New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NZ_CP009273	= 287112	NA (NA)	14 (0.670)	11/166	0.6	87.5%	intergenic (‑55/‑99)	BW25113_RS01405/BW25113_RS01410	IS1‑like element IS1B family transposase/hypothetical protein
	?	NZ_CP009273	1903038 =	2 (0.100)					intergenic (‑15/‑144)	mgrB/yobH	PhoP/PhoQ regulator MgrB/YobH family protein

AGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCGAATTTTCAGCCCGGATGTTTCACGTACCTATGTCGAATATCTGGCCGATAAGGTTGCGGATCGAGAAGAGGATGCAGAGGAATA  >  NZ_CP009273/287030‑287197                                                                                   |                                                                                      aggGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCGAAtttt                                                                                <  2:517230/90‑1 (MQ=37)      cAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCGAATTTTCAGcc                                                                           <  2:339362/90‑1 (MQ=255)             tAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCGAATTTTCAGCCCGGATGt                                                                    <  1:242841/90‑1 (MQ=255)             tAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCGAATTTTCAGCCCGGATGt                                                                    >  1:322638/1‑90 (MQ=255)                     gAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCGAATTTTCAGCCCGGATGTTTCACGTa                                                            >  2:88118/1‑90 (MQ=255)                     gAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCGAATTTTCAGCCCGGATGTTTCACGTa                                                            >  1:432813/1‑90 (MQ=255)                       aGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCGAATTTTCAGCCCGGATGTTTCACGTAcc                                                          <  2:322638/90‑1 (MQ=255)                              ggAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCGAATTTTCAGCCCGGATGTTTCACGTACCTATGTCg                                                   <  2:432813/90‑1 (MQ=255)                                    ccTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCGAATTTTCAGCCCGGATGTTTCACGTACCTa                                                        >  1:227671/1‑79 (MQ=255)                                    ccTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCGAATTTTCAGCCCGGATGTTTCACGTACCTa                                                        <  2:227671/79‑1 (MQ=255)                                    ccTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCGAATTTTCAGCCCGGATGTTTCACGTACCTATGTCGAATATc                                             >  1:457747/1‑90 (MQ=255)                                      tCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCGAATTTTCAGCCCGGATGTTTCACGTACCTATGTCGAATATCTg                                           >  2:5870/1‑90 (MQ=255)                                              cccATCATACACTAAATCAGTAAGTTGGCAGCATCACCGAATTTTCAGCCCGGATGTTTCAc                                                               <  2:451450/61‑1 (MQ=255)                                              acCATCATACACTAAATCAGTAAGTTGGCAGCATCACCGAATTTTCAGCCCGGATGTTTCAc                                                               >  1:451450/1‑62 (MQ=255)                                              acCATCATACACTAAATCAGTAAGTTGGCAGCATCACCGAATTTTCAGCCCGGATGTTTCACGTACCTATGTCGAATATCTGGCCGATaa                                   >  2:440243/1‑90 (MQ=255)                                                         cTAAATCAGTAAGTTGGCAGCATCACCGAATTTTCAGCCCGGATGTTTCACGTACCTATGTCGAATATCTGGCCGATAAGGTTGCGGATc                        >  1:363244/1‑90 (MQ=255)                                                           aaaTCAGTAAGTTGGCAGCATCACCGAATTTTCAGCCCGGATGTTTCACGTACCTATGTCGAATATCTGGCCGATAAGGTTGCGGATCga                      >  2:207926/1‑90 (MQ=255)                                                            aaTCAGTAAGTTGGCAGCATCACCGAATTTTCAGCCCGGATGTTTCAc                                                               >  2:300195/1‑48 (MQ=255)                                                            aaTCAGTAAGTTGGCAGCATCACCGAATTTTCAGCCCGGATGTTTCAc                                                               <  1:300195/48‑1 (MQ=255)                                                              tCAGTAAGTTGGCAGCATCACCGAATTTTCAGCCCGGATGTTTCACGTACCTATGTCGAATATCTGGCCGATAAGGTTGCGGATCGagaa                   <  1:566163/90‑1 (MQ=255)                                                                 gTAAGTTGGCAGCATCACCGAATTTTCAGCCCGGATGTTTCACGTAcc                                                          >  2:220985/1‑48 (MQ=255)                                                                 gTAAGTTGGCAGCATCACCGAATTTTCAGCCCGGATGTTTCACGTAcc                                                          <  1:220985/48‑1 (MQ=255)                                                                 gTAAGTTGGCAGCATCACCGAATTTTCAGCCCGGATGTTTCACGTACCTATGTCGAATATCTGGCCGATAAGGTTGCGGATCGAGAagag                >  1:24707/1‑90 (MQ=255)                                                                      ttGGCAGCATCACCGAATTTTCAGCCCGGATGTTTCACGTACCTATGTCGAATATCTGGCCGATAAGGTTGCGGATCGAGAAGAGGATGc           >  1:608826/1‑90 (MQ=255)                                                                       tGGCAGCATCACCGAATTTTCAGCCCGGATGTTTCACGTACCTATGTCGAATATCTGGCCGATAAGGTTGCGGATCGAGAAGAGGATGCa          >  1:419864/1‑90 (MQ=255)                                                                             caTCACCGAATTTTCAGCCCGGATGTTTCACGTACCTATGTCGAATATCTGGCCGATAAGGTTGCGGATCGAGAAGAGGATGCAGAGGaa    <  1:327821/90‑1 (MQ=255)                                                                               tCACCGAATTTTCAGCCCGGATGTTTCACGTACCTATGTCGAATATCTGGCCGATAAGGTTGCGGATCGAGAAGAGGATGCAGAGGAata  >  2:253257/1‑90 (MQ=255)                                                                                   |                                                                                      AGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCGAATTTTCAGCCCGGATGTTTCACGTACCTATGTCGAATATCTGGCCGATAAGGTTGCGGATCGAGAAGAGGATGCAGAGGAATA  >  NZ_CP009273/287030‑287197

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ 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.