Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	357,890	0	C	A	42.5%	37.0 / 18.9	40	L267F (TTG→TTT)	cynR	transcriptional activator of cyn operon; autorepressor
Reads supporting (aligned to +/- strand):  ref base C (14/9);  new base A (0/17);  total (14/26)
Fisher's exact test for biased strand distribution p-value = 3.76e-05
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

ATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCC‑TTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCG‑CAACAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGA‑GAAATAG‑C‑TTTAAGCCCGTCATGTTGTGT‑GGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCGCCTCAA  >  NC_000913/357743‑358035                                                                                                                                                      |                                                                                                                                                       aTAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCC‑TTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCG‑CAACaaa                                                                                                                                                     <  2:550581/151‑1 (MQ=255)   aaGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCC‑TTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCG‑CAACaaaa                                                                                                                                                    <  2:561489/150‑1 (MQ=255)    aGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCC‑TTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCG‑CAACAAAAcc                                                                                                                                                  <  1:997692/151‑1 (MQ=255)    aGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCC‑TTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCG‑CAACAAAAcc                                                                                                                                                  >  1:567955/1‑151 (MQ=255)     gCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCGTTTATCCAACGCCATGTGCAAAAATGCC‑TTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCG‑CAACAAAAccg                                                                                                                                                 <  2:224599/151‑1 (MQ=255)      cGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCC‑TTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCG‑CAACAAAAccgc                                                                                                                                                >  1:492500/1‑151 (MQ=255)             cATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCC‑TTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCG‑CAACAAAACCGCCGTtctc                                                                                                                                         >  1:616919/1‑151 (MQ=255)                     aaTTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCC‑TTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCG‑CAACAAAACCGCCGTTCTCTCCagt                                                                                                                                   >  1:108111/1‑149 (MQ=255)                          cAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCC‑TTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCG‑CAACAAAACCGCCGTTCTCTCCAGTAGTGGC‑g                                                                                                                           >  1:238861/1‑151 (MQ=255)                             ccGCAGCCTTGTGTCGGCGGCTACCGTGTTTCTTTCCCCCCAACACCCGCGCTTTTCCCCACCGCAATGTGAAAAAATCCT‑TTCGCGGCGGTTGTCTGCCAGTTTTTTTCCCGCCG‑CAAAAAAACCGCCGTTCTCTCCAGTAGTGGC‑ggg                                                                                                                         <  2:898104/150‑1 (MQ=255)                                         gtCGGCGGCCACCGTATTTCATTCCCCCCACCACCCGCGCTTTTCCCCAACGCCATGTGAAAAAATCCC‑TTCGCGGCGGCTGTCTGCCATCTTTTTTCCCGCCA‑CAAAAAACCCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGA‑GAAATa                                                                                                            <  1:848540/150‑1 (MQ=255)                                         gtCAGCGGCTCCCGTGATTCATTCCCGCAAACACCCGCCCTTTTACCCACCCCCTTGTGAAAAAATCCC‑TTCGCGGGGGCTGTCTCCCAGTTTTTTTCCCGCCG‑CAAAAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCa                                                                                                                      <  2:733032/141‑1 (MQ=255)                                              cGGCTACCGTGATTCATTCCCCCCAACACCCGCGCTTTTACCCACCGCCATGTCAAAAAATGCC‑TCCGCGGCGGCTGTCGGCAGGTTATTTTCCCGCCG‑AAAAAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGA‑GAAATAG‑C‑tt                                                                                                      <  