Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	357,890	0	C	A	44.4%	43.9 / 23.5	45	L267F (TTG→TTT)	cynR	transcriptional activator of cyn operon; autorepressor
Reads supporting (aligned to +/- strand):  ref base C (17/8);  new base A (0/20);  total (17/28)
Fisher's exact test for biased strand distribution p-value = 1.09e-06
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAA‑CC‑GCGCATTTATCCAACGCCATGTGCAAAAATGCCTTC‑GCGGCGGCTGT‑CTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAG‑AGAAATAGC‑TTTAAGCCCGTCATGTTGTGT‑GGCAATCG‑CTGCTGGTAACAATGT‑GGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCGCCT  >  NC_000913/357741‑358032                                                                                                                                                           |                                                                                                                                                    tGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAA‑CC‑GCGCATTTATCCAACGCCATGTGCAAAAATGCCTTC‑GCGGCGGCTGT‑CTGCCAGCTATTTTT‑CCGCCGcaac                                                                                                                                                     >  2:858728/1‑150 (MQ=255)   aTAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAA‑CC‑GCGCATTTATCCAACGCCATGTGCAAAAATGCCTTC‑GCGGCGGCTGT‑CTGCCAGCTATTTTT‑CCGCCGcaacaa                                                                                                                                                   >  1:599395/1‑150 (MQ=255)     aaGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAA‑CC‑GCGCATTTATCCAACGCCATGTGCAAAAATGCCTTC‑GCGGCGGCTGT‑CTGCCAGCTATTTTT‑CCGCCGCAACaaaa                                                                                                                                                 <  1:265299/150‑1 (MQ=255)     aaGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAA‑CC‑GCGCATTTATCCAACGCCATGTGCAAAAATGCCTTC‑GCGGCGGCTGT‑CTGCCAGCTATTTTT‑CCGCCGCAACAAAAc                                                                                                                                                <  2:273221/151‑1 (MQ=255)      aGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAA‑CC‑GCGCATTTATCCAACGCCATGTGCAAAAATGCCTTC‑GCGGCGGCTGT‑CTGCCAGCTATTTTT‑CCGCCGCAACAAAAcc                                                                                                                                               <  2:367314/151‑1 (MQ=255)          tAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAA‑CC‑GCGCATTTATCCAACGCCATGTGCAAAAATGCCTTC‑GCGGCGGCTGT‑CTGCCAGCTATTTTT‑CCGCCGCAACAAAAccgccg                                                                                                                                           >  1:334198/1‑151 (MQ=255)           aGCCCATCGGGAAATTCCAGCCGCAGCCCTGTGTCAGCGGCTACCGTGATTCATTCCCGCCAACAA‑CC‑GCGCTTTTATCCAACGCCATGTGCAAAAATGCCTTC‑GCGGCGGCTGT‑CTGCCAGCTATTTTT‑CCGCCGCAACAAAAccgccg                                                                                                                                           <  2:567646/150‑1 (MQ=18)              gcATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAA‑CC‑GCGCATTTATCCAACGCCATGTGCAAAAATGCCTTC‑GCGGCGGCTGT‑CTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTtct                                                                                                                                       >  2:1054293/1‑151 (MQ=255)                        aTTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAA‑CC‑GCGCATTTATCCAACGCCATGTGCAAAAATGCCTTC‑GCGGCGGCTGT‑CTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCagtag                                                                                                                              >  1:139608/1‑150 (MQ=255)                           ccAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTCCCGCAAACAC‑CC‑GCCCTTTTACCAAACGCCATGTGAAAAAATGCTTTC‑GCGGCGGCTGT‑CTGCCAGTTATTTTC‑CCGCCGAAACAAAACCGCCGTTCTCTCCagtagt                                                                                                                             <  1:50916/148‑1 (MQ=18)                               ccGCGGACCTGTGTCGGCGGCTCCCGTTTTTCATCCCCGCCACCAC‑CC‑GCGCTTTTACCCACCCCCTTGTGAAAAAAT‑CCTTCGGGGGCGGTTGT‑CTCCCGGCTTTTTTC‑CCCCCAAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCgggg                                                                                                                      <  2:632587/151‑1 (MQ=255)                                  cAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAA‑CC‑GCGCATTTATCCAACGCCATGTGCAAAAATGCCTTC‑GCGGCGGCTGT‑CTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGcggcgg                                                                                                                        >  2:586374/1‑146 (MQ=255)                                   aGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAA‑CC‑GCGCATTTATCCAACGCCATGTGCAAAAATGCCTTC‑GCGGCGGCTGT‑CTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCgggg                                                                                                                      >  1:938752/1‑147 (MQ=255)                                   aGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAA‑CC‑GCGCATTTATCCAACGCCATGTGCAAAAATGCCTTC‑GCGGCGGCTGT‑CTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGAGc                                                                                                                     >  1:107979/1‑148 (MQ=255)                                       cTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAA‑CC‑GCGCATTTATCCAACGCCATGTGCAAAAATGCCTTC‑GCGGCGGCTGT‑CTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCacg                                                                                                                  >  2:628079/1‑145 (MQ=255)                                            tccgCGGCTCCCGTAATTC‑TTTCCCCCAAAAA‑CCGGCGAATTTACCCACCGCTATGTGCAAAAA‑GCCCTC‑CGGGGGGCTTTCCCCCCGGCTATTTTT‑CCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAG‑AGAAATa                                                                                                          <  1:927110/146‑1 (MQ=255)                                            tCAGCGGCTACCGTGATTCATTTCCGCCAACAA‑CC‑GCGCATTTATCCAACGCCATGTGCAAAAATGCCTTC‑GCGGCGGCTGT‑CTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGcggcag                                                                                                                >  2:73328/1‑139 (MQ=255)                                              aGCGGCTACCGTGATTCATTTCCGCCAACAA‑CC‑GCGCATTTATCCAACGCCATGTGCAAAAATGCCTTC‑GCGGCGGCTGT‑CTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGTGGGAG‑AGAAATaa                                                                                                         >  2:875644/1‑147 (MQ=255)                                                    tACCGTGATTCATTTCCGCCAACAA‑CC‑GCGCATTTATCCAACGCCATGTGCAAAAATGCCTTC‑GCGGCGGCTGT‑CTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGAAG‑AGaaaaaaagtttaagc                                                                                                >  2:933910/1‑139 (MQ=255)                                                         tttttCTTTCCCCCCAACAC‑CC‑GCCCTTTTCCCCACCGCCATGTGAAAAAAGCCCTCC‑GCGGCGGCTGT‑CTGCCAGTTTTTTTC‑CCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAG‑AGAAATAGC‑TTTAAGCCCGt                                                                                            <  2:420044/146‑1 (MQ=255)                                                            ttCATTTCCGCCAACAA‑CC‑GCGCATTTATCCAACGCCATGTGCAAAAATGCCTTC‑GCGGCGGCTGT‑CTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGAAG‑AAAAAAAAC‑ttttaaaacctcatg                                                                                        >  1:1008753/1‑138 (MQ=25)                                                                ttccccccaccaC‑CC‑GCGCTTTTACCCACCGCCTTTTGAAAAAATCCCTTC‑GCGGCGGCTGT‑CTCCCAGCTTTTTTC‑CCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAG‑AGAAATAGC‑TTTAAGCCCGTCAtgttg                                                                                     <  2:700852/143‑1 (MQ=255)                                                                  tCCGCCAACAA‑CC‑GCGCATTTATCCAACGCCATGTGCAAAAATGCCTTC‑GCGGCGGCTGT‑CTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCCAG‑AGAAAAAAA‑TTTAAACCCCCCCTGTtttgt‑g                                                                                >  1:899376/1‑151 (MQ=25)                                                                  tCCCCCAACCACCC‑GCGCTTTTACCCACCCCCATGTAAAAAATGGCCTTC‑GCGGGGGCTGT‑CTCCCAGTTTTTTTC‑CCGCCAAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAG‑AGAAATAGC‑TTTAAg                                                                                                 <  2:474925/136‑1 (MQ=255)                                                                  