Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	357,890	0	C	A	45.6%	43.6 / 22.4	46	L267F (TTG→TTT)	cynR	transcriptional activator of cyn operon; autorepressor
Reads supporting (aligned to +/- strand):  ref base C (19/6);  new base A (0/21);  total (19/27)
Fisher's exact test for biased strand distribution p-value = 5.07e-08
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGC‑GGCGGCTGTCTGCCAGCTATTTTTCCGCCGC‑AACAAAACCGCCGTTCTCTCCAGTAGTGGCGGG‑GCAAGA‑G‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCGCCTCAA  >  NC_000913/357742‑358035                                                                                                                                                       |                                                                                                                                                     gATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGC‑GGCGGCTGTCTGCCAGCTATTTTTCCGCCGc‑aac                                                                                                                                                      <  2:945439/149‑1 (MQ=255)   tAAGCGTAGCGCTTCAGACAATTCCAGCCGCAGACCTGTGTCAGCGCCTACCTTGATTCACTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGC‑GGCGGCTGTCTGCCAGCTATTTTTCCGCCGc‑aac                                                                                                                                                      <  2:231873/147‑1 (MQ=255)      gCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGC‑GGCGGCTGTCTGCCAGCTATTTTTCCGCCGC‑AACAAAAccg                                                                                                                                               <  2:767357/151‑1 (MQ=255)         tAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGC‑GGCGGCTGTCTGCCAGCTATTTTTCCGCCGC‑AACAAAAccgccg                                                                                                                                            >  1:796779/1‑151 (MQ=255)         tAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGC‑GGCGGCTGTCTGCCAGCTATTTTTCCGCCGC‑AACAAAAccgccg                                                                                                                                            >  1:429306/1‑151 (MQ=255)             gcATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGC‑GGCGGCTGTCTGCCAGCTATTTTTCCGCCGC‑AACAAAACCGCCGTtct                                                                                                                                        >  2:681272/1‑151 (MQ=255)             gcATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGC‑GGCGGCTGTCTGCCAGCTATTTTTCCGCCGC‑AACAAAACCGCCGTtct                                                                                                                                        >  2:614271/1‑151 (MQ=255)               aTCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGC‑GGCGGCTGTCTGCCAGCTATTTTTCCGCCGC‑AACAAAACCGCCGTtctct                                                                                                                                      >  1:439517/1‑151 (MQ=255)                           cAGCCGCAGCCTTGTGTCGGCGGCTCCCGTGTTTCATTCCCGCCAACACCCGCGCATTTACCCAACCCCATGTGAAAAAATGCCTTCGC‑GGCGGCTGTCTCCCAGCTTTTTTCCCGCCGC‑AACAAAACCGCCGTTCTCTCCAGTAGTGGCg                                                                                                                          <  1:849127/151‑1 (MQ=255)                           cAGCCGCAGCCTTGTGTCAGCGCCTACCGTGTTTCTTTCCCCCAAACACCCGCGCTTTTACCCACCGCCTTGTAAAAAAATGCTTCCGG‑GGCGGCTTTCTCCCAGTTTTTTTCCCGCCGA‑AAAAAAACCGCCGTTCTCTCCAGTAGTGGCg                                                                                                                          <  1:531203/151‑1 (MQ=255)                              ccGCAGACCTGTGCCCGCGCCTCCCGTGATTCTTCCCCGCCAAAACCCGCGCTTTTCCCCACCGCCATGTGAAAAAGTGCCTTCGC‑GGCGCTTGCCTGCCAGTTTTTTTCCCGCCGC‑AAAAAAACCGCCGTTCTCTCCAGTAGTGGCg                                                                                                                          <  2:174773/148‑1 (MQ=255)                                  aGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGC‑GGCGGCTGTCTGCCAGCTATTTTTCCGCCGC‑AACAAAACCGCCGTTCTCTCCAGTAGTGGCggg‑g                                                                                                                      >  1:917456/1‑147 (MQ=255)                                  