New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	82395 =	176 (0.860)	9 (0.050)	5/152	NT	5.3%	coding (500/957 nt)	nikB_1	Nickel transport system permease protein NikB
	?	USA300TCH1516_ALE	82432 =	152 (0.790)					coding (537/957 nt)	nikB_1	Nickel transport system permease protein NikB

TGTGTAATCAGATGTGCTGTCATCAATAAGATATGACACCCTTCTATAACAACAATTGTGAAGATTGGCAGCACAAAGTGTTGCCATGAATCAC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  USA300TCH1516_ALE/82488‑82395 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑tcacAATTGTTGTTATAGAAGGGTGTCATATCTTATTGATGACAGCACATCTGATTACACAAACGTTAGATCAAGATGCGTATCAACTGGCGCA  >  USA300TCH1516_ALE/82432‑82521                                                                                                                                                                                          TGTGTAATCAGATGTGCTGTCATCAATAAGATATGACACCCTTCTATAACAACAATTGTGAAGATTGGCAGCACAAAGTGTTGCCATGAAT                                                                                               >  2:1441660/1‑91  GTGTAATCAGATGTGCTGTCATCAATAAGATATGACACCCTTCTATAACAACAATTGTGAAGATTGGCAGCACAAAGTGTTGCCATGAATC                                                                                              >  2:2614915/1‑91    GTAATCAGATGTGCTGTCATCAATAAGATATGACACCCTTCTATAACAACAATTGTGAAGATTGGCAGCACAAAGTGTTGCCATGAATCAC                                                                                            <  2:418089/91‑1    GTAATCAGATGTGCTGTCATCAATAAGATATGACACCCTTCTATAACAACAATTGTGAAGATTGGCAGCACAAAGTGTTGCCATGAATCAC                                                                                            >  1:2834030/1‑91                                           TCTATAACAACAATTGTGAAGATTGGCAGCACAAAGTGTTGCCAATCTTCACAATTGTTGTTATAGAAGGGTGTCATATCTTATTGATGAC                                                     >  1:3317121/1‑91                                                          GTGAAGATTGGCAGCACAAAGTGTTGCCATGAATCACAATTGTTGTTATAGAAGGGTGTCATACCTTATTGATGACAGCACATCTGATTAC                                      >  2:228882/1‑91                                                           TGAAGATTGGCAGCACAAAGTGTTGCCATGAATCACAATTGTTGTTATAGAAGGGTGTCATATCTTATTGATGACAGCACATCTGATTACA                                     >  1:2296755/1‑91                                                           TGAAGATTGGCAGCACAAAGTGTTGCCATGAATCACAATTGTTGTTATAGAAGGGTGTCATATCTTATTGATGACAGCACATCTGATTACA                                     >  1:2296767/1‑91                                                           TGAAGATTGGCAGCACAAAGTGTTGCCATGAATCACAATTGTTGTTATAGAAGGGTGTCATATCTTATTGATGACAGCACATCTGATTACA                                     >  1:1654103/1‑91                                                           TGAAGATTGGCAGCACAAAGTGTTGCCATGAATCACAATTGTTGTTATAGAAGGGTGTCATATCTTATTGATGACAGCACATCTGATTACA                                     >  1:3192547/1‑91                                                             AAGATTGGCAGCACAAAGTGTTGCCATGAATCACAATTGTTGTTATAGAAGGGTGTCATATCTTATTGATGACAGCACATCTGATTACACA                                   >  1:3236939/1‑91                                                             AAGATTGGCAGCACAAAGTGTTGCCATGAATCACAATTGTTGTTATAGAAGGGTGTCATATCTTATTGATGACAGCACATCTGATTACACA                                   >  1:3237910/1‑91                                                              AGATTGGCAGCACAAAGTGTTGCCATGAATCACAATTGTTGTTATAGAAGGGTGTCATATCTTATTGATGACAGCACATCTGATTACACAA                                  >  1:2185107/1‑91                                                                                           