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

AACTGATGGTACAGACTATTCTAGCTTCATCAGTTATCATATATTCTTTGAAACACTTGTAAGAAAATATAATGAGTATTTACTACATAATGATATTTCAAATTAGAAAAAAGGAAGTTATGATTTAATGGCCTTGAGCCTATCATAACTTCCTTTTATCATTTTATTGTTGTGTTGATGTTTCGATAACGTGGTACATCTTATCAAACATCAATTCGAAACCATGCACCATGGCATCATGATATTCTTTTTTCTTTTGCTTGTATTCTAAATTAGTAA  >  USA300TCH1516_ALE/2442698‑2442976                                                                                                                                             |                                                                                                                                           aaCTGATGGTACAGACTATTCTAGCTTCATCAGTTATCATATATTCTTTGAAACACTTGTAAGAAAATATAATGAGTATTTACTACATAATGATATTTCAAATTAGAAAAAAGGAAGTTATGATTTAATGGCCTTGAGCCt                                                                                                                                            >  2:357726/1‑141 (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)                     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)                                               tttGAAACACTTGTAAGAAAATATAATGAGTATTTACTACATAATGATATTTCAAATTAGAAAAAAGGAAGTTATGATTTAATGGCCTTGAGCCTATCATAACTTCCTTTTATCATTTTATTGTTGTGTTGATGTTTCGAt                                                                                              <  1:217514/141‑1 (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)                                                                              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                                                >  2:602189/1‑141 (MQ=255)                                                                                             atatTTCAAATTAGAAAAAAGGAAGTTATGATTTAATGGCCTTGAGCCTATCATAACTTCCTTTTATCATTTTATTGTTGTGTTGATGTTTCGATAACGTGGTACATCTTATCAAACATCAATTCGAAACCATGCACCATg                                                >  2:461397/1‑141 (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)                                                                                                                   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)                                                                                                                             ttAATGGCCTTGAGCCTatcataacttccttttatataatttgaaatatcattatgtaataaatactcattatattttcttacaagtgtttcaaagaatatatgataactgataaagctagaatggtcggtaccattagtt                <  1:40815‑M2/141‑125 (MQ=255)                                                                                                                                 tGGCCTTGAGCCTATCATAACTTCCTTTTATCATTTTATTGTTGTGTTGATGTTTCGATAACGTGGTACATCTTATCAAACATCAATTCGAAACCATGCACCATGGCATCATGATATTCTTTTTTCTTTTGCTTGTATTCt            >  2:390530/1‑141 (MQ=255)                                                                                                                                  ggCCTTGAGCCTATCATAACTTCCTTTTATCATTTTATTGTTGTGTTGATGTTTCGATAACGTGGTACATCTTATCAAACATCAATTCGAAACCATGCACCATGGCATCATGATATTCTTTTTTCTTTTGCTTGTATTCTa           <  1:267555/141‑1 (MQ=255)                                                                                                                                           ccTATCATAACTTCCTTTTATCATTTTATTGTTGTGTTGATGTTTCGATAACGTGGTACATCTTATCAAACATCAATTCGAAACCATGCACCATGGCATCATGATATTCTTTTTTCTTTTGCTTGTATTCTAAATTAGTaa  <  2:540765/141‑1 (MQ=255)                                                                                                                                             |                                                                                                                                           AACTGATGGTACAGACTATTCTAGCTTCATCAGTTATCATATATTCTTTGAAACACTTGTAAGAAAATATAATGAGTATTTACTACATAATGATATTTCAAATTAGAAAAAAGGAAGTTATGATTTAATGGCCTTGAGCCTATCATAACTTCCTTTTATCATTTTATTGTTGTGTTGATGTTTCGATAACGTGGTACATCTTATCAAACATCAATTCGAAACCATGCACCATGGCATCATGATATTCTTTTTTCTTTTGCTTGTATTCTAAATTAGTAA  >  USA300TCH1516_ALE/2442698‑2442976

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.