New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NZ_CP009273	1242342 =	24 (0.680)	3 (0.090)	3/160	2.6	10.8%	coding (491/1698 nt)	treA	alpha,alpha‑trehalase
	?	NZ_CP009273	1242352 =	26 (0.760)					coding (481/1698 nt)	treA	alpha,alpha‑trehalase
Rejected: Frequency below/above cutoff threshold.

CTATTTCATGAGCAAAATTGGCCACCATATCCGCGACTTTATCCCAGTGACCGCTTTCGGCAAGTCCTAACATGGTGAAGTAACTGTCCCAGTAATATACCTCGCGAAAGCGTCCGCCCGGCACGACATAAGGTTCCGGCAGCGGTAACAGAGAATCCCATTTT  >  NZ_CP009273/1242268‑1242431                                                                           |                                                                                          cTATTTCATGAGCAAAATTGGCCACCATATCCGCGACTTTATCCCAGTGACCGCTTTCGGCAAGTCCTAACATGGTGAAGTAACTGTccc                                                                            <  1:113717/90‑1 (MQ=255) cTATTTCATGAGCAAAATTGGCCACCATATCCGCGACTTTATCCCAGTGACCGCTTTCGGCAAGTCCTAACATGGTGAAGTAACTGTccc                                                                            <  2:679280/90‑1 (MQ=255) cTATTTCATGAGCAAAATTGGCCACCATATCCGCGACTTTATCCCAGTGACCGCTTTCGGCAAGTCCTAACATGGTGAAGTAACTGTccc                                                                            <  2:23994/90‑1 (MQ=255) cTATTTCATGAGCAAAATTGGCCACCATATCCGCGACTTTATCCCAGTGACCGCTTTCGGCAAGTCCTAACATGGTGAAGTAACTGTccc                                                                            <  1:774408/90‑1 (MQ=255) cTATTTCATGAGCAAAATTGGCCACCATATCCGCGACTTTATCCCAGTGACCGCTTTCGGCAAGTCCTAACATGGTGAAGTAACTGTccc                                                                            <  1:566163/90‑1 (MQ=255) cTATTTCATGACCAAAATTGGCCACGATAACCGCGACTTTATCCCAGTTACCGCTTTCGGCAAGTCCTAACATGGTGAAGTAACTGTccc                                                                            <  2:941616/90‑1 (MQ=255)        aTGAGCAAAATTGGCCACCATATCCGCGACTTTATCCCAGTGACCGCTTTCGGCAAGTCCTAACATGGTGAAGTAACTGTCCCAGTAata                                                                     >  1:626248/1‑90 (MQ=255)         tGAGCAAAATTGGCCACCATATCCGCGACTTTATCCCAGTGACCGCTTTCGGCAAGTCCTAACATGGTGAAGTAACTGTCCCAGTAatat                                                                    <  2:626248/90‑1 (MQ=255)                           atatCCGCGACTTTATCCCAGTGACCGCTTTCGGCAAGTCCTAACATGGTGAAGTAACTGTCCCAGTAATATACCTCGCGAAAGCGTCCg                                                  >  1:325368/1‑90 (MQ=255)                                 gcgACTTTATCCCAGTGACCGCTTTCGGCAAGTCCTAACATGGTGAAGTAACTGTCCCAGTAATATACCTCGCGAAAGCGTCCGCCCGGc                                            <  2:325368/90‑1 (MQ=255)                                   gttccgggcggactctttcgcgaggtatattactgggacaGTGAAGTAACTGTCCCAGTAATATACCTCGCGAAAGCGTCCGCCCGGCAc                                          <  2:549575‑M1/50‑1 (MQ=255)                                   gACTTTATCCCAGTGACCGCTTTCGGCAAGTCCTAACATGGTGAAGTAACTGTCCCAGTAATATACCTCGCGAAAGCGTCCGCCCGGCAc                                          <  1:1067868/90‑1 (MQ=255)                                       ttATCCCAGTGACCGCTTTCGGCAAGTCCTAACATGGTGAAGTAACTGTccc                                                                            >  1:82705/1‑52 (MQ=255)                                       ttATCCCAGTGACCGCTTTCGGCAAGTCCTAACATGGTGAAGTAACTGTccc                                                                            <  2:82705/52‑1 (MQ=255)                                       ttATCCCAGTGACCGCTTTCGGCAAGTCCTAACATGGTGAAGTAACTGTCCCAGTAATATACCTCGCGAAAGCGTCCGCCCGGCACGACa                                      >  1:883651/1‑90 (MQ=255)                                          gcggacgctttcgcgaggtatattactgggacaGTGAAGTAACTGTCCCAGTAATATACCTCGCGAAAGCGTCCGCCCGGCACGACATaa                                   <  1:238344‑M1/57‑1 (MQ=255)                                              aGTGACCGCTTTCGGCAAGTCCTAACATGGTGAAGTAACTGTCCCAGTAATATACCTCGCGAAAGCGTCCGCCCGGCACGACATAAGGtt                               >  1:23606/1‑90 (MQ=255)                                                 gACCGCTTTCGGCAAGTCCTAACATGGTGAAGTAACTGTccc                                                                            <  2:394909/42‑1 (MQ=255)                                                 gACCGCTTTCGGCAAGTCCTAACATGGTGAAGTAACTGTccc                                                                            >  1:394909/1‑42 (MQ=255)                                                 gACCGCTTTCGGCAAGTCCTAACATGGTGAAGTAACTGTCCCAGTAatat                                                                    >  1:933957/1‑50 (MQ=255)                                                 gACCGCTTTCGGCAAGTCCTAACATGGTGAAGTAACTGTCCCAGTAatat                                                                    <  2:933957/50‑1 (MQ=255)                                                   ccGCTTTCGGCAAGTCCTAACATGGTGAAGTAACTGTCCCAGTAATATACCTCGCGAAAGCGTCCGCCCGGCACGACATAAGGTTCCGGc                          >  2:1018317/1‑90 (MQ=255)                                                      cTTTCGGCAAGTCCTAACATGGTGAAGTAACTGTCCCAGTAATATACCTCGCGAAAGCGTCCGCCCGGCACGACATAAGGTTCCGGCAGc                       <  2:776045/90‑1 (MQ=255)                                                                       gacaGTGAAGTAACTGTCCCAGTAATATACCTCGCGAAAGCGTCCGCCCGGCACGACATAAGGTTCCGGCAGCGGTAACAGAGAATCCCa      >  2:238344‑M1/5‑90 (MQ=255)                                                                          ggTGAAGTAACTGTCCCAGTAATATACCTCGCGAAAGCGTCCGCCCGGCACGACATAAGGTTCCGGCAGCGGTAACAGAGAATCCCAttt   >  2:194388/1‑90 (MQ=255)                                                                          ggTGAAGTAACTGTCCCAGTAATATACCTCGCGAAAGCGTCCGCCCGGCACGACATAAGGTTCCGGCAGCGGTAACAGAGAATCCCAttt   >  1:632436/1‑90 (MQ=255)                                                                          ggTGAAGTAACTGTCCCAGTAATATACCTCGCGAAAGCGTCCGCCCGGCACGACATAAGGTTCCGGCAGCGGTAACAGAGAATCCCAttt   >  1:229877/1‑90 (MQ=255)                                                                           GTGAAGTAACTGTCCCAGTAATATACCTCGCGAAAGCGTCCGCCCGGCACGACATAAGGTTCCGGCAGCGGTAACAGAGAATCCCAtttt  <  1:584941‑M1/90‑1 (MQ=255)                                                                           |                                                                                          CTATTTCATGAGCAAAATTGGCCACCATATCCGCGACTTTATCCCAGTGACCGCTTTCGGCAAGTCCTAACATGGTGAAGTAACTGTCCCAGTAATATACCTCGCGAAAGCGTCCGCCCGGCACGACATAAGGTTCCGGCAGCGGTAACAGAGAATCCCATTTT  >  NZ_CP009273/1242268‑1242431

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 20 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 34 ≤ 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.