New junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? USA300TCH1516_ALE = 135390640 (1.430)3 (0.120) 3/252 3.5 8.2% intergenic (+99/+44) nucH/USA300HOU_RS06735 Thermonuclease/hypothetical protein
?USA300TCH1516_ALE = 1353932 31 (1.230)intergenic (+125/+18) nucH/USA300HOU_RS06735 Thermonuclease/hypothetical protein
Rejected: Coverage evenness skew score above cutoff.
Rejected: Frequency below/above cutoff threshold.

AAGCTAAACAACAGAAATTAAATATTTGGAGTAAATAATTAAATAGGTGATTATATATATTAAAGTAAAATATACTTGAAGCATCGATTTATTATTACCATAAATTTATATATAGAAATAATTTAAAGGCATAATAACCATAGTGCGTATCGAGCGTAATGGATTATTATGCCTTTGATTTTACTTGAATATAGCTGTGATTTGATCAACCTGTTCTTTATTTAAAGGGTGTTTAGATAGCTCTATGGCTTCGCTAATAATAC  >  USA300TCH1516_ALE/1353770‑1354032
                                                                                                                                        |                                                                                                                              
aaGCTAAACAACAGAAATTAAATATTTGGAGTAAATAATTAAATAGGTGATTATATATATTAAAGTAAAATATACTTGAAGCATCGATTTATTATTACCATAACTTTATATATAGAAATAATTTAAAGGCATAATAACCa                                                                                                                             >  2:96989/1‑140 (MQ=255)
  gCTAAACAACAGAAATTAAATATTTGGAGTAAATAATTAAATAGGTGATTATATATATTAAAGTAAAATATACTTGAAGCATCGATTTATTATTACCATAAATTTATATATAGAAATAATTTAAAGACATAATAACCATa                                                                                                                           >  2:130045/1‑140 (MQ=255)
            aGAAATTAAATATTAGGAGTAAATAATTAAATAGGAGATTATATATATTAAAGTAAAATATACTTGAAGCATCGATTTATTATTACCATAAATTTATATATAGAAATAATTTAAAGGAATAATAATCATAATGCGTATca                                                                                                                 >  2:202965/1‑139 (MQ=255)
            aGAAAATTAATAGTTGGAGTAAATAATTAAATAGGTGATTATATATATTAAAGTAAAATATACTTTAAGCATCGATTTATTATTACCATAAATTTATATATAGAAATAATTTAAAGGCATAATAACCATAGTGCGTATCg                                                                                                                 <  2:113333/140‑1 (MQ=255)
              aaaTTAAATATTTGGAGTAAATAATTAAATAGGTGATTATATATATTAAAGTAAAATATACTTGAAGCATCGATTTATTATTACCATAAATTTATATATAGAAATAATTTAAAGGCATAATAACCATAGTGCGTATCGAg                                                                                                               <  2:124578/140‑1 (MQ=255)
              aaaTTAAATATTTGGAGTAAATAATTAAATAGGTGATTATATATATTAAAGTAAAATATACTTGAAGCATCGATTTATTATTACCATAAATTTATATATAGAAATAATTTAAAGGCATAATAACCATAGTGCGTATCGAg                                                                                                               <  1:55084/140‑1 (MQ=255)
              aaaTTAAATATTTGGAGTAAATAATTAAATAGGTGATTATATATATTAAAGTAAAATATACTTGAAGCATCGATTTATTATTACCATAAATTTATATATAGAAATAATTTAAAGGCATAATAACCATAGTGCGTATCGAg                                                                                                               <  1:45995/140‑1 (MQ=255)
              aaaTTAAATATTTGGAGTAAATAATTAAATAGGTGATTATATATATTAAAGTAAAATATACTTGAAGCATCGATTTATTATTACCATAAATTTATATATAGAAATAATTTAAAGGCACAATAACCATAGTGCGTATCGAg                                                                                                               <  1:271247/140‑1 (MQ=255)
