New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NZ_CP009273	3512437 =	17 (0.700)	3 (0.130)	3/164	1.8	15.6%	intergenic (‑14/+387)	aroK/hofQ	shikimate kinase AroK/DNA uptake porin HofQ
	?	NZ_CP009273	3645396 =	NA (NA)					pseudogene (746/747 nt)	BW25113_RS18155	hypothetical protein
Rejected: Frequency below/above cutoff threshold.

AGCTAACTGGCGCCCAATAGTGCTTTTTCCGGCACCCATAGGCCCAACCAGAAAGATATTGCGTTTCTCTGCCATTTTTTCGGTACTACTAAGACTATTCGTTAATGATAAACCCGCTTCGCTCAGAGAGCGCCGCAGGACATGAACTGAAACCTCATAAGATATTGCGAGAGTC  >  NZ_CP009273/3512349‑3512523                                                                                         |                                                                                       atttacgggagaaaaaatcggctcaaacatgaagaaatgaaatgactgagtcagccgagaagaatttccccgcttattcgcaccttccCt                                                                                       <  1:165779‑M1/2‑1 (MQ=255) atttacgggagaaaaaatcggctcaaacatgaagaaatgaaatgactgagtcagccgagaagaatttccccgcttattcgcaccttccCt                                                                                       <  1:437111‑M1/2‑1 (MQ=255) atttacgggagaaaaaatcggctcaaacatgaagaaatgaaatgactgagtcagccgagaagaatttccccgcttattcgcaccttccCt                                                                                       <  1:372448‑M1/2‑1 (MQ=255)  tttacgggagaaaaaatcggctcaaacatgaagaaatgaaatgactgagtcagccgagaagaatttccccgcttattcgcaccttccCTa                                                                                      <  1:293914‑M1/3‑1 (MQ=255)   ttacgggagaaaaaatcggctcaaacatgaagaaatgaaatgactgagtcagccgagaagaatttccccgcttattcgcaccttccCTaa                                                                                     <  1:143637‑M1/4‑1 (MQ=255)   cTAACTGGCGCCCAATAGTGCTTTTTCCGGCACCCATAGGCCCAACCAGAAAGATATTGCGTTTCTCTGCCATTTTTTCGGTACTACTaa                                                                                     <  1:55781/90‑1 (MQ=255)    tAACTGGCGCCCAATAGTGCTTTTTCCGGCACCCATAGGCCCAACCAGAAAGATATTGCGTTTCTCTGCCATTTTTTCGGTACTACTAAg                                                                                    >  1:408859/1‑90 (MQ=255)          gcgcCCAATAGTGCTTTTTCCGGCACCCATAGGCCCAACCAGAAAGATATTGCGTTTCTCTGCCATTTTTTCGGTACTACTAAGACTAtt                                                                              <  2:365399/90‑1 (MQ=255)               cAATAGTGCTTTTTCCGGCACCCATAGGCCCAACCAGAAAGATATTGCGTTTCTCTGCCATTTTTTCGGTACTACTAAGACTATTCGTTa                                                                         <  1:166192/90‑1 (MQ=255)               cAATAGTGCTTTTTCCGGCACCCATAGGCCCAACCAGAAAGATATTGCGTTTCTCTGCCATTTTTTCGGTACTACTAAGACTATTCGTTa                                                                         <  1:494524/90‑1 (MQ=255)               cAATAGTGCTTTTTCCGGCACCCATAGGCCCAACCAGAAAGATATTGCGTTTCTCTGCCATTTTTTCGGTACTACTAAGACTATTCGTTa                                                                         <  2:616373/90‑1 (MQ=255)                    gTGCTTTTTCCGGCACCCATAGGCCCAACCAGAAAGATATTGCGTTTCTCTGCCATTTTTTCGGTACTACTAAGACTATTCGTTAATGAt                                                                    <  2:331432/90‑1 (MQ=255)                                    aatgaaatgactgagtcagccgagaagaatttccccgcttattcgcaccttccc                                                                                        <  1:311988‑M1/1‑1 (MQ=255)                                    aatgaaatgactgagtcagccgagaagaatttccccgcttattcgcaccttccc                                                                                        >  2:311988‑M1/54‑54 (MQ=255)                                             cAACCAGAAAGATATTGCGTTTCTCTGCCATTTTTTCGGTACTACTAAGACTATTCGTTAATGATAAACCCGCTTCGCTCAGAGAGcgcc                                           >  2:485297/1‑90 (MQ=255)                                             cAACCAGAAAGATATTGCGTTTCTCTGCCATTTTTTCGGTACTACTAAGACTATTCGTTAATGATAAACCCGCTTCGCTCAGAGAGcgcc                                           >  2:201192/1‑90 (MQ=255)                                             cAACCAGAAAGATATTGCGTTTCTCTGCCATTTTTTCGGTACTACTAAGACTATTCGTTAATGATAAACCCGCTTCGCTCAGAGAGcgcc                                           >  1:505800/1‑90 (MQ=255)                                                              gaatttccccgcttattcgcaccttccCTAAGACTATTCGTTAATGATAAACCCGCTTCGCTCAGAGAGCGCCGCAGGACATGAACTGaa                          >  2:235613‑M1/28‑90 (MQ=255)                                                                tttCTCTGCCATTTTTTCGGTACTACTAAGACTATTCGTTAATGATAAACCCGCTTCGCTCAGAGAGCGCCGCAGGACATGAACTGAAAc                        <  1:655987/90‑1 (MQ=255)                                                                tttCTCTGCCATTTTTTCGGTACTACTAAGACTATTCGTTAATGATAAACCCGCTTCGCTCAGAGAGCGCCGCAGGACATGAACTGAAAc                        <  2:212003/90‑1 (MQ=255)                                                                tttCTCTGCCATTTTTTCGGTACTACTAAGACTATTCGTTAATGATAAACCCGCTTCGCTCAGAGAGCGCCGCAGGACATGAACTGAAAc                        <  1:438136/90‑1 (MQ=255)                                                                  tctcTGCCATTTTTTCGGTACTACTAAGACTATTCGTTAATGATAAACCCGCTTCGCTCAGAGAGCGCCGCAGGACATGAACTGAAACCt                      >  1:673038/1‑90 (MQ=255)                                                                   tccccgcttattcgcaccttccCTAAGACTATTCGTTAATGATAAACCCGCTTCGCTCAGAGAGCGCCGCAGGACATGAACTGAAACCTc                     <  1:58103‑M1/68‑1 (MQ=255)                                                                       gCCATTTTTTCGGTACTACTAAGACTATTCGTTAATGATAAACCCGCTTCGCTCAGAGAGCGCCGCAGGACATGAACTGAAACCTCATaa                 >  1:282210/1‑90 (MQ=255)                                                                       gCCATTTTTTCGGTACTACTAAGACTATTCGTTAATGATAAACCCGCTTCGCTCAGAGAGCGCCGCAGGACATGAACTGAAACCTCATaa                 <  1:100719/90‑1 (MQ=255)                                                                                      tccCTAAGACTATTCGTTAATGATAAACCCGCTTCGCTCAGAGAGCGCCGCAGGACATGAACTGAAACCTCATAAGATATTGCGAGAGTc  >  2:639336‑M1/4‑90 (MQ=255)                                                                                      ctactaAGACTATTCGTTAATGATAAACCCGCTTCGCTCAGAGAGCGCCGCAGGACATGAACTGAAACCTCATAAGATATTGCGAGAGTc  <  2:511811/90‑1 (MQ=255)                                                                                         |                                                                                       AGCTAACTGGCGCCCAATAGTGCTTTTTCCGGCACCCATAGGCCCAACCAGAAAGATATTGCGTTTCTCTGCCATTTTTTCGGTACTACTAAGACTATTCGTTAATGATAAACCCGCTTCGCTCAGAGAGCGCCGCAGGACATGAACTGAAACCTCATAAGATATTGCGAGAGTC  >  NZ_CP009273/3512349‑3512523

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