Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	357,875	0	A	T	44.0%	62.7 / 19.3	50	N272K (AAT→AAA)	cynR	transcriptional activator of cyn operon; autorepressor
Reads supporting (aligned to +/- strand):  ref base A (21/7);  new base T (0/22);  total (21/29)
Fisher's exact test for biased strand distribution p-value = 2.63e-08
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

ACTGAACTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGC‑GGCGGCTGTCTGCCAGCTATTTTTCCGCCGC‑AACAAAACCGCCGTTCTCTCCAGTAGTGGCGGG‑GCAAGA‑G‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGC  >  NC_000913/357725‑358017                                                                                                                                                        |                                                                                                                                                   aCTGAACTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGC‑GGCGGCTGTCTGCCAGCTa                                                                                                                                                    <  1:590358/151‑1 (MQ=255)  cTGAACTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGC‑GGCGGCTGTCTGCCAGCTAt                                                                                                                                                   >  2:702225/1‑151 (MQ=255)    gAACTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGC‑GGCGGCTGTCTGCCAGCTAttt                                                                                                                                                 <  2:89926/151‑1 (MQ=255)              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)                                                                                                                                                        |                                                                                                                                                   ACTGAACTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGC‑GGCGGCTGTCTGCCAGCTATTTTTCCGCCGC‑AACAAAACCGCCGTTCTCTCCAGTAGTGGCGGG‑GCAAGA‑G‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGC  >  NC_000913/357725‑358017

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: ‑