New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	= 368778	52 (1.130)	3 (0.070)	3/250	NT	6.4%	intergenic (+212/+66)	bglK/ybbH_2	Beta‑glucoside kinase/putative HTH‑type transcriptional regulator YbbH
	?	USA300TCH1516_ALE	= 368819	38 (0.860)					intergenic (+253/+25)	bglK/ybbH_2	Beta‑glucoside kinase/putative HTH‑type transcriptional regulator YbbH

ACCAACAGTGTGCCACGGGCAAATTAAATTGAAGAAGCTGAGATATTAAAATTTTAGAAAATGTAAAAAAATATTTGGTATTGAAATTAAAAAAGCACCTAGCAACTCGTTGGGACAATCACGATGATTGTCTACAGTTGCAGGTGGATTTGAATATACTACTAGTTATTTGTTGTCTAGGATAATAGATTTAGTATGTTGATAAGTTTGACTCAGATTCGTATTTTCTAATAAATGATAACTCACGATATCGATTAAAAAGAGTGTCGCAATT  >  USA300TCH1516_ALE/368679‑368952                                                                                                                                             |                                                                                                                                      accaacAGTGTGCCACGGGCAAATTAAATTGAAGAAGCTGAGATATTAAAATTTTAGAAAATGTAAAAAAATATTTGGTATTGAAATTAAAAAAGCACCTAGCAACTCGTTGGGACAATCACGATGATTGTCTACAGTTGc                                                                                                                                       <  1:767670/141‑1 (MQ=255)     aCAGTGTGCCACGGGCAAATTAAATTGAAGAAGCTGAGATATTAAAATTTTAGAAAATGTAAAAAAATATTTGGTATTGAAATTAAAAAAGCACCTAGCAACTCGTTGGGACAATCACGATGATTGTCTACAGTTGCaggt                                                                                                                                   >  2:43914‑M2/1‑137 (MQ=255)      cAGTGTGCCACGGGCAAATTAAATTGAAGAAGCTGAGATATTAAAATTTTAGAAAATGTAAAAAAATATTTGGTATTGAAATTAAAAAAGCACCTAGCAACTCGTTGGGACAATCACGATGATTGTCTACAGTTGCaggtg                                                                                                                                  <  1:648858‑M2/141‑6 (MQ=255)       aGTGTGCCACGGGCAAATTAAATTGAAGAAGCTGAGATATTAAAATTTTAGAAAATGTAAAAAAATAGTTGGTATTGAAATTAAAAAAGCACCTAGCAACTCGTTGGGACAATCACGATGATTGTCTACAGTTGCAGGTgg                                                                                                                                 >  1:163972/1‑141 (MQ=255)          gtgCCACGGGCAAATTAAATTGAAGAAGCTGAGATATTAAAATTTTAGAAAATGTAAAAAAATATTTGGTATTGAAATTAAAAAAGCACCTAGCAACTCGTTGGGACAATCACGATGATTGTCTACAGTTGCAGGTGGAtt                                                                                                                              >  2:55862/1‑141 (MQ=255)          gtgCCACGGACAAATTAAATTGAAGAAGCTGAGATATTAAAATTTTAGAAAATGTAAACAAATATTTGGTATTGAAATTAAAAAAGCACCTAGCAACTCGTTGGGACAATCACGATGATTGTCTACAGTTGCAGGTGGAtt                                                                                                                              <  1:590854/141‑1 (MQ=255)           tgCCACGGGCAAATTAAATTGAAGAAGCTGAGATATTAAAATTTTAGAAAATGTAAAAAAATATTTGGTATTGAAATTAAAAAAGCACCTAGCAACTCGTTGGGACAATCACGATGATTGTCTACAGTTGCAGGTGGAttt                                                                                                                             >  2:325014/1‑141 (MQ=255)           tgCCACGGGCAAATTAAATTGAAGAAGCTGAGATATTAAAATTTTAGAAAATGTAAAAAAATATTTGGTATTGAAATTAAAAAAGCACCTAGCAACTCGTTGGGACAATCACGATGATTGTCTACAGTTGCAGGTGGAttt                                                                                                                             <  1:473973/141‑1 (MQ=255)           