New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NZ_CP009273	2282398 =	NA (NA)	17 (1.020)	9/166	0.5	100%	pseudogene (3/2532 nt)	yejO	autotransporter YejO
	?	NZ_CP009273	3512437 =	0 (0.000)					intergenic (‑14/+387)	aroK/hofQ	shikimate kinase AroK/DNA uptake porin HofQ

TTTACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  NZ_CP009273/2282484‑2282398 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑CTAAGACTATTCGTTAATGATAAACCCGCTTCGCTCAGAGAGCGCCGCAGGACATGAACTGAAACCTCATAAGATATTGCGAGAGTC  >  NZ_CP009273/3512437‑3512523                                                                                                                                                                                TTTACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTA                                                                                      >  1:180592/1‑90              AAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAAGACTATTCGTTA                                                                         <  2:271456/90‑1                            ATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAAGACTATTCGTTAATGATAAACCCGCT                                                           <  2:327127/90‑1                                               GAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAAGACTATTCGTTAATGATAAACCCGCTTCGCTCAGAGAGCGCCGCA                                        >  1:214316/1‑90                                               GAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAAGACTATTCGTTAATGATAAACCCGCTTCGCTCAGAGAGCGCCGCA                                        <  1:335907/90‑1                                               GAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAAGACTATTCGTTAATGATAAACCCGCTTCGCTCAGAGAGCGCCGCA                                        >  2:130904/1‑90                                               GAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAAGACTATTCGTTAATGATAAACCCGCTTCGCTCAGAGAGCGCCGCA                                        <  2:234562/90‑1                                                     GCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAAGACTATTCGTTAATGATAAACCCGCTTCGCTCAGAGAGCGCCGCAGGACAT                                  >  1:171835/1‑90                                                     GCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCC                                                                                        >  1:155276/1‑36                                                     GCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCC                                                                                        <  2:155276/36‑1                                                      CCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAAGACTATTCGTTAATGATAAACCCGCTTCGCTCAGAGAGCGCCGCAGGACATG                                 <  1:137541/90‑1                                                               ATTTCCCCGCTTATTCGCACCTTCCCTAAGACTATTCGTTAATGATAAACCCGCTTCGCTCAGAGAGCGCCGCAGGACATGAACTGAAAC                        <  2:100872/90‑1                                                               ATTTCCCCGCTTATTCGCACCTTCCCTAAGACTATTCGTTAATGATAAACCCGCTTCGCTCAGAGAGCGCCGCAGGACATGAACTGAAAC                        <  2:214316/90‑1                                                                                    TTCCCTAAGACTATTCGTTAATGATAAACCCGCTTCGCTCAGAGAGCGCCGCAGGACATGAACTGAAACCTCATAAGATATTGCGAGAGT   >  2:467654/1‑90                                                                                    TTCCCTAAGACTATTCGTTAATGATAAACCCGCTTCGCTCAGAGAGCGCCGCAGGACATGAACTGAAAC                        >  1:419688/1‑69                                                                                    TTCCCTAAGACTATTCGTTAATGATAAACCCGCTTCGCTCAGAGAGCGCCGCAGGACATGAACTGAAAC                        <  2:419688/69‑1                                                                                     TCCCTAAGACTATTCGTTAATGATAAACCCGCTTCGCTCAGAGAGCGCCGCAGGACATGAACTGAAACCTCATAAGATATTGCGAGAGTC  >  1:3188/1‑90                                                                                                                                                                                TTTACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  NZ_CP009273/2282484‑2282398 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑CTAAGACTATTCGTTAATGATAAACCCGCTTCGCTCAGAGAGCGCCGCAGGACATGAACTGAAACCTCATAAGATATTGCGAGAGTC  >  NZ_CP009273/3512437‑3512523

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 33 ≤ 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.