1:460114/149‑1 (MQ=21)                                               ggCTCCCGTTTTTCTTTCCCCCCAACACCCGCGCTTTTACCCACCGCCTTGTGAAAAAATCCT‑TCCGCGGCGGCTTTCTCCCAGTTTTTTTCCCGCCG‑CAAAAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGA‑GAAATa                                                                                                            <  2:508775/144‑1 (MQ=255)                                                          ttCTTTCCCGCCAACACCCGCCCTTTTACCAAACGCCGTGTGAAAAAAGCCC‑TGCGGGGCGTCTGTCTGCAAGCTTTTTTCCCGCCG‑CAACAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGA‑GAAATAG‑C‑TTTAAGCCCGTCa                                                                                           <  2:122259/148‑1 (MQ=255)                                                           tCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCC‑TTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCG‑CAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGCGGGG‑GAAAAAG‑A‑TTTAACCCCgcc                                                                                            >  1:38149/1‑145 (MQ=25)                                                                cccGCCACCAACCGCCCATTTACCCACCCCCTTGT‑CAAAAATTCCTTTGGCGGCGGCTTTCTGCCAGCTTTTTTCCCGCCC‑CAAAAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGA‑GAAATAG‑C‑TTTAAGCCCGTCAtgtt                                                                                       <  2:617016/145‑1 (MQ=255)                                                                      aacaccCGCCCATTTATCCACCGCCATGTGAAAAAATGCC‑TGCGCGGCGGCTGTCTCCCATTTTTTTTCCCGCCG‑CAAAAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGA‑GAAATAG‑C‑TTTAAGCCCGTCATGTTGTGT‑GGCAAt                                                                            <  2:824537/150‑1 (MQ=255)                                                                         acccgcctaTTTACCCACCCCCATGGAAAAAAATGCC‑TCCGCGGGGGCTGTCTGCCAGTTTTTTTCCCGCCA‑AAAAAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGA‑GAAATAG‑C‑TTTAAGCCCGTCATGTTGTGT‑GGCAATc                                                                           <  1:749714/140‑1 (MQ=255)                                                                           ccGCGCTTTCACCCACCCCCTTGTAAAAAAATGCT‑TCGGCGGCGCCTGTCGGCCGGTTTTTTTCCCGCCA‑AAAAAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGA‑GAAATAG‑C‑TTTAAGCCCGTCATGTTGTGT‑GGCAATCgct                                                                        <  1:639351/149‑1 (MQ=255)                                                                           ccGCGCATTTATCCAACGCCATGTGCAAAAATGCC‑TTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCG‑CAACAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGGGAGA‑GGAAAAA‑C‑TTTTAACCCCCCCTTTTGTGT‑ggggctc                                                                           >  1:873764/1‑141 (MQ=25)                                                                              cgcATTTATCCAACGCCATGTGCAAAAATGCC‑TTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCG‑CAACAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGGAAGA‑GAAAAAGAA‑TTTAAACCC‑CCCTGTTGTGT‑gggg                                                                              >  1:677624/1‑138 (MQ=25)                                                                                           cGCCAGGTAAAAAAAGGCC‑TCCGCGGCGGCTGTCTGCCAGTTTTTTTCCCGCCG‑CAACAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGA‑GAAATAG‑C‑TTTAAGCCCGTCATGTTGTGT‑GGCAATCGCTGCTGGTAACAAtgt                                                          <  2:372325/147‑1 (MQ=255)                                                                                              cATGTGCAAAAATGCC‑TTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCG‑CAACAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCGAGA‑GAAAAAA‑CATTTAAACCC‑TCCTTTTGTGT‑GGGGAAAGCTGCTGGTTAAAAAGTGGgaa                                                     >  2:567873/1‑149 (MQ=25)                                                                                                  tgCAAAAATGCC‑TTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCG‑CAACAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGA‑GAAAAAA‑A‑ATTAATCCCCTCCCGTTGTGT‑GGGGAACGCCGCCGGGGACAATTTGGGAAggg                                                  >  1:294712/1‑148 (MQ=255)                                                                                                  gaaaaaaaTCCT‑TCCGCGGGGGCGGTCGGCCAGCTTTTTTCCCGCCG‑AAAAAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGA‑GAAATAG‑C‑TTTAAGCCCGTCATGTTGTGT‑GGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAg                                               <  1:28160/148‑1 (MQ=255)                                                                                                   gCAAAAATGCC‑TTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCG‑CAACAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGGCAGAGGAAAAAA‑A‑TTTAACCCCG‑CCTGTTTTGTGGGCAATGGCGCGGGGTGACAATGTgg                                                        >  1:311040/1‑142 (MQ=255)                                                                                                     