Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	357,880	0	T	C	55.0%	23.3 / 55.6	40	K271E (AAA→GAA)	cynR	transcriptional activator of cyn operon; autorepressor
Reads supporting (aligned to +/- strand):  ref base T (14/4);  new base C (0/22);  total (14/26)
Fisher's exact test for biased strand distribution p-value = 1.32e-07
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 2.14e-08

CGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCC‑AA‑CAACCGCGCATTTATCCAACGCCATGTGCAAAAATG‑CCTT‑CGCGGCGGCTGT‑CTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTC  >  NC_000913/357733‑358006                                                                                                                                                         |                                                                                                                                cGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCC‑AA‑CAACCGCGCATTTATCCAACGCCATGTGCAAAAATG‑CCTT‑CGCGGCGGCTGT‑CTGCCAGCTATTTTTc                                                                                                                                <  2:181129/149‑1 (MQ=255)  gTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCC‑AA‑CAACCGCGCATTTATCCAACGCCATGTGCAAAAATG‑CCTT‑CGCGGCGGCTGT‑CTGCCAGCTATTTTTccgc                                                                                                                             >  2:750639/1‑151 (MQ=255)         tGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCC‑AA‑CAACCGCGCATTTATCCAACGCCATGTGCAAAAATG‑CCTT‑CGCGGCGGCTGT‑CTGCCAGCTATTTTTCCGCCGcaac                                                                                                                       >  1:564929/1‑150 (MQ=255)          gATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCC‑AA‑CAACCGCGCATTTATCCAACGCCATGTGCAAAAATG‑CCTT‑CGCGGCGGCTGT‑CTGCCAGCTATTTTTCCGCCGcaaca                                                                                                                      <  1:15617/150‑1 (MQ=255)           aTAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCC‑AA‑CAACCGCGCATTTATCCAACGCCATGTGCAAAAATG‑CCTT‑CGCGGCGGCTGT‑CTGCCAGCTATTTTTCCGCCGCAACaaa                                                                                                                    <  1:415236/151‑1 (MQ=255)                    gcgcATCAGGAAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCC‑AA‑CACCCGCGCATTTATCCACCGCCATGTGCAAAAATG‑CCTT‑CGCGGCGGCTGT‑CTGCCAGCTATTTTTCCGCCGCAACAAAAccgccg                                                                                                             <  1:192510/149‑1 (MQ=255)                      gcATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCC‑AA‑CAACCGCGCATTTATCCAACGCCATGTGCAAAAATG‑CCTT‑CGCGGCGGCTGT‑CTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTtct                                                                                                         >  1:482654/1‑151 (MQ=255)                           aGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCC‑AA‑CAACCGCGCATTTATCCAACGCCATGTGCAAAAATG‑CCTT‑CGCGGCGGCTGT‑CTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTcc                                                                                                     >  2:260626/1‑150 (MQ=255)                              cAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCC‑AA‑CAACCGCGCATTTATCCAACGCCATGTGCAAAAATG‑CCTT‑CGCGGCGGCTGT‑CTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCagt                                                                                                  >  2:258051/1‑150 (MQ=255)                                  cccACCCGCGGCCTTGTGCCAGCGCCTCCGGTGATTCTTTCCCCCC‑AA‑CACCCGCGCTTTTACCCACCCCCATGTAAAAAAATC‑CCTC‑CGGGGCGCCTGC‑CGGCCATTTTTTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCagtagt                                                                                               <  2:348496/148‑1 (MQ=255)                                       ccccagccttgttTCCGCGGCTACGTTAATTATTTCCCGCC‑AA‑CACCCGCGTTTTTACCCACCCCCGTTGGAAAAATTT‑CCTT‑CGGGGCGGCTCT‑CTGCCTGTTTTTTTCCCCCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCg                                                                                           <  2:562962/139‑1 (MQ=255)                                       