Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	1,182,430	0	C	A	55.6%	3.9 / 10.6	9	N377K (AAC→AAA)	pepT	peptidase T
Reads supporting (aligned to +/- strand):  ref base C (0/4);  new base A (5/0);  total (5/4)
Fisher's exact test for biased strand distribution p-value = 7.94e-03
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.17e-02
Rejected as consensus: E-value score below prediction cutoff.
Rejected as consensus: Frequency below/above cutoff threshold.

AACCGATCCGCGGTGGTACCGACGGCGCGCAGTTGTCGTTTATGGGATTACCGTGCCCGAACCTGTTCACTGGCGGTTACAACTATCATGGTAAGCATGAGTTTGTGACTCTGGAAGGTATGGAAAAAGCGGTGCAGGTGATCGTCCGTATTGCCGAGTTAAC  >  NZ_CP009273/1182348‑1182510                                                                                   |                                                                                 aaCCGATCCGCGGTGGTACCGACGGCGCGCAGTTGTCGTTTATGGGATTACCGTGCCCGAACCTGTTCACTGGCGGTTTCAAATATCATg                                                                           >  1:792536/1‑90 (MQ=255)                    cGACGGCGCGCAGTTGTCGTTTATGGGATTACCGTGCCCGAACCTGTTCACTGGCGGTTACAACTATCATGGTAAGCATGAGTTTGTGAc                                                        <  2:373775/90‑1 (MQ=255)                         gcgcgcAGTTGTCGTTTATGGGATTACCGTGCCCGAACCTGTTCACTGGCGGGTACAAACATCATTGTAAGCAAGAGGTTGTGTGTCTgg                                                   >  2:96475/1‑90 (MQ=255)                                         tATGGGATTACCGTGCCCGAACCTGTTCACTGGCGGTTACAACTATCATGGTAAGCATGAGTTTGTGACTCTGGAAGGTATGGAAAAAGc                                   <  2:334191/90‑1 (MQ=255)                                          aTGGGATTACCGTGCCCGAACCTGTTCACTGGCGGTTTCAAATATTATTGTAAGAATGAGGTTTTGGCTCTGGGAGGGATGGgaaaaaag                                  >  1:507411/1‑87 (MQ=255)                                          aTGGGATTACCGTGCCCGAACCTGTTCACTGGCGGTTTCAAATATCATGGGAAACATGAGGTTTTGGCTCTGGGAGGGATTGaaaaaaag                                  >  1:792687/1‑87 (MQ=255)                                              gATTACCGTGCCCGAACCTGTTCACTGGCGGTTACAACTATCATGGTAAGCATGAGTTTGTGACTCTGGAAGGTATGGAAAAAGCGGTGc                              <  2:550685/90‑1 (MQ=255)                                                                 gTTCACTGGCGGTTACAAATATTATTGTAAGCATGAGGTTGTGGCTCTGGGAGGGGTGGGAAAAAAGGGGGAGGGGGTCGTCCGTAtttc           >  2:104660/1‑88 (MQ=255)                                                                          cGGTTACAACTATCATGGTAAGCATGAGTTTGTGACTCTGGAAGGTATGGAAAAAGCGGTGCAGGTGATCGTCCGTATTGCCGAGTTAAc  <  1:104660/90‑1 (MQ=255)                                                                                   |                                                                                 AACCGATCCGCGGTGGTACCGACGGCGCGCAGTTGTCGTTTATGGGATTACCGTGCCCGAACCTGTTCACTGGCGGTTACAACTATCATGGTAAGCATGAGTTTGTGACTCTGGAAGGTATGGAAAAAGCGGTGCAGGTGATCGTCCGTATTGCCGAGTTAAC  >  NZ_CP009273/1182348‑1182510

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