New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	CP009273	= 1391495	NA (NA)	4 (0.260)	4/272	NT	40.0%	intergenic (+146/‑127)	insH1/ynaJ	IS5 transposase and trans‑activator/DUF2534 family putative inner membrane protein
	?	CP009273	= 1972751	6 (0.390)					intergenic (‑297/‑483)	flhD/uspC	flagellar class II regulon transcriptional activator, with FlhC/universal stress protein

AAATGGGTCTTTACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAACTCACCGTAA  >  CP009273/1972614‑1972887                                                                                                                                          |                                                                                                                                         aaaTGGGTCTTTACACTTATCTAAGATTTTTCCTAAATCAACGCAACAGTAATCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAggaaggtgcga                                                                                                                               <  2:12503‑M2/149‑12 (MQ=255)                              ttCATAACTCAACGCCACTATATTCGTCACTACACGCACATACAACGGAGGGTGGCTGCGATTTTCAATAATGTGTGATGCATATCACACAAAACACTCAATTACTTAACATAAATGTATAAGTCATACTTTTGTTTTGGgtgt                                                                                                       <  1:166368/144‑1 (MQ=255)                                     aTCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGAGATGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAggaaggtgcgaataagcggggaaattcttctcggctgactcagtcat                                                                                           <  2:33434‑M2/149‑48 (MQ=255)                                      tCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAggaaggtgcgaataagcggggaaattcttctcggctgactcag                                                                                               >  1:11389‑M2/1‑101 (MQ=255)                                                tGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGAGCACACAAAACACTCAATTACTTAACATAAATGTATAAGTAATACTTTTGTTTTGGGTGTATTTCAATCTGTTaaaaa                                                                                     >  1:80313/1‑144 (MQ=255)                                                              cacGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTagca                                                                  >  2:203170/1‑149 (MQ=255)                                                                         aaCGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACACAAATACTTAACATAAATATATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGa                                                       >  2:54484/1‑149 (MQ=255)                                                                                              tCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATggg                                  <  2:76566/149‑1 (MQ=255)                                                                                                      gCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATg                               >  1:35642/1‑144 (MQ=255)                                                                                                              cAGATCACACAAAACACTCAATTACTTAAggaaggtgcgaataagcggggaaattcttctcggctgactcagtcatttcatttcttcatgtttgagccgattttttctcccgtaaatgccttgaatcagcctatttagaccgtttcttc                  <  2:222532‑M2/149‑121 (MQ=255)                                                                                                                              gcaccttccTTAACATAAATGTATAAGTCATACTTTTGTTTAGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAACTCACCGTaa  >  2:45236/9‑149 (MQ=255)                                                                                                                               caccttccTTAACATAAATGTATAAGTCATACTTTTATTCTTGTTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAAGGAAACACGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAACTAAcc      >  1:158453/8‑144 (MQ=255)                                                                                                                                          |                                                                                                                                         AAATGGGTCTTTACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAACTCACCGTAA  >  CP009273/1972614‑1972887

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ 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.