Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	357,880	0	T	C	43.6%	39.8 / 14.8	40	K271E (AAA→GAA)	cynR	transcriptional activator of cyn operon; autorepressor
Reads supporting (aligned to +/- strand):  ref base T (13/9);  new base C (0/17);  total (13/27)
Fisher's exact test for biased strand distribution p-value = 7.83e-05
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCC‑GCCAACAACCGCGCATTTATCCAACGCCA‑TGTGCAAAAATGCC‑TT‑CGC‑GGCGGCTGTCTGCCAGCTATTTTTCCGCCGC‑AACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGT  >  NC_000913/357733‑358026                                                                                                                                                         |                                                                                                                                                    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‑GGCGGCTGTCTGCCAGCTATTTTTCCGCCGc‑aac                                                                                                                                          >  2:888182/1‑151 (MQ=255)          gATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCC‑GCCAACAACCGCGCATTTATCCAACGCCA‑TGTGCAAAAATGCC‑TT‑CGC‑GGCGGCTGTCTGCCAGCTATTTTTCCGCCGc‑aacaa                                                                                                                                        <  2:343341/151‑1 (MQ=255)             aaGCGTAGCGCATCAGGCAATTCCAGCCGCAGTCCTGTTTCAGCGGCTACCGTGATTCATTTCC‑GCCAACAACCGCGCATTTATCCAACGCCA‑TGTGCAAAAATGCC‑TT‑CGC‑GGCGGCTGTCTGCCAGCTATTTTTCCGCCGC‑AACAAAAc                                                                                                                                     <  2:671430/151‑1 (MQ=255)             aaGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCC‑GCCAACAACCGCGCATTTATCCAACGCCA‑TGTGCAAAAATGCC‑TT‑CGC‑GGCGGCTGTCTGCCAGCTATTTTTCCGCCGC‑AACAAAAc                                                                                                                                     <  2:900028/151‑1 (MQ=255)                 gTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCC‑GCCAACAACCGCGCATTTATCCAACGCCA‑TGTGCAAAAATGCC‑TT‑CGC‑GGCGGCTGTCTGCCAGCTATTTTTCCGCCGC‑AACAAAAccgcc                                                                                                                                 >  1:1115619/1‑151 (MQ=255)                         tCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCC‑GCCAACAACCGCGCATTTATCCAACGCCA‑TGTGCAAAAATGCC‑TT‑CGC‑GGCGGCTGTCTGCCAGCTATTTTTCCGCCGC‑AACAAAACCGCCGTtctctc                                                                                                                         >  2:22555/1‑151 (MQ=255)                              cAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCC‑GCCAACAACCGCGCATTTATCCAACGCCA‑TGTGCAAAAATGCC‑TT‑CGC‑GGCGGCTGTCTGCCAGCTATTTTTCCGCCGC‑AACAAAACCGCCGTTCTCTCCagt                                                                                                                     >  2:263536/1‑150 (MQ=255)                               aaTTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCC‑GCCAACAACCGCGCATTTATCCAACGCCA‑TGTGCAAAAATGCC‑TT‑CGC‑GGCGGCTGTCTGCCAGCTATTTTTCCGCCGC‑AACAAAACCGCCGTTCTCTCCagt                                                                                                                     >  2:989536/1‑149 (MQ=255)                                aTTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCC‑GCCAACAACCGCGCATTTATCCAACGCCA‑TGTGCAAAAATGCC‑TT‑CGC‑GGCGGCTGTCTGCCAGCTATTTTTCCGCCGC‑AACAAAACCGCCGTTCTCTCCagtagt                                                                                                                  >  2:136863/1‑151 (MQ=255)                                   ccAGCCACGGCCCTGTGTCGGCGCCTACCGTGTTTCATTCCC‑CCCAACACCCGCG‑TTTTAACCAAGCCCATTGTGAAAAAATGCC‑TT‑CGG‑GGCGGCTTTCGCCCAGTTTTTTTCCCGCCGA‑AAAAAAACCGCCGTTCTCTCCAGTAGTGGc                                                                                                               <  2:1115871/151‑1 (MQ=255)                                       ccgccgACCTGTTTCCGCGTCTCCCGTGATTCTTCCCC‑CCCAACACCCCCGATTTTCCCCACCCCCG‑TGTCCAAAAACGCT‑TC‑CGC‑GGCGTCGGTCTCCCAGCTTTTTTTCCGCCCC‑AAAAAAACCGCCGTTCTCTCCAGTAGTGGc                                                                                                               <  2:381892/147‑1 (MQ=255)                                       ccGCACCCCTGTGTCAGCGTCTCCGGTGTTTCATTCCC‑CCAAACACCCGCTCATTTACCCACCGCCT‑TTTCAAAAAATGCT‑TT‑CGC‑GGCGGCTTCCGGCCCGTTTTTTTCCCGCCCC‑AAAAAAACCGCCGTTCTCTCCAGTAGTGGCgg                                                                                                             <  2:1133747/149‑1 (MQ=255)                                        