Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	357,880	0	T	C	55.1%	29.5 / 67.0	50	K271E (AAA→GAA)	cynR	transcriptional activator of cyn operon; autorepressor
Reads supporting (aligned to +/- strand):  ref base T (16/6);  new base C (0/27);  total (16/34)
Fisher's exact test for biased strand distribution p-value = 2.23e-08
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.40e-08

ACTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACC‑TGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACC‑GCGCATTTATCCAACGCCATGTGCAAAAAT‑G‑CCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAG  >  NC_000913/357730‑358025                                                                                                                                                           |                                                                                                                                                    aCTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACC‑TGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACC‑GCGCATTTATCCAACGCCATGTGCAAAAAT‑G‑CCTTCGCGGCGGCTGTCTGCCAGCTAttttt                                                                                                                                                     <  1:543245/151‑1 (MQ=255)    cGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACC‑TGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACC‑GCGCATTTATCCAACGCCATGTGCAAAAAT‑G‑CCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑c                                                                                                                                                   <  1:287310/149‑1 (MQ=255)        ggCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACC‑TGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACC‑GCGCATTTATCCAACGCCATGTGCAAAAAT‑G‑CCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑ccgccg                                                                                                                                              >  2:738367/1‑150 (MQ=255)           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)                                                                                                                                                           |                                                                                                                                                    ACTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACC‑TGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACC‑GCGCATTTATCCAACGCCATGTGCAAAAAT‑G‑CCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAG  >  NC_000913/357730‑358025

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: ‑