Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	2,141,241	0	C	A	55.6%	3.0 / 10.6	9	N29K (AAC→AAA)	yegD	molecular chaperone
Reads supporting (aligned to +/- strand):  ref base C (1/3);  new base A (5/0);  total (6/3)
Fisher's exact test for biased strand distribution p-value = 4.76e-02
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.

TTTTGATTACGGTACAGCAAACTGTTCAGTGGCGGTCATGCGTGACGGTAAACCGCATTTGCTAAAAATGGAAAACGACAGCACGCTGCTGCCTTCAATGCTTTGCGCGCCAACGCGTGAAGCGGTAAGCGAATGGCTGTACCGC  >  NZ_CP009273/2141166‑2141310                                                                            |                                                                      ttttGATTACGGTACAGCAAACTGTTCAGTGGCGGGCATTCGTGGCGGGAAACCGCATTTTGTAAAAAAGGAAAAAGACAGCACgccgct                                                         >  2:188391/1‑90 (MQ=255)               cAGCAAACTGTTCAGTGGCGGTCATGCGTGGCGGGAAAACCCATTTTCTAAAAAAGGAAAAAAACAGCACGCCGCTGCCTTCAATGCttt                                           >  2:20125/1‑90 (MQ=255)               cAGCAAACTGTTCAGTGGCGGTCATGCGTGACGGGAAAACGCATTTTCTAAAAATGGAAAAAGACAGCACGCTGCTGCCTTCAATGCttt                                           >  1:18458/1‑90 (MQ=255)                      cTGTTCAGTGGCGGTCATGCGTGACGGGAAAACGCATTTTCTAAAAAAGGGAAAAGACAGCACGCTGCTGCCTTCCATGCTTTTCGCGcc                                    >  1:53989/1‑90 (MQ=255)                       tGTTCAGTGGCGGTCATGCGTGACGGTAAACCGCATTTGCTAAAAATGGAAAACGACAGCACGCTGCTGCCTTCAATGCTTTGCGCGCCa                                   <  1:213640/90‑1 (MQ=255)                       tGTTCAGTGGCGGTCATGCGTGACGGTAAACCGCATTTGCTAAAAATGGAAAACGACAGCACGCTGCTGCCTTCAATGCTTTGCGCGCCa                                   <  2:53989/90‑1 (MQ=255)                        gTTCAGTGGCGGTCATGCGTGACGGTAAAACGCATTTTCTAAAAAAGGAAAAAGACAACACGCCGCCGCCTTCAATGCTTTTCGCGCCaa                                  >  1:76012/1‑90 (MQ=255)                                             aCGGTAAACCGCATTTGCTAAAAATGGAAAACGACAGCACGCTGCTGCCTTCAATGCTTTGCGCGCCAACGCGTGAAGCGGTAAGCGAAt             >  2:224860/1‑90 (MQ=255)                                                        cATTTGCTAAAAATGGAAAACGACAGCACGCTGCTGCCTTCAATGCTTTGCGCGCCAACGCGTGAAGCGGTAAGCGAATGGCTGTACCGc  <  1:197294/90‑1 (MQ=255)                                                                            |                                                                      TTTTGATTACGGTACAGCAAACTGTTCAGTGGCGGTCATGCGTGACGGTAAACCGCATTTGCTAAAAATGGAAAACGACAGCACGCTGCTGCCTTCAATGCTTTGCGCGCCAACGCGTGAAGCGGTAAGCGAATGGCTGTACCGC  >  NZ_CP009273/2141166‑2141310

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 5 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 20 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