New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NZ_CP009273	= 729706	NA (NA)	3 (0.110)	3/152	2.3	NA	pseudogene (103/1506 nt)	BW25113_RS03635	RHS repeat protein
	?	NZ_CP009273	= 729729	NA (NA)					pseudogene (126/1506 nt)	BW25113_RS03635	RHS repeat protein

GCACCCTCAGCATGTGGCCGGATAACCGTATCGCCCGTGACGCGCACTATCTTTACCGGTATGACCGTCACGGCAGGCTGACGGAGAAAACCGACCTCATCCCGGAAGGGGTTATCCGCACGGATGATGAGCGCACCCACCGGTACCATTACGA  >  NZ_CP009273/729665‑729818                                                                 |                                                                                          gCACCCTCAGCATGTGGCCGGATAACCGTATCGCCCGTGACGCGCACTATCTTTACCGGTATGACCGTCACGGCAGGCTGACGGAGaaaa                                                                  >  1:417208/1‑90 (MQ=33) gCACCCTCAGCATGTGGCCGGATAACCGTATCGCCCGTGACGCGCACTATCTTTACCGGTATGACCGTCACGGCAGGCTGACGGAGaaaa                                                                  >  1:450629/1‑90 (MQ=33)       tCAGCATGTGGCCGGATAACCGTATCGCCCGTGACGCGCACTATCTTTACCGGTATGACCGTCACGGCAGGCTGACGGAGAAAACCGAcc                                                            <  2:173289/90‑1 (MQ=35)         aGCATGTGGCCGGATAACCGTATCGCCCGTGACGCGCACTATCTTTACCGGTATGACCGTCACGGCAGGCTGACGGAGAAAACCGACCTc                                                          <  1:845080/90‑1 (MQ=35)                            gTATCGCCCGTGACGCGCACTATCTTTACCGGTATGACCGTCACGGCAGACTGACGGAGAAAACCGACCTCATCCCGGaa                                                 >  2:794824/1‑80 (MQ=21)                            gTATCGCCCGTGACGCGCACTATCTTTACCGGTATGACCGTCACGGCAGACTGACGGAGAAAACCGACCTCATCCCGGaa                                                 <  1:794824/80‑1 (MQ=255)                               tCGCCCGTGACGCGCACTATCTTTACCGGTATGACCGTCACGGCAGGCTGACGGAGAAAACCGACCTCATCCCGGAAGGGGTTATCCGCa                                    >  1:673447/1‑90 (MQ=33)                                cGCCCGTGACGCGCACTATCTTTACCGGTATGACCGTCACGGCAGGCTGACGGAGAAAACCGACCTCATCCCGGAAGGGGTTATCCGCAc                                   <  2:44069/90‑1 (MQ=33)                                cGCCCGTGACGCGCACTATCTTTACCGGTATGACCGTCACGGCAGGCTGACGGAGAAAACCGACCTCATCCCGGAAGGGGTTATCCGCAc                                   <  1:736547/90‑1 (MQ=33)                                 gCCCGTGACGCGCACTATCTTTACCGGTATGACCGTCACGGCAGGCTGACGGAGAAAACCGACCTCATCCCGGAAGGGGTTATCCGc                                     >  2:566191/1‑87 (MQ=33)                                 gCCCGTGACGCGCACTATCTTTACCGGTATGACCGTCACGGCAGGCTGACGGAGAAAACCGACCTCATCCCGGAAGGGGTTATCCGc                                     <  1:566191/87‑1 (MQ=33)                                 gCCCGTGACGCGCACTATCTTTACCGGTATGACCGTCACGGCAGGCTGACGGAGAAAACCGACCTCATCCCGGAAGGGGTTATCCGc                                     <  1:681424/87‑1 (MQ=33)                                 gCCCGTGACGCGCACTATCTTTACCGGTATGACCGTCACGGCAGGCTGACGGAGAAAACCGACCTCATCCCGGAAGGGGTTATCCGc                                     >  2:681424/1‑87 (MQ=33)                                          gcgcACTATCTTTACCGGTATGACCGTCACGGCAGGCTGACGGAGAAAACCGACCTCATCCCGGAAGGGGTTATCCGCACGGATGATGAg                         <  1:396026/90‑1 (MQ=33)                                               