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

TTATGTCCACATTGTGTACATATCTGTACATCATCTTGTGCTTGTTGTCCGCACTTCGGGCAAGATTTCATACTTTCACCTCAATTCTGTTCCTCTTCAATTGTTATATGTATATCACAAAAATTATTTCATTATTTTACCATTATTATTTTACAAATATTATCCCAAGAATACAATTCAAGAAATGATTAACTTTACTTTAGAATTGTACCTTATTACATTATTTATGAAAGTACTCTCTCAATTATAACTAAAAAGAAGGTGTTCAATACATAC  >  USA300TCH1516_ALE/2476185‑2476460                                                                                                                                             |                                                                                                                                        ttATGTCCACATTGTGTACATATCTGTACATCATCTTGTGCTTGTTGTCCGCACTTCGGGCAAGATTTCATACTTTCACCTCAATTCTGTTCCTCTTCAATTGTTATATGTATATCACAAAAATTATTTCATTATTTTAcc                                                                                                                                         <  1:256295/141‑1 (MQ=255)               tgcaCATATCTGTACATCATCTTGTGCTTGTTGTCCGCACTTCGGGCAAGATTTCATACTTTCACCTCAATTCTGTTCCTCTTCAATTGTTATATGTATATCACAAAAATTATTTCATTATTTTACCATTATTATTTTACa                                                                                                                           >  1:138344/4‑141 (MQ=255)                gtACATATCTGTACATCATCTTGTGCTTGTTGTCCGCACTTCGGGCAAGATTTCATACTTTCACCTCAATTCTGTTCCTCTTCAATTGTTATATGTATATCACAAAAATTATTTCATTATTTTACCATTATTATTTTACaa                                                                                                                          >  2:89434/1‑141 (MQ=255)                 tACATATCTGTACATCATCTTGTGCTTGTTGTCCGCACTTCGGGCAAGATTTCATACTTTCACCTCAATTCTGTTCCTCTTCAATTGTTATATGTATATCACAAAAATTATTTCATTATTTTACCATTATTATTTTACaaa                                                                                                                         >  1:149698/1‑141 (MQ=255)                                catcTTGTGCTTGTTGTCCGCACTTCGGGCAAGATTTCATACTTTCACCTCAATTCTGTTCCTCTTCAATTGTTATATGTATATCACAAAAATTATTTCATTATTTTACCattattttacaaatattatcccaagaataca                                                                                                          <  1:2580‑M2/141‑32 (MQ=255)                                    ttGTGCTTGTTGTCCGCACTTCGGGCAAGATTTCATACTTTCACCTCAATTCTGTTCCTCTTCAATTGTTATATGTATATCACAAAAATTATTTCATTATTTTACCattattttacaaatattatcccaagaatacaattc                                                                                                      >  2:72874‑M2/1‑106 (MQ=255)                                    ttGTGCTTGTTGTCCGCACTTCGGGCAAGATTTCATACTTTCACCTCAATTCTGTTCCTCTTCAATTGTTATATGTATATCACAAAAATTATTTCATTATTTTACCattattttacaaatattatcccaagaatacaattc                                                                                                      >  1:24695‑M2/1‑106 (MQ=255)                                     tgtgCTTGTTGTCCGCACTTCGGGCAAGATTTCATACTTTCACCTCAATTCTGTTCCTCTTCAATTGTTATATGTATATCACAAAAATTATTTCATTATTTTACCATTATTATTTTACAAATATTATCCCAAGAATACAAt                                                                                                     <  2:99044/141‑1 (MQ=255)                                     tgtgCTTGTTGTCCGCACTTCGGGCAAGATTTCATACTTTCACCTCAATTCTGTTCCTCTTCAATTGTTATATGTATATCACAAAAATTATTTCATTATTTTACCATTATTATTTTACAAATATTATCCCAAGAATACAAt                                                                                                     <  2:264037/141‑1 (MQ=255)                                       tgCTTGTTGTCCGCACTTCGGGCAAGATTTCATACTTTCACCTCAATTCTGTTCCTCTTCAATTGTTATATGTATATCACAAAAATTATTTTATTATTTTACCATTATTATTTTACAAATATTATCCCAAGAATACAATTc                                                                                                   <  1:296888/141‑1 (MQ=255)                                       tgCTTGTTGTCCGCACTTCGGGCAAGATTTCATACTTTCACCTCAATTCTGTTCCTCTTCAATTGTTATATGTATATCACAAAAATTATTTCATTATTTTACCATTATTATTTTACAAATATTATCCCAAGAATACAATTc                                                                                                   >  1:304298/1‑141 (MQ=255)                                        