Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	357,873	0	C	T	44.9%	37.3 / 26.0	50	S273N (AGC→AAC)	cynR	transcriptional activator of cyn operon; autorepressor
Reads supporting (aligned to +/- strand):  ref base C (14/13);  new base T (0/22);  total (14/36)
Fisher's exact test for biased strand distribution p-value = 5.01e-05
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GCACTGAACTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGA‑TTCATTTCCGCCAA‑CAACCGCGCATTTA‑TCCAACGCC‑ATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACC  >  NC_000913/357723‑358013                                                                                                                                                            |                                                                                                                                             gCACTGAACTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGA‑TTCATTTCCGCCAA‑CAACCGCGCATTTA‑TCCAACGCC‑ATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGc                                                                                                                                              >  1:551805/1‑151 (MQ=255)   aCTGAACTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGA‑TTCATTTCCGCCAA‑CAACCGCGCATTTA‑TCCAACGCC‑ATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGCt                                                                                                                                             >  2:812364/1‑150 (MQ=255)      gAACTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGA‑TTCATTTCCGCCAA‑CAACCGCGCATTTA‑TCCAACGCC‑ATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGCTAtt                                                                                                                                          <  1:1190321/150‑1 (MQ=255)      gAACTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGA‑TTCATTTCCGCCAA‑CAACCGCGCATTTA‑TCCAACGCC‑ATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGCTAtt                                                                                                                                          <  2:1021583/150‑1 (MQ=255)       aaCTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGA‑TTCATTTCCGCCAA‑CAACCGCGCATTTA‑TCCAACGCC‑ATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGCTAtttt                                                                                                                                        >  2:965942/1‑151 (MQ=255)        aCTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGA‑TTCATTTCCGCCAA‑CAACCGCGCATTTA‑TCCAACGCC‑ATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGCTAttttt                                                                                                                                       >  2:1218880/1‑151 (MQ=255)           cGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGA‑TTCATTTCCGCCAA‑CAACCGCGCATTTA‑TCCAACGCC‑ATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTccg                                                                                                                                    <  1:180967/151‑1 (MQ=255)            gTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGA‑TTCATTTCCGCCAA‑CAACCGCGCATTTA‑TCCAACGCC‑ATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTccgc                                                                                                                                   >  1:1254192/1‑151 (MQ=255)              aGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGA‑TTCATTTCCGCCAA‑CAACCGCGCATTTA‑TCCAACGCC‑ATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTccgccg                                                                                                                                 >  2:604139/1‑151 (MQ=255)              aGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGA‑TTCATTTCCGCCAA‑CAACCGCGCATTTA‑TCCAACGCC‑ATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTccgccg                                                                                                                                 >  2:145744/1‑151 (MQ=255)                gCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGA‑TTCATTTCCGCCAA‑CAACCGCGCATTTA‑TCCAACGCC‑ATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGca                                                                                                                               <  1:302631/151‑1 (MQ=255)                       aaGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGA‑TTCATTTCCGCCAA‑CAACCGCGCATTTA‑TCCAACGCC‑ATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAAc                                                                                                                        <  1:527466/151‑1 (MQ=255)                                   tCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGA‑TTCATTTCCGCCAA‑CAACCGCGCATTTA‑TCCAACGCC‑ATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTtctctc                                                                                                            >  2:1002227/1‑151 (MQ=255)                                      gcaaaTCCCAGCCGAGGCCTTGTGTCAGCGGCTCCCGTGA‑TTCATTCCCGCAAA‑CACCCGCGCTTTTA‑TCCAACGCC‑ATGTGCAAAAATGCCTC‑CGCGGCGGCTGTCTGCAAGTTATTTTTCCGCCGCAAAAAAAccgccg                                                                                                                   <  1:1185898/138‑1 (MQ=17)                                           tcccACCCGCAGCCTGGTGCCGGGGGCTACGGTGT‑TTATTTCCCGCAAA‑AACCCGCGCTTTTA‑CCCAACCCC‑TTGTAAAAAAATGCTTC‑CGGGGGGGCTGTCGGCCAGTTTTTTTCCCGCCGAAACAAAACCGCCGTTCTCTCCagtagt                                                                                                     <  2:1211666/148‑1 (MQ=255)                                            tCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGA‑TTCATTTCCGCCAA‑CAACCGCGCATTTA‑TCCAACGCC‑ATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTgg                                                                                                   >  1:851415/1‑151 (MQ=255)                                             ccggCCGGAGCCTTGTGCCGGCGGCTACCTTGA‑TTTTTTCCCCCAAA‑CACCCGCACATTTA‑CCCACCCCC‑TTTGGAAAAATTGCCTC‑CGCGGCGGCTGTCTGCAAGTTTTTTTCCCGCCCCAAAAAAACCGCCGTTCTCTCCAGTAGTg                                                                                                    <  2:1015942/146‑1 (MQ=255)                                              cAGCCGCAGACCTGTGTCAGCGGCTACCGTGA‑TTCATTTCCGCCAA‑CAACCGCGCATTTA‑TCCAACGCC‑ATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCg                                                                                                 >  2:998059/1‑151 (MQ=255)                                               aGCCGCAGACCTGTGTCAGCGGCTACCGTGA‑TTCATTTCCGCCAA‑CAACCGCGCATTTA‑TCCAACGCC‑ATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCgg                                                                                                >  2:97630/1‑151 (MQ=255)                                                 ccGCAGCCCTGGGCCAGCGCCTACCGTAT‑TTCTTTCCCCCCAA‑CACCCGCGCTTTTA‑CCCACCGCC‑ATGTGAAAAAATCCCTC‑CGGGGCGGTTGTCTCCCAGTTTTTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCggg                                                                                               <  2:642170/150‑1 (MQ=255)                                                 ccGCAGACCTGT‑TCAGCCGGAACCCTTATTTCATTCCCGCAAA‑CACCCGCG‑ATTTACCCCAACGCA‑AGGTAC‑AAAATGCCTTGCGCGGGGGCTGTCTGCAACCTATTTTCCCGCCAAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCgggg                                                                                              <  2:1198551/151‑1 (MQ=255)                                                  cgcaacctggtgcCAGCGGCTCCCGTTT‑TTCATTCCCCCCAA‑CACCCGCGCTTTAA‑CCCAACGCC‑TTGTAAAAAAATCCCTC‑CGCGGCGGCTGTCGGCCAGTTTTTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCgggg                                                                                              <  1:1209561/141‑1 (MQ=255)                                                  cgaagcccTGTGTCAGGGGCTCCCGTGT‑TTCTTTCCCGCCAC‑CACCCGCGCTTTTA‑‑CCAACCCCAATGTGAAAAATTGCCTC‑CGGGGCGGCTTTCTGCTAGTTTTTTTCCCGCCAAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGc                                                                                             <  2:1139967/145‑1 (MQ=255)                                                    cggccgtttgccggCGTCTACCGTAA‑TTCTTTCCCCCCAC‑CACCCGCGTTTTTA‑CCCACCCCC‑ATGAGAAAAAAGGCCTC‑CGGGGGGGTTTTCTGCCAGTTTTTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGc                                                                                             <  1:922202/136‑1 (MQ=255)                                                      gACCTGTGTCAGCGGCTACCGTGA‑TTCATTTCCGCCAA‑CAACCGCGCATTTA‑TCCAACGCC‑ATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCgg                                                                                                >  2:187327/1‑144 (MQ=255)                                                               cggcgcCTACCGTAA‑TTCTTTCCCCCCAA‑CACCCCCCCTTTTA‑TCCAACCCA‑ATGTGCAAAAATGCCTT‑CGGGGCGGCTGTCGGCCCGTTATTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAg                                                                                  <  2:515583/147‑1 (MQ=255)                                                                   gcctccgttGA‑TTCTTTCCCCCCAA‑CACCCCCGCATTTA‑CCCACCGCC‑ATGTGAAAAAATCCCTC‑CGCGGCGGTTTCCGGCCAGTTTTTTTCCCGCCAAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATa                                                                                   <  1:115389/136‑1 (MQ=255)                                                                   gcctcccGTGA‑TTCTTTCCCCCCAA‑CACCCGCGCTTTTA‑CCCACCGCC‑ATGTGAAAAAATGCCTC‑CGGGGGGGCTGTCTGCCAGCTTTTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCt                                                                                <  2:825477/142‑1 (MQ=255)                                                                      tACCGTGA‑TTCATTTCCGCCAA‑CAACCGCGCATTTA‑TCCAACGCC‑ATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGGAGAGAAAAAGAttt                                                                              >  1:584735/1‑146 (MQ=255)                                                                       cccGTGT‑TTCTTTCCCCCCAA‑CACCCGCCCTTTTA‑‑CCAACCCCAAGGTGAAAAAATCCCTC‑CGGGGGGGCTGTCGGCAAGTTATTTTCCCGCCAAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGccc                                                                        <  1:139969/150‑1 (MQ=255)                                                                       cccGTGT‑TTC‑TTTCCCCCAACCACCCGCGCTTTTA‑CCCACCGCC‑TGGTAAAAAAATGCCTC‑CGGGGCGGTTGTCGGCAAGTTTTTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGc                                                                          <  1:1061724/148‑1 (MQ=255)                                                                       aCCGTGA‑TTCATTTCCGCCAA‑CAACCGCGCATTTA‑TCCAACGCC‑ATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGGAGAGAAAAAAATTTaaaacc                                                                        >  2:556077/1‑147 (MQ=25)                                                                        ccGTGT‑TTTTTTCCCCCCAA‑CACCCGCGCATTTA‑CCCAACGCC‑ATGTGCAAAAATGCCTC‑CGGGGCGGCTGTCTGCCAGCTTTTTTCCCGCCGAAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGccc                                                                        <  2:159503/150‑1 (MQ=25)                                                                        ccGTGA‑TTCTTTCCCCCCAA‑CACCCGCGCATTTA‑CCCACCGCC‑TTGTGAAAAAATGCCTT‑CGCGGCGGCTGTCGGCCAGTTTTTTTTCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGc                                                                          <  2:788332/148‑1 (MQ=255)                                                                           tGA‑TTCATTTCCGCCAA‑CAACCGCGCATTTA‑TCCAACGCC‑ATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGCAGAGgaaaaagttt                                                                              >  2:592861/1‑134 (MQ=25)                                                                            gA‑TTCTTTCCCCCCAA‑CACCCGCCTATTTA‑CCCACCCCC‑AGGTCCAAAAAGCCCTC‑CGGGGGGCTTGTCCGCCAGTTTTTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGt                                                                      <  1:171552/148‑1 (MQ=255)                                                                               ttCTTTCCCGCAAA‑CACCCGCGATTTTA‑CCAAACGCC‑ATGTGAAAAATTGCCTC‑CGGGGGGGTTGTCGGCCACTTATTTTCCCCCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCAtg                                                                  <  2:452240/150‑1 (MQ=255)                                                                                     ccccccAA‑CACCCCCCCTTTTA‑CCCACCGCC‑ATGTGAAAAAATCCCTC‑CGCGGCGGCTGTCTGCAAGCTTTTTTCCCGCCAAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTtgtgtg                                                           <  1:556026/147‑1 (MQ=255)                                                                                               acccGCGCATTTA‑CCCACCGCA‑ATGTGAAAAAATCCCTT‑CGGGGCGGTTGTCTCCCAGTTTTTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATc                                                     <  2:845587/146‑1 (MQ=255)                                                                                                        tttA‑TCCACCGCC‑ATGAAAAAAAGTCCCTG‑CGCGGGGGTTTCCGCCCAGTTTTTTTCCCCCCACAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGt                                            <  1:786247/148‑1 (MQ=255)                                                                                                              ccACCGCC‑ATGTGAAAAAATGCCTC‑CGCGGCGGCTGTCTGCCAGCTTTTTTCCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAAt                                      <  1:370226/149‑1 (MQ=255)                                                                                                              ccAACGCC‑ATGTGAAAAAATGCCTC‑CGCGGCGGCTGTCTGCCAGCTTTTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACaa                                       <  2:954857/148‑1 (MQ=255)                                                                                                                  cGCC‑ATGTAAAAAAATGCCTT‑CGGGGCGGCTTTCTGCCAGTTTTTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGACAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAAtgt                                    <  2:14748/147‑1 (MQ=255)                                                                                                                    cc‑ATGTGAAAAAAGCCCTC‑CGCGGCGGCTGTCGGCCAGTTTTTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGaaa                               <  2:449158/150‑1 (MQ=255)                                                                                                                             aaaaaTGCTTG‑CGTGGCGGATGACTGCAACAAATTTTCCCGCCGAAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAg                         <  2:462029/148‑1 (MQ=255)                                                                                                                             aaaaaGGCCTG‑CGCGGCGGCTTTCTCCCATCTTTTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGt                        <  1:568480/149‑1 (MQ=255)                                                                                                                                aaaccctcccgcgCCGGTTGTCAGCCGTTTTTTTTCCCCCCCCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTgcgg                    <  1:278901/142‑1 (MQ=255)                                                                                                                                          gggggggcTGTCGGCCGGTTTTTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATc              <  2:1066980/142‑1 (MQ=255)                                                                                                                                              cggcTTTCCGCCAGCTATTTCCCCGCCACAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCa       <  1:812295/150‑1 (MQ=255)                                                                                                                                                     cTGCCAGTTTTTTTCCCCCCCCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAg      <  1:1143432/144‑1 (MQ=255)                                                                                                                                                        ccAGTTTTTTTCCCGCCGAAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAAcc  <  1:145731/145‑1 (MQ=255)                                                                                                                                                            |                                                                                                                                             GCACTGAACTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGA‑TTCATTTCCGCCAA‑CAACCGCGCATTTA‑TCCAACGCC‑ATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACC  >  NC_000913/357723‑358013

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: ‑