New junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? USA300TCH1516_ALE 895785 =10 (0.390)6 (0.270) 6/226 NT 28.1% coding (806/822 nt) metQ_2 Methionine‑binding lipoprotein MetQ
?USA300TCH1516_ALE = 909740 22 (1.000)intergenic (‑663/‑371) USA300HOU_RS04500/csbD_1 hypothetical protein/Stress response protein CsbD

AAATCTGAGCGTATTTTTTTGTTTAAAATTCGATAATTTGCATATACTGCCCCTTTTGTGCCCTTTTTTATTTTCAATACCACAAAAATAACCCCTTAATCGTTGTTATTAAAGGGTATTTTTATTTAATTGGTATTATTTAGCAGGAATAA‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  USA300TCH1516_ALE/895936‑895785
‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑ttatttagcaggaataaTTAGCCAGATTATCAAGGAAGTTCAAGGGCAATCAAAACATTGTTATATATGCATTTATAAAATTTTCAAGATAATTTATTATTCATACCCTTGCCCTTTGTTTCAAAATTATGCCCTTTTTTTGCCCTTGAAAAC  <  USA300TCH1516_ALE/909740‑909605
                                                                                                                                                                                                                                                                                                
aaattgGAGCGCATTTTTTTTTTTAAAATTCGATAGTTTGCATATACTGCCCCTTTTGTGCCCTTTTTTATTTTCAATACCACAAAAATAATCCCTTAATCGTTGTTATTAAAGGGTATTTTTATTTAATTGGTATTATTT                                                                                                                                                     <  2:69346/135‑1
   ctTGAGCGTATTTTTTGGTTTAAAATTCGATAATTTGCATATACTGCCCCTTTTGTGCCCTTTTTTATTTTCAATACCACAAAAATAACCCCTTAATCGTTGTTATTAAAGGGTATTTTTATTTAATTGGTATTATTTAGC                                                                                                                                                  <  1:188214/139‑1
     tgagaaTATTTTTTTGTTTAAAATTCGATAATTTGCATATACTGCCCCTTTTGTGCCCTTTTTTATATTCAATACCACAAAAATAACCCCTTAATCGTTGTTATTAAAGGGTATTTTTATTTAATTGGTATTATTTAGCAG                                                                                                                                                <  1:15698/135‑1
     TGAGCGTATTTTTTTGTGTAAAATTCGATAATTTGCATATACTGCCCCTTTTGTGCCCTTTTTTATTTTCAATACCACAAAAATAACCCCTTAATCGTTGTTATTAAAGGGTATTTTTATTTAATTGGTATTATTTAGCAG                                                                                                                                                <  2:247909/141‑1
       AGCGTATTTTTTTGTTTAAAATTCGATAATTTGCATATACTGCCCCTTTTGTGCCCTTTTTTATTTTCAATACCACAAAAATAACCCCTTAATCGTTGTTATTAAAGGGTATTTTTATTTAATTGGTATTATTTAGCAGGA                                                                                                                                              <  2:91545/141‑1
        GCGTATTTTTTTGTTTAAAATTCGATAATTTGCATATACTGCCCCTTTTGTGCCCTTTTTTATTTTCAATACCACAAAAATAACCCCTTAATCGTTGTTATTAAAGGGTATTTTTATTTAATTGGTATTATTTAGCAGGAA                                                                                                                                             <  1:168385/141‑1
                              cgttagTTTGCATATACAGCCCTTTTTGTGCCCTTTTTTATTTTCAATACCACAAAAATATCCCCTTAATCGTTGTTATTAAAGGGTATTTGTATTTAATTGGTATTATTTAGCAGGAATAATTAGCCAGATTATCAAGGA                                                                                                                       <  2:131704/135‑1
                                               TGCCTCTTTTGTGCCCTTTTTTATTTTCAATACCAAAAAAATAACCCCTTAATCGTTGTTATTAAAGGGTATTTTTATTTAATTGGTATTATTTGGCAGGAATAATTAGCCAGATTATCAAGGAAGTTCAAGGGCAATCAA                                                                                                      <  2:39775/141‑1