ccGCAGCCCTGTGTCAGCGGCTCCCGTGATTCTTTCCCCCA‑AA‑CACCCGCGCTTTTACCCAACGCCTTGTGAAAAAATC‑CCTT‑CGGGGCGGCTTT‑CGGCCAGTTATTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCg                                                                                           <  1:504421/148‑1 (MQ=255)                                       ccGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCC‑AA‑CAACCGCGCATTTATCCAACGCCATGTGCAAAAATG‑CCTT‑CGCGGCGGCTGT‑CTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCgg                                                                                          >  1:75664/1‑149 (MQ=255)                                          cAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCC‑AA‑CAACCGCGCATTTATCCAACGCCATGTGCAAAAATG‑CCTT‑CGCGGCGGCTGT‑CTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCgggg                                                                                        >  2:242796/1‑148 (MQ=255)                                           aGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCC‑AA‑CAACCGCGCATTTATCCAACGCCATGTGCAAAAATG‑CCTT‑CGCGGCGGCTGT‑CTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCgggg                                                                                        >  1:300431/1‑147 (MQ=255)                                              cttgtgTCAGCGGCTCCCGTAATTCTTTCCCGCC‑AA‑CACCCGCGCTTTTACCCACCCCCATGTGAAAAAATC‑CCTC‑CGGGGCGGCTGT‑CTCCCAGTTTTTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAaga‑g                                                                                 <  1:355927/148‑1 (MQ=255)                                                tgtgccggggcctgccGTGATTCATTTCCGCA‑AA‑CACCCCCTAATTTACCCACCCCCTTGT‑AAAAAATT‑CCTTCCGGGGGGCCTGC‑CTCCCGCCTTTTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAag                                                                                    <  1:550893/132‑1 (MQ=255)                                                  tgccAGCGCCCACCGTTATTCTTTCCCCCA‑AA‑CACCCGCGCTTTTACCCACCGCCATGTGAAAAAAGG‑CCTC‑CGGGGCGGCTTT‑CGGCCAGTTTTTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑Gaaa                                                                              <  2:564926/146‑1 (MQ=255)                                                        cGGCTACCGTGATTCATTTCCGCC‑AA‑CAACCGCGCATTTATCCAACGCCATGTGCAAAAATG‑CCTT‑CGCGGCGGCTGT‑CTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCGAGA‑Gaaaaaaaat                                                                        >  1:100384/1‑143 (MQ=255)                                                         ggCTCCCGTGTTTCATTCCCCCC‑AA‑CACCCGCGCTTTTACCCACCCCCATGTGAAAAAAGC‑CCTT‑CGCGGCGGTTGT‑CTGCCAGTTTTTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGCttt                                                                       <  1:680777/149‑1 (MQ=255)                                                            cacccgtgttCCTTTCCCCCAAA‑CACCCGCG‑ATTTACCCCACCCCGTTGGCAAAAAAT‑CCTTCCGGGGGGGCTGC‑CCGCCAGTTTTTTTCCCGCGACAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑Gaa                                                                               <  2:70761/131‑1 (MQ=255)                                                              ccGTGTTTCTTTCCCCCC‑AA‑CACCCGCCCTTTTACCCACCCCCATGTGAAAAAAGG‑CCTC‑CGCGGCGGCTTT‑CTGCCATTTTTTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGCTTTaa                                                                     <  1:424260/146‑1 (MQ=255)                                                                gTGATTCATTCCCCCC‑AA‑CACCCGCGATTTTACCCACCCCCGTGTGAAAAATTG‑CCTC‑GGCGGCGCTTGT‑CTCCCATTTTTTTTCCCGCCACAAAAAAGCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGCt                                                                         <  1:515083/140‑1 (MQ=255)                                                                     ttaattCCCCC‑AACCACCCGCCCTTTTACCCAACGCCATGTGAAAAAATC‑CCTC‑CGGGGCGCTTGT‑CTCCCAGTTTTTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGCTTTAAGCCCGt                                                               <  1:760354/142‑1 (MQ=255)                                                                           ccccc‑ac‑caCCCGCCCTTTTACCCACCCCCTTGTCAAAAAATC‑CCTC‑CGGGGCGGTTGC‑CGCCCAGTTTTTTTCCCCCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGCTTTAAGCCCGTCATGTtgtgt                                                     <  1:132182/146‑1 (MQ=255)                                                                            