New junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? REL606 3809862 =86 (0.840)7 (0.100) 4/34 NT 8.2% coding (207/1503 nt) uhpB sensory histidine kinase in two‑component regulatory sytem with UhpA
?REL606 3882315 = 96 (1.320)coding (103/816 nt) atpB F0F1 ATP synthase subunit A

GCGCGGATACTGGCCGGTGCTGCTGGGCGCGGAGTGGCTG‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  REL606/3809901‑3809862
‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑gtggctgGGGGGTTTTGTGGA  >  REL606/3882315‑3882328
                                                      
GCGCGGATACTGGCCGGTGCTGCTGGGCGCGGAGT                     <  1:9441669/35‑1
 nGCGGATACTGGCCGGTGCTGCTGGGCGCGGAGTG                    <  1:7398537/34‑1
 CGCGGATTCTGGCCGGTGCTGCTGGGCGCGGAGTG                    <  1:19386055/35‑1
 CGCGGATACTGGCCGGTGCTGCTGGGCGCGGAGTG                    <  1:10492491/35‑1
 CGCGGATACTGGCCGGTGCTGCTGGGCGCGGAGTG                    <  1:10917132/35‑1
 CGCGGATACTGGCCGGTGCTGCTGGGCGCGGAGTG                    <  1:19902757/35‑1
  GCGGATACTGGCCTGTGCTGCTGGGCGCGGAGTGG                   >  1:14573148/1‑35
  GCGGATACTGGCAGGTGCTGCTGGGCGCGGAGTGG                   <  1:12325232/35‑1
   CGGATACTGGCCGGTGCTGCTGGGCGCGGAGTGGC                  <  1:15070948/35‑1
    GGATACTGGCCGGTGCTGCTGGGCGCGGAGTGGCT                 <  1:8600766/35‑1
    GGATACTGGCCGGTGCTGCTGGGCGCGGAGGGGCT                 >  1:11123580/1‑35
       TACTGGCCGGTGCTGCTGGGCGCGGGGTGGCTGGG              >  1:5829660/1‑35
       TACTGGCCGGTGCTGCTGGGCGCGGGGTGGCTGGG              >  1:10257085/1‑35
          TGGCCGGTGCTGCTGGGCGCGGAGTGGCTGGGGGG           >  1:2498400/1‑35
          TGGCCGGTGCTGCTGGGCGCGGAGTGGCTGGGGGG           >  1:14259775/1‑35
          TGGCCGGTGCTGCTGGGCGCGGAGTGGCTGGGGGG           >  1:9302866/1‑35
           GGCCGGTGCTGCTGGGCGCGGAGTGGCTGGGGGGT          >  1:7619774/1‑35
            GCCGGTGCTGCTGGGCGCGGAGTGGCTGGGGGTTT         >  1:11936483/1‑35
             CCGGTGCTGCTGGGCGCGGAGTGGCTGGGGGGTTT        >  1:16493296/1‑35
             CCGGTGCTGCTGGGCGCGGAGTGGCTGGGGGGTTT        >  1:5036265/1‑35
               GGTGCTGCTGGGCGCGGAGTGGCTGGGGGGGTTTc      >  1:5542116/1‑34
                  GCTGCTGGGCGCGGAGTGGCTGGGGGGTTTTTTGG   >  1:1683037/1‑35
                   CTGCTGGGCGCGGAGTGGCTGGGGGGTTTTTTGGt  >  1:15075308/1‑34
                                                      
GCGCGGATACTGGCCGGTGCTGCTGGGCGCGGAGTGGCTG‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  REL606/3809901‑3809862
‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑gtggctgGGGGGTTTTGTGGA  >  REL606/3882315‑3882328

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 28 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 34 ≤ 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.