Missing coverage evidence...
			seq id	start	end	size	←reads	reads→	gene	description
*	*	÷	NZ_CP009273	1407378	1407383	6	2 [0]	[0] 3	intR	site‑specific integrase

TTGTAATCTCCCAGCCTTTTAATGTTTCCCGACATCGTTTTCCTCGAAACATGAACCAGATGCGAATGTATCTACCTCTAATCTCGACAC  >  NZ_CP009273/1407384‑1407473 |                                                                                          ttGTAATCTCCCAGCCTTTTAATGTTTCCCGACATCGTTTTCCTCGAAACATGAACCAGATGCGaa                          >  1:92561/1‑66 (MQ=255) ttGTAATCTCCCAGCCTTTTAATGTTTCCCGACATCGTTTTCCTCGAAACATGAACCAGATGCGaa                          <  2:92561/66‑1 (MQ=255) ttGTAATCTCCCAGCCTTTTAATGTTTCCCGACATCGTTTTCCTCGAAACATGAACCAGATGCGAATGTATCTACCTCTAATCTCGacac  >  1:629590/1‑90 (MQ=255) |                                                                                          TTGTAATCTCCCAGCCTTTTAATGTTTCCCGACATCGTTTTCCTCGAAACATGAACCAGATGCGAATGTATCTACCTCTAATCTCGACAC  >  NZ_CP009273/1407384‑1407473

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