New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	= 1427028	41 (0.520)	4 (0.050)	4/268	8.6	9.3%	intergenic (‑759/+213)	pstS/cvfB	Phosphate‑binding protein PstS/Conserved virulence factor B
	?	USA300TCH1516_ALE	1442915 =	NA (NA)					intergenic (+148/+120)	USA300HOU_RS07165/USA300TCH1516_01342	TelA‑like protein/hypothetical protein
Rejected: Coverage evenness skew score above cutoff.
Rejected: Frequency below/above cutoff threshold.

TTAGATATAACAAAAAAGAGCTTGGGACATTAAGTTCCTTAAAGTTCTTAGGCAATGTAAAAAAGCTGATTTCTATTATTTATTTGATAGAAATCAGCTTTTTTGATATGTATTTTATAATGTACAGCTCGTTGAGCTGCTATTTTCCTTATATTAAGTGCCATTAATACAAAACCTAGCTCTCGTTTAACTTTATTTATTCCTCGAACTGACATTCGAGTGAAACCCAAAATAGCCTTCATAAATCCAAAAACAGGCTCTACATC  >  USA300TCH1516_ALE/1442776‑1443041                                                                                                                                            |                                                                                                                               ttAGATATAACAAGAAAGAGCTTGGGACATTAAGTTCCTTAAAGTGCTTAGGCAATGTAAAAAAGCTGATTTCTATTATTTATTTGATAGAAATCAGCTTGTTTGATATGTATTTTATAATGTACAGCTCGTTGAgctgct                                                                                                                               <  1:495238/141‑1 (MQ=255)   aGATATAACAAAAAAGAGCTTGGGACATTAAGTTCCTTAAAGTTCTTAGGCAATGTAAAAAAGCTGATTTCTATTATTTATTTGATAGAAATCAGCTTTTTTGATATGTATTTTATAATGTACAGCTCGTTGAGCTGCTAt                                                                                                                             <  2:553417/141‑1 (MQ=255)       ataACAAAAAAGAGCTTGGGACATTAAGTTCCTTAAAGTTCTTAGGCAATGTAAAAAAGCTGATTTCTATTATTTATTTGATAGAAATCAGCTTTTTTGATATGTATTTTATAATGTACAGCTCGTTGAGCTGCTATTTTc                                                                                                                         >  2:533582/1‑141 (MQ=255)            aaaaaaGAGCTTGGGACATTAAGTTCCTTAAAGTTCTTAGGCAATGTAAAAAAGCTGATTTCTATTATTTATTTGATAGAAATCAGCTTTTTTGATATGTATTTTATAATGTACAGCTCGTTGAGCTGCTATTTTCCTtat                                                                                                                    <  1:49270/141‑1 (MQ=255)               aaaGAGCTTGGGACATTAAGTTCCTTAAAGTTCTTAGGCAATGTAAAAAAGCTGATTTCTATTATTTATTTGATAGAAATCAGCTTTTTTGATATGTATTTTATAATGTACAGCTCGTTGAGCTGCTATTTTCCTTATAtt                                                                                                                 <  2:496841/141‑1 (MQ=255)                aaGAGCTTGGGACATTAAGTTCCTTAAAGTTCTTAGGCAATGTAAAAAAGCTGATTTCTATTATTTATTTGATAGAAATCAGCTTTTTTGATATGTATTTTATAATGTACAGCTCGTTGAGCTGCTATTTTCCTTATATTa                                                                                                                <  2:604378/141‑1 (MQ=255)                 agagCTTGGGACATTAAGTTCCTTAAAGTTCTTAGGCAATGTAAAAAAGCTGATTTCTATTATTTATTTGATAGAAATCAGCTTTTTTGATATGTATTTTATAATGTACAGCTCGTTGAGCTGCTATTTTCCTTATATTaa                                                                                                               >  1:57074/1‑141 (MQ=255)                 agagCTTGGGACATTAAGTTCCTTAAAGTTCTTAGGCAATGTAAAAAAGCTGATTTCTATTATTTATTTGATAGAAATCAGCTTTTTTGATATGTATTTTATAATGTACAGCTCGTTGAGCTGCTATTTTCCTTATATTaa                                                                                                               >  1:87085/1‑141 (MQ=255)                  gagCTTGGGACATTAAGTTCCTTAAAGTTCTTAGGCAATGTAAAAAAGCTGATTTCTATTATTTATTTGATAGAAATCAGCTTTTTTGATATGTATTTTATAATGTACAGCTCGTTGAGCTGCTATTTTCCTTATATTaat                                                                                                              >  2:37107/1‑140 (MQ=255)                       tGGGACATTAAGTTCCTTAAAGTTCTTAGGCAATGTAAAAAAGCTGATTTCTATTATTTATTTGATAGAAATCAGCTTTTTTGATATGTATTTTATAATGTACAGCTCGTTGAGCTGCTATTTTCCTTATATTAAGTGCCa                                                                                                         <  1:548237/141‑1 (MQ=255)                                                       aTGTAAAAAAGCTGATTTCTATTATTTATTTGATAGAAATCAGCTTTTTTGATATGTATTTTATAATGTACAGCTCGTTGAGCTGCTATTTTCCTTATATTAAGTGCCATTAATACAAAACCTAGCTCTCGTTTAACttta                                                                         <  1:924546/141‑1 (MQ=32)                                                            aaaaaGCTGATTTCTATTATTTATTTGATAGAAATCAGCTTTTTTGATATGTATTTTATAATGTACAGCTCGTTGAGCTGCTATTTTCCTTATATTAAGTGCCATTAATACAAAACCTAGCTCTCGTTTAACTttatttat                                                                    >  1:526473/1‑141 (MQ=32)                                                            aaaaaGCTGATTTCTATTATTTATTTGATAGAAATCAGCTTTTTTGATATGTATTTTATAATGTACAGCTCGTTGAGCTGCTATTTTCCTTATATTAAGTGCCATTAATACAAAACCTAGCTCTCGTTTAACTttatttat                                                                    >  1:881623/1‑141 (MQ=32)                                                            aaaaaGCTGATTTCTATTATTTATTTGATAGAAATCAGCTTTTTTGATATGTATTTTATAATGTACAGCTCGTTGAGCTGCTATTTTCCTTATATCAAGTGCCATTAATACAAAACCTAGCTCTCGTTTAACTttatttat                                                                    >  2:901036/1‑141 (MQ=17)                                                            aaaaaGCTGATTTCTATTATTTATTTGATAGAAATCAGCTTGTTTGATATGTATTTTATAATGTACAGCTCGTTGAGCTGCTAGTTTCCTTGTATTAAGTGCCATTAATACAAAACCTAGCTCTCGTTTAACTttatttat                                                                    >  2:183334/1‑141 (MQ=12)                                                             aaaaGCTGATTTCTATTATTTATTTGATAGAAATCAGCTTTTTTGATATGTATTTTTTACTGTAAAGCTCGTTGTGCTTCTGTTTTCGTTACATTTAGTGCCATTTGTACAAAACCTATCTCTCGTTTAACTTtatttatt                                                                   >  2:216777/1‑141 (MQ=11)                                                             aaaaGCTGATTTCTATTATTTATTTGATAGAAATCAGCTTTTTTGATATGTATTTTATAATGTACAGCTCGTTGAGCTGCTATTTTCCTTATATTACGTGCCATTAATACAAAACCTTGGTCTCGTTTAACTTtatttttt                                                                   >  2:821943/1‑141 (MQ=255)                                                               aaGCTGATTTCTATTATTTATTTGATAGAAATCAGCTTTTTTGATATGTATTTTATAATGTACAGCTCGTTGAGCTGCTATTTTCCTTATATTAAGTGCCATTAATACAAAACCTAGCTCTCGTTTAACTTTATTTATTcc                                                                 <  2:830711/141‑1 (MQ=32)                                                                  cTGATTTCTATTATTTATTTGATAGAAATCAGCTTTTATGATATGTATTTTATAATGTACAGCTCGTTGAGCTGCTATTTTCCTTATATTAAGTGCCATTAATACAAAACCTAGCTCTCGTTTAACTTTATTTATTCCTCg                                                              >  2:372517/1‑141 (MQ=17)                                                                   tGATTTCTATTATTTATTTGATAGAAATCAGCTTTTTTGATATGTATTTTATAATGTACAGCTCGTTGAGCTGCTATTTTCCTTATATTAAGTGCCATTAATACAAAACCTAGCTCTCGTTCAACTTTATTTATTCCTCGa                                                             <  1:600136/141‑1 (MQ=17)                                                                         ttattatTTATTTGATAGAAATCAGCTTTTTTGATATGTATTTTATAATGTACAGCTCGTTGAGCTGCTATTTTCCTTATATTAAGTGCCATTAATACAAAACCTAGCTCTCGTTTAACTTTATTTATTCCTCGAACTGAc                                                       <  2:126476/140‑1 (MQ=17)                                                                         cTATTATTTATTTGATAGAAATCAGCTTTTTTGATATGTATTTTATAATGTACAGCTCGTTGAGCTGCTATTTTCCTTATATTAAGTGCCATTAATACAAAACCTAGCTCTCGTTTAACTTTATTTATTCCTCGAACTGAc                                                       >  2:334224/1‑141 (MQ=32)                                                                         cTATTATTTATTTGATAGAAATCAGCTTTTTTGATACTGATTTTATAATGTACAGCTCGTTGAGCTGCTATTTTCCTTAGATTAAGTGCCATTAATACAAAACCTAGCTCTCGTTTAACTTTATTTATTCCTCGAACTGAc                                                       <  1:353194/141‑1 (MQ=255)                                                                            ttatttatTTGATAGAAATCAGCTTTTTTGATATGTATTTTATAATGTACAGCTCGTTGAGCTGCTATTTTCCTTATATTAAGTGCCATTAATACAAAACCTAGCTCTCGTTTAACTTTATTTATTCCTCGAACTGACAtt                                                    <  1:533582/141‑1 (MQ=32)                                                                                                                              agttCGTTGAGAAGATATTTTACATAGATTAAGTGCCATTAATACAAAACCTAGATCACGTTTAACTTTATTTATTCCTCGAACTGACAATCGAGTGAAACCCAAAATAGCCTAAAAAAAAAAAAAAACAGGCTCTACATc  <  2:260348/138‑1 (MQ=1)                                                                                                                                            |                                                                                                                               TTAGATATAACAAAAAAGAGCTTGGGACATTAAGTTCCTTAAAGTTCTTAGGCAATGTAAAAAAGCTGATTTCTATTATTTATTTGATAGAAATCAGCTTTTTTGATATGTATTTTATAATGTACAGCTCGTTGAGCTGCTATTTTCCTTATATTAAGTGCCATTAATACAAAACCTAGCTCTCGTTTAACTTTATTTATTCCTCGAACTGACATTCGAGTGAAACCCAAAATAGCCTTCATAAATCCAAAAACAGGCTCTACATC  >  USA300TCH1516_ALE/1442776‑1443041

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.