cGCC‑AA‑CAACCGCGCATTTATCCAACGCCATGTGCAAAAATG‑CCTT‑CGCGGCGGCTGT‑CTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAAA‑GAAAAAAATTTAAAACCCTCCCGTtgtgt                                                     >  1:629615/1‑148 (MQ=25)                                                                                        cgcgCATTTATCCAACGCCATGTGCAAAAATG‑CCTT‑CGCGGCGGCTGT‑CTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGAAGAGGAAAAACATTTAAACCCg                                                                >  2:258472/1‑128 (MQ=37)                                                                                                     atcgcggtgcaaaaaaaCG‑CCTG‑CGCGGCGCTTGT‑CTGCGTGTTTTTTTCCCGCCGCAAAAAAGCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAAtg                              <  1:94712/136‑1 (MQ=255)                                                                                                      aCGCCATGTGCAAAAATG‑CCTT‑CGCGGCGGCTGT‑CTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGCGAA‑GGAAAAAAACTAAGCCCGCCACGTTTTGTGGGAGTCgctggcggggaaaaagagg                           >  2:507225/1‑135 (MQ=19)                                                                                                       cGCCATGTGAAAAAAGC‑CCTC‑CGGGGCGGTTGT‑CGGCAAGTTTTTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTgg                           <  2:338590/149‑1 (MQ=255)                                                                                                       cGCCAGGTG‑AAAAATGCCCTC‑CGCGGCGGCTTT‑CTCCCAGTTTTTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGa                          <  1:242798/150‑1 (MQ=255)                                                                                                        gCCATGTGCAAAAATG‑CCTT‑CGCGGCGGCTGT‑CTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGGAGA‑GAAAAAAATTTTAAACCCCCCTGTTTTGTGGGGATCGCCGCTggggaaaaagtgg                           >  1:721268/1‑137 (MQ=21)                                                                                                               gCAAAAATG‑CCTT‑CGCGGCGGCTGT‑CTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCCAGA‑GAAAAAAATTTAAAACCCCCATTTTTTGTGGGAAACGCCGCTGGGGACAAATTGGGAAgggga                   >  1:571346/1‑147 (MQ=255)                                                                                                                 aaaaaGG‑CC‑T‑CGGGGGGGCTTTCCTGCCTGTTTTTTTCCCGCCAAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTgc               <  2:545779/151‑1 (MQ=255)                                                                                                                   aaattccttt‑CGGGGCGCTTGT‑CGCCCACCTTTTTTCCCGCCCCAACAAACCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTgcg              <  1:434462/143‑1 (MQ=255)                                                                                                                    aaTC‑CCTT‑GGCGGCGGCTTC‑CGGCCATTTTTTTGCCCGCCACAACAAACCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTgcggc            <  1:759902/151‑1 (MQ=255)                                                                                                                      aatccctcgggggcggcGGT‑CGGCCGTTTTTTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTgcggc            <  2:732378/140‑1 (MQ=255)                                                                                                                               ggggcggcTGT‑CTGCAATTTTTTTTCCCGCCGAAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGc    <  2:518819/148‑1 (MQ=255)                                                                                                                                 ggcggtTGT‑CGCCCATTTTTTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTc  <  2:346351/150‑1 (MQ=255)                                                                                                                                 ggcggcTGT‑CTGCCAGCTTTTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCa      <  1:260628/146‑1 (MQ=255)                                                                                                                                                         |                                                                                                                                CGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCC‑AA‑CAACCGCGCATTTATCCAACGCCATGTGCAAAAATG‑CCTT‑CGCGGCGGCTGT‑CTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTC  >  NC_000913/357733‑358006

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: ‑