Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	357,890	0	C	A	43.5%	42.5 / 27.5	46	L267F (TTG→TTT)	cynR	transcriptional activator of cyn operon; autorepressor
Reads supporting (aligned to +/- strand):  ref base C (22/4);  new base A (0/20);  total (22/24)
Fisher's exact test for biased strand distribution p-value = 1.94e-09
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACA‑ACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCT‑TCGCGGCGGCTGTCTGCCAG‑CTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGG‑CAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGT‑GGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCGCCTC  >  NC_000913/357744‑358033                                                                                                                                                      |                                                                                                                                                   tAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACA‑ACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCT‑TCGCGGCGGCTGTCTGCCAG‑CTATTTTTCCGCCGCAACaaa                                                                                                                                                 >  1:1041214/1‑150 (MQ=255) tAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACA‑ACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCT‑TCGCGGCGGCTGTCTGCCAG‑CTATTTTTCCGCCGCAACaaa                                                                                                                                                 <  2:299647/150‑1 (MQ=255)        aGCGCATCAGGCAATTCCAGCCGCAGCCTTGTGTCAGCGGCTACCTTGATTCATTTCCGCCAACA‑ACCGCGCATTTATCCACCGCCATTTGCAAAAATGCCT‑TCGCGGCGGCTGTCTGCCAG‑CTTTTTTTCCGCCGCAACAAAAccgccg                                                                                                                                          <  1:639631/150‑1 (MQ=18)                aGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACA‑ACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCT‑TCGCGGTGGCTGTCTGCCAG‑CTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTcc                                                                                                                                  >  2:216824/1‑150 (MQ=255)                     aTTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACA‑ACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCT‑TCGCGGCGGCTGTCTGCCAG‑CTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCagtagt                                                                                                                            >  2:851338/1‑151 (MQ=255)                     aTTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACA‑ACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCT‑TCGCGGCGGCTGTCTGCCAG‑CTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCagtag                                                                                                                             >  2:339860/1‑150 (MQ=255)                        ccACCCGCAGCCTTGTGCCAGCGGCTCCCGTGTTTCTTTCCCGCAAACA‑CCCGCGCTTTTACCCACCCCCATGTGAAAAAATCCTT‑CCGCGGCGGCTGTCGGCAGG‑TTTTTTTCCCGCCGCAACAAAACCGCCGTTCTCTCCagt                                                                                                                               <  2:33215/145‑1 (MQ=255)                          aGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACA‑ACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCT‑TCGCGGCGGCTGTCTGCCAG‑CTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCgg                                                                                                                       >  1:559027/1‑151 (MQ=255)                          aGCCGCAGACCTGCGTCAGCGGCTACCGTGATTCATTTCCGCCAACA‑ACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCT‑TCGCGGCGGCTGTCTGCCAG‑CTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCgg                                                                                                                       >  1:213715/1‑151 (MQ=255)                            ccGCAGCCCTGTGTCGGGGCCTCCCGTGTTTCATTCCCCCAAACA‑CCCGCGCTTTTACCCACCCCCTTGTGAAAAAATCCCT‑TCGCGGCGGCTTTCTCCAAG‑TTTTTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCgggg                                                                                                                     <  1:215880/151‑1 (MQ=255)                            ccGCAGACTTGTGTCGGCGGCTCCCTTTTTTCATTCCCGCCACCA‑CCCGCGTTTTTACCCACCGCAATGTGAAAAATTCCTT‑TGGCGGGGGCTGTCTGCCAG‑TTTTTTTCCCGCCTCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCgggg                                                                                                                     <  1:693992/151‑1 (MQ=255)                                 gACTTGTTTCAGCCGCTCCGCTGATTCATTCCCACCAACC‑CCCGCCTATTTCCCCACCGCCTTGCCAAAAACTCCCC‑TCCGGGCGCCTCCTTCCCTC‑CTTTTTTCCCGCCCACACAAACCCGCCGTTCTCTCCAGTAGTGGCGGGG‑CAaga                                                                                                               <  1:63776/151‑1 (MQ=255)                                   cttttgccggCGGCTCCGGTTTTTCTTTCCCCCCAACA‑CCCGCGATTTTACCCACCCCCTTGTGAAAAAATCCTT‑CCGCGGCGGCGTTCGCCCAG‑TTTTTTTCCCCCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGG‑CAagag                                                                                                              <  1:742870/141‑1 (MQ=255)                                     tgtgTCAGCGGCTACCGTGATTCATTTCCGCCAACA‑ACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCT‑TCGCGGCGGCTGTCTGCCAG‑CTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCggggggggag                                                                                                               >  2:1044858/1‑142 (MQ=255)                                     