Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	353,586	0	A	T	53.3%	7.8 / 18.7	18	N272K (AAT→AAA)	cynR	transcriptional regulator CynR
Reads supporting (aligned to +/- strand):  ref base A (4/3);  new base T (0/8);  total (7/11)
Fisher's exact test for biased strand distribution p-value = 2.56e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.72e-04
Rejected as consensus: E-value score below prediction cutoff.
Rejected as consensus: Frequency below/above cutoff threshold.

CAACGCCATGTGCAAAAATGCCTTCGCAGCGGCTGTCTGCCAGCTGTAGTTTATGCCGGATGCGGCGTGAACGCCTTATCCGGCCTACGTAGAGCACTGAACTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTC‑GCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCGCCTCAATGACCACCTGTGGATGTAGCCCCGCTTTCTCGCAGTAGTGGTCAATTTGCTCTCTGGTGGCAAATTCCGCGCTGAGCAGGAC  >  NZ_CP009273/353341‑353828                                                                                                                                                                                                                                                       |                                                                                                                                                                                                                                                   cAACGCCATGTGCAAAAATGCCTTCGCAGCGGCTGTCTGCCAGCTGTAGTTTATGCCGGATGCGGCGTGCACGCCTTATCCGGCCTACGGAGAGCACTGAAATCGTAGGCCTGATAAGCGTAGCGCCTCAGGCCATTCCAGCCGCAGACCCGGGTCAGCGGCTACCGGGAATCCTTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTC‑CAGGCGGCTTTCTTCCCGCTCtttt                                                                                                                                                                                                                                                >  2:807061/1‑250 (MQ=255)        aTGTGCAAAAATGCCTTCGCAGCGGCTGTCTGCCAGCTGTAGTTTATGCCGGATGCGGCGTGAACGCCTTATCCGGCCTACGTAGAGCACTGAACTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTC‑GCGGCGGCTGTCTGCCAGCTATTTTTccgccg                                                                                                                                                                                                                                         >  1:368159/1‑250 (MQ=255)        aTGTGCAAAAATGCCTTCGCAGCGGCTGTCTGCCAGCTGTAGTTTATGCCGGATGCGGCGTGAACGCCTTATCCGGCCTACGTAGAGCACTGAACTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGGGGTTCCTTTCCCCCAACAACCGCGCCTTTATCCAACGCCATGTGCCAAAATGCCTTC‑GCCGCGGCCGTCTGCCAGCTCTTTTTtcgccg                                                                                                                                                                                                                                         >  2:137377/1‑250 (MQ=18)              aaaaaTGCCTTCGCAGCGGCTGTCTGCCAGCTGTAGTTTATGCCGGATGCGGCGTGAACGCCTTATCCGGCCTACGTAGAGCACTGAACTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTC‑GCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGccaca                                                                                                                                                                                                                                    >  1:857416/1‑249 (MQ=255)                  aTGCCTTCCCGGCGGCTGTCTGCCAGCTGTAGTTTATGCCGGATGCGGCGTGAACGCCTTATCCGGCCTACGTAGAGCCCTGAACTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTC‑GCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAAcc                                                                                                                                                                                                                               <  1:573946/250‑1 (MQ=255)                  aTGCCTTCACTGCGGCTTTCTGCCAGCTGTAGTTTATGCCGGATGCGGCGTGAACGCCTTATCCGGCCTACGTAGAGCACTGAACTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACTCCATGTGCTAAAATTCCTTC‑GCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAAcc                                                                                                                                                                                                                               <  1:389463/250‑1 (MQ=255)                               ggCTGTCTGCCAGCTGTAGTTTATGCCGGATGCGGCGTGAACGCCTTATCCGGCCTACGTAGAGCACTGAACTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTC‑GCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTccc                                                                                                                                                                                                                  >  1:728958/1‑249 (MQ=255)                                  tGTCTGCCAGCTGTAGTTTATGCCGGATGCGGCGTGAACGCCTTATCCGGCCTACGTAGAGCACTGAACTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAACCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTC‑GCGGCGGCTGCCCGCCCGCTCTTTTTTCGCCCCAACAAAACCCCCGCtctctctcg                                                                                                                                                                                                                 >  2:273829/1‑245 (MQ=17)                                                                                                                                                         