New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	895785 =	25 (1.010)	7 (0.320)	5/246	2.1	27.0%	coding (806/822 nt)	metQ_2	Methionine‑binding lipoprotein MetQ
	?	USA300TCH1516_ALE	= 909740	16 (0.730)					intergenic (‑663/‑371)	USA300HOU_RS04500/csbD_1	hypothetical protein/Stress response protein CsbD

GGTTGTTTTCAAGGGCAAAAAAAGGGCATAATTTTGAAACAAAGGGCAAGGGTATGAATAATAAATTATCTTGAAAATTTTATAAATGCATATATAACAATGTTTTGATTGCCCTTGAACTTCCTTGATAATCTGGCTAATTATTCCTGCTAAATAAATCATATTAATGGCTCAGTAACGTGATGTTGCTGGGCTTTTTAATTTAAACAGGTATTTATATGATATTTAGGAATGAGATGCTATTACGGATAAAGTAAAATCCTATATGCATGCGTGCT  >  USA300TCH1516_ALE/909601‑909878                                                                                                                                            |                                                                                                                                           ggTTGTTTTCAAGGGCAAAAAAAGGGCATAATTTTGAAACAAAGGGCAAGGGTATGAATAATAAATTATCTTGAAAATTTTATAAATGCATATATAACAATGTTTTGATTGCCCTTGAACTTCCTTGATAATCTGGCTAAt                                                                                                                                           >  1:196949‑M2/1‑140 (MQ=255)   ttgttTTCAAGGGCAAAAAAAGGGCGTAATTTTGAAACAAAGGGCAAGGGTATGAATAATAAATTATCTTGAAAATTTTATAAATGCATATATAACAATGTTTTGATTTCTCTTGAACTTCCTTGATAATCTGGCTAAtta                                                                                                                                         <  2:20494‑M2/141‑4 (MQ=255)   ttgttTTCAAGGGCAAAAAAAGGGCATAATTTTGAAACAAAGGGCAAGGGTATGAATAATAAATTATCTTGAAAATTTTATAAATGCATATATAACAATGTTTTGATTGCCCTTGAACTTCCTTGATAATCTGGCTAAtta                                                                                                                                         <  2:126891‑M2/141‑4 (MQ=255)     gttTTCAAGGGCAAAAAAAGGGCATAATTTTGAAACAAAGGGCAAGGGTATGAATAATAAATTATCTTGAAAATTTTATAAATGCATATATAACAATGTTTTGATTGCCCTTGAACTTCCTTGATAATCTGGCTAAttatt                                                                                                                                       <  2:171622‑M2/141‑6 (MQ=255)                     aaaGGGCATAATTTTGAAACAAAGGGCAAGGGTATGAATAATAAATTATCTTGAAAATTTTATAAATGCATATATAACAATGTTTTGATTGCCCTTGAACTTCCTTGATAATCTGGCTAATTATTCCTGCTAAATAAATCa                                                                                                                       <  1:151533/141‑1 (MQ=255)                     aaaGGGCATAATTTTGAAACAAAGGGCAAGGGTATGAATAATAAATTATCTTGAAAATTGTATAAATGCATATATAACAATGTTTTGATTGCCCTTGAACTTCCTTGATAATCTGGCTAATTATTCTTGCTAAATAAATCa                                                                                                                       >  1:116138/1‑141 (MQ=255)                     aaaGGGCATAATTTTGAAAAAAAGGGCAAGGGTATGAATAATAAATTATCTTGAAAATTTTATAAATGCATATATAACAATGTTTTGATTGCCCTTGAACTTCCTTGATAATCTGGCTAATTATTCCTGCTAAATAAATCa                                                                                                                       <  1:89092/141‑1 (MQ=255)                              aagtatgaaacAAAGGGCAAGGGTATGAATAATAAATTATCTTGAAAATTTTATAAATGCATATATAACAATGTTTTGATTGCCCTTGAACTTCCTTGATAATCTGGCTAAttattcctgctaaataataccaattaaata                                                                                                              >  2:194218‑M2/6‑111 (MQ=255)                              aaTTTTGAAACAAAGGGCAAGGGTATGAATAATAAATTATCTTGAAAATTTTATAAATGCATATATAACAATGTTTTGATTGCCCTTGAACTTCCTTGATAATCTGGCTAAttattcctgctaaataataccaattaaata                                                                                                              >  1:70462‑M2/1‑111 (MQ=255)                              aaTGTTGAAACAAAGGGCAAGGGTATGAATAATAAATTATCTTGAAAATTTTATAAATGCATATATAACAATGTTTTGATTGCCCTTGAACTTCCTTGATAATCTGGCTAAttattcctgctaaataataccaattaaata                                                                                                              >  2:88585‑M2/1‑111 (MQ=255)                                       aCAAAGGGCAAGGGTATGAATAATAAATTATCTTGAAAATTTTATAAATGCATATATAACAATGTTTTGATTGCCCTTGAACTTCCTTGATAATCTGGCTAAttattcctgctaaataataccaattaaataaaaataccc                                                                                                     >  1:171622‑M2/1‑102 (MQ=255)                                         aaaGGGCAAGGGTATGAATAATAAATTATCTTGAAAATTTTATAAATGCATATATAACAATGTTTTGATTGCCCTTGAACTTCCTTGATAATCTGGCTAATTATTCCTGCTAAATAAATCATATTAATGGCTCAGTAACGt                                                                                                   <  2:113954/141‑1 (MQ=255)                                                        gAATAATAAATTATCTTGAGAATTTTATAAATGCATATATAACAATGTTTTGATTGCCCTTGAACTTCCTTGATAATCTGGCTAATTATTCCTGCTAAATAAATCATATTAATGGCTCAGTAACGTGATGTTGCTGGGCtt                                                                                    <  2:137727/141‑1 (MQ=255)                                                          ataataACTTATCTTTAAAATTTTATAAATGCATATATAACAACGTTTTGATTGCCCTTGAACTTCCCTGATAATCTGGCTAATTATTCCTGCTAAATAAATCATACTAATTGCTCAGTAACGTGATTTTGCTGGGCtttt                                                                                  <  1:70296/141‑1 (MQ=255)                                                                  ttATCTTGAAAATTTTATAAATGCATATATAACAATGTTTTGATTGCCCTTGAACTTCCTTGATAATCTGGCTAATTATTCCTGCTAAATAAATCATATTAATGGCTCAGTAACGTGATGTTGCTGGGCTTtttaatttaa                                                                          <  1:210517/141‑1 (MQ=255)                                                                       ttGAAAATTTTATAAATGCATATATAACAATGTTTTGATTGTCCTTTAACTTCCTTGATAATCTGGCTGTTTGTTGGCCCGAAACAACAACTAGAAACATGTCAGTAACTGGATGTTGCTGGGCTTTTTAATTTAAACAgg                                                                     <  1:135966/141‑1 (MQ=255)                                                                                ttATAAATGCATATATAACAATGTTTTGATTGCCCTTGAACTTCCTTGATAATCTGGCTAAttattcctgctaaataataccaattaaataaaaataccctttaataacaacgattaaggggttatttttgtggtattgaa                                                            >  1:126891‑M2/1‑61 (MQ=255)                                                                                            atataATAATGTTTTTATTGCTCTTGAACTTCCTTGATAATCTGGCTAATTATTCGTGTTAAATAAATCATATTAATGGCTCAGTAACGTGATGTTGCTGGGCTTTTTAATTTAAACAGGTATTTATATGATATTTAGGaa                                                <  2:181625/141‑1 (MQ=255)                                                                                            atataACAATGTTTTGATTGCCCTTGCACTACCTTGATAATCTGGCTAATTATTCCTGCTAAATAAATCATATTAATGGCTCAGTAACGTGATGTTGCTGGGCTTTTTAATTTAAACAGGTATTTATATGATATTTAGGaa                                                <  2:70699/141‑1 (MQ=255)                                                                                                   aaTGTTTTGATTGTCCTTGAACTTCCTTGATAATCTGGCTAAttattcctgctaaataataccaattaaataaaaataccctttaataacaacgattaaggggttatttttgtggtattgaaaataaaaaagggcacaaaa                                         >  1:146375‑M2/1‑42 (MQ=255)                                                                                                           gATTGCCCTTGAACTTCCTTGATGATATGGCTAATTATTCCTGCTAAATAAATCATATTAATCGCACGGGAACGTGAGGTTCCTGGGCTTTTTCATTTATACAGGTATTTATATTATATTTAGGATTGAGTTGCAAttctt                                 >  2:157843/1‑138 (MQ=255)                                                                                                           gATTGCCCTTGAACTTCCTTGATAATCTGGCTAATTATTCCTGCTAAATAAATCATATTAATGGCTCAGTAACGTGATGTTGCTGGGCTTTTTAATTTAAACAGGTATTTATATGATATTTAGGAATGAGATGCTATTACg                                 >  1:105087/1‑141 (MQ=255)                                                                                                             ttGCCCTTGAACTTCCTTGATAATCTGGCTAATTATTCCTGCTAAATAAATCATATTAATGGCTCAGTAACGTGATGTTGCTGGGCTTTTTAATTTAAACAGGTATTTATATGATATTTAGGAATGAGATGCTATTACGGa                               >  1:119119/1‑141 (MQ=255)                                                                                                                        cTTCCTTGATAATCTGGCTAAttattcctgctaaataataccaattaaataaaaataccctttaataacaacgattaaggggttatttttgtggtattgaaaataaaaaagggcccaaaaggggcagtatatgcaacttat                    <  1:35006‑M2/141‑121 (MQ=255)                                                                                                                          tCCTTGATAATCTGGCTAATTATTCCTGCTAAATAAATCATATTAATAGCTAAATAACGTGATGTTACTAATCTTTTTAATTTAAACATTTATTTATATAATATTTAGAAATGAAATATTATTAATTATAAAGTAAAAtat                  >  2:112521/1‑139 (MQ=255)                                                                                                                                      tGGATAATTATTCATGATAAGTAAATCATATTAATGGCTCAGTAACGTGATGTTGCTGGGCTTTTTAATTTAAACAGGCATTTAGATGATATTTAGGAATGAGATGCTATTACGGATAAAGTAAAAACCTATATGCATGCg      <  2:282126/141‑1 (MQ=255)                                                                                                                                          tAATTATTCCTGCTAAATAAATCATATTAATGGCTCAGTAACGTGATGTTGCTGGGCTTTTTAATTTAAACAGGTATTTATATGATATTTAGGAATGAGATGCTATTACGGATAAAGTAAAATCCTATATGCATGCGTGCt  >  2:70135/1‑141 (MQ=255)                                                                                                                                            |                                                                                                                                           GGTTGTTTTCAAGGGCAAAAAAAGGGCATAATTTTGAAACAAAGGGCAAGGGTATGAATAATAAATTATCTTGAAAATTTTATAAATGCATATATAACAATGTTTTGATTGCCCTTGAACTTCCTTGATAATCTGGCTAATTATTCCTGCTAAATAAATCATATTAATGGCTCAGTAACGTGATGTTGCTGGGCTTTTTAATTTAAACAGGTATTTATATGATATTTAGGAATGAGATGCTATTACGGATAAAGTAAAATCCTATATGCATGCGTGCT  >  USA300TCH1516_ALE/909601‑909878

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.