Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	357,890	0	C	A	46.9%	41.3 / 22.9	50	L267F (TTG→TTT)	cynR	transcriptional activator of cyn operon; autorepressor
Reads supporting (aligned to +/- strand):  ref base C (21/5);  new base A (0/23);  total (22/28)
Fisher's exact test for biased strand distribution p-value = 2.87e-09
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.65e-01

AGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATG‑CCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGG‑CAAGA‑GAAATAGC‑TTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGG‑AAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCGCCTCAATG  >  NC_000913/357746‑358037                                                                                                                                                   |                                                                                                                                                         aGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATG‑CCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAA‑cc                                                                                                                                                   >  1:788458/1‑151 (MQ=255)     tAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATG‑CCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAA‑ccgcc                                                                                                                                                >  2:516436/1‑150 (MQ=255)       tcgcATCAGGCAATTCCAGCCGCAGCCCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAACATG‑CCTT‑CGCGGCGGCCGTCGCCCAGCTAATTTTCCGCCGCAAGACAA‑CCGCCGt                                                                                                                                              >  2:408778/2‑150 (MQ=18)       gcgcATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATG‑CCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAA‑CCGCAGt                                                                                                                                              <  1:1587500/150‑1 (MQ=255)            tCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATG‑CCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAA‑CCGCCGTtctctc                                                                                                                                        >  1:837912/1‑151 (MQ=255)              aGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATG‑CCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAA‑CCGCCGTTCTCTcc                                                                                                                                       >  1:1130935/1‑150 (MQ=255)                  attcccACCCGCAGCCTTGTGCCGGCGCCTCCCGTGTTCCTTTCCCCCCAACACCCGCGCTTTTACCCAACGCCATGTGAAAAAATG‑CTTT‑CGCGGCGTCTGTCTCCCATTTTTTTTCCCGCCGAAAAAAAA‑CCGCCGTTCTCTCCagtag                                                                                                                                  <  1:1407055/147‑1 (MQ=255)                    ttCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATG‑CCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAA‑CCGCCGTTCTCTCCAGTAGTg                                                                                                                                >  2:565791/1‑151 (MQ=255)                      ccAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATG‑CCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAA‑CCGCCGTTCTCTCCAGTAGTGGc                                                                                                                              >  2:221257/1‑151 (MQ=255)                              agccttgtgTCAGCGCCTCCCGTGATTCTTTTCCCCCACCACCCGGTCTTTACCCCACCGCCATGTGCAAAAATG‑CTTC‑CGCGGGGGCTGCCTGCCAGTTATTTTCCCGCCGAAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGG‑Ca                                                                                                                       <  2:489743/144‑1 (MQ=255)                                   tgtgTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATG‑CCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGG‑cga                                                                                                                      >  1:497668/1‑143 (MQ=255)                                    gtgtCAGCGGTTCCCGTGTTTCTTTCCCGCAAACACCCGCACATTTACCCACCCCCATG‑GCAAAAATGCCCTG‑CGGGGGGGCTTTCTGCCGTCTTTTTTCCCGCCGAAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGG‑CAAGA‑Gaa                                                                                                                <  2:1151513/149‑1 (MQ=255)                                     tgtCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATG‑CCTT‑CGCGGCGGCTGTCTGCCAGCTCTTTTTCCGCCGCAACAAAA‑CCGCCGTTCTCTCCAGTAGTGGCggggggggagg                                                                                                                   >  2:838638/1‑140 (MQ=255)                                            ggCTCCGGTGATTCATTCCCGCCAACACCCGCGCATTTACCCACCGCCATGTGAAAAAATG‑CCTT‑CGGGGCGGCTGTCTGCCAGTTTTTTTCCCGCCGCAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGG‑CAAGA‑GAAATAGC‑TTTa                                                                                                      <  1:370328/150‑1 (MQ=255)                                            ggCTACGGGAATTCATTCCCCCAAACACCCGCGCTTTTACCCACCGCCATGTGAAAAAAGC‑CCTT‑GGGGGGGGCTGTCGGCCAGTTTTTTTCCCGCCGCAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGG‑CAAGA‑GAAATAGC‑ttt                                                                                                       <  1:1195636/149‑1 (MQ=255)                                               tACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATG‑CCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGG‑GGAGA‑GAAAAAGA‑ttttaaac                                                                                                  >  1:1123604/1‑146 (MQ=25)                                                       