New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	1442900 =	NA (NA)	4 (0.080)	3/246	NT	NA	intergenic (+133/+135)	USA300HOU_RS07165/USA300TCH1516_01342	TelA‑like protein/hypothetical protein
	?	USA300TCH1516_ALE	1442915 =	NA (NA)					intergenic (+148/+120)	USA300HOU_RS07165/USA300TCH1516_01342	TelA‑like protein/hypothetical protein

ATAACAAAAAAGAGCTTGGGACATTAAGTTCCTTAAAGTTCTTAGGCAATGTAAAAAAGCTGATTTCTATTATTTATTTGATAGAAATCAGCTTTTTTGATATGTATTTTATAATGTACAGCTCGTTGAGCTGCTATTTTCCTTATATTAAGTGCCATTAATACAAAACCTAGCTCTCGTTTAACTTTATTTATTCCTCGAACTGACATTCGAGTGAAACCCAAAATAGCCTTCATAAATCCAAAAAC  >  USA300TCH1516_ALE/1442782‑1443029                                                                                                                                      |                                                                                                                   ataACAAAAAAGAGCTTGGGACATTAAGTTCCTTATAGTTCTTAGGCAATGTAAAAAAGCTGATTTCTATTATTTATTTGATAGAAATCAGCTTTTTTGATATGTATTTTATATTGTACAGCTCGTTGAGCTGCTAtttt                                                                                                              >  1:356796/1‑140 (MQ=255)   aaCAAAAAAGAGCTTGGGACATTAAGTTCCTTAAAGTTCTTAGGCAATGTAAAAAAGCTGATTTCTATTATTTATTTGATAGAAATCAGCTTTTTTGATATGTATTTTATAATGTACAGCTCGTTGAGCTGCTATTTTcc                                                                                                            >  1:260289/1‑140 (MQ=255)      aaaaaaGAGCTTGGGACATTAAGTTCCTTAAAGTTCTTAGGCAATGTAAAAAAGCTGATTTCTATTATTTATTTGATAGAAATCAGCTTTTTTGATATGTATTTTATAATGTACAGCTCGTTGAGCTGCTATTTTCCTta                                                                                                         >  2:641362/1‑140 (MQ=255)      aaaaaaGAGCTTGGGACATTAAGTTCCTTAAAGTTCTTAGGCAATGTAAAAAAGCTGATTTCTATTATTTATTTGATAGAAATCAGCTTTTTTGATATGTATTTTATAATGTACAGCTCGTTGAGCTGCTATTTTCCTta                                                                                                         >  1:592964/1‑140 (MQ=255)        aaaaGAGCTTGGGACATTAAGTTCCTTAAAGTTCTTAGGCAATGTAAAAAAGCTGATATCTATTATTTATTTGATAGAAATCAGCTTATTTGATATGTATTTTATAATGTACAGCTCGTTGAGCTGCTATTTTCCTtata                                                                                                       >  1:593849/1‑140 (MQ=255)             agCTTGGGACATTAAGTTCCTTAAAGTTCTTAGGCAATGTAAAAAAGCTGATTTCTATTATTTATTTGATAGAAATCAGCTTTTTTGATATGTATTTTATAATGTACAGCTCGTTGAGCTGCTATTTTCCTTTTATTAAg                                                                                                  >  1:465927/1‑140 (MQ=255)                  gggACATTAAGTTCCTTAAAGTTCTTAGGCAATGTAAAAAAGCTGATTTCTATTATTTTTTTGCTAGAAATCAGCTTTTTTGATATGTATTTTATAATGTACACCTCGTTGAGCTGCTATTTTCCTTATATTATCTGCCa                                                                                             >  1:303767/1‑140 (MQ=14)                  gggACATTAAGTTCCTTAAAGTTCTTAGGCAATGTAAAAAAGCTGATTTCTATTATTTATTTGATAGAAATCAGCTTTTTTGATATGTATTTTATAATGTACAGCTCGTTGAGCTGCTATTTTCCTTATATTAAGTGCCa                                                                                             >  2:629253/1‑140 (MQ=255)                   ggACATTAAGTTCCTTAAAGTTCTTAGGCAATGTAAAAAAGCTGATTTCTATTATTTATTTGATAGAAATCAGCTTTTTTGATATGTATTTTATAATGTACAGCTCGTTGAGCTGCTATTTTCCTTATATTAAGTGCCAt                                                                                            >  2:567748/1‑140 (MQ=255)                   ggACATTAAGTTCCTTAAAGTTCTTAGGCAATGTAAAAAAGCTGATTTCTATTATTTATTTGATAGAAATCAACTTTTTTGCTATGTATTTTGAGTTTAACAGCTCGTTGAGCTGCTATTTTCCTTATATTAAGTGCCAt                                                                                            >  1:50812/1‑140 (MQ=14)                    gACATTAAGTTCCTTAAAGTTCTTAGGCAATGTAAAAAAGCTGATTTCTATTATTTTTTTCACTTAAAGCAGCTTTTTTGATATGTATTTTATAATGTACAGCTCGTTGAGCTGCTATTTTCCTTATATTAAGTGCCAtt                                                                                           <  1:317276/140‑1 (MQ=14)                    gACATTAAGTTCCTTAAAGTTCTTAGGCAATGTAAAAAAGCTGATTTCTATTATTTATTTGATAGAAATCAGCTTTTTTGATATGTATTTTATAATGTACAGCTCGTTGAGCTGCTATTTTCCTTATATTAAGTGCCAtt                                                                                           >  1:195175/1‑140 (MQ=255)                           aGTTCCTTAAAGTTCTTAGGCAATGTAAAAAAGCTGATTTCTATTATTTATTTGATAGAAATCAGCTTTTTTGATATGTATTTTATAATGTACAGCTCGTTGAGCTGCTATTTTCCTTATATTAAGTGCCATTAATACaa                                                                                    >  2:313585/1‑140 (MQ=40)                                        tCTTAGGCAATGTAAAACAGCTCCTTTCTATTATTTATTTGATAGAAATCAGCTTTTTTTATATGGATTTTATAATTTACAGCTCGTTGAGCTGCTATTTTCCTTATATTAAGTGCCATTAATACAAAACCTAGCTCTCg                                                                       <  2:627851/140‑1 (MQ=11)                                         cTTAGGCAATGTAAAAAAGCTGATTTCTATTATTTATTTGATAGAAATCAGCTTTTTTGATATGTATTTTATAATGTACAGCTCGTTGAGCTGCTATTTTCCTTATATTAAGTGCCATTAATACAAAACCTAGCTCTCGt                                                                      <  1:488674/140‑1 (MQ=33)                                         aatatgCAATGTAAAAAATCTTAATTATAATATTTATTTTATAGAAATCAGCTTTTTTGATATGTATTTTATAATGTACAGCTCGTTGAGCTGCTATTTACCTTATATTAAGTGCCATTAATACAAAACCTAGCTCTCGt                                                                      <  1:283619/135‑1 (MQ=11)                                           tAGGCAATGTAAAAAAGCTGATTTCTATTATTTATTTGATAGAAATCAGCTTTTTTGATATGTATTTTATAATGTACAGCTCGTTGAGCTGCTATTTTCCTTATATTAAGTGCCATTAATACAAAACCTAGCTCTCGttt                                                                    <  2:370120/140‑1 (MQ=33)                                           tAGGCAATGTAAAAAAGCTGATTTCTATTATTTATTTGATAGAAATCAGCTTTTTTGATATGTATTTTATAATGTACAGCTCGTTGAGCTGCTATTTTCCTTATATTAAGTGCCATTAATACAAAACCTAGCTCTCGttt                                                                    >  2:602912/1‑140 (MQ=33)                                            