cgaccgcgcCTACCGATATTCATCCCCGCCACACCCCCCGCTTTTCCCCACCGCCGTGTGAAAAAATCCCGCG‑GCGGCGGTTTGCGCCCAGTTTTTCTCCCGCCGAAACAAACCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCg                                                                                          <  2:268186/243‑1 (MQ=255)                                                                                                                                                                   tACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTC‑GCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCACCGTtct                                                                                                                                                                                                                       >  1:649336/1‑113 (MQ=255)                                                                                                                                                                    cccGTGTTTCATTCCCGCCAACACCCGCGCTTTTACCCAACGCCATGTAAAAAAATCCTTTC‑GGGGCGGCTGTCTCCCATTTTTTTTCCCCCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCGCCTCAATGaccac                                                                             <  1:463370/249‑1 (MQ=255)                                                                                                                                                                    aCCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTC‑GCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCACCGTtctc                                                                                                                                                                                                                      <  2:649336/113‑1 (MQ=255)                                                                                                                                                                                        acaccCGCCCATTAACCCAACGCGTGGTAAAAAAATGCCTCC‑GGGGCGCCTTACTGCTATCTTTTTTCCCGCCACAACAAAGCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCGCCTCAATGACCACCTGTGGATGTAGCCCCGCtt                                                         <  1:363682/250‑1 (MQ=255)                                                                                                                                                                                          acccGCGCATTTACCCACCCCCTTGAGCAAAATTCCCTCC‑GCGGCGGCTTTCTCCCAGTTTTTTTCCCGCCCCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCGCCTCAATGACCACCTGTGGATGTAGCCCCGCTTtc                                                       <  1:620631/248‑1 (MQ=255)                                                                                                                                                                                                     tccccacccccATGTAAAAAAATCCTTCC‑GCGGCGCCTGTCCCCCATTTTTTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCGCCTCAATGACCACCTGTGGATGTAGCCCCGCTTTCTCGCagtagt                                             <  1:60658/240‑1 (MQ=255)                                                                                                                                                                                                        ccAACCCCATGTGAAAAAATTCCTGCGGGGGGGGTTTTCTCCCAGTTTTTTTCCCCCCGAAAAAAACCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCGCCTCAATGACCACCTGTGGATGTAGCCCCGCTTTCTCGCAGTAGTgg                                           <  1:335806/249‑1 (MQ=255)                                                                                                                                                                                                                   tgaaaaagTGCTTGC‑GCGGGGTCTGCCTGCCAGTTTTTTCCCCCCCCAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCGCCTCAATGACCACCTGTGGATGTAGCCCCGCTTTCTCGCAGTAGTGGTCAATTTGctct                               <  1:391860/246‑1 (MQ=255)                                                                                                                                                                                                                                                gCCAGTTTTTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCGCCTCAATGACCACCTGTGGATGTAGCCCCGCTTTCTCGCAGTAGTGGTCAATTTGCTCTCTGGTGGCAAATTCCGCGCTGAGCAGGAc  <  1:137377/250‑1 (MQ=255)                                                                                                                                                                                                                                                       |                                                                                                                                                                                                                                                   CAACGCCATGTGCAAAAATGCCTTCGCAGCGGCTGTCTGCCAGCTGTAGTTTATGCCGGATGCGGCGTGAACGCCTTATCCGGCCTACGTAGAGCACTGAACTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTC‑GCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCGCCTCAATGACCACCTGTGGATGTAGCCCCGCTTTCTCGCAGTAGTGGTCAATTTGCTCTCTGGTGGCAAATTCCGCGCTGAGCAGGAC  >  NZ_CP009273/353341‑353828

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