Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	357,880	0	T	C	58.5%	26.3 / 52.9	41	K271E (AAA→GAA)	cynR	transcriptional activator of cyn operon; autorepressor
Reads supporting (aligned to +/- strand):  ref base T (15/2);  new base C (0/24);  total (15/26)
Fisher's exact test for biased strand distribution p-value = 2.14e-09
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 2.27e-09

GGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCT‑TCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAAC‑AAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGTAACAAT‑GT‑GGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGA  >  NC_000913/357737‑358024                                                                                                                                                 |                                                                                                                                                     ggCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCT‑TCGCGGCGGCTGTCTGCCAGCTATTTTTCcgccgc                                                                                                                                               >  1:750000/1‑151 (MQ=255)         aaGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCT‑TCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAAC‑AAAAc                                                                                                                                      <  1:687361/151‑1 (MQ=255)          aGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCT‑TCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAAC‑AAAAcc                                                                                                                                     >  2:536901/1‑151 (MQ=255)            cGTAGCGCATCAGGCAATTCCAGCCGCAGACCCGTTTCACCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCT‑TCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAAC‑AAAAccgc                                                                                                                                   <  2:477643/151‑1 (MQ=255)                        ggCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCT‑TCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAAC‑AAAACCGCCGTTCTCTcc                                                                                                                         >  1:226583/1‑149 (MQ=255)                                   ccGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCT‑TCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAAC‑AAAACCGCCGTTCTCTCCAGTAGTGGCgggg                                                                                                            >  2:880860/1‑151 (MQ=255)                                    cGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCT‑TCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAAC‑AAAACCGCCGTTCTCTCCAGTAGTGGCgggg                                                                                                            >  1:503980/1‑150 (MQ=255)                                     gCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCT‑TCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAAC‑AAAACCGCCGTTCTCTCCAGTAGTGGCgggggg                                                                                                          >  2:191584/1‑149 (MQ=255)                                      cAGCCCGGTGTCGGCGGCTACCTTGTTTCTTTCCCCCCAACACCCGCGTTTTTACCCACCCCCAGGTAAAAAAATGCCT‑CCGGGGGGGCTGTCTGCCAGTTTTTTTCCCGCCGCAAA‑AAAACCGCCGTTCTCTCCAGTAGTGGCGGGGc                                                                                                           <  2:554430/149‑1 (MQ=255)                                       agcccTGTGTCAGCGGCTCCCGTGATTCTTTCCCGCCAACACCCGCGCTTTTACCCAACGCCATGTGAAAAAATGCTT‑TCGGGGCGGCTGTCTGCCAGTTTTTTTCCCGCCGCAAC‑AAAACCGCCGTTCTCTCCAGTAGTGGCg                                                                                                               <  1:192028/141‑1 (MQ=255)                                        gactggtgtCGGCGGCTACCGTGTTTCATTCCCGCCAACACCCGCGCATTTACCCAACGCCATGTGAAAAAATGCTT‑TCGGGGCGGCTGTCTCCCAGCTTTTTTCCCGCCGAAAC‑AAAACCGCCGTTCTCTCCAGTAGTGGCGGGGc                                                                                                           <  1:903192/142‑1 (MQ=255)                                                     ggCTCCCGTTTTTCATTCCCCCCAACACCCGCGCTTTTACCCACCGCCATGTGCAAAAATGCCT‑CCGGGGCGGCTGTCGGCCAGTTTTTTTCCCGCCAAAAA‑AAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCttt                                                                                            <  2:822142/149‑1 (MQ=255)                                                       cTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCT‑TCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAAC‑AAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGGAGGGaaaaaaaatt                                                                                            >  2:451843/1‑140 (MQ=25)                                                          ccgtttttCATTCCCGCCAACACCCGCGCTTTTCCCCACCGCCTTGTGAAAAATTCCCT‑TCGCGGCGTTTGTCTCCCAGTTTTTTTCCCGCCGAAAA‑AAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGcc                                                                                       <  1:3976/143‑1 (MQ=255)                                                                ttCTTTCCCCCCAACACCCCCGCTTTTCCCCAACGCAATGTGAAAAATTGCCT‑GCGGGGCGTTTGTCGGCCATTTTTTTTCCCGCCGCAAA‑AAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCAtg                                                                                <  2:884284/150‑1 (MQ=255)                                                                      ccccccAACACCCGCGCTTTTACCCACCCCCATGTAAAAAAATCCCT‑CCGGGGCGCCTGTCGCCCAGTTTTTTTCCCGCCAAAAA‑AAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTtgtgtg                                                                         <  2:914311/147‑1 (MQ=255)                                                                        ccccAACACCCGCGTTTTTACCCACCGCCATGTGAAAAAATGCCT‑CCGCGGCGGCTGTCTGCCAGCTTTTTTCCCGCCGCAAA‑AAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGc                                                                       <  1:820495/149‑1 (MQ=255)                                                                               acccGCGTTTTTACCCACCGCCATGAGAAAAATCCCCT‑CCGCGGCGGCTGTCTGCCAGTTTTTTTCCCGCCGCAAA‑AAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCgc                                                                 <  2:251532/148‑1 (MQ=255)                                                                               acccGCGCATTTACCCACCGCCATGTGAAAAAAGGCCT‑CCGCGGCGGCTTTCTGCCAGTTATTTTCCCGCCGCAAA‑AAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCgct                                                                <  1:742080/149‑1 (MQ=255)                                                                                 ccGCGCATTTATCCAACGCCATGTGCAAAAATGCCT‑TCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAAC‑AAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGAAGAGAAAAAAATTTAAACCCCCCCtgttgttggggg                                                                      >  2:388868/1‑137 (MQ=25)                                                                                   gcgcATTTATCCAACGCCATGTGCAAAAATGCCT‑TCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAAC‑AAAACCGCCGTTCTCTCCAGTAGTGGCGGAGGACGAAAGAAAGATTTTAGCACGCCCTGTTGTggggggaaccgct                                                               >  1:552294/1‑139 (MQ=21)                                                                                        tttccccACCGCCATGTGAAAAAATGCCT‑GGGCGGCGGCTGTCTGCCAGTTATTTTCCCGCCGCAAA‑AAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGt                                                         <  1:290667/143‑1 (MQ=255)                                                                                        tttACCCACCGCCATGTGAAAAAATGCCT‑TCGGGGCGGTTGTCGCCCAGTTTTTTTCCCGCCGAAAA‑AAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGTaa                                                       <  1:31160/150‑1 (MQ=255)                                                                                                 cGCCATGT‑CAAAAACTCCTGCCGGGGCGGCTGTCCCCGACTTTTTTTCCCGCCAAAAA‑AAATCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGTAACAAT‑GT‑GGaa                                           <  2:1029779/151‑1 (MQ=255)                                                                                                          cAAAAATGCCT‑TCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAAC‑AAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCGAGAGAAAAAACTTTTAAACCCTCCTTTTTTGTGGGGATCGCTGCG‑GGTGACAAA‑GT‑GGGAAggg                                       >  2:391726/1‑146 (MQ=255)                                                                                                           aaaagTGTCT‑CCGCGGCGGCTTTCGCCCAGTTTTTTTCCCGCCCCAAA‑AAAGCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGTAACAAT‑GT‑GGAAAGGGAAGTgc                                 <  2:226536/151‑1 (MQ=255)                                                                                                           aaaaaTGCCT‑TCGCGGGGGCTGTCTCCCAGTTTTTTTCCCGCCGAAAA‑AAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGTAACAAT‑GT‑GGAAAGGGAAGt                                   <  1:898130/149‑1 (MQ=255)                                                                                                           aaaaaTGCCT‑CCGCGGCGGCTGTCTGCCAGTTTTTTTCCCGCCGCAAA‑AAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGTAACAAT‑GT‑gg                                             <  1:864915/139‑1 (MQ=255)                                                                                                           aaaaaTCCCT‑GGGGGGCGGCTGCCGGCCAGTTTTTTTCCCGCCGAAAA‑AAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGTAACAAT‑GT‑GGAAAGGGAAGTgc                                 <  2:382014/151‑1 (MQ=255)                                                                                                           aaaaaCCCCT‑CCGCGGCGGCTGTCTGCAAGTTTTTTTCCCGCCGCAAA‑AAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGTAACAAT‑GT‑GGAAAGGGAAGTgc                                 <  2:13508/151‑1 (MQ=255)                                                                                                              aacgccctcggcgcgggcGGTCTGCCAGTTTTTTTCCCGCCAAAAA‑AAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGTAACAAT‑GT‑GGAAAGGGAAGTgcgg                               <  2:746003/136‑1 (MQ=255)                                                                                                                   cT‑TCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAAC‑AAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGGAGAGAAAAAAATTTAAAACCCCCATGTTTTGTGGGGATAGCTGCTGGGTAAAAAG‑TT‑GGAAGGGGagggggggg                              >  1:188972/1‑139 (MQ=255)                                                                                                                     