New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	CP009273	= 4532507	7 (0.390)	9 (0.540)	7/258	NT	53.7%	intergenic (+57/‑425)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
	?	CP009273	= 4532803	9 (0.540)					intergenic (+353/‑129)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)

GCGTTATACCGCCAGTAATGCTGCTCGTTTTGCCGGATTATGGGAAAGAAATAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTCACATCACCTCCGCTATATGTAAAGCTAACGTT  >  CP009273/4532360‑4532655                                                                                                                                                    |                                                                                                                                                     gCGTTATTCCGCCAGTAATGCTGCTCGCTTTGCCGGATTATGGCAAAGAAATAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGAGTTATCGTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCaa                                                                                                                                                     <  2:177548/149‑1 (MQ=255)         ccGCCAGTAATGCTGCTCGTTTTGCCGGATTATGGGAAAGAAATAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCa                                                                                                                                             >  2:118157/1‑149 (MQ=255)          cGCCAGTAATGCTGCTCGTTTTGCCGGATTATGGGAAAGAAATAACCTCATAAACGAACAATCAACAAGTGAAGCGGCTTGTTTTAACTGATTGATAATAAAGTTAAAAAAACAAATAAATACAAGAGAATTGGGGCCAAACTGTCCat                                                                                                                                            >  2:216457/1‑149 (MQ=255)                    gctgctCGTTTTGCCGGATTATGGGAAAGAAATAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAttttgactcatagaggaaag                                                                                                                                  >  2:31833‑M1/1‑129 (MQ=255)                     gctgctttcctttcaaaaaactatttctaaatcgacatgggcagtcgttctgtacactttgttttgtaaacgagtttgactgccaacactgcacagttttcccccaaaagatgaaacatTTGGGGCCAAACTGTCCATATCataaataa                                                                                                                                 >  2:96037‑M1/120‑149 (MQ=255)                     ctgctCGTTTTGCCGGATTATGGGAAAGAAATAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCataaataa                                                                                                                                 >  1:46541/1‑149 (MQ=255)                         ctttcctttcaaaaaactatttctaaatcgacatgggcagtcgttctgtacactttgttttgtaaacgagtttgactgccaacactgcacagttttccccaaaaagatgaaacatTTGGGGCCAAACTGTCCATATCATAAATAAGTTa                                                                                                                             <  2:140820‑M1/34‑1 (MQ=255)                           gTTTTGCCGGATTATGGGAAAGAAATAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAttttgactcatagaggaaagcatcgcg                                                                                                                           <  2:121282‑M1/149‑28 (MQ=255)                           gTTTGGCCGGATTATGGGAAAGAAATAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAAGAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAttttgactcatagaggaaagcatcgcg                                                                                                                           <  2:121281‑M1/149‑28 (MQ=255)                                     aTTATGGGAAAGAAATAATCTCATAATCGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTtct                                                                                                                 <  1:72992/149‑1 (MQ=255)                                                    tcgacatgggcagtcgttctgtacactttgttttgtaaacgagtttgactgccaacactgcacaattttcccccaaaagatgaaacatTTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAatat                                                                                                  <  1:49902‑M1/61‑1 (MQ=255)                                                           aTAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAttttgactcatagaggaaagcatcgcgcacaaactctttcagtttatttgttggcttaa                                                                                           >  2:289582‑M1/1‑90 (MQ=255)                                                                          acactttgttttgtaaacgagtttgactgccaacactgcacagttttccgccaaaagatgaaagatTTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTTTCAAGCTTAAAAATTTTAAAAAACGCCAAAAAGAATCt                                                                            <  1:133673‑M1/83‑1 (MQ=255)                                                                          acactttgttttgtaaacgagtttgactgccaacactgcacagttttcccccaaaagatgaaacatTTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCt                                                                            <  1:253555‑M1/83‑1 (MQ=255)                                                                                gaagagGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAACACAAGACAATTGGGGCCAttttgactcatagaggaaagcatcgcggacaaactttttcagtttatttgttggcttaatattctattgttatctttatt                                                                      <  2:103305‑M1/149‑81 (MQ=255)                                                                                        ttGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAttttgactcatagaggaaagcatcgcggacaaactttttcagtttatttgttggcttaatattctattgttatctttatttatagatg                                                              <  2:188781‑M1/149‑89 (MQ=255)                                                                                                   taatGATAATAAAGTTAAAAAAACAAATAAATACAAGCCAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTc                                                   <  1:197834/146‑1 (MQ=255)                                                                                                   tATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAttttgactcatagaggaaagcatcgcggacaaactttttcagtttatttgttggcttaatattctattgttatcttta                                                                        <  2:284890‑M1/128‑79 (MQ=255)                                                                                                   tATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAgtttgactcatagaggaaagcatcgcggacaaactttttcagtttatttgttggcttaatattctattgttatcttta                                                                        >  1:284890‑M1/1‑50 (MQ=255)                                                                                                                     aaaaaCAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTca                                 <  1:118157/149‑1 (MQ=255)                                                                                                                        aaCAAATAAATACAAGACAATTGGGGCCAAACTGCTCATGTCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTCACAt                              <  2:162546/149‑1 (MQ=255)                                                                                                                             ataaataCAAGACAATTGGGGCCAttttgactcatagaggaaagcatcgcggacaaactttttcagtttatttgttggcttaatattctattgttatctttatttatagatgtttatattgcatgaggtggtttttggagaggaagagc                         <  2:160084‑M1/149‑126 (MQ=255)                                                                                                                                  gatgaaacatTTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTCACATCACCTCCGCt                    >  2:49902‑M1/11‑149 (MQ=255)                                                                                                                                            TTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTCACATCACCTCCGCTATATGTAAAg          <  1:245018‑M1/149‑1 (MQ=255)                                                                                                                                                GGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTCACATCACCTCCGCTATATGTAAAGCTaa      >  1:288403‑M1/1‑149 (MQ=255)                                                                                                                                                    attttgactcatagaggaaagcatcgcggacaaactttttcagtttatttgttggcttaatattctattgttatctttatttatagatgtttatattgcatgaggtggtttttggagagaagaatgaggaagatgcgtcgagccacaga  >  1:248241‑M1/1‑1 (MQ=255)                                                                                                                                                    AAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTAATTCTTGGGTAAATTAATTTCACATCACCTCCGCTATATGTAAAGCTAACGtt  <  2:59617‑M1/149‑1 (MQ=255)                                                                                                                                                    |                                                                                                                                                     GCGTTATACCGCCAGTAATGCTGCTCGTTTTGCCGGATTATGGGAAAGAAATAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTCACATCACCTCCGCTATATGTAAAGCTAACGTT  >  CP009273/4532360‑4532655

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.