New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	= 1443583	98 (0.700)	5 (0.040)	3/248	NT	6.6%	intergenic (‑156/+197)	USA300TCH1516_01342/brnQ_3	hypothetical protein/Branched‑chain amino acid transport system 2 carrier protein
	?	USA300TCH1516_ALE	2317554 =	48 (0.360)					intergenic (+207/‑249)	iucC_3/USA300TCH1516_02193	Aerobactin synthase/hypothetical protein

TAATTTAGTTTAGTAGTATTTATTAAATTATACGAAGGGATCCAACACAGAAAATTTATTTTATTGAATTTTACATTTATGTGCAAGTTGGGCAAAGTGTCTTATTTTTTTAAAGTATTTCAAAGTAAAATTACACGTTAATAC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  USA300TCH1516_ALE/1443440‑1443583 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑aatacTTCGTATTGAATGGCTTCGCTTTCCTAGGGTGCCGTCTCAGCCTCGGTCTTCGACTGGCACTGCTCCCTCAGGAGTCTCGCCATTAATACTACGTATTAACATGTAATTTTACTTTTACATACTTTTAAAAAATAAGAC  >  USA300TCH1516_ALE/2317554‑2317692                                                                                                                                                                                                                                                                                             TAATTTAGTTTAGTAGTATTTATTAAATTATACGAAGGGATCCAACACAGAAAATTTATTTTATTGAATTTTACATTTATGTGCAAGTTGGGCAAAGTGTCTTATTTTTTTAAAGTATTTCAAAGTAAAATTACACGTTAA                                                                                                                                                <  1:89476/141‑1  AATTTAGTTTAGTAGTATTTATTAAATTATACGAAGGGATCCAACACAGAAAATTTATTTTATTGAATTTTACATTTATGTGCAAGTTGGGCAAAGTGTCTTATTTTTTTAAAGTATTTCAAAGTAAAATTACACGTTAAT                                                                                                                                               <  1:72964/141‑1  AATTTAGTTTAGTAGTATTTATTAAATTATACGAAGGGATCCAACACAGAAAATTTATTTTATTGAATTTTACATTTATGTGCAAGTTGGGCAAAGTGTCTTATTTTTTTAAAGTATTTCAAAGTAAAATTACACGTTAAT                                                                                                                                               <  3:339386/141‑1      TAGTTTAGTAGTATTTATTAAATTATACGAAGGGATCCAACACAGAAAATTTATTTTATTGAATTTTACATTTATGTGCAAGTTGGGCAAAGTGTCTTATTTTTTTAAAGTATTTCAAAGTAAAATTACACGTTAATACTa                                                                                                                                           <  1:541518/141‑2        tTTTAGTAGTATTTATTAAATTATACGAAGGGATCCAACACAGAAATTTTATTTTATTGAATTTTACATTTATGTGCAAGTTGGGAAAAGTGTCTTATTTTTTTAAAGTATTTCAAAGTAAAATTACACGTTAATACTacg                                                                                                                                         <  4:196863/140‑4             GTAGTATTTATTAAATTATACGAAGGGATCCAACACAGAAAATTTATTTTATTGAATTTTACATTTATGTGCAAGTTGGGCAAAGTGTCTTATTTTTTTAAAGTATTTCAAAGTAAAATTACACGTTAATACTACGTATTa                                                                                                                                    >  2:366067/1‑140                                                                                        TTGGGCAAAGTGTCTTATTTTTTTAAAGTATTTCAAAGTAAAATTACATGTTAATACGTAGTATTGAATGGCTTCGCTTTCCTAGGGTGCCGTCTCAGCCTCGGTCTTCGACTGGCACTGCTCCCTCAGGAGTCTCGCCAT                                                         <  2:1155817/141‑1                                                                                             CAAAGTGTCTTATTTTTTTAAAGTATTTCAAAGTAAAATTACATGTTAATACTTCGTATTGAATGGCTTCGCTTTCCTAGGGTGCCGTCTCAGCCTCGGTCTTCGACTGGCACTGCTCCCTCAGGAGTCTCGCCATTAATA                                                    <  4:148831/141‑1                                                                                                  