Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	357,873	0	C	T	43.2%	44.6 / 22.5	45	S273N (AGC→AAC)	cynR	transcriptional activator of cyn operon; autorepressor
Reads supporting (aligned to +/- strand):  ref base C (17/8);  new base T (0/19);  total (17/28)
Fisher's exact test for biased strand distribution p-value = 1.61e-06
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

ACTGAACTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGG‑GGCAAG‑AGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCA  >  NC_000913/357725‑358008                                                                                                                                                     |                                                                                                                                          aCTGAACTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCt                                                                                                                                          >  2:48028/1‑150 (MQ=255)  cTGAACTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTAt                                                                                                                                        >  1:83354/1‑151 (MQ=255)    gAACTCGTAGGCCTGACAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTAt                                                                                                                                        <  1:198445/149‑1 (MQ=255)        tCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTcc                                                                                                                                  >  1:918274/1‑151 (MQ=255)         cGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTcc                                                                                                                                  <  1:480910/150‑1 (MQ=255)                 tGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGcaac                                                                                                                          >  1:955610/1‑150 (MQ=255)                     aaGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAAc                                                                                                                     <  1:1030269/151‑1 (MQ=255)                      aGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAAcc                                                                                                                    <  2:633357/151‑1 (MQ=255)                        cGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAAccgc                                                                                                                  <  2:739455/151‑1 (MQ=255)                            gcgcATCGGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTCCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAAccgccg                                                                                                                <  2:300977/149‑1 (MQ=255)                                  cAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTcc                                                                                                        >  1:942805/1‑151 (MQ=255)                                       attcccgcccGCGGCCCTGTGCCGGCGCCCCCGGTGATTCATTCCCCCAAACACCCCCTCTTTTACCAACCCCCTTGTGAAAAATTCCCTCGGCGGCGGCGTTCCGCCAGTTTTTTTCCCGCCGCAACAAAACCGCCGTTCTCTCCa                                                                                                       <  1:569439/139‑1 (MQ=255)                                           ccACCCGCAGCCCTGTGCCAGGGGCTCCCGTGATTCTTTCCCGCCAACACCCGCGCATTTCCCAACCCCCTTGTCAAAAAATGCTTCCGGGGCGGCTGTCTGCCAGTTATTTTCCCCCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGc                                                                                               <  2:134436/151‑1 (MQ=255)                                           ccACCCGCAGACTTGTGTCAGCGGCTCCCTTTTTTCTTCCCCCCCACCACCCGCGCTTTTACCCACCCCCATGTCAAAAAATCCCTCCGGGGGGGCTGTCTGCCAGTTTTTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGc                                                                                               <  1:713278/151‑1 (MQ=255)                                                cGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCgg‑g                                                                                           >  1:832260/1‑149 (MQ=255)                                                   aGACCTGTGTCAGCGGCTCCCGTGATTCATTCCCCCCAACACCCGCGCTTTTACCCACCCCCATGTGAAAAAATCCCTTCGCGGCGGCTGTCTCCCAGCTTTTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGG‑GGc                                                                                         <  2:221807/148‑1 (MQ=255)                                                    gccgtgtgcaggcgcCTCCCGTGATTCTTTCCCGCAAACACCCGCGCTTTTACCCACCCCAATGTAAAAAATGGCCTCCGCGCCGGCTGTCGCCCAGTTTTTTTCCCCCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGG‑GGCAag                                                                                      <  2:898341/139‑1 (MQ=255)                                                     cccTGTGTCAGCGCCTACGGTGATTCATTCCCCCAAACAACCGCGCATTTACCCAACCCCATGTAAAAAAATGCCTTCGCGGCGGCTGTCTGCCAGTTATTTTCCCGCCACAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGG‑GGCAag‑ag                                                                                   <  2:467816/150‑1 (MQ=255)                                                     cccTGTGGCGGCGGCTCCCGTAATTCTTTCCCGCCAACACCCGCGCTTTTACCCACCGCCATGTGCAAAAAGCCCTCCGGGGCGGCTGTCTGCCAGTTATTTTCCCCCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGG‑GGCAag‑ag                                                                                   <  2:893415/150‑1 (MQ=255)                                                     aCCTGTGTCAGCGGCTACCGTAATTCATTCCCGCCAACAACCGCGCATTTACCAACCGCCATGTAAAAAAATGCCTTCGCGGCGGCTGTCTGCCAGTTATTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGG‑GGCAag‑a                                                                                    <  2:390671/150‑1 (MQ=21)                                                      ccTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGG‑GGGGag‑ag                                                                                   >  1:776423/1‑150 (MQ=255)                                                        tgtgTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCgg‑ggggcgag                                                                                    >  2:871764/1‑142 (MQ=255)                                                           gtCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGG‑GGGTCG‑AGaaa                                                                                >  2:1071892/1‑148 (MQ=255)                                                                  gCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGG‑GGGAAG‑AGgaaaaaaatt                                                                         >  2:49384/1‑141 (MQ=255)                                                                     aCCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGG‑GGGGAG‑AGGAAAAGCatt                                                                         >  1:957750/1‑145 (MQ=255)                                                                     aCCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGG‑GGCGAG‑AGaaaaaaattttatgc                                                                    >  2:556878/1‑138 (MQ=255)                                                                      ccGTGTTTCATTCCCCCAAACACCCGCGAATTTACCAACCCCCTTGTGAAAAAATCCTTCCGGGGCGGCTGTCTCCCATTTTTTTTCCCGCCACAAAAAACCCGCCGTTCTCTCCAGTAGTGGCGG‑GGCAAG‑AGAAATAGCTTTAAGccc                                                                   <  2:917175/150‑1 (MQ=255)                                                                         tGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGTGGAAAG‑GGCAAAAACGTTAAGcc                                                                    >  1:607173/1‑147 (MQ=25)                                                                         tGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGG‑GGGCAG‑AGgaagaacattgttatc                                                                   >  1:29668/1‑134 (MQ=25)                                                                          gATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGG‑GGCGAG‑AGaaaaaagttttaaac                                                                    >  2:531156/1‑133 (MQ=255)                                                                            ttcttccccccaaacaccCGCGCTTTTACCCAACGCATTGTAAAAAAAGGCCTCCGGGGCGGCTTCCGGCCAGTTTTTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGG‑GGCAAG‑AGAAATAGCTTTAAGCCCGTCAt                                                              <  1:341218/137‑1 (MQ=255)                                                                                ttccccccAACACCCGCCCTTTTCCCCACCGCCTTGGGAAAAAATGCCTCCGCGGGGGTTGTCTGCCACTTTTTTTCCCGCCACAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGG‑GGCAAG‑AGAAATAGCTTTAAGCCCGTCAtgt                                                            <  1:374898/141‑1 (MQ=255)                                                                                          cacccccccttttACCCACCCCCATGTAAAAAACTGCCTCCGCGCCGGCTGCCTGCCAGTTTTTTTCCCGCCAAAACAAAACCGCCGTTCTCTCCAGTAGTGGCGG‑GGCAAG‑AGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCgc                                              <  1:528614/141‑1 (MQ=255)                                                                                                      tATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGG‑GGCGAG‑AGAAAAAAATTTTAATCCGCCACGTTTTGTggggaatgatcgcgg                                        >  2:703606/1‑132 (MQ=25)                                                                                                           accaccATGTGAAAAAACCCCTCCGGGGCGGCTTTCTCCAAGTTTTTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGG‑GGCAAG‑AGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAAtg                                <  2:475069/144‑1 (MQ=255)                                                                                                           accGCCTTGTGAAAAATTCCCTTCGCGGCGGTTTTCGGCAAGTTTTTTTCCCGCCGAAACAAAACCGCCGTTCTCTCCAGTAGTGGCGG‑GGCAAG‑AGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAAtgt                               <  1:516524/147‑1 (MQ=255)                                                                                                            accataTGTGAAAAAATGCCTCCGCGGCGCCGGTCCCCCACTTTTTTTTCCCCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGG‑GGCAAG‑AGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAAtgtg                              <  2:99094/144‑1 (MQ=255)                                                                                                               caatttgCAAAAATGCTTTGGCGGCGGCTGTCTGCAACATTTTTTCCCCCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGG‑GGCAAG‑AGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAAt                                 <  2:170755/138‑1 (MQ=255)                                                                                                                   gtgCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGG‑GGCGAGCAGAAAAAACTTTAATCCC‑CCCTGTTTTGTGGGGATCGCCTCTgg                                        >  1:258969/1‑132 (MQ=255)                                                                                                                   gggaaaaaaTGCCTCCGCGGCGGCTGTCTGCCGTTTTTTTTCCCCCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGG‑GGCAAG‑AGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGa                      <  1:627731/146‑1 (MQ=255)                                                                                                                       aaaaaTCCCTCCGCGGCGGCTGTCGGCCAGTTTTTTTCCCGCCACAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGG‑GGCAAG‑AGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTg                  <  1:73007/150‑1 (MQ=255)                                                                                                                                  cgcgGCGCTTGTCCCCCTTCTTTTTTTCCCCCGAAACAAAACCGCCGTTCTCTCCAGTAGTGGCGG‑GGCAAG‑AGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCa        <  1:76074/149‑1 (MQ=255)                                                                                                                                   gcggggGTTGTCGCCCAGTTTTTTTCCCGCCGAAAAAAACCCGCCGTTCTCTCCAGTAGTGGCGG‑GGCAAG‑AGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAg       <  1:362259/149‑1 (MQ=255)                                                                                                                                     ggcggcTTTCTGCCAGTTTTTTTCCCCCCAAAACAAAGCCGCCGTTCTCTCCAGTAGTGGCGG‑GGCAAG‑AGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTgcggcg             <  1:379658/141‑1 (MQ=255)                                                                                                                                        ggcTGTCTGCCAGTTTTTTTCCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGG‑GGCAAG‑AGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCa  <  2:717084/149‑1 (MQ=255)                                                                                                                                                     |                                                                                                                                          ACTGAACTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGG‑GGCAAG‑AGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCA  >  NC_000913/357725‑358008

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: ‑