New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NZ_CP009273	= 3512449	2 (0.220)	12 (1.320)	10/166	0.1	85.7%	intergenic (‑26/+375)	aroK/hofQ	shikimate kinase AroK/DNA uptake porin HofQ
	?	NZ_CP009273	3576788 =	NA (NA)					coding (391/417 nt)	BW25113_RS17825	YrhA family protein

TTTTCCGGCACCCATAGGCCCAACCAGAAAGATATTGCGTTTCTCTGCCATTTTTTCGGTACTACTAAGACTATTCG‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  NZ_CP009273/3512373‑3512449 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑GGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCAGCTGTCCCTCC  >  NZ_CP009273/3576788‑3576872                                                                                                                                                                    TTTTCCGGCACCCATAGGCCCAACCAGAAAGATATTGCGTTTCTCTGCCATTTTTTCGGTACTACTAAGACTATTCGGGTGATGCTGCCA                                                                          >  2:221139/1‑90       GGCACCCATAGGCCCAACCAGAAAGATATTGCGTTTCTCTGCCATTTTTTCGGTACTACTAAGACTATTCGGGTGATGCTGCCAACTTAC                                                                    <  2:102928/90‑1                                    TGCGTTTCTCTGCCATTTTTTCGGTACTACTAAGACTATTCGGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGG                                       <  2:261821/90‑1                                     GCGTTTCTCTGCCATTTTTTCGGTACTACTAAGACTATTCGGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGT                                      <  1:221139/90‑1                                                   TTTTTTCGGTACTACTAAGACTATTCGGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTC                        <  1:221789/90‑1                                                                    AGACTATTCGGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCAGCTGTC       <  1:90670/90‑1                                                                        TATTCGGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCAGCTGTCCCTC   >  1:13422/1‑90                                                                        TATTCGGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGG                                       <  1:162620/54‑1                                                                        TATTCGGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGG                                       >  2:162620/1‑54                                                                         ATTCGGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCAGCTGTCCCTCC  >  1:194473/1‑90                                                                          TTCGGGTGATGCTGCCAACTTACTGATTTAGTGTAT                                                       >  1:149165/1‑36                                                                          TTCGGGTGATGCTGCCAACTTACTGATTTAGTGTAT                                                       <  2:149165/36‑1                                                                                                                                                                    TTTTCCGGCACCCATAGGCCCAACCAGAAAGATATTGCGTTTCTCTGCCATTTTTTCGGTACTACTAAGACTATTCG‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  NZ_CP009273/3512373‑3512449 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑GGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCAGCTGTCCCTCC  >  NZ_CP009273/3576788‑3576872

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 38 ≤ 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.