New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	321549 =	74 (1.140)	7 (0.110)	6/248	NT	9.6%	intergenic (+468/‑59)	rclR/ykgE	reactive chlorine species (RCS)‑specific activator of the rcl genes/cysteine‑rich LutA family protein; putative electron transport chain YkgEFG component
	?	NC_000913	321566 =	61 (0.990)					intergenic (+485/‑42)	rclR/ykgE	reactive chlorine species (RCS)‑specific activator of the rcl genes/cysteine‑rich LutA family protein; putative electron transport chain YkgEFG component

GACAGCCGAGTTTTTCCAGTAGCAGCACGGAGTCTCGTGCCATTCTTGATTTCAGGGCGTCACCAATACAGGTGACAAAGAAATTGACATTCACAACTAATACTCCATTACTTCATGCCCATTTATGCCCGATGTTTCCCCCCCACC‑‑GGGGGA‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  NC_000913/321701‑321549 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑gggggaAACATCGGGCATAAATGGGCATGAAGTAATGGAGTATTAGTTGTGAATGTCAATTTCTTTGTCACCTGTATTGGTGACGCCCTGAAATCAAGAATGGCACGAGACTCCGTGCTGCTACTGGAAAAACTC  >  NC_000913/321566‑321694                                                                                                                                                                                                                                                                                              GACAGCCGAGTTTTTCCAGTAGCAGCACGGAGTCTCGTGCCATTCTTGATTTCAGGGAGTCACCAATACAGGTGACAAAGAAATTGACATTCACAACTAATACTCCATTACTTCATGCCCATTTATGCCCGATGTTTCCCCCCCACC‑‑GG                                                                                                                                       >  3:485044/1‑149   CAGCCGAGTTTTTCCAGTAGCAGCACGGAGTCTCGTGCCATTCTTGATTTCAGGGCGTCACCAATACAGGTGACAAAGAAATTGACATTCACAACTAATACTCCATTACTTCATGCCCATTTATGCCCGATGTTTCCCCCCCACC‑‑GGGG                                                                                                                                     <  1:496217/149‑1   CAGCCGAGTTTTTCCAGTAGCAGCACGGAGTCTCGTGCCATTCTTGATTTCAGGGCGTCACCAATACAGGTGACAAAGAAATTGACATTCACAACTAATACTCCATTACTTCATGCCCATTTATGCCCGATGTTTCCCCCCCACC‑‑GGGG                                                                                                                                     <  2:137650/149‑1                                                                                                                                 CCGATGTTTCCCCCCCACC‑‑GGGGGAAACATCGGGCATAAATGGGCATGAAGTAATGGAGTATTAGTTGTGAATGTCAATTTCTTTGTCACCTGTATTGGTGACGCCCTGAAATCAA                                        <  1:312800/116‑1                                                                                                                                 CCGATGTTTCCCCCCCACC‑‑GGGGGAAACATCGGGCATAAATGGGCATGAAGTAATGGAGTATTAGTTGTGAATGTCAATTTCTTTGTCACCTGTATTGGTGACGCCCTGAAATCAA                                        >  2:312800/1‑116                                                                                                                                 CCGATGTTTCCCCCCCACC‑‑GGGGGAAACATCGGGCATAAATGGGCATGAAGTAATG                                                                                                    >  1:153566/1‑56                                                                                                                                 CCGATGTTTCCCCCCCACC‑‑GGGGGAAACATCGGGCATAAATGGGCATGAAGTAATG                                                                                                    <  2:153566/56‑1                                                                                                                                       TTTCCCCCCCACCGGGGGGGAAACATCGGGCATAAATGGGCATGAAGTAATGGAGTATTAGTTGTGAATGTCAATTTCTTTGTCACCTGTATTGGTGACGCCCTGAAATCAAGA                                      <  1:305211/114‑1                                                                                                                                       TTTCCCCCCCACCGGGGGGGAAACATCGGGCATAAATGGGCATGAAGTAATGGAGTATTAGTTGTGAATGTCAATTTCTTTGTCACCTGTATTGGTGACGCCCTGAAATCAAGA                                      >  2:305211/1‑114                                                                                                                                        TTCCCCCCCACCGGGGGGGAAACATCGGGCATAAATGGGCATGAAGTAATGGAGTATTAGTTGTGAATGTCAATTTCTTTGTCACCTGTATTGGTGACGCCCTGAAATCAAGAATGGCACGAGACTCCGTGCTGCTACTGGAAAAACTC  >  2:219228/1‑149                                                                                                                                                                                                                                                                                              GACAGCCGAGTTTTTCCAGTAGCAGCACGGAGTCTCGTGCCATTCTTGATTTCAGGGCGTCACCAATACAGGTGACAAAGAAATTGACATTCACAACTAATACTCCATTACTTCATGCCCATTTATGCCCGATGTTTCCCCCCCACC‑‑GGGGGA‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  NC_000913/321701‑321549 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑gggggaAACATCGGGCATAAATGGGCATGAAGTAATGGAGTATTAGTTGTGAATGTCAATTTCTTTGTCACCTGTATTGGTGACGCCCTGAAATCAAGAATGGCACGAGACTCCGTGCTGCTACTGGAAAAACTC  >  NC_000913/321566‑321694

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ 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.