New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	= 2442821	45 (0.870)	5 (0.110)	5/228	NT	11.6%	intergenic (+18/+40)	glvR/USA300HOU_RS12585	HTH‑type transcriptional regulator GlvR/hypothetical protein
	?	USA300TCH1516_ALE	= 2442838	37 (0.810)					intergenic (+35/+23)	glvR/USA300HOU_RS12585	HTH‑type transcriptional regulator GlvR/hypothetical protein

AGTAACACATTCTACTTAACTGATGGTACAGACTATTCTAGCTTCATCAGTTATCATATATTCTTTGAAACACTTGTAAGAAAATATAATGAGTATTTACTACATAATGATATTTCAAATTAGAAAAAAGGAAGTTATGATTTAATGGCCTTGAGCCTATCATAACTTCCTTTTATCATTTTATTGTTGTGTTGATGTTTCGATAACGTGGTACATCTTATCAAACATCAATTCGAAACCATGCACCATGGCATCATGATATTCTTTTTTCTTTTGC  >  USA300TCH1516_ALE/2442681‑2442957                                                                                                                                             |                                                                                                                                         aGTAACACATTCTACTTAACTGATGGTACAGACTATTCTAGCTTCATCAGTTATCATATATTCTTTGAAACACTTGTAAGAAAATATAATGAGTATTTACTACATAATGATATTTCAAATTAGAAAAAAGGAAGTTATGAT                                                                                                                                          <  1:36227‑M1/141‑1 (MQ=255)   tAACACATTCTACTTAACTGATGAGACAGACTATTCTAGCTTCATCAGTTATCATATATTCTTTGAAACACTTGTAAGAAAATATAATGAGTATTTACTACATAATGATATTTCAAATTAGAAAAAAGGAAGTTATGAttt                                                                                                                                        <  2:358140/141‑1 (MQ=255)      cacaTTCTACTTAACTGATGGTACAGACTATTCTAGCTTCATCAGTTATCATATATTCTTTGAAACACTTGTAAGAAAATATAATGAGTATTTACTACATAATGATATTTCAAATTAGAAAAAAGGAAGTTATGATTTAAt                                                                                                                                     <  1:569024/141‑1 (MQ=255)       acaTTCTACTTAACTGATGGTACAGACTATTCTAGCTTCATCAGTTATCATATATTCTTTGAAACACTTGTAAGAAAATATAATGAGTATTTACTACATAATGATATTTCAAATTAGAAAAAAGGAAGTTATGATTTAATg                                                                                                                                    >  2:422456/1‑141 (MQ=255)          ttCTACTTAACTGATGGTACAGACTATTCTAGCTTCATGAGTTATCATATATTCTTTGAAACACTTGTAAGAAAATATAATGAGTATTTACTACATAATGATATTTCAAATTAGAAAAAAGGAAGTTATGATTTAATGGcc                                                                                                                                 >  1:392625/1‑141 (MQ=255)          ttCTACTTAACTGATGGTACAGACTATTCTAGCTTCATCAGTTATCATATATTCTTTGAAACACTTGTAAGAAAATATAATGAGTATTTACTACATAATGATATTTCAAATTAGAAAAAAGGAAGTTATGATTTAATGGcc                                                                                                                                 <  1:152840/141‑1 (MQ=255)          ttCTACTTAACTGATGGTACAGACTATTCTAGCTTCATCAGTTATCATATATTCTTTGAAACACTTGTAAGAAAATATAATGAGTATTTACTACATAATGATATTTCAAATTAGAAAAAAGGAAGTTATGATTTAATGGcc                                                                                                                                 >  1:219348/1‑141 (MQ=255)            cTACTTAACTGATGGTACAGACTATTCTAGCTTCATCAGTTATCATATATTCTTAGACTCAGAGTTAAGAAAATATAATGAGTATTTACTACATAATGATATTTCAAATTAGAAAAAAGGAAGTTATGATTTAATGGCCtt                                                                                                                               <  1:443875/141‑1 (MQ=255)                  