tgCCACGGGCAAATTAAATTGAAGAAGCTGAGATATTAAAATTTTAGAAAATGTAAAAAAATATTTGGTATTGAAATTAAAAAAGCACCTAGCAACTCGTTGGGACAATCACGATGATTGTCTACAGTTGCAGGTGGAttt                                                                                                                             <  1:372956/141‑1 (MQ=255)           tgCCACGGGCAAATTAAATTGAAGAAGCTGAGATATTAAAATTTTAGAAAATGAAAAAAAATATTTGGTATTGAAATTAAAAAAGCACCTAGCAACTCGTTGGGACAATCACGATGATTGTCTACAGTTGCAGGTGGAttt                                                                                                                             >  1:595530/1‑141 (MQ=255)                          aaattGAAGAAGCTGAGATATTAAAATTTTAGAAAATGTAAAAAAATATTTGGTATTGAAATTAAAAAAGCACCTAGCAACTCGTTGGGACAATCACGATGATTGTCTACAGTTGCAGGTGGATTTGAATATACTACTAGt                                                                                                              <  2:225019/141‑1 (MQ=255)                             ttGAAGAAGCTGAGATATTAAAATTTTAGAAAATGTAAAAAAATATTTGGTATTGAAATTAAAAAAGCACCTAGCAACTCGTTGGGACAATCACGATGATTGTCTACAGTTGCAGGTGGATTTGAATATACTACTAGTTAt                                                                                                           >  1:337821/1‑141 (MQ=255)                              tGAAGAAGCTGAGATATTAAAATTTTAGAAAATGTAAAAAAATATTTGGTATTGAAATTAAAAAAGCACCTAGCAACTCGTTGGGACAATCACGATGATTGTCTACAGTTGCAGGTGGATTTGAATATACTACTAGTTAtt                                                                                                          <  1:194926/141‑1 (MQ=255)                                 agaagCTTATATATTAAAATTTTAGAAAATGTAAAAAAATATTTGGTATTGAAATTAAAAAAGCACCTAGCAACTCGTTGGGACAATCACGATGATTGTCTACAGTTGCAGGTGGATTTGAATATACTACTAGTTATttgt                                                                                                       <  1:144811/141‑1 (MQ=255)                                    aacTGAGGTATTAAAATTTTAGACAATGTAAAAAAATATTTGGTATTGAAATTAAAAAAGCACCTAGCAACTCGTTGGGACAATCACGATGATTGTCTACAGTTGCAGGTGGATTTGAATATACTACTAGTTATTtgttgt                                                                                                    <  1:755664/139‑1 (MQ=255)                                       tGAGATATTAAAATTTTAGAAAATGTAAAAAAATATTTGGTATTGAAATTAAAAAAGCACCTAGCAACTCGTTGGGACAATCACGATGATTGTCTACAGTTGCAGGTGGATTTGAATATACTACTAGTTATTTGTTGTCTa                                                                                                 >  1:751770/1‑141 (MQ=255)                                         agaTATTAACATTTTAGAAAATGTAAAAAAATATTTGGTATTGAAATTAAAAAAGCACCTAGCAACTCGTTGGGACAATCACGATGATTGTCTACAGTTGCAGGTGGATTTGAATATACTACTAGTTATTTGTTGTCTAgg                                                                                               >  1:692415/1‑141 (MQ=255)                                            tatTAAAATTTTAGAAAATGTAAAAAAATATTTGGTATTGAAATTAAAAAAGCACCTAGCAACTCGTTGGGACAATCACGATGATTGTCTACAGTTGCAGGTGGATTTGAATATACTACTAGTTATTTGTTGTCTAGGata                                                                                            <  1:240037/141‑1 (MQ=255)                                                    ttttAGAAAATGTAAAAAAATATTTGGTATTGAAATTAAAAAAGCACCTAGCAACTCGTTGGGACAATCACGATGATTGTCTACAGTTGCAGGTGGATTTGAATATACTACTAGTTATTTGTTGTCTAGGATAATAGAttt                                                                                    <  1:45324/141‑1 (MQ=255)                                                     