New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	2088022 =	38 (0.820)	3 (0.070)	3/226	NT	8.8%	intergenic (+39/+56)	chp/USA300HOU_RS10560	Chemotaxis inhibitory protein/Glycyl‑glycine endopeptidase ALE‑1
	?	USA300TCH1516_ALE	2088070 =	29 (0.720)					intergenic (+87/+8)	chp/USA300HOU_RS10560	Chemotaxis inhibitory protein/Glycyl‑glycine endopeptidase ALE‑1

AATCATCTTATGTAATTAATGGTCCTGGAAAAACTAATGAATATGCATACTAATAGTAGTTACATAAATTAAAAGGTAGATATTTCTTTTTTATATAAAGGTTTGGCA‑GACATTTCATAACT‑TGCCAAACCTTTATATATCTAATTATCAAACTGCACTAAACTTACCAAAACTGCTTATTCTATTACCTGCCTTGTCTACCTCTCCTGTCGCTATATAACGACGTTGTCCACTATTAGCAATATAAGTAATCCATCTATAGCCATTA  >  USA300TCH1516_ALE/2087931‑2088198                                                                                                                                              |                                                                                                                                 aaTCATCTTATGTAATTAATGGTCCTGGAAAAACTAATGAATATGCATACTAATAGTAGTTACATAAATTAAAAGGTAGATATTTCTTTTTTATATAAAGGTTTGGCA‑GACATTTCATAACT‑TGCCAAACCTTTATATATc                                                                                                                                 >  1:201467/1‑141 (MQ=255)   tcatcTTATGTAATTAATGGTCCTGGAAAAACTAATGAATATGCATACTAATAGTAGTTACATAAATTAAAAGGTAGATATTTCTTTTTTATATAAAGGTTTGGCA‑GACATTTCATAACT‑TGCCAAACCTTTATATATCTa                                                                                                                               <  1:753738/141‑1 (MQ=255)    catcTTATGTAATTAATGGTCCTGGAAAAACTAATGAATATGCATACTAATAGTAGTTACATAAATTAAAAGGTAGATATTTCTTTTTTATATAAAGGTTTGGCA‑GACATTTCATAACT‑TGCCAAACCTTTATATATCTaa                                                                                                                              >  1:145726/1‑141 (MQ=255)    catcTTATGTAATTAATGGTCCTGGAAAAACTAATGAATATGCATACTAATAGTAGTTACATAAATTAAAAGGTAGATATTTCTTTTTTATATAAAGGTTTGGCA‑GACATTTCATAACT‑TGCCAAACCTTTATATATCTaa                                                                                                                              >  1:145753/1‑141 (MQ=255)      tcTTATGTAATTAATGGTCCTGGAAAAACTAATGAATATGCATACTAATAGTAGTTACATAAATTAAAAGGTAGATATTTCTTTTTTATATAAAGGTTTGGCA‑GACATTTCATAACT‑TGCCAAACCTTTATATATCTAAtt                                                                                                                            >  2:222920/1‑141 (MQ=255)          aTGTAATTAATGGTCCTGGAAAAACTAATGAATATGCATACTAATAGTAGTTACATAAATTAAAAGGTAGATATTTCTTTTTTATATAAAGGTTTGGCA‑GACATTTCATAACT‑TGCCAAACCTTTATATATCTAATTATCa                                                                                                                        >  2:43372/1‑141 (MQ=255)                 taatGGTCCTGGAAAAACTAATGAATATGCATACTAATAGTAGTTACATAAATTAAAAGGTAGATATTTCTTTTTTATATAAAGGTTTGGCA‑GACATTTCATAACT‑TGCCAAACCTTTATATATCTAATTATCAAACTGCa                                                                                                                 <  1:45129/141‑1 (MQ=255)                  aatGGTCCTGGAAAAACTAATGAATATGCATACTAATAGTAGTTACATAAATTAAAAGGTAGATATTTCTTTTTTATATAAAGGTTTGGCA‑GACATTTCATAACT‑TGCCAAACCTTTATATATCTAATTATCAAACTGCAc                                                                                                                >  1:134081/1‑141 (MQ=255)                   