Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	357,890	0	C	A	44.7%	23.8 / 25.2	47	L267F (TTG→TTT)	cynR	transcriptional activator of cyn operon; autorepressor
Reads supporting (aligned to +/- strand):  ref base C (12/14);  new base A (0/21);  total (12/35)
Fisher's exact test for biased strand distribution p-value = 3.66e-04
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.99e-01

CTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACC‑TGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACC‑GCGCATTTATCCAACGCCATGTGCAAAAAT‑G‑CCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCGCCT  >  NC_000913/357740‑358032                                                                                                                                                            |                                                                                                                                                cTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACC‑TGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACC‑GCGCATTTATCCAACGCCATGTGCAAAAAT‑G‑CCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGcaac                                                                                                                                                 >  1:859900/1‑151 (MQ=255)   gATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACC‑TGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACC‑GCGCATTTATCCAACGCCATGTGCAAAAAT‑G‑CCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGcaaca                                                                                                                                                >  2:1000102/1‑150 (MQ=255)    aTAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACC‑TGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACC‑GCGCATTTATCCAACGCCATGTGCAAAAAT‑G‑CCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGcaacaa                                                                                                                                               >  2:1020031/1‑150 (MQ=255)    aTAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACC‑TGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACC‑GCGCATTTATCCAACGCCATGTGCAAAAAT‑G‑CCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACaaa                                                                                                                                              <  1:384608/151‑1 (MQ=255)      aaGCGTAGCGCATCAGGCAATTCCAGCCGCAGACC‑TGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACC‑GCGCATTTATCCAACGCCATGTGCAAAAAT‑G‑CCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACaaaa                                                                                                                                             <  1:830150/150‑1 (MQ=255)                          ttCCAGCCGCAGACC‑TGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACC‑GCGCATTTATCCAACGCCATGTGCAAAAAT‑G‑CCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTg                                                                                                                        >  2:443160/1‑151 (MQ=255)                           tCCCGCCCCAAACCTTGTGCCGGCGCCTCCGGTGTTCCATTCCCCCAAACACCG‑GCCCTTTTACCCACCGCCATGTAAAAAAAT‑C‑CCTCCGCGGCGGTTGTCT‑CCAGTTTTTTTTCCCGCCGAAACAAAACCGCCGTTCTCTCCagtag                                                                                                                          <  2:582051/149‑1 (MQ=255)                           tCCAGCCGCAGACC‑TGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACC‑GCGCATTTATCCAACGCCATGTGCAAAAAT‑G‑CCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTgg                                                                                                                       >  1:811100/1‑151 (MQ=255)                                ccGCAGCCG‑TGTGTCGGGGGCTCCGGTGATTCATTCCCGCCAAAACCC‑GCCCTTTTACCCACCCCCATGTGAAAAAGG‑G‑CCTGCGGGGCGGTTGTCGGCCGGTTTTTTTC‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCgg                                                                                                                    <  2:212083/149‑1 (MQ=255)                                ccGCAGCCC‑TGTGTCGGCGGCTCCCGTGATTCATTCCCGCCAACACCC‑GCGCTTTTACCCACCGCCTTGTGAAAAAAT‑G‑CCTCGGCGGGGGCTGTCTCCCAGTTTTTTTC‑CCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCgg                                                                                                                    <  1:995978/149‑1 (MQ=21)                                 cGCAGACC‑TGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACC‑GCGCATTTATCCAACGCCATGTGCAAAAAT‑G‑CCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCgggg                                                                                                                  >  1:790049/1‑150 (MQ=255)                                     gACC‑TGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACC‑GCGCATTTATCCAACGCCATGTGCAAAAAT‑G‑CCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCggggg                                                                                                                 >  2:382210/1‑146 (MQ=255)                                        cttgtgTCAGCGCCTCCCGTGATTCTTTCCCCCCAACAACC‑CCGCATTTACCCACCCCCTTGTGAAAAAAT‑C‑CTTCCGCGGCGGCTTTCGGCCAGTTTTTTTC‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAag                                                                                                              <  2:689646/146‑1 (MQ=255)                                        c‑TGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACC‑GCGCATTTATCCAACGCCATGTGCAAAAAT‑G‑CCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCgggg                                                                                                                  >  1:490305/1‑143 (MQ=255)                                          tgtgTCCGCGCTTCCCGTGTTTCTTTCCCCCCACCACCC‑CCTCTTTTACCCACCCCCTTGTGAAAAAAT‑C‑CCTTCGCGGCGGCTGTCTGCCAG‑TTTTTTC‑CCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAag                                                                                                              <  2:394763/145‑1 (MQ=255)                                           gtgtCAGCGTCTCCGGTGTTTCATTCCCGCCAACACCC‑GCGCTTTTACCCACCGCCATGTGAAAAAAT‑G‑CTTTGGGGGCGGTTTTCTGCAAGTTATTTTC‑CCGCCGAAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAAt                                                                                                       <  1:790925/151‑1 (MQ=255)                                             gtCAGCGGCTACCGTGATTCATTTCCGCCAACAACC‑GCGCATTTATCCAACGCCATGTGCAAAAAT‑G‑CCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGACGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGGAGGG‑AAATa                                                                                                      >  1:161416/1‑150 (MQ=255)                                                 gCGGTTACTGTTTTTCCTTCCCCCCAACCCCC‑GCTTTTTTACCCACCGCCATGTAAAAAATC‑G‑CTTCCGCGGCGTTTGTCTGCCATTTTTTTTC‑CCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCtt                                                                                                  <  2:390098/150‑1 (MQ=255)                                                 gCGGCTCCCGTGATTCTTTCCCCCCAACACCC‑GCGCATTTATCCACCGCCATGTGAAAAAAT‑G‑CCTTCGCGGCGGCTGTCTGCCAGTTATTTTC‑CCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAg                                                                                                     <  1:493191/147‑1 (MQ=255)                                                      tACCGTGATTCATTTCCGCCAACAACC‑GCGCATTTATCCAACGCCATGTGCAAAAAT‑G‑CCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGCagaggcaaaaatttaaaac                                                                                             >  1:992883/1‑136 (MQ=25)                                                             attcattcCCCCCAACACCC‑GCGCTTTTACCCAACCCCATTTAAAAAAAT‑C‑CCTCCGCGGCGCCTGCCTCCCATCTTTTTTC‑CCGCCCAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTc                                                                                        <  1:660382/148‑1 (MQ=255)                                                              ttatttccccccAACACCC‑GCGCATTTACCCACCGCCTTGTGAAAAAAT‑C‑CCTTCGCGGCGGCTGTCTGCCAGTTTTTTTC‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCAtg                                                                                     <  1:207729/140‑1 (MQ=255)                                                               ttctttCCCCCAACCACCGGCGTTTTTATCAAACG‑CATGTTGAAAAAG‑GCCCTCCGCGGCGGCTGTCTGCCCTTTTTTTTC‑CCGCCACAACAAACCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTc                                                                                        <  2:215093/144‑1 (MQ=255)                                                                cATTTCCGCCAACAACC‑GCGCATTTATCCAACGCCATGTGCAAAAAT‑G‑CCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGGAGAG‑GAAAAGCttttatacccccctgtt                                                                                   >  1:734968/1‑136 (MQ=25)                                                                  tcccccccAACACCC‑GCCTTTTTACCAACCCCCATGTACAAAAAT‑G‑CTTCCGGGGCGGTTGTCTGCCGGCTTTTTTC‑CCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCAtgttgt                                                                                 <  2:938836/144‑1 (MQ=255)                                                                   tccccccAAAACCC‑GCGCTTTTATCCAACGCCTTTTCAAAAAAT‑G‑CCTCCGGGGCGGCGGTCTGCCAGTTTTTTTT‑CCGCCCAAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCAtgttg                                                                                  <  1:915268/143‑1 (MQ=255)                                                                        ccAACAACC‑GCGCATTTATCCAACGCCATGTGCAAAAAT‑G‑CCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAAAG‑AAAAAAGTTTAAAACCGCAATGCtgtgt                                                                               >  1:292342/1‑146 (MQ=25)                                                                           accacccgccaaTTTACCCACCGCCTTGTGAAAAAAT‑G‑CCTCCGGGGCGGCTGTCGCCCAGTTTTTTTC‑CCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAAt                                                                         <  2:571800/139‑1 (MQ=255)                                                                           aacaccccctcttttATCCAACGCCATGTGAAAAAAT‑G‑CCTTCGCGGCGGCTGTCGCCCCGTTATTTTC‑CCGCCGAAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATc                                                                        <  1:910122/139‑1 (MQ=255)                                                                            caccc‑GCGCATTTACCCACCGCCATGTAAAAAAAT‑C‑CCTTCGCGGCGGCTGTCTCCCAGCTTTTTTC‑CCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATc                                                                        <  1:453782/146‑1 (MQ=255)                                                                                 cgcataTTTATCCAACGCAATGTGCAAAAAT‑T‑CTTGGGCGGCGGCTGCCTGCCAGCTTTTTTG‑CCGCCGCAAAAAATCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCgctgct                                                                  <  1:950110/146‑1 (MQ=255)                                                                                     