New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NZ_CP009273	= 1972821	0 (0.000)	5 (0.240)	5/166	1.4	100%	intergenic (‑367/‑413)	flhD/uspC	flagellar transcriptional regulator FlhD/universal stress protein UspC
	?	NZ_CP009273	2095230 =	NA (NA)					pseudogene (1/354 nt)	wbbL	N‑acetylglucosaminyl‑diphospho‑decaprenol L‑rhamnosyltransferase WbbL

AAACACTCAATTACTTAACATAAATGTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAACTCACCGTAAATAATCATC  >  NZ_CP009273/1972734‑1972896                                                                                        |                                                                            taagttgatgactcatgatgaaccctgttctatggctccagatgacaaacatgatctcatatcagggacttgttcgcaccttccCTagca                                                                           >  1:465591‑M1/85‑90 (MQ=255)                      accctgttctatggctccagatgacaaacatgatctcatatcagggacttgttcgcaccttccCTAGCAAGCAAAAATGAAACAGGaata                                                      <  1:325160‑M1/27‑1 (MQ=255)                         ctgttctatggctccagatgacaaacatgatctcatatcagggacttgttcgcaccttccCTAGCAAGCAAAAATGAAACAGGAATAATc                                                   >  1:457100‑M1/61‑90 (MQ=255)                             taAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGggaaggtgcgaataagcggggaaattcttc                                               <  1:81235‑M1/90‑31 (MQ=255)                                atggctccagatgacaaacatgatctcatatcagggacttgttcgcaccttccCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATgg                                            >  1:379346‑M1/54‑90 (MQ=255)                                atggctccagatgacaaacatgatctcatatcagggacttgttcgcaccttccCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATgg                                            <  2:161046‑M1/37‑1 (MQ=255)                                  ggctccagatgacaaacatgatctcatatcagggacttgttcgcaccttccCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGa                                          >  1:264336‑M1/52‑90 (MQ=255)                                  ggctccagatgacaaacatgatctcatatcagggacttgttcgcaccttccCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGa                                          >  1:387789‑M1/52‑90 (MQ=255)                                  cATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGggaaggtgcgaataagcggggaaattcttctcggc                                          >  1:356543‑M1/1‑55 (MQ=255)                                     tccagatgacaaacatgatctcatatcagggacttgttcgcaccttccCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGt                                       <  2:583866‑M1/42‑1 (MQ=255)                                           tgacaaacatgatctcatatcagggacttgttcgcaccttccCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGca                                 >  1:583866‑M1/43‑90 (MQ=255)                                                     tATTTAAATCTGTTAAAAAGTTTTTCGCTACGCTAGggaaggggcgaataagcggggaaattcttctcggctgactcactcattttattt                       >  2:361979‑M1/1‑36 (MQ=255)                                                     gatctcatatcagggacttgttcgcaccttccCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGcac                                >  2:367613‑M1/33‑81 (MQ=255)                                                     gatctcatatcagggacttgttcgcaccttccCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGcac                                <  1:367613‑M1/49‑1 (MQ=255)                                                         tCAATCTGTTAAAAAGTTTTTCGCTACTCTAGggaaggtgctaataagcggggaaattcttctcggctgactcagtcatttcatttcttc                   <  2:106039‑M1/90‑59 (MQ=255)                                                           atatcagggacttgttcgcaccttccCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGcac                                <  1:426743‑M1/49‑1 (MQ=255)                                                           atatcagggacttgttcgcaccttccCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGcac                                >  2:426743‑M1/27‑75 (MQ=255)                                                            tatcagggacttgttcgcaccttccCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAACTCAc                <  2:375788‑M1/65‑1 (MQ=255)                                                                          ttttCGCTACGCTAGggaaggtgcgaataagcggggaaattcttctcggctgactcagtcatttcatttcttcatgtttgagccgatttt  >  1:238420‑M1/1‑15 (MQ=255)                                                                                 ttccCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATgg                                            >  1:90699‑M1/5‑41 (MQ=255)                                                                                 ttccCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATgg                                            <  2:90699‑M1/37‑1 (MQ=255)                                                                                        |                                                                            AAACACTCAATTACTTAACATAAATGTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAACTCACCGTAAATAATCATC  >  NZ_CP009273/1972734‑1972896

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 23 ≤ 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.