New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NZ_CP009273	2282398 =	NA (NA)	15 (0.890)	11/168	0.4	93.8%	pseudogene (3/2532 nt)	yejO	autotransporter YejO
	?	NZ_CP009273	= 3629487	1 (0.060)					intergenic (+234/+81)	yhiM/yhiN	DUF2776 domain‑containing protein/NAD(P)/FAD‑dependent oxidoreductase

AAAGATCTGGCCACTGAGTGAGTTTTCAATCACCTTTCCATCCACCTTATATTAAGCATGGAGGGTTTCAGTTCACGGGCTCATTAGAAAATAATCACAAGATAACCACTATCAAAATTAGCTCATTTTTAATGCGACTCTAATAATTTTCATCTTTAGGAAATAGGTCAGGAC  >  NZ_CP009273/3629401‑3629574                                                                                       |                                                                                        aaaGATCTGGCCACTGAGTGAGTTTTCAATCACCTTTCCATCCACCTTATATTAAGCATGGAGGGTTTCAGTTCACGGGCTCATTAGgga                                                                                      >  2:28968‑M2/1‑87 (MQ=255)  aaGATCTGGCCACTGAGTGAGTTTTCAATCACCTTTCCATCCACCTTATATTAAGCATGGAGGGTTTCAGTTCACGGGCTCATTAGggaa                                                                                     >  1:412810‑M2/1‑86 (MQ=255)  aaGATCTGGCCACTGAGTGAGTTTTCAATCACCTTTCCATCCACCTTATATTAAGCATGGAGGGTTTCAGTTCACGGGCTCATTAGggaa                                                                                     >  1:67498‑M2/1‑86 (MQ=255)       cTGGCCACTGAGTGAGTTTTCAATCACCTTTCCATCCACCTTATATTAAGCATGGAGGGTTTCAGTTCACGGGCTCATTAGggaaggtgc                                                                                >  2:171888‑M2/1‑81 (MQ=255)         ggCCACTGAGTGAGTTTTCAATCACCTTTCCATCCACCTTATATTAAGCATGGAGGGTTTCAGTTCACGGGCTCATTAGggaaggtgcga                                                                              <  1:149244‑M2/90‑12 (MQ=255)              cTGAGTGAGTTTTCAATCACCTTTCCATCCACCTTATATTAAGCATGGAGGGTTTCAGTTCACGGGCTCATTAGggaaggtgcgaataag                                                                         <  2:175373‑M2/90‑17 (MQ=255)                     agtTTTCAATCACCTTTCCATCCACCTTATATTAAGCATGGAGGGTTTCAGTTCACGGGCTCATTAGgggaggtgcgaataagcggggaa                                                                  <  1:471114‑M2/90‑24 (MQ=255)                                               ttATATTAAGCATGGAGGGTTTCAGTTCACGGGCTCATTAGggaaggtgcgaataagcggggaaattcttctcggctgactcagtcattt                                        <  2:104308‑M2/90‑50 (MQ=255)                                                      aaGCATGGAGGGTTTCAGTTCACGGGCTCATTAGggaaggtgcgaataagcggggaaattcttctcggctgactcagtcatttcatttct                                 <  1:356836‑M2/90‑57 (MQ=255)                                                       aGCATGGAGGGTTTCAGTTCACGGGCTCATTAGggaaggtgcgaataagcggggaaattcttctcggctgactcagtcatttcatttctt                                <  1:27465‑M2/90‑58 (MQ=255)                                                           tGGAGGGTTTCGGTTCACGGGCTCATTAGAAAATAATCACAAGATAACCACTATCAAAATTAGCTCATTTTTAATGCGACTCTAATAAtt                            >  2:403093/1‑90 (MQ=255)                                                                         tCACGGGCTCATTAGggaaggtgcgaataagcggggaaattcttctcggctgactcagtcatttcatttcttcatgtttgagccgatttt              <  2:65732‑M2/90‑76 (MQ=255)                                                                                 tCATTAGggaaggtgcgaataagcggggaaattcttctcggctgactcagtcatttcatttcttcatgtttgagccgattttttctcccg      <  1:256448‑M2/90‑84 (MQ=255)                                                                                    ttAGggaaggtgcgaataagcggggaaattcttctcggctgactcagtcatttcatttcttcatgtttgagccgattttttctcccgtaa   <  1:380665‑M2/90‑87 (MQ=255)                                                                                     tAGggaaggtgcgaataagcggggaaattcttctcggctgactcagtcatttcatttcttcatgtttgagccgattttttctcccgtaaa  >  1:36702‑M2/1‑3 (MQ=255)                                                                                     tAGggaaggtgcgaataagcggggaaattcttctcggctgactcagtcatttcatttcttcatgtttgagccgattttttctcccgtaaa  >  2:309856‑M2/1‑3 (MQ=255)                                                                                       |                                                                                        AAAGATCTGGCCACTGAGTGAGTTTTCAATCACCTTTCCATCCACCTTATATTAAGCATGGAGGGTTTCAGTTCACGGGCTCATTAGAAAATAATCACAAGATAACCACTATCAAAATTAGCTCATTTTTAATGCGACTCTAATAATTTTCATCTTTAGGAAATAGGTCAGGAC  >  NZ_CP009273/3629401‑3629574

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 36 ≤ 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.