               aaTTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATG‑CCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCagt                                                                                                        >  2:663866/1‑149 (MQ=255)                                 ttCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATG‑CCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTg                                                                                                    >  1:374290/1‑151 (MQ=255)                                    cAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCTGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAACG‑CCTTCGCGGCCGCTGGCTGCCAGCTATTTTTCCGCCGCAACAACACCGCCGTTCTCTCCagta                                                                                                       >  1:580728/1‑145 (MQ=255)                                       ccGCAGCCTTGTGCCAGCGCCTCCCGTGTTTCTTTCCCCCCACCACCCGCGCTTTTACCCAACCCCAGGTAAAAAAATG‑CCTCCGCGGGGGTTGTCTGCAGGTTTTTTTCCCCCCGAAAAAAAACCGCCGTTCTCTCCagtagt                                                                                                     <  1:196350/144‑1 (MQ=255)                                          cagccttgtgCCAGCGGCTCCCGTAATTCATTCCCGCCAACACCCGCCCTTTTACCAACCGCAATGTGAAAAAATC‑CTTCCGCGGGGGCTGTCTCCCAGTTTTTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCgggg                                                                                              <  2:472767/142‑1 (MQ=255)                                           aGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATG‑CCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCgggg                                                                                              >  1:354072/1‑147 (MQ=255)                                             ccttttgtCGGCGCCTCCCGTAATTCTTTCCCCCCACCACCCGCCCATTGTCCCAACGCCATGTACAAAATTG‑CCTCCGGGGGGGCTGTCCGCCAGCTTTTTTCCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGc                                                                                             <  2:267592/141‑1 (MQ=255)                                              ccTGTGTCAGCGGCTCCCTTGATTCTTTCCCGCCAACACCCGCGCATTTATCCAACGCCATGTGAAAAAATG‑CCTTCGCGGCGGCTGTCTGCCAGTTTTTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAgaga                                                                                       <  2:98725/151‑1 (MQ=255)                                                         ggCTACCGTAATTCTTTCCCGCAAACACCCGCGCATTTACCCACCCCCATGTGAAAAAATG‑CTTCCGCGGCGGCTGTCTGCCAGTTTTTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTa                                                                             <  2:440160/150‑1 (MQ=255)                                                               cGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATG‑CCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGCAGAGaaaaaaattttaaccc                                                                        >  2:574997/1‑136 (MQ=25)                                                                gTGATTCATTCCCCCCAACACCCGCCCATTTACCCACCGCCATGTGAAAAAATC‑CCTCGGCGGCGGTTGTCTGCCAGTTTTTTTTCCGCCGAAAAAAAGCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTc                                                                     <  2:649885/151‑1 (MQ=255)                                                                       aTTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATG‑CCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGAAGAGAAAAAACttttaaaccctcacg                                                                  >  2:794597/1‑135 (MQ=25)                                                                                     ccGCTCTTTTACCCACCCCCATGTGAAAAATTG‑CCTCCGCGGCGGTTTTCGGCCAGTTTTTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCgc                                                   <  1:52822/148‑1 (MQ=255)                                                                                     ccGCGCTTTTACCCAGCTCCATGTG‑AAAAATGCCCTTGGGGGCGGCTTTCTGCCAGTTTTTTTCCCGCCCCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAAt                                                      <  2:682217/145‑1 (MQ=255)                                                                                        cgcATTTACCCACCGCCATGTGCAAAAATG‑CCTTCGCGGCGGCTGTCTGCCAGTTTTTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCgctgct                                               <  2:437362/149‑1 (MQ=38)                                                                                                  cAACGCCATGTGCAAAAATG‑CCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGAAGAGAAAAAAAGTTAAACACTGCAAGTTGTGTGGGGAACGCTGCT‑ggggaaaa                                      >  1:326636/1‑141 (MQ=25)                                                                                                     ctccgcgaaaaaaagTC‑CCTTCGCGGTGGCTGCCTGCAGACAATTTCTCCCCCACAAAAAATCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGTAACAAtgt                                   <  1:665375/137‑1 (MQ=255)                                                                                                           gtaaaaaaaTC‑CCTCCGGGGCGGCGGTCGGCCAGTTATTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGTAACAATGTGGAAAGGGaa                         <  2:33037/147‑1 (MQ=255)                                                                                                               aaaaaTG‑CTTCCGCGGGGGTTGTCTGCCGGTTTTTTTTCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGTAACAATGTGGAAAGGGAAg                        <  2:789412/148‑1 (MQ=255)                                                                                                               aaaaaTG‑CCTCCGCGGGGCCTATTCGCCAGTTTTTTTCCCGCCACAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGTAACAATGTGGAAAGGGaa                         <  2:308253/147‑1 (MQ=255)                                                                                                                   aTG‑CCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGGAGAAAAAAAAAATTTAACCCCTCCTGTTTTGTTGGGATCCCTGCTGGGTAAAAAATGGGAAAGGGagggggggg                  >  2:115631/1‑143 (MQ=255)                                                                                                                              gggggtggccggCCAGTTTTTTTCCCCCCAAAAAAAACCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTcc       <  2:244612/140‑1 (MQ=255)                                                                                                                                          ccAGTTATTTTCCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGa    <  2:26946/142‑1 (MQ=255)                                                                                                                                             gCTTTTTTCCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAAc  <  2:529338/141‑1 (MQ=255)                                                                                                                                                |                                                                                                                                           CGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATG‑CCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAAC  >  NC_000913/357733‑358012

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