aGACCTGTGTCAGCGGCTAACGTGATTAATTTCCTCCAACAAACGTGCTTTTATCCCAAGCCATGTGCAAAAATGCCTTCGC‑GGCGGCCCGCTGCCAGCTATTTTTCCGCCGC‑AACAAAAACCCCGTTCTCTccgttcggggaggtg                                                                                                                       >  2:501998/1‑134 (MQ=18)                                   gcccTGTGTCAGCGGCTACCGTGATTCATTCCCGCCAACACCCGCGCTTTTACCCACCCCCATGTCAAAAAATGCCTTCGC‑GGCGGCTGTCTGCCAGTTTTTTTCCCGCCGC‑AAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGG‑GCaa                                                                                                                   <  1:499860/147‑1 (MQ=21)                                       tgtgTCAGCGGCTCCCGTAATTCTTTCCCCCCAACACCCGCGCTTTTCCCCACCGCATTGTGAAAAAATGCTTTCGC‑GGCGGCTTTCTGCCAGTTTTTTTCCCCCCGC‑AAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGG‑GCAAGA‑G‑aa                                                                                                            <  1:722669/150‑1 (MQ=255)                                       tgtgTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGC‑GGCGGCTGTCTGCCAGCTATTTTTCCGCCGC‑AACAAAACCGCCGTTCTCTCCAGTAGTGGCggg‑gggaaaaaa                                                                                                              >  1:612557/1‑142 (MQ=255)                                        gtgtCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGC‑GGCGGCTGTCTGCCAGCTATTTTTCCGCCGC‑AACAAAACCGCCGTTCTCTCCAGTAGTGGCGGG‑Gcca                                                                                                                   >  1:810560/1‑142 (MQ=255)                                            cAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGC‑GGCGGCTGTCTGCCAGCTATTTTTCCGCCGC‑AACAAAACCGCCGTTCTCTCCAGTAGTGGCGGG‑GGGAGG‑G‑aaaaaaat                                                                                                      >  1:344710/1‑146 (MQ=255)                                              ggggCTACCGTGATTCTTTCCCCCAAACACCCGCGCTTTTACCCACCGCCATGGGAAAAAATGCTTTCGG‑GGCGGCTGTCGGCCAGTTTTTTTCCCGCCGC‑AAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGG‑GCAAGA‑G‑AAATAGCtt                                                                                                     <  1:266506/148‑1 (MQ=255)                                                gcctcccGTGATTCTTTCCCCCCAACACCCGCGCTTTTACCCACCCCCATGTAAAAAAATGCCTCCGG‑GGGGGCTTTCTCCCAGTTTTTTTCCCCCCCC‑AAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGG‑GCAAGA‑G‑AAATAGCTTTaa                                                                                                  <  1:853538/146‑1 (MQ=255)                                                  cTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGC‑GGCGGCTGTCTGCCAGCTATTTTTCCGCCGC‑AACAAAACCGCCGTTCTCTCCAGTAGTGGCGGG‑Gcgcggg                                                                                                                >  2:549877/1‑132 (MQ=255)                                                     ccGTGTTTCATTCCCGCAAACACCCGCCCTTTTACCCAACGCCATGTACAAAAATCCCTCCGC‑GGCGGCTGTCTGCCATCTTTTTTCCCCCCGC‑AACAAAACCGCCGTTCTCTCCAGTAGTGGCGGG‑GCAAGA‑G‑AAATAGCTTTAAGccc                                                                                              <  1:828905/150‑1 (MQ=255)                                                        taatttatttCCGCCAACACCCGCGCTTTTATCCACCCCCATGTGAAAAAATGCCTGCGC‑GGCGGCTGCCTGCCATCTTTTTTCCCGCCAC‑AACAAAACCGCCGTTCTCTCCAGTAGTGGCGGG‑GCAAGA‑G‑AAATAGCTTTaa                                                                                                  <  1:77197/141‑1 (MQ=255)                                                           ttCTTTCCCCCCAACACCCGCGCTTTTACCCAACGCCATGTGAAAAAATGCTTCGGG‑GGGGGTTGTCTGCCAGTTTTTTTCCCGCCGA‑AAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGG‑GCAAGA‑G‑AAATAGCTTTAAGCCCGTCAtg                                                                                        <  1:437407/150‑1 (MQ=255)                                                           ttCTTTCCCCCCAACACCCGCGCATTTACCCACCGCCATGTGAAAAAATGCCTCCGC‑GGCGGCTTTCTGCCAGTTTTTTTCCCGCCGA‑AAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGG‑GCAAGA‑G‑AAATAGCTTTAAGCCCGTc                                                                                           <  1:738332/147‑1 (MQ=255)                                                           