Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	357,880	0	T	C	51.1%	38.0 / 70.4	47	K271E (AAA→GAA)	cynR	transcriptional activator of cyn operon; autorepressor
Reads supporting (aligned to +/- strand):  ref base T (15/8);  new base C (0/24);  total (15/32)
Fisher's exact test for biased strand distribution p-value = 6.52e-07
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.93e-08

CGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCC‑ATGTGCAAAAATG‑CCTT‑C‑GCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCG  >  NC_000913/357733‑358029                                                                                                                                                        |                                                                                                                                                        cGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCC‑ATGTGCAAAAATG‑CCTT‑C‑GCGGCGGCTGTCTGCCAGCTATTTTTc                                                                                                                                                        <  2:1256757/149‑1 (MQ=255) cGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCCGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCC‑ATGTGCAAAAATG‑CCTT‑C‑GCGGCGGCTGTCTGCCAGCTATTTTTccg                                                                                                                                                      <  1:514005/151‑1 (MQ=255)       ccTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCC‑ATGTGCAAAAATG‑CCTT‑C‑GCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGcaa                                                                                                                                                <  2:215505/151‑1 (MQ=255)         tGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCC‑ATGTGCAAAAATG‑CCTT‑C‑GCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGcaac                                                                                                                                               >  2:26463/1‑150 (MQ=255)          gATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCC‑ATGTGCAAAAATG‑CCTT‑C‑GCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGcaacaa                                                                                                                                             <  2:435296/151‑1 (MQ=255)             aaGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCC‑ATGTGCAAAAATG‑CCTT‑C‑GCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACaaaa                                                                                                                                           <  2:37153/150‑1 (MQ=255)             aaGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCC‑ATGTGCAAAAATG‑CCTT‑C‑GCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACaaaa                                                                                                                                           <  1:352/150‑1 (MQ=255)              aGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCC‑ATGTGCAAAAATG‑CCTT‑C‑GCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAAcc                                                                                                                                         >  1:313012/1‑151 (MQ=255)                           aGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCC‑ATGTGCAAAAATG‑CCTT‑C‑GCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTcc                                                                                                                             >  1:713679/1‑150 (MQ=255)                             gCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCC‑ATGTGCAAAAATG‑CCTT‑C‑GCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCagt                                                                                                                          >  1:1099945/1‑151 (MQ=255)                             gCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCC‑ATGTGCAAAAATG‑CCTT‑C‑GCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCagt                                                                                                                          >  2:41566/1‑151 (MQ=255)                              cAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCC‑ATGTGCAAAAATG‑CCTT‑C‑GCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCagt                                                                                                                          >  2:1089009/1‑150 (MQ=255)                                  tCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCC‑ATGTGCAAAAATG‑CCTT‑C‑GCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTgg                                                                                                                     >  1:1328342/1‑151 (MQ=255)                                   ccacccccaccctggtgtCAGCGTCTCCGGTTATTCTTTCCCGCCAACACCCGCGCTTTTATCCACCGCT‑ATGTGAAAAAATG‑CCTT‑C‑GCGGCGGCTGTTTGCCAGTTTTTTTTCCCCCCAAAAAAAACCGCCGTTCTCTCCAGTAGTg                                                                                                                      <  2:1104056/135‑1 (MQ=255)                                   ccAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCC‑ATGTGCAAAAATG‑CCTT‑C‑GCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGc                                                                                                                    >  1:929754/1‑151 (MQ=255)                                       ccGCAGCCCTGTGCCAGCGGCTCCCGTGTTTCTTTCCCGCCAACACCCGCGCTTTTA‑CCCACCCC‑CTTTTCAAAAATGCCCTT‑G‑GGGGCGGCTTTCGGCCAGCTTTTTTCCCGCCCCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCg                                                                                                                   <  2:688148/148‑1 (MQ=255)                                        cgcagcctttgctCAGCGCCTACCGGGTTTCATTCCCGCCAACACCCGCCCTTTTATCCACCGCA‑TTGTGCAAAAATG‑CCTT‑C‑GGGGCGGCTGTCTGCAAGCTTTTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCg                                                                                                                   <  2:398269/135‑1 (MQ=255)                                                tgtgTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCC‑ATGTGCAAAAATG‑CCTT‑C‑GCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGAagcgga                                                                                                        >  2:443109/1‑146 (MQ=255)                                                 gtgtCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCC‑ATGTGCAAAAATG‑CCTT‑C‑GCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGGAGAG‑aaa                                                                                                      >  2:275825/1‑150 (MQ=255)                                                 gtgccggcgcCTCCCGTATTTCTTTCCCCCCAACACCCGCTCTTTTACCCACCGCC‑AGGTAAAAAAATG‑CCTC‑G‑GCGGCGGCTGTCTGCCAGTTTTTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAagag                                                                                                          <  1:710642/141‑1 (MQ=255)                                                   gtCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCC‑ATGTGCAAAAATG‑CCTT‑C‑GCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCggtcacaatgacaaa                                                                                                     >  1:326928/1‑137 (MQ=255)                                                    tCAGCGGCTCCCGTGTTTCATTCCCCCCAACACCCGCGCTTTTACCCACCGCC‑ATGGGAAAAATGG‑CCTT‑C‑GCGGCGCCTGTCTCCCAGTTTTTTTCCCCCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAg                                                                                                   <  2:31090/150‑1 (MQ=255)                                                       gcgcCTACCGTTTTTCATTCCCGACAACACCCGCGATTTTACCAAACCCA‑GTGTGAAAAAATC‑CCTC‑C‑GCGGCGGCTTCCGGCAAGTTTTTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑aaa                                                                                                      <  1:616661/144‑1 (MQ=255)                                                         gcctcccGTGATTCATTCCCCCCAACACCCGCCCTTTTACCCACCGCA‑ATGTAAAAAAATG‑CCTG‑C‑GGGGCGCCTGTCTGCCAGTTTTTTTCCCGCCAAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCtt                                                                                                <  1:191507/143‑1 (MQ=255)                                                         gcctcccGTGATTCATTCCCCCAAACACCCGCGCTTTTCCCCACCGCC‑ATGTGAAAAAAGG‑CTTC‑C‑GGGGCGGTTGTCGGCCGGTTTTTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAag                                                                                                            <  1:199946/132‑1 (MQ=255)                                                         gccTACCGTAATTCATTCCCCCCACCACCCGCGCATTTACCCACCGCA‑AGGTGAAAAAATG‑CCTT‑C‑GGGGCGGCTGTCTGCCAGCTTTTTTCCCGCCGAAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATa                                                                                                    <  2:1269329/142‑1 (MQ=255)                                                           ctcccGTGATTCATTCCCCCCAACACCCGCGCTTTTA‑CCAACCCCAATGTGAAAAAAGC‑CCTG‑C‑GGGGGGGCTGTCTGCCAGTTTTTTTCCCGCGCAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTa                                                                                              <  1:980603/145‑1 (MQ=255)                                                           caaCCGTAATTATTTCCCGCAAACACCCGCAAATTATTCCACCGCC‑GTG‑AAAAAAATC‑CCTT‑CGGCGGCGGGTGTCGGCCAGATATTTTCCCCCCTCACAAAAGCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGc                                                                                           <  2:436222/149‑1 (MQ=255)                                                                      cATTCCCCCAAACACCCGCGCATTTATCCAACGCC‑ATGTGCAAAAATG‑CCTT‑C‑GGGGCGGTTGTCTGCCAGCTTTTTTTCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCAtgt                                                                                  <  2:537106/149‑1 (MQ=37)                                                                        ttccccccAACACCGGCGTATTTACCCACCCCC‑ATGTAAAAAATTG‑CCTC‑C‑GCGGCGGCTTTCGCCCAGTTTTTTTCCCCCCCCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTc                                                                                      <  2:714756/137‑1 (MQ=255)                                                                        ttcccGCCAACACCCGCGCATTTACCCAACGCC‑ATGTGAAAAAATG‑CCTT‑C‑GGGGCGGCTGTCTGCCAGTTATTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCAtgtt                                                                                 <  2:1073043/145‑1 (MQ=255)                                                                        tccccGCCAAAACCCGCCAATTTACCAACCCCC‑CTGTGCAAAAACG‑CTTG‑C‑GGGGCGGTTGTCCGCCATCTTTTTTCCCGCCGAAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCAtg                                                                                   <  2:234688/143‑1 (MQ=255)                                                                                      cgcacttttACCCACCCCC‑ATGTAAAAAAATG‑CCTC‑G‑GCGGCGGCTGTCTCCCAGCTTTTTTCCCGCCCAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCgctgct                                                                <  2:396197/145‑1 (MQ=255)                                                                                            tttACCCACCGCC‑ATGTG‑AAAAAAG‑CCTTGC‑GGGGCGGCTGTCTGCCGTTTTTTTTCCCGCCACAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGt                                                            <  1:753979/148‑1 (MQ=255)                                                                                                   aaCGCC‑ATGTGCAAAAATG‑CCTT‑C‑GCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGAAGGGAAAAAAGATTTAATCCC‑TCATTTTTTGTGGGGATCgctccgggggacaa                                                        >  1:1290858/1‑135 (MQ=25)                                                                                                    aaccctttgtaaaaaaaTG‑CCTC‑C‑GCGGGGGCTTTCGGCCAGTTTTTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGTAACAAtg                                                     <  2:834062/136‑1 (MQ=255)                                                                                                         caggtcgaaaaaTG‑CCGG‑C‑GGGGCGGCTGTCTGCCGGCTTTTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGTAACAATGTGGAAAgg                                             <  2:1071704/144‑1 (MQ=255)                                                                                                            gtgAAAAAGTC‑CCTC‑G‑GCGGGGGTTGTCTCCCAGTTTTTTTCCCCCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGTAACAATGTGGAAAGGGa                                           <  2:1199636/150‑1 (MQ=255)                                                                                                                aaaaaTG‑CCTC‑C‑GCGGCGGCTTTCTGCCATTTTTTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGTAACAATGTGGAAAGGGAAg                                         <  2:249186/148‑1 (MQ=255)                                                                                                                aaaaaTC‑CCTT‑C‑GCGGCGGCTTTCTCCAAGTTTTTTTCCCCCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGTAACAATGTGGAAAGGGAAGt                                        <  2:571262/149‑1 (MQ=255)                                                                                                                aaaaaTC‑CCTC‑C‑GGGGGGGCTGTCTCCCATTTTTTTTCCCGCCACAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGTAACAATGTGGAAAGGGAAGTgc                                      <  1:1202249/151‑1 (MQ=255)                                                                                                                aaaaaGG‑CCTG‑C‑GGGGCGGTTGTCTCCCAGTTTTTTTCCCGCCGCAAAAAAGCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGTAACAATGTGGaa                                                <  1:1300540/141‑1 (MQ=255)                                                                                                                 aaaaTG‑CCTT‑C‑GCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGGAGAG‑GAAAAAATTTAAAGACCCCCTTTTTTGTGGCGATCGCTGGT‑GGGGACCAATTGGAAAGGGAAggg                                       >  2:396467/1‑147 (MQ=255)                                                                                                                    aatcccgtgc‑gcgCCGCCTGTCTCCCTCCTTTTTTCCCCCCGCAACAAACCCGCCGTTCTCTCCAGTAGTGGCGGTGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGTAACAATGTGGAAAGGGAAGTgcgg                                    <  1:474821/142‑1 (MQ=255)                                                                                                                    aacgcttt‑C‑GGGGGGGCTGTCTGCCGTCTTTTTTCCCGCCAAAACAAATCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGTAACAATGTGGAAAGGGAAGTgcggc                                   <  2:807196/145‑1 (MQ=255)                                                                                                                                 ggcggcTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCGAGAG‑AAAAAAATTTTAGACCGGCCTTTTTTGTGGGAATCGCTGCTGGGTAAAAAGTGGGAAAGGGAAGGGGGGGGaaaaacccc                         >  2:1129257/1‑144 (MQ=255)                                                                                                                                       tGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGAAGAG‑AAAAAACTTTTAACCCCTCCTGTTGTGTGGGGATCGCTGCT‑GGGAAAAAAGTGGGAAAGGGAGGGGGGGGGATCAACTCCaaaaac                  >  2:477572/1‑149 (MQ=255)                                                                                                                                                    ttttcCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAg      <  2:832256/150‑1 (MQ=255)                                                                                                                                                    ttttcCCCCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGTAACAATGTGGAAAGGGAAGTGCGGCGAATCa                             <  2:671595/127‑1 (MQ=255)                                                                                                                                                        tCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGGAGAG‑GAAAAAATTTTAACCCGGCATGTTTTGTGGGGAACGCCGCT‑GGGTACAAAGTGGAAAGGGGAGAGGGGGGGATCAACCCCCCAAACGCGCTCATTGAGtttg  >  2:643437/1‑148 (MQ=255)                                                                                                                                                        tCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGAAGAG‑AAAAAAAATTAAACCCCTCATTTTTTGTGGGCATCGCTGCC‑GGGAAAAAAGTGGGAAGGGGAGGGGGGGGGAGCAGCCCCACAACCGCGCCCATTGAGt     >  1:851969/1‑147 (MQ=255)                                                                                                                                                        |                                                                                                                                                        CGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCC‑ATGTGCAAAAATG‑CCTT‑C‑GCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCG  >  NC_000913/357733‑358029

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: ‑