aaCTGATGGTACAGACTATTCTAGCTTCATCAGTTATCATATATTCTTTGAAACACTTGTAAGAAAATATAATGAGTATTTACTACATAATGATATTTCAAATTAGAAAAAAGGAAGTTATGATTTAATGGCCTTGAGCCt                                                                                                                         >  2:357726/1‑141 (MQ=255)                  aaCTAATGGTACCGACCATTCTAGCTTTATCAGTTATCATATATTCTTTGAAACACTTGTAAGAAAATATAATGAGTATTTATTACATAATGATATTTCAAATTATATAAAAGGAAGTTATGATaggctcaaggccattaa                                                                                                                         <  1:40815‑M1/141‑18 (MQ=255)                    ctgctcgTACAGCTTATTCTAGCTTCATCAGGTATTATATATTCTTTGAAACACTTGTAAGAAAATATAATGAGTATTTACTACATAATGATATTTCATATTAGAAAAAAGGAAGTTATGATTTAATGGCCTTGAGCCTAt                                                                                                                       <  2:173295/135‑1 (MQ=255)                            aCAGACTATTCTAGCTTCATCAGTTATCATATATTCTTTGAAACACTTGTAAGAAAATATAATGAGTATTTACTACATAATGATATTTCAAATTAGAAAAAAGGAAGTTATGATTTAATGGCCTTGAGCCTatcataaatt                                                                                                               <  1:576655‑M2/141‑11 (MQ=255)                                 cTATTCTAGCTTCATCAGTTATCATATATTCTTTGAAACACTTGTAAGAAAATATACTGCGTATTTACTACATAAAGAATTATCAAATTAGAAAAAAGGAAGTTATGATTTACTGGCCTTGAGCCTatcataacttccttt                                                                                                          <  2:218520‑M2/141‑16 (MQ=255)                                    ttttAGCTTCATAAGGAATGATAGAGTCTTGGAAACACTTATAGGAAAAGTTAATGAGTATTTTCCACATATTGATATTAAAAAAAAAAAAAAAGGAAGTTATGATTTAATGGCCTTGAGCCTATCATAACTTCCTTTTAt                                                                                                       <  2:103404/138‑1 (MQ=255)                                    ttCTAGCTTCATCAGTTATCATATATTCTTTGAAACACTTGTAAGAAAATATAATGAGTATTTACTACATAATGATATTTCAAATTAGAAAAAAGGAAGTTATGATTTAATGGCCTTGAGCCTATCATAACTTCCTTTTAt                                                                                                       <  1:300020/141‑1 (MQ=255)                                    ttCTAGCTCCATTAGTTATCATATATACCTTGAAACCCTTGTAAGAAAATATAAGGAGTATTTACTACATAATGATATTTCAAATTAGAAAAAAGGAAGTTATGATagtctcaaggccattcaatcataacttcctttttt                                                                                                       <  2:272561‑M1/141‑36 (MQ=255)                                      cTAGCTTCATCAGTTATCATATATTCTTTGAAACACTTGTAAGAAACAATAATGTTTTTGTACTACATAATGATATTTCAAATTAGAAAAAAGGAAGTTATGATTTAATGGCCTTGAGCCTATCATAACTTCCTTTTATCa                                                                                                     <  1:114966/141‑1 (MQ=255)                                       tAGTTTCATCAGTTATCTTATCTTCTTTGAAACACTTGTAAGAAAATATAATGAGTATTTACTACATAATGATATTTCAAATTAGAAAAAAGGAAGTTCTGATTTAATGGCCTTGAGCCTATCATAACTTCCTTTTATCAt                                                                                                    <  1:75936/141‑1 (MQ=255)                                         gCTTCATCAGTTATCATATATTCTTTGAAACACTTGTAAGAAAATATAATGAGTATTTACTACATAATGATATTTCAAATTAGAAAAAAGGAAGTTATGATTTAATGGCCTTGAGCCTATCATAACTTCCTTTTATCAttt                                                                                                  >  1:490120/1‑141 (MQ=255)                                         