New junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? AE015451 = 598667966 (1.070)3 (0.050) 3/328 NT 4.4% coding (946/987 nt) PP_5245 Transcriptional regulator, AraC family
?AE015451 = 5986783 69 (1.170)intergenic (+63/‑136) PP_5245/kefB‑III Transcriptional regulator, AraC family/glutathione‑regulated potassium/H+ antiporter
Rejected: Frequency below/above cutoff threshold.

TTCACCGTGCAGAAAATGGCCGAACTGGTGGCCATGAGCGGGCGTAACTTTGCCCGGACGTTTCTGCGCGAGGTGGGCATTACGCCGCTGCAGTACCTGCAGAATGCGCGCATCGATCGTACGCGCAAGTTGCTCGAATGCGGTGACCTGCCGATGAAGGTGGTGGCGGCGCAGTGCGGGTTTGGCAGTGACCGACACATGCGCAAGGTATTCTTTGAGCGAATTGGCATGACGCCGGCGC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  AE015451/5986439‑5986679
‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑gccggcgcTTACCTGGGCTCAAGGCCTGTGCTATCTCTGTGGGAGCGGGCGCGCCCGCGAAGAAGGCAGCGCTAATCGGACTGTTCACCGCCACCAAACTGTGCCCGATACTGCGCCGGCGTCATGCCAATTCGCTCAAAGAATACCTTGCGCATGTGTCGGTCACTGCCAAACCCGCACTGCGCCGCCACCACCTTCATCGGCAGGTCACCGCATT  <  AE015451/5986783‑5986575
                                                                                                                                                                                                                                                                                                                                                                                                                                                                  
TTCACCGTGCAGAAAATGGCCGAACTGGTGGCCATGAGCGGGCGTAACTTTGCCCGGACGTTTCTGCGCGAGGTGGGCATTACGCCGCTGCAGTACCTGCAGAATGCGCGCATCGATCGTACGCGCAAGTTGCTCGAATGCGGTGACCTGCCGATGAAGGTGGTGGCGGCGCAGTGCGGGTTTGGCAGTGACCGACACATGCGCAAGGTATTCTTTGAGCGAATTGGCATGACGCC                                                                                                                                                                                                                        >  1:1008129/1‑236
 TCACCGTGCAGAAAATGGCCGAACTGGTGGCCATGAGCGGGCGTAACTTTGCCCGGACGTTTCTGCGCGAGGTGGGCATTACGCCGCTGCAGTACCTGCAGAATGCGCGCATCGATCGTACGCGCAAGTTGCTCGAATGCGGTGACCTGCCGATGAAGGTGGTGGCGGCGCAGTGCGGGTTTGGCAGTGACCGACACATGCGCAAGGTATTCTTTGAGCGAATTGGCATGACGCCG                                                                                                                                                                                                                       >  1:407532/1‑236
   ACCGTGCAGAAAATGGCCGAACTGGTGGCCATGAGCGGGCGTAACTTTGCCCGGACGTTTCTGCGCGAGGTGGGCATTACGCCGCTGCAGTACCTGCAGAATGCGCGCATCGATCGTACGCGCAAGTTGCTCGAATGCGGTGACCTGCCGATGAAGGTGGTGGCGGCGCAGTGCGGGTTTGGCAGTGACCGACACATGCGCAAGGTATTCTTTGAGCGAATTGGCATGACGCCGGC                                                                                                                                                                                                                     <  1:849959/236‑1
      GTGCAGAAAATGGCCGAACTGGTGGCCATGAGCGGGCGTAACTTTGCCCGGACGTTTCTGCGCGAGGTGGGCATTACGCCGCTGCAGTACCTGCAGAATGCGCGCATCGATCGTACGCGCAAGTTGCTCGAATGCGGTGACCTGCCGATGAAGGTGGTGGCGGCGCAGTGCGGGTTTGGCAGTGACCGACACATGCGCAAGGTATTCTTTGAGCGAATTGGCATGACGCCGGC                                                                                                                                                                                                                     <  2:534341/233‑1
                                                                                                                                                                                               CCGACACATGCGCAAGGTATTCTTTGAGCGAATTGGCATGACGCCGGCGCTTACCTGGGCTCAAGGCCTGTGCTATCTCTGTGGGAGCGGGCG                                                                                                                                                                        >  2:1103365/1‑93
                                                                                                                                                                                                           CAAGGTATTCTTTGAGCGAATTGGCATGACGCCGGCGCTTACCTGGGCTCAAGGCCTGTGCTATCTCTGTGGGAGCGGGCGCGCCCGCGAAGAAGGCAGCGCTAATCGGACTGTTCACCGCCCACAAAATGTGCCCGA                                                                                                               >  2:396656/1‑138
                                                                                                                                                                                                                 ATTCTTTGAGCGAATTGGCATGACGCCGGCGCTTACCTGGGCTCAAGGCCTGTGCTATCTCTGTGGGAGCGGGCG                                                                                                                                                                        >  2:1097891/1‑75
                                                                                                                                                                                                                                           CGGCGCTTACCTGGGCTCAAGGCCTGTGCTATCTCTGTGGGAGCGGGCGCGCCCGCGAAGAAGGCAGCGCTAATCGGACTGTTCACCGCCACCAAACTGTGCCCGATACTGCGCCGGCGTCATGCCAATTCGCTCAAAGAATACCTTGCGCATGTGTCGGTCACTGCCAAACCCGCACTGCGCCGCCACCACCTTCATCGGCAGGTCACCGCATT  >  2:779678/1‑215
                                                                                                                                                                                                                                           CGGCGCTTACCTGGGCTCAAGGCCTGTGCTATCTCTGTGGGAGCGGGCGCGCCCGCGAAGAAGGCAGCGCTAATCGGACTGTTCACCGCCACCAAACTGTGCCCGATACTGCGCCGGCGTCATGCCAATTCGCTCAAAGAATACCTTGCGCATGTGTCG                                                          <  1:1089131/159‑1
                                                                                                                                                                                                                                                                                                                                                                                                                                                                  
TTCACCGTGCAGAAAATGGCCGAACTGGTGGCCATGAGCGGGCGTAACTTTGCCCGGACGTTTCTGCGCGAGGTGGGCATTACGCCGCTGCAGTACCTGCAGAATGCGCGCATCGATCGTACGCGCAAGTTGCTCGAATGCGGTGACCTGCCGATGAAGGTGGTGGCGGCGCAGTGCGGGTTTGGCAGTGACCGACACATGCGCAAGGTATTCTTTGAGCGAATTGGCATGACGCCGGCGC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  AE015451/5986439‑5986679
‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑gccggcgcTTACCTGGGCTCAAGGCCTGTGCTATCTCTGTGGGAGCGGGCGCGCCCGCGAAGAAGGCAGCGCTAATCGGACTGTTCACCGCCACCAAACTGTGCCCGATACTGCGCCGGCGTCATGCCAATTCGCTCAAAGAATACCTTGCGCATGTGTCGGTCACTGCCAAACCCGCACTGCGCCGCCACCACCTTCATCGGCAGGTCACCGCATT  <  AE015451/5986783‑5986575

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 40 ≤ 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.