Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	357,880	0	T	C	54.8%	27.6 / 53.6	43	K271E (AAA→GAA)	cynR	transcriptional activator of cyn operon; autorepressor
Reads supporting (aligned to +/- strand):  ref base T (14/5);  new base C (0/23);  total (14/29)
Fisher's exact test for biased strand distribution p-value = 2.20e-07
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 2.33e-06

CTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTT‑CCGCCAACAACCGCGCATTTATCCAACGCC‑ATGTGCAAAAATGCCTT‑C‑GC‑GGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTG  >  NC_000913/357731‑358023                                                                                                                                                           |                                                                                                                                                  cTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTT‑CCGCCAACAACCGCGCATTTATCCAACGCC‑ATGTGCAAAAATGCCTT‑C‑GC‑GGCGGCTGTCTGCCAGCTAttttt                                                                                                                                                   >  2:219324/1‑150 (MQ=255)  tCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTT‑CCGCCAACAACCGCGCATTTATCCAACGCC‑ATGTGCAAAAATGCCTT‑C‑GC‑GGCGGCTGTCTGCCAGCTATTTTT‑cc                                                                                                                                                >  2:587084/1‑151 (MQ=255)   cGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTT‑CCGCCAACAGCCGCTCATTTATCCAACGCC‑ATGTGCAAAAATGCCTT‑C‑GC‑GGCGGCTGTCTGCCAGCTATTTTT‑cc                                                                                                                                                <  2:882643/150‑1 (MQ=255)     tAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTT‑CCGCCAACAACCGCGCATTTATCCAACGCC‑ATGTGCAAAAATGCCTT‑C‑GC‑GGCGGCTGTCTGCCAGCTATTTTT‑ccgcc                                                                                                                                             >  1:760232/1‑151 (MQ=255)     tAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTT‑CCGCCAACAACCGCGCATTTATCCAACGCC‑ATGTGCAAAAATGCCTT‑C‑GC‑GGCGGCTGTCTGCCAGCTATTTTT‑ccgcc                                                                                                                                             >  2:72690/1‑151 (MQ=255)           tGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTT‑CCGCCAACAACCGCGCATTTATCCAACGCC‑ATGTGCAAAAATGCCTT‑C‑GC‑GGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGcaac                                                                                                                                        >  1:990337/1‑150 (MQ=255)             aTAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTT‑CCGCCAACAACCGCGCATTTATCCAACGCC‑ATGTGCAAAAATGCCTT‑C‑GC‑GGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGcaacaa                                                                                                                                      >  1:495037/1‑150 (MQ=255)                   gttgcgcTTCAGCCAATTCAAGCCGCAGCCCTGTGTCAGCGGCTACCGTACTTAATTT‑CCGCCAAAAACCGGGCTTTTATCCAACGCC‑ATGTGCAAAAAGGCCTT‑C‑GC‑GGCGGTTGTCTGCCAGCTATTTTA‑CCGCCGCAAGAAAAccgcc                                                                                                                               <  2:978285/148‑1 (MQ=18)                     aGCCCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGGGATTCATTC‑CCGCCAACAACCGCGCATTTATCCAACGCC‑ATGGGCAAAAATGCCTT‑C‑GC‑GGCGGCTGTCTGCCGGCTATTTTT‑CCGCCGCAACAAAAccgcc                                                                                                                               <  2:605195/149‑1 (MQ=255)                           ccggccattccccgCCCCAGCCCTGGTTCAGCGCCTGCCGTGATTCTTCC‑CCCCCACCACCCGCGCTTTCATCCACCGCC‑TTGGGCAAAAATCCCTT‑C‑GC‑GGCGGCTGTCTGCCGGCTTTTTTC‑CCGCCGCAACAAAACCGCCGTtctctc                                                                                                                       <  2:113128/138‑1 (MQ=255)                                cAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTT‑CCGCCAACAACCGCGCATTTATCCAACGCC‑ATGTGCAAAAATGCCTT‑C‑GC‑GGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCagt                                                                                                                   >  2:253838/1‑150 (MQ=255)                                 aaTTCCAGCCGCAGACCTGTGTCAGGGGCTACCGTGATTCATTT‑CCGCCAACAACCGCGCATTTATCCAACGCC‑ATGTGCAAAAATGCCTC‑C‑TC‑GGCGGCGGTCTGCCAGCTATCTTT‑CCGACTCCACAAAAcccacgcgctaccc                                                                                                                      >  2:532583/1‑134 (MQ=17)                                    tCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTT‑CCGCCAACAACCGCGCATTTATCCAACGCC‑ATGTGCAAAAATGCCTT‑C‑GC‑GGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAAACGCCGTTCTCTCCAGTAGTgg                                                                                                              >  1:621988/1‑151 (MQ=255)                                      