New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	= 1353906	40 (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.

TGGAGTAAATAATTAAATAGGTGATTATATATATTAAAGTAAAATATACTTGAAGCATCGATTTATTATTACCATAAATTTATATATAGAAATAATTTAAAGGCATAATAACCATAGTGCGTATCGAGCGTAATGGATTATTATGCCTTTGATTTTACTTGAATATAGCTGTGATTTGATCAACCTGTTCTTTATTTAAAGGGTGTTTAGATAGCTCTATGGCTTCGCTAATAATACGTCGTAACGAAGATTTTGTTGAAACTGTATCAACATA  >  USA300TCH1516_ALE/1353796‑1354069                                                                                                                                         |                                                                                                                                          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                                                                 <  1:293093/140‑1 (MQ=255)                                                                        ccATAAATTTATATATAGAAATAATTTAAAGGCATAATAACCATAGTGCGTATCGAGCGTAATGGATTATTATGCCTTTGATTTTACTTGAATATAGCTGTGATTTGATCAACCTGTTCTTTATTTAAAGGGTGTTTAGa                                                                 <  2:204455/140‑1 (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)                                                                                                                 catgtttcGTATCGAGCTTAATGGATTATTATGCCTTTGATGTTACTTGAATATAGCTGTGATTTGATCAACCTGTTCTTTATTTAAAGGGTGTTTAGATAGCTCTATGGCTTCGCTAATAATACGTCGTAACGAAGAtt                        <  2:265823/133‑1 (MQ=255)                                                                                                                     gTGCGTATCGAGCGTAATGGATTATTATGCCTTTGATTTTACTTGAATATAGCTGTGATTTGATCAACCTGTTCTTTATTTAAAGGGTGTTTAGATAGCTCTATGGCTTCGCTAATAATACGTCGTAACGAAGATTttgt                    <  2:72956/140‑1 (MQ=255)                                                                                                                        cGTATCGAGCGTAATTGATTATTATGACTTTAATTTTACTTGAATATAGCTGTGATTTGATCAACCTGTTCTTTATTTAAATGGTGTTTAGATAGCTCTATGGCTTCGCTAATAATACGTCGTAACGAAGATTTTGTTGa                 <  1:293537/140‑1 (MQ=255)                                                                                                                        cGTATCGAGCGTAATGGATTATTATGCTTTTGATTTTACTTGAATTTTGCTGTGATTTGATTCACCTGTTTTTTATTTAAAGGGTGTTTAGATAGCTCTATGGCTTCGCTAATAATACGTCGTAACGAAGATTTTGTTGa                 <  1:119542/140‑1 (MQ=255)                                                                                                                          tATCGAGCGTAATGGATTATTATGCCTTTGATTTTACTTGAATATAGCTGTGCTTTGATCAACCTGTTCTTTATTTAAAGGGTGTTTAGATAGCTCTATGGCTTCACTAATAATACGTCTTAACGAAGATTTTGTTGaga               >  1:6751/1‑138 (MQ=255)                                                                                                                                       ggATTATTATGCCTTTGATTTTACTTGAATATAGCTGTGATTTGATCAACCTGTTCTTTATTTAAAGGGTGTTTAGATAGCTCTATGGCTTCGCTAATAATACGTCGTAACGAAGATTTTGTTGAAACTGTATCAACata  <  1:179760/140‑1 (MQ=255)                                                                                                                                         |                                                                                                                                          TGGAGTAAATAATTAAATAGGTGATTATATATATTAAAGTAAAATATACTTGAAGCATCGATTTATTATTACCATAAATTTATATATAGAAATAATTTAAAGGCATAATAACCATAGTGCGTATCGAGCGTAATGGATTATTATGCCTTTGATTTTACTTGAATATAGCTGTGATTTGATCAACCTGTTCTTTATTTAAAGGGTGTTTAGATAGCTCTATGGCTTCGCTAATAATACGTCGTAACGAAGATTTTGTTGAAACTGTATCAACATA  >  USA300TCH1516_ALE/1353796‑1354069

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.