aaaagcccc‑TCCGCGGGGCCTGTC‑GCCAAGTTTTTTTCCCCCGAAAACAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGA‑GAAATAG‑C‑TTTAAGCCCGTCATGTTGTGT‑GGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGt                                              <  1:290741/142‑1 (MQ=255)                                                                                                     aaaaaTGCT‑TTGGCGGCGGCTTTCTGCCAGTTTTTTTCCCCCCA‑CAAAAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGA‑GAAATAG‑C‑TTTAAGCCCGTCATGTTGTGT‑GGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTgc                                            <  2:82823/151‑1 (MQ=255)                                                                                                      aaaaTGCT‑TCCGCGGCGGCTGTCTGCCAGTTTTTTTCCCGCCC‑CAAAAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGA‑GAAATAG‑C‑TTTAAGCCCGTCATGTTGTGT‑GGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTgcg                                           <  2:873892/151‑1 (MQ=255)                                                                                                       aaaGGCC‑TCGGCGGGGGCTTTCTCCCAGTTTTTTTCCCCCCG‑CAAAAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGA‑GAAATAG‑C‑TTTAAGCCCGTCATGTTGTGT‑GGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTgcgg                                          <  2:503130/151‑1 (MQ=255)                                                                                                             c‑TTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCG‑CAACAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGGCAGG‑GGAAAAA‑A‑TTTAAACCCCCCGTGTTGTGT‑GGGGAACGCAGCTGGGGAAAAAGTGGGAAGGGGAgggggg                                          >  2:452225/1‑140 (MQ=255)                                                                                                                   cggcggCTGTCTGCCAGCTATTTTTCCGCCG‑CAACAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGGCAGA‑GAAAAAA‑A‑TTTAAAACCCTCATTTTGTGT‑GGGAAAAACCGCTGGGAAAAAAGTgggaagggaaaggggggg                                        >  2:759690/1‑134 (MQ=255)                                                                                                                       ggcTGTCTGCCAGTTTTTTTCCCGCCG‑CAAAAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGA‑GAAATAG‑C‑TTTAAGCCCGTCATGTTGTGT‑GGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTc                               <  2:250759/147‑1 (MQ=255)                                                                                                                                    tttttttcCCGCCG‑CAAAAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGA‑GAAATAG‑C‑TTTAAGCCCGTCATGTTGTGT‑GGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAAtt               <  1:297566/147‑1 (MQ=255)                                                                                                                                        tttcCCCCCA‑CAACAAATCCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGA‑GAAATAG‑C‑TTTAAGCCCGTCATGTTGTGT‑GGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGt           <  1:101846/150‑1 (MQ=255)                                                                                                                                         tccccgccg‑CAACAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGA‑GAAATAG‑C‑TTTAAGCCCGTCATGTTGTGT‑GGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGtt          <  1:308114/147‑1 (MQ=255)                                                                                                                                           cccgccc‑AAAAAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGA‑GAAATAG‑C‑TTTAAGCCCGTCATGTTGTGT‑GGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCg        <  1:999940/149‑1 (MQ=255)                                                                                                                                               ccg‑aAAAAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGA‑GAAATAG‑C‑TTTAAGCCCGTCATGTTGTGT‑GGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCGCCTc    <  2:294657/150‑1 (MQ=255)                                                                                                                                                 g‑cAACAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCGAGA‑GGAAAAA‑C‑ATTAAACCCCCCCTTTTGTGT‑GGCGATCGCCGGTGGGTACAATTTGGGAAGGGGAGGGGGGCGGATCAACTCCCGAAAACCGCCAATTTAGGTTGCCTcca  >  1:390066/1‑148 (MQ=255)                                                                                                                                                      |                                                                                                                                                       ATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCC‑TTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCG‑CAACAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGA‑GAAATAG‑C‑TTTAAGCCCGTCATGTTGTGT‑GGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCGCCTCAA  >  NC_000913/357743‑358035

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