New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	AP009048	2026073 =	88 (1.760)	4 (0.090)	3/96	NT	5.6%	intergenic (+258/‑32)	fliR/rcsA	flagellar export pore protein/DNA‑binding transcriptional co‑regulator with RcsB
	?	AP009048	2026120 =	53 (1.130)					coding (16/624 nt)	rcsA	DNA‑binding transcriptional co‑regulator with RcsB

GTCGGGTGTAACTACATAAATCCATAATAATCGTTGACATGGCATACCCTCACTCAATGCGTAACGATAATT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  AP009048/2026144‑2026073 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑attATGGATTTATGTAGTTACACCCGACTAGGTTTAACCGGGTATCTGTTGAGTAGAGGGGTTAAAAAAA  >  AP009048/2026120‑2026186                                                                                                                                             GTCGGGTGTAACTTCATAAATCCATAATAATCGTTGACATGGCATACCCTCACTCAATGCGTAACGATAAT                                                                      <  1:2761416/71‑1 GTCGGGTGTAACTACATAAATCCATAATAATCGTTGACATGGCATACCCTCACTCAATGCGTAACGATAAT                                                                      >  1:3919762/1‑71            CTACATAAATCCATAATAATCGTTGACATGGCATACCCTCACTCAATGCGTAACGATAATTATGGATTTAT                                                           >  1:2787216/1‑71               CATAAATCCATAATAATCGTTGACATGGCATACCCTCACTCAATGCGTAACGATAA                                                                       >  1:364755/1‑56                    ATCCATAATAATCGTTGACATGGCATACCCTCACTCAATGCGTAACGATAATT                                                                     <  1:3815942/53‑1                          AATAATCGTTGACATGGCATACCCTCACTCAATGCGTAACGATAATTATGGATTTATGTAGTTACACCCGA                                             >  1:3502641/1‑71                            TAATCGTTGACATGGCATACCCTCACTCAATGCGTAACGATAATTATGGATTTATGTAGTTACACCCGAC                                            >  1:81997/1‑70                                                             tcAACGATAATTATGGATTTATGTAGTTACACCCGACTAGGTTTAACCGGGTATCTGTTGAGTAGAGGGGT          >  1:1633975/3‑71                                                                      ATTATGGATTTATGTAGTTACACCCGACTAGGTTTAACCGGGTATCTGTTGAGTAGAGGGGTTAAAAAAA  <  1:2224625/70‑1                                                                      ATTATGGATTTATGTAGTTACACCCGACTAGGTTTAACCGGGTATCTGTTGAGTAGAGGGGTTAAAAAAA  <  1:332922/70‑1                                                                                                                                             GTCGGGTGTAACTACATAAATCCATAATAATCGTTGACATGGCATACCCTCACTCAATGCGTAACGATAATT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  AP009048/2026144‑2026073 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑attATGGATTTATGTAGTTACACCCGACTAGGTTTAACCGGGTATCTGTTGAGTAGAGGGGTTAAAAAAA  >  AP009048/2026120‑2026186

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ 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.