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

TAACTGGCGCCCAATAGTGCTTTTTCCGGCACCCATAGGCCCAACCAGAAAGATATTGCGTTTCTCTGCCATTTTTTCGGTACTACTAAGACTATTCGTTAATGATAAACCCGCTTCGCTCAGAGAGCGCCGCAGGACATGAACTGAAACCTCATAAGATATTGCGAGAGTCAGACTG  >  NZ_CP009273/3512352‑3512529                                                                                          |                                                                                         tgtcgttctcaaaatcggtggagctgcatgacaaagtcatcgggcattatctgaacataaaacactatcaataagttggagtcattaccg                                                                                          <  1:118307‑M2/1‑1 (MQ=255) tgtcgttctcaaaatcggtggagctgcatgacaaagtcatcgggcattatctgaacataaaacactatcaataagttggagtcattaccg                                                                                          <  1:87599‑M2/1‑1 (MQ=255)   tcgttctcaaaatcggtggagctgcatgacaaagtcatcgggcattatctgaacataaaacactatcaataagttggagtcattaccGAc                                                                                        <  1:227019‑M2/3‑1 (MQ=255)   tcgttctcaaaatcggtggagctgcatgacaaagtcatcgggcattatctgaacataaaacactatcaataagttggagtcattaccGAc                                                                                        <  2:74056‑M2/3‑1 (MQ=255)   aCTGGCGCCCAATAGTGCTTTTTCCGGCACCCATAGGCCCAACCAGAAAGATATTGCGTTTCTCTGCCATTTTTTCGGTACTACTAAGAc                                                                                        <  1:262861/90‑1 (MQ=255)                  gtggagctgcatgacaaagtcatcgggcattatctgaacataaaacactatcaataagttggagtcattaccGACTATTCGTTAATGATa                                                                         >  1:64059‑M2/73‑90 (MQ=255)                      ttttCCGGCACCCATAGGCCCAACCAGAAAGATATTGCGTTTCTCTGCCATTTTTTCGGTACTACTAAGACTATTCGggtgatgctgcca                                                                     >  2:221139‑M1/1‑77 (MQ=255)                            ggCACCCATAGGCCCAACCAGAAAGATATTGCGTTTCTCTGCCATTTTTTCGGTACTACTAAGACTATTCGggtgatgctgccaacttac                                                               <  2:102928‑M1/90‑20 (MQ=255)                                                         tGCGTTTCTCTGCCATTTTTTCGGTACTACTAAGACTATTCGggtgatgctgccaacttactgatttagtgtatgatggtgtttttgagg                                  <  2:261821‑M1/90‑49 (MQ=255)                                                          gCGTTTCTCTGCCATTTTTTCGGTACTACTAAGACTATTCGggtgatgctgccaacttactgatttagtgtatgatggtgtttttgaggt                                 <  1:221139‑M1/90‑50 (MQ=255)                                                           aaaacactatcaataagttggagtcattaccGACTATTCGTTAATGATAAACCCGCTTCGCTCAGAGAGCGCCGCAGGACATGAACTGaa                                <  1:136558‑M2/59‑1 (MQ=255)                                                                 ctatcaataagttggagtcattaccGACTATTCGTTAATGATAAACCCGCTTCGCTCAGAGAGCGCCGCAGGACATGAACTGAAACCTCa                          >  1:137921‑M2/26‑90 (MQ=255)                                                                        ttttttCGGTACTACTAAGACTATTCGggtgatgctgccaacttactgatttagtgtatgatggtgtttttgaggtgctccagtggcttc                   <  1:221789‑M1/90‑64 (MQ=255)                                                                                         aGACTATTCGggtgatgctgccaacttactgatttagtgtatgatggtgtttttgaggtgctccagtggcttctgtttctatcagctgtc  <  1:90670‑M1/90‑81 (MQ=255)                                                                                          |                                                                                         TAACTGGCGCCCAATAGTGCTTTTTCCGGCACCCATAGGCCCAACCAGAAAGATATTGCGTTTCTCTGCCATTTTTTCGGTACTACTAAGACTATTCGTTAATGATAAACCCGCTTCGCTCAGAGAGCGCCGCAGGACATGAACTGAAACCTCATAAGATATTGCGAGAGTCAGACTG  >  NZ_CP009273/3512352‑3512529

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.