gCTTCATCAGTTATCATATATTCTTTGAAACACTTGTAAGAAAATATAATGAGTATTTACTACATAATGATATTTCAAATTAGAAAAAAGGAAGTTATGATTTAATGGCCTTGAGCCTATCATAACTTCCTTTTATCAttt                                                                                                  <  2:317977/141‑1 (MQ=255)                                            tcatcaGTTATCATATATTCTTTGAAACACTTGTAAGAAAATATAATGAGTATTTACTACATAATGATATTTCAAATTAGAAAAAAGGAAGTTATGATTTAATGGCCTTGAGCCTATCATAACTTCCTTTTATCATTTTAt                                                                                               <  2:391017/141‑1 (MQ=255)                                              atcaGTTATCATATATTCTTTGAAACACTTGTAAGAAAATATAATGAGTATTTACTACATAATGATATTTCAAATTAGAAAAAAGGAAGTTATGATTTAATGGCCTTGAGCCTATCATAACTTCCTTTTATCATTTTAttg                                                                                             <  2:543924/141‑1 (MQ=255)                                                   ttATCATATATTCTTTGAAACACTTGTAAGAAAATATAATGAGTATTTACTACATAATGATATTTCAAATTAGAAAAAAGGAAGTTATGATTTAATGGCCTTGAGCCTATCATAACTTCCTTTTATCATTTTATtgttgtg                                                                                        <  1:573287/141‑1 (MQ=255)                                                      tCATATATTCTTTGAAACACTTGTAAGAAAATATAATGAGTATTTACTACATAATGATATTTCAAATTAGAAAAAAGGAAGTTATGATTTAATGGCCCTGAGCCTATCATAACTTCCTTTTATCCTTTTAttgttttgttt                                                                                     >  1:587052/1‑140 (MQ=255)                                                      tCATATATTCTTTGAAACACTTGTAAAAAAATATAATGAGTATTTATTACATAATGATATTTCAAATTAGAAAAAA‑GAAGTTATGATaggctcaaggccattaaatcataacttccttttttctaatttgaaatatcatta                                                                                    <  2:31997‑M1/141‑55 (MQ=255)                                                                tttGAAACACTTGTAAGAAAATATAATGAGTATTTACTACATAATGATATTTCAAATTAGAAAAAAGGAAGTTATGATTTAATGGCCTTGAGCCTATCATAACTTCCTTTTATCATTTTATTGTTGTGTTGATGTTTCGAt                                                                           <  1:217514/141‑1 (MQ=255)                                                                 ttGAAACACTTGTAAGAAAATATAATGAGTATTTACTACATAATGATATTTCAAATTAGAAAAAAGGAAGTTATGATaggctcaaggccattaaatcataacttccttttttctaatttgaaatatcattatgtagtaaat                                                                          >  2:156228‑M1/1‑77 (MQ=255)                                                                 ttGAAACACTTGTAAGAAAATATAATGAGTATTTACTACATAATGATATTTCAAATTAGAAAAAAGGAAGTTATGATTTAATGGCCTTGAGCCTatcataacttccttttttctaatttgaaatatcattatgtagtaaat                                                                          <  1:156228‑M2/141‑48 (MQ=255)                                                                 ttGAAACACTTGTAAGAAAATATAATGAGTATTTACTACATAATGATATTTCAAATTAGAAAAAAGGAAGTTATGATTTAATGGCCTTGAGCCTATCATAACTTCCTTTTATCATTTTATTGTTGTGTTGATGTTTCGATa                                                                          >  2:561322/1‑141 (MQ=255)                                                                  tGAAACACTTGTAAGAAAATATAATGAGTATTTACTACATAATGATATTTCAAATTAGAAAAAAGGAAGTTATGATTTAATGGCCTTGAGCCTATCATAACTTCCTTTTATCATTTTATTGTTGTGTTGATGTTTCGAtga                                                                         >  2:81844/1‑139 (MQ=255)                                                                  