New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	2476329 =	30 (0.840)	9 (0.260)	5/268	2.6	23.5%	intergenic (‑74/+166)	tcaA/tcaR	Membrane‑associated protein TcaA/HTH‑type transcriptional regulator TcaR
	?	USA300TCH1516_ALE	= 2476325	30 (0.880)					intergenic (‑70/+170)	tcaA/tcaR	Membrane‑associated protein TcaA/HTH‑type transcriptional regulator TcaR

TGTACATATCTGTACATCATCTTGTGCTTGTTGTCCGCACTTCGGGCAAGATTTCATACTTTCACCTCAATTCTGTTCCTCTTCAATTGTTATATGTATATCACAAAAATTATTTCATTATTTTACCATTATTATTTTACAAATATTATCCCAAGAATACAATTCAAGAAATGATTAACTTTACTTTAGAATTGTACCTTATTACATTATTTATGAAAGTACTCTCTCAATTATAACTAAAAAGAAGGTGTTCAATACATAC  >  USA300TCH1516_ALE/2476199‑2476460                                                                                                                                   |                                                                                                                                    tgcaCATATCTGTACATCATCTTGTGCTTGTTGTCCGCACTTCGGGCAAGATTTCATACTTTCACCTCAATTCTGTTCCTCTTCAATTGTTATATGTATATCACAAAAATTATTTCATTATTTTACCATTATTATTTTACa                                                                                                                           >  1:138344/4‑141 (MQ=255)  gtACATATCTGTACATCATCTTGTGCTTGTTGTCCGCACTTCGGGCAAGATTTCATACTTTCACCTCAATTCTGTTCCTCTTCAATTGTTATATGTATATCACAAAAATTATTTCATTATTTTACCATTATTATTTTACaa                                                                                                                          >  2:89434/1‑141 (MQ=255)   tACATATCTGTACATCATCTTGTGCTTGTTGTCCGCACTTCGGGCAAGATTTCATACTTTCACCTCAATTCTGTTCCTCTTCAATTGTTATATGTATATCACAAAAATTATTTCATTATTTTACCATTATTATTTTACaaa                                                                                                                         >  1:149698/1‑141 (MQ=255)                     catcttgtgcttgttgtccgcacttcgggcaagatttcatactttcacctcaattctgttcctcttcaattgttatatgtatatcacaaaaattatttcattattttaccATTATTTTACAAATATTATCCCAAGAATACa                                                                                                       <  1:2580‑M1/31‑1 (MQ=255)                       tgtgCTTGTTGTCCGCACTTCGGGCAAGATTTCATACTTTCACCTCAATTCTGTTCCTCTTCAATTGTTATATGTATATCACAAAAATTATTTCATTATTTTACCATTATTATTTTACAAATATTATCCCAAGAATACAAt                                                                                                     <  2:99044/141‑1 (MQ=255)                       tgtgCTTGTTGTCCGCACTTCGGGCAAGATTTCATACTTTCACCTCAATTCTGTTCCTCTTCAATTGTTATATGTATATCACAAAAATTATTTCATTATTTTACCATTATTATTTTACAAATATTATCCCAAGAATACAAt                                                                                                     <  2:264037/141‑1 (MQ=255)                         ttgtgcttgttgtccgcacttcgggcaagatttcatactttcacctcaattctgttcctcttcaattgttatatgtatatcacaaaaattatttcattattttaccATTATTTTACAAATATTATCCCAAGAATACAATTc                                                                                                   >  1:24695‑M1/107‑141 (MQ=255)                         ttgtgcttgttgtccgcacttcgggcaagatttcatactttcacctcaattctgttcctcttcaattgttatatgtatatcacaaaaattatttcattattttaccATTATTTTACAAATATTATCCCAAGAATACAATTc                                                                                                   >  2:72874‑M1/107‑141 (MQ=255)                         tgCTTGTTGTCCGCACTTCGGGCAAGATTTCATACTTTCACCTCAATTCTGTTCCTCTTCAATTGTTATATGTATATCACAAAAATTATTTTATTATTTTACCATTATTATTTTACAAATATTATCCCAAGAATACAATTc                                                                                                   <  1:296888/141‑1 (MQ=255)                         tgCTTGTTGTCCGCACTTCGGGCAAGATTTCATACTTTCACCTCAATTCTGTTCCTCTTCAATTGTTATATGTATATCACAAAAATTATTTCATTATTTTACCATTATTATTTTACAAATATTATCCCAAGAATACAATTc                                                                                                   >  1:304298/1‑141 (MQ=255)                           cTTGTTGTCCGCACTTCGGGCAAGATTTCATACTTTCACCTCAATTCTGTTCCTCTTCAATTGTTATATGTATATCACAAAAATTATTTCATTATTTTACCATTATTATTTTACAAATATTATCCCAAGAATACAATTCaa                                                                                                 <  1:23369/141‑1 (MQ=255)                             gcttgttgtccgcacttcgggcaagatttcatactttcacctcaattctgttcctcttcaattgttatatgtatatcacaaaaattatttcattattttaccATTATTTTACAAATATTATCCCAAGAATACAATTCAAGa                                                                                               <  1:209052‑M1/39‑1 (MQ=255)                             gcttgttgtccgcacttcgggcaagatttcatactttcacctcaattctgttcctcttcaattgttatatgtatatcacaaaaattatttcattattttaccATTATTTTACAAATATTATCCCAAGAATACAATTCAAGa                                                                                               <  1:139945‑M1/39‑1 (MQ=255)                                    cGCACTTCGGGCAAGATTTCATACTTTCACCTCAATTCTGTTCCTCTTCAATTGTTATATGTATATCACAAAAATTATTTCATTATTTTACCATTATTATTTTACAAATATTATCCCAAGAATACAATTCAAGAAATGAtt                                                                                        >  2:72887/1‑141 (MQ=255)                                           cGGGCAAGATTTCATACTTTCACCTCAATTCTGTTCCTCTTCAATTGTTATATGTATATCACAAAAATTATTTCATTATTTTACCATTATTATTTTACAAATATTATCCCAAGAATACAATTCAAGAAATGATTAacttta                                                                                 >  1:307066/1‑141 (MQ=255)                                           cGGGCAAGATTTCATACTTTCACCTCAATTCTGTTCCTCTTCAATTGTTATATGTATATCACAAAAATTATTTCATTATTTTACCATTATTATTTTACAAATATTATCCCAAGAATACAATTCAAGAAATGATTAacttta                                                                                 >  1:327717/1‑141 (MQ=255)                                           cGGGCAAGATTTCATACTTTCACCTCAATTCTGTTCCTCTTCAATTGTTATATGTATATCACAAAAATTATTTCATTATTTTACCATTATTATTTTACAAATATTATCCCAAGAATACAATTCAAGAAATGATTAacttta                                                                                 >  1:250652/1‑141 (MQ=255)                                                  gATTTCATACTTTCACCTCAATTCTGTTCCTCTTCAATTGTTATATGTATATCACAAAAATTATTTCATTATTTTACCATTATTATTTTACAAATATTATCCCAAGAATACAATTCAAGAAATGATTAACTTTACTTTAGa                                                                          >  1:290207/1‑141 (MQ=255)                                                  gATTTCATACTTTCACCTCAATTCTGTTCCTCTTCAATTGTTATATGTATATCACAAAAATTATTTCATTATTTTACCATTATTATTTTACAAATATTATCCCAAGAATACAATTCAAGAAATGATTAACTTTACTTTAGa                                                                          >  1:174831/1‑141 (MQ=255)                                                  gATTTCATACTTTCACCTCAATTCTGTTCCTCTTCAATTGTTATATGTATATCACAAAAATTATTTCATTATTTTACCATTATTATTTTACAAATATTATCCCAAGAATACAATTCAAGAAATGATTAACTTTACTTTAGa                                                                          >  2:153315/1‑141 (MQ=255)                                                       cATACTTTCACCTCAATTCTGTTCCTCTTCAATTGTTATATGTATATCACAAAAATTATTTCATTATTTTACCATTATTATTTTACAAATATTATCCCAAGAATACAATTCAAGAAATGATTAACTTTACTTTAGAATTGt                                                                     <  2:138344/141‑1 (MQ=255)                                                         tACTTTCACCTCAATTCTGTTCCTCTTCAATTGTTATATGTATATCACAAAAATTATTTCATTATTTTACCATTATTATTTTACAAATATTATCCCAAGAATACAATTCAAGAAATGATTAACTTTACTTTAGAATTGTAc                                                                   >  2:383972/1‑141 (MQ=255)                                                                aCCTCAATTCTGTTCCTCTTCAATTGTTATATGAAAAAAACAAAAATTATTTCATTATTTTACCATTATTATTTTACAAATATTATCCCAAGAATACAATTCAAGAAATGATTAACTTTACTTTAGAATTGTACCttatta                                                            <  2:364028/141‑1 (MQ=255)                                                                   tCAATTCTGTTCCTCTTCAATTGTTATATGTATATCACAAAAATTATTTCATTATTTTACCATTATTATTTTACAAATATTATCCCAAGAATACAATTCAAGAAATGATTAACTTTACTTTAGAATTGTACCTTATTACat                                                         >  2:374509/1‑141 (MQ=255)                                                                     ctcaattctgttcctcttcaattgttatatgtatatcacaaaaattatttcattattttaccATTATTTTACAAATATTATCCCAAGAATACAATTCAAGAAATGATTAACTTTACTTTAGAATTGTACCTTATTACatta                                                       <  2:105178‑M1/79‑1 (MQ=255)                                                                     ctcaattctgttcctcttcaattgttatatgtatatcacaaaaattatttcattattttaccATTATTTTACAAATATTATCCCAAGAATACAATTCAAGAAATGATTAACTTTACTTTAGAATTGTACCTTATTACatta                                                       <  1:399757‑M1/79‑1 (MQ=255)                                                                        