tttAGAAAATGTAAAAAAATATTTGGTATTGAAATTAAAAAAGCACCTAGCAACTCGTTGGGACAATCACGATGATTGTCTACAGTTGCAGGTGGATTTGAATATACTACTAGTTATTTGTTGTCTAGGATAATAGATTTa                                                                                   >  2:71800/1‑141 (MQ=255)                                                        aGAAAATGTAAAAAAATATTTGGTATTGAAATTAAAAAAGCACCTAGCAACTCGTTGGGACAATCACGATGATTGTCTACAGTTGCAGGTGGATTTGAATATACTACTAGTTATTTGTTGTCTAGGATAATAGATTTAGTa                                                                                >  2:21966/1‑141 (MQ=255)                                                         gAAAATGTAAAAAAATATTTGGTATTGAAATTAAAAAAGCACCTAGCAACTCGTTGGGACAATCACGATGATTGTCTACAGTTGCAGGTGGATTTGAATATACTACTAGTTATTTGTTGTCTAGGATAATAGATTTAGTAt                                                                               <  1:768560/141‑1 (MQ=255)                                                           aaaTGTAAAAAAATATTTGGTATTGAAATTAAAAAAGCACCTAGCAACTCGTTGGGACAATCACGATGATTGTCTACAGTTGCAGGTGGATTTGAATATACTACTAGTTATTTGTTGTCTAGGATAATAGATTTAGTATGt                                                                             <  1:473564/141‑1 (MQ=255)                                                            aaTGTAAAAAAATATTTGGTATTGAAATTAAAAAAGCACCTAGCAACTCGTTGGGACAATCACGATGATTGTCTACAGTTGCAGGTGGATTTGAATATACTACTAGTTATTTGTTGTCTAGGATAATAGATTTAGTATGtt                                                                            <  1:196400/141‑1 (MQ=255)                                                            aaTGTAAAAAAATATTTGGTATTGAAATTAAAAAAGCACCTAGCAACTCGTTGGGACAATCACGATGATTGTCTACAGTTGCAGGTGGATTTGAATATACTACTAGTTATTTGTTGTCTAGGATAATAGATTTAGTATGtt                                                                            <  1:222145/141‑1 (MQ=255)                                                            aaTGTAAAAAAATATTTGGTATTGAAATTAAAAAAGCACCTAGCAACTCGTTGGGACAATCACGATGATTGTCTACAGTTGCAGGTGGATTTGAATATACTACTAGTTATTTGTTGTCTAGGATAATAGATGTAGTATGtt                                                                            <  1:693690/141‑1 (MQ=255)                                                               gTAAAAAAATATTTGGTATTGAAATTAAAAAAGCACCTAGCAACTCGTTGGGACAATCACGATGATTGTCTACAGTTGCAGGTGGATTTGAATATACTACTAGTTATTTGTTGTCTAGGATAATAGATTTAGTATGTTGAt                                                                         >  1:535051/1‑141 (MQ=255)                                                                   aaaaaTATTTGGTATTGAAATTAAAAAAGCACCTAGCAACTCGTTGGGACAATCACGATGATTGTCTACAGTTGCAGGTGGATTTGAATATACTACTAGTTATTTGTTGTCTAGGATAATAGATTTAGTATGTTGATAAGt                                                                     <  1:523458/141‑1 (MQ=255)                                                                   aaaaaTATTTGGTATTGAAATTAAAAAAGCACCTAGCAACTCGTTGGGACAATCACGATGATTGTCTACAGTTGCAGGTGGATTTGAATATACTACTAGTTATTTGTTGTCTAGGATAATAGATTTAGTATGTTGATAAGt                                                                     >  1:232848/1‑141 (MQ=255)                                                                       atatTTGGTATTGAAATTAAAAAAGCACCTAGCAACTCGTTGGGACAATCACGATGATTGTCTACAGTTGCAGGTGGATTTGAATATACTACTAGTTATTTGTTGTCTAGGATAATAGATTTAGTATGTTGATAAGTTTGa                                                                 <  1:437307/141‑1 (MQ=255)                                                                       atatTTGGTATTGAAATTAAAAAAGCACCTAGCAACTCGTTGAGACAATCACGATGATTGTCTACAGTTGCAGGTGGATTTTAATATACTACTAGTTATTTGTTGTCTAGGATAATAGATTTAGTATGTTGATAAGTTTGa                                                                 <  2:224418/141‑1 (MQ=255)                                                                         atTTGGTATTGAAATTAAAAAAGCACCTAGCAACTCGTTGGGACAATCACGATGATTGTCTACAGTTGCAGGTGGATTTGAATATACTACTAGTTATTTGTTGTCTAGGATAATAGATTTAGTATGTTGATAAGTTTGACt                                                               >  2:38699/1‑141 (MQ=255)                                                                         atTTGGTATTGAAATTAAAAAAGCACCTAGCAACTCGTTGGGACAATCACGATGATTGTCTACAGTTGCAGGTGGATTTGAATATACTACTAGTTATTTGTTGTCTAGGATAATAGATTTAGTATGTTGATAAGTTTGACt                                                               >  2:69134/1‑141 (MQ=255)                                                                            tGGTATTGAAATTAAAAAAGCACCTAGCAACTCGTTGGGACAATCACGATGATTGTCTACAGTTGCtaggtgcttttttaatttcaataccaaatatttttttacattttctaaaattttaatatctcagcttcttcaatt                                                            <  1:738873‑M2/141‑76 (MQ=255)                                                                            tGGTATTGAAATTAAAAAAGCACCTAGCAACTCGTTGGGACAATCACGATGATTGTCTACAGTTGCAGGTGGATTTGAATATACTACTAGTTATTTGTTGTCTAGGATAATAGATTTAGTATGTTGATAAGTTTGACTCAg                                                            >  1:79069/1‑141 (MQ=255)                                                                                aTTGAAATTAAAAAAGCACCTAGCAACTCGTTGGGACAATCACGATGATTGTCTACAGTTGCAGGTGGATTTGAATATACTACTAGTTATTTGTTGTCTAGGATAATAGATTTAGTATGTTGATAAGTTTGACTCAGATTc                                                        <  1:737575/141‑1 (MQ=255)                                                                                aTTGAAATTAAAAAAGCACCTAGCAACTCGTTGGGACAATCACGATGATTGTCTACAGTTGCAGGTGGATTTGAATATACTACTAGTTATTTGTTGTCTAGGATAATAGATTTAGTATGTTGATAAGTTTGACTCAGATTc                                                        <  2:168423/141‑1 (MQ=255)                                                                                 ttGAAATTAAAAAAGCACCTAGCAACTCGTTGGGACAATCACGATGATTGTCTACAGTTGCAGGTGGATTTGAATATACTACTAGTTATTTGTTGTCTAGGATAATAGATTTAGTATGTTGATAAGTTTGACTCAGATTCg                                                       <  1:10882/141‑1 (MQ=255)                                                                                   gAAATTAAAAAAGCACCTAGCAACTCGTTGGGACAATCACGATGATTGTCTACAGTTGCAGGTGGATTTGAATATACTACTAGTTATTTGTTGTCTAGGATAATAGATTTAGTATGTTGATAAGTTTGACTCAGATTCGTa                                                     <  1:87609/141‑1 (MQ=255)                                                                                      aTTAAAAAAGCACCTAGCAACTCGTTGGGACAATCACGATGATTGTCTACAGTTGCTGGTGGATTTGAATATACTACTAGTTATTTGTTGTCTAGGATAATAGATTTAGTATGTTGATAAGTTTGACTCAGATTCGTAttt                                                  <  1:624260/141‑1 (MQ=255)                                                                                      aTTAAAAAAGCACCTAGCAACTCGTTGGGACAATCACGATGATTGTCTACAGTTGCAGGTGGATTTGAATATACTACTAGTTATTTGTTGTCTAGGATAATAGATTTAGTATGTTGATAAGTTTGACTCAGATTCGTAttt                                                  >  1:258303/1‑141 (MQ=255)                                                                                           aaaaGCACCTAGCAACTCGTTGGGACAATCACGATGATTGTCTACAGTTGCAGGTGGATTTGAATATACTACTAGTTATTTGTTGTCTAGGATAATAGATTTAGTATGTTGATAAGTTTGACTCAGATTCGTATTTTCtaa                                             <  2:12558/141‑1 (MQ=255)                                                                                             aaGCACCTAGCAACTCGTTGGGACAATCACGATGATTGTCTACAGTTGCAGGTGGATTTGAATATACTACTAGTTATTTGTTGTCTAGGATAATAGATTTAGTATGTTGATAAGTTTGACTCAGATTCGTATTTTCtaata                                           >  1:734712/1‑141 (MQ=255)                                                                                               gCACCTAGCAACTCGTTGGGACAATCACGATGATTGTCTACAGTTGCaggtgcttttttaatttcaataccaaatatttttttacattttctaaaattttaatatctcagcttcttcaatttaatttgcccgtggcacact                                         <  1:441502‑M2/141‑95 (MQ=255)                                                                                                cACCTAGCAACTCGTTGGGACAATCACGATGATTGTCTACAGTTGCAGGTGGATTTGAATATACTACTAGTTATTTGTTGTCTAGGATAATAGATTTAGTATGTTGATAAGTTTGACTCAGATTCGTATTTTCTAATAAAt                                        >  1:161164/1‑141 (MQ=255)                                                                                                          cTCGTTGGGACAATCACGATGATTGTCTACAGTTGCaggtgcttttttaatttcaataccaaatatttttttacattttctaaaattttaatatctcagcttcttcaatttaatttgcccgtggcacactgttggttgata                              <  1:58584‑M2/141‑106 (MQ=255)                                                                                                                       tCACGATGATTGTCTACAGTTGCAGGTGGATTTGAATATACTACTAGTTATTTGTTGTCTAGGATAATAGATTTAGTATGTTGATAAGTTTGACTCAGATTCGTATTTTCTAATAAATGATAACTCACGATATCGATTaaa                 <  1:348774/141‑1 (MQ=255)                                                                                                                        cACGATGATTGTCTACAGTTGCAGGTGGATTTGAATATACTACTAGTTATTTGTTGTCTAGGATAATAGATTTAGTATGTTGATAAGTTTGACTCAGATTCGTATTTTCTAATAAATGATAACTCACGATATCGATTaaaa                <  1:186045/141‑1 (MQ=255)                                                                                                                                 tGTCTACAGTTGCAGGTGTATTTGAATATACTACTAGTTATTTGTTGTCTAGGATAATAGATTTAGTATGTTGATAAGTTTGACTCAGATTCGTATTTTCTAATAAATGATAACTCACGATATCGATTAAAAAGAGTGTCg       <  1:439701/141‑1 (MQ=255)                                                                                                                                  gTCTACAGTTGCAGGTGGATTTGAATATACTACTAGTTATTTGTTGTCTAGGATAATAGATTTAGTATGTTGATAAGTTTGACTCAGATTCGTATTTTCTAATAAATGATAACTCACGATATCGATTAAAAAGAGTGTCGc      <  1:53113/141‑1 (MQ=255)                                                                                                                                      aCAGTTGCAGGTGGATTTGAATATACTACTAGTTATTTGTTGTCTAGGATAATAGATTTAGTATGTTGATAAGTTTGACTCAGATTCGTATTTTCTAATAAATGATAACTCACGATATCGATTAAAAAGAGTGTCGCAAtt  <  2:143069/141‑1 (MQ=255)                                                                                                                                             |                                                                                                                                      ACCAACAGTGTGCCACGGGCAAATTAAATTGAAGAAGCTGAGATATTAAAATTTTAGAAAATGTAAAAAAATATTTGGTATTGAAATTAAAAAAGCACCTAGCAACTCGTTGGGACAATCACGATGATTGTCTACAGTTGCAGGTGGATTTGAATATACTACTAGTTATTTGTTGTCTAGGATAATAGATTTAGTATGTTGATAAGTTTGACTCAGATTCGTATTTTCTAATAAATGATAACTCACGATATCGATTAAAAAGAGTGTCGCAATT  >  USA300TCH1516_ALE/368679‑368952

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