ttCATTCCCCCCACCAACCGCACATCTATCCCGCGCCTGGTCAAAAAAGGCCCTCGG‑GGGGGCGGACAGCCGTTTATTTTGCCCCCCA‑AAAAAACCCGCCGTTCTCTCCAGTAGTGGCGGG‑GCAAGA‑G‑AAATAGCTTTAAGCCCGTCAt                                                                                         <  2:90436/149‑1 (MQ=255)                                                               ttccccccAACACCCGCGCTTTTACCCAACGCCATGTCCAAAAATGCTTTCGC‑GGCGGCTGTCTGCCATTTTTTTTCCCGCCGC‑AAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGG‑GCAAGA‑G‑AAATAGCTTTAAGCCCGTc                                                                                           <  1:869338/137‑1 (MQ=255)                                                               ttccccccAACACCCGCGATTTTACCCACCGCCTTTTGAAAAAATGCTTCCGC‑GGCGGCTTTCGGCAAGCTATTTTCCCGCCGC‑AAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGG‑GCAAGA‑G‑AAATAGCTTTAAGCCCGt                                                                                            <  1:703468/136‑1 (MQ=255)                                                               ttccccccAACACCCGCCCTTTTACCCACCCCCTTGTGCAAAAATCCCTTCGC‑GGCGGCTGTCTCCCAGTTTTTTTCCCGCCGC‑AAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGG‑GCAAGA‑G‑AAATAGCTTTAAGCCCGTCAtgt                                                                                       <  1:218814/141‑1 (MQ=255)                                                                  cccccaccaCCCCCGCTTTTCCCCAGCCCCTTGTGAAAAAAGCCCTCCGG‑GGGGGGTTTTGGCCAGGTTTTTTCCCGCCCA‑AAAAAACCCGCCGTTCTCTCCAGTAGTGGCGGG‑GCAAGA‑G‑AAATAGCTTTAAGCCCGTCATGTTGTGTgg                                                                                <  1:735071/148‑1 (MQ=255)                                                                  ccGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGC‑GGCGGCTGTCTGCCAGCTATTTTTCCGCCGC‑AACAAAACCGCCGTTCTCTCCAGTAGTGGCGGG‑GGCAGA‑G‑AAAAAGATTTTAAcccccccctgt                                                                                      >  2:472239/1‑137 (MQ=25)                                                                         cacccGCGCTTTTACCCACCCCCATGTGAAAAAATGCCTCCGC‑GGCGGCTGTCTCCAAGTTTTTTTCCCGCCGC‑AAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGG‑GCAAGA‑G‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCg                                                                          <  1:702502/147‑1 (MQ=255)                                                                           acCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGC‑GGCGGCTGTCTGCCAGCTATTTTTCCGCCGC‑AACAAAACCGCCGTTCTCTCCAGTAGTGGCGGG‑GGAAGA‑G‑GAAAAACTTTTAACCCCCCACGTTGTGTgggcagc                                                                           >  2:823264/1‑142 (MQ=25)                                                                           acCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGC‑GGCGGCTGTCTGCCAGCTATTTTTCCGCCGC‑AACAAAACCGCCGTTCTCTCCAGTAGTGGCGGG‑GCCAGG‑G‑AAAAAAATTTAAATCCCCCCGGTTGTGTgg                                                                                >  2:357089/1‑142 (MQ=25)                                                                                     tATCCAACGCCATGTGCAAAAATGCCTTCGC‑GGCGGCTGTCTGCCAGCTATTTTTCCGCCGC‑AACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGTGCACAA‑G‑AAAAAATTTTATACCCGTCAGTTTTGGTGGCATTCgcgcttggtac                                                                >  2:594125/1‑140 (MQ=21)                                                                                        ccACCGCCATGTGAAAAAATCCTTTCGC‑GGCGGCTTTCTCCCAGCTTTTTTCCCGCCGC‑AAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGG‑GCAAGA‑G‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAAtg                                                           <  1:943367/150‑1 (MQ=255)                                                                                          accGCCTTGTAAAAAAATCCCTTCGG‑GGCGGCTGTCGGCCAGTTTTTTTCCCGCCGC‑AACAAAACCGCCGTTCTCTCCAGTAGTGGCGGG‑GCAAGA‑G‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAAtgtg                                                         <  1:70644/148‑1 (MQ=255)                                                                                            cGCCATGTGCAAAAATGCCTTCGC‑GGCGGCTGTCTGCCAGCTATTTTTCCGCCGC‑AACAAAACCGCCGTTCTCTCCAGTAGTGGCGGG‑GCGAGAGG‑AAAAAAATTTAA‑CCCCCCCCGTTGTGTGGGGAACGCCGCTTGTGACAAAGTgg                                                        >  2:489734/1‑149 (MQ=21)                                                                                                      