TCACAATTGTTGTTATAGAAGGGTGTCATATCTTATTGATGACAGCACATCTGATTACACAAACGTTAGATCAAGATGCGTATCAACTGtc     >  2:1185899/1‑89                                                                                           TCACAATTGTTGTTATAGAAGGGTGTCATATCTTATTGATGACAGCACATCTGATTACACAAACGTTAGATCAAGATGCGTATCAACTGGC     >  2:3518185/1‑91                                                                                           TCACAATTGTTGTTATAGAAGGGTGTCATATCTTATTGATGACAGCACATCTGATTACACAAACGTTAGATCAAGATGCGTATAAACTGGC     >  2:3518071/1‑91                                                                                           TCACAATCGTTGTTATAGAAGGGTGTCATATCTTATTGATGACAGCACATCTGATTACACAAACGTTAGATCAAGATGCGTATCAACTGGC     >  2:1314685/1‑91                                                                                            CACAATTGTTGTTATAGAAGGGTGTCATATCTTATTGATGACAGCACATCTGATTACACAAACGTTAGATCAAGATGCGTATCAACTGGCG    <  2:2044461/91‑1                                                                                             ACAATTGTTGTTATAGAAGGGTGTCATATCTTATTGATGACAGCACATCTGATTACACAAACGTTAGATCAAGATGCGTATCAACTGGCGC   >  1:3521195/1‑91                                                                                             ACAATTGTTGTTATAGAAGGGTGTCATATCTTATTGATGACAGCACATCTGATTACACAAACGTTAGATCAAGATGCGTATCAACTGGCGC   >  2:1384470/1‑91                                                                                             ACAATTGTTGTTATAGAAGGGTGTCATATCTTATTGATGACAGCACATCTGATTACACAAACGTTAGATCAAGATGCGTATCAACTGGCGC   <  2:2473655/91‑1                                                                                             ACAATTGTTGTTATAGAAGGGTGTCATATCTTATTGATGACAGCACATCTGATTACACAAACGTTAGATCAAGATGCGTATCAACTGGCGC   >  1:2686134/1‑91                                                                                             ACAATTGTTGTTATAGAAGGGTGTCATATCTTATTGATGACAGCACATCTGATTACACAAACGTTAGATCAAGATGCGTATCAACTGGCGC   >  2:3146825/1‑91                                                                                              CAATTGTTGTTATAGAAGGGTGTCATATCTTATTGATGACAGCACATCTGATTACACAAACGTTAGATCAAGATGCGTATCAACTGGCGCA  >  1:1220577/1‑91                                                                                              CAATTGTTGTTATAGAAGGGTGTCATATCTTATTGATGACAGCACATCTGATTACACAAACGTTAGATCAAGATGCGTATCAACTGGCGCA  >  1:1741826/1‑91                                                                                              CAATTGTTGTTATAGAAGGGTGTCATATCTTATTGATGACAGCACATCTGATTACACAAACGTTAGATCAAGATGCGTATCAACTGGCGCA  >  1:1741782/1‑91                                                                                              CAATTGTTGTTATAGAAGGGTGTCATATCTTATTGATGACAGCACATCTGATTACACAAACGTTAGATCAAGATGCGTATCAACTGGCGCA  >  1:1741813/1‑91                                                                                              CAATTGTTGTTATAGAAGGGTGTCATATCTTATTGATGACAGCACATCTGATTACACAAACGTTAGATCAAGATGCGTATCAACTGGCGCA  >  1:1220629/1‑91                                                                                                                                                                                          TGTGTAATCAGATGTGCTGTCATCAATAAGATATGACACCCTTCTATAACAACAATTGTGAAGATTGGCAGCACAAAGTGTTGCCATGAATCAC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  USA300TCH1516_ALE/82488‑82395 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑tcacAATTGTTGTTATAGAAGGGTGTCATATCTTATTGATGACAGCACATCTGATTACACAAACGTTAGATCAAGATGCGTATCAACTGGCGCA  >  USA300TCH1516_ALE/82432‑82521

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