New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NZ_CP009273	= 1972751	0 (0.000)	50 (1.610)	32/160	0.0	100%	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 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑GGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGAGCCATAGAACAGGGTTCATCATGAGTCATCAACTTACCTTCG  <  NZ_CP009273/2283592‑2283503                                                                                                                                                                                   CTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAGGAA                                                                                        <  2:179447/91‑1   CGTCACTACACGCACATACAACGGCGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAGGA                                                                                         >  2:226211/1‑88   CGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAGGAAGG                                                                                      >  1:895710/1‑91   CGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAGGA                                                                                         <  1:226211/88‑1          ACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAGGAAGGTGCGAAC                                                                               <  2:1034487/91‑1                 CATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAGGAAGGTGCGAACAAGTCCC                                                                        <  2:54802/91‑1                 CATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAGGAAGGTGCGAACAAGTCCC                                                                        <  1:716981/91‑1                  ATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAGGAAGGTGCGAACAAGTCCCT                                                                       >  1:136897/1‑91                  ATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAGGAAGGTGCGAACAAGTCCCT                                                                       <  2:902164/91‑1                      AACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAGGAAGGTGCGAACAAGTCCCTGATA                                                                   <  2:667770/91‑1                      AACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAGGAAGGTGCGAACAAGTCCCTGATA                                                                   <  2:136897/91‑1                       ACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAGGAAGGTGCGAACAAGTCCCTGATAT                                                                  <  1:962155/91‑1                       ACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAGGAAGGTGCGAACAAGTCCCTGATAT                                                                  >  2:300099/1‑91                       ACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAGGAAGGTGCGAACAAGTCCCTGATAT                                                                  <  1:723277/91‑1                           AGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCAGACAAAACACTCAATTACTTAAGGAAGGTGCGAACAAGTCCCTGATATGAGA                                                              >  2:1006798/1‑91                           AGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAGGAAGGTGCGAACAAGTCCCTGATATGAGA                                                              >  1:465117/1‑91                           AGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAGGAAGGTGCGAACAAGTCCCTGATATGAGA                                                              >  1:326307/1‑91                                    GCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAGGAA                                                                                        <  2:440800/56‑1                                    GCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAGGAA                                                                                        >  1:440800/1‑56                                      GATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTC                                                   >  2:565472/1‑91                                      GATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTC                                                   <  2:465117/91‑1                                             AATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGA                                            <  1:300099/91‑1                                              ATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAGGAAGG                                                                                      >  1:226782/1‑48                                              ATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAGGAAGG                                                                                      <  2:226782/48‑1                                                 ATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGG                                             >  2:445844/1‑86                                                 ATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGG                                             <  1:445844/86‑1                                                 ATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAGGAAGGTGCGAACAAGT                                                                           <  1:55812/56‑1                                                 ATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAGGAAGGTGCGAACAAGT                                                                           >  2:55812/1‑56                                                   GCGTGATGCAGATCACACAAAACACTCAATTACTTAAGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGAGCCATA                                      >  2:420014/1‑91                                                      TGATGCAGATCACACAAAACACTCAATTACTTAAGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGAGCCATAGAA                                   <  1:23954/91‑1                                                        ATGCAGATCACACAAAACACTCAATTACTTAAGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGAGCCATAGAACA                                 >  1:53460/1‑91                                                            AGATCACACAAAACACTCAATTACTTAAGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGAGCCATAGAACAGGGT                             <  1:420014/91‑1                                                             GATCACACAAAACACTCAATTACTTAAGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGAGCCATAGAACAGGGTT                            >  2:344835/1‑91                                                                  CACAAAACACTCAATTACTTAAGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGAGCCATAGAACAGGGTTCATCA                       >  1:677030/1‑91                                                                  CACAAAACACTCAATTACTTAAGGAAGGTGCGAACAAGTCCCTGATATGAGATCA                                                           >  2:9335/1‑55                                                                  CACAAAACACTCAATTACTTAAGGAAGGTGCGAACAAGTCCCTGATATGAGATCA                                                           <  1:9335/55‑1                                                                       AACACTCAATTACTTAAGGAAGGTGCGAACAAGTCCCTGATATGAGATGATGTTTGTCATCTGGA                                            >  2:814550/1‑65                                                                       AACACTCAATTACTTAAGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGAGCCAT                                       <  1:806931/70‑1                                                                       AACACTCAATTACTTAAGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGAGCCAT                                       >  2:806931/1‑70                                                                       AACACTCAATTACTTAAGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGA                                            <  1:814550/65‑1                                                                         CACTCAATTACTTAAGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGAGCCATAGAACAGGGTTCATCATGAGTCA                <  1:482719/91‑1                                                                           CTCAATTACTTAAGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGAGCCATAGAACAGGGTTCATCATGAGTCATC              <  1:1006798/91‑1                                                                           CTCAATTACTTAAGGAAGGCGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGAGCCATAGAACAGGGTTCATCATGAGTCATa              >  1:342441/1‑90                                                                                      AAGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGAGCCATAGAACAGGGTTCATCATGAGTCATCAACTTACCTTC   >  2:843181/1‑91                                                                                       AGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGAGCCATAGAACAGGGTTCATCATGAGTCATCAACTTACCTTCG  >  1:188651/1‑91                                                                                       AGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGAGCCATAGAACAGGGTTCATCATGAGTCATCAACTTACCTTCG  >  2:1060952/1‑91                                                                                       AGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGAGCCATAGAACAGGGT                             <  1:857511/64‑1                                                                                       AGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGAGCCATAGAACAGGGT                             >  2:857511/1‑64                                                                                       AGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGAGCCAT                                       <  2:979288/54‑1                                                                                       AGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGAGCCAT                                       >  1:979288/1‑54                                                                                                                                                                                   CTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAA‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  NZ_CP009273/1972665‑1972751 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑GGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGAGCCATAGAACAGGGTTCATCATGAGTCATCAACTTACCTTCG  <  NZ_CP009273/2283592‑2283503

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 29 ≤ 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.