cacccGCAGCCTTGTGTGAGGGCCTACGGTAATTCATCC‑CCCCCAACACCCGCGCTTTTTCCCACCGCC‑TTGTGAAAAATTCCTTT‑C‑GC‑GGCGGTTGTCGGCCGGTTTTTTTC‑CGGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGc                                                                                                             <  2:730909/147‑1 (MQ=255)                                         ccGCAGCCTTGTGTCAGCGGCTCCCGTGTTTCTTTC‑CCCCCAACACCCGCCCATTTACCCAACCCC‑TTGTGAAAAAATCCTTC‑C‑GC‑GGCGGCTTTCTGCCAGTTTTTTTC‑CCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCgg                                                                                                           <  1:339502/149‑1 (MQ=255)                                          cgcggccttgtgTCAGCGGCTCCCGTGTTTCATTC‑CCCCCAACAACCGCGCTTTTCCCCAGCGCC‑ATGTAAAAAAATCCCTC‑C‑GG‑GGCGGCTGCCTCCCAGTTATTTTT‑CCGCCCCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCggg                                                                                                          <  1:280781/141‑1 (MQ=255)                                               cccTGTGTCAGGGGCTCCCGTTTTTCATTC‑CCCCCAACACCCGCGCATTTACCCACCGCC‑ATGTGAAAAAATGCTTT‑C‑GG‑GGCGGCTGTCTGCCAGCTTTTTTC‑CCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAagag                                                                                                   <  1:53541/150‑1 (MQ=255)                                                 cTGTGTCAGCGGCTACCGTGATTCATTT‑CCGCCAACAACCGCGCATTTATCCAACGCC‑ATGTGCAAAAATGCCTT‑C‑GC‑GGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGctgga                                                                                                    >  2:548655/1‑144 (MQ=255)                                                  tgtgTCAGCGGCTACCGTGATTCATTT‑CCGCCAACAACCGCGCATTTATCCAACGCC‑ATGTGCAAAAATGCCTT‑C‑GC‑GGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGGAGAG‑aa                                                                                                >  1:808153/1‑150 (MQ=255)                                                    tgtCAGCGGCTACCGTGATTCATTT‑CCGCCAACAACCGCGCATTTATCCAACGCC‑ATGTGCAAAAATGCCTT‑C‑GC‑GGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCgggggcgggag                                                                                                  >  2:890196/1‑140 (MQ=255)                                                     gtaaggggCTCCCGT‑ATTTATTTCCCCCCAAAACCCGCGCTTTTA‑CCAACCCCAATGT‑CAAAAATGCCTTCC‑GC‑GCCGGCTGTCT‑CCCGCTTTTTTTCCCCCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑aaa                                                                                               <  1:254449/142‑1 (MQ=255)                                                          cGGCTACCGTGATTCATTT‑CCGCCAACAACCGCGCATTTATCCAACGCC‑ATGTGCAAAAATGCCTT‑C‑GC‑GGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGAGGTAGAG‑aaaaaagatt                                                                                        >  1:152580/1‑143 (MQ=25)                                                           ggCTCCCGTGATTATTTC‑CCCCCAACACCCGCGCTTTTACCAAACGCA‑ATGTGAAAAAATGCTTT‑C‑GC‑GGCGGCTTTCGGCCAGTTTTTTTC‑CCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTa                                                                                       <  1:876614/150‑1 (MQ=255)                                                                  gtgtTTCTTTC‑CCGCCAACACCCGCGCTTTTACCCACCGCC‑ATGTGAAAAAATGCCTT‑C‑GG‑GGCGGCTGTCTCCCAGCTTTTTTC‑CCCCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAg                                                                                     <  1:487485/145‑1 (MQ=255)                                                                  gTGATTCATTC‑CCGCCAACACCCGCGCTTTTACCCAACGCC‑ATGTGAAAAAATGCTTC‑C‑GG‑GGCGGCTGTCTGCCAGTTTTTTTC‑CCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGt                                                                                <  1:284559/150‑1 (MQ=255)                                                                              ccgaccacccccGCGCACTTCTCCACCGCC‑TTGTCCAAAACTGCCTG‑C‑GG‑GGGGCTTGTCGCCGAGTTGTTTTC‑CCCCCAAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTgg                                                                    <  2:539611/141‑1 (MQ=255)                                                                              cccccAACACCCGCGCTTTTACCCACCCCC‑TGGTAAAAAAATGCCTC‑C‑GG‑GGCGGCTGTCTCCCAGTTTTTTTC‑CCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTtgtgt                                                                      <  1:890944/146‑1 (MQ=255)                                                                              ccGCCACCACCCGCGCATTTACCCACCCCC‑ATGTGAAAAAATGCCTC‑C‑GC‑GGCGGCTGTCTGCCAGTTTTTTTC‑CCGCCACAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTtgtg                                                                       <  1:147574/148‑1 (MQ=255)                                                                                 ccAACACCCGCGCATTTATCCACCGCC‑ATGTACAAAAATCCCTT‑C‑GC‑GGCGGCTGTCTGCCAGTTTTTTTC‑CCGCCGAAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCaa                                                                 <  1:300337/151‑1 (MQ=255)                                                                                 