New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NZ_CP009273	19796 =	NA (NA)	7 (0.770)	3/166	0.8	87.5%	intergenic (‑1/+15)	BW25113_RS25960/BW25113_RS00100	fimbrial family protein/IS1‑like element IS1A family transposase
	?	NZ_CP009273	3512441 =	1 (0.110)					intergenic (‑18/+383)	aroK/hofQ	shikimate kinase AroK/DNA uptake porin HofQ

TGTCGTTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  NZ_CP009273/19884‑19796 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑GACTATTCGTTAATGATAAACCCGCTTCGCTCAGAGAGCGCCGCAGGACATGAACTGAAACCTCA  >  NZ_CP009273/3512441‑3512505                                                                                                                                                            TGTCGTTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCG                                                                  <  1:118307/90‑1 TGTCGTTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCG                                                                  <  1:87599/90‑1   TCGTTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGAC                                                                <  1:227019/90‑1   TCGTTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGAC                                                                <  2:74056/90‑1                  GTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGACTATTCGTTAATGATA                                                 >  1:64059/1‑90                                                           AAAACACTATCAATAAGTTGGAGTCATTACCGACTATTCGTTAATGATAAACCCGCTTCGCTCAGAGAGCGCCGCAGGACATGAACTGAA        <  1:136558/90‑1                                                                 CTATCAATAAGTTGGAGTCATTACCGACTATTCGTTAATGATAAACCCGCTTCGCTCAGAGAGCGCCGCAGGACATGAACTGAAACCTCA  >  1:137921/1‑90                                                                                                                                                            TGTCGTTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  NZ_CP009273/19884‑19796 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑GACTATTCGTTAATGATAAACCCGCTTCGCTCAGAGAGCGCCGCAGGACATGAACTGAAACCTCA  >  NZ_CP009273/3512441‑3512505

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