              aaaTTAAATATTTGGAGTAAATAAGTAAATAGGTGATTATATATATTAAAGTAAAATATACTTGAAGCATCGATTTATTATTACCATAAATTTATATATAGAAATAATTTAAAGGCATAATAACCATAGTGCGTATCGAg                                                                                                               <  2:174156/140‑1 (MQ=255)
                aTTAAATATTTGGAGTAAATAATTAAATAGGTGATTATATATATTAAATTAAAATATACTTGAAGCATCGATTTATTATTACCATAAATTTATATATAGAAATAATTTAAAGGCATAATAACCATAGTGCGTATCGAGCg                                                                                                             <  1:285357/140‑1 (MQ=255)
                 ttAAATATTTGGAGTAAATAATTAAATATGTTATTATATATATTAAAGTAAAATATACTTGAAGCATCGATTTATTATTACCATAAATTTATATATAGAAATAATTTAAAGGCATAATAACCATAGTGCGTATCGAGCGt                                                                                                            <  1:280705/140‑1 (MQ=255)
                          tGGAGTAAATATTTAAATATGTGATTATATATATTAAAGTAAAATATACTTGAAGCATCGATTTATTATTACCATAAATTTATATATAGAAATAATTTAAAGGCATAATAACCATAGTGCGTATCGAGCGTAATGGatta                                                                                                   <  2:113639/140‑1 (MQ=255)
                          tGGAGTAAATAATTAAATAGGTGATTATATATATTAAAGTAAAATATACTTGAAGCATCGATTTATTATTACCATAAATTTATATATAGCAATAATTTAAAGGCATAATACCCCTAGTGCGTATCGCGCGTACTGGatta                                                                                                   >  1:204455/1‑140 (MQ=255)
                          tGGAGTAAATAATTAAATAGGTGATTATATATATTAAAGTAAAATATACTTGAAGCATCGATTTATTATTACCATAAATTTATATATAGAAATAATTTAAAGGCATAATAACCATAGTGCGTATCGAGCGTAATGGatta                                                                                                   >  2:293093/1‑140 (MQ=255)
                                    tatTAAATAGGTGATTATATATATTAAAGTAAAATATACTTGCAGCATCGATTTATTATTACCATAAATTTATATATAGAAATAATTTAAAGGCATAATAACCATAGTGCGTATCGAGCGTAATGGATTATTATGCCttt                                                                                         <  1:280001/139‑1 (MQ=255)
                                     atTAAATAGGTGATTATATATATTAAAGTAAAATATACTTGAAGCATCGATTTATTATTACCATAAATTTATATATAGAAATAATTTAAAGGCATAATAACCATAGTGCGTATCGAGCGTAATGGATTATTATGCCTTTg                                                                                        >  2:209782/1‑140 (MQ=255)
                                           tAGGTGATTATATATATTAAAGTAAAATATACTTGAAGCATCGATTTATTATTACCATAAATTTATATATAGAAATAATTTAAAGGCATAATAACCATAGTGCGTATCGAGCGTACTGGATGATAAAGCCTTTGATTTTa                                                                                  >  1:290613/1‑140 (MQ=255)
                                                     tatatatTAAAGTAAAATATATTTGAAGTATCGATTTATTATTACCATAAATTTATATATAGAAATAATTTAAAGGCATAATAACCATAGTGCGTATCGAGCGTAATGGATTATTATGCCTTTGATTTTACTTGAAtata                                                                        <  1:198783/140‑1 (MQ=255)
                                                      atatatTAAAGTAAAATATACTTGAAGCATCGATTTATTATTACCATAAATTTATATATAGAAATAATTTAAAAGCATAATACCCATAGTACGTATCGAGCGTAATGGATTATTATGCCTTTGATTTTACTTGAATATAg                                                                       >  1:124328/1‑140 (MQ=255)
