New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NZ_CP009273	= 1972751	1 (0.020)	50 (1.240)	30/172	0.1	98.0%	intergenic (‑297/‑483)	flhD/uspC	flagellar transcriptional regulator FlhD/universal stress protein UspC
	?	NZ_CP009273	= 2283592	NA (NA)					intergenic (‑68/‑387)	BW25113_RS11435/narP	IS5‑like element IS5 family transposase/nitrate/nitrite response regulator protein NarP

CTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAA‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  NZ_CP009273/1972665‑1972751 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑GGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGAGCCATAGAACAGGGTTCATCATGAGTCATCAACTTACCTTC  <  NZ_CP009273/2283592‑2283504                                                                                                                                                                                  CTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAGGA                                                                                        <  2:517456/90‑1  TCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAGGAA                                                                                       <  1:685717/90‑1   CGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAGGAAG                                                                                      >  2:538061/1‑90      CACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAGGAAGGTG                                                                                   <  2:1022976/90‑1       accACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAGGAAGGTGC                                                                                  <  1:215667/87‑1        CTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAGGAAGGTGCG                                                                                 >  1:250794/1‑90            ACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAGGAAGGTGCGAACA                                                                             <  1:538061/90‑1            ACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAGGAAGGTGCGAACA                                                                             <  1:123422/90‑1               CACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAGGAAGGTGCGAACAAGT                                                                          >  1:937102/1‑90               CACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAGGAAGGTGCGAACAAGT                                                                          >  2:1023613/1‑90               CACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAGGAAGGTGCGAACAAGT                                                                          >  1:499033/1‑90                  ATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAGGAAGGTGCGAACAAGTCCC                                                                       <  2:632036/90‑1                       ACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAGGAAGGTGCGAACAAGTCCCTGATA                                                                  >  1:841025/1‑90                       ACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAGGAAGGTGCGAACAAGTCCCTGATA                                                                  >  1:1020970/1‑90                        CGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAGGAAGGTGCGAACAAGTCCCTGATAT                                                                 <  2:806948/90‑1                           AGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAGGAAGGTGCGAACAAGTCCCTGATATGAG                                                              >  1:1096305/1‑90                           AGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAGGAAGGTGCGAACAAGTCCCTGATATGAG                                                              >  1:1040836/1‑90                            GGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAGGAAGGTGCGAACAAGTCCCTGATATGAGA                                                             >  2:1085446/1‑90                            GGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAGGAAGGTGCGAACAAGTCCCTGATATGAGA                                                             >  1:654256/1‑90                              GGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAGGAAGGTGCGAACAAGTCCCTGATATGAGATC                                                           <  1:684508/90‑1                              GGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAGGAAGGTGCGAACAAGTCCCTGATATGAGATC                                                           <  1:849057/90‑1                               GGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAGGAAGGTGCGAACAAGTCCCTGATATGAGATCA                                                          >  2:249305/1‑90                               GGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAGGAAGGTGCGAACAAGTCCCTGATATGAGATCA                                                          <  2:935296/90‑1                               GGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAGGAAGGCGCGAACAAGTCCCTGATAGGAGATCA                                                          >  1:690148/1‑90                                 GCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAGGAAGGTGCGAACAAGTCCCTGATATGAGATCATG                                                        >  2:1081206/1‑90                                   TGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTT                                                      <  1:96550/90‑1                                    GCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTT                                                     >  1:631260/1‑90                                      GATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGT                                                   <  1:502570/90‑1                                              ATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGA                                           <  2:937102/90‑1                                              ATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGA                                           <  1:305233/90‑1                                                   GCGTGATGCAGATCACACAAAACACTCAATTACTTAAGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGAGCCAT                                      <  2:683020/90‑1                                                   GCGTGATGCAGATCACACAAAACACTCAATTACTTAAGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGAGCCAT                                      >  1:987794/1‑90                                                   GCGTGATGCAGATCACACAAAACACTCAATTACTTAAGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGAGCCAT                                      >  1:278512/1‑90                                                   GCGTGATGCAGATCACACAAAACACTCAATTACTTAAGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGA                                           >  1:683062/1‑85                                                   GCGTGATGCAGATCACACAAAACACTCAATTACTTAAGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGA                                           <  2:683062/85‑1                                                   GCGTGATGCAGATCACACAAAACACTCAATTACTTAAGGAAGGTGCGAACAAGTCCCTGATATGAGATCATG                                                        <  1:964594/72‑1                                                   GCGTGATGCAGATCACACAAAACACTCAATTACTTAAGGAAGGTGCGAACAAGTCCCTGATATGAGATCATG                                                        >  2:964594/1‑72                                                        ATGCAGATCACACAAAACACTCAATTACTTAAGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGAGCCATAGAAC                                 <  2:420061/90‑1                                                          GCAGATCACACAAAACACTCAATTACTTAAGGAAGGTGCGAACAACTCCCTGATATGAGATCATGTTTGTCATCTGGAGCCATAGAACAG                               <  1:367581/90‑1                                                              ATCACACAAAACACTCAATTACTTAAGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGAGCCATAGAACAGGGTT                           <  2:726585/90‑1                                                                  CACAAAACACTCAATTACTTCAGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGAGCCATAGAACAGGGTTCATC                       >  1:328845/1‑90                                                                          ACTCAATTACTTAAGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGAGCCATAGAACAGGGTTCATCATGAGTCA               <  2:710825/90‑1                                                                          ACTCAATTACTTAAGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGAGCCATAGAACAGGGTTCATCATGAGTCA               <  1:1023613/90‑1                                                                          ACTCAATTACTTAAGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGAGCCATAGAACAGGGTTCATCATGAGTCA               <  1:532997/90‑1                                                                            TCAATTACTTAAGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGAGCCATAGAACAGGGTTCATCATGAGTCATC             <  1:107294/90‑1                                                                                    TTAAGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGAGCCATAGAACAGGGTTCATCATGAGTCATCAACTTACC     >  1:898276/1‑90                                                                                     TAAGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGAGCCATAGAACAGGGTTCATCATGAGTCATCAACTTACCT    >  1:816364/1‑90                                                                                       AGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGAGCCATAGAACAGGGTTCATCATGAGTCATCAACTTACCTTC  >  2:563841/1‑90                                                                                       AGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGAGCCATAGAACAGGGTTCATCATGAGTCATCAACTTACCTTC  >  2:476190/1‑90                                                                                       AGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGAGCCATAGAACAGGGTTCATCATGAGTCATCAACTTACCTTC  >  2:427699/1‑90                                                                                                                                                                                  CTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAA‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  NZ_CP009273/1972665‑1972751 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑GGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGAGCCATAGAACAGGGTTCATCATGAGTCATCAACTTACCTTC  <  NZ_CP009273/2283592‑2283504

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 34 ≤ 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.