caaacaccCGCGCTTTTACCCAACGCC‑ATGTGAAAAAAGGCTTC‑C‑GC‑GGCGGCTGTCTCCCAGTTTTTTTC‑CCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCa                                                                  <  1:984024/148‑1 (MQ=255)                                                                                   aacaccCGCGCTTTTCCCCAGCGCC‑ATGTACAAAAAGGCCTG‑C‑GG‑GGGGGCTGTCGGCCGGCTTTTTTC‑CCGCCAAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCa                                                                  <  2:54120/148‑1 (MQ=255)                                                                                      acccGCGCATTTATCCACCGCC‑TTGTGAAAAAATGCCTC‑C‑GC‑GGCGGCTGTCTGCCAGCTTTTTTC‑CCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCgc                                                             <  1:220189/148‑1 (MQ=255)                                                                                        ccccgatttgaTCCACGGCC‑GTGAGAAAAAAGGCC‑T‑C‑GCGGGCGGTTGTCACCGAGTTTTTTTC‑CCGCCACAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCgctg                                                           <  2:571721/140‑1 (MQ=255)                                                                                                 gaTCCCACCCC‑ATTGGGAAAAATTCCCT‑CGGC‑GGCGGCGTTCTCCCGGCTTTTTCC‑CCGCCGAAACAAACCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTa                                                     <  2:839285/147‑1 (MQ=255)                                                                                                  aTCCAACGCC‑ATGTGCAAAAATGCCTT‑C‑GC‑GGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGGAGAGAAAAAAAATTTAATCCC‑TCATGTTTTGTGGGGATAGCTGCTggggaaaa                                                 >  1:86467/1‑144 (MQ=25)                                                                                                   cccACCGCC‑GTGTGAAAAAAGGCTTT‑G‑GG‑GGCGGCTGTCTGCCAGTTATTTTC‑CCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAAtg                                               <  1:230875/150‑1 (MQ=255)                                                                                                      accGCC‑ATGTCAAAAAATCCCTC‑C‑GC‑GGCGGCTGTCTGCCAGTTTTTTTC‑CCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAAtg                                               <  1:946600/146‑1 (MQ=255)                                                                                                      aaCGCC‑ATGGGAAAAAATGCCTC‑C‑GC‑GGCGGCTGTCTGCCGTTTTTTTTC‑CCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAAtgtg                                             <  1:845435/150‑1 (MQ=255)                                                                                                           cattgtaaaaaaaTGCCTC‑C‑GC‑GGGGGCTGTCTCCCAGTTTTTTTC‑CCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAg                                        <  1:956107/143‑1 (MQ=255)                                                                                                                   aaaaaTGCCTC‑C‑GC‑GGCGGCTTTCTGCCAGTTTTTTTC‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTgc                                <  1:298847/151‑1 (MQ=255)                                                                                                                     aaaTGCCTC‑G‑GG‑GGCGGCTTTCTTCCAGTTATTTCC‑CCGCCCAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTgcgg                              <  2:928119/151‑1 (MQ=255)                                                                                                                      aaaaaggcttcgggggcggtGGTCTCCCAGTTTTTTTC‑CCCCCGAAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGaa                                    <  1:282545/133‑1 (MQ=255)                                                                                                                                       ggcTCTCTCCAAGCTTTTTTT‑CCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCa                       <  2:385901/143‑1 (MQ=255)                                                                                                                                             cTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGGAGAG‑AAAAAAATTTTAAACCCCCATGTTTTTTGGGGATAGCCGCTGGGGAAAAATTGGGAAGGGGAGGGGGGGGGATCAACTCCCGaa              >  1:891325/1‑146 (MQ=255)                                                                                                                                                     ttttttc‑CCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTg  <  1:186668/148‑1 (MQ=255)                                                                                                                                                           |                                                                                                                                                  CTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTT‑CCGCCAACAACCGCGCATTTATCCAACGCC‑ATGTGCAAAAATGCCTT‑C‑GC‑GGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTG  >  NC_000913/357731‑358023

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 24 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