tGAAACACTTGTAAGAAAATATAATGAGTATTTACTACATAATGATATTTCAAATTAGAAAAAAGGAAGTTATGATTTAATGGCCTTGAGCCTATCATAACTTCCTTTTATCATTTTATTGTTGTGTTGATGTTTCGATat                                                                         >  1:175182/1‑140 (MQ=255)                                                                   gAAACACTTGTAAGAAAATATAATGAGTATTTACTACATAATGATATTTCAAATTAGAAAAAAGGAAGTTATGATTTAATGGCCTTGAGCCTATCATAACTTCCTTTTATCATTTTATTGTTGTGTTGATGTTTCGATAAc                                                                        <  1:183122/141‑1 (MQ=255)                                                                      acacTTGTAAGAAAATATAATGAGTATTTACTACATAATGATATTTCAAATTAGAAAAAAGGAAGTTATGATTTAATGGCCTTGAGCCTATCATAACTTCCTTTTATCATTTTATTGTTGTGTTGATGTGTCGATAACTTg                                                                     >  2:475825/1‑141 (MQ=255)                                                                         cTTGTAAGAAAATATAATGAGTATTTACTACATAATGATATTTCAAATTAGAAAAAAGGAAGTTATGATTTAATGGCCTTGAGCCTATCATAACTTCCTTTTATCATTTTATTGTTGTGTTGATGTTTCGATAACGTGCTa                                                                  >  2:445538/1‑141 (MQ=255)                                                                           tGTAAGAAAATATAATGAGTATTTACTACATAATGATATTTCAAATTAGAAAAAAGGAAGTTATGATTTAATGGCCTTGAGCCTATCATAACTTCCTTTTATCATTTTATTGTTGTGTTGATGTTTCGATAACGTGGTCCa                                                                >  2:149744/1‑141 (MQ=255)                                                                            gTAAGAAAATATAATGAGTATTTACTACATAATGATATTTCAAATTAGAAAAAAGGAAGTTATGATTTAATGGCCTTGAGCCTATCATAACTTCCTTTTATCATTTTATTGTTGTGTTGATGTTTCGATAACGTGGTACAt                                                               <  1:599294/141‑1 (MQ=255)                                                                             tAAGAAAATATAATGAGTATTTACTACATAATGATATTTCAAATTAGAAAAAAGGAAGTTATGATTTAATGGCCTTGAGCCTATCATAACTTCCTTTTATCATTTTATTGTTGTGTTGATGTTTCGATAACGTGGTACATc                                                              <  2:77853/141‑1 (MQ=255)                                                                                     tataATGAGTATTTACTACATAATGATATTTCAAATTAGAAAAAAGGAAGTTATGATTTAATGGCCTTGAGCCTATCATAACTTCCTTTTATCATTTTATTGTTGTGTTGATGTTTCGATAACGTGGTACATCTTATCaaa                                                      >  2:253477/1‑141 (MQ=255)                                                                                               aTTTACTACATAATGATATTTCAAATTAGAAAAAAGGAAGTTATGATaggctcaaggccattaaatcataacttccttttttctaatttgaaatatcattatgtagtaaatactcattatattttcttacaagtgtttcaa                                            <  1:156228‑M1/141‑95 (MQ=255)                                                                                               aTTTACTACATAATGATATTTCAAATTAGAAAAAAGGAAGTTATGATTTAATGGCCTTGAGCCTatcataacttccttttttctaatttgaaatatcattatgtagtaaatactcattatattttcttacaagtgtttcaa                                            >  2:156228‑M2/1‑64 (MQ=255)                                                                                               aTTTACTACATAATGAAATTTCAAATTAGAAAAAAGGAAGTTATGATTTAATGGCCTTGAGCCTATCATAACTTCCTTTTATCATTTTATTGTTGTGTTGATGTTTCGATAACGTGGTACATCTTATCAAACATCAATTCg                                            <  1:76824/141‑1 (MQ=255)                                                                                                tttACTACATAATGATATTTCAAATTAGAAAAAAGGAAGTTATGATTTAATGGCCTTGAGCCTATCATAACTTCCTTTTATCATTTTATTGTTGTGTTGATGTTTCGATAACGTGGTACATCTTATCAAACATCAATTCGa                                           <  1:357726/141‑1 (MQ=255)                                                                                                tttACTACATAATGATATTTAAAATTAGAAAAAAGGAAGTTATGATTTAATGGCCTTGAGCCTATCATAACTTCCTTTTATCATTTTATTGTTGTGTTGATGTTTCGATAACGTGGTACATCTTATCAAACATCAATTCGa                                           <  2:91942/141‑1 (MQ=255)                                                                                                   actacATAATGATATTTCAAATTAGAAAAAAGGAAGTTATGATTTAATGGCCTTGAGCCTATCATAACTTCCTTTTATCATTTTATTGTTGTGTTGATGTTTCGATAACGTGGTACATCTTATCAAACATCAATTCGAAAc                                        >  2:267555/1‑141 (MQ=255)                                                                                                    ctaaATAAAGATATTTCAAATTAGAAAAAAGGAAGTTATGATTTAATGGCCTTGAACCGCTTATCACTTCCTTTTATCATTTTATTATTGTGTTGATATTTCGATAACGTTGTACATCTTCTCAAACATCAATTCGataac                                       >  2:155419/1‑137 (MQ=255)                                                                                                     tacATAATGATATTTCAAATTAGAAAAAAGGAAGTTATGATTTAATGGCCTTGAGCCTATCATAACTTCCTTTTATCATTTTATTGTTGTGTTGATGTTTCGATAACGTGGTACATCTTATCAAACATCAATTCGAAACCa                                      <  1:49443/141‑1 (MQ=255)                                                                                                         tAATGATATTTCAAATTAGAAAAAAGGAAGTTATGATTTAATGGCCTTGAGCCTatcataacttcttttttctaatttgaaatatcattatgtaataaatactcattatatttttttacaagtgtttcaaagaatatatga                                  <  2:31997‑M2/141‑88 (MQ=255)                                                                                                              atatTTCAAATTAGAAAAAAGGAAGTTATGATTTAATGGCCTTGAGCCTATCATAACTTCCTTTTATCATTTTATTGTTGTGTTGATGTTTCGATAACGTGGTACATCTTATCAAACATCAATTCGAAACCATGCACCATg                             >  2:461397/1‑141 (MQ=255)                                                                                                              atatTTCAAATTAGAAAAAAGGAAGTTATGATTTAATGGCCTTGAGCCTATCATAACTTCCTTTTATCATTTTATTGTTGTGTTGATGTTTCGATAACGTGGTACATCTTATCAAACATCAATTCGAAACCATGCACCATg                             >  2:602189/1‑141 (MQ=255)                                                                                                                     aaaTTAGAAAAAAGGAAGTTATGATTTAATGGCCTTGAGCCTATCATAACTTCCTTTTATCATTTTATTGTTGTGTTGATGTTTCGATAACGTGGTACATCTTATCAAACATCAATTCGAAACCATGCGCCATGTcatcat                      >  1:71798/1‑141 (MQ=255)                                                                                                                          aGAAAAAAGGAAGTTATGATTTAATGGCCTTGAGCCTATCATAACTTCCTTTTATCATTTTATTGTTGTGTTGATGTTTCGATAACGTGGTACATCTTATCAAACATCAATTCGAAACCATGCACCATGGCATCATGatat                 >  1:596631/1‑141 (MQ=255)                                                                                                                          aGAAAAAAGGAAGTTATGATTTAATGGCCTTGAGCCTATCATAACTTCCGTATATCATTTTATTGTTGTGTTGATGCTTCGATAACGTGGTACATCTTATAAAACAGCAATTCGAAACCATGCACCCTCGCACCATGatat                 >  2:478350/1‑141 (MQ=255)                                                                                                                            aaaaaaGGAAGTTATGATTTAATGGCCTTGAGCCTATCATAACTTCCTTTTATCATTTTATTGTTGTGTTGATGTTTCGATAACGTGGTACATCTTATCAAACATCAATTCGAAACCATGCACCATGGCATCATGATAttc               <  