New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	1030884 =	55 (1.060)	3 (0.060)	3/234	NT	5.9%	intergenic (+7/‑129)	ktrB_1/yfkN_2	Ktr system potassium uptake protein B/Trifunctional nucleotide phosphoesterase protein YfkN
	?	USA300TCH1516_ALE	1030933 =	47 (1.010)					intergenic (+56/‑80)	ktrB_1/yfkN_2	Ktr system potassium uptake protein B/Trifunctional nucleotide phosphoesterase protein YfkN

GTTTTCATTTTTTTCCATCATGTTACACCTCTCATTGTTACTAGTTTACCATTTTCGAAACCAATCGTCTTATAAAATAAGTTAAAAATACAAACTAAAAAAGCAATCTAAGTTCCAGTTAAAATCTACATTAACT‑AAACTTAGATTGCT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  USA300TCH1516_ALE/1031033‑1030884 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑aacttagattgctTTTTTAGTTTGTATTTTTAACTTATTTTATAAGACGATTGGTTTCGAAAATGGTAAACTAGTAACAATGAGAGGTGTAACATGATGGAAAAAAATGAAAACATTAATGTAGAGATTTTAACTACGTCAGATATGCAT  >  USA300TCH1516_ALE/1030933‑1031069                                                                                                                                                                                                                                                                                                  GTTTTCATTTTTTTCCATCATGTTACACCTCTCATTGTTACTAGTTTACCATTTTCGAAACCAATCGTCTTATAAAATAAGTTAAAAATACAAACTAAAACAGCAATCTAAGTTCCAGTTAAAATCTACATTAACT‑AAACT                                                                                                                                                    <  2:459688/141‑1   TTTCATTTTTTTCCATCATGTTACACCTCTCATTGTTACTAGTTTACCATTTTCGAAACCAATCGTCTTATAAAATAAGTTAAAAATACAAACTAAAAAAGCAATCTAAGTTCCAGTTAAAATCTACATTAACT‑AAACT                                                                                                                                                    <  1:319835/139‑1   TTTCATTTTTTTCCATCATGTTACACCTCTCATTGTTACTAGTTTACCATTTTCGAAACCAATCGTCTTATAAAATAAGTTAAAAATACAAACTAAAAAAGCAATCTAAGTTCCAGTTAAAATCTACATTAACT‑AAACT                                                                                                                                                    >  2:319835/1‑139                                                 CCATTTTCGAAACCAATCGTCTTATAAAATAAGTTAAAAATACAAACTAAAAAAGCAATCTAAGTT‑TAGTTAATGTAGATTTTAACTGGAACTTAGATTGCTTTTTTAGTTTGTATTTTTAACTTATTTTATAAGACGATT                                                                                                    >  2:497200/1‑141                                                                                                           TCTAAGTTCCAGTTAAAATCTACATTAACT‑AAACTTAGATTGCTTTTTTAGTTTGTATTTTTAACTTATTTTATAAGACGATTGGTTTCGAAAATGGTAAACTAGTAAAAATGAGAGGTGTAACATGATGGAAAAAAATGA                                          >  2:348153/1‑141                                                                                                                       TTAAAATCTACATTAACT‑AAACTTAGATTGCTTTTTTAGTTTGTATTTTTAACTTATTTTATAAGACGATTGGTTTCGAAAATGGTAAACTAGTAACAATGAGAGGTGTAACATGATGGAAAAAAATGAAAACATTAATGT                              >  1:529924/1‑141                                                                                                                                       ctgAAATTTAGATTGCTTTTTTAGTGTGTATTTTTAACTTATTTTATAAGACGATTGGTTTCGAAAATGGTAAAATAGTAACAATGAGAGGTGTAACATGATGGAAAAAAATGAAAACATTAATGTAGAGATTTTAACTAC               <  1:287852/138‑1                                                                                                                                            ACTTAGATTGCTTTTTTAGTTTGTCTTTTTAAATTATTATATAAGGCGATTGGTTTCGAACATGGTAAAATAGTAACAATGAGAGGAGTAACATGATGGAAAAAAATGAAAACATTAATGTAGAGATTTTAACTACGTAAG          >  2:142525/1‑141                                                                                                                                              TTAGATTGCTTTTTTAGTTTGTATTTTTAACTTATTTTATAAGACGATTGGTTTCGAAAATGGTAAACTAGTAACAATGAGAGGTGTAACATGATGGAAAAAAATGAAAACATTAATGTAGAGATTTTAACTACGTCAGAT        <  1:234513/141‑1                                                                                                                                               TAGATTGCTTTTTTAGTTTGTATTTTTAACTTATTTTATAAGACGATTGGTTTCGAAAATGGTAAACTAGTAACAATGAGAGGTGTAACATGATGGAAAAAAATGAAAACATTAATGTAGAGATTTTAACTACGTCAGATA       <  1:116196/141‑1                                                                                                                                                   TTGCTTTTTTAGTTTGTAGTTTTAACTTATTTTATAAGACGATTGGTTTCGAAAATGGTAAACTAGTAACAATGAGAGGTGTAACATGATGGAAAAAAATGAAAACATTAATGTAGAGATTTTAACTACGTCAGATATGCA   <  1:196540/141‑1                                                                                                                                                    TGCTTTTTTAGTTTGTATTTTTAACTTATTTTATAAGACGATTGGTTTCGAAAATGGTAAACTCGTAACAATGAGAGGTGTAACATGATGGAAAAAAATGAAAACATTAATGTAAAGCTTTTACATAAGTACGATATGCAT  >  2:191399/1‑141                                                                                                                                                                                                                                                                                                  GTTTTCATTTTTTTCCATCATGTTACACCTCTCATTGTTACTAGTTTACCATTTTCGAAACCAATCGTCTTATAAAATAAGTTAAAAATACAAACTAAAAAAGCAATCTAAGTTCCAGTTAAAATCTACATTAACT‑AAACTTAGATTGCT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  USA300TCH1516_ALE/1031033‑1030884 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑aacttagattgctTTTTTAGTTTGTATTTTTAACTTATTTTATAAGACGATTGGTTTCGAAAATGGTAAACTAGTAACAATGAGAGGTGTAACATGATGGAAAAAAATGAAAACATTAATGTAGAGATTTTAACTACGTCAGATATGCAT  >  USA300TCH1516_ALE/1030933‑1031069

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 27 ≤ 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.