New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NZ_CP009273	= 3512457	1 (0.090)	12 (1.130)	11/168	0.1	92.3%	intergenic (‑34/+367)	aroK/hofQ	shikimate kinase AroK/DNA uptake porin HofQ
	?	NZ_CP009273	4487998 =	NA (NA)					intergenic (+241/‑91)	BW25113_RS22170/BW25113_RS22180	tyrosine‑type recombinase/integrase/IS3‑like element IS2 family transposase

TGCTTTTTCCGGCACCCATAGGCCCAACCAGAAAGATATTGCGTTTCTCTGCCATTTTTTCGGTACTACTAAGACTATTCGTTAATGATAAACCCGCTTCGCTCAGAGAGCGCCGCAGGACATGAACTGAAACCTCATAAGATATTGCGAGAGTCAGACTGAAAATTATCTCAA  >  NZ_CP009273/3512369‑3512542                                                                                         |                                                                                      tGCTTTTTCCGGCACCCATAGGCCCAACCAGAAAGATATTGCGTTTCTCTGCCATTTTTTCGGTACTACTAAGACTATTCGTTAATGATt                                                                                      <  1:189952‑M1/90‑2 (MQ=255)         cacgggaatatctgcggcagcgggcttgtaatgggttaagtgataacagatgtctggaaatataggggcaaatccAATGATAAACCCGCt                                                                              <  2:149242‑M2/15‑1 (MQ=255)                      gcggcagcgggcttgtaatgggttaagtgataacagatgtctggaaatataggggcaaatccAATGATAAACCCGCTTCGCTCAGAGAgc                                                                 >  1:112764‑M2/63‑90 (MQ=255)                               gAAAGATATTGCGTTTCTCTGCCATTTTTTCGGTACTACTAAGACTATTCGTTAATGATtagactggccccctgaatctccagacaacca                                                        >  2:186868‑M1/1‑59 (MQ=255)                                  aGATATTGCGTTTCTCTGCCATTTTTTCGGTACTACTAAGACTATTCGTTAATGATtagactggccccctgaatctccagacaaccaata                                                     <  2:147237‑M1/90‑35 (MQ=255)                                         gCGTTTCTCTGCCATTTTTTCGGTACTACTAAGACTATTCGTTAATGATtagactggccccctgaatctccagacaaccaatatcactta                                              <  2:207924‑M1/90‑42 (MQ=255)                                          ggataagtgataagagatcgctggaaatataggggcaaatccAATGATAAACCCGCTTCGCTTATAGAGCGACGCAGGACATGAACGGaa                                             <  1:236411‑M2/48‑1 (MQ=255)                                             ttCTCTGCCATTTTTTCGGTACTACTAAGACTATTCGTTAATGATtagactggccccctgaatctccagacaaccaatatcacttaaata                                          <  2:66896‑M1/90‑46 (MQ=255)                                                   gCCATTTTTTCGGTACTACTAAGACTATTCGTTAATGATtagactggccccctgaatctccagacaaccaatatcacttaaataagtgat                                    >  1:224338‑M1/1‑39 (MQ=255)                                                   ataacagatgtctggaaatataggggcaaatccAATGATAAACCCGCTTCGCTCAGAGAGCGCCGCAGGACATGAACTGAAACCTCATaa                                    >  1:34765‑M2/34‑90 (MQ=255)                                                   ataacagatgtctggaaatataggggcaaatccAATGATAAACCCGCTTCGCTCAGAGAGCGCCGCAGGACATGAACTGAAACCTCATaa                                    >  1:264107‑M2/34‑90 (MQ=255)                                                    taacagatgtctggaaatataggggcaaatccAATGATAAACCCGCTTCGCTCAGAGAGCGCCGCAGGACATGAACTGAAACCTCATAAg                                   <  1:33106‑M2/58‑1 (MQ=255)                                                                tactacTAAGACTATTCGTTAATGATtagactggccccctgaatctccagacaaccaatatcacttaaataagtgatagtcttaatacta                       <  1:186868‑M1/90‑65 (MQ=255)                                                                         gACTATTCGTTAATGATtagactggccccctgaatctccagacaaccaatatcacttaaataagtgatagtcttaatactagtttttaga              >  1:36183‑M1/1‑17 (MQ=255)                                                                         gACTATTCGTTAATGATtagactggccccctgaatctccagacaaccaatatcacttaaataagtgatagtcttaatactagtttttaga              >  1:270300‑M1/1‑17 (MQ=255)                                                                          gggcaaatccAATGATAAACCCGCTTCGCTCAGAGAGCGCCGCAGGACATGAACTGAAACCTCATAAGATATTGCGAGAGTCAGACTGaa             >  2:144185‑M2/11‑90 (MQ=255)                                                                            tATTCGTTAATGATtagactggccccctgaatctccagacaaccaatatcacttaaataagtgatagtcttaatactagtttttagacta           >  1:303158‑M1/1‑14 (MQ=255)                                                                               tCGTTAATGATtagactggccccctgaatctccagacaaccaatatcacttaaataagtgatagtcttaatactagtttttagactagtc        <  1:168035‑M1/90‑80 (MQ=255)                                                                                 gTTAATGATtagactggccccctgaatctccagacaaccaatatcacttaaataagtgctagtcttaatactagtttttagactagtcat      <  2:234711‑M1/90‑82 (MQ=255)                                                                                     aTGATAAACCCGCTTCGCTCAGAGAGCGCCGCAGGACATGAACTGAAACCTCATAAGATATTGCGAGAGTCAGACTGAAAATTATCTCaa  <  2:112764/90‑1 (MQ=255)                                                                                         |                                                                                      TGCTTTTTCCGGCACCCATAGGCCCAACCAGAAAGATATTGCGTTTCTCTGCCATTTTTTCGGTACTACTAAGACTATTCGTTAATGATAAACCCGCTTCGCTCAGAGAGCGCCGCAGGACATGAACTGAAACCTCATAAGATATTGCGAGAGTCAGACTGAAAATTATCTCAA  >  NZ_CP009273/3512369‑3512542

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 24 ≤ ATCG/ATCG < 32 ≤ 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.