Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	357,873	0	C	T	42.9%	38.2 / 20.7	43	S273N (AGC→AAC)	cynR	transcriptional activator of cyn operon; autorepressor
Reads supporting (aligned to +/- strand):  ref base C (15/9);  new base T (0/18);  total (15/28)
Fisher's exact test for biased strand distribution p-value = 1.40e-05
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CACTGAACTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCC‑GCCAACAACCGCGCATTTATCCAACGCCA‑TGTGCAAAAATGCC‑TT‑CGC‑GGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGC  >  NC_000913/357724‑358015                                                                                                                                                           |                                                                                                                                               cACTGAACTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCC‑GCCAACAACCGCGCATTTATCCAACGCCA‑TGTGCAAAAATGCC‑TT‑CGC‑GGCGGCTGTCTGCCAGCt                                                                                                                                               <  1:648140/151‑1 (MQ=255)  aCTGAACTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCC‑GCCAACAACCGCGCATTTATCCAACGCCA‑TGTGCAAAAATGCC‑TT‑CGC‑GGCGGCTGTCTGCCAGCt                                                                                                                                               <  2:265691/150‑1 (MQ=255)     gAACTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCC‑GCCAACAACCGCGCATTTATCCAACGCCA‑TGTGCAAAAATGCC‑TT‑CGC‑GGCGGCTGTCTGCCAGCTAttt                                                                                                                                           >  1:14712/1‑151 (MQ=255)      aaCTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCC‑GCCAACAACCGCGCATTTATCCAACGCCA‑TGTGCAAAAATGCC‑TT‑CGC‑GGCGGCTGTCTGCCAGCTAtttt                                                                                                                                          >  1:256401/1‑151 (MQ=255)          cGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCC‑GCCAACAACCGCGCATTTATCCAACGCCA‑TGTGCAAAAATGCC‑TT‑CGC‑GGCGGCTGTCTGCCAGCTATTTTTccg                                                                                                                                      >  2:1018808/1‑151 (MQ=255)          cGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCC‑GCCAACAACCGCGCATTTATCCAACGCCA‑TGTGCAAAAATGCC‑TT‑CGC‑GGCGGCTGTCTGCCAGCTATTTTTcc                                                                                                                                       <  2:1146097/150‑1 (MQ=255)           gTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCC‑GCCAACAACCGCGCATTTATCCAACGCCA‑TGTGCAAAAATGCC‑TT‑CGC‑GGCGGCTGTCTGCCAGCTATTTTTccgc                                                                                                                                     >  1:787391/1‑151 (MQ=255)                 cTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCC‑GCCAACAACCGCGCATTTATCCAACGCCA‑TGTGCAAAAATGCC‑TT‑CGC‑GGCGGCTGTCTGCCAGCTATTTTTCCGCCGcaac                                                                                                                               >  2:888182/1‑151 (MQ=255)                   gATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCC‑GCCAACAACCGCGCATTTATCCAACGCCA‑TGTGCAAAAATGCC‑TT‑CGC‑GGCGGCTGTCTGCCAGCTATTTTTCCGCCGcaacaa                                                                                                                             <  2:343341/151‑1 (MQ=255)                      aaGCGTAGCGCATCAGGCAATTCCAGCCGCAGTCCTGTTTCAGCGGCTACCGTGATTCATTTCC‑GCCAACAACCGCGCATTTATCCAACGCCA‑TGTGCAAAAATGCC‑TT‑CGC‑GGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAAc                                                                                                                          <  2:671430/151‑1 (MQ=255)                      aaGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCC‑GCCAACAACCGCGCATTTATCCAACGCCA‑TGTGCAAAAATGCC‑TT‑CGC‑GGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAAc                                                                                                                          <  2:900028/151‑1 (MQ=255)                          gTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCC‑GCCAACAACCGCGCATTTATCCAACGCCA‑TGTGCAAAAATGCC‑TT‑CGC‑GGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAAccgcc                                                                                                                      >  1:1115619/1‑151 (MQ=255)                                  tCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCC‑GCCAACAACCGCGCATTTATCCAACGCCA‑TGTGCAAAAATGCC‑TT‑CGC‑GGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTtctctc                                                                                                              >  2:22555/1‑151 (MQ=255)                                       cAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCC‑GCCAACAACCGCGCATTTATCCAACGCCA‑TGTGCAAAAATGCC‑TT‑CGC‑GGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCagt                                                                                                          >  2:263536/1‑150 (MQ=255)                                        aaTTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCC‑GCCAACAACCGCGCATTTATCCAACGCCA‑TGTGCAAAAATGCC‑TT‑CGC‑GGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCagt                                                                                                          >  2:989536/1‑149 (MQ=255)                                         aTTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCC‑GCCAACAACCGCGCATTTATCCAACGCCA‑TGTGCAAAAATGCC‑TT‑CGC‑GGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCagtagt                                                                                                       >  2:136863/1‑151 (MQ=255)                                            ccAGCCACGGCCCTGTGTCGGCGCCTACCGTGTTTCATTCCC‑CCCAACACCCGCG‑TTTTAACCAAGCCCATTGTGAAAAAATGCC‑TT‑CGG‑GGCGGCTTTCGCCCAGTTTTTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGc                                                                                                    <  2:1115871/151‑1 (MQ=255)                                                ccgccgACCTGTTTCCGCGTCTCCCGTGATTCTTCCCC‑CCCAACACCCCCGATTTTCCCCACCCCCG‑TGTCCAAAAACGCT‑TC‑CGC‑GGCGTCGGTCTCCCAGCTTTTTTTCCGCCCCAAAAAAACCGCCGTTCTCTCCAGTAGTGGc                                                                                                    <  2:381892/147‑1 (MQ=255)                                                ccGCACCCCTGTGTCAGCGTCTCCGGTGTTTCATTCCC‑CCAAACACCCGCTCATTTACCCACCGCCT‑TTTCAAAAAATGCT‑TT‑CGC‑GGCGGCTTCCGGCCCGTTTTTTTCCCGCCCCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCgg                                                                                                  <  2:1133747/149‑1 (MQ=255)                                                 cGCAGCCCTGTGTCAGCGGCACCGGTAATTCTTTCCC‑GCCAACACCCGCGCTTTTACCCACCGCCT‑TGTGAAAAAATGCC‑TC‑CGC‑GGCGGCTGCCGGCCAGCTTTTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGc                                                                                               <  2:867724/151‑1 (MQ=255)                                                  gCAGTCCTGTTTCAGCGCCCCCGGTATTTCTTTCCC‑GCCAACAACCGCCATTTTACCCACCCCCA‑TGTCAAAAAAGGCT‑TT‑CGG‑GGCGGCTGTCTGCCATTTTTTTTCCCCCCGCAACAAAGCCGCCGTTCTCTCCAGTAGTGGCgg                                                                                                  <  2:580148/147‑1 (MQ=255)                                                   cAGACCTGTGTCAGCGGCTACCGTGATTCATTTCC‑GCCAACAACCGCGCATTTATCCAACGCCA‑TGTGCAAAAATGCC‑TT‑CGC‑GGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCgggg                                                                                                >  1:370142/1‑148 (MQ=255)                                                       cttgtgTCGGCGGCTCCCGTGATTCTTTCCC‑CCCAACACCCCCGCATTTACCCAACGCCA‑TGTGAAAAAATGCC‑TT‑CGC‑GGCGGCTGTCTGCCAGTTATTTTCCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGc                                                                                               <  2:304765/143‑1 (MQ=255)                                                         tgtgTCGGCGGCTACCGTGATTCATTCCC‑GCCAACACCCGCGCATTTACCAACCGCCT‑TGTGAAAAAATGCT‑TT‑CGC‑GGCGGCTGTCTGCCAGTTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGaa                                                                                        <  2:129248/150‑1 (MQ=25)                                                           tgtCAGCGGCTACCGTGATTCATTTCC‑GCCAACAACCGCGCATTTATCCAACGCCA‑TGTGCAAAAATGCC‑TT‑CGC‑GGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGCGCCaggggaa                                                                                       >  1:895747/1‑144 (MQ=255)                                                            gtCGGCGGCTCCCGTGTTTCTTTCCC‑CCAAACACCCGCGCTTTTACCCACCGCCT‑TGTGAAAAAATCCC‑TT‑CGG‑GGGGGCTGTCTGCCAGTTTTTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAagag                                                                                          <  2:143965/145‑1 (MQ=255)                                                                    gcccccgttttCCTTTCCGGCCAAAAACCGC‑CTTTTTCCCAACCCCA‑TTGTCAAAAACGCCTTT‑CGG‑GGCGGCTGTCTCCCGGCTTTTTTTCCGCCGAAAAAAAGCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTaa                                                                              <  2:190144/141‑1 (MQ=255)                                                                            ttttcctcccccccaccaGCCGCACTTTTACCCACCGCCA‑TGTG‑AAAAATGTC‑TTCCGG‑GGCGGCTGTCAGCAATTTATTTTGCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTc                                                                       <  1:590019/137‑1 (MQ=255)                                                                             