Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	357,890	0	C	A	52.6%	15.2 / 53.1	38	L267F (TTG→TTT)	cynR	transcriptional activator of cyn operon; autorepressor
Reads supporting (aligned to +/- strand):  ref base C (13/5);  new base A (0/20);  total (13/25)
Fisher's exact test for biased strand distribution p-value = 1.58e-06
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.38e-05

TGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCC‑AA‑CAACCGCGCATTTATCCAACGCCATGTGCAAAAATG‑CCTT‑CGCGGCGGCTGT‑CTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑G‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTC  >  NC_000913/357741‑358028                                                                                                                                                           |                                                                                                                                             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‑G‑aaa                                                                                                    <  2:564926/146‑1 (MQ=255)                                                cGGCTACCGTGATTCATTTCCGCC‑AA‑CAACCGCGCATTTATCCAACGCCATGTGCAAAAATG‑CCTT‑CGCGGCGGCTGT‑CTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCGAGA‑G‑aaaaaaaat                                                                                              >  1:100384/1‑143 (MQ=255)                                                 ggCTCCCGTGTTTCATTCCCCCC‑AA‑CACCCGCGCTTTTACCCACCCCCATGTGAAAAAAGC‑CCTT‑CGCGGCGGTTGT‑CTGCCAGTTTTTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑G‑AAATAGCttt                                                                                             <  1:680777/149‑1 (MQ=255)                                                    cacccgtgttCCTTTCCCCCAAA‑CACCCGCG‑ATTTACCCCACCCCGTTGGCAAAAAAT‑CCTTCCGGGGGGGCTGC‑CCGCCAGTTTTTTTCCCGCGACAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑G‑aa                                                                                                     <  2:70761/131‑1 (MQ=255)                                                      ccGTGTTTCTTTCCCCCC‑AA‑CACCCGCCCTTTTACCCACCCCCATGTGAAAAAAGG‑CCTC‑CGCGGCGGCTTT‑CTGCCATTTTTTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑G‑AAATAGCTTTaa                                                                                           <  1:424260/146‑1 (MQ=255)                                                        gTGATTCATTCCCCCC‑AA‑CACCCGCGATTTTACCCACCCCCGTGTGAAAAATTG‑CCTC‑GGCGGCGCTTGT‑CTCCCATTTTTTTTCCCGCCACAAAAAAGCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑G‑AAATAGCt                                                                                               <  1:515083/140‑1 (MQ=255)                                                             ttaattCCCCC‑AACCACCCGCCCTTTTACCCAACGCCATGTGAAAAAATC‑CCTC‑CGGGGCGCTTGT‑CTCCCAGTTTTTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑G‑AAATAGCTTTAAGCCCGt                                                                                     <  1:760354/142‑1 (MQ=255)                                                                   ccccc‑ac‑caCCCGCCCTTTTACCCACCCCCTTGTCAAAAAATC‑CCTC‑CGGGGCGGTTGC‑CGCCCAGTTTTTTTCCCCCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑G‑AAATAGCTTTAAGCCCGTCATGTtgtgt                                                                           <  1:132182/146‑1 (MQ=255)                                                                    cGCC‑AA‑CAACCGCGCATTTATCCAACGCCATGTGCAAAAATG‑CCTT‑CGCGGCGGCTGT‑CTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAAA‑G‑AAAAAAATTTAAAACCCTCCCGTtgtgt                                                                           >  1:629615/1‑148 (MQ=25)                                                                                cgcgCATTTATCCAACGCCATGTGCAAAAATG‑CCTT‑CGCGGCGGCTGT‑CTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGAAGAGG‑AAAAACATTTAAACCCg                                                                                      >  2:258472/1‑128 (MQ=37)                                                                                             atcgcggtgcaaaaaaaCG‑CCTG‑CGCGGCGCTTGT‑CTGCGTGTTTTTTTCCCGCCGCAAAAAAGCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑G‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAAtg                                                    <  1:94712/136‑1 (MQ=255)                                                                                              aCGCCATGTGCAAAAATG‑CCTT‑CGCGGCGGCTGT‑CTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGCGAA‑G‑GAAAAAAACTAAGCCCGCCACGTTTTGTGGGAGTCgctggcggggaaaaagagg                                                 >  2:507225/1‑135 (MQ=19)                                                                                               cGCCATGTGAAAAAAGC‑CCTC‑CGGGGCGGTTGT‑CGGCAAGTTTTTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑G‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTgg                                                 <  2:338590/149‑1 (MQ=255)                                                                                               cGCCAGGTG‑AAAAATGCCCTC‑CGCGGCGGCTTT‑CTCCCAGTTTTTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑G‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGa                                                <  1:242798/150‑1 (MQ=255)                                                                                                gCCATGTGCAAAAATG‑CCTT‑CGCGGCGGCTGT‑CTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGGAGA‑G‑AAAAAAATTTTAAACCCCCCTGTTTTGTGGGGATCGCCGCTggggaaaaagtgg                                                 >  1:721268/1‑137 (MQ=21)                                                                                                       gCAAAAATG‑CCTT‑CGCGGCGGCTGT‑CTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCCAGA‑G‑AAAAAAATTTAAAACCCCCATTTTTTGTGGGAAACGCCGCTGGGGACAAATTGGGAAgggga                                         >  1:571346/1‑147 (MQ=255)                                                                                                         aaaaaGG‑CC‑T‑CGGGGGGGCTTTCCTGCCTGTTTTTTTCCCGCCAAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑G‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTgc                                     <  2:545779/151‑1 (MQ=255)                                                                                                           aaattccttt‑CGGGGCGCTTGT‑CGCCCACCTTTTTTCCCGCCCCAACAAACCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑G‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTgcg                                    <  1:434462/143‑1 (MQ=255)                                                                                                            aaTC‑CCTT‑GGCGGCGGCTTC‑CGGCCATTTTTTTGCCCGCCACAACAAACCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑G‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTgcggc                                  <  1:759902/151‑1 (MQ=255)                                                                                                              aatccctcgggggcggcGGT‑CGGCCGTTTTTTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑G‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTgcggc                                  <  2:732378/140‑1 (MQ=255)                                                                                                                       ggggcggcTGT‑CTGCAATTTTTTTTCCCGCCGAAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑G‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGc                          <  2:518819/148‑1 (MQ=255)                                                                                                                         ggcggtTGT‑CGCCCATTTTTTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑G‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTc                        <  2:346351/150‑1 (MQ=255)                                                                                                                         ggcggcTGT‑CTGCCAGCTTTTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑G‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCa                            <  1:260628/146‑1 (MQ=255)                                                                                                                                                 cccgcccCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑G‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTc  <  1:549652/148‑1 (MQ=255)                                                                                                                                                   cgccgcAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGACGA‑GAAAAAAACTTTAA‑CCCCCCCTGTTTTGTTGGGATCGCTGCCTGTTACAAAGTGGGGAGGGGAGGGGGGGGGATGAACCCCCGAAACGCGCCAAtt        >  2:703472/1‑141 (MQ=255)                                                                                                                                                           |                                                                                                                                             TGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCC‑AA‑CAACCGCGCATTTATCCAACGCCATGTGCAAAAATG‑CCTT‑CGCGGCGGCTGT‑CTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑G‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTC  >  NC_000913/357741‑358028

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 26 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