ttCTTTCCCCCCAACACCCGCGAATTAACCCACCGCAATGGGAAAAAGGC‑CCTG‑CGGGGGGGTTGTCTGCCAGTTTTTTTTCCGCGGAAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGG‑CAAGA‑GAAATAGC‑TTTaa                                                                                                     <  2:1632082/140‑1 (MQ=255)                                                          aTTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATG‑CCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAA‑c                                                                                                                                                    <  1:269601/93‑1 (MQ=255)                                                          aTTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATG‑CCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAA‑c                                                                                                                                                    >  2:269524/1‑93 (MQ=255)                                                          aTTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATG‑CCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAA‑ACGCCGTTCTCTCCAGTAGTGGCGGGG‑GGAGA‑GAAACAGA‑TTTaaaaac                                                                                                 >  2:1473851/1‑137 (MQ=25)                                                           ttcccGCCAACACCCGCGCTTTTACCCAACGCCATGTGAAAAAATG‑CCTC‑CGCGGCGGCTGTCGGCCAGTTTTTTTCCCGCCGAAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGG‑CAAGA‑GAAATAGC‑TTTAAGCCCGTCAtgttgt                                                                                       <  1:661929/147‑1 (MQ=255)                                                                      aacCGCGCATTTATCCAACGCCATGTGCAAAAATG‑CCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCCAGGG‑GAAATAAC‑TTTagcaagtcgttct                                                                                          >  2:466029/1‑125 (MQ=25)                                                                      aacCGCGCATTTATCCAACGCCATGTGCAAAAATG‑CCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGG‑GGAGA‑GAAAAAAA‑TTTTAACCCGTCCtgttgt                                                                                       >  1:749339/1‑139 (MQ=37)                                                                         cgcgCATTTACCCACCGCATTGTGAAAAAATG‑CGTG‑CGGGGCGCCTGTCGGCCAGTTTTTTTCCCGCCGCAACAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGG‑CAAGA‑GAAATAGC‑TTTAAGCCCGTCATGTTGTGTGGCAATCgctgct                                                                        <  2:928454/151‑1 (MQ=255)                                                                          gcgcATTTATCCAACGCCATGTGCAAAAATG‑CCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGG‑CCAAA‑GAAAAAAA‑TTTAATCTCGT‑‑TGTTGTGTgggggtatcg                                                                           >  1:1473668/1‑137 (MQ=25)                                                                                     cAACGCCATGTGCAAAAATG‑CCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGG‑GCAGA‑GAAAAAAA‑TTTTAAACCCTCATGTTTTGTGGGCATCGCGGTTggggacca                                                                >  2:516924/1‑141 (MQ=25)                                                                                      aaCGCCATGTGCAAAAATG‑CCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGG‑TGAGA‑GGAAAAAA‑TTTATATCCGCCATGATGTGTGGGaa                                                                                >  1:39863/1‑130 (MQ=25)                                                                                       ccGCCAGGGGAAAAAATC‑CCTT‑CGCGGCGCCTTTCGGGCAGCTTTTTTCCCCCCAAAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGG‑CAAGA‑GAAATAGC‑TTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGG‑a                                                         <  2:342882/150‑1 (MQ=255)                                                                                          ccATGTGAAAAAATG‑CCTT‑CGCGGCGGCTGTCTGCCAGTTATTTTCCCGCCGCAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGG‑CAAGA‑GAAATAGC‑TTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGG‑AAAg                                                      <  1:566042/151‑1 (MQ=255)                                                                                             ggtgAAAAAAGG‑CCTT‑CGCGGGGCCTGTCTGCCGGTTATTTTCCCGCCGAAAAAAAG‑CCGCCGTTCTCTCCAGTAGTGGCGGGG‑CAAGA‑GAAATAGC‑TTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGG‑AAAg                                                      <  2:654218/147‑1 (MQ=255)                                                                                              tgacAAAAATG‑CTTC‑CGCGGCGTCTTCCTGCAAGCTATTTTCCCGCCCAAAAAAAT‑CCGCCGTTCTCTCCAGTAGTGGCGGGG‑CAAGA‑GATATAGC‑TTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTTG‑AAAgg                                                     <  2:778216/145‑1 (MQ=255)                                                                                              gtgAAAAAATG‑CTTC‑CGGGGCGGCTGTCTGCCAGTTTTTTTCCCGCCGCAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGG‑CAAGA‑GAAATAGC‑TTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGG‑AAAGGGaa                                                  <  1:1525079/151‑1 (MQ=255)                                                                                              gtacAAAAATG‑CCTC‑CGCGGCGGCTTTCTGCCGGTTATTTTCCCGCCCCAAAAAAT‑CCGCCGTTCTCTCCAGTAGTGGCGGGG‑CAAGA‑GAAATAGC‑TTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGG‑AAAGGGa                                                   <  2:238843/147‑1 (MQ=255)                                                                                              gtaaaaaaaTC‑CCTT‑CGCGGCGGCTGTCTGCCAGTTTTTTTCCCGCCGAAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGG‑CAAGA‑GAAATAGC‑TTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGG‑AAAggg                                                    <  1:1045546/145‑1 (MQ=255)                                                                                                  aaaaaTG‑CCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGG‑GCAGA‑GAAAAAAA‑ATTAAACCCCCCATGTTGTGTGGGGAACGCCGCTGGGAACAAAGTGG‑AAAaggggggg                                               >  1:1252837/1‑145 (MQ=255)                                                                                                  aaaaaTC‑CCTC‑CGCGGCGGTTGTCCCCCATTTGTTTTCCCGCCCAAAAAAAG‑CCGCCGTTCTCTCCAGTAGTGGCGGGG‑CAAGA‑GAAATAGC‑TTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGG‑AAAGGGAAGt                                                <  2:1374865/149‑1 (MQ=255)                                                                                                  aaaaaGC‑CCTC‑CGGGGGGGCTGTCGCCCAGCTTTTTTCCCGCCGAAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGG‑CAAGA‑GAAATAGC‑TTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGG‑AAAGGGAAGTgc                                              <  1:342298/151‑1 (MQ=255)                                                                                                    aaaCG‑CCTTCCGCGGCGGCGGTCTCCAGGCTTTTTCCCCGCCCAAAAAAAG‑CCGCCGTTCTCTCCAGTAGTGGCGGGG‑CAAGA‑GAAATAGC‑TTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGG‑AAAGGGAAGTgcg                                             <  2:1163311/151‑1 (MQ=255)                                                                                                        g‑CCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGG‑GGAGA‑GAAAAAAC‑CTTAAACCCCCCCTGTTTTGTGGGAATCCCCGCTTGGAAAAAAGGGG‑GAAGGGGAgggggggg                                          >  1:1186139/1‑142 (MQ=255)                                                                                                                gcggcgGCTGTCTGCCAGTTATTTTCCCGCCGAAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGG‑CAAGA‑GAAATAGC‑TTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGG‑AAAGGGAAGTGCGGCGAATCa                                     <  1:691808/148‑1 (MQ=255)                                                                                                                 cggcggCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGCG‑GAAGA‑GAAAAAAA‑TTTTAACCCGTAATGTTTTGGGGGGATCGGTGACTGTAACAATGAGGAAAAGGGAAgggggcgga                                         >  1:1286499/1‑136 (MQ=255)                                                                                                                  ggggccTGTCTGCCTGTTATTTTCCCG‑CGAAACAAAACCCGCCGTTCTCTCCAGTAGTGGCGGGG‑CAAGA‑GAAATAGC‑TTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGG‑AAAGGGAAGTGCGGCGaa                                        <  2:1123426/138‑1 (MQ=255)                                                                                                                              ccAGTTTTTTTCCCGCCGCAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGG‑CAAGA‑GAAATAGC‑TTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGG‑AAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTa                    <  1:699849/151‑1 (MQ=255)                                                                                                                                ccattttgtcccgccaCACAAAAT‑CCGCCGTTCTCTCCAGTAGTGGCGGGG‑CAAGA‑GAAATAGC‑TTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGG‑AAAGGGAAGTGCGGCGAATCAGCTCCAGAACTGCGCTa                    <  2:92490/139‑1 (MQ=255)                                                                                                                                  cTATTTTTCCGCCGCAACAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGG‑GCAGAGGAAAAAAA‑TTTAAACCCCT‑ATGGTTTGGGGGGATCGCTGCTGGGGAAAAAGTGG‑GAAGGGGAGGGGGGGGGAAAAGCTCCaaaaaaggggtaa                   >  1:289904/1‑139 (MQ=255)                                                                                                                                   ttttttcCCGCCGAAACAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGG‑CAAGA‑GAAATAGC‑TTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGG‑AAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTaa                   <  2:124991/145‑1 (MQ=255)                                                                                                                                     ttttcCCGCCGCAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGG‑CAAGA‑GAAATAGC‑TTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGG‑AAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAAtt                 <  1:350110/147‑1 (MQ=255)                                                                                                                                     ttttcCCCCCGCAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGG‑CAAGA‑GAAATAGC‑TTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGG‑AAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAg              <  1:633655/150‑1 (MQ=255)                                                                                                                                     tttgcccgccaCAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGG‑CAAGA‑GAAATAGC‑TTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGG‑AAAGGGAAGTGCGGCGAATCAGCTCCAGAACcgcg                       <  2:1211878/136‑1 (MQ=255)                                                                                                                                       tttCCGCCGCAACAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGG‑CCAGA‑GAAAAAACTTTTAACCCCGCCTTGTT‑TGTGGGCAACGCTGCTGGGGACAATGTGG‑GGAGGGGAGGGGGGGGGAACAACCCCCGAAACGCGCCAATTTAGttt           >  1:617385/1‑150 (MQ=255)                                                                                                                                                 aacaaAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGG‑CAAGA‑GAAATAGC‑TTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGG‑AAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCGCCTCAATg  <  1:617952/150‑1 (MQ=255)                                                                                                                                                   |                                                                                                                                                         AGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATG‑CCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGG‑CAAGA‑GAAATAGC‑TTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGG‑AAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCGCCTCAATG  >  NC_000913/357746‑358037

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: ‑