ttCTTTCCC‑GCAACCACCCGCGCTTTTACCCACCCCCA‑TGTAAAAAAATCCT‑TC‑CGG‑GGGGGCTGTCTCCCAGTTTTTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCAtg                                                                    <  2:737220/150‑1 (MQ=255)                                                                                 tttCC‑GCCAACAACCGCGCATTTATCCAACGCCA‑TGTGCAAAAATGCC‑TT‑CGC‑GGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGGAGAGaaaaaaatgtttgcacc                                                                         >  2:144618/1‑127 (MQ=25)                                                                                    cc‑GCCAACACCCGCGCTTTTACCCACCGCCA‑TGTGAAAAAATCCC‑TC‑CGC‑GGCGGCTGTCGGCCAGTTATTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTtgtgtg                                                             <  2:1059290/150‑1 (MQ=255)                                                                                     ccacaaacaacCGCGAATTCACCCACCACCT‑TGTGAAAAAATCCC‑TC‑GGC‑TGGGGTGGTGCCCCGGATTTTTTTCCGCCAAACCAAACCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTc                                                                       <  2:631195/135‑1 (MQ=255)                                                                                             aacCGCGCATTTATCCAACGCCA‑TGTGCAAAAATGCC‑TT‑CGC‑GGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGGAGAGAAAAAACATTTAACCCCTCCTGTTTTGTgggga                                                         >  2:596628/1‑143 (MQ=25)                                                                                               ccGCGCTTTTACCCAACCCCA‑TGTGCAAAAATCCT‑TT‑GGC‑GGCGGCTGTCTGCCAGTTATTTTCCCGCCGAAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCgctg                                                   <  2:673213/150‑1 (MQ=255)                                                                                                             aaCCCCA‑GGTGAAAAAAGCCC‑TC‑CGG‑GGCGGCTTTCTGCCAGTTTTTTTCCCCCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAAtg                                       <  2:849629/148‑1 (MQ=255)                                                                                                               ccccA‑TGTGAAAAAATGCT‑TC‑CGC‑GGCGGTTGTCTCCCGGTTTTTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGaa                                  <  1:845712/149‑1 (MQ=255)                                                                                                                 cgcaatataaaaaaaTCC‑TT‑CGGGGGCGTCTTTCTCCCGGTTTTTTTCCCCCCGAAAAAAACCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACaa                                         <  2:899331/135‑1 (MQ=255)                                                                                                                       ggaaaaaaTTCC‑TTGCGG‑GGCGGCTGTCTCCCGTTTTTTTTCCCGCCCAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAgg                               <  1:169803/145‑1 (MQ=255)                                                                                                                          aaaaaTCCC‑TC‑CGG‑GGGGGCTCTCTGCCATTTTTTTTCCCCCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAggg                              <  1:714827/145‑1 (MQ=255)                                                                                                                           aaaaTGCT‑TC‑CGC‑GGCGGTTGTCTGCCAGTTTTTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTgcg                       <  2:508814/151‑1 (MQ=255)                                                                                                                                         gggggggcTGTCTGCCAGTTTTTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATc                <  2:370231/142‑1 (MQ=255)                                                                                                                                           ggcggtTGTCTGCCAGTTATTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCa               <  1:243762/146‑1 (MQ=255)                                                                                                                                                   tctgctttcTATTTTTCCGCCACAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAAc     <  2:256457/140‑1 (MQ=255)                                                                                                                                                    cTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGTCAGAGAAAAAAATTTTAACTCCTCCTGTTGTGTGGCAAATGGTCCTGCTGAAAAATTGGTAAGGGGAGGGGGGCGAATCAGCTcccgcaacgc  >  1:585064/1‑142 (MQ=255)                                                                                                                                                           |                                                                                                                                               CACTGAACTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCC‑GCCAACAACCGCGCATTTATCCAACGCCA‑TGTGCAAAAATGCC‑TT‑CGC‑GGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGC  >  NC_000913/357724‑358015

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