tCTGTTCCTATTTAATTGTTATATGTATATCACAAAAATTATTTCATTATTTTACCATTATTATTTTACAAATATTATCCCAAGAATACAATTCAAGAAATGATTAACTTTACTTTAGAATTGTACCTTATTACAttattt                                                    <  2:115241/141‑1 (MQ=255)                                                                           gTTCCTCTTCAATTGTTATATGTATATCACAAAAATTATTTCATTATTTTACCATTATTATTTTACAAATATTATCCCAAGAATACAATTCAAGAAATGATTAACTTTACTTTAGAATTGTACCTTATTACATTATTTATg                                                 >  2:204618/1‑141 (MQ=255)                                                                             tCCTCTTCAATTGTTATATGTATATCACAAAAATTATTTCATTATTTTACCATTATTATTTTACAAATATTATCCCAAGAATACAATTCAAGAAATGATTAACTTTACTTTAGAATTGTACCTTATTACATTATTTATGaa                                               <  1:285328/141‑1 (MQ=255)                                                                                      aTTGTTATATGTATATCACAAAAATTATTTCATTATTTTACCATTATTATTTTACAAATATTATCCCAAGAATACAATTCAAGAAATGATTAACTTTACTTTAGAATTGTACCTTATTACATTATTTATGAAAGTActctc                                      >  2:13413/1‑141 (MQ=255)                                                                                      aTTGTTATATGTATATCACAAAAATTATTTCATTATTTTACCATTATTATTTTACAAATATTATCCCAAGAATACAATTCAAGAAATGATTAACTTTACTTTAGAATTGTACCTTATTACAATGGTTATTAAAGTActctc                                      >  1:230892/1‑141 (MQ=255)                                                                                                 atgtatatcacaaaaattatttcattattttaccATTATTTTACAAATATTATCCCAAGAATACAATTCAAGAAATGATTAACTTTACTTTAGAATTGTACCTTATTACATTATTTATGAAAGTACTCTCTCAATTATAAc                           >  2:209052‑M1/35‑141 (MQ=255)                                                                                                 atgtatatcacaaaaattatttcattattttaccATTATTTTACAAATATTATCCCAAGAATACAATTCAAGAAATGATTAACTTTACTTTAGAATTGTACCTTATTACATTATTTATGAAAGTACTCTCTCAATTATAAc                           >  2:139945‑M1/35‑141 (MQ=255)                                                                                                       acaAAAATTATTTCATTATTTTACCATTATTATTTTACAAATATTATCCCAAGAATACAATTCAAGAAATGATTAACTTTACTTTAGAATTGTACCTTATTACATTATTTATGGAAGTACTCTCTCAATTATAACTaaaaa                     <  2:90563/141‑1 (MQ=255)                                                                                                        caAAAATTATTTCATTATTTTACCATTATTATTTTACAAATATTATCCCAAGAATACAATTCAAGAAATGATTAACTTTACTTTAGAATTGTACCTTATTACATTATTTATGAAAGTACTCTCTCAATTATAACTAAAaag                    >  2:65102/1‑141 (MQ=255)                                                                                                        caAAAATTATTTCATTATTTTACCATTATTATTTTACAAATATTATCCCAAGAATACAATTCAAGAAATGATTAACTTTACTTTAGAATTGTACCTTATTACATTATTTATGAAAGTACTCTCTCAATTATAACTAAAaag                    >  2:114557/1‑141 (MQ=255)                                                                                                        caAAAATTATTTCATTATTTTACCATTATTATTTTACAAATATTATCCCAAGAATACAATTCAAGAAATGATTAACTTTACTTTAGAATTGTACCTTATTACATTATTTATGAAAGTACTCTCTCAATTATAACTAAAaag                    <  1:110020/141‑1 (MQ=255)                                                                                                             attattTCATTATTTTACCATTATTATTTTACAAATATTATCCCAAGAATACAATTCAAGAAATGATTAACTTTACTTTAGAATTGTACCTTATTACATTATTTATGAAAGTACTCTCTCAATTATAACTAAAAAGAAGgt               >  2:199014/1‑141 (MQ=255)                                                                                                                          tttACCATTATTATTTTACAAATATTATCCCAAGAATACAATTCAAGAAATGATTAACTTTACTTTAGAATTGTACCTTATTACATTATTTATGAAAGTACTCTCTCAATTATAACTAAAAAGAAGGTGTTCAatacatac  >  1:171217/1‑141 (MQ=255)                                                                                                                                   |                                                                                                                                    TGTACATATCTGTACATCATCTTGTGCTTGTTGTCCGCACTTCGGGCAAGATTTCATACTTTCACCTCAATTCTGTTCCTCTTCAATTGTTATATGTATATCACAAAAATTATTTCATTATTTTACCATTATTATTTTACAAATATTATCCCAAGAATACAATTCAAGAAATGATTAACTTTACTTTAGAATTGTACCTTATTACATTATTTATGAAAGTACTCTCTCAATTATAACTAAAAAGAAGGTGTTCAATACATAC  >  USA300TCH1516_ALE/2476199‑2476460

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ 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.