New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NZ_CP009273	= 1127367	15 (0.470)	3 (0.110)	3/150	2.5	21.1%	coding (58/696 nt)	flgD	flagellar hook assembly protein FlgD
	?	NZ_CP009273	= 1127421	9 (0.320)					coding (112/696 nt)	flgD	flagellar hook assembly protein FlgD

CTGAAAACCCTTACGCTCGGTCAATAAAGGAGAAAGCTATGTCCATTGCGGTAACCACCACCGATCCGACAAATACCGGCGTCAGTACCACCAGCA‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  NZ_CP009273/1127272‑1127367 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑ccaccagcaAAGTCAGAAAACTGCTTTGTAAATCTGCGGCGTTGCTGCCCGTGAGCGAACTACTGCTGGTGGTACTGACGCCGGTATTTGTCGGATC  <  NZ_CP009273/1127421‑1127334                                                                                                                                                                                          CTGAAAACCCTTACGCTCGGTCAATAAAGGAGAAAGCTATGTCCATTGCGGTAACCACCACCGATCCGACAAATACCGGCGTCAGTACCA                                                                                                <  2:390516/90‑1   GAAAACCCTTACGCTCGGTCAATAAAGGAGAAAGCTATGTCCATTGCGGTAACCACCACCGATCCGACAAATACCGGCGTCAGTACCACC                                                                                              >  1:155425/1‑90                                                     AACCACCACCGATCCGACAAATACCGGCGTCAGTACCACCAGCAAAGTCAGAAAACTGCTTTGTAAATCTGC                                                              <  1:593180/72‑1                                                     AACCACCACCGATCCGACAAATACCGGCGTCAGTACCACCAGCAAAGTCAGAAAACTGCTTTGTAAATCTGC                                                              >  2:593180/1‑72                                                                 TCCGACAAATACCGGCGTCAGTACCACCAGCAAAGTCAGAAAACTGCTTTGTAAATCTGCGGCGTTGCTGCCCGTGAGCGAACTACTGCT                                >  2:107789/1‑90                                                                                             AGCAAAGTCAGAAAACTGCTTTGTAAATCTGCGGCGTTGCTGCCCGTGAGCGAACTACTGCTGGTGGTACTGACGCCGGTATTTGTCGGA    <  2:261339/90‑1                                                                                               CAAAGTCAGAAAACTGCTTTGTAAATCTGCGGCGTTGCTGCCCGTGAGCGAACTACTGCTGGTGGTACTGACGCCGGTATTTGTCGGATC  <  1:791780/90‑1                                                                                                                                                                                          CTGAAAACCCTTACGCTCGGTCAATAAAGGAGAAAGCTATGTCCATTGCGGTAACCACCACCGATCCGACAAATACCGGCGTCAGTACCACCAGCA‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  NZ_CP009273/1127272‑1127367 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑ccaccagcaAAGTCAGAAAACTGCTTTGTAAATCTGCGGCGTTGCTGCCCGTGAGCGAACTACTGCTGGTGGTACTGACGCCGGTATTTGTCGGATC  <  NZ_CP009273/1127421‑1127334

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 33 ≤ 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.