cGCAGCCCTGTGTCAGCGGCACCGGTAATTCTTTCCC‑GCCAACACCCGCGCTTTTACCCACCGCCT‑TGTGAAAAAATGCC‑TC‑CGC‑GGCGGCTGCCGGCCAGCTTTTTTCCCGCCGC‑AAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGc                                                                                                          <  2:867724/151‑1 (MQ=255)                                         gCAGTCCTGTTTCAGCGCCCCCGGTATTTCTTTCCC‑GCCAACAACCGCCATTTTACCCACCCCCA‑TGTCAAAAAAGGCT‑TT‑CGG‑GGCGGCTGTCTGCCATTTTTTTTCCCCCCGC‑AACAAAGCCGCCGTTCTCTCCAGTAGTGGCgg                                                                                                             <  2:580148/147‑1 (MQ=255)                                          cAGACCTGTGTCAGCGGCTACCGTGATTCATTTCC‑GCCAACAACCGCGCATTTATCCAACGCCA‑TGTGCAAAAATGCC‑TT‑CGC‑GGCGGCTGTCTGCCAGCTATTTTTCCGCCGC‑AACAAAACCGCCGTTCTCTCCAGTAGTGGCgggg                                                                                                           >  1:370142/1‑148 (MQ=255)                                              cttgtgTCGGCGGCTCCCGTGATTCTTTCCC‑CCCAACACCCCCGCATTTACCCAACGCCA‑TGTGAAAAAATGCC‑TT‑CGC‑GGCGGCTGTCTGCCAGTTATTTTCCCGCCGC‑AACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGc                                                                                                          <  2:304765/143‑1 (MQ=255)                                                tgtgTCGGCGGCTACCGTGATTCATTCCC‑GCCAACACCCGCGCATTTACCAACCGCCT‑TGTGAAAAAATGCT‑TT‑CGC‑GGCGGCTGTCTGCCAGTTATTTTTCCGCCGC‑AACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGaa                                                                                                   <  2:129248/150‑1 (MQ=25)                                                  tgtCAGCGGCTACCGTGATTCATTTCC‑GCCAACAACCGCGCATTTATCCAACGCCA‑TGTGCAAAAATGCC‑TT‑CGC‑GGCGGCTGTCTGCCAGCTATTTTTCCGCCGC‑AACAAAACCGCCGTTCTCTCCAGTAGTGGCGGCGCCaggggaa                                                                                                  >  1:895747/1‑144 (MQ=255)                                                   gtCGGCGGCTCCCGTGTTTCTTTCCC‑CCAAACACCCGCGCTTTTACCCACCGCCT‑TGTGAAAAAATCCC‑TT‑CGG‑GGGGGCTGTCTGCCAGTTTTTTTCCCGCCGC‑AAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAagag                                                                                                     <  2:143965/145‑1 (MQ=255)                                                           gcccccgttttCCTTTCCGGCCAAAAACCGC‑CTTTTTCCCAACCCCA‑TTGTCAAAAACGCCTTT‑CGG‑GGCGGCTGTCTCCCGGCTTTTTTTCCGCCGA‑AAAAAAGCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTaa                                                                                         <  2:190144/141‑1 (MQ=255)                                                                   ttttcctcccccccaccaGCCGCACTTTTACCCACCGCCA‑TGTG‑AAAAATGTC‑TTCCGG‑GGCGGCTGTCAGCAATTTATTTTGCCGCCGA‑AAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTc                                                                                  <  1:590019/137‑1 (MQ=255)                                                                    ttCTTTCCC‑GCAACCACCCGCGCTTTTACCCACCCCCA‑TGTAAAAAAATCCT‑TC‑CGG‑GGGGGCTGTCTCCCAGTTTTTTTCCCGCCGA‑AAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCAtg                                                                               <  2:737220/150‑1 (MQ=255)                                                                        tttCC‑GCCAACAACCGCGCATTTATCCAACGCCA‑TGTGCAAAAATGCC‑TT‑CGC‑GGCGGCTGTCTGCCAGCTATTTTTCCGCCGC‑AACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGGAGAGaaaaaaatgtttgcacc                                                                                    >  2:144618/1‑127 (MQ=25)                                                                           cc‑GCCAACACCCGCGCTTTTACCCACCGCCA‑TGTGAAAAAATCCC‑TC‑CGC‑GGCGGCTGTCGGCCAGTTATTTTCCCGCCGC‑AAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTtgtgtg                                                                        <  2:1059290/150‑1 (MQ=255)                                                                            ccacaaacaacCGCGAATTCACCCACCACCT‑TGTGAAAAAATCCC‑TC‑GGC‑TGGGGTGGTGCCCCGGATTTTTTTCCGCCAA‑ACCAAACCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTc                                                                                  <  2:631195/135‑1 (MQ=255)                                                                                    aacCGCGCATTTATCCAACGCCA‑TGTGCAAAAATGCC‑TT‑CGC‑GGCGGCTGTCTGCCAGCTATTTTTCCGCCGC‑AACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGGAGAGAAAAAACATTTAACCCCTCCTGTTTTGTgggga                                                                    >  2:596628/1‑143 (MQ=25)                                                                                      