Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	357,890	0	C	A	47.8%	37.9 / 30.7	46	L267F (TTG→TTT)	cynR	transcriptional activator of cyn operon; autorepressor
Reads supporting (aligned to +/- strand):  ref base C (15/9);  new base A (0/22);  total (15/31)
Fisher's exact test for biased strand distribution p-value = 2.89e-06
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTAT‑CCAA‑CGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCT‑GCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCG‑CTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCG  >  NC_000913/357742‑358029                                                                                                                                                         |                                                                                                                                             gATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTAT‑CCAA‑CGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCT‑GCCAGCTATTTTTCCGCCGcaacaa                                                                                                                                            <  1:602581/151‑1 (MQ=255)  aTAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTAT‑CCAA‑CGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCT‑GCCAGCTATTTTTCCGCCGcaacaa                                                                                                                                            >  2:135003/1‑150 (MQ=255)          aGCGAATCGGTCATTCCCAGCCACACACATGTCTCGGCGGCTACCTTGATTCATTCCCGCCAACACCCGCGCATTTTC‑CCAA‑CGCCATGTGCAAAAATGCTTT‑CGCGGCGGCTGTCT‑GCCAGCTATTTTCCCGCCGCAAAAAAAccgccg                                                                                                                                    <  2:196032/150‑1 (MQ=17)           gcgcATCAGGAAATTCCAGCCGCAGACCTGTGTCAGCGGCTCCCGTGATTCATTCCCGCCAACAACCGCGCATTTAC‑CCAA‑CGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCT‑GCCAGTTATTTTTCCGCCGCAACAAAAccgccg                                                                                                                                    <  1:842782/149‑1 (MQ=255)            cgcATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACTGTGATTCATTTCCGCCAACAACCGCGCATTTAT‑CCAA‑CGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCT‑GCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTtc                                                                                                                                 >  1:196317/1‑151 (MQ=255)            cgcATCAGGAAATTCCAGCCGCAGACCTGTGTCAGCGGCTCCCGTGATTCATTCCCGCCAACAACCGCGCATTTAT‑CCAA‑CGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCT‑GCCAGCTATTTTTCCGCCGCAACAAAAccgccg                                                                                                                                    <  1:209318/148‑1 (MQ=255)             gcATCAGGCATTTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTCCCGCCAACAACCGCGCATTTAC‑CCAA‑CGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCT‑GCCAGCTATTTTTCCGCCGCAAC‑AAACCGCCGTtct                                                                                                                                <  1:978990/150‑1 (MQ=255)                      aaTTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTAT‑CCAA‑CGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCT‑GCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCagt                                                                                                                         >  1:978624/1‑149 (MQ=255)                      aaTTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTAT‑CCAA‑CGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCT‑GCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCagt                                                                                                                         >  2:213567/1‑149 (MQ=255)                      aaTTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTAT‑CCAA‑CGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCT‑GCCAGCGATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCag                                                                                                                          >  2:506247/1‑148 (MQ=255)                       aTTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTAT‑CCAA‑CGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCT‑GCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCagtagt                                                                                                                      >  2:743260/1‑151 (MQ=255)                       aTTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTAT‑CCAA‑CGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCT‑GCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCagtag                                                                                                                       >  1:22861/1‑150 (MQ=255)                        ttCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTAT‑CCAA‑CGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCT‑GCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTg                                                                                                                     >  2:849391/1‑151 (MQ=255)                            aGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTAT‑CCAA‑CGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCT‑GCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCgg                                                                                                                 >  