New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NZ_CP009273	4532499 =	0 (0.000)	12 (0.590)	8/146	0.8	68.6%	intergenic (+49/‑433)	fimE/fimA	type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA
	?	NZ_CP009273	4532813 =	11 (0.540)					intergenic (+363/‑119)	fimE/fimA	type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA

AATAGAATATTAAGCCAACAAATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAGTGTACAGAACGACTGCCCAT  >  NZ_CP009273/4532736‑4532895                                                                              |                                                                                   aaTAGAATATTAAGCCAACAAATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCC‑AATGTTTCATCtttt                                                                       <  1:657800/90‑1 (MQ=255)       atatTAAGCCAACAAATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTTggggg                                                                  >  1:498251/1‑90 (MQ=255)          ttAAGCCAACAAATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTTGGGGGaaa                                                               >  2:95210/1‑90 (MQ=255)          ttAAGCCAACAAATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTTGGGGGaaa                                                               >  2:345200/1‑90 (MQ=255)                 aacaaATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTTGGGGGAAAAc                                                             <  2:279141/85‑1 (MQ=255)                 aacaaATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTTGGGGGAAAAc                                                             >  1:279141/1‑85 (MQ=255)                 aacaaATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGc                                                        >  1:121408/1‑90 (MQ=255)                             ttgagaaaaaatacgtaacttatttatgatatggacagtttggccccaaATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGt                                            >  2:180457‑M2/50‑90 (MQ=255)                                       gTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGtt                                  >  1:455936/1‑90 (MQ=255)                                              acttatttatgatatggacagtttggccccaaATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTacaaaa                           <  1:180457‑M2/58‑1 (MQ=255)                                                      ctctATGAGTCAAAATGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAgtgt                   <  1:95210/90‑1 (MQ=255)                                                        gatatggacagtttggccccaaATGTTTCATTTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTTGTTTacaaaacaa                        >  2:306080‑M2/23‑83 (MQ=255)                                                        gatatggacagtttggccccaaATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTacaaaacaa                        <  1:306080‑M2/61‑1 (MQ=255)                                                             aGTCAAAATGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAGTGTACAGAAc            >  1:288863/1‑90 (MQ=255)                                                             aGTCAAAATGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAGTGTACAGAAc            >  1:268897/1‑90 (MQ=255)                                                                  gtttggccccaaATGTTTCATCTTTTGGGGGAAAACtgtg                                                         <  2:259789‑M2/28‑1 (MQ=255)                                                                  gtttggccccaaATGTTTCATCTTTTGGGGGAAAACtgtg                                                         >  1:259789‑M2/13‑40 (MQ=255)                                                                  gtttggccccaaATGTTTCATCTTTTGGGGGAAAACTGTGc                                                        >  2:203955‑M2/13‑41 (MQ=255)                                                                  gtttggccccaaATGTTTCATCTTTTGGGGGAAAACTGTGc                                                        <  1:203955‑M2/29‑1 (MQ=255)                                                                  gtttggccccaaATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAGTGTACAGAACGACt        <  1:651964‑M2/77‑1 (MQ=255)                                                                  gtttggccccaaATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAGTGTACAGAACGACt        >  2:651964‑M2/13‑89 (MQ=255)                                                                  gtttggccccaaATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAGTGTACAGAACGACTg       >  1:574080‑M2/13‑90 (MQ=255)                                                                  gtttggccccaaATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAGTGTACAGAACGACTg       >  2:151774‑M2/13‑90 (MQ=255)                                                                     tggccccaaATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAGTGTACAGAACGACTGccc    <  2:268897‑M2/81‑1 (MQ=255)                                                                       gccccaaATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAGTGTACAGAACGACTGCCCAt  >  1:200207‑M2/8‑90 (MQ=255)                                                                              |                                                                                   AATAGAATATTAAGCCAACAAATAAACTGAAAAAGTTTGTCCGCGATGCTTTCCTCTATGAGTCAAAATGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAGTGTACAGAACGACTGCCCAT  >  NZ_CP009273/4532736‑4532895

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 26 ≤ 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.