Missing coverage evidence...
			seq id	start	end	size	←reads	reads→	gene	description
*	*	÷	NZ_CP009273	1407244	1407275	32	3 [1]	[1] 2	intR	site‑specific integrase

ATTTTTGCCCCAGTGCTGGACTGGGGAAAACGTCTTAAATACTCAAATTCACCGGAGTTTATTTCATGAACTATCAGCGCTCTTAAATTTCCGG  >  NZ_CP009273/1407272‑1407365     |                                                                                          aTTTTTGCCCCAGTGCTGGACTGGGGAAAACGTCTTAAATACTCAAATTCACCGGAGTTTATTTCATGAACTATCAGCGCTCTTAAAttt      >  1:68906/1‑90 (MQ=255)     ttGCCCCAGTGCTGGACTGGGGAAAACGTCTTAAATACTCAAATTCACCGGAGTTTATTTCATGAACTATCAGCGCTCTTAAATTTCCgg  >  1:33035/1‑90 (MQ=255)     |                                                                                          ATTTTTGCCCCAGTGCTGGACTGGGGAAAACGTCTTAAATACTCAAATTCACCGGAGTTTATTTCATGAACTATCAGCGCTCTTAAATTTCCGG  >  NZ_CP009273/1407272‑1407365

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 26 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