New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NZ_CP009273	4532499 =	21 (0.340)	13 (0.230)	9/144	2.1	23.7%	intergenic (+49/‑433)	fimE/fimA	type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA
	?	NZ_CP009273	4532813 =	65 (1.170)					intergenic (+363/‑119)	fimE/fimA	type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA

ACATATCAAACAGTTAGATGCTTTTTGTCGTTTTTTAATATTTTTATGCTTGAGAAAAAATACGTAACTTATTTATGATATGGACAGTTTGGCCCCAA‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  NZ_CP009273/4532596‑4532499 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑tggccccaaATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAGTGTACAGAACGACTGCCCATGTCGA  >  NZ_CP009273/4532813‑4532900                                                                                                                                                                                            ACATATCAAACAGTTAGATGCTTTTTGTCGTTTTTTAATATTTTTATGCTTGAGAAAAAATACGTAACTTATTTATGATATGGACAGTTT                                                                                                  >  2:78472/1‑90    TATCAAACAGTTAGATGCTTTTTGTCGTTTTTTAATATTTTTATGCTTGAGAAAAAATACGTAACTTATTTATGATATGGACAGTTTGGC                                                                                               >  1:401884/1‑90     ATCAAACAGTTAGATGCTTTTTGTCGTTTTTTAATATTTTTATGCTTGAGAAAAAATACGTAACTTATTTATGATATGGACAGTTTGGCC                                                                                              <  2:1713715/90‑1      TCAAACAGTTAGATGCTTTTTGTCGTTTTTTAATATTTTTATGCTTGAGAAAAAATACGTAACTTATTTATGATATGGACAGTTTGGCCC                                                                                             >  2:1295014/1‑90               TAGATGCTTTTTGTCGTTTTTTAATATTTTTATGCTTGAGAAAAAATACGTAACTTATTTATGATATGGACAGTTTGGCCCCAAATGTTT                                                                                    >  1:1325573/1‑90               TAGATGCTTTTTGTCGTTTTTTAATATTTTTATGCTTGAGAAAAAATACGTAACTTATTTATGATATGGACAGTTTGGCCCCAAATGTTT                                                                                    >  1:1044747/1‑90                       TTTTGTCGTTTTTTAATATTTTTATGCTTGAGAAAAAATACGTAACTTATTTATGATATGGACAGTTTGGCCCCAAATGTTTCATCTTTT                                                                            >  2:1869243/1‑90                                     AATATTTTTATGCTTGAGAAAAAATACGTAACTTATTTATGATATGGACAGTTTGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTG                                                              <  1:996394/90‑1                                                                     TTATTTATGATATGGACAGTTTGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACA                              >  2:259298/1‑90                                                                     TTATTTATGATATGGACAGTTTGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACA                              <  1:273844/90‑1                                                                      TATTTATGATATGGACAGTTTGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAA                             <  2:401884/90‑1                                                                              ATATGGACAGTTTGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAGTGTACA                     >  2:1240832/1‑90                                                                                 TGGACAGTTTGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAGTGTACAGAA                  >  1:791925/1‑90                                                                                 TGGACAGTTTGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAGTGTACAGAA                  >  1:1816017/1‑90                                                                                 TGGACAGTTTGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAA                             <  2:1094540/79‑1                                                                                 TGGACAGTTTGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAA                             >  1:1094539/1‑79                                                                                       GTTTGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAGTGTACAGAACGACTG            >  1:1629971/1‑90                                                                                          TGGCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAGTGTACAGAACGACTGCCC         >  1:640302/1‑90                                                                                            GCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAG                           >  2:175982/1‑70                                                                                            GCCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAG                           <  1:175982/70‑1                                                                                             CCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAA                                              <  1:767938/50‑1                                                                                             CCCCAAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAA                                              >  2:767938/1‑50                                                                                                 AAATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAGTGTACAGAACGACTGCCCATGTCGA  >  1:227990/1‑90                                                                                                                                                                                            ACATATCAAACAGTTAGATGCTTTTTGTCGTTTTTTAATATTTTTATGCTTGAGAAAAAATACGTAACTTATTTATGATATGGACAGTTTGGCCCCAA‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  NZ_CP009273/4532596‑4532499 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑tggccccaaATGTTTCATCTTTTGGGGGAAAACTGTGCAGTGTTGGCAGTCAAACTCGTTTACAAAACAAAGTGTACAGAACGACTGCCCATGTCGA  >  NZ_CP009273/4532813‑4532900

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 35 ≤ 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.