New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NZ_CP009273	4532499 =	18 (0.340)	11 (0.240)	9/148	1.8	33.3%	intergenic (+49/‑433)	fimE/fimA	type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA
	?	NZ_CP009273	4532813 =	28 (0.600)					intergenic (+363/‑119)	fimE/fimA	type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA

ATCAAACAGTTAGATGCTTTTTGTCGTTTTTTAATATTTTTATGCTTGAGAAAAAATACGTAACTTATTTATGATATGGACAGTTTGGCCCCAA‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  NZ_CP009273/4532592‑4532499 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑tggccccaaATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAGTGTACAGAACGACTGCCCATGTCGA  >  NZ_CP009273/4532813‑4532900                                                                                                                                                                                        ATCAAACAGTTAGATGCTTTTTGTCGTTTTTTAATATTTTTATGCTTGAGAAAAAATACGTAACTTATTTATGATATGGACAGTTTGGCC                                                                                              <  1:1126102/90‑1     AACAGTTAGATGCTTTTTGTCGTTTTTTAATATTTTTATGCTTGAGAAAAAATACGTAACTTATTTATGATATGGACAGTTTGGCCCCAA                                                                                          >  2:23201/1‑90                 CTTTTTGTCGTTTTTTAATATTTTTATGCTTGAGAAAAAATACGTAACTTATTTATGATATGGACAGTTTGGCCCCAAATGTTTCATCTT                                                                              >  1:539422/1‑90                                                   AAAAAATACGTAACTTATTTATGATATGGACAGTTTGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAAC                                            <  2:1511824/90‑1                                                                 TTATTTATGATATGGACAGTTTGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACA                              <  1:654644/90‑1                                                                  TATTTATGATATGGACAGTTTGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAA                             >  2:22365/1‑90                                                                    TTTATGATATGGACAGTTTGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAG                           <  1:1074184/90‑1                                                                    TTTATGATATGGACAGTTTGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAG                           <  2:1342891/90‑1                                                                                 CAGTTTGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAA                                <  1:241537/72‑1                                                                                 CAGTTTGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAA                                >  2:241537/1‑72                                                                                   GTTTGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAGTGTACAGAACGACTG            >  2:408283/1‑90                                                                                   GTTTGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAGTGTACAGAACGAC              >  1:552424/1‑88                                                                                   GTTTGGCCCCAAATGTTTCATCATTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAGTGTACAGAACGAC              <  2:552424/88‑1                                                                                             AAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAGTGTACAGAACGACTGCCCATGTCGA  >  1:258815/1‑90                                                                                             AAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAGTGTACAGAACGACTGCCCATGTCGA  >  2:981236/1‑90                                                                                                                                                                                        ATCAAACAGTTAGATGCTTTTTGTCGTTTTTTAATATTTTTATGCTTGAGAAAAAATACGTAACTTATTTATGATATGGACAGTTTGGCCCCAA‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  NZ_CP009273/4532592‑4532499 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑tggccccaaATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAGTGTACAGAACGACTGCCCATGTCGA  >  NZ_CP009273/4532813‑4532900

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