New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NZ_CP009273	= 1046001	NA (NA)	8 (0.740)	8/166	0.3	66.7%	intergenic (+15/+418)	BW25113_RS05135/cspH	IS1‑like element IS1D family transposase/cold shock‑like protein CspH
	?	NZ_CP009273	= 1903046	4 (0.370)					intergenic (‑23/‑136)	mgrB/yobH	PhoP/PhoQ regulator MgrB/YobH family protein

ATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  NZ_CP009273/1045926‑1046001 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑AGGTAGGTGAAACGGAGATTGGAGTGAAAAAGTTTCGATGGGTCGTTCTGGTTGTCGTGGTGTTGGCTTGCTTGCTGCTTTGGGC  <  NZ_CP009273/1903046‑1902962                                                                                                                                                                   ATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCAGGTAGGTGAAACG                                                                         <  2:299619/90‑1    GGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCAGGTAGGTGAAACGGAG                                                                      >  1:134398/1‑90                                 ATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCAGGTAGGTGAAACGGAGATTGGAGTGAAAAAGTTTCGATGGGTCGT                                         >  2:154097/1‑90                                   TATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCAGGTAGGTGAAACGGAGATTGGAGTGAAAAAGTTTCGATGGGTCGTTC                                       >  1:129801/1‑90                                             TAAAACACTATCAATAAGTTGGAGTCATTACCAGGTAGGTGAAACGGAGATTGGAGTGAAAAAGTTTCGATGGGTCGTTCTGGTTGTCGT                             <  2:180572/90‑1                                                    CTATCAATAAGTTGGAGTCATTACCAGGTAGGTGAAACGGAGATTGGAGTGAAAAAGTTTCGATGGGTCGTTCTGGTTGTCGTGGTGTTG                      >  1:83080/1‑90                                                             AGTTGGAGTCATTACCAGGTAGGTGAAACGGAGATTGGAGTGAAAAAGTTTCGATGGGTCGTTCTGGTTGTCGTGGTGTTGGCTTGCTTG             <  2:175945/90‑1                                                                        TTACCAGGTAGGTGAAACGGAGATTGGAGTGAAAAAGTTTCGATGGGTCGTTCTGGTTGTCGTGGTGTTGGCTTGCTTGCTGCTTTGGGC  >  1:312209/1‑90                                                                                                                                                                   ATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  NZ_CP009273/1045926‑1046001 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑AGGTAGGTGAAACGGAGATTGGAGTGAAAAAGTTTCGATGGGTCGTTCTGGTTGTCGTGGTGTTGGCTTGCTTGCTGCTTTGGGC  <  NZ_CP009273/1903046‑1902962

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 20 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 35 ≤ 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.