aGGCAATGTAAAAAAGCTGATTTCTATTATTTATTTGATAGAAATCAGCTTTTTTGATATGTATTTTATAATGTACAGCTCGTTGAGCTGCTATTTTCCTTATATTAAGTGCCATTAATACAAAACCTAGCTCTCGTTTa                                                                   >  2:447606/1‑140 (MQ=33)                                                      aaaaaGCTGATTTCTATTATTTATTTGATAGAAATCAGCTTTTTTGATATGTATTTTATAATGTACAGCTCGTTGAGCTGCTATTTTCCTTATATTAAGTGCCATTAATAGAAAACCTAGCTCTCGTTTAACtttattta                                                         >  2:422794/1‑140 (MQ=18)                                                      aaaaaGCTGATTTCTATTATTTATTTGATAGAAATCAGCTTTTTTGATATGTATTTTATAATGTACAGCTCGTTGAGCTGCTATTTTCCTTATATTAAGTGCCATTAATACAAAACCTAGCTCTCGTTTAACtttattta                                                         >  1:565422/1‑140 (MQ=33)                                                      aaaaaGCTGATTTCTATTATTTATTTGATAGAAATCAGCTTTTTTGATATGTATTTTATAATGTACAGCTCGTTGAGCTGCTATTTTCCTTATATTAAGTGCCATTAATACAAAACCTAGCTCTCGTTTAACtttattta                                                         >  1:250377/1‑140 (MQ=33)                                                                tttCTATTATTTATTTGATAGAAATCAGCTTTTTTGATATGTATTTTATAATGTACAGCTCGTTGAGCTGCTATTTTCCTTATATTAAGTGCCATTAATACAAAACCTAGCTCTCGTTTAACTTTATTTATTCCTCGAAc                                               >  1:442919/1‑140 (MQ=33)                                                                tttCTATTATTTATTTGATAGAAATCAGCTTTTTTGATATGTATTTTATAATGTACAGCTCGTTGAGCTGCTATTTTCCTTATATTAAGTGCCATTAATACAAAACCTAGCTCTCGTTTAACTTTATTTATTCCTCGAAc                                               >  1:133121/1‑140 (MQ=33)                                                                        atttatttGATAGAAATCAGCTTTTTTGATATGTATTTTATAATGTACAGCTCGTTGAGCTGCTATTTTCCTTATATTAAGTGCCATTAATACAAAACCTAGCTCTCGTTTAACTTTATTTATTCCTCGAACTGACATTc                                       <  1:453699/140‑1 (MQ=31)                                                                        atttatttGATAGAAATCAGCTTTTTTGATATGTATTTTATAATGTACAGCTCGTTGAGCTGCTATTTTCCTTATATTAAGTGCCATTAATACAAAACCTAGCTCTCGTTTAACTTTATTTATTCCTCGAACTGACATTc                                       <  2:426552/140‑1 (MQ=31)                                                                                                             ttttaATGTACAGCTCGTTGAGCTGCTATTTTCCTTATATTAAGTGCCATTAATACAAAACCTAGCTCTCGTTTAACTTTATTTATTCCTCGAACTGACATTCGAGTGAAACCCAAAATAGCCTTCATAAATCCAAAAAc  <  2:468708/137‑1 (MQ=1)                                                                                                                                      |                                                                                                                   ATAACAAAAAAGAGCTTGGGACATTAAGTTCCTTAAAGTTCTTAGGCAATGTAAAAAAGCTGATTTCTATTATTTATTTGATAGAAATCAGCTTTTTTGATATGTATTTTATAATGTACAGCTCGTTGAGCTGCTATTTTCCTTATATTAAGTGCCATTAATACAAAACCTAGCTCTCGTTTAACTTTATTTATTCCTCGAACTGACATTCGAGTGAAACCCAAAATAGCCTTCATAAATCCAAAAAC  >  USA300TCH1516_ALE/1442782‑1443029

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 32 ≤ 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.