1:101518/141‑1 (MQ=255)                                                                                                                            aaaaaaGGAAGTTATGATTGAATGGCCTTGAGACTatcataacttccttttttctaatttgaaatatcattatgtagtaaatactccttatattttcttacaagggtttcaaggtatatatgataactaatggagctagaa               <  2:272561‑M2/141‑107 (MQ=255)                                                                                                                             aaaaaGGAAGTTATGATTTAATGGCCTTGAGCCTATCATAACTTCCTTTTATCATTTTATTGTTGTGTTGATGTTTCGATAACGTGGTACATCTTATCAAACATCAATTCGAAACCATGCACCATGGCATCATGATAttct              >  2:485592/1‑141 (MQ=255)                                                                                                                              aaaaGGAAGTTATGATTTAATGGCCTTGAGCCTATCATAACTTCCTTTTATCATTTTATTGTTGTGTTGATGTTTCGATAACGTGGTACATCTTATCAAACATCAATTCGAAACCATGCACCATGGCATCATGATAttctt             >  2:113307/1‑141 (MQ=255)                                                                                                                               aaaGGAAGTTATGATaggctcaaggccagtaaatcataacttccttttttctaatttgataattctttatgtagtaaatacgcagtatattttcttacaagtgtttcaaagaatatatgataactgatgaagctagaatag            <  2:218520‑M1/141‑127 (MQ=255)                                                                                                                                    aatttatgATaggctcaaggccattaaatcataacttccttttttctaatttgaaatatcattatgtagtaaatactcattatattttcttacaagtgtttcaaagaatatatgataactgatgaagctagaatagtctgt       <  1:576655‑M1/138‑132 (MQ=255)                                                                                                                                    aaGTTATTATTTAATGGCCTTGAGCCTATCATAACTTCCTTTTATCATTTTATTGTTGTGTTGATGTTTCGATAACGTGGTACATCTTATCAAACATCAATTCGAAACCATGCACCATGGCATCATGATAttcttttttct       <  1:179595/141‑1 (MQ=255)                                                                                                                                     aGTTATGATTTAATGGCCTTGAGCCTATCATAACTTCCTTTTATCATTTTATTGTTGGGTTGATGTTTCGATAACGTGGTACATCTTATCAAACATCAATTCGAAACCATGCACCATGGCATCATGATAttcttttttctt      >  1:327620/1‑141 (MQ=255)                                                                                                                                        tATGATTTAATGGCCTTGAGCCTATCATAACTTCCTTTTATCATTTTATTGTTGTGTTGATGTTTCGATAACGTGGTACATCTTATCAAACATCAATTCGAAACCATGCACCATGGCATCATGATATTCTTTTTTCTTTTg   <  1:580207/141‑1 (MQ=255)                                                                                                                                         aTGATTTAATGGCCTTGAGCCTATCATAACTTCCTTTTATCATTTTATTGTTGTGTTGATGTTTCGATAACGTGGTACATCTTATCAAACATCAATTCGAAACCATGCACCATGGCATCATGATATTCTTTTTTCTTTTGc  <  1:74251/141‑1 (MQ=255)                                                                                                                                             |                                                                                                                                         AGTAACACATTCTACTTAACTGATGGTACAGACTATTCTAGCTTCATCAGTTATCATATATTCTTTGAAACACTTGTAAGAAAATATAATGAGTATTTACTACATAATGATATTTCAAATTAGAAAAAAGGAAGTTATGATTTAATGGCCTTGAGCCTATCATAACTTCCTTTTATCATTTTATTGTTGTGTTGATGTTTCGATAACGTGGTACATCTTATCAAACATCAATTCGAAACCATGCACCATGGCATCATGATATTCTTTTTTCTTTTGC  >  USA300TCH1516_ALE/2442681‑2442957

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.