Missing coverage evidence...
			seq id	start	end	size	←reads	reads→	gene	description
*	*	÷	NZ_CP009273	1195573	1195581	9	2 [1]	[1] 4	intE	site‑specific integrase

CCTAACCGCTGACCAGTAACCAGCGCTAACAGCATGGCATTTCCCATGTAACGATGAGTAGCGTCTGCGATATCGAAGATTTTTTTCCATTC  >  NZ_CP009273/1195580‑1195671   |                                                                                          ccTAACCGCTGACCAGTAACCAGCGCTAACAGCATGGCATTTCCCATGTAACGATGAGTAGCGTCTGCGATATCGAAGATTTTTTTCCAt    <  2:354408/90‑1 (MQ=255)   tAACCGCTGACCAGTAACCAGCGCTAACAGCATGGCATTTcc                                                  <  1:218887/42‑1 (MQ=255)   tAACCGCTGACCAGTAACCAGCGCTAACAGCATGGCATTTcc                                                  >  2:218887/1‑42 (MQ=255)   tAACCGCTGACCAGTAACCAGCGCTAACAGCATGGCATTTCCCATGTAACGATGAGTAGCGTCTGCGATATCGAAGATTTTTTTCCAttc  >  2:2229/1‑90 (MQ=255)   |                                                                                          CCTAACCGCTGACCAGTAACCAGCGCTAACAGCATGGCATTTCCCATGTAACGATGAGTAGCGTCTGCGATATCGAAGATTTTTTTCCATTC  >  NZ_CP009273/1195580‑1195671

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