Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	357,890	0	C	A	41.9%	51.1 / 21.0	43	L267F (TTG→TTT)	cynR	transcriptional activator of cyn operon; autorepressor
Reads supporting (aligned to +/- strand):  ref base C (18/7);  new base A (0/18);  total (18/25)
Fisher's exact test for biased strand distribution p-value = 8.66e-07
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTT‑CCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAAT‑GCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGC‑AACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGC‑AAGAG‑AAATAGC‑TTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCGCCTCAATG  >  NC_000913/357742‑358037                                                                                                                                                        |                                                                                                                                                        gATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTT‑CCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAAT‑GCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGc‑aaca                                                                                                                                                        <  1:942002/150‑1 (MQ=255)  aTAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTT‑CCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAAT‑GCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGC‑AACaaa                                                                                                                                                      <  2:803467/151‑1 (MQ=255)  aTAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTT‑CCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAAT‑GCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGC‑AACaaa                                                                                                                                                      <  2:45886/151‑1 (MQ=255)    aaGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTTTCAGCGGCTACCGTGATTCATTT‑CCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAAT‑GCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGC‑AACAAAAc                                                                                                                                                    <  2:146263/151‑1 (MQ=255)    aaGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTT‑CCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAAT‑GCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGC‑AACaaaa                                                                                                                                                     <  1:202772/150‑1 (MQ=255)    aaGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTT‑CCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAAT‑GCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGC‑AACAAAAc                                                                                                                                                    <  2:663451/151‑1 (MQ=255)       cGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTT‑CCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAAT‑GCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGC‑AACAAAAccgc                                                                                                                                                 >  1:638709/1‑151 (MQ=255)         tAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTT‑CCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAAT‑GCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGC‑AACAAAAccgccg                                                                                                                                               >  1:917100/1‑151 (MQ=255)                       aTTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTT‑CCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAAT‑GCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGC‑AACAAAACCGCCGTTCTCTCCagtagt                                                                                                                                 >  2:573016/1‑151 (MQ=255)                              ccGCAAACTTGGGCCGGCGGCTCCCGTTATTCTTCC‑CCCCCAACACCCGCGCTTTTCCCAACCCCCATGTCAAAAAAT‑GCCTCCGGGGGGGCTGTCTCCCAGCTTTTTTCCCCCCGA‑AAAAAAACCGCCGTTCTCTCCAGTAGTGGCgggg                                                                                                                          <  1:619567/151‑1 (MQ=255)                                   gACCTGTGTCAGCGGCTACCGTGATTCATTT‑CCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAAT‑GCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGC‑AACAAAACCGCCGTTCTCTCCAGTAGTGGCgggg                                                                                                                          >  1:74030/1‑146 (MQ=255)                                            cAGCGGCTACCGTGATTCATTT‑CCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAAT‑GCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGC‑AACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGG‑AAGAG‑gaaaa                                                                                                             >  1:65504/1‑146 (MQ=255)                                                gcctcccGTGATTCATTC‑CCGCCAACACCCGCGCTTTTACCAACCGCCATGTGCAAAAAT‑GCCTTCGCGGCGGCTGTCGCCCATTTTTTTTCCCGCCGC‑AAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGC‑AAGAG‑AAATAGC‑TTTa                                                                                                      <  2:765269/145‑1 (MQ=25)                                                  cTACCGTGATTCATTT‑CCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAAT‑GCCTTCGCGGCGGCTGTCTGCCAGCTACTTTTCCGCCGC‑AACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGC‑gaaag‑aaaaaaattt                                                                                                        >  2:415490/1‑140 (MQ=25)                                                    ccggttttctaTTC‑CCCCCAACACCCGCGTTTTTACCCACCCCCGTGTAAAAAAAT‑GCCTCCGGGGCGGCTGCCGCCCATTTTTTTTCCCGCCAA‑AAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGC‑AAGAG‑AAATAGC‑TTTAAGcc                                                                                                  <  1:1080509/140‑1 (MQ=255)                                                     ccttatttCATTC‑CCCCCAACACCCGCACTTTTCCCCAACCCCTTGTAAAAAAAT‑GCTGCCGCGGCGGTTTTCTGCAAGTTTTTTTCCCGCCAA‑AAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGC‑AAGAG‑AAATAGC‑ttt                                                                                                       <  1:423194/138‑1 (MQ=255)                                                            tCATTTCCCGCCAACACCCGCGCTTTTCCCCACCG‑CTTGGCAAAAAATGGCCTCCGCGGCGGTTGCCGCCCATTTTTTTTCCCGCCAA‑AAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGC‑AAGAG‑AAATAGC‑TTTAAGCCCGTc                                                                                              <  1:944635/147‑1 (MQ=255)                                                                    cGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAAT‑GCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGC‑AACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGG‑CAAAG‑aaaaaaattttaaacc                                                                                                  >  2:477906/1‑123 (MQ=25)                                                                      ccAACACCCGCTCTTTTCCCCACCGCCATGTGAAAAAAT‑CCTTCCGCGGCGGTTTTCTGCCAGTTTTTTTCCCGCCGC‑AAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGC‑AAGAG‑AAATAGC‑TTTAAGCCCGTCATGTTGTGTGGCa                                                                                 <  2:51544/150‑1 (MQ=255)                                                                             ccGCGTTTTTCTCCAACCCCGTGAAAAAAAAT‑CCCTCGGGGGCGGTTTTTTGCCAGTTTTTTGCCCGCCGA‑AAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGC‑AAGAG‑AAATAGC‑TTTAAGCCCGTCATGTTGTGTGGCAATCgct                                                                           <  1:118705/149‑1 (MQ=255)                                                                                cgcATTTATCCAACGCCATGTGCAAAAAT‑GCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGC‑AACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGG‑GAGAGAAAAAAGA‑TTTAA‑CCCACCATGTTGTGTGGGGAATGCTGCT‑gg                                                                     >  2:858481/1‑151 (MQ=25)                                                                                cgcATTTATCCAACGCCATGTGCAAAAAT‑GCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGC‑AACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGG‑GAGAG‑AAAAAAA‑ATTAAAACCCCCGTTTTGTGTGGGGATCCctgct‑g                                                                      >  1:315208/1‑150 (MQ=25)                                                                                     ttATCCAACGCCATGTGCAAAAAT‑GCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGC‑AACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGC‑GAGAG‑AAAAAAC‑TTTAAAACCCCCCTGTTTTGTGGGGAACGCGGCT‑GGGaaa                                                                 >  2:1136750/1‑149 (MQ=25)                                                                                         ccAACGCCATGTGCAAAAAT‑GCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGC‑AACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGG‑GAAAG‑AAAAAAA‑TTTTATCCCCCCCTGTTTTGTGGGGATCGCCGCT‑GGTGACaa                                                               >  2:1387976/1‑148 (MQ=25)                                                                                          cAACGCCATGTGCAAAAAT‑GCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGC‑AACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCGAAAGG‑AAAAAAC‑TTTAAACCC‑CCATTGTGTGTGGGGATTGCCGCT‑GGGGACaa                                                               >  2:920732/1‑147 (MQ=21)                                                                                           acccccatggaaaaaagT‑CCCTCCGGGGCGGCTGTCTGCCGTTTTTTTCCCCGCCGC‑AACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGC‑AAGAG‑AAATAGC‑TTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGTAACAATGTgg                                                          <  1:1117714/139‑1 (MQ=255)                                                                                                 aTGTGCAAAAAT‑GCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGC‑AACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGG‑AAGGG‑GAAAAAA‑ATTAAACACGCCGCGTGGTGTGGGGATCGCGGCT‑GGGAaaaaatgagggaagg                                                    >  2:736442/1‑140 (MQ=255)                                                                                                    gaaaaaaaggccccgcgcgGCGGGTTTCGGCAATTTTTTTTCCCGCCAA‑AAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGC‑AAGAG‑AAATAGC‑TTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGTAACAATGTGGAAAGGGa                                                   <  1:1451461/135‑1 (MQ=255)                                                                                                     gCAAAAAT‑GCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGC‑AACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGC‑AAAAG‑AAAAAAC‑TTTTAAACCCCCCCGTTTTGGGGGGAACGCTGCT‑GGTGACaaaaaggaaaagg                                                    >  2:396833/1‑136 (MQ=255)                                                                                                       aaaaaT‑GCCTGCGCGGCGGCTTTCTCCAAGTTTTTTTCCCGCCGC‑AAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGC‑AAGAG‑AAATAGC‑TTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGTAACAATGTGGAAAGGGAAGt                                                <  2:355594/149‑1 (MQ=255)                                                                                                       aaaaaG‑CCCTCCGGGGCGGCTTTCTGCCAGCTTTTTTCCCCCCAC‑AAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGC‑AAGAG‑AAATAGC‑TTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGTAACAATGTGGAAAGGGAAGTgc                                              <  1:51606/151‑1 (MQ=255)                                                                                                       aaaaaC‑GCCTCCGGGGGGGCTTTCTGCCGGTTTTTTTCCCGCCGC‑AACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGC‑AAGAG‑AAATAGC‑TTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGTAACAATGTGGAAAGGGAAg                                                 <  1:107195/148‑1 (MQ=255)                                                                                                         aaaT‑GCCTTCGGGGGGGTGGTCGCCAAGTTTTTTTCCCGCCGA‑AAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGC‑AAGAG‑AAATAGC‑TTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGTAACAATGTGGAAAGGGAAGTgcgg                                            <  1:644597/151‑1 (MQ=255)                                                                                                           aatccttccgcgGCGGTTTTCTGCCAGTTTTTTTCCCGCCGA‑AAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGC‑AAGAG‑AAATAGC‑TTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGTAACAATGTGGAAAGGGAAGTgcggc                                           <  1:969119/143‑1 (MQ=255)                                                                                                                    gcggggctgttcggCCAGTTTTTTTCCCCCCAA‑AAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGC‑AAGAG‑AAATAGC‑TTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGTAACAATGTGGAAAGGGAAGTGCGGCGAATc                                      <  1:171365/134‑1 (MQ=255)                                                                                                                             tgccgCCAGTTTTTTTTCCCCCCCAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGC‑AAGAG‑AAATAGC‑TTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAAc                           <  1:766467/146‑1 (MQ=255)                                                                                                                               cTGCCAGTTTTTTTCCCCCCGC‑AAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGC‑AAGAG‑AAATAGC‑TTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCa                               <  2:253382/143‑1 (MQ=255)                                                                                                                                cgccaagtttttttCCCCCCCAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGC‑AAGAG‑AAATAGC‑TTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACcgcg                       <  2:529203/142‑1 (MQ=255)                                                                                                                                  ccattttttttcCCGCCGA‑AAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGC‑AAGAG‑AAATAGC‑TTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCt                     <  2:140149/143‑1 (MQ=255)                                                                                                                                      cTATTTTTCCGCCGC‑AACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGG‑AAAAG‑AAAAAAG‑TTTTAAACCGCCATGTTGTGTGGGAATCGCCGCTGGGGAAAAAGGTGG‑AAGGGGAGGGGGGGGGATCAACTCCAGAACCGCGCCAAtt                 >  2:98943/1‑150 (MQ=255)                                                                                                                                         ttttcCCGCCGA‑AAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGC‑AAGAG‑AAATAGC‑TTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAg              <  2:297701/150‑1 (MQ=255)                                                                                                                                          ttttCCGCCGC‑AACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGC‑AAGAGAAAAAACC‑TTTAATACC‑TCATGTTTTGTGGCCAAAACTGCT‑GGGGACAAAGTGGGAAGGGGAGGGAGGGGGATCAGCCCCCCAAACGCCCCCATTGAggt            >  2:951121/1‑149 (MQ=255)                                                                                                                                             tCCGCCGC‑AACAAAACCGCCGTTCTCTCCAGTGGTGGCGGGGC‑AAGAG‑AAATAGC‑TTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCGc         >  2:570455/1‑151 (MQ=255)                                                                                                                                               cgccgc‑AACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGC‑GAGGG‑AAAAAACTTTTAAGCAC‑TCACGTTTTTGGGGGAACCCTGCT‑GGTGACAATGTGGGGAGGGGGGTGGGGGGGAACAGATCCACAAACCCGCCAATTGAGTTTGcc        >  2:802730/1‑150 (MQ=255)                                                                                                                                                       acaaAACCGCCGTTCTCTCCAGTAGTGGCGGGGG‑GAGAGAAAAAAAA‑TTTAAACCC‑CCATGTTTTGTGGCAATCGCTGCT‑TGGGACAAAGTGGGAAGGGGAGGGGGGGGGATCAGCTCCACAAACCCGCCAATTTAGTTCTCCTCCATg  >  2:649593/1‑149 (MQ=255)                                                                                                                                                        |                                                                                                                                                        GATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTT‑CCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAAT‑GCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGC‑AACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGC‑AAGAG‑AAATAGC‑TTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCGCCTCAATG  >  NC_000913/357742‑358037

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