cccGCCAACAC‑CC‑GCGTATTTACCCACCCCCATGTGC‑AAAATCCCTCC‑GCGGCGGCTGT‑CGGCCAGTTATTTTC‑CCGCCGAAAAAAAGCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAG‑AGAAATAGC‑TTTAAGCCCGTCATGTtgtg                                                                                   <  2:362779/147‑1 (MQ=255)                                                                       caacac‑CC‑GCGCTTTCACCAACCGCCGTGTAAAAAAATGCCTCC‑GGGGCGGCTTT‑CTGCCAGTTATTTTC‑CCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAG‑AGAAATAGC‑TTTAAGCCCGTCATGTTGTGT‑GGCaa                                                                            <  2:567331/150‑1 (MQ=255)                                                                       caacaa‑CC‑GCGCATTTATCCAACGCCATGTGCAAAAATGCCTTC‑GCGGCGGCTGT‑CTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGGAG‑GGGAAAAGA‑TTTTATACCGCCATTTTGTTT‑gggggg                                                                           >  2:31943/1‑147 (MQ=21)                                                                        aacac‑cC‑GCGCTTTTACCCAACGCAATGTGAAAAAATGCTTCC‑GCGGCGGCTGT‑CTGCCAGTTTTTTTC‑CCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAG‑AGAAATAGC‑TTTAAGCCCGTCATGTTGTGT‑GGCAATc                                                                          <  1:173277/151‑1 (MQ=255)                                                                               c‑gcgCATTTATCCAACGCCATGTGCAAAAATGCCTTC‑GCGGCGGCTGT‑CTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCCAG‑AAAAAAAAC‑TTTTAACCCCTCCTTTTTTGT‑GGGGAACg‑ctgc                                                                    >  1:800105/1‑150 (MQ=25)                                                                                  cgcATTTATCCAACGCCATGTGCAAAAATGCCTTC‑GCGGCGGCTGT‑CTGCCAGTTATTTTT‑CCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAG‑AGAAATAGC‑TTTAAGCCCGTCATGTTGTGT‑GGCAATCG‑CTGCTgg                                                                 <  1:712734/151‑1 (MQ=255)                                                                                      tccccccACCGCCTTGTAAAAAAATCCCTCC‑GCGGCGCCTGT‑CTGCCATTTTTTTTC‑CCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAG‑AGAAATAGC‑TTTAAGCCCGTCATGTTGTGT‑GGCAATCG‑CTGCTGGTa                                                               <  2:431613/144‑1 (MQ=255)                                                                                         aTCCAACGCCATGTGCAAAAATGCCTTC‑GCGGCGGCTGT‑CTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGGAG‑AGAAAAAAA‑TTTTAACCCCCCATATTTTGT‑GGGAAACg‑ctctttggtaaaa                                                           >  1:910464/1‑139 (MQ=21)                                                                                               cccaaTGTGCAAAAATCCTTGC‑GCGGCGGCTTT‑CTCCCAGCTTTTTTC‑CCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAG‑AGAAATAGC‑TTTAAGCCCGTCATGTTGTGT‑GGCAATCG‑CTGCTGGTAACAATGT‑GGa                                                    <  1:573000/146‑1 (MQ=255)                                                                                                     gtaaaaaaaTGCCTCC‑GCGGCGGCTGT‑CGGCCAGTTTTTTTC‑CCGCCCCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAG‑AGAAATAGC‑TTTAAGCCCGTCATGTTGTGT‑GGCAATCG‑CTGCTGGTAACAATGT‑GGAAAgg                                                <  2:639798/144‑1 (MQ=255)                                                                                                     ggtaaaaaaaGGCTTCGGCGGGGGCTTT‑CTGCCATTTTTTTTC‑CCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAG‑AGAAATAGC‑TTTAAGCCCGTCATGTTGTGT‑GGCAATCG‑CTGCTGGTAACAATGT‑gg                                                     <  2:911337/140‑1 (MQ=255)                                                                                                      tgaaaaaaTCCCTTC‑GCGGGGGCTTT‑CGGCCAGTTATTTTC‑CCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAG‑AGAAATAGC‑TTTAAGCCCGTCATGTTGTGT‑GGCAATCG‑CTGCTGGTAACAATGT‑GGAAAGGGaa                                             <  1:750786/147‑1 (MQ=255)                                                                                                       gCAAAAATGCCTTC‑GCGGCGGCTGT‑CTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGGAGAAGAAAAAAT‑TTTAAACCC‑CCCTGTTGTGT‑GGGGAACGCCTGCTGGGAAAAAATG‑GGAAAgg                                                >  1:1065993/1‑147 (MQ=255)                                                                                                        aaaaaaTCCCTCC‑GGGGCGGCTGT‑CTGCCATTTTTTTTC‑CCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAG‑AGAAATAGC‑TTTAAGCCCGTCATGTTGTGT‑GGCAATCG‑CTGCTGGTAACAATGT‑GGAAAGGGAAGTg                                          <  2:15599/150‑1 (MQ=255)                                                                                                                ccTCC‑GCGGCGGCTGT‑CTGCCAGTTTTTTTC‑CCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAG‑AGAAATAGC‑TTTAAGCCCGTCATGTTGTGT‑GGCAATCG‑CTGCTGGTAACAATGT‑GGAAAGGGAAGTGCGGCGAAt                                  <  1:792874/151‑1 (MQ=255)                                                                                                                   tC‑GCGGCGGCTGT‑CTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGGAG‑AGAAAAAACATTTAAACCC‑CCCTTTTGTGTGGGGAATC‑‑CCGCTGGTGACAAAGTGGGAAAgggggaggggggg                                     >  1:321052/1‑136 (MQ=255)                                                                                                                        ggcggcTGT‑CTGCCAGTTTTTTTC‑CCGCCGAAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAG‑AGAAATAGC‑TTTAAGCCCGTCATGTTGTGT‑GGCAATCG‑CTGCTGGTAACAATGT‑GGAAAGGGAAGTGCGGCGAATCAGCTcc                           <  1:184898/151‑1 (MQ=255)                                                                                                                           ggcTGT‑CT‑CCATCTTTTTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAG‑AGAAATAGC‑TTTAAGCCCGTCATGTTGTGT‑GGCAATCG‑CTGCTGGTAACAATGT‑GGAAAGGGAAGTGCGGCGAATCAGCTCCAg                         <  1:577320/150‑1 (MQ=255)                                                                                                                                       agtttttttc‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAG‑AGAAATAGC‑TTTAAGCCCGTCATGTTGTGT‑GGCAATCG‑CTGCTGGTAACAATGT‑GGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTa               <  1:465522/144‑1 (MQ=255)                                                                                                                                            ttttc‑CCGCCAAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAG‑AGAAATAGC‑TTTAAGCCCGTCATGTTGTGT‑GGCAATCG‑CTGCTGGTAACAATGT‑GGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAg         <  1:687212/150‑1 (MQ=255)                                                                                                                                                 cccgccgAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAG‑AGAAATAGC‑TTTAAGCCCGTCATGTTGTGT‑GGCAATCG‑CTGCTGGTAACAATGT‑GGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTc      <  2:64108/148‑1 (MQ=255)                                                                                                                                                  cccccaaaacaaAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAG‑AGAAATAGC‑TTTAAGCCCGTCATGTTGTGT‑GGCAATCG‑CTGCTGGTAACAATGT‑GGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTc      <  2:116339/141‑1 (MQ=255)                                                                                                                                                     ccgcAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAG‑AGAAATAGC‑TTTAAGCCCGTCATGTTGTGT‑GGCAATCG‑CTGCTGGTAACAATGT‑GGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCGCCt  <  1:447245/149‑1 (MQ=255)                                                                                                                                                     ccgaAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAG‑AGAAATAGC‑TTTAAGCCCGTCATGTTGTGT‑GGCAATCG‑CTGCTGGTAACAATGT‑GGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCg     <  2:802451/146‑1 (MQ=255)                                                                                                                                                        caacaaAACCGCCGTTCTCTCCAGTAGTGGCGGGGCCAG‑AGAAAAAAA‑AATTAACACCCCCTTTTTTGT‑GGGGATCG‑CCGCTGGGGACAATGT‑GGGAAGGGAAGGGGGGGGGAGCAACCCCCGAACACCGCCAATTTAGTTTGcc   >  2:554832/1‑145 (MQ=255)                                                                                                                                                           |                                                                                                                                                    TGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAA‑CC‑GCGCATTTATCCAACGCCATGTGCAAAAATGCCTTC‑GCGGCGGCTGT‑CTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAG‑AGAAATAGC‑TTTAAGCCCGTCATGTTGTGT‑GGCAATCG‑CTGCTGGTAACAATGT‑GGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCGCCT  >  NC_000913/357741‑358032

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