aaaaaTGCTTCCGG‑GGCGGCTTCCTG‑CAGGTTTTTTTCCCGCGCAAACAAATCCGCCGTTCTCTCCAGTAGTGGCGGG‑GCAAGA‑G‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGt                                              <  2:91342/149‑1 (MQ=255)                                                                                                      aaaaaTGCCTCCGC‑GGCGGCTGTCTCCCAGTTTTTTTCCCGCCGC‑AAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGG‑GCAAGA‑G‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTgc                                            <  1:944088/151‑1 (MQ=255)                                                                                                       aaaaTGCCTTCGC‑GGCGGCTGTCTGCCAGCTATTTTTCCGCCGC‑AACAAAACCGCCGTTCTCTCCAGTAGTGGCGGG‑GGCAGA‑GAAAAAAAATTTAATCCC‑TCTTGTTTTGGGGGAATCGCTGCCGGGGACAATGTgggga                                                     >  2:898837/1‑138 (MQ=255)                                                                                                       aaaaTGCCTCCGC‑GGCGCCTGTCCGCCAGTTTTTTTCCCCCCAC‑AAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGG‑GCAAGA‑G‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTgcg                                           <  2:932356/151‑1 (MQ=255)                                                                                                         aaTGCCCTCGGGGGCGCCTGTCTCCCAGTTTTTTTCCCGCCAA‑AAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGG‑GCAAGA‑G‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTgcgg                                          <  2:917117/151‑1 (MQ=255)                                                                                                               ttCGC‑GGCGGCTGTCTGCCAGCTATTTTTCCGCCGC‑AACAAAACCGCCGTTCTCTCCAGTAGTGGCGGG‑GGGAGA‑A‑AAAAAAATTTTAACCCCCCCTTTTTTGTGGGGAAAGCTGCTGGTTAAAATGTGGGAAGGGaggggggggggaaa                                    >  1:300193/1‑137 (MQ=255)                                                                                                                                 ccAGCTTTTTTCCCCCCGC‑AAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGG‑GCAAGA‑G‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCgcgc                    <  1:832203/149‑1 (MQ=255)                                                                                                                                      tttttccccgccgC‑AAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGG‑GCAAGA‑G‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAAt                <  2:796485/141‑1 (MQ=255)                                                                                                                                        tttcccccccac‑aaaaaAACCGCCGTTCTCTCCAGTAGTGGCGGG‑GCAAGA‑G‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACcg                       <  2:429081/128‑1 (MQ=255)                                                                                                                                             ccgccgC‑AACAAAACCGCCGTTCTCTCCAGTAGTGGCGGG‑GGAAGA‑GAAAAAAGGTTTAAACCC‑TCCTGTTTTGTGGGCAACGCCGCTGGGGACAAATTGGGAAGGGAAGGGGGGGGGATCAACTCCCCAAACGCGCCCATTTAGTTCGcc      >  1:667274/1‑151 (MQ=255)                                                                                                                                                ccgc‑AAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGG‑GCAAGA‑G‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGATCCAGAACCGCGCTAATTGAGTTc         <  1:705308/145‑1 (MQ=255)                                                                                                                                                   c‑aacaaAACCGCCGTTCTCTCCAGTAGTGGCGGG‑GCGAGA‑GAAAAAAAATTTAACCCCTTCTTCTT‑TGTGGGGAATGCTGTTGGGGAAAATTTGGGAAGGGGAGGGGGGGGGGGCAGATCCCGAACCGCGCCAATTGAATTCGCCTcca  >  2:846174/1‑147 (MQ=255)                                                                                                                                                       |                                                                                                                                                     GATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGC‑GGCGGCTGTCTGCCAGCTATTTTTCCGCCGC‑AACAAAACCGCCGTTCTCTCCAGTAGTGGCGGG‑GCAAGA‑G‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCGCCTCAA  >  NC_000913/357742‑358035

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 25 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