New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	= 3798186	11 (0.140)	4 (0.050)	4/496	NT	27.8%	coding (1240/1260 nt)	waaL	O‑antigen ligase
	?	NC_000913	= 3798668	10 (0.130)					coding (644/1074 nt)	waaU	lipopolysaccharide core biosynthesis

GTACGTGAATTAGGGTAAAATGCAAGCGTTGGTTTATGATAAGCCGCAGCGATATGAACAAGAGCTGTATCAACAGAAATGACAAAATCACTATACTTGGTCAACGCAACGGTATAAATAAACTCATCAAATGGTAGTGTTTCGATTTCAAGTATTGGTATTGTCAATAAATCTTGCGGTAACCCGGTAAATATAATCCGATAATTTTCAAAGTGTGTTTTCACTTCTTGATATATAACTTTTATTTGCTCAAACGTAAGACGGCATATTTTTTTTGCACCTAATGGATTAATAATGACTATTCTTGTATCTCCAATAAATTCTTTTATTTTATCTTCAACATCTACTGGTAAATGCAAGTCGTAGTTGGTGGAAAATTTACCCTCACCATAAATATGCTTCAGTATTTCTATTGCTCGTGTACTCATATGTTCTTTTAAACATTCATCGTGGGGATGGTAAAATGAATAGTAACGCTTATACCAATGATCAAAACCCAGAATGTAAGAATCTTTTAAACTTGATAATATTAAGCTATGCTTAAATGAGGGCATAGTTTCAAAG  >  NC_000913/3798383‑3798946                                                                                                                                                                                                                                                                                              |                                                                                                                                                                                                                                                                                       gTACGTGAATTAGGGTAAAATGCAAGCGTTGGTTTATGATAAGCCGCAGCGATATGAACAAGAGCTGTATCAACAGAAATGACAAAATCACTATACTTGGTCAACGCAACGGTATAAATAAACTCATCAAATGGTAGTGTTTCGATTTCAAGTATTGGTATTGTCAATAAATCTTGCGGTAACCCGGTAAATATAATCCGATAATTTTCAAAGTGTGTTTTCACTTCTTGATATATAACTTTTATTTGCTCAAACGTAAGACGGCATATTTTTTTTGCACCTAATGga                                                                                                                                                                                                                                                                                      >  1:350695‑M2/1‑286 (MQ=255)    cGTGAATTAGGGTAAAATGCAAGCGTTGGTTTATGATAAGCCGCAGCGATATGAACAAGAGCTGTATCAACAGAAATGACAAAATCACTATACTTGGTCAACGCAACGGTATAAATAAACTCATCAAATGGTAGTGTTTCGATTTCAAGTATTTGTATTGTCAATAAATCTTGCGGTAACCCGGTAAATATAATCCGATAATTTTCAAAGTGTGTTTTCACTTCTTGATATATAACTTTTATTTGCTCAAACGTAAGACGGCATATTTTTTTTGCACCTAATGGATtaa                                                                                                                                                                                                                                                                                  >  2:326865/1‑289 (MQ=255)     gggAAGTAGGGTAAAATGCAAGCTTTGGTTTATGATAAGCCGCAGCGATATGAACAAGAGCTGTATCAACAGAAATGACAAAATCACTATACTTGGTCAACGCAACGGTATAAATAAACTCATCAAATGGTAGTGTTTCGATTTCAAGTATTGGTATTGTCAATAAATCTTGCGGTAACCCGGTAAATATAATCCGATAATTTTCAAAGTGTGTTTTCACTTCTTGATATATAACTTTTATTTGCTCAAACGTAAGACGGCATATTTTTTTTGCACCTAATGGATtaat                                                                                                                                                                                                                                                                                 <  1:441094/287‑1 (MQ=255)        aaTTAGGGTAAAATGCAAGCGTTGGTTTATGATAAGCCGCAGCGATATGAACAAGAGCTGTATCAACAGAAATGACAAAATCACTATACTTGGTCAACGCAACGGTATAAATAAACTCATCAAATGGTAGTGTTTCGATTTCAAGTATTTGTATTGTCAATAAATCTTGCGGTAACCCGGTAAATATAATCCGATAATTTTCAAAGTGTGTTTTCACTTCTTGATATATAACTTTTATTTGCTCAAACGTAAGACGGCATATTTTTTTTGCACCTAATGGATTaataat                                                                                                                                                                                                                                                                              <  1:326865/289‑1 (MQ=255)                                                                                                   ggTCAACGCAACGGTATAAATAAACTCATCAAATGGTAGTGTTTCGATTTCAAGTATTGGTATTGTCAATAAATCTTGCGGTAACCCGGTAAATATAATCCGATAATTTTCAAAGTGTGTTTTCACTTCTTGATATATAACTTTTATTTGCTCAAACGTAAGACGGCATATTTTTTTTGCACCTAATGGATTaataat                                                                                                                                                                                                                                                                              >  2:63029/1‑198 (MQ=255)                                                                                                   ggTCAACGCAACGGTATAAATAAACTCATCAAATGGTAGTGTTTCGATTTCAAGTATTGGTATTGTCAATAAATCTTGCGGTAACCCGGTAAATATAATCCGATAATTTTCAAAGTGTGTTTTCACTTCTTGATATATAACTTTTATTTGCTCAAACGTAAGACGGCATATTTTTTTTGCACCTAATGGATTaataat                                                                                                                                                                                                                                                                              <  1:63029/198‑1 (MQ=255)                                                                                                    gTCAACGCAACGGTATAAATAAACTCATCAAATGGTAGTGTTTCGATTTCAAGTATTGGTATTGTCAATAAATCTTGCGGTAACCCGGTAAATATAATCCGATAATTTTCAAAGTGTGTTTTCACTTCTTGATATATAACTTTTATTTGCTCAAACGTAAGACGGCATATTTTTTTTGCACCTAATGGATTAATAATGACTATTCTTGTATCTCCAATAAATTCTTTTATTTTATCTTCAACATCTACTGGTAAATGCAAGTCGTAGTTGGTGGAAAATTTAcc                                                                                                                                                                                       <  2:340551/284‑1 (MQ=255)                                                                                                    gTCAACGCAACGGTATAAATAAACTCATCAAATGGTAGTGTTTCGATTTCAAGTATTGGTATTGTCAATAAATCTTGCGGTAACCCGGTAAATATAATCCGATAATTTTCAAAGTGTGTTTTCACTTCTTGATATATAACTTTTATTTGCTCAAACGTAAGACGGCATATTTTTTTTGCACCTAATGGATTAATAATGACTATTCTTGTATCTCCAATAAATTCTTTTATTTTATCTTCAACATCTACTGGTAAATGCAAGTCGTAGTTGGTGGAAAATTTAcc                                                                                                                                                                                       >  1:340551/1‑284 (MQ=255)                                                                                                              cgGTATAAATAAACTCATCAAATGGTAGTGTTTCGATTTCAAGTATTGGTATTGTCAATAAATCTTGCGGTAACCCGGTAAATATAATCCGATAATTTTCAAAGTGTGTTTTCACTTCTTGATATATAACTTTTATTTGCTCAAACGTAAGACGGCATATTTTTTTTGCACCTAATGgattattaatgacgagtaagaggactatagcggatataatgataattggaatgctgcgtgcccatatgatcacatcactgagtccaatccccacaatgccaagcgttaata                                                                                                                                                                         <  1:31284‑M2/288‑112 (MQ=255)                                                                                                                              atcaAATGGTAGTGTTTCGATTTCAAGTATTGGTATTGTCAATAAATCTTGCGGTAACCCGGTAAATATAATCCGATAATTTTCAAAGTGTGTTTTCACTTCTTGATATATAACTTTTATTTGCTCAAACGTAAGACGGCATATTTTTTTTGCACCTAATGGATTAATAATGACTATTCTTGTATCTCCAATAAATTCTTTTATTTTATCTTCAACATCTACTGGTAAATGCAAGTCGTAGTTGGTGGAAAATTTACCCTCACCATAAATATGCTTc                                                                                                                                                                    >  1:704843/1‑277 (MQ=255)                                                                                                                              atcaAATGGTAGTGTTTCGATTTCAAGTATTGGTATTGTCAATAAATCTTGCGGTAACCCGGTAAATATAATCCGATAATTTTCAAAGTGTGTTTTCACTTCTTGATATATAACTTTTATTTGCTCAAACGTAAGACGGCATATTTTTTTTGCACCTAATGGATTAATAATGACTATTCTTGTATCTCCAATAAATTCTTTTATTTTATCTTCAACATCTACTGGTAAATGCAAGTCGTAGTTGGTGGAAAATTTACCCTCACCATAAATATGCTTc                                                                                                                                                                    <  2:704843/277‑1 (MQ=255)                                                                                                                                       tAGTGTTTCGATTTCAAGTATTGGTATTGTCAATAAATCTTGCGGTAACCCGGTAAATATAATCCGATAATTTTCAAAGTGTGTTTTCACTTCTTGATATATAACTTTTATTTGCTCAAACGTAAGACGGCATATTTTTTTTGCACCTAATGgattattaatgacgagtaagaggactatagcggatataatgataattggaatgctgcgtgcccatatgatcacatcactgagtccaatccccacaatgccaagcgttaatatcaacaaacccaaagctcgtttttt                                                                                                                                                >  2:31284‑M2/1‑152 (MQ=255)                                                                                                                                                                   gTCAATAAATCTTGCGGTAACCCGGTAAATATAATCCGATAATTTTCAAAGTGTGTTTTCACTTCTTGATATATAACTTTTATTTGCTCAAACGTAAGACGGCATATTTTTTTTGCACCTAATGgattattaatgacgagtaagaggactatagcggatataatgataattggaatgctgcgtgcccatatgatcacatcactgagtccaatccccacaatgccaagcgttaatatcaacaaacccaaagctcgttttttatatgctatataaaatagtgaaaaataga                                                                                                                   <  2:605428‑M2/289‑166 (MQ=255)                                                                                                                                                                         aaaTCTTGCGGTAACCCGGTAAATATAATCCGATAATTTTCAAAGTGTGTTTTCACTTCTTGATATATAACTTTTATTTGCTCAAACGTAAGACGGCATATTTTTTTTGCACCTAATGGATTAATAATGACTATTCTTGTATCTCCAATAAATTCTTTTATTTTATCTTCAACATCTACTGGTAAATGCAAGTCGTAGTTGGTGGAAAATTTACCCt                                                                                                                                                                                     <  1:291971/217‑1 (MQ=255)                                                                                                                                                                         aaaTCTTGCGGTAACCCGGTAAATATAATCCGATAATTTTCAAAGTGTGTTTTCACTTCTTGATATATAACTTTTATTTGCTCAAACGTAAGACGGCATATTTTTTTTGCACCTAATGGATTAATAATGACTATTCTTGTATCTCCAATAAATTCTTTTATTTTATCTTCAACATCTACTGGTAAATGCAAGTCGTAGTTGGTGGAAAATTTACCCt                                                                                                                                                                                     >  2:291971/1‑217 (MQ=255)                                                                                                                                                                              ttGCGGTAACCCGGTAAATATAATCCGATAATTTTCAAAGTGTGTTTTCACTTCTTGATATATAACTTTTATTTGCTCAAACGTAAGACGGCATATTTTTTTTGCACCTAATGGATTAATAATGACTATTCTTGTATCTCCAATAAATTCTTTTATTTTATCTTCAACATCTACTGGTAAATGCAAGTCGTAGTTGGTGGAAAATTTACCCTCACCATAAATATGCTTCAGTATTTCTATTGCTCGTGTACTCATATGTTCTTTTAAACATTCATCGTGGGGATGGTaa                                                                                                        >  1:327898/1‑289 (MQ=255)                                                                                                                                                                                                                        tgtTTTCACTTCTTGATATATAACTTTTATTTGCTCAAACGTAAGACGGCATATTTTTTTTGCACCTAATGGATTAATAATGACTATTCTTGTATCTCCAATAAATTCTTTTATTTTATCTTCAACATCTACTGGTAAATGCAAGTCGTAGTTGGTGGAAAATTTACCCTCACCATAAATATGCTTCAGTATTTCTATTGCTCGTGTACTCATATGTTCTTTTAAACATTCATCGTGGGGATGGTAAAATGAATAGTAACGCTTATACCAATGATCAAAACCCAGAATg                                                              >  1:86472/1‑289 (MQ=255)                                                                                                                                                                                                                            ttCACTTCTTGATATATAACTTTTATTTGCTCAAACGTAAGACGGCATATTTTTTTTGCACCTAATGgattattaatgacgagtaagaggactatagcggatataatgataattggaatgctgcgtgcccatatgatcacatcactgagtccaatccccacaatgccaagcgttaatatcaacaaacccaaagctcgttttttatatgctatataaaatagtgaaaaatagaggaaaagtgtggaaaaaattcccatcagacctttcagtgaccctgcttcaattatct                                                          >  1:605428‑M2/1‑67 (MQ=255)                                                                                                                                                                                                                                                                          atatTTTTTTTGCACCTAATGGATTAATAATGACTATTCTTGTATCTCCAATAAATTCTTTTATTTTATCTTCAACATCTACTGGTAAATGCAAGTCGTAGTTGGTGGAAAATTTACCCTCACCATAAATATGCTTCAGTATTTCTATTGCTCGTGTACTCATATGTTCTTTTAAACATTCATCGTGGGGATGGTAAAATGAATAGTAACGCTTATACCAATGATCAAAACCCAGAATGTAAGAATCTTTTAAACTTGATAATATTAAGCTATGCTTAAATGAGGGCa             <  2:327898/288‑1 (MQ=255)                                                                                                                                                                                                                                                                                    tGCACCTAATGGATTAATAATGACTATTCTTGTATCTCCAATAAATTCTTTTATTTTATCTTCAACATCTACTGGTAAATGCAAGTCGTAGTTGGTGGAAAATTTACCCTCACCATAAATATGCTTCAGTATTTCTATTGCTCGTGTACTCATATGTTCTTTTAAACATTCATCGTGGGGATGGTAAAATGAATAGTAACGCTTATACCAATGATCAAAACCCAGAATGTAAGAATCTTTTAAACTTGATAATATTAAGCTATGCTTAAATGAGGGCATAGTTTCAAAg  <  2:86472/289‑1 (MQ=255)                                                                                                                                                                                                                                                                                              |                                                                                                                                                                                                                                                                                       GTACGTGAATTAGGGTAAAATGCAAGCGTTGGTTTATGATAAGCCGCAGCGATATGAACAAGAGCTGTATCAACAGAAATGACAAAATCACTATACTTGGTCAACGCAACGGTATAAATAAACTCATCAAATGGTAGTGTTTCGATTTCAAGTATTGGTATTGTCAATAAATCTTGCGGTAACCCGGTAAATATAATCCGATAATTTTCAAAGTGTGTTTTCACTTCTTGATATATAACTTTTATTTGCTCAAACGTAAGACGGCATATTTTTTTTGCACCTAATGGATTAATAATGACTATTCTTGTATCTCCAATAAATTCTTTTATTTTATCTTCAACATCTACTGGTAAATGCAAGTCGTAGTTGGTGGAAAATTTACCCTCACCATAAATATGCTTCAGTATTTCTATTGCTCGTGTACTCATATGTTCTTTTAAACATTCATCGTGGGGATGGTAAAATGAATAGTAACGCTTATACCAATGATCAAAACCCAGAATGTAAGAATCTTTTAAACTTGATAATATTAAGCTATGCTTAAATGAGGGCATAGTTTCAAAG  >  NC_000913/3798383‑3798946

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 38 ≤ 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.