New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	CP009273	4532499 =	15 (0.780)	3 (0.170)	3/258	NT	18.7%	intergenic (+49/‑433)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
	?	CP009273	4532813 =	12 (0.670)					intergenic (+363/‑119)	fimE/fimA	tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)

ACTGTGCGTTATACCGCCAGTAATGCTGCTCGTTTTGCCGGATTATGGGAAAGAAATAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTCACATCACCTCCGCTATATGTAAA  >  CP009273/4532355‑4532646                                                                                                                                                 |                                                                                                                                                    aCTGTGCGTTATACCGCCAGTAATGCTGCTCGTTTTGCCGGATTATGGAAAAGAAATAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGG                                                                                                                                                 >  1:112489‑M1/1‑149 (MQ=255)   attgccagagttttaattttcatgctgctttcctttcaaaaaactatttataaatcaacatgggcagtcgttctgtacactttgttttgtaaacgagtttgactgccaacactgcacagttttcccccaaaagttgaaacatTTGGGGc                                                                                                                                               <  1:262853‑M1/7‑1 (MQ=255)                      aaTGCTGCTCGTTTTGCCGGATTATGGGAAAGAAATAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATAAAAGACAATTGGGGCCAttttgagtcatagagga                                                                                                                            >  2:316423‑M1/1‑132 (MQ=255)                             ctCGTTTTGCCGGATTATGGGAAAGAAATAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGtt                                                                                                                     <  2:34921/149‑1 (MQ=255)                                      ccGGATTATGGGAAAGAAAGAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACATTTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTAtttt                                                                                                            <  1:253413/149‑1 (MQ=255)                                         gATTATGGGAAAGAAATAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACATGACTATTGGGGTCAAACTGTCCATATCATAAATAAGTTACGTATTTTTtc                                                                                                         <  1:128897/149‑1 (MQ=255)                                            tATGGGAAAGAAATAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCa                                                                                                      >  2:309979/1‑149 (MQ=255)                                                 gaaagaaaTAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAAACAATTGGGGCCAAACTGTCCATATGATAAATAAGTTACGTATTTTTTCTaaaagtt                                                                                                 >  2:183635/1‑145 (MQ=255)                                                               cATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATAAAAGACAATTGGGGCCAttttgactcatagaggaaagcatcgaggacaaactttttcagtttatttgttgggtta                                                                                   >  1:173044‑M1/1‑91 (MQ=255)                                                                gggcagtcgttctgtacactttgctttgtaaacgagtttgactgccaacactgcacagttttcccccaaaagatgaaacatTTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTaaaaaa                                                                                  >  1:25140‑M1/82‑149 (MQ=255)                                                                ataacacaaaaaTTAAAAAGAGACAATGTTTGATTAAACTTATTTATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTaaaaaa                                                                                  <  2:64471/142‑1 (MQ=255)                                                                             gaaaaaGAGAAGAGGTTTGATTCAACTTATTAATAATAAAGTCAAAAAAACAAAGAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCAt                                                                     <  2:100198/148‑1 (MQ=255)                                                                                aaaGAGAAGCGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAttttgactcatagaggaaagcatcgcggacaaactttttcagtttatttgttggcttaatattctattgttatct                                                                  <  2:34909‑M1/149‑76 (MQ=255)                                                                                 actttgttttgtaaacgagtttgactgccaacactgcacagttttcccccaaaagatgaaacatTTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTaa                                                                 <  2:182861‑M1/85‑1 (MQ=255)                                                                                          ggTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGat                                                        <  1:270750/149‑1 (MQ=255)                                                                                                   tAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTTTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAatt                                               <  1:231524/149‑1 (MQ=255)                                                                                                   tAACTTATGGATAATAAAGTTAAAAATACAAATAAATACAATTCAATTGGGGTCAATCTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGTATAAAAATATTAAATAACGACAAAAAGCATCTAACTGTTTGATATGTAAatt                                               <  1:231529/149‑1 (MQ=255)                                                                                                           tGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTCTTTTTTCTCAAGCATAAAAATATTAAAAAAAAACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTAt                                       <  1:248683/149‑1 (MQ=255)                                                                                                           tGAAAATAAAGTTAAAAAAACAAATAAATACAATACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTAt                                       <  1:69947/149‑1 (MQ=255)                                                                                                                     gTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAttttgactcatagaggaaagcatcgcggacaaactttttcagtttatttgttggcttaatattctattgttatctttatttatagatgtttatattgcatgaggtggttttt                             >  1:182861‑M1/1‑37 (MQ=255)                                                                                                                        aaaaaaaCAAATAAATACAAGACAATTGGGGCCAttttgactcatagaggaaagcatcgcggacaaactttttcagtttatttgttggcttaatattctattgttatctttatttatagatgtttatattgcatgaggtggtttctgaa                          >  1:328778‑M1/1‑34 (MQ=255)                                                                                                                         aaaaaaCAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAATAGTATCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTc                         <  1:267697/149‑1 (MQ=255)                                                                                                                            aaaCAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAAAAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTcaca                      >  1:300259/1‑149 (MQ=255)                                                                                                                               cAAATAAATACAAGACAATTGGGGCCAACCTTTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAATTATTAAAAAAAAAAAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTCACATCa                   <  2:327946/149‑1 (MQ=255)                                                                                                                                 ccaaaagatgaaacatTTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTCACATCAcc                 <  2:328778‑M1/133‑1 (MQ=255)                                                                                                                                   taaataCAAGACAATTGGGGCCAttttgactcatagaggaaagcatcgcggacaaactttttcagattatttgttggcttaatattctattgttatctttatttatagatgtttatattgcatgaggtggtttttggagagaagaatga               >  1:133984‑M1/1‑23 (MQ=255)                                                                                                                                                aTTGGGGCCATACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTCACATCACCTCCGCTATATGTaaa  <  2:102226/149‑1 (MQ=255)                                                                                                                                                 |                                                                                                                                                    ACTGTGCGTTATACCGCCAGTAATGCTGCTCGTTTTGCCGGATTATGGGAAAGAAATAATCTCATAAACGAAAAATTAAAAAGAGAAGAGGTTTGATTTAACTTATTGATAATAAAGTTAAAAAAACAAATAAATACAAGACAATTGGGGCCAAACTGTCCATATCATAAATAAGTTACGTATTTTTTCTCAAGCATAAAAATATTAAAAAACGACAAAAAGCATCTAACTGTTTGATATGTAAATTATTTCTATTGTAAATTAATTTCACATCACCTCCGCTATATGTAAA  >  CP009273/4532355‑4532646

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 27 ≤ 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.