New junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? REL606 = 3741965NA (NA)80 (0.780) 37/48 NT 93.0% noncoding (1/768 nt) IS1 repeat region
?REL606 3742143 = 6 (0.060)pseudogene (223/405 nt) waaT UDP‑galactose:(Glucosyl) LPS alpha1,2‑galactosyltransferase WaaT

ACTAAATCAGTAAGTTGGCAGCATCACCGAATGTTGAGGCGTTTTGCACATGCCGCCTGAGT  >  REL606/3741938‑3741999
                           |                                  
acTAAATCAGTAAGTTGGCAGCATCACCGAATGtt                             <  1:1053844/35‑1 (MQ=40)
    aaTCAGTAAGTTGGCAGCATCACCGAATGTTGAgg                         <  1:41399/35‑1 (MQ=255)
                    gcaTCACCGAATGTTGAGGCGTTTTGCACATgccg         <  1:6440523/35‑1 (MQ=255)
                    gcaTCACCGAATGTTGAGGCGTTTTGCACATgccg         >  1:8514773/1‑35 (MQ=255)
                           cGAATGTTGAGGCGTTTTGCACATGCCGCCTGAGt  <  1:5324969/35‑1 (MQ=255)
                           |                                  
ACTAAATCAGTAAGTTGGCAGCATCACCGAATGTTGAGGCGTTTTGCACATGCCGCCTGAGT  >  REL606/3741938‑3741999

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 31 ≤ 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.