Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	357,890	0	C	A	44.9%	48.5 / 23.5	49	L267F (TTG→TTT)	cynR	transcriptional activator of cyn operon; autorepressor
Reads supporting (aligned to +/- strand):  ref base C (21/6);  new base A (0/22);  total (21/28)
Fisher's exact test for biased strand distribution p-value = 7.74e-09
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.67e-01

AAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGA‑TTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCAT‑GTGCAAAAATG‑CCTT‑CGCGGC‑GGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAA  >  NC_000913/357745‑358011                                                                                                                                                       |                                                                                                                             aaGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGA‑TTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCAT‑GTGCAAAAATG‑CCTT‑CGCGGC‑GGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAAc                                                                                                                         <  2:980881/151‑1 (MQ=255)  aGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGA‑TTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCAT‑GTGCAAAAATG‑CCTT‑CGCGGC‑GGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAAcc                                                                                                                        >  1:1333699/1‑151 (MQ=255)            aTCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGA‑TTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCAT‑GTGCAAAAATG‑CCTT‑CGCGGC‑GGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTtctct                                                                                                              >  1:87304/1‑151 (MQ=255)                 gCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGA‑TTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCAT‑GTGCAAAAATG‑CCTT‑CGCGGC‑GGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCag                                                                                                          >  1:1109801/1‑150 (MQ=255)                   aaTTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGA‑TTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCAT‑GTGCAAAAATG‑CCTT‑CGCGGC‑GGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCagt                                                                                                         >  2:524045/1‑149 (MQ=255)                    aTTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGA‑TTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCAT‑GTGCAAAAATG‑CCTT‑CGCGGC‑GGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCagtagt                                                                                                      >  1:315271/1‑151 (MQ=255)                       ccAGCCGCAGCCTTGTGCCAGCGGCTACCGTGT‑TTCTTTCCCCCCAACACCCGCGCTTTTACCCAACCCCAT‑GTAAAAAAATC‑CCTC‑CGGGGC‑GGCTGTCTCCCAGTTTTTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTg                                                                                                     <  1:1523284/149‑1 (MQ=255)                          gCCGCAGACCTGTGTCAGCGGCTACCGTGA‑TTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCAT‑GTGCAAAAATG‑CCTT‑CGCGGC‑GGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGC‑ggg                                                                                               >  1:1227948/1‑151 (MQ=255)                            cGCAGCCCTGTGTCAGGGCCTCCCGTGA‑TTCATTCCCGCCAACAACCGCGCTTTTACCCACCCCAAT‑GTGAAAAAAGC‑CCTT‑CGCGGC‑GGCTGTCTGCCAGTTTTTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGC‑g                                                                                                 <  1:1020155/147‑1 (MQ=18)                            cGCAGACCTGTGTCAGCGGCTACCGTGA‑TTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCAT‑GTGCAAAAATG‑CCTT‑CGCGGC‑GGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGC‑ggggg                                                                                             >  1:548763/1‑150 (MQ=255)                              caccccTGTGTCAGCGTCTACCGTGT‑TTCTTTCCCCCAAACACCCGCCCTTTTACCCAACCCCAT‑GTCCAAAAATG‑CCTT‑CGCGGC‑GGCTGTCGCCCAATTTTTTTCCCGCCGAAACAAAACCGCCGTTCTCTCCAGTAGTGGC‑ggg                                                                                               <  1:480785/143‑1 (MQ=255)                                gccgggtggCAGGGGCTGCCGTGA‑TTCTTTCCCTCAAACACCCGCGCTTTTACCCACCGCCGT‑GTGAAAAAGTG‑CTTC‑CGCGGG‑GGTTGTCTGCCATCTATTTTCCCCCCCAAAAAAACCCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAag                                                                                          <  1:1380098/145‑1 (MQ=255)                                   cTGTGTCAGCGGCTACCGTGA‑TTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCAT‑GTGCAAAAATG‑CCTT‑CGCGGC‑GGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGGAaga                                                                                         >  1:1476667/1‑148 (MQ=255)                                      tgtCGGCGCCTA‑CGTGATTTCATTCCCGCCAACACCGGCCCTTTTACCCACCGCCAT‑GTGAAAAAATC‑CTTC‑CGGGGC‑GGCTGTCTGCAAGTTTTTTTCCGGCCAAAACAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAG‑aa                                                                                     <  2:810564/148‑1 (MQ=255)                                      tgtCAGCGGCTCCCGTTT‑TTCATTCCCGCCAACACCCGCGCTTTTACCCACCCCCAT‑GTGCAAAAATG‑CCTT‑CGGGGC‑GGCTGTCTGCCAGTTTTTTTTCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAG‑aa                                                                                     <  1:489548/148‑1 (MQ=255)                                      tgccggCGGCTCCGGTGT‑TTCATTCCCCCCACCACCCGCGCATTTCCCCACCGCATT‑GTGAAAAAATG‑CCTG‑CGGGGC‑GGCGGCCTGCCAGTTTTTTTCCCGCCCCAAAAAACCCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAagag                                                                                        <  2:227872/141‑1 (MQ=255)                                       gtCAGCGGCTACCGTGA‑TTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCAT‑GTGCAAAAATG‑CCTT‑CGCGGC‑GGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGGAAAAG‑aaaa                                                                                   >  1:603323/1‑148 (MQ=255)                                         cggcgccccccGTGT‑TTCTTTCCCCCCAACACCCCCGCTTTTACCCACCCCATT‑GTGAAAAAAGG‑CCTT‑CGGGGC‑GGCTGTCTGCCAGTTTTTTTCCCCCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAG‑AAATAGCt                                                                               <  1:17421/142‑1 (MQ=255)                                           gCGGCTACCGTGA‑TTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCAT‑GTGCAAAAATG‑CCTT‑CGCGGC‑GGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGGAaggggaaaaaaaat                                                                              >  1:544813/1‑139 (MQ=255)                                            cgactcctgtgt‑TTCATTCCCCCCACCACCCGCGCTTTTACCAACCCCCAT‑GTGAAAAAATG‑CCTC‑GGGGGC‑GGTTTTCCCCCAGTTATTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAG‑AAATAGc                                                                                <  1:495306/139‑1 (MQ=255)                                             ggCTCCCGTGT‑TTCATTCCCCCCAACACCCGCGCTTTTATCCAACGCCAT‑GTGAAAAAATG‑CCTT‑CGGGGC‑GGCTGTCTCCCAGCTATTTTCCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAG‑AAATAGCt                                                                               <  1:241994/147‑1 (MQ=255)                                             ggCTCCCGTGA‑TTCTTTCCCCCAAACACCCGCCCTTTTACCAACCGCCAT‑GTGAAAAAATC‑CTTC‑CGCGGC‑GGCTGTCCCCCAGTTTTTTTTCCCCCGAAACAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAG‑AAATAGCtt                                                                              <  1:841104/148‑1 (MQ=255)                                             ggCTACCGTGA‑TTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCAT‑GTGCAAAAATG‑CCTT‑CGCGGC‑GGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGGGAGAG‑AAAAAACttt                                                                             >  1:1417204/1‑149 (MQ=255)                                               cTACCGTGA‑TTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCAT‑GTGCAAAAATG‑CCTT‑CGCGGC‑GGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGTGGAAGAG‑AAAAAggatt                                                                             >  1:615413/1‑143 (MQ=255)                                               cTACCGTGA‑TTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCAT‑GTGCAAAAATG‑CCTT‑CGCGGC‑GGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCacggaaaaaaaaat                                                                               >  1:1135726/1‑133 (MQ=255)                                                tACCGTGA‑TTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCAT‑GTGCAAAAATG‑CCTT‑CGCGGC‑GGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCGAGAG‑AAAAAGCttt                                                                             >  1:1315254/1‑146 (MQ=255)                                                 aCCGTGA‑TTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCAT‑GTGCAAAAATG‑CCTT‑CGCGGC‑GGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACTGCCGTTCTCTCCAGTAGTGGCGGGGGCAGGAG‑AAAAAATTTTAAccc                                                                        >  2:712911/1‑151 (MQ=21)                                                  cgttta‑TTCTTTCCCACCAACACCGGCACATTTACCCACCGCTTT‑GTG‑AAAAATG‑CCTTCCGGGGC‑GGCTGTCTCCCAGTTATTTTCCCCCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAG‑AAATAGCTTTAAGc                                                                         <  1:695364/143‑1 (MQ=255)                                                   ccttgtttCATTTCCCCAAACACCCGC‑CTTTTTCCCAACCCCCTGGTGAAAAAAT‑‑CCTT‑GGGGGCGGGCTGCCTGCCGGTTTTTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAG‑AAATAGCTTTAAGCCCg                                                                      <  2:266862/145‑1 (MQ=255)                                                             ttccccccAACACCCGCGTTTTTACCCAACGCATT‑GTGAAAAAATC‑CCTC‑CGGGGC‑GGTTGTCGCCCATTTTTTTTTCCCCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAG‑AAATAGCTTTAAGCCCGTCAtgttg                                                              <  1:838362/143‑1 (MQ=255)                                                             ttccccccAACACCCGCGCATTTACCCACCCCCAT‑GTGAAAAAATC‑CTTC‑CGCGGC‑GGTTGTCTGCCACCTATTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAG‑AAATAGCTTTAAGCCCGTCAtg                                                                 <  1:886039/140‑1 (MQ=255)                                                               cccccaaacaccCGCGCATTTACCCACCGCCAT‑GT‑AAAAAAAG‑CCTTCCGCGGC‑GGCTGTCTGCCAGTTTTTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTtgtg                                                            <  1:1268615/143‑1 (MQ=255)                                                                ccccaaacaccCGCGCTTTTACCCACCGCCAT‑GTGAAAAAAGG‑CCTT‑CGGGGC‑GGCTGTCTGCCAGTTATTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTgg                                                         <  1:1034416/146‑1 (MQ=255)                                                                          ccGCGC‑TTTATCCCACCGCAT‑GTGAAAAAAAGCCCTC‑CGGGGC‑GGTTGTCTGCCAGTTTTTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCgct                                                 <  2:189732/149‑1 (MQ=255)                                                                                  ttACCCAACCCCAT‑GTGAAAAAATG‑CCTT‑CGCGGG‑GGTTTTCTGCCAGCTTTTTTCCCGCCAAAAAAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGTAAc                                       <  1:576704/150‑1 (MQ=255)                                                                                       cAACGCCAT‑GTGCAAAAATG‑CCTT‑CGCGGC‑GGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGGGAGAGAAAAAAAATTTAATCCC‑TCCTTTTTTGTGGGGATCGCCGCC‑GGTAAAAAagtg                                 >  1:749622/1‑151 (MQ=21)                                                                                          cGCCAT‑GTGCAAAAATG‑CCTT‑CGCGGC‑GGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGGACGGG‑AAAAAGAATTAAAACCCCCCTGTTTTGTGGGAATCGCTGCT‑GGtgaaa                                      >  2:432858/1‑139 (MQ=25)                                                                                            cgcgatggaaaaaaTGCCCTC‑CGGGGG‑GGCTGTCTGCCAGTTATTTTCCCGCCGAAACAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGTAACAAtgt                                  <  2:1174745/138‑1 (MQ=255)                                                                                            ccAT‑GTGCAAAAATG‑CCTT‑CGCGGC‑GGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGGGAGAGAAAAAAAATTTAAACCC‑CCCTGTTGTGTGGGGATCGCCGCT‑ggggaaaa                                     >  1:176975/1‑136 (MQ=25)                                                                                            ccAT‑GTAAAAAAAGG‑CTTC‑CGCGGC‑GGCTGTCTGCCATTTTTTTTCCCCCCGCAAAAAATCCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGTAACAATGTGGAAAg                            <  2:997667/151‑1 (MQ=255)                                                                                                 gtgCAAAAATG‑CCTT‑CGCGGC‑GGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGGGAGAG‑AAAAAAATTTTAAACCCCCCTGTTTTGTGGGAATTGCCTCT‑GGGGACAAATTGGGAAggg                          >  1:637463/1‑149 (MQ=255)                                                                                                  tgaaaaaaTG‑CTTT‑CGGGGC‑GGCTGTCTGCCAGTTTTTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGTAACAATGTGGAAAggg                          <  1:926333/145‑1 (MQ=255)                                                                                                   aaaaaaaTC‑CCTC‑CGCGGC‑GCCTTCCGCCCAGTTTTTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGTAACAATGTGGAAAGGGAAg                       <  2:436459/148‑1 (MQ=255)                                                                                                      aaaaTG‑CCTT‑CGCGGC‑GGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGGGAGAG‑AAAAAAATTTTAAACCGCCCTGTTTTGTGGGGATTGCCGCT‑TGGGAAAATGTGGGAAGGGagggggg                   >  1:11832/1‑145 (MQ=255)                                                                                                           g‑CCTT‑CGCGGC‑GGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGGGAGAG‑AAAAAAAATTAAAACCCTCCTGTTTTTTGGGGATCGCTGGTGGGTAAAAAATGGGAAAGGGagggggggg                 >  1:1256080/1‑141 (MQ=255)                                                                                                                      gggggcTGTCGCCCAGTTTTTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTc       <  1:30801/147‑1 (MQ=255)                                                                                                                         ggcTGTCTCCCAGTTTTTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAg    <  1:366286/150‑1 (MQ=255)                                                                                                                                tgccattttttttcCCGCAGCAAAAAACCCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGaa  <  2:1233984/136‑1 (MQ=255)                                                                                                                                      attttttcCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGaa  <  2:544804/136‑1 (MQ=255)                                                                                                                                                       |                                                                                                                             AAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGA‑TTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCAT‑GTGCAAAAATG‑CCTT‑CGCGGC‑GGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAA  >  NC_000913/357745‑358011

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 25 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