Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	357,890	0	C	A	48.5%	20.8 / 16.7	33	L267F (TTG→TTT)	cynR	transcriptional activator of cyn operon; autorepressor
Reads supporting (aligned to +/- strand):  ref base C (11/6);  new base A (0/16);  total (11/22)
Fisher's exact test for biased strand distribution p-value = 8.65e-05
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATG‑CCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCGCCTCAA  >  NC_000913/357741‑358035                                                                                                                                                       |                                                                                                                                                  tGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATG‑CCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGcaac                                                                                                                                                   >  1:384996/1‑150 (MQ=255)  gATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATG‑CCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGcaaca                                                                                                                                                  >  2:676761/1‑150 (MQ=255)  gATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATG‑CCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGcaaca                                                                                                                                                  >  1:434143/1‑150 (MQ=255)   aTAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATG‑CCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGcaacaa                                                                                                                                                 >  1:255298/1‑150 (MQ=255)   aTAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATG‑CCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGcaaca                                                                                                                                                  >  2:1877/1‑149 (MQ=255)      aGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATG‑CCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAAcc                                                                                                                                             <  1:343001/151‑1 (MQ=255)                       aaTTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATG‑CCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCagt                                                                                                                              >  2:50921/1‑149 (MQ=255)                        aTTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATG‑CCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCagtagt                                                                                                                           >  1:758295/1‑151 (MQ=255)                         tcccgcccGCAGCCCTGTGTCGGCGGCTCCGGTGATTCATTCCCGCAAACACCCGCGCTTTTCCCAAACGCATTGTGAAAAAATC‑CCTTCGCGGCGGCTGTTTCCCAGTTTTTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCag                                                                                                                               <  2:787732/140‑1 (MQ=255)                          tCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATG‑CCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTgg                                                                                                                         >  1:70064/1‑151 (MQ=255)                           ccAGCCGAAGCCTTGTGTCAGCGGTTCCGGTGATTCTTTCCCCCCAACACCCGCGCATTTATCCAACGCCATGTGAAAAAATG‑CCTTCGCGGCGGCTGTCGGCCAGTTATTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTgg                                                                                                                         <  1:450224/150‑1 (MQ=255)                                cGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATG‑CCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCgggg                                                                                                                    >  2:893423/1‑150 (MQ=255)                                cGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATG‑CCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCgggg                                                                                                                    >  2:732024/1‑150 (MQ=255)                                         gtgtCAGCGGCTCCCGTGATTCTTTCCCGCAAACACCCGCGCTTTTATCCACCCCCATGTGAAAAAATG‑CCTTCGCGGCGGCTGTCTGCCAGTTTTTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGaa                                                                                                            <  1:265947/149‑1 (MQ=255)                                             cAGCGGCTACCGTGTTTCATTCCCCCAAACACCCGCGCATTTACCCACCCCCATGTGAAAAAATG‑CCTTCGCGGCGGCTGTCTGCCAGCTATTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGc                                                                                                       <  1:498824/150‑1 (MQ=255)                                                cggcccccGTGATTCATTCCCCCCAACACCGGCGCATTTACCCAACGCGTTGTACAAAAAGG‑CCTCCCCGGCGGCTGTCGGCCCGCTATTTTCCCGCCGCAAAAAATCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCt                                                                                                      <  1:118872/142‑1 (MQ=255)                                                  gCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATG‑CCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGGAGAGgaaaaaatttt                                                                                                   >  1:82505/1‑141 (MQ=25)                                                      ccGTGATTCATTCCCGCCAACACCCGCGCTTTTATCCACCGCCATGTGCAAAAATG‑CCTTCGCGGCGGCTGTCTGCCAGTTTTTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGcc                                                                                               <  1:703275/149‑1 (MQ=25)                                                                