New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_002947	1311774 =	45 (0.920)	3 (0.070) +GCATCCACT	3/232	NT	7.5%	intergenic (‑236/+42)	PP_1144/rapA	membrane protein/RNA polymerase‑associated protein RapA
	?	NC_002947	3963035 =	35 (0.710)					intergenic (+37/+80)	PP_3492/PP_3493	acyl‑CoA dehydrogenase/LysR family transcriptional regulator

GACGCCCTGCGCAAGCGGCGCGAAGATGGCCTGGCAATGCTGGAGAAGGCCGCCCTGCGCCTGGAAGCCATTCGCGTGCTGGTGGCTGGCTAGCGCAGGCCCCGCGCCCCTTGTGGGAGCGGGCACGCCCGCGAA‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  NC_002947/1311908‑1311774 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑GCGGTGGAGGGCACCGGCTTTGCCGGTGTTCGCGGGCGCGCCCGCTCCC  >  NC_002947/3963035‑3963083                                                                                                                                        |||||||||                                                  GACGCCCTGCGCAAGCGGCGCGAAGATGGCCTGGCAATGCTGGAGAAGGCCGCCCTGCGCCTGGAAGCCATTCGCGTGCTGGTGGCTGGCTAGCGCAGGCCCCGCGCCCCCTGTGGGAGCGGGCGAGCCCGCGAAGCATCCACTGCGGTG                                             >  2:701489/1‑150                  GCGCGAAGATGGCCTGGCAATGCTGGAGAAGGCCGCCCTGCGCCTGGAAGCCATTCGCGTGCTGGTGGCTGGCTAGCGCAGGCCCCGCGCCCCTTGTGGGAGCGGGCGAGCCCGCGAAGCATCCACTGCGGTGGATGCCACCGGCTTTGC                            <  1:268488/150‑1                                            AGAAGGCCGCCCTGCGCCTGGAAGCCATTCGCGTGCTGGTGGCTGGCTAGCGCAGGCCCCGCGCCCCCTGTGGGAGCGGGCGAGCCCGCGAAGCATCCACTGCGGTGGATGCCACCGGCTTTGCCGGTGTTCGCGGGCGTGCCCGCTCCC  <  1:701489/150‑1                                                                                                                                        |||||||||                                                  GACGCCCTGCGCAAGCGGCGCGAAGATGGCCTGGCAATGCTGGAGAAGGCCGCCCTGCGCCTGGAAGCCATTCGCGTGCTGGTGGCTGGCTAGCGCAGGCCCCGCGCCCCTTGTGGGAGCGGGCACGCCCGCGAA‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  NC_002947/1311908‑1311774 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑GCGGTGGAGGGCACCGGCTTTGCCGGTGTTCGCGGGCGCGCCCGCTCCC  >  NC_002947/3963035‑3963083

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.