New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_002947	447140 =	53 (1.010)	6 (0.150) +TTACGTCTTCAGGTTCAGCGTGGTCCCT	4/190	NT	11.7%	intergenic (+17/‑285)	PP_0368/PP_0369	acyl‑CoA dehydrogenase/diguanylate cyclase
	?	NC_002947	= 3252686	64 (1.220)					intergenic (+173/+70)	ureG/PP_2851	urease accessory protein/hypothetical protein

CCAGCAGGGCCGGCCTCTTCGCGGGTAAACCCGCTCCTACGAGGGACCACGCTGAACCTGAAGACGTAAAAAACCCGCCTCCCGGTCAGGGCAGGCGGGTTTT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  NC_002947/447242‑447140 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑CGTAGGAGCGGGTTTACCCGCGAAGAGGCCGGCCCTGCTG  <  NC_002947/3252686‑3252647                                                                                                        ||||||||||||||||||||||||||||                                         CCAGCAGGGCCGGCCTCTTCGCGGGTAAACCCGCTCCTACGAGGGACCACGCTGAACCTGAAGACGTAAAAAACCCGCCTCCCGGTCAGGGCAGGCGGGTTTTTTAC                                                                  <  1:651546/107‑1 CCAGCAGGGCCGGCCTCTTCGCGGGTAAACCCGCTCCTACGAGGGACCACGCTGAACCTGAAGACGTAAAAAACCCGCCTCCCGGTCAGGGCAGGCGGGTTTTTTAC                                                                  >  2:651546/1‑107                                                                         ACCCGCCTCCCGGTCAGGGCAGGCGGGTTTTTTACGTCTTCAGGTTCAGCGTGGTCCCTCGTAGGAGCGGGTTTACCCGCGAAGAGGCCGGCCCTGCTG  <  1:1303872/99‑1                                                                         ACCCGCCTCCCGGTCAGGGCAGGCGGGTTTTTTACGTCTTCAGGTTCAGCGTGGTCCCTCGTAGGAGCGGGTTTACCCGCGAAGAGGCCGGCCCTGCTG  >  2:1303872/1‑99                                                                                TCCCGGTCAGGGCAGGCGGGTTTTTTACGTCTTCAGGTTCAGCGTGGTCCCTCGTAGGAGCGGGTTTACCCGCGAAGAG               >  1:389593/1‑79                                                                                TCCCGGTCAGGGCAGGCGGGTTTTTTACGTCTTCAGGTTCAGCGTGGTCCCTCGTAGGAGCGGGTTTACCCGCGAAGAG               <  2:389593/79‑1                                                                                                 GGGTTTTTTACGTCTTCAGGTTCAGCGTGGTCCCTCGTAGGAGCGGGTTTACCC                       >  1:899730/1‑54                                                                                                 GGGTTTTTTACGTCTTCAGGTTCAGCGTGGTCCCTCGTAGGAGCGGGTTTACCC                       <  2:899730/54‑1                                                                                                        ||||||||||||||||||||||||||||                                         CCAGCAGGGCCGGCCTCTTCGCGGGTAAACCCGCTCCTACGAGGGACCACGCTGAACCTGAAGACGTAAAAAACCCGCCTCCCGGTCAGGGCAGGCGGGTTTT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  NC_002947/447242‑447140 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑CGTAGGAGCGGGTTTACCCGCGAAGAGGCCGGCCCTGCTG  <  NC_002947/3252686‑3252647

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 37 ≤ 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.