                                                        atatTAAAGTAAAATATACTTGAAGCATCTATTTATTATTACCATAAATTTATATATAGAAATAATTTAAAGGTATAATAAGTATAGTGTGTATCGAGCGTAATGGATTATTATGCCTTTGATTTTACTTGAATATAGCt                                                                     <  2:39016/140‑1 (MQ=255)
                                                        atatTAAAGTAAAATATACTTGAAGCATCGATTTATTATTACCATAAATTTATATATAGAAATAATTTAAAGGCATAATAACCATAGTGCGTATCGAGCGTAATGGATTATTATGCCTTTGATTTTACTTGAATATAGCt                                                                     <  1:304476/140‑1 (MQ=255)
                                                          atTAAAGTAAAATATACTTGAAGCATTATTTTATTATTACCATAAATTTATATATAGAATGCTTTGAATCGCGTAATAACCATAGTGCGTATCGAGCGTAATGGATTATTATGCCTTTGATTTTACTTGAATATAGCtgt                                                                   <  1:154567/140‑1 (MQ=255)
                                                                   aaaTATACTTGAAGCATCGATTTATTATTACCATAAATTTATATATAGAAATAATTTAAAGGCATAATAACCATAGTGCGTATCGAGCGTAATGGATTATTATGCCTTTGATTTTACTTGAATATAGCTGTGATTTGATc                                                          <  1:210070/140‑1 (MQ=255)
                                                                      tataCTTGAAGCATCGATTTATTATTACCATAAATTTATATATAGAAATAATTTAAAGGCATAATAACCATAGTGCGTATCGAGCGTAATGGATTATTATGCCTTTGATTTTACTTGAATATAGCTGTGATTTGATCAAc                                                       <  1:93487/140‑1 (MQ=255)
                                                                         acatGAAGCATCGATTTATTATTACCATAAATTTATAGATGTAAAGAATTTAAAGGCATAGTAACCATAGTGCGTATCGAGCGTAATGGATTATTATGCCTTTGATTTTACTTGAATATAGCTGTGATTTGATCAACCTg                                                    <  2:193940/137‑1 (MQ=255)
                                                                             gAAGCATCGATTTATTATTACCATAAATTTATATATTGATATAAAGAAAAGGCATAATAACCATAGTGCGTATCGAGCGTAATGGATTATTATGCCTTTGATTTTACTTGAATATAGCTGTGATTTGATCAACCTGTTCt                                                <  1:139596/140‑1 (MQ=255)
                                                                             gAAGCATCGATTTATGATTACCATAAATTTATATATAGATATAATTTAAAGGCATAATAACCATAGTGCGTATCGAGGGTAATGGATTATTATGCCTTTGATTTTACTTGAATATAGCTGTGATTTGATCAACCTGTTCt                                                <  1:80610/140‑1 (MQ=255)
                                                                                    tgATTTATTATTACCATAAATTTATATATAGAAATAATTTAAAGGCATAATAACCATAGTGCGTATCGAGCGTAATGGATTATTATGCCTTTGATTTTACTTGAATATAGCTGTGATTTGATCAACCTGTTCtttattta                                         <  2:16857/139‑1 (MQ=255)
                                                                                     gATTTATTATTACCATAAATTTATATATAGAAATAATTTAAAGGCATAATAACCATAGTGCGTATCGAGCGTAATGGATTATTATGCCTTTGATTTTACTTGAATATAGCTGTGATTTGATCAACCTGTTCTTTATTTaa                                        >  2:155568/1‑140 (MQ=255)
                                                                                          attattaCCATAAATTTATATATAGAAATAATTTAAAGGCATAATAACCATAGTGCGTATCGAGCGTAATGGATTATTATGCCTTTGATTTTACTTGAATATAGCTGTGATTTGATCAACCTGTTCTTTATTTAAAGGgt                                   <  1:96989/140‑1 (MQ=255)
                                                                                            tattaCCATAAATTTATATATAGAAATAATTTAAAGGCATAATAACCATAGTGCGTATCGAGCGTAATGGATTATTATGCCTTTGATTTTACTTGAATATAGCTGTGATTTGATCAACCTGTTCTTTATTTAAAGGgtgt                                 >  1:255887/1‑140 (MQ=255)
