Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	357,880	0	T	C	46.3%	39.3 / 18.2	41	K271E (AAA→GAA)	cynR	transcriptional activator of cyn operon; autorepressor
Reads supporting (aligned to +/- strand):  ref base T (19/3);  new base C (0/19);  total (19/22)
Fisher's exact test for biased strand distribution p-value = 8.01e-09
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCC‑AACAACCGCGC‑ATTTATCCAACGCCATGTGCAAAAA‑TG‑CC‑TT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGG‑GGCAAGA‑GAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTG  >  NC_000913/357733‑358023                                                                                                                                                          |                                                                                                                                                  cGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCC‑AACAACCGCGC‑ATTTATCCAACGCCATGTGCAAAAA‑TG‑CC‑TT‑CGCGGCGGCTGTCTGCCAGCTATTTTTcc                                                                                                                                                 <  2:437353/150‑1 (MQ=255)  gTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCC‑AACAACCGCGC‑ATTTATCCAACGCCATGTGCAAAAA‑TG‑CC‑TT‑CGCGGCGGCTGTCTGCCAGCTATTTTTccgc                                                                                                                                               >  1:375350/1‑151 (MQ=255)     ggCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCC‑AACAACCGCGC‑ATTTATCCAACGCCATGTGCAAAAA‑TG‑CC‑TT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCcgccgc                                                                                                                                            >  2:605177/1‑151 (MQ=255)             aaGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCC‑AACAACCGCGC‑ATTTATCCAACGCCATGTGCAAAAA‑TG‑CC‑TT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACaaaa                                                                                                                                     <  1:761712/150‑1 (MQ=255)             aaGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCC‑AACAACCGCGC‑ATTTACCCAACGCCATGTGCAAAAA‑TG‑CC‑TT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACaaaa                                                                                                                                     >  2:59017/1‑150 (MQ=255)                  tAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCC‑AACCACCGCGC‑ATTTATCCAACGCCATGTGCAAAAA‑TG‑CC‑TT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACCAAAccgccg                                                                                                                               >  2:94287/1‑151 (MQ=255)                   aGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCC‑AACAACCGCGC‑ATTTATCCAACGCCATGTGCAAAGA‑TG‑CC‑TT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGt                                                                                                                              >  1:26615/1‑151 (MQ=255)                   aGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCC‑AACAACCGCGC‑ATTTATCCAACGCCATGTGCAAAAA‑TG‑CC‑TT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGt                                                                                                                              >  1:260633/1‑151 (MQ=255)                        aTCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCC‑AACAACCGCGC‑ATTTATCCAACGCCATGTGCAAAAA‑TG‑CC‑TT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTtctct                                                                                                                         >  1:196590/1‑151 (MQ=255)                        aTCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCC‑AACAACCGCGC‑ATTTATCCAACGCCATGTGCAAAAA‑TG‑CC‑TT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTtctc                                                                                                                          >  2:388186/1‑150 (MQ=255)                                       ccgcagtctttttgcAGGGGCTCCTGTGTTTCATCCCCCCC‑ACCACCCGCGT‑TTTCCCCCAACGCCTTGTGCAAAAA‑GC‑CC‑TG‑CGGGGCGGCTTTCTCCCTGTTATTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCgg‑g                                                                                                          <  2:215064/136‑1 (MQ=255)                                       ccGCAGCCCTGTGTCCGCGCCTCCGGTG‑TTTATTTCCCCCAAACACCCCCGC‑ATTAACCCACCCCCTTGGAAAAAAA‑TC‑CC‑TT‑CGCGGCGCCTGTCGGCGAGTTTTTTTCCCGCCCCAAAAAGACCGCCGTTCTCTCCAGTAGTGGCgg‑gg                                                                                                         <  2:296849/151‑1 (MQ=255)                                       ccGCAGACCTGTGTAAGCGCCTCCCGTTATTCTTTCCCCCA‑AACACCCGCGC‑TTTTACCCAACGCCATGTGCAAAAA‑TG‑CC‑TC‑CGGGGCGGCTGTCTCCCAGCTTTTTTCCCCCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCgg‑g                                                                                                          <  1:1022243/150‑1 (MQ=21)                                        cGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCC‑AACAACCGCGC‑ATTTATCCAACGCCATGTGCAAAAA‑TG‑CC‑TT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCgg‑ggg                                                                                                        >  1:735118/1‑150 (MQ=255)                                          cAGACCTGGGTCAGCGGCTACCGTGATTCATTTCCGCC‑AACAACCGCGC‑ATTTATCCAACGCCATGTGCAAAAT‑TG‑CC‑TT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCgg‑ggg                                                                                                        >  2:145922/1‑148 (MQ=255)                                           agccttgtgCCAGGGTCTCCCGTGATCCATTCCCCCA‑AAAAACCGCCC‑TTTTACCAAGCGCTATGCGAAAAAA‑CC‑CC‑TT‑GGGGGGGGTTGTCTCCCGGTTATTTTTCGCCCGCAAAAAAACCGCCGTTCTCTCCagtagt                                                                                                                 <  1:937300/135‑1 (MQ=255)                                           aGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCC‑AACAACCGCGC‑ATTTATCCAACGCCATGTGCAAAAA‑TG‑CC‑TT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCgg‑gggg                                                                                                       >  2:695605/1‑147 (MQ=255)                                             aCCTGTGTCAGCGGCTACCGTGATTCATTTCCGCC‑AACAACCGCGC‑ATTTATCCAACGCCATGTGCAAAAA‑TG‑CC‑TT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCggcggc                                                                                                        >  2:844196/1‑143 (MQ=255)                                             aCCTGTGTCAGCGGCTACCGTGATTCATTTCCGCC‑AACAACCGCGC‑ATTTATCCAACGCCATGTGCAAAAA‑TG‑CC‑TT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCgg‑gg                                                                                                         >  2:1041627/1‑145 (MQ=255)                                                      ggcggttaccaataTTCATTTCCACA‑AACCCCCGCCC‑TTTTATCCACCGCAGTGTCCAAAAA‑GC‑CC‑TT‑GGGGGGGGCTGCCGGCAATTTTTTTCCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGACGG‑GGCAAGA‑GAAATAGCt                                                                                          <  1:43143/137‑1 (MQ=255)                                                       gCGGCTACCGTGATTCATTTCCGCC‑AACAACCGCGC‑ATTTATCCAACGCCATGTGCAAAAA‑TG‑CC‑TT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGG‑GGGGAGA‑GGAAAAGcagt                                                                                        >  1:368400/1‑148 (MQ=255)                                                          gCTACCGTGTTTCATTCCCCCA‑AACACCCGCCC‑TTTTACCCACCGCTATGTGAAAAAA‑TG‑CT‑TT‑CGGGGCGGCTTTCTGCCAGTTATTTTCCCGCCAAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGG‑GGCAAGA‑GAAATAGCttt                                                                                        <  1:382289/148‑1 (MQ=255)                                                          gCTACCGTGATTCATTTCCGCC‑AACAACCGCGC‑ATTTATCCAACGCCATGTGCAAAAA‑TG‑CC‑TT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGCGGCAGGG‑GAACAAGCTTTat                                                                                      >  1:469690/1‑150 (MQ=25)                                                                gTGATT‑ATTTCCCGC‑AACCACC‑CGCTATTTTTCCAACCCCTTTTAAAAAAATTC‑CC‑TG‑CGCGGCGGTTTTCTGCAAGCTATTTTCCCCCCGCAAAAAACCCGCCGTTCTCTCCAGTAGTGGCGG‑GGCAAGA‑GAAATAGCTTTAAGc                                                                                    <  1:767837/146‑1 (MQ=255)                                                                 tGATTCATTTCCGCC‑AACAACCGCGC‑ATTTATCCAACGCCATGTGCAAAAA‑TG‑CC‑TT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGG‑GGGGAGG‑Gaaaaaaattttaaacc                                                                                  >  1:556809/1‑134 (MQ=25)                                                                    ttCTTTCCCGCA‑AACACCCGCGC‑TTTTACCCAACCCCATGTGAAAAAA‑TC‑CT‑TT‑CGGGGGGGCTTTCTGCCAGTTTTTTTCCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGG‑GGCAAGA‑GAAATAGCTTTAAGCCCGTCAtg                                                                            <  1:759317/150‑1 (MQ=255)                                                                         ttcccccaaacaccCGCCC‑TTTTACCCAACCCCTTTTGCAAAAA‑TC‑CC‑TC‑CCCGGCGGTTGTCTGCCATTTTTTTTCCCCCCCAAACAAACCCGCCGTTCTCTCCAGTAGTGGCGG‑GGCAAGA‑GAAATAGCTTTAAGCCCGTCAtgttgt                                                                        <  1:616662/142‑1 (MQ=255)                                                                           ccGCA‑AACAACCCCCT‑TTTTACCCACCTCCGTGAACAAAAA‑TG‑CC‑TT‑CGCGGCGGCTGTCTCCCATTTTTTTTCCCGCCCAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGG‑GGCAAGA‑GAAATAGCTTTAAGCCCGTCAtgtt                                                                          <  2:446898/145‑1 (MQ=255)                                                                               c‑aacaaCCGCGC‑ATTTATCCAACGCCATGTGCAAAAA‑TG‑CC‑TT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGG‑GGGCAAA‑Gaaaaaaattttattcc                                                                                  >  1:303013/1‑120 (MQ=25)                                                                                     cccGCGC‑TTTTACCCACCCCCATG‑GCAAAAAGTC‑CC‑TC‑CGGGGCGGCTGTCTGCCAGCTTTTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGG‑GGCAAGA‑GAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCgctg                                                           <  1:1048935/150‑1 (MQ=255)                                                                                     acCGCGC‑ATTTATCCAACGCCATGTGCAAAAA‑TG‑CC‑TT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGG‑GGGGAGA‑GAAAAAAATTTAAACCCCTCCTGTTGTGTggggaac                                                               >  1:493312/1‑142 (MQ=37)                                                                                              tttATCCAACGCCATGTGCAAAAA‑TG‑CC‑TT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGG‑GGCAGGAGGAAAAAACTTTagcaccccatgt                                                                            >  2:1049924/1‑116 (MQ=25)                                                                                              tttACCCACCGCTATGTAAAAAAA‑TG‑CT‑TT‑CGGGGGGGCTGTCTGCCAGTTTTTTTCCCGCCAAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGG‑GGCAAGA‑GAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGt                                                      <  1:220587/148‑1 (MQ=255)                                                                                                   ccAACGCCATTTACAAAAA‑TG‑CC‑TC‑CGCGGCGGCTGTCTGCCGTCTTTTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGG‑GGCAAGA‑GAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAAtgt                                              <  1:219812/151‑1 (MQ=255)                                                                                                    ccccccccatgccAAAAA‑TT‑CCTTT‑CGCGGCGTCTGTCTGCCAGTTTTGTCCCCGCGACAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGG‑GGCAAGA‑GAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAAtg                                               <  2:423331/138‑1 (MQ=255)                                                                                                       cGCCATGTGAAAAAA‑TG‑CC‑TC‑CGGGGCGGCTGTCTGCCAGTTTTTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGG‑GGCAAGA‑GAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGa                                           <  1:1038373/150‑1 (MQ=255)                                                                                                       cGCCATGT‑CAAAAA‑GT‑CC‑TTCCGCGGCGGCTGTCTGCCATTTTTTTTCCCCCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGG‑GGCAAGA‑GAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAAtgt                                              <  2:967878/147‑1 (MQ=255)                                                                                                        cgctatgtaaaaaa‑TGCCC‑TG‑CGCGGCGGCTGTCTCCAAGCTTTTTTCCCCCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGG‑GGCAAGA‑GAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTgg                                            <  1:905624/140‑1 (MQ=255)                                                                                                                     attG‑CC‑TC‑CGGGGCGGCTGTCCGCCACTTTTTTTCCCGCCACAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGG‑GGCAAGA‑GAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTgcggc                             <  1:640494/149‑1 (MQ=255)                                                                                                                        agtggccccggggcgtcTGTCTGCCTGCTTTTTTCCCCCCGAAACAAAACCGCCGTTCTCTCCAGTAGTGGCGG‑GGCAAGA‑GAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTgcggc                             <  2:189638/140‑1 (MQ=255)                                                                                                                                    ggggcgttctcCCAGTTTTTTCCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGG‑GGCAAGA‑GAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCa                       <  1:670692/138‑1 (MQ=255)                                                                                                                                                 agtttttttcCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGG‑GGCAAGA‑GAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAAt    <  1:605383/146‑1 (MQ=255)                                                                                                                                                    ttttttcCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGG‑GGCAAGA‑GAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTg  <  1:460503/148‑1 (MQ=255)                                                                                                                                                      ttttcCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGG‑GGCAAGA‑GAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAAcc            <  1:603066/138‑1 (MQ=255)                                                                                                                                                          |                                                                                                                                                  CGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCC‑AACAACCGCGC‑ATTTATCCAACGCCATGTGCAAAAA‑TG‑CC‑TT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGG‑GGCAAGA‑GAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTG  >  NC_000913/357733‑358023

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