TGTCTTATTTTTTTAAAGTATTTCAAAGTAAAATTACACGTTAATACTTCGTATTGAATGGCTTCGCTTTCCTAGGGTGCCGTCTCAGCCTCGGTCTTCGACTGGCACTGCTCCCTCAGGAGTCTCGCCATTAATACTACG                                               <  1:949216/141‑1                                                                                                    TCTTATTTTTTTAAAGTATTTCAAAGTAAAATTACACGTTAATACTTCGTATTGAATGGCTTCGCTTTCCTTGGGTGCCGTCTCAGCCTCGGTCTTCGACTGGCACTGCTCCCTCAGGAGTCTCGCCATTAATACTACGTA                                             <  1:813451/141‑1                                                                                                                                            AATACTTCGTATTGAATGGCTTCGCTTTCCTAGGGTGCCGTCTCAGCCTCGGTCTTCGACTGGCACTGCTCCCTCAGGAGTCTCGCCATTAATACTACGTATTAACATGTAATTTTACTTTTACATACTTTTAAAAAATAA     >  1:112955/1‑141                                                                                                                                            AATACTTCGTATTGAATGGCTTCGCTTTCCTAGGGTGCCGTCTCAGCCTCGGTCTTCGACTGGCACTGCTCCCTCAGGAGTCTCGCCATTAATACTACGTATTAACATGTAATTTTACTTTTACATACTTTTAAAAAATAA     <  2:453052/141‑1                                                                                                                                            AATACTTCGTATTGAATGGCTTCGCTTTCCTAGGGTGCCGTCTCAGCCTCGGTCTTCGACTGGCACTGCTCCCTCAGGAGTCTCGCCATTAATACTACGTATTAACATGTAATTTTACTTTTACATACTTTTAAAAAATAA     >  2:902821/1‑141                                                                                                                                             ATACTTCGTATTGAATGGCTTCGCTTTCCTAGGGTGCCGTCTCAGCCTCGGTCTTCGACTGGCACTGCTCCCTCAGGAGTCTCGCCATTAATACTACGTATTAACATGTAATTTTACTTTTACATACTTTTAAAAAATAAG    <  2:605631/141‑1                                                                                                                                              TACTTCGTATTGAATGGCTTCGCTTTCCTAGGGTGCCGTCTCAGCCTCGGTCTTCGACTGGCACTGCTCCCTCAGGAGGCTCGCCATTAATACTACGTATTAACATGTAATTTTACTTTTACATACTTTTAAAAAATAAGA   >  4:283466/1‑141                                                                                                                                               ACTTCGTATTGAATGGCTTCGCTTTCCTAGGGTGCCGTCTCAGCCTCGG                                                                                              >  2:388839/1‑49                                                                                                                                               ACTTCGTATTGAATGGCTTCGCTTTCCTAGGGTGCCGTCTCAGCCTCGG                                                                                              <  1:388839/49‑1                                                                                                                                               ACTTCGGATTGAATGGCTTCGCTTTCCTAGGGTGCCGTCTCAGCCTCGGTCTTCGACTGGCACTGCTCCCTCAGGAGTCTCGCCATTAATACTACGTATTAACATGTAATTTTACTTTTACATACTTTTAAAAAATAAGAC  <  2:33147/141‑1                                                                                                                                                                                                                                                                                             TAATTTAGTTTAGTAGTATTTATTAAATTATACGAAGGGATCCAACACAGAAAATTTATTTTATTGAATTTTACATTTATGTGCAAGTTGGGCAAAGTGTCTTATTTTTTTAAAGTATTTCAAAGTAAAATTACACGTTAATAC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  USA300TCH1516_ALE/1443440‑1443583 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑aatacTTCGTATTGAATGGCTTCGCTTTCCTAGGGTGCCGTCTCAGCCTCGGTCTTCGACTGGCACTGCTCCCTCAGGAGTCTCGCCATTAATACTACGTATTAACATGTAATTTTACTTTTACATACTTTTAAAAAATAAGAC  >  USA300TCH1516_ALE/2317554‑2317692

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ 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.