New junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? NZ_CP009273 = 377441029 (1.600)3 (0.190) 3/148 1.5 10.1% intergenic (+33/‑165) lldD/trmL quinone‑dependent L‑lactate dehydrogenase/tRNA (uridine(34)/cytosine(34)/5‑ carboxymethylaminomethyluridine(34)‑2'‑O)‑ methyltransferase TrmL
?NZ_CP009273 = 3774411 28 (1.750)intergenic (+34/‑164) lldD/trmL quinone‑dependent L‑lactate dehydrogenase/tRNA (uridine(34)/cytosine(34)/5‑ carboxymethylaminomethyluridine(34)‑2'‑O)‑ methyltransferase TrmL
Rejected: Frequency below/above cutoff threshold.

GTGCAGGGGCTGGGTAAAGAGTTGCCTGCGGCACTGGCTCCCATGGCGAAAGGGAATGCGGCATAGTCGTTTGCGCCCCCTCACCCTAACCCTCTCCCT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  NZ_CP009273/3774312‑3774410
‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑ccctctccctGAGGGAGAGGGTTAGGGTGAGGGGGCGCAAACGACTATGCCGCATTCCCTTTCGCCATGGGAGCCAGTGCCGCAGGCAACTCTT  <  NZ_CP009273/3774411‑3774328
                                                                                                                                                                                       
GTGCAGGGGCTGGGTAAAGAGTTGCCTGCGGCACTGGCTCCCATGGCGAAAGGGAATGCGGCATAGTCGTTTGCGCCCCCTCACCCTAAC                                                                                               <  1:256505/90‑1
    AGGGGCTGGGTAAAGAGTTGCCTGCGGCACTGGCTCCCATGGCGAAAGGGAATGCGGCATAGTCGTTTGCGCCCCCTCACCCTAACCCTC                                                                                           <  1:442350/90‑1
                     TTGCCTGCGGCACTGGCTCCCATGGCGAAAGGGAATGCGGCATAGTCGTTTGCGCCCCCTCACCCTAACCCTC                                                                                           <  1:42700/73‑1
                     TTGCCTGCGGCACTGGCTCCCATGGCGAAAGGGAATGCGGCATAGTCGTTTGCGCCCCCTCACCCTAACCCTC                                                                                           >  2:42700/1‑73
                                                 AAGGGAATGCGGCATAGTCGTTTGCGCCCCCTCACCCTAACCCTCTCCCTGAGGGAGAGGGTTAGGGTGAGGGGGCGCAAACGACTATGC                                              >  1:43717/1‑90
                                                                      TTGCGCCCCCTCACCCTAACCCTCTCCCTGAGGGAGAGGGTTAGGGTGAGGGGGCGCAAACGACTATGCCGCATTCCCTTTCGCCATGGG                         >  1:269258/1‑90
                                                                                       AACCCTCTCCCTGAGGGAGAGGGTTAGGGTGAGGGGGCGCAAACGACTATGCCGCATTCCCTTTCGCCATGGGAGCCAGTGCCGCAGGCA        <  2:269258/90‑1
                                                                                               CCCTGAGGGAGAGGGTTAGGGTGAGGGGGCGCAAACGACTATGCCGCATTCCCTTTCGCCATGGGAGCCAGTGCCGCAGGCAACTCTT  >  1:168438/1‑88
                                                                                               CCCTGAGGGAGAGGGTTAGGGTGAGGGGGCGCAAACGACTATGCCGCATTCCCTTTCGCCATGGGAGCCAGTGCCGCAGGCAACTCTT  <  2:168438/88‑1
                                                                                                                                                                                       
GTGCAGGGGCTGGGTAAAGAGTTGCCTGCGGCACTGGCTCCCATGGCGAAAGGGAATGCGGCATAGTCGTTTGCGCCCCCTCACCCTAACCCTCTCCCT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  NZ_CP009273/3774312‑3774410
‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑ccctctccctGAGGGAGAGGGTTAGGGTGAGGGGGCGCAAACGACTATGCCGCATTCCCTTTCGCCATGGGAGCCAGTGCCGCAGGCAACTCTT  <  NZ_CP009273/3774411‑3774328

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 31 ≤ 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.