Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	357,890	0	C	A	48.8%	18.1 / 27.4	41	L267F (TTG→TTT)	cynR	transcriptional activator of cyn operon; autorepressor
Reads supporting (aligned to +/- strand):  ref base C (17/4);  new base A (0/20);  total (17/24)
Fisher's exact test for biased strand distribution p-value = 4.70e-08
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.30e-01

AAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCC‑AACAACCGCGC‑ATTTATCCAACGCCATGTGCAAAAA‑TG‑CC‑TT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGG‑GGCAAGA‑GAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCGCCTC  >  NC_000913/357745‑358033                                                                                                                                                        |                                                                                                                                                  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)                                                                                                                                                   cacaaaaaAACCGCCGTTCTCTCCAGTAGTGGCGG‑GGCAAGA‑GAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCGCCTc  <  2:698488/147‑1 (MQ=255)                                                                                                                                                        |                                                                                                                                                  AAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCC‑AACAACCGCGC‑ATTTATCCAACGCCATGTGCAAAAA‑TG‑CC‑TT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGG‑GGCAAGA‑GAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCGCCTC  >  NC_000913/357745‑358033

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: ‑