Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	357,880	0	T	C	46.8%	48.2 / 14.8	48	K271E (AAA→GAA)	cynR	transcriptional activator of cyn operon; autorepressor
Reads supporting (aligned to +/- strand):  ref base T (20/5);  new base C (0/22);  total (20/28)
Fisher's exact test for biased strand distribution p-value = 9.41e-09
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGC‑GGCGGCTGTCTGCCAGCTATTTTTCCGCCGC‑AACAAAACCGCCGTTCTCTCCAGTAGTGGCGGG‑GCAAGA‑G‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGC  >  NC_000913/357738‑358017                                                                                                                                                |                                                                                                                                              gCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGCGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGC‑GGCGGCTGTCTGCCAGCTATTTTTCcgccgc                                                                                                                                        >  2:610370/1‑150 (MQ=255)  ccTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGC‑GGCGGCTGTCTGCCAGCTATTTTTCCGCCGc‑aa                                                                                                                                     <  2:57640/151‑1 (MQ=255)  ccTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGC‑GGCGGCTGTCTGCCAGCTATTTTTCCGCCGc‑a                                                                                                                                      >  1:932700/1‑150 (MQ=255)     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                                                                                                                          >  1:429306/1‑151 (MQ=255)             tAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGC‑GGCGGCTGTCTGCCAGCTATTTTTCCGCCGC‑AACAAAAccgccg                                                                                                                          >  1:796779/1‑151 (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)                                                                                                                                                |                                                                                                                                              GCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGC‑GGCGGCTGTCTGCCAGCTATTTTTCCGCCGC‑AACAAAACCGCCGTTCTCTCCAGTAGTGGCGGG‑GCAAGA‑G‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGC  >  NC_000913/357738‑358017

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 26 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