New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	= 2551423	94 (0.880)	3 (0.030)	3/250	12.9	3.7%	intergenic (‑367/+85)	bioD1/USA300HOU_RS13150	ATP‑dependent dethiobiotin synthetase BioD 1/putative ABC transporter ATP‑binding protein
	?	USA300TCH1516_ALE	= 2555628	71 (0.750)					intergenic (‑599/+270)	irtA/yfdG	Iron import ATP‑binding/permease protein IrtA/Prophage bactoprenol‑linked glucose translocase
Rejected: Coverage evenness skew score above cutoff.
Rejected: Frequency below/above cutoff threshold.

TAATTGCATTATTTCTTAATAAAAAGACATCCTAGCTTTACCATCTTGTGAAACAATCCATTAATTGTAATATTACGTTGAGCGCCTTGTTCATCAATGCTATAATTAGTTACATAATAAATTGAACATCTAAATACACCAAATCCCCTCACTAT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  USA300TCH1516_ALE/2551269‑2551423 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑aaatcccctcactatGGCAGTAGTGAGGGGATTTGGTGTATTTAGATGTTCAATTTATTATGTAATTAATTATAGCATTGATGAACAAGGTGTGCAATGTATTTTTGCAATATTACAATAAATGAATTTAATTATATTAGAATTAAGTATTTCGA  <  USA300TCH1516_ALE/2555628‑2555489                                                                                                                                                                                                                                                                                                         TAATTGCATTATTTCTTAATAAAAAGACATCCTAGCTTTACCATCTTGTGAAACAATCCATTAATTGTAATATTACGTTGAGCGCCTTGTTCATCAATGCTATAATTAGTTACATAATAAATTGAACATCTAAATACACCA                                                                                                                                                            >  1:1163156/1‑141 TAATTGCATTATTTCTTAATAAAAAGACATCCTAGCTTTACCATCTTGTGAAACAATCCATTAATTGTAATATTACGTTGAGCGCCTTGTTCATCAATGCTATAATTAGTTACATAATAAATTGAACATCTAAATACACCA                                                                                                                                                            >  1:317516/1‑141   ATTGCATTATTTCTTAATAAAAAGACATCCTAGCTTTACCATCTTGTGAAACAATCCATTAATTGTAATATTACGTTGAGCGCCTTGTTCATCAATGCTATAATTAGTTACATAATAAATTGAACATCTAAATACACCAAA                                                                                                                                                          >  2:157448/1‑141   ATTGCATTATTTCTTAATAAAAAGACATCCTAGCTTTACCATCTTGTAAAACAATACATTAATTGTATTATTACGTTGAGCGACTTGACCACCAATGCTATAATTAGTTACATAATAACTTGAACATCTAAATACACCAAA                                                                                                                                                          >  2:546308/1‑141     TGCATTATTTCTTAATAAAAAGACATCCTAGCTTTACCATCTTGTGAAACAATCCATTAATTGTAATATTACGTTGAGCGCCTTGTTCATCAATGCTATAATTAGTTACATAATAAATTGAACATCTAAATACACCAAATC                                                                                                                                                        >  2:815227/1‑141     TGCATTATTTCTTAATAAAAAGACATCCTAGCTTTACCATCTTGTGAAACAATCAATTAATTGTAATATTACCTTGAGCGCCTTGTTCTTCAATGCTTTAATTAGTTAAATAAAGAATTGAACATATATAAACACCAAAac                                                                                                                                                        >  2:713679/1‑139      GCATTATTTCTTAATAAACCGACATTCTAGCTTTACCATCTTGTGAAACAGTACATTAATTGTAATATTACGTTGAGCGCTTTGTTCATCAATGCTATAATTAGTTACATAATAAATTGAACATCTAAATACACCAAATCC                                                                                                                                                       >  2:69288/1‑141      GCATTATTTCTTAATAAAAAGACATCCTAGCTTTACCATCTTGTGAAACAATCCATTAATTGTAATATTACGTTGAGCGCCTTGTTCATCAATGCTATAATTAGTTACATAATAAATTGAACATCTAAATACACCAAATCC                                                                                                                                                       >  1:1178026/1‑141       CATTATTTCTTAATAAAAAGACATCCTAGCTTTACCATCTTGTGAAACAATCCATTAATTGTAATATTACGTTGAGCGCCTTGTTCATCAATGCTATAATTAGTTACATAATAAATTGAACATCTAAATACACCAAATCCC                                                                                                                                                      <  1:861783/141‑1        ATTATTTCTTAATAAAAAGACATCCTAGCTTTACCATCTTGTGAAACAATCCATTAATTGTAATATTACGTTGAGCGCCTTGTTCATCAATGCTATAATTAGTTACATAATAAATTGAACATCTAAATACACCAAATCCCC                                                                                                                                                     <  1:802268/141‑1         TTATTTCTTAATAAAAAGACATCCTAGCTTTACCATCTTGTGAAACAATCCATTAATTGTAATATTACGTTGAGCGCCTTGTTCATCAATGCTATAATTAGTTACATAATAAATTGAACATCTAAATACACCAAATCCCCT                                                                                                                                                    <  1:1055056/141‑1           ATTTCTTAATAAAAAGACATCCTAGCTTTACCATCTTGTGAAACAATCCATTAATTGTAATATTACGTTGAGCGCCTTGTTCATCAATGCTATAATTAGTTACATAATAAATTGAACATCTATATACACCAAATCCCCTCA                                                                                                                                                  <  2:23680/141‑1            TTTCTTAATAAAAAGACATCCTAGCTTTACCATCTTGTGAAACAATCCATTAATTGTAATATTACGTTGAGCGCCTTGTTCATCAATGCTATAATTAGTTACATAATAAATTGAACATCTAAATACACCAAATCCCCTCAC                                                                                                                                                 <  2:774985/141‑1            TTTCTTAATAAAAAGACATCCTAGCTTTACCATCTTGTGAAACAATCCATTAATTGTAATATTACGTTGAGCGCATTGTTCATCAATGCTATAATTAGTTACATAATAAATTGAACATCTAAATACACCAAATCCCCTCAC                                                                                                                                                 >  1:573183/1‑141              TCTTAATAAAAAGACATCCTAGCTTTACCATCTTGTGAAACAATCCATTAATTGTAATATTACGTTGAGCGCCTTGTTCATCAATGCTATAATTAGTTACATAATAAATTGAACATCTAAATACACCAAATCCCCTCACTA                                                                                                                                               >  2:246989/1‑141               CTTAATAAAAAGACATCCTAGCTTTACCATCTTGTGAAACAATCCATTAATTGTAATATTACGTTGAGCGCCTTGTTCATCAATGCTATAATTAGTTACATAATAAATTGAACATCTAAATACACCAAATCCCCTCACTAT                                                                                                                                              <  1:364762/141‑1               CTTAATAAAAAGACATCCTAGCTTTACCATCTTGTGAAACAATCCATTAATTGTAATATTACGTTGAGCGCCTTGTTCATCAATGCTATAATTAGTTACATAATAAATTGAACATCTAAATACACCAAATCCCCTCACTAT                                                                                                                                              <  1:953069/141‑1               CTTAATAAAAAGACATCCTAGCTTTACCAAACTTTTTAACAATCCATTAATTGAAAGATTACGTTGAGCGCCTTGTTCATCAATGCTATAATTAGTTACATAATAAATTGAACATCTAAATACACCAAATCCCCTCACTAT                                                                                                                                              >  2:850299/1‑141                   ATAAAAAGACATCCTAGCTTTACCATCTTGTGAAACAATCCATTAATTGTAATATTACGTTGAGCGCCTTGTTCATCAATGCTATAATTAGTTAGATAATAAATTGAACATCTAAATACACCAAATCCGCTCACTATGGCA                                                                                                                                          <  1:849766/141‑1                                                                                               CAATGCTATAATTAATTACATAATAAATTGAACATCTAAATACACCAAATCCCCTCACTATGGCAGTAGTGAGGGGATTTGGTGTATTTAGATGTTCAATTTATTATGTAATTAATTATAGCATTG                                                                             <  1:605647/126‑1                                                                                               CAATGCTATAATTAATTACATAATAAATTGAACATCTAAATACACCAAATCCCCTCACTATGGCAGTAGTGAGGGGATTTGGTGTATTTAGATGTTCAATTTATTATGTAATTAATTATAGCATTG                                                                             >  