cTATCTTTACCGGTATGACCGTCACGGCAGGCTGACGGAGAAAACCGACCTCATCCCGGAAGGGGTTATCCGCACGGATGATGAGCGcac                    <  1:738706/90‑1 (MQ=33)                                                 aTCTTTACCGGTATGACCGTCACGGCAGGCTGACGGAGAAAACCGACCTCATCCCGGAAGGGGTTATCCGCACGGATGATGAGCGcaccc                  <  2:562416/90‑1 (MQ=33)                                                    tttACCGGTATGACCGTCACGGCAGGCTGACGGAGAAAACCGACCTCATCCCGGAAGGGGTTATCCGCACGGATGATGAGCGcacccacc               <  2:59277/90‑1 (MQ=33)                                                      tACCGGTATGACCGTCACGGCAGGCTGACGGAGAAAACCGACCTCATCCCGGAAGGGGTTATCCGCACGGATGATGAGCGCACCCACCgg             >  1:823827/1‑90 (MQ=33)                                                        ccGGTATGACCGTCACGGCAGGCTGACGGAGAAAACCGACCTCATCCCGGAAGGGGTTATCCGCACGGATGATGAGCGCACCCACCGGTa           <  1:597835/90‑1 (MQ=33)                                                        ccGGTATGACCGTCACGGCAGGCTGACGGAGAAAACCGACCTCATCCCGGAAGGGGTTATCCGCACGGATGATGAGCGCACCCACCGGTa           <  2:830901/90‑1 (MQ=33)                                                           gTATGACCGTCACGGCAGGCTGACGGAGAAAACCGACCTCATCCCGGAAGGGGTTATCCGCACGGATGATGAGCGCACCCACCGGTACCa        >  2:743967/1‑90 (MQ=33)                                                           gTATGACCGTCACGGCAGGCTGACGGAGAAAACCGACCTCATCCCGGAAGGGGTTATCCGCACGGATGATGAGCGCACCCACCGGTACCa        >  1:186359/1‑90 (MQ=35)                                                           gTATGACCGTCACGGCAGGCTGACGGAGAAAACCGACCTCATCCCGGAAGGGGTTATCCGCACGGATGATGAGCGCACCCACCGGTACCa        >  1:834272/1‑90 (MQ=35)                                                           gTATGACCGTCACGGCAGGCTGACGGAGAAAACCGACCTCATCCCGGAAGGGGTTATCCGCACGGATGATGAGCGCACCCACCGGTACCa        >  1:44085/1‑90 (MQ=33)                                                           gTATGACCGTCACGGCAGGCTGACGGAGAAAACCGACCTCATCCCGGAAGGGGTTATCCGCACGGATGATGAGCGCACCCACCGGTACCa        >  1:418982/1‑90 (MQ=35)                                                             aTGACCGTCACGGCAGGCTGACGGAGAAAACCGACCTCATCCCGGAAGGGGTTATCCGCACGGATGATGAGCGCACCCACCGGTACCAtt      >  1:33804/1‑90 (MQ=33)                                                               gACCGTCACGGCAGGCTGACGGAGAAAACCGACCTCATCCCGGAAGGGGGTATCCGCACGGATGATGAGCGCACCCACCGGTACCATTAc    >  2:309750/1‑90 (MQ=18)                                                                 ccGTCACGGCAGGCTGACGGAGAAAACCGACCTCATCCCGGAAGGGGTTATCCGCACGGATGATGAGCGCACCCACCGGTACCATTACGa  <  2:855213/90‑1 (MQ=33)                                                                 ccGTCACGGCAGGCTGACGGAGAAAACCGACCTCATCCCGGAAGGGGTTATCCGCACGGATGATGAGCGCACCCACCGGTACCATTACGa  <  1:818425/90‑1 (MQ=33)                                                                 |                                                                                          GCACCCTCAGCATGTGGCCGGATAACCGTATCGCCCGTGACGCGCACTATCTTTACCGGTATGACCGTCACGGCAGGCTGACGGAGAAAACCGACCTCATCCCGGAAGGGGTTATCCGCACGGATGATGAGCGCACCCACCGGTACCATTACGA  >  NZ_CP009273/729665‑729818

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 20 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 34 ≤ 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.