New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NZ_CP009273	= 287112	NA (NA)	29 (0.590)	24/246	0.6	96.7%	intergenic (‑55/‑99)	BW25113_RS01405/BW25113_RS01410	IS1‑like element IS1B family transposase/hypothetical protein
	?	NZ_CP009273	1972826 =	1 (0.020)					intergenic (‑372/‑408)	flhD/uspC	flagellar transcriptional regulator FlhD/universal stress protein UspC

CACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  NZ_CP009273/287007‑287112 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑CAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAACTCACCGTAAATAATCATCTGCTATAAATAATCACTTTCATGCAATACCAGATAAGCTATTTTTAAACAG  >  NZ_CP009273/1972826‑1972947                                                                                                                                                                                                                                      CACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCAAAAATGAAACAGGAATAATCGAAATGGGATG                                                                                           >  2:356953/1‑139      CGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCG                                                                                      >  2:29673/1‑139      CGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCG                                                                                      <  1:288718/139‑1       GTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGC                                                                                     <  1:400351/139‑1                  AACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAA                                                                           >  1:552413/1‑138                       GAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCACCACCCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAACT                                                                      >  2:443411/1‑138                        AGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAACTCA                                                                    <  1:366673/139‑1                            ACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAACTCACCG                                                                 >  2:432620/1‑138                                   ATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCAAAAATGAAACAGGAATAA                                                                                                        >  2:556238/1‑92                                   ATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCAAAAATGAAACAGGAATAA                                                                                                        <  1:556238/92‑1                                      GAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAACTCACCGTAAATAATCAT                                                      <  1:31010/139‑1                                             AAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAACTCACCGTAAATAATCATCTGCTA                                                >  1:30316/1‑138                                                      GAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCACCACCCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAACTCACCGTAAATAATCATCTGCTATAAATAAT                                        <  1:443411/137‑1                                                         CACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAACTCACCGTAAATAATCATCTGCTATAAATAATCACTT                                   <  1:432620/139‑1                                                               AAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAACTCACCGTAAATAATCATCTGCTATAAATAATCACTTTCATG                              <  2:256086/138‑1                                                                      CCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAACTCACCGTAAATAATCATCTGCTATAAATAATCACTTTCATGCAATAC                        >  1:595363/1‑137                                                                         TCATACACTAAATCAGTAAGTTGGCAGCATCACCCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAACTCACCGTAAATAATCATCTGCTATAAATAATCACTTTCATGCAATACCAGAT                   <  2:881850/139‑1                                                                                 TAAATCAGTAAGTTGGCAGCATCACCCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAACTCACCGTAAATAATCATCTGCTATAAATAATCACTTTCATGCAATACCAGATAAGCTATT           >  2:522876/1‑139                                                                                   AATCAGTAAGTTGGCAGCATCACCCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAACTCACCGTAAATAATCATCTGCTATAAATAATCACTTTCATGCAATACCAGATAAGCTATTTT         >  2:459913/1‑139                                                                                   AATCAGTAAGTTGGCAGCATCACCCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAACTCACCGTAAATAATCAT                                                      >  1:466848/1‑94                                                                                   AATCAGTAAGTTGGCAGCATCACCCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAACTCACCGTAAATAATCAT                                                      <  2:466848/94‑1                                                                                    ATCAGTAAGTTGGCAGCATCACCCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAACTCACCGTAAATAATCATCTGCTATAAATAAT                                        <  1:585733/107‑1                                                                                    ATCAGTAAGTTGGCAGCATCACCCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAACTCACCGTAAATAATCATCTGCTATAAATAAT                                        >  2:585733/1‑107                                                                                         TAAGTTGGCAGCATCACCCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAACTCACCGTAAATAATCATCTGCTATAAATAATCACTTTCATG                              <  2:404646/112‑1                                                                                         TAAGTTGGCAGCATCACCCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAACTCACCGTAAATAATCATCTGCTATAAATAATCACTTTCATG                              >  1:404646/1‑112                                                                                             TTGGCAGCATCACCCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAACTCACCGTAAATAATCATCTGCTATAAATAATCACTTTCATG                              >  1:731678/1‑108                                                                                             TTGGCAGCATCACCCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAACTCACCGTAAATAATCATCTGCTATAAATAATCACTTTCATG                              <  2:731678/108‑1                                                                                                     ATCACCCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAACTCACCGTAAATAATCATCTGCTATAAATAATCACTTTCATGCAATACCAGATAAGCTATTTTTAAACAG  >  2:451803/1‑128                                                                                                     ATCACCCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAACTCACCGTAAATAATCATCTGCTATAAATAATCACTTTCATGCAATACCAGATAAGCTATTTTTAAACAG  <  1:451803/128‑1                                                                                                                                                                                                                                      CACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  NZ_CP009273/287007‑287112 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑CAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAACTCACCGTAAATAATCATCTGCTATAAATAATCACTTTCATGCAATACCAGATAAGCTATTTTTAAACAG  >  NZ_CP009273/1972826‑1972947

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ 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.