tgcggggcggcTGTCTGCCAGTTATTTTCCCCCCGCAAA‑AAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGTAACAAT‑GT‑GGAAAGGGAAGTGCGGCGa                            <  1:1052712/142‑1 (MQ=255)                                                                                                                       cgcgGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAAC‑AAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGGAGAGGAAAAAATTTTAACCCCCCCTGTTTTGTTGGGATCGCTGCT‑GGGGAAAAT‑GTGGGAAAGGGagagggggg                              >  2:659435/1‑136 (MQ=255)                                                                                                                          gccggcTTTCTGCCAGTTATTTTCCCCCCGCAAA‑AAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGTAACAAT‑GT‑GGAAAGGGAAGTGCGGCGAATc                         <  1:451973/143‑1 (MQ=255)                                                                                                                           gcggcTGTCTGCCAGCTATTTTTCCGCCGCAAC‑AAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGAAGAGAAAAAAATTTTAAACCCTCATGTTGTGTGGGAAACGCTGCT‑GGGAACAAA‑AT‑GGGAAAGGGAGGGCGGGGGAACAACTcc                   >  1:3407/1‑150 (MQ=255)                                                                                                                                tGTCTCCCAGTTTTTTTCCCGCCAAAAA‑AAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGTAACAAT‑GT‑GGAAAGGGAAGTGCGGCGAATCAGCTCCAg                 <  2:480716/147‑1 (MQ=255)                                                                                                                                tGTCGGCGAGTTTTTTTCCCGCCGCAAA‑AAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGTAACAAT‑GT‑GGAAAGGGAAGTGCGGCGAATCAGCTcc                   <  1:754979/145‑1 (MQ=255)                                                                                                                                    gcctgcttttttttCCCCCGAAAC‑AAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGTAACAAT‑GT‑GGAAAGGGAAGTGCGGCGAATCAGCTCCAGAAcc             <  1:537052/138‑1 (MQ=255)                                                                                                                                      ccgctttttttcCCCCCGAAAC‑AAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGTAACAAT‑GT‑GGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACcgcg          <  1:377061/141‑1 (MQ=255)                                                                                                                                      cccgtttttttcCCGCCAAAAA‑AAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGTAACAAT‑GT‑GGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTa       <  1:811599/144‑1 (MQ=255)                                                                                                                                      ccAGTTTTTTTCCCGCCGAAAA‑AAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGTAACAAT‑GT‑GGAAAGGGAAGTGCGGCGAATCAGCTCCAGaa               <  1:884130/143‑1 (MQ=255)                                                                                                                                        actttttttcCCCCCGAAAA‑AAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGTAACAAT‑GT‑GGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCt        <  1:842528/143‑1 (MQ=255)                                                                                                                                        aGCTATTTTTCCGCCGCAAC‑AAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGCAGAGAAAAAACCTTTAAACCACCCTGTTTTGTGGGGATCGCTGCC‑GGTTAAAAA‑GT‑GGGAAGGGAAGAGGGGCGGAACCGCTCCACAACCacgccca      >  1:123452/1‑147 (MQ=255)                                                                                                                                           ttttttcCCGCCGAAAC‑AAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGTAACAAT‑GT‑GGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTaa      <  1:615890/145‑1 (MQ=255)                                                                                                                                           tATTTTTCCGCCGCAAC‑AAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGCAGAGAAAAAAATTTAAAACCGCCCTTTTTTGTGGGGAACGCCGCT‑GGGGACAATGGG‑GGGAAGGGAGGGGGGGGGAA‑CAGCTCCAGAAACgcgccga      >  2:216266/1‑144 (MQ=255)                                                                                                                                             tttttCCGCCGAAAA‑AAACCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGTAACAAT‑GT‑GGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGa  <  2:385212/149‑1 (MQ=255)                                                                                                                                              ttttCCCCCCCAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGTAACAAT‑GT‑GGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGa  <  2:749769/149‑1 (MQ=255)                                                                                                                                                 |                                                                                                                                                     GGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCT‑TCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAAC‑AAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGTAACAAT‑GT‑GGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGA  >  NC_000913/357737‑358024

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: ‑