                                                                     ATTTTCAATACCACAAAAATAACCCCTTAATCGTTGTTATTAAAGGGTATTTTTATTTACTTGGTATTATTTCGCAGGAATAATTAGCCAGATTATCAAGTAAGTTCAAGGGCAATCAAAACATTGTTATATAATCATTTA                                                                                >  2:11430/1‑141
                                                                                                      TTGTTATTAAAGGGTATTTTTATTTAATTGGTATTATTTAGCAGGAATAATTAGCCAGATTATCAAGGAAGTTCAAGGGCAATCAAAACATTGTTATATATGCATTTATAAAATTTTCAAGATAATTTATTATTCATACCC                                               <  1:145723/141‑1
                                                                                                                           ATTTAATTGGTATTATTTAGCAGGAATAATTAGCCAGATTATCAAGGAAGTTCAAGGGCAAGCAAAACATTGTTATATATGCATTTATAAAATTTTCAAGATAATTTATTATTCATACTCTTGCACTTTGTTTCAAAATTA                          >  2:9178/1‑141
                                                                                                                              TAAATGGTATTATTTAGCAGGAATAATTAGCCAGATTATCAAGGAAGTTCAAGGGCAATCAAAACATTGTTATATATGCATTTATAAAATTTTCAAGATAATTTATTATTCATACCCTTGCCCTTTGTTTCAAAATTATGC                       <  2:147605/141‑1
                                                                                                                                            TAGCAGGAATAATTAGCCAGATTATCAAGGAAGTTCAAGGGCAATCAAAACATTGTTATATATGCATTTATAAAATTTTCAAGATAATTTATTATTCATACCCTTGCCCTTTGTTTCAAAATTATGCCCTTTTTTTGCCCT         >  2:131379/1‑141
                                                                                                                                             AGCAGGAATAATTAGCCAGATTATCAAGGAAGTTCAAGGGCAATCAAAACATTGTTATATATGCATTTATAAAATTTTCAAGATAATTTATTATTCATACCCTTGCCCTTTGTTTCAAAATTATGCCCTTTTTTTGCCCTT        <  1:237671/141‑1
                                                                                                                                               CAGGAATAATTAGCCAGATTATCAAGGAAGTTCAAGGGCAATCAAAACATTGTTATATATGCATTTATAAAATTTTCAAGATAATTTATTATTCATACCCTTGCCCTTTGTTTCAAAATTATGCCCTTTTTTTGCCCTTGA      <  1:3551/141‑1
                                                                                                                                                   AATAATTAGCCAGATTATCAAGGAAGTTCAAGGGCAATCAAAACATTGTTATATATGCATTTATAAAATTTTCAAGATAATTTATTATTCATACCCTTGCCCTTTGTTTCAAAATTATGCCCTTTTTTTGCCCTTGAAAAC  <  1:10111/141‑1
                                                                                                                                                                                                                                                                                                
AAATCTGAGCGTATTTTTTTGTTTAAAATTCGATAATTTGCATATACTGCCCCTTTTGTGCCCTTTTTTATTTTCAATACCACAAAAATAACCCCTTAATCGTTGTTATTAAAGGGTATTTTTATTTAATTGGTATTATTTAGCAGGAATAA‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  USA300TCH1516_ALE/895936‑895785
‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑ttatttagcaggaataaTTAGCCAGATTATCAAGGAAGTTCAAGGGCAATCAAAACATTGTTATATATGCATTTATAAAATTTTCAAGATAATTTATTATTCATACCCTTGCCCTTTGTTTCAAAATTATGCCCTTTTTTTGCCCTTGAAAAC  <  USA300TCH1516_ALE/909740‑909605

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 32 ≤ 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.