2:588693/1‑151 (MQ=255)                              ccgcggttttgtgTCGGCGGCTCCCGTGATTCATCCCCCCCAACACCCGCGCATTCCC‑CCAC‑CGCCATGTGAAAAAATGCCTC‑CGCGGGGGCTGTCT‑GCCAGTTATTTTTCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCggg                                                                                                                <  1:427178/141‑1 (MQ=255)                                 cAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTAT‑CCAA‑CGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCT‑GCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCgggg                                                                                                               >  2:870887/1‑148 (MQ=255)                                  aGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTAT‑CCAA‑CGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCT‑GCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCCGTAGTGGCggtgg                                                                                                              >  2:153824/1‑145 (MQ=255)                                   gccttgtaacgggggCTCCGGTGATACATTCCCGCCAACACCCGCGTTTTTAT‑CCAA‑CGCTGTGTGAAAAATTGCCTT‑CGGGGGGGGTTTCT‑GCCAGTTATTTTCCCCCCGCAAAAAAGCCGCCGTTCTCTCCAGTAGTGGCGGGGCAag                                                                                                           <  1:315808/137‑1 (MQ=255)                                     cttgtgCCGGCGCCTCCGGTGATTCTTTCCCCCCAACACCCGCGCTTTTAC‑CCAC‑CGCCTTGTGAAAAATCCCCTT‑CGGGGCGGTTGTCG‑GCCCGTTTTTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAagag                                                                                                         <  2:738165/148‑1 (MQ=255)                                          gtCGGCGGCTCCCGTGATTCTTTCCCCCCAACACCCGCCCTTTTAC‑CCAC‑CCCCATGTGCAAAAATGCCTT‑CGGGGCGGCTGTCT‑GCCAGTTTTTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATa                                                                                                    <  1:846329/150‑1 (MQ=255)                                              ggggCTCCCGTGTTTCTTTCCCCCAAACACCCGCGCATTTAC‑CCAC‑CGCCATGTGAAAAAATGCTTC‑CGGGGCGGCTGTCG‑GCCAGCTTTTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAgaga                                                                                                        <  1:730675/140‑1 (MQ=255)                                              gCGGCTCCCGTGTTTCTTTCCCGCCAACACCCGCGCTTTTAC‑CCAC‑CCCCATGTGAAAAAATCCCTC‑CGCGGCGGCTGTCT‑GCCAGCTTTTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAg                                                                                                   <  1:979285/147‑1 (MQ=255)                                                ggCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTAT‑CCAA‑CGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCT‑GCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCgggggcatggaaaaaa                                                                                                   >  2:709588/1‑133 (MQ=255)                                                   tACCGTGATTCATTTCCGCCAACAACCGCGCATTTAT‑CCAA‑CGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCT‑GCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGAATAGAAATaaaatttaagc                                                                                          >  1:822339/1‑141 (MQ=255)                                                     ccGTGTTTCATTCCCCCCAAAACCCGCGCTTTTCC‑CAAC‑CCCCATGTCAAAAAATCCCTC‑CGGGGGGGCTGTCT‑GCCAGTTTTTTTCCCGCCAAAAAAAACCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCt                                                                                                 <  2:874362/142‑1 (MQ=255)                                                                 cccGCCAACACCCGCGTATTTAT‑CCAC‑CGCCATGTGCAAAAATGCTTT‑CGGGGCGGCTGTCG‑GCCAGCTTTTTTCCCGCCGCAACAAAGCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTtgtgtg                                                                            <  1:329218/150‑1 (MQ=255)                                                                  ccGCAAACACCCGCCCTTTTAT‑CCAC‑CCCAGTGTAAAAAATTCCCTG‑CGGGGCGGCTGTCT‑CCCGGTTTTTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTtgtgtg                                                                            <  1:71023/150‑1 (MQ=255)                                                                    ccccaaaaaaccgcATTTTTACCAACCGCCATGTCAAAAATTCCCTT‑CGGGGCGGCTTTCT‑CCCAGTTTTTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTtgtgt                                                                             <  1:555876/138‑1 (MQ=255)                                                                                   tttAC‑CCAC‑CGCCATGTGAAAAAATCCCTC‑CGCGGCGGCTGTCT‑GCCAGTTTTTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCG‑CTGCTGGt                                                            <  1:173426/148‑1 (MQ=255)                                                                                    ttAT‑CCAA‑CGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCT‑GCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCGAGAGAAAAAAATTTAAAACCGTCCTGTTGTGTgggga                                                                        >  1:26017/1‑133 (MQ=37)                                                                                         ccAC‑CGCCATGTGAAAAAATGCCTC‑CGCGGCGGCTGTCT‑GCCAGCTATTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCG‑CTGCTGGTAACa                                                        <  1:83898/147‑1 (MQ=255)                                                                                                    