New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_002947	= 4449631	32 (1.380)	3 (0.130)	3/242	NT	10.7%	intergenic (+102/‑340)	nicR/nicA	HTH‑type transcriptional repressor NicR/nicotinate dehydrogenase subunit A
	?	NC_002947	= 4449683	19 (0.850)					intergenic (+154/‑288)	nicR/nicA	HTH‑type transcriptional repressor NicR/nicotinate dehydrogenase subunit A

CTGCCGCCATTGCCGTCACAGATACGCGGCCTGAGAGATCAAGCGCATCGCGAGCAAGCTCGCTCACATTGGACACGCATCGGTGGTTGG‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  NC_002947/4449542‑4449631 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑ttggCCAGCAGGGCCGGCCCATTCGCGGGTGAACCCGCTCCTACGGCGGCCTGTGTCCAACCACCGATGCGTGTCCAATGTGAGCGAGCTTGCTCGCGATGCGCTTGATCTCTCAGGC  <  NC_002947/4449683‑4449570                                                                                                                                                                                                              CTGCCGCCATTGCCGTCACAGATACGCGGCCTGAGAGATCAAGCGCATCGCGAGCAAGCTCGCTCACATTGGACACGCATCGGTGGTTGGCCAGCAGGGCCGGCCCATTCGCGGGTGAACCCGCTCCTACGGCGGCCTGTGTCCAACCAC                                                        <  2:487594/150‑1                                TGAGAGATCAAGCGCATCGCGAGCAAGCTCGCTCACATTGGACACGCATCGGTGGTTGGCCAGCAGGGCCGGCCCATTCGCGGGTGAACCCGCTCCTACGGCGGCCTGTGTC                                                               >  1:93026/1‑112                                TGAGAGATCAAGCGCATCGCGAGCAAGCTCGCTCACATTGGACACGCATCGGTGGTTGGCCAGCAGGGCCGGCCCATTCGCGGGTGAACCCGCTCCTACGGCGGCCTGTGTC                                                               <  2:93026/112‑1                                                                                          GCCAGCAGGGCCGGCCCATTCGCGGGTGAACCCGCTCCTACGGCGGCCTGTGTCCAACCACCGATGCGTGTCCAATGTGAGCGAGCTTGCTCGCGATGCGCTTGATCTCTCAGGC  <  1:40805/115‑1                                                                                          GCCAGCAGGGCCGGCCCATTCGCGGGTGAACCCGCTCCTACGGCGGCCTGTGTCCAACCACCGATGCGTGTCCAATGTGAGCGAGCTTGCTCGCGATGCGCTTGATCTCTCAGGC  >  2:40805/1‑115                                                                                                                                                                                                              CTGCCGCCATTGCCGTCACAGATACGCGGCCTGAGAGATCAAGCGCATCGCGAGCAAGCTCGCTCACATTGGACACGCATCGGTGGTTGG‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  NC_002947/4449542‑4449631 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑ttggCCAGCAGGGCCGGCCCATTCGCGGGTGAACCCGCTCCTACGGCGGCCTGTGTCCAACCACCGATGCGTGTCCAATGTGAGCGAGCTTGCTCGCGATGCGCTTGATCTCTCAGGC  <  NC_002947/4449683‑4449570

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ 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.