New junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? NZ_CP009273 = 1391494NA (NA)9 (0.820) 6/164 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

AATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAACTAATCAATGCGTTGATTGTAAATCCAGCTAAGAGGTGAGGTTTTCAGAGCAGACAACGGTGAAATGTCATGG  >  NZ_CP009273/1391423‑1391572
                                                                       |                                                                              
aaTCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAACTAATCAATGCGt                                                              <  2:199977/90‑1 (MQ=255)
                         aatgaCTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAACTAATCAATGCGTTGATTGTAAATCCAGCTAAgaggtg                                     <  1:152327/90‑1 (MQ=255)
                                           gaagaaTTTCCCCGCTTATTCGCACCTTCCCTAACTAATCAATGCGTTGATTGTAAATCCAGCTAAGAGGTGAGGTTTTCAGAGCAGACa                   >  1:235237/1‑90 (MQ=255)
                                                            aTTCGCACCTTCCCTAACTAATCAATGCGTTGATTGTAAATCCAGCTAAGAGGTGAGGTTTTCAGAGCAGACAACGGTGAAATGTCATgg  <  2:235237/90‑1 (MQ=255)
                                                                       |                                                                              
AATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAACTAATCAATGCGTTGATTGTAAATCCAGCTAAGAGGTGAGGTTTTCAGAGCAGACAACGGTGAAATGTCATGG  >  NZ_CP009273/1391423‑1391572

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