New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NZ_CP009273	= 1391494	NA (NA)	14 (0.870)	9/166	0.5	100%	intergenic (+145/‑128)	BW25113_RS06980/ynaJ	IS5‑like element IS5 family transposase/DUF2534 family protein
	?	NZ_CP009273	1972747 =	0 (0.000)					intergenic (‑293/‑487)	flhD/uspC	flagellar transcriptional regulator FlhD/universal stress protein UspC

AACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAA  >  NZ_CP009273/1972658‑1972831                                                                                          |                                                                                     gcatttccgggagaaaaaatcggctcaaacatgaagaaatgaaatgactgagtcagccgagaagaatttccccgcttattcgcaccttcc                                                                                      <  2:288204‑M2/1‑1 (MQ=255)   atttacgggagaaaaaatcggctcaaacatgaagaaatgaaatgactgagtcagccgagaagaatttccccgcttattcgcaccttcctt                                                                                    >  2:467689‑M2/88‑90 (MQ=255)   atttacgggagaaaaaatcggctcaaacatgaagaaatgaaatgactgagtcagccgagaagaatttccccgcttattcgcaccttcctt                                                                                    >  2:395239‑M2/88‑90 (MQ=255)    tttacgggagaaaaaatcggctcaaacatgaagaaatgaaatgactgagtcagccgagaagaatttccccgcttattcgcaccttcCTTa                                                                                   >  1:147331‑M2/87‑90 (MQ=255)           gagaaaaaatcggctcaaacatgaagaaatgaaatgactgagtcagccgagaagaatttccccgcttattcgcaccttcCTTAACATaaa                                                                            <  2:147331‑M2/11‑1 (MQ=255)                       gctcaaacatgaagaaatgaaatgactgagtcagccgagaagaatttccccgcttattcgcaccttcCTTAACATAAATGTATAAGTCAt                                                                <  1:402120‑M2/23‑1 (MQ=255)                       gctcaaacatgaagaaatgaaatgactgagtcagccgagaagaatttccccgcttattcgcaccttcCTTAACATAAATGTATAAGTCAt                                                                <  2:435536‑M2/23‑1 (MQ=255)                         aTACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAggaaggtgcgaacaagtccc                                                              <  2:119426‑M1/90‑21 (MQ=255)                           aaacatgaagaaatgaaatgactgagtcagccgagaagaatttccccgcttattcgcaccttcCTTAACATAAATGTATAAGTCATACtt                                                            <  1:32022‑M2/27‑1 (MQ=255)                           aCAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAggaaggtgcgaacaagtccctg                                                            >  2:417371‑M1/1‑68 (MQ=255)                            aacatgaagaaatgaaatgactgagtcagccgagaagaatttccccgcttattcgcaccttcCTTAACATAAATGTATAAGTCATACttt                                                           <  2:30814‑M2/28‑1 (MQ=255)                                ggAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAggaaggtgcgaacaagtccctgata                                                         >  2:452805‑M1/1‑63 (MQ=255)                                ggAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAggaaggtgcgaacaagtccctgata                                                         <  1:452805‑M1/88‑26 (MQ=255)                                  aGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAggaaggtgcgaacaagtccctgata                                                         <  1:297574‑M1/86‑26 (MQ=255)                                  aGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAggaaggtgcgaacaagtccctgata                                                         >  2:297574‑M1/1‑61 (MQ=255)                                   ggggggCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAggaaggtgcgaacaagtccctgatatgaga                                                    >  1:254646‑M1/1‑60 (MQ=255)                                    gggggCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAggaaggtgcgaacaagtccctgatatgagat                                                   <  1:376669‑M1/90‑32 (MQ=255)                                      aatgaaatgactgagtcagccgagaagaatttccccgcttattcgcaccttcCTTAACATAAATGTATAAGTCATACttt                                                           >  1:179059‑M2/53‑80 (MQ=255)                                      aatgaaatgactgagtcagccgagaagaatttccccgcttattcgcaccttcCTTAACATAAATGTATAAGTCATACttt                                                           <  2:179059‑M2/28‑1 (MQ=255)                                                    gtcagccgagaagaatttccccgcttattcgcaccttcCTTAACATAAATGta                                                                        >  2:224123‑M2/39‑53 (MQ=255)                                                    gtcagccgagaagaatttccccgcttattcgcaccttcCTTAACATAAATGta                                                                        <  1:224123‑M2/15‑1 (MQ=255)                                                              aagaatttccccgcttattcgcaccttcCTTAACATAAATGTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGttt                         <  1:421739‑M2/62‑1 (MQ=255)                                                                tGCAGATCACACAAAACACTCAATTACTTAAggaaggtgcgaacaagtccctgatatgagatcatgtttgtcatctggagccatagaaca                       <  1:417371‑M1/90‑60 (MQ=255)                                                                              aaCACTCAATTACTTAAggaaggtgcgaacaagtccctgatatgagatcatgtttgtcatctggagccatagaacagggttcatcatgag         >  1:333851‑M1/1‑17 (MQ=255)                                                                                   tCAATTACTTAAggaaggtgcgaacaagtccctgatatgagatcatgtttgtcatctgga                                  <  1:68418‑M1/60‑49 (MQ=255)                                                                                   tCAATTACTTAAggaaggtgcgaacaagtccctgatatgagatcatgtttgtcatctgga                                  >  2:68418‑M1/1‑12 (MQ=255)                                                                                     ccttcCTTAACATAAATGTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCaaaaa  >  2:307360‑M2/6‑90 (MQ=255)                                                                                     aaTTACTTAAggaaggtgcgaacaagtccctgatatgagatcatgtttgtcatctggagccatagaacagggttcatcatgagtcatcaa  >  2:213482‑M1/1‑10 (MQ=255)                                                                                          |                                                                                     AACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGTATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAA  >  NZ_CP009273/1972658‑1972831

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 31 ≤ 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.