New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NZ_CP009273	= 3512457	1 (0.090)	12 (1.130)	11/168	0.1	92.3%	intergenic (‑34/+367)	aroK/hofQ	shikimate kinase AroK/DNA uptake porin HofQ
	?	NZ_CP009273	4487998 =	NA (NA)					intergenic (+241/‑91)	BW25113_RS22170/BW25113_RS22180	tyrosine‑type recombinase/integrase/IS3‑like element IS2 family transposase

CACAGGGTGATGCGGGATAACTGACGTAAGGAGTGCTGCAGGGATTTGATGGTCCCTTGTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTA  >  NZ_CP009273/4487939‑4488061                                                            |                                                                cacaGGGTGATGCGGGATAACTGACGTAAGGAGTGCTGCAGGGATTTGATGGTCCCTTGTAGACTGGCCCCCTGAATCTCCAGACAACCa                                   >  2:167698/1‑90 (MQ=255)        tGATGCGGGATAACTGACGTAAGGAGTGCTGCAGGGATTTGATGGTCCCTTGTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCAc                            >  2:305945/1‑90 (MQ=255)         gATGCGGGATAACTGACGTAAGGAGTGCTGCAGGGATTTGATGGTCCCTTGTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACt                           >  1:124630/1‑90 (MQ=255)                       gACGTAAGGAGTGCTGCAGGGATTTGATGGTCCCTTGTAGACTGGCCCCCTGAATCTCCAGAc                                        <  1:230682/63‑1 (MQ=255)                       gACGTAAGGAGTGCTGCAGGGATTTGATGGTCCCTTGTAGACTGGCCCCCTGAATCTCCAGAc                                        >  2:230682/1‑63 (MQ=255)                           tAAGGAGTGCTGCAGGGATTTGATGGTCCCTTGTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCtt         <  2:277568/90‑1 (MQ=255)                                 gTGCTGCAGGGATTTGATGGTCCCTTGTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACt   >  2:184121/1‑90 (MQ=255)                                 gTGCTGCAGGGATTTGATGGTCCCTTGTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACt   >  2:36711/1‑90 (MQ=255)                                  tgctgcAGGGATTTGATGGTCCCTTGTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTa  <  1:3930/90‑1 (MQ=255)                                   gctgcAGGGATTTGATGGTCCCTTGTAGACTGGCCCCCTGAATCTCCAGAc                                        >  1:18324/1‑51 (MQ=255)                                   gctgcAGGGATTTGATGGTCCCTTGTAGACTGGCCCCCTGAATCTCCAGAc                                        <  2:18324/51‑1 (MQ=255)                                                            |                                                                CACAGGGTGATGCGGGATAACTGACGTAAGGAGTGCTGCAGGGATTTGATGGTCCCTTGTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTA  >  NZ_CP009273/4487939‑4488061

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑
Reads not counted as support for junction
read_name Not counted due to insufficient overlap past the breakpoint.
read_name Not counted due to not crossing MOB target site duplication.