New junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? NC_000913_3_pae_tpiA 164559 =47 (1.210)4 (0.110) 4/268 5.1 9.6% intergenic (+25/‑171) hrpB/mrcB putative ATP‑dependent helicase/fused glycosyl transferase and transpeptidase
?NC_000913_3_pae_tpiA 289255 = 31 (0.850)intergenic (‑93/+46) yagI/argF CP4‑6 prophage; putative DNA‑binding transcriptional regulator/ornithine carbamoyltransferase 2, chain F; CP4‑6 prophage
Rejected: Coverage evenness skew score above cutoff.
Rejected: Frequency below/above cutoff threshold.

CAGGCGCAAAAGCCCGATTTTCTGTTCTTCTGTTACAAGACAGAAGAAGATATCTCTCAAAATTTGTGCTCGATCGGTCCCCTCTCCCTTGAGGGAGAGGGTTAGGGTGAGGGTGAACGTGCGCGCTGATGCCCTCACCCCGGCCCTCTCCC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  NC_000913_3_pae_tpiA/164710‑164559
‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑ccctctcccTGTGGGAGAGGGCCGGGGTGAGGGCACCAACGCGCAGCGGACCCAATCACTCCCCAAGCGTTGCCATCATCACCGCCTTAATCGTATGCATCCGGTTTTCCGCCTGGTCGAACACGATGCTCGCCGCCGACTCAAACACCTCGTCCGT  >  NC_000913_3_pae_tpiA/289255‑289402
                                                                                                                                                                                                                                                                                                            
CAGGCGCAAAAGCCCGATTTTCTGTTCTTCTGTTACAAGACAGAAGAAGATATCTCTCAAAATTTGTGCTCGATCGGTCCCCTCTCCCTTGAGGGAGAGGGTTAGGGTGAGGGTGAACGTGCGCGCTGATGCCCTCACCCCGGCCCTCT                                                                                                                                                         <  1:349305/149‑1
                             CTGTTACAAGACAGAAGAAGATATCTCTCAAAATTTGTGCTCGATCGGTCCCCTCTCCCTTGAGGGAGAGGGTTAGGGTGAGGGTGAACGTGCGCGCTGATGCCCTCACCCCGGCCCTCTCCCTGTGGGAGAGGG                                                                                                                                          >  1:358207/1‑135
                             CTGTTACAAGACAGAAGAAGATATCTCTCAAAATTTGTGCTCGATCGGTCCCCTCTCCCTTGAGGGAGAGGGTTAGGGTGAGGGTGAACGTGCGCGCTGATGCCCTCACCCCGGCCCTCTCCCTGTGGGAGAGGG                                                                                                                                          <  2:358207/135‑1
                                                                                                                                     CTCACCCCGGCCCTCTCCCTGTGGGAGAGGGCCGGGGTGAG                                                                                                                                >  1:221121/1‑41
                                                                                                                                     CTCACCCCGGCCCTCTCCCTGTGGGAGAGGGCCGGGGTGAG                                                                                                                                <  2:221121/41‑1
                                                                                                                                             ccCCCTCGCCCTGGGGGAGAGGGCCGGGGTGAGGGCACCAACGCGAAGCGGACCCGATCACTCCCCAAGCTGTGCCATCATCACCGCCTTAATCGTATGCATCCGGTTTTCCGCCTGGTCGAACACGATGCTCGCCGCCGACTCAAACA            <  2:247225/147‑1
                                                                                                                                                      CCTGTGGGAGAGGGCCGGGGTGAGGGCACCAACGCGCAGCGGACCCAATCACTCCCCAAGCGTTGCCATCATCACCGCCTTAATCGTATGCATCCGGTTTTCCGCCTGGTCGAACACGATGCCCGCCGCCGACTCAAACACCTCGTCCG   >  2:243247/1‑149
                                                                                                                                                       CTGTGGGAGAGGGCCGGGGTGAGGGCACCAACGCGCAGCGGACCCAATCACTCCCCAAGCGTTGCCATCATCACCGCCTTCATCGTATGCATCCGGTTTTCCGCCTGGTGGAACACGATGCTCGCCGCCGACTCAACCCCCTCGTCCGT  >  2:166014/1‑149
                                                                                                                                                                                                                                                                                                            
CAGGCGCAAAAGCCCGATTTTCTGTTCTTCTGTTACAAGACAGAAGAAGATATCTCTCAAAATTTGTGCTCGATCGGTCCCCTCTCCCTTGAGGGAGAGGGTTAGGGTGAGGGTGAACGTGCGCGCTGATGCCCTCACCCCGGCCCTCTCCC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  NC_000913_3_pae_tpiA/164710‑164559
‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑ccctctcccTGTGGGAGAGGGCCGGGGTGAGGGCACCAACGCGCAGCGGACCCAATCACTCCCCAAGCGTTGCCATCATCACCGCCTTAATCGTATGCATCCGGTTTTCCGCCTGGTCGAACACGATGCTCGCCGCCGACTCAAACACCTCGTCCGT  >  NC_000913_3_pae_tpiA/289255‑289402

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 37 ≤ 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.