2:605647/1‑126                                                                                                                                             AAATCCCCTCACTATGGCAGTAGTGAGGGGATTTGGTGTATTTCGATGTTCAATTTATTATGTAATTAATTATAGCATTCGTCAAATTGGGCATCGATGTATGTTTGCAATATTACAATAAATGAATTTAATTATATTAta                >  1:521338/1‑139                                                                                                                                                TCCCCTCACTATGGCAGTAGTGAGGGGATTTGGTGTATTTAGATGTTCAATTTATTATGTAATTAATTATAGCATTGATGAACAAGGTGTGCAATGTATTTTTGCAATATTACAATAAATGAATTAAATTATATTAGAATT             <  1:897468/141‑1                                                                                                                                                 CCCCTCACTATGGCAGTAGTGAGGGGATTTGGTGTATTTAGATGTTCAATTTATTATGTAATTAATTATAGCATTGATGAACAAGGTGTGCAATGTATTTTTGCAATATTACAATAAATGAATTTAATTATATTAGAATTA            >  1:968171/1‑141                                                                                                                                                   CCTCACTATGGCAGTAGTGAGGGGATTTGGTGTATTTAGATGTTCAATTTATTATGTAATTAATTATAGCATTGATGAACAAGGTGTGCAATGTATTTTTGCAATATTACAATAAATGAATTTAATTATATTAGAATTAAG          <  1:309223/141‑1                                                                                                                                                    cttACTATGGCAGTAGTGAGGGGATTTGGTGTATTTAGATGTTCAATTTATTATGTAATTAATTATAGCATTGATGAACAAGGTGTGCAATGTATTTTTGCAATATTACAATAAATGAATTTAATTATATTAGAATTAAGT         <  2:375260/138‑1                                                                                                                                                    CTCACTATGTGAGTAGGGAGGGGATTTGGTGTATTTAGATGTTCAATTTATTATGTAATTAATTATAGCATTGATGAACAAGGTGTGTAATGTATTTTTGCAATATTACAATAAATGAATTTAATTATATTAGAATTAAGT         <  1:14372/141‑1                                                                                                                                                    CTCACTATGGCAGTAGTGAGGGGATTTGGTGTATTTAGATGTTCAATTTATTATGTAATTAATTATAGCATTGATGAACAAGGTGTGCAATGTATTTTTGCAATATTACAATAAATGAATTTAATTATATTAGAATTAAGT         <  2:162710/141‑1                                                                                                                                                       ACTATGGCAGTAGTGAGGGGATTTGGTGTATTTAGATGTTCCATTTATTATGTAATTAATTATAGCATTGATGAACAAGGTGTGCAATGTATTTTTGCAATATTACAATAAATGAATTTAATTATATTAGAATTAAGTATT      <  1:686588/141‑1                                                                                                                                                           TGGCAGTAGTGAGGGGATTGGGTGTATTTAGATGTTCAATTTATTATGTAATTAATTATAGCATTGATGAACAAGGTGTGCAATGTATTTTTGCAATATTACAATAAATGAATTTAATTATATTAGAATTAAGTATTTCGA  <  1:255629/141‑1                                                                                                                                                           TGGCAGGAGTGAGGGGATTTGGTGTATTTAGATGTTCAATTGATTATGTAATTAATTATAGCATTGATGAACAAGGTGTGCAATGTATTTTTGCAATATTACAATAAATGAATTTAATTATATTAGAATTAAGTATTTCGA  <  1:1082183/141‑1                                                                                                                                                                                                                                                                                                         TAATTGCATTATTTCTTAATAAAAAGACATCCTAGCTTTACCATCTTGTGAAACAATCCATTAATTGTAATATTACGTTGAGCGCCTTGTTCATCAATGCTATAATTAGTTACATAATAAATTGAACATCTAAATACACCAAATCCCCTCACTAT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  USA300TCH1516_ALE/2551269‑2551423 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑aaatcccctcactatGGCAGTAGTGAGGGGATTTGGTGTATTTAGATGTTCAATTTATTATGTAATTAATTATAGCATTGATGAACAAGGTGTGCAATGTATTTTTGCAATATTACAATAAATGAATTTAATTATATTAGAATTAAGTATTTCGA  <  USA300TCH1516_ALE/2555628‑2555489

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 37 ≤ 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.