cATTTATCCAACGCCATGTGCAAAAAT‑G‑CCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGGAGGGAAAAAAACTTTAAACCCGTctcttt                                                                                   >  2:564710/1‑126 (MQ=25)                                                                                       tttACCCACCGCCATGTGAAAAAAT‑G‑CTTTCGCGGCGGCTGTCTGCCAGTTATTTTC‑CCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTaa                                                             <  1:386599/150‑1 (MQ=255)                                                                                           tCCAACGCCATGTGCAAAAAT‑G‑CCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGCAGAG‑AAAAAAATTTTATACCCGCATGTTTTGTGGGGAACGCCGCTggggaaaa                                                          >  1:341585/1‑143 (MQ=21)                                                                                           acccaccgcATTTGCAAAAATCG‑CCTTCGGGGCGGCTGTCAGCAAGTTATTTTC‑CCGCGCCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTaa                                                             <  2:121796/139‑1 (MQ=255)                                                                                                cccaaTGTGAAAAAAT‑C‑CTTGCGGGGCGGCTGTCTGCAAGTTTTTTTC‑CCGCCGAAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAAt                                                         <  1:990493/141‑1 (MQ=255)                                                                                                      gtaaaaaaaT‑C‑CCTTCGGGGCGGCTGTCGGCCAGTTTTTTTC‑CCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTgg                                                     <  1:711055/139‑1 (MQ=255)                                                                                                      ggaaaaaaaT‑C‑CTTCCGGGGCGGCTGTCTGCCGGTTTTTTTC‑CCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAgg                                                <  2:361016/144‑1 (MQ=255)                                                                                                       tgaaaaaaT‑G‑CTTCCGGGGCGGCTTTCTGCAAGCTTTTTTC‑CCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGaa                                             <  1:39466/147‑1 (MQ=255)                                                                                                       tgaaaaaaT‑C‑CCTGCGCGGCGGCTTTCTGCCAGTTATTTTC‑CCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGa                                              <  1:162497/146‑1 (MQ=255)                                                                                                         cAAAAAT‑G‑CCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGGAGAG‑AAAAAAAATTTAAACCGCCATGTTGTGTGGGGATCGCCGCTGGTGAAAAAGTGGGAAagg                                               >  1:105548/1‑146 (MQ=255)                                                                                                         aaaaaaT‑G‑CCTGCGGGGGGGTTGTCTCCCAGTTTTTTTC‑CCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGt                                           <  1:97403/149‑1 (MQ=255)                                                                                                            aaaT‑G‑CCTCCGGGGCGGCTGTCTGCCAGTTTTTTTC‑CCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTgcgg                                       <  1:134177/151‑1 (MQ=255)                                                                                                                        gcggcgGCTGTCTGCCAGTTTTTTTC‑CCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCa                                <  1:793671/148‑1 (MQ=255)                                                                                                                          gggggcTGTCGCCCATCTATTTTC‑CCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCa                                <  1:7815/143‑1 (MQ=255)                                                                                                                                   cTGCCAGTTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAAcc                     <  1:159936/148‑1 (MQ=255)                                                                                                                                      ccAGTTTTTTTC‑CCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACcg                    <  1:811888/146‑1 (MQ=255)                                                                                                                                      ccAGTTTTTTTC‑CCGCCCAAACAAACCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAg                               <  2:431880/135‑1 (MQ=255)                                                                                                                                             ttttc‑CCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAg         <  2:296375/150‑1 (MQ=255)                                                                                                                                                      ccgcAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCGCCt  <  1:745418/149‑1 (MQ=255)                                                                                                                                                            |                                                                                                                                                CTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACC‑TGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACC‑GCGCATTTATCCAACGCCATGTGCAAAAAT‑G‑CCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCGCCT  >  NC_000913/357740‑358032

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: ‑