ttcccGCAAACACCCGCGCATTTACCCAACGCCATGTGAAAAAATG‑CCTTCGCGGCGGCTGTCTGCCAGCTATTTTCCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCAtgttgt                                                                                    <  1:682057/147‑1 (MQ=255)                                                                      ccAACACCCGCGCATTTACCCAACCCCATGTGCAAAAATG‑CCTTCGCGGCGGCTGTCTGCCAGTTTTTTTCCCGCCGAAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCa                                                                              <  1:898836/150‑1 (MQ=38)                                                                        aacaccCGCGCATTTCCCCACCCCAGTGTAAAAAAACC‑CCTTCGGGGGGGGTTTCTCCCAGTTTTTTCCCCGCCCAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCa                                                                              <  2:851032/148‑1 (MQ=255)                                                                        aacaccCGCCCATTTACCCACCCCCATGTGAAAAAATG‑CCTCCGCGGCGGTTGCCTGCCGGTTTTTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAAt                                                                            <  2:905195/150‑1 (MQ=255)                                                                                cgcTTTTACCCAACGCCATGTGAAAAAATG‑CCTCCGGGGCGGCTGTCGGCGAGTTATTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCgctgct                                                                     <  1:453934/149‑1 (MQ=255)                                                                                 gcATTTATCCAACGCCATGTGCAAAAATG‑CCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAAAAAAATTAAAACCCTCCTGTTGTGTggggagcg                                                                          >  1:205567/1‑137 (MQ=37)                                                                                             ccgccggtgCAAAAAAGCCCTCCGCGGCGGTTCTCTCCCGTTTATTTTTCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGa                                                       <  2:1813/145‑1 (MQ=255)                                                                                             cccctgggaaaaaaaTC‑CCTCGGGGGCGGTTGTCTCCCAGCTTTTTTCCCCCCGAAAAAAACCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGaa                                                      <  2:530813/141‑1 (MQ=255)                                                                                               ccATGTGCAAAAAGG‑CCTCCGCGGCGCTTGTCCGCCAGTTATTTTCCCGCGGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAg                                                    <  2:809501/151‑1 (MQ=255)                                                                                                    tgCAAAAATG‑CCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGAAAAGAAAAAGCTTTTTAACCGGCATGTTTTGTGGGGATAGCCGCTGGTTACaaagagg                                                        >  1:718992/1‑137 (MQ=255)                                                                                                       aaaaaTG‑CCTCCGCGGCGGCTGTCTGCCAGTTTTTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTg                                             <  1:153973/150‑1 (MQ=255)                                                                                                            tG‑CCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGCAGAAAAAAAAGCTTAAGACCCCCATTTTGTGTGGGGATCGCTGCTGGGATAAAAATGGGAAGGGGAGGgcggggg                                       >  2:613385/1‑148 (MQ=255)                                                                                                              cccTCCGCGGCGGTTTTCTCCCAGTTTTTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGa                                       <  2:170183/149‑1 (MQ=255)                                                                                                                 ttCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGAAGAGAAAAAAATTTTAACCCCTCCTGTTGTGTGGGGATCGCTGCTGGGTAAAAAGTGGGAAGGGGAggggggggg                                       >  1:459059/1‑139 (MQ=255)                                                                                                                      gggggttGTCTGCCAGTTTTTTTCCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCt                                <  1:357163/143‑1 (MQ=255)                                                                                                                               cgccaagtttttttcCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGa                           <  2:918193/135‑1 (MQ=255)                                                                                                                                tGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGAAGAGAAAAAACTTTTAACCCCTCCTGTTTTGTGGGGATCGCCGCTGGGAACAAAGTGGGAAAGGGAGGGCGGGGGGTCAACTCCCGaa                          >  1:376625/1‑145 (MQ=255)                                                                                                                                         ttttcCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAAt                <  1:50925/146‑1 (MQ=255)                                                                                                                                           tttCCCCCGAAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGtt          <  2:553515/150‑1 (MQ=255)                                                                                                                                                 ccgaAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCGcc      <  1:345064/148‑1 (MQ=255)                                                                                                                                                    caaaaaAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCGCCTCaa  <  2:727934/149‑1 (MQ=255)                                                                                                                                                       |                                                                                                                                                  TGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATG‑CCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCGCCTCAA  >  NC_000913/357741‑358035

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