Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	357,880	0	T	C	48.9%	47.3 / 15.2	45	K271E (AAA→GAA)	cynR	transcriptional activator of cyn operon; autorepressor
Reads supporting (aligned to +/- strand):  ref base T (17/6);  new base C (0/22);  total (17/28)
Fisher's exact test for biased strand distribution p-value = 1.15e-07
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCAT‑GTGCAAAAATG‑CCTTCGCGGCGGCTGT‑CTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATT  >  NC_000913/357734‑358022                                                                                                                                                      |                                                                                                                                               gTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCAT‑GTGCAAAAATG‑CCTTCGCGGCGGCTGT‑CTGCCAGCTATTTTTccgc                                                                                                                                            <  2:1002818/151‑1 (MQ=255)             aGCGTACCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCAT‑GTGCAAAAATG‑CCTTCGCGGCGGCTGT‑CTGCCAGCTATTTTTCCGCCGCAACaaaa                                                                                                                                  <  2:1058707/149‑1 (MQ=255)              gCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCAT‑GTGCAAAAATG‑CCTTCGCGGCGGCTGT‑CTGCCAGCTATTTTTCCGCCGCAACAAAAcc                                                                                                                                <  2:954826/150‑1 (MQ=255)               cGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCAT‑GTGCAAAAATG‑CCTTCGCGGCGGCTGT‑CTGCCAGCTATTTTTCCGCCGCAACAAAAccg                                                                                                                               <  1:161081/150‑1 (MQ=255)                    cgcATCAGGCCATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCAT‑GTGCAAAAATG‑CCTTCGCGGCGGCTGC‑CTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGtt                                                                                                                          >  2:196202/1‑150 (MQ=255)                    cgcATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCAT‑GTGCAAAAATG‑CCTTCGCGGCGGCTGT‑CTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTtc                                                                                                                         >  2:757402/1‑151 (MQ=255)                    cgcACCAGCCATTCCCACCCGCAGCCCTGTGTCAGCGGCTACGGTAATTCATTCCCGCCAACACCCGCGCTTTTCTCCACCGCCAT‑GTGCAAAAATG‑CCTCCGCGGGGGCTGT‑CTGCCATCTATTTTCCCCCCGCACCAAAAccgccg                                                                                                                            <  2:24159/148‑1 (MQ=12)                      cATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCAT‑GTGCAAAAATG‑CCTTCGCGGCGGCTGT‑CTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTtctc                                                                                                                       >  2:453941/1‑151 (MQ=255)                         cAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCAT‑GTGCAAAAATG‑CCTTCGCGGCGGCTGT‑CTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTcc                                                                                                                    >  2:268543/1‑151 (MQ=255)                         cAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCAT‑GTGCAAAAATG‑CCTTCGCGGCGGCTGT‑CTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTcc                                                                                                                    >  2:315209/1‑151 (MQ=255)                          aGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCAT‑GTGCAAAAATG‑CCTTCGCGGCGGCTGT‑CTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTcc                                                                                                                    >  2:39356/1‑150 (MQ=255)                              aaTTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCAT‑GTGCAAAAATG‑CCTTCGCGGCGGCTGT‑CTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCagt                                                                                                                 >  1:744556/1‑149 (MQ=255)                              aaTTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCAT‑GTGCAAAAATG‑CCTTCGCGGCGGCTGT‑CTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCagt                                                                                                                 >  2:63987/1‑149 (MQ=255)                              aaTTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCAT‑GTGCAAAAATG‑CCTTCGCGGCGGCTGT‑CTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCagt                                                                                                                 >  2:563277/1‑149 (MQ=255)                              aaTTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCAT‑GTGCAAAAATG‑CCTTCGCGGCGGCTGT‑CTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCa                                                                                                                   >  2:1035668/1‑147 (MQ=255)                                 cccACCCGCAGACCTGTGCCGGCGCCTCCGGTGATTCTTTCCCGCAACCACCCGCGCATTTACCCACCGCCAT‑GTGAAAAAATC‑CCTCCGCGGCGGCTTT‑CTCCCAGTTTTTTTCCCCCCGCAAAAAAACCGCCGTTCTCTCCagtagt                                                                                                              <  2:761588/148‑1 (MQ=255)                                  ccAGCCGCAGCCCTGTGTCGGCGGCTCCCGTGATTCATTCCCCCCAACACCCGCGCATTTATCCACCCCCAT‑GTGCAAAAATG‑CCTTCGCGGCGGCTGT‑CTGCCAGCTATTTTTCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGc                                                                                                           <  1:596365/151‑1 (MQ=255)                                  ccACCCGCGGATCGGTGCCAGCGCCTCCCGTTTTTCTTCCCCGCCAACACCCGCGCATTTA‑CCCACCCCATGGTGAAAAAATG‑CCTCCGCGGCGGCTGC‑CGGCCAGTTTTTTTCCCGCCCCAACAAAACCGCCGTTCTCTCCAGTAGTgg                                                                                                            <  2:369629/150‑1 (MQ=255)                                    aGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCAT‑GTGCAAAAATG‑CCTTCGCGGCGGCTGT‑CTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCgg                                                                                                         >  1:1016234/1‑151 (MQ=255)                                      ccgcggccttgtgTCGGCGGCACCGGTGATTCTTCCCCCCCAACACCCGCCTTTTTACCCACCCCCAT‑GTAAAAAATTG‑CCTGCGGGGCGGCTGT‑CTGCCAGTTTTTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCgg                                                                                                         <  2:838282/140‑1 (MQ=255)                                      ccGAAGCCCTGGTTCGGCGCCTCCCGTGTTTCTTTCCCCCAAACACCCGCGCTTTTACCAACCGCCTT‑GTGAAAAAATG‑CTTCCGCGGCGGCTGT‑CGGCCAGTTTTTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCgggg                                                                                                       <  2:245426/151‑1 (MQ=255)                                       cGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCAT‑GTGCAAAAATG‑CCTTCGCGGCGGCTGT‑CTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCgg                                                                                                         >  2:348229/1‑148 (MQ=255)                                                 tgtCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCAT‑GTGCAAAAATG‑CCTTCGCGGCGGCTGT‑CTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGGAGAGgaaa                                                                                             >  1:914991/1‑149 (MQ=255)                                                   tCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCAT‑GTGCAAAAATG‑CCTTCGCGGCGGCTGT‑CTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGgaaagaaaa                                                                                             >  1:980809/1‑147 (MQ=255)                                                    cggggcctccggTGCTTCTTTTCCCCAAAAACCCGCGCTTTTACCCACCCCATT‑GTGAAAAAATC‑CCTTCGGGGCGTTTTT‑CTGCCAGCTTTTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGaa                                                                                               <  1:967285/134‑1 (MQ=255)                                                        gcctcccGTGATTCTTTCCCCCCAAC‑ACCCCCCATTTAACCAACCCCCTGGTCAAAAAATC‑CCTCCGCGGCGGCTTT‑CTGCCAGCTTTTTTCCCCCCCCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGc                                                                                                      <  2:1010604/129‑1 (MQ=255)                                                          cTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCAT‑GTGCAAAAATG‑CCTTCGCGGCGGCTGT‑CTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGGAGGGaaaaaaattt                                                                                       >  1:383234/1‑140 (MQ=25)                                                           tACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCAT‑GTGCAAAAATG‑CCTTCGCGGCGGCTGT‑CTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGGTGAGaaaaaaattttatac                                                                                  >  1:1076355/1‑139 (MQ=25)                                                             ccGTGATTCATTCCCCCAAACACCCGCGCTTTTACCCACCCCAAT‑GTGAAAAAATG‑CCTCCGGGGCGGCTGT‑CGGCCAGCTTTTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCg                                                                                <  1:172326/151‑1 (MQ=255)                                                              cGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCAT‑GTGCAAAAATG‑CCTTCGCGGCGGCTGT‑CTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGgaaagaaaaaaaattaaaac                                                                                  >  1:731231/1‑136 (MQ=25)                                                                tGATCCTTTCCCCCCAACACCCGCGCTTTTACCCAACCCCAT‑GTGAAAAAATG‑CCTTCGGGGCGGCTGT‑CTCCCAGCTATTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGc                                                                                   <  1:91301/145‑1 (MQ=255)                                                                   ttCATTCCCGCAAACACCCGCGCTTTTACCCACCGCCAT‑GTGAAAAAATG‑CCTTCGCGGCGG‑TGTCCTGCCATTTATTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTc                                                                              <  1:667011/147‑1 (MQ=255)                                                                         cccGCCACCACCCCCGCTTTTACCCACCCCCTG‑GTCAAAAAAGC‑CCTCCGCGGCGCCTTT‑CGGCCAGTTTTTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTtgtgtg                                                                    <  2:972405/150‑1 (MQ=255)                                                                                   cccGCGCATTTACCCACCGCCAT‑GTGAAAAAGTC‑CTCGCGGGGGGCCTGC‑CGGCGAGCTATTCGCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCgctg                                                          <  2:488842/150‑1 (MQ=255)                                                                                   cccGCGCATTTACCCAACCCCTT‑GTAAAAAAATG‑CCTTCGGGGCGGCTGT‑CTGCCAGTTTTTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCgctg                                                          <  2:158083/150‑1 (MQ=255)                                                                                           ttaacccACCGCCAT‑GGGAAAAAAGC‑CCTTCGGGGGGGTTTT‑CTGCCAGCTTTTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTaa                                                   <  1:966086/145‑1 (MQ=255)                                                                                                ccACCGCCAT‑GTGAAAAAATG‑CCTTCGCGGCGGTTGT‑CTGCCAGTTATTTTCCCCCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACaa                                                <  1:882535/148‑1 (MQ=255)                                                                                                    accccctttgCAAAAAAGCCCTCCGCGGCGCTTTT‑CTGCCGGTTTTTTTCCCGCCCAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAAtgtg                                            <  2:402448/142‑1 (MQ=255)                                                                                                       ctatgtaaaaaaaGC‑CCTCCGGGGGGGCTTT‑CTGCAGGTTTTTTTCCCGCCGAAAAAAAGCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTgg                                           <  2:786762/139‑1 (MQ=255)                                                                                                           gtgAAAAAATG‑CCTCCGGGGCGGCTGC‑CTGCCATTTTTTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGa                                    <  1:54851/150‑1 (MQ=255)                                                                                                           gacaaaaaaTG‑CGTCCGCGGCGCCTGT‑CCCCCCGTTCTTCTCCCGCCGCACAAAGCCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGaga                                        <  2:785034/142‑3 (MQ=255)                                                                                                               aaaaaTC‑CCTCGGCGGCGGTTGC‑CGGCAAGTTTTTTTCCCGCCAAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGa                                    <  2:269910/146‑1 (MQ=255)                                                                                                                            gcggcgGCTGT‑CGGCCAGCTTTTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCa                      <  1:101486/148‑1 (MQ=255)                                                                                                                              ggcggtTGT‑CTGCCATTTTTTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAg                     <  1:565812/147‑1 (MQ=255)                                                                                                                              ggcggcTGT‑CGGCCGGTTATTTTCCCGCCAAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTcc                 <  2:818917/151‑1 (MQ=255)                                                                                                                                      gtcggcgactttttttcCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAg               <  2:58474/134‑1 (MQ=255)                                                                                                                                                  ttttcCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAAt   <  1:31104/146‑1 (MQ=255)                                                                                                                                                  ttttcCCCCCCCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAAtt  <  1:257003/147‑1 (MQ=255)                                                                                                                                                      |                                                                                                                                               GTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCAT‑GTGCAAAAATG‑CCTTCGCGGCGGCTGT‑CTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATT  >  NC_000913/357734‑358022

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: ‑