gCTTGTTGTCCGCACTTCGGGCAAGATTTCATACTTTCACCTCAATTCTGTTCCTCTTCAATTGTTATATGTATATCACAAAAATTATTTCATTATTTTACCattattttacaaatattatcccaagaatacaattcaaga                                                                                                  <  1:139945‑M2/141‑40 (MQ=255)                                        gCTTGTTGTCCGCACTTCGGGCAAGATTTCATACTTTCACCTCAATTCTGTTCCTCTTCAATTGTTATATGTATATCACAAAAATTATTTCATTATTTTACCattattttacaaatattatcccaagaatacaattcaaga                                                                                                  <  1:209052‑M2/141‑40 (MQ=255)                                         cTTGTTGTCCGCACTTCGGGCAAGATTTCATACTTTCACCTCAATTCTGTTCCTCTTCAATTGTTATATGTATATCACAAAAATTATTTCATTATTTTACCATTATTATTTTACAAATATTATCCCAAGAATACAATTCaa                                                                                                 <  1:23369/141‑1 (MQ=255)                                                  cGCACTTCGGGCAAGATTTCATACTTTCACCTCAATTCTGTTCCTCTTCAATTGTTATATGTATATCACAAAAATTATTTCATTATTTTACCATTATTATTTTACAAATATTATCCCAAGAATACAATTCAAGAAATGAtt                                                                                        >  2:72887/1‑141 (MQ=255)                                                         cGGGCAAGATTTCATACTTTCACCTCAATTCTGTTCCTCTTCAATTGTTATATGTATATCACAAAAATTATTTCATTATTTTACCATTATTATTTTACAAATATTATCCCAAGAATACAATTCAAGAAATGATTAacttta                                                                                 >  1:250652/1‑141 (MQ=255)                                                         cGGGCAAGATTTCATACTTTCACCTCAATTCTGTTCCTCTTCAATTGTTATATGTATATCACAAAAATTATTTCATTATTTTACCATTATTATTTTACAAATATTATCCCAAGAATACAATTCAAGAAATGATTAacttta                                                                                 >  1:307066/1‑141 (MQ=255)                                                         cGGGCAAGATTTCATACTTTCACCTCAATTCTGTTCCTCTTCAATTGTTATATGTATATCACAAAAATTATTTCATTATTTTACCATTATTATTTTACAAATATTATCCCAAGAATACAATTCAAGAAATGATTAacttta                                                                                 >  1:327717/1‑141 (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)                                                                                cTCAATTCTGTTCCTCTTCAATTGTTATATGTATATCACAAAAATTATTTCATTATTTTACCattattttacaaatattatcccaagaatacaattcaagaaatgattaactttactttagaattgtaccttattacatta                                                          <  2:105178‑M2/141‑80 (MQ=255)                                                                                cTCAATTCTGTTCCTCTTCAATTGTTATATGTATATCACAAAAATTATTTCATTATTTTACCattattttacaaatattatcccaagaatacaattcaagaaatgattaactttactttagaattgtaccttattacatta                                                          <  1:399757‑M2/141‑80 (MQ=255)                                                                                 tCAATTCTGTTCCTCTTCAATTGTTATATGTATATCACAAAAATTATTTCATTATTTTACCATTATTATTTTACAAATATTATCCCAAGAATACAATTCAAGAAATGATTAACTTTACTTTAGAATTGTACCTTATTACat                                                         >  2:374509/1‑141 (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‑M2/1‑34 (MQ=255)                                                                                                            atGTATATCACAAAAATTATTTCATTATTTTACCattattttacaaatattatcccaagaatacaattcaagaaatgattaactttactttagaattgtaccttattacattatttatgaaagtactctctcaattataac                              >  2:139945‑M2/1‑34 (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)                                                                                                                                             |                                                                                                                                        TTATGTCCACATTGTGTACATATCTGTACATCATCTTGTGCTTGTTGTCCGCACTTCGGGCAAGATTTCATACTTTCACCTCAATTCTGTTCCTCTTCAATTGTTATATGTATATCACAAAAATTATTTCATTATTTTACCATTATTATTTTACAAATATTATCCCAAGAATACAATTCAAGAAATGATTAACTTTACTTTAGAATTGTACCTTATTACATTATTTATGAAAGTACTCTCTCAATTATAACTAAAAAGAAGGTGTTCAATACATAC  >  USA300TCH1516_ALE/2476185‑2476460

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.