gccaaaaaaGCCCTC‑CGCGGGGGCTGGCT‑GCCGGTTTTTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCG‑CTGCTGGTAACAATGTGGAAAGGGa                                           <  2:850671/146‑1 (MQ=255)                                                                                                    ataaaaaaaTCCTTC‑CGCGCCTGCTCCCT‑CCCATTTATTTTTCCCCCGAAAAAAACCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCG‑CTGCTGGTAACAATGTGGaaa                                               <  2:36207/142‑1 (MQ=255)                                                                                                       aaaaaaGGCCTC‑CGGGGCGGCTGCCT‑GCCAGTTTTTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCG‑CTGCTGGTAACAATGTGGAAAGGGAAg                                         <  1:538701/148‑1 (MQ=255)                                                                                                         aaaaTGCCTT‑CGCGGCGGCTGTCT‑GCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGCGCCAGGGAAAAAGAATTAAAACCCTTCTGTTTTTTGGGGATAGCCTCCGGGGAACAAGGGGGAAAGGGaaaggg                                      >  2:531136/1‑147 (MQ=255)                                                                                                         aaaaTCCCTT‑CGGGGCGGCTGTCT‑GCCCGTTTTTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCG‑CTGCTGGTAACAATGTGGAAAGGGAAGTgcg                                     <  1:816946/151‑1 (MQ=255)                                                                                                         aaaaAGCCTTCCGGGGCGGCTGTCG‑GCCAGTTTTTTTCCCCCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCG‑CTGCTGGTAACAATGTGGAAAGGGAAg                                         <  2:814374/148‑1 (MQ=255)                                                                                                                  tccgcgGCGGCGTTCT‑CCAAGCTATTTTCCCGCCGAAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCG‑CTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAAt                               <  1:298639/147‑1 (MQ=255)                                                                                                                       ggcggcTGTCG‑CCCAGTTTTTTTCCCGCCGAAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCG‑CTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGaa                                <  2:914391/143‑1 (MQ=255)                                                                                                                        ggggcTGTCCGGCCTGCTTTTTGTCACCCGAAACAAAGCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCG‑CTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAAt                               <  2:151971/142‑1 (MQ=255)                                                                                                                         cggcTGTCT‑GCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCGAGAGGAAAAAAATTAAACCCGCCACACTGGGTGGTAATCG‑CCGGTGGGTACAAAATGGGAAAGGGAGGGCGGGGGATCAGCTcc                        >  1:186039/1‑149 (MQ=255)                                                                                                                             tGTCG‑GCCAGTTTTTTTCCCCCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCG‑CTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGaa                    <  1:865924/149‑1 (MQ=255)                                                                                                                                  tgccggttttttccccgccgAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCG‑CTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAAc                   <  2:945961/132‑1 (MQ=255)                                                                                                                                    ccAGTTTTTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCG‑CTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACcgcg               <  1:564484/148‑1 (MQ=255)                                                                                                                                    ccAGTTTTTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCG‑CTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTa            <  2:77676/151‑1 (MQ=255)                                                                                                                                    ccAGTTATTTTCCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCG‑CTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCt             <  1:204538/150‑1 (MQ=255)                                                                                                                                          ttttccccgccgCAAAAAAGCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCG‑CTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAAtt         <  1:135015/142‑1 (MQ=255)                                                                                                                                                ccgccgCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCG‑CTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCg  <  1:579035/149‑1 (MQ=255)                                                                                                                                                         |                                                                                                                                             GATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTAT‑CCAA‑CGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCT‑GCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCG‑CTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCG  >  NC_000913/357742‑358029

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: ‑