                                                                                              ttaTCATAAATTTATATATAGAAATAATTTAAAGGCATACTAGCGATAGGGCGTATCGACCGTAATGGATTATTATGCCTTTGATTTTACTTGAATATAGCTGTGATTTGATCAACCTGTTCTTTATTTAAAGGGTGttt                               <  1:300869/140‑1 (MQ=255)
                                                                                                 ccATAAATTTATATATAGAAATAATTTAAAGGCATAATAACCATAGTGCGTATCGAGCGTAATGGATTATTATGCCTTTGATTTTACTTGAATATAGCTGTGATTTGATCAACCTGTTCTTTATTTAAAGGGTGTTTAGa                            <  2:204455/140‑1 (MQ=255)
                                                                                                 ccATAAATTTATATATAGAAATAATTTAAAGGCATAATAACCATAGTGCGTATCGAGCGTAATGGATTATTATGCCTTTGATTTTACTTGAATATAGCTGTGATTTGATCAACCTGTTCTTTATTTAAAGGGTGTTTAGa                            <  1:293093/140‑1 (MQ=255)
                                                                                                   aTAAATTTATATATAGAAATAATTTAAAGGCATAATAACCATAGTGCGTATCGAGCGTAATGGATTATTATGCCTTTGATTTTACTTGAATATAGCTGTGATTTGATCAATCTGTTCTTTATTTAAAGTGTGTTtatata                          >  2:153142/1‑140 (MQ=255)
                                                                                                       agttATATACAGAAATATTTTAAAGGCATAATAAGCATTGTGCGTATCGAGCGTAATGGATTATTCTGCCTTTGATTTTACTTGAATATAGCTGTGATTTGATCAACCTGTTCTTTATTTAAAGGGTGTTTAGATAGctc                      <  2:228240/138‑1 (MQ=255)
                                                                                                       aTTTATATATAGAAATAATTTAAAGGCATAATAACCATAGTGCGTATCGAGCGTAATGGATTATTATGCCTTTGATTTTACTTGAATATAGCTGTGATTTGATCAACCTGTTCTTTATTTAAAGGGTGTTTAGATAGctc                      <  2:313145/140‑1 (MQ=255)
                                                                                                            tatataGAAATAATTTAAAGGCATAATAACCATAGTGCGTATCGAGCGTAATGGATTATTATGCCTTTGATTTTACTTGAATATAGCTGTGATTTGATCAACCTGTTCTTTATTTAAAGGGTGTTTAGATAGCTCTATgg                 <  2:258901/140‑1 (MQ=255)
                                                                                                                           tAAAGGCATCAAAACCATAGTGCGTATCGAGCGTAATGGATTATTATGCCTTTGATTTTACTTGAATATAGCTGTGATTTGATCAACCTGTTCTTTATTTAAAGTGTGTTTAGATAGCTCTATGGCTTCGCTAATAATAc  >  2:41443/1‑140 (MQ=255)
                                                                                                                           tAAAGGCATAATAACCATAGTGCGTATCGAGCGTAATGGATTATTATGCCTTTGATTTTACTTGAATATAGCTGTGATTTGATCAACCTGTTCTTTATTTAAAGGGTGTTTAGATAGCTCTATGGCTTCGCTAATAATAc  >  2:104179/1‑140 (MQ=255)
                                                                                                                                        |                                                                                                                              
AAGCTAAACAACAGAAATTAAATATTTGGAGTAAATAATTAAATAGGTGATTATATATATTAAAGTAAAATATACTTGAAGCATCGATTTATTATTACCATAAATTTATATATAGAAATAATTTAAAGGCATAATAACCATAGTGCGTATCGAGCGTAATGGATTATTATGCCTTTGATTTTACTTGAATATAGCTGTGATTTGATCAACCTGTTCTTTATTTAAAGGGTGTTTAGATAGCTCTATGGCTTCGCTAATAATAC  >  USA300TCH1516_ALE/1353770‑1354032

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.