tgtgTCAGCGGCTACCGTGATTCATTTCCGCCAACA‑ACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCT‑TCGCGGCGGCTGTCTGCCAG‑CTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCggg                                                                                                                      >  2:832268/1‑141 (MQ=255)                                           cgccgtctccagtgttCTTTTCCCCCAACACCCCTCTCTTTCATCCACCCCCCTGTGC‑AAAATGCCTCTGGAGGCGGCTTCCGGCCAC‑TTTTTTGTCCGCAAAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGG‑CAAGAG‑AAATAg                                                                                                       <  2:71564/135‑1 (MQ=255)                                                ctcccGTGATTATTTCCCCCCACCA‑CCCGCGCTTTTACCAACCCCCTTGTAAAAAAATGCTT‑CCGCGGCGGCTGTCTGCCAG‑TTTTTTTCCCGCCAAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGG‑CAAGAG‑AAATAGCtt                                                                                                    <  2:377118/143‑1 (MQ=255)                                                cTACCGTGATCCATTTCCGCCAACA‑ACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCT‑TCGCGGCGGCTGTCTGCCAG‑CTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCggagatggagacaa                                                                                                           >  2:693157/1‑129 (MQ=255)                                                 tACCGTGATTCATTTCCGCCAACA‑ACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCT‑TCGCGGCGGCTGTCTGCCAG‑CTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGG‑GCGGAG‑aaaaaacaatt                                                                                                  >  1:379721/1‑139 (MQ=25)                                                             ttcccGCCAACA‑CCCGCGCTTTTATCCACCGCCATGTGAAAAAATGCCT‑TCGCGGCGGCTGTCTGCCAG‑TTTTTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGG‑CAAGAG‑AAATAGCTTTAAGCCCGTCAtgtt                                                                                     <  1:249676/145‑1 (MQ=255)                                                                 ccgccagcccgcggtcATTTACCCACCCCCATGTAAAAAAGTTCCC‑GGGCGG‑GGCTGTCTTGCAGTTTATTTTTCCGCAAAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGG‑CAAGAG‑AAATAGCTTTAAGCCCGTCATGTtgtgtg                                                                                <  2:968663/135‑1 (MQ=255)                                                                     aaca‑ccCCCGCTTTTACCCACCCCCATGTGAAAAAATCCCT‑CCGCGGCGGCTTTCTGCCAG‑TTTTTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGG‑CAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAAt                                                                           <  1:985746/150‑1 (MQ=255)                                                                        a‑acCGCGCATTTATCCAACGCCATGTGCAAAAATGCCT‑TCGCGGCGGCTGTCTGCCAG‑CTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGG‑GGAGGG‑GAAAAGATTTTAAACCGGCAAGTTGTGTggggagag                                                                         >  1:148481/1‑143 (MQ=25)                                                                        a‑acCGCGCATTTATCCAACGCCATGTGCAAAAATGCCT‑TCGCGGCGGCTGTCTGCCAG‑CTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGG‑GGAGAG‑AAAAAAATTTTAGCCCGCCCTGTtttgtg                                                                                >  2:768244/1‑142 (MQ=25)                                                                          acCGCGCATTTATCCAACGCCATGTGCAAAAATGCCT‑TCGCGGCGGCTGTCTGCCAG‑CTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCCAGGGG‑AAAAAGATTTAAAACC‑TCCTGTtgtgt                                                                                 >  1:830320/1‑140 (MQ=25)                                                                               gcATTTATCCAACGCCATGTGCAAAAATGCCT‑TCGCGGCGGCTGTCTGCCAG‑CTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGG‑GAAGAGAAAAAAAATTTAAACCC‑TCATGTTGTGTggggaaagc                                                                        >  1:838333/1‑137 (MQ=25)                                                                                cATTTATCCAACGCCATGTGCAAAAATGCCT‑TCGCGGCGGCTGTCTGCCAG‑CTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGG‑GCAGAG‑AAAAAAACTTAAACCCCGCAATTTGTGGGGGAAGCGCTGCTgg                                                                  >  1:302775/1‑149 (MQ=25)                                                                                  tttccccAACCCCATGTGAAAAAATCCCT‑CCGCGGGGGCTGCCTCCCGG‑TTTTTTTCCCGCCAAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGG‑CAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTa                                                                <  2:112238/144‑1 (MQ=255)                                                                                   ttACCCACCGCCATGGGAAAAAAGCCCT‑CCGCGGCGGCTTTCCGCCAG‑TTTTTTTCCCGCCCAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGG‑CAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAAc                                                              <  2:774491/150‑1 (MQ=255)                                                                                      tCCAACGCCATGTGCAAAAATGCCT‑TCGCGGCGGCTGTCTGCCAG‑CTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGG‑GGAAAG‑AAAAAAATTTTAACCCCTCACGTTTTGTGGGGATCGCTGCTGGtgaaa                                                             >  1:821206/1‑144 (MQ=25)                                                                                         aaCGCCATGTGCAAAAATGCCT‑TCGCGGCGGCTGTCTGCCAG‑CTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGG‑GGAGAG‑GAAAAACTTTTAACACCTCCTTTTGTGTGGTGATAGCCGCTgggggcaaagagg                                                       >  1:73349/1‑140 (MQ=21)                                                                                           cGCCATGTGCAAAAATGCCT‑TCGCGGCGGCTGTCTGCCAG‑CTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGG‑GAAGAG‑AAAAAACTTTTAACCCCCCCTTTTTTGTGGGGAACGCTGCTggggaaaaagttg                                                       >  1:59940/1‑138 (MQ=25)                                                                                           cGCCATGTAAAAAAATCCCT‑CCGCGGGGGCTGTCTCCCAG‑TTTTTTTCCCGCCCAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGG‑CAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGT‑GGa                                                     <  1:840324/150‑1 (MQ=255)                                                                                                       aaaTCCCT‑GCGCGGGGGCTGTCTGCCAG‑TTTTTTTCCCCCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGG‑CAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGT‑GGAAAGGGAAGTgcgg                                        <  1:1074211/151‑1 (MQ=255)                                                                                                            ccT‑CCGCGGGGGCTGTCTGCCGG‑TTTTTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGG‑CAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCGATCGCTGCTGGTAACAATGT‑GGAAAGGGAAGTGCGGCGaa                                    <  2:93623/150‑1 (MQ=255)                                                                                                                    ggcggcTGTCGGCAAT‑TTTTTTTCCCGCCAAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGG‑CAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGT‑GGAAAGGGAAGTGCGGCGAAt                                   <  2:267706/144‑1 (MQ=255)                                                                                                                     gcggcTGTCGGCAGG‑TTTTTTTCCCCCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGG‑CAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGT‑GGAAAGGGAAGTGCGGCGAATCAGCTcc                            <  1:906450/150‑1 (MQ=255)                                                                                                                           gTCTGCCAG‑CTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGG‑GCAGAG‑AAAAAACTTTTAACCCCCCCTGTTTTGTGGGAATCGCTGGTGGTGAAAAAGT‑GGAAAGGGGAGGGCGGGGGAACAGCCCCCGaaac                      >  1:520464/1‑148 (MQ=255)                                                                                                                            tctcCCAG‑CTTTTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGG‑CAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGT‑GGAAAGGGAAGTGCGGCGAATCAGCTCCAg                          <  2:516459/145‑1 (MQ=255)                                                                                                                              ccgccattttttttcCCGCCACAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGG‑CAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGT‑GGAAAGGGAAGTGCGGCGAATCAGCTCCAGAAcc                      <  2:830292/138‑1 (MQ=255)                                                                                                                                ccAG‑TTTTTTTCCCGCCACAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGG‑CAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGT‑GGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACcgcg                   <  2:104823/148‑1 (MQ=255)                                                                                                                                  aG‑CTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGG‑CCAGAG‑AAAAAACTTTAAAACCCCCCTGTTTTGTGGGGATCGCTCCTGGTGAAAAAAT‑GGGAAGGGGAGAGGGGCGAAACAACACCCGAAACccgccca               >  1:609830/1‑147 (MQ=255)                                                                                                                                     cTATTTTTCCGCCGCGACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGG‑GAAGAG‑AAAAAAATTTTAAACCCTCCTGTTTTGTGGGGATCGCTGCTGGGGACAAAGT‑GGGAAGGGGAGGGGGGGGGAACAGCTCCACAAACCCGCTAAtt             >  1:905282/1‑150 (MQ=255)                                                                                                                                      tttttccccgccgAAAAAAACCCGCCGTTCTCTCCAGTAGTGGCGGGG‑CAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGT‑GGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTg            <  1:505591/143‑1 (MQ=255)                                                                                                                                      tATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGCG‑CCAGAG‑GAAAAACTTTTAACCCCTCCTGTTGTGTGGGAATAGCCGCTGGGAACAATGTGGGAAGGGGAGGGGGGGGGAAACA‑CCCCAAAACCGCGCTaa               >  1:976405/1‑147 (MQ=255)                                                                                                                                             ccgccgCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGG‑CAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGT‑GGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCg      <  2:690856/149‑1 (MQ=255)                                                                                                                                                ccacaaaaaAACCGCCGTTCTCTCCAGTAGTGGCGGGG‑CAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGT‑GGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCGCCTc  <  2:956396/147‑1 (MQ=255)                                                                                                                                                      |                                                                                                                                                   TAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACA‑ACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCT‑TCGCGGCGGCTGTCTGCCAG‑CTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGG‑CAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGT‑GGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCGCCTC  >  NC_000913/357744‑358033

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: ‑