Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	357,875	0	A	T	48.0%	43.3 / 24.2	50	N272K (AAT→AAA)	cynR	transcriptional activator of cyn operon; autorepressor
Reads supporting (aligned to +/- strand):  ref base A (13/13);  new base T (0/24);  total (13/37)
Fisher's exact test for biased strand distribution p-value = 3.63e-05
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GAACTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGA‑TTCATTTCCGCCAA‑CAACCGCGCATTTA‑TCCAACGCC‑ATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACC  >  NC_000913/357728‑358013                                                                                                                                                         |                                                                                                                                           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)                                                                                                                                                 ggccggttATTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAAc   <  1:1218756/139‑1 (MQ=255)                                                                                                                                                   ccAGTTTTTTTCCCGCCGAAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAAcc  <  1:145731/145‑1 (MQ=255)                                                                                                                                                         |                                                                                                                                           GAACTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGA‑TTCATTTCCGCCAA‑CAACCGCGCATTTA‑TCCAACGCC‑ATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACC  >  NC_000913/357728‑358013

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: ‑