ccGCGCTTTTACCCAACCCCA‑TGTGCAAAAATCCT‑TT‑GGC‑GGCGGCTGTCTGCCAGTTATTTTCCCGCCGA‑AACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCgctg                                                              <  2:673213/150‑1 (MQ=255)                                                                                                    aaCCCCA‑GGTGAAAAAAGCCC‑TC‑CGG‑GGCGGCTTTCTGCCAGTTTTTTTCCCCCCGA‑AAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAAtg                                                  <  2:849629/148‑1 (MQ=255)                                                                                                      ccccA‑TGTGAAAAAATGCT‑TC‑CGC‑GGCGGTTGTCTCCCGGTTTTTTTCCCGCCGC‑AAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGaa                                             <  1:845712/149‑1 (MQ=255)                                                                                                        cgcaatataaaaaaaTCC‑TT‑CGGGGGCGTCTTTCTCCCGGTTTTTTTCCCCCCGA‑AAAAAACCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACaa                                                    <  2:899331/135‑1 (MQ=255)                                                                                                              ggaaaaaaTTCC‑TTGCGG‑GGCGGCTGTCTCCCGTTTTTTTTCCCGCCCA‑AAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAgg                                          <  1:169803/145‑1 (MQ=255)                                                                                                                 aaaaaTCCC‑TC‑CGG‑GGGGGCTCTCTGCCATTTTTTTTCCCCCCGA‑AAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAggg                                         <  1:714827/145‑1 (MQ=255)                                                                                                                  aaaaTGCT‑TC‑CGC‑GGCGGTTGTCTGCCAGTTTTTTTCCCGCCGC‑AAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTgcg                                  <  2:508814/151‑1 (MQ=255)                                                                                                                                gggggggcTGTCTGCCAGTTTTTTTCCCGCCGA‑AAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATc                           <  2:370231/142‑1 (MQ=255)                                                                                                                                  ggcggtTGTCTGCCAGTTATTTTCCCGCCGA‑AAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCa                          <  1:243762/146‑1 (MQ=255)                                                                                                                                          tctgctttcTATTTTTCCGCCAC‑AACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAAc                <  2:256457/140‑1 (MQ=255)                                                                                                                                           cTGCCAGCTATTTTTCCGCCGC‑AACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGTCAGAGAAAAAAATTTTAACTCCTCCTGTTGTGTGGCAAATGGTCCTGCTGAAAAATTGGTAAGGGGAGGGGGGCGAATCAGCTcccgcaacgc             >  1:585064/1‑142 (MQ=255)                                                                                                                                              catgttgttttcCCGCCAA‑AAAAAATCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACcg              <  1:184651/139‑1 (MQ=255)                                                                                                                                               ccactttttttCCCCCGCAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACcgc             <  1:227040/141‑1 (MQ=255)                                                                                                                                                agtttttttcCCCCCGA‑AAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAAt       <  1:1032711/146‑1 (MQ=255)                                                                                                                                                      tttcCCCCCGA‑AAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGt  <  2:844502/150‑1 (MQ=255)                                                                                                                                                         |                                                                                                                                                    CGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCC‑GCCAACAACCGCGCATTTATCCAACGCCA‑TGTGCAAAAATGCC‑TT‑CGC‑GGCGGCTGTCTGCCAGCTATTTTTCCGCCGC‑AACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGT  >  NC_000913/357733‑358026

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: ‑