atGGTCCTGGAAAAACTAATGAATATGCATACTAATAGTAGTTACATAAATTAAAAGGTAGATATTTCTTTTTTATATAAAGGTTTGGCA‑GACATTTCATAACT‑TGCCAAACCTTTATATATCTAATTATCAAACTGCACt                                                                                                               <  1:232254/141‑1 (MQ=255)                     ggTCCTGGAAAAACTAATGTATATGCATACTAATAGTAGTTACATAAATTAAAAGGTAGATATTTCTTTTTTATATAAAGGTTTGGCA‑GACATTTCATAACT‑TGCCAAACCTTTATATATCTAATTATCAAACTGCACTaa                                                                                                             <  1:387805/141‑1 (MQ=255)                     ggTCCTGGAAAAACTAATGAATATGCATACTAATAGTAGTTACATAAATTAAAAGGTAGATATTTCTTTTTTATATAAAGGTTTGGCA‑GACATTTCATAACT‑TGCCAAACCTTTATATATCTAATTATCAAACTGCACTaa                                                                                                             <  1:155910/141‑1 (MQ=255)                     ggTCCTGGAAAAACTAATGAATATGCATACTAATAGTAGTTACATAAATTAAAAGGTAGATATTTCTTTTTTATATAAAGGTTTGGCA‑GACATTTCATAACT‑TGCCAAACCTTTATATATCTAATTATCAAACTGCACTaa                                                                                                             >  1:515990/1‑141 (MQ=255)                       tCCTGGAAAAACTAATGAATATGCATACTAATAGTAGTTACATAAATTAAAAGGTAGATATTTCTTTTTTATATAAAGGTTTGGCA‑GACATTTCATAACT‑TGCCAAACCTTTATATATCTAATTATCAAACTGCACTAAAc                                                                                                           >  1:477869/1‑141 (MQ=255)                             gaggtagacaaggcaggtaatagaataagcagttttggtaagtttagtgcagtttgataattagatatataaaggtttggcagacatttcataacttgccaaacctttatataTCTAATTATCAAACTGCACTAAACTTAc                                                                                                       <  1:342905‑M2/28‑1 (MQ=255)                                  cTAATGAATATGCATACTAATAGTAGTTACATAAATTAAAAGGTAGATATTTCTTTTTTATATAAAGGTTTGGCA‑GACATTTCATAACT‑TGCCAAACCTTTATATATCTAATTATCAAACTGCACTAAACTTACCAAAACt                                                                                                >  1:328167/1‑141 (MQ=255)                                     aTGAATATGCATACTAATAGTAGTTACATAAATTAAAAGGTAGATATTTCTTTTTTATATAAAGGTATGGCA‑GACATTTCATAACT‑TGCCAAACCTTTATATATCTAATTATCAAACTGCACTAAACTTACCAAAACTgta                                                                                             >  1:584545/1‑139 (MQ=255)                                      tGAATATGCATACTAATAGTAGTTACATAAATTAAAAGGTAGATATTTCTTTTTTATATAAAGGTTTGGCA‑GACATTTCATAACT‑TGCCAAACCTTTATATATCTAATTATCAAACTGCACTAAACTTACCAAAACTGCtt                                                                                            <  1:715601/141‑1 (MQ=255)                                      tGAATATGCATACTAATAGTAGTTACATAAATTAAAAGGTAGATATTTCTTTTTTATATAAAGGTTTGGCA‑GACATTTCATAACT‑TGCCAAACCTTTATATATCTAATTATCAAACTGCACTAAACTTACCAAAACTGCtt                                                                                            <  1:259184/141‑1 (MQ=255)                                       aggcaggtaatagaataagcagttttggtaagtttagtgcagtttgataattagatatataaaggtttggcagacatttcataacttgccaaacctttatataTCTAATTATCAAACTGCACTAAACTTACCAAAACTGCt                                                                                             >  1:311918‑M2/104‑141 (MQ=255)                                            tGCATACTAATAGTAGTCACATAAATTAAAAGGTAGATATTTCTTTTTTATATAAAGGACTGGCA‑GACGTTTCATAAGG‑GGCCATACCTTTAGAGATCTAATTATCAAACTGCACTAAACTTACCAAAACTTCTTATTCTa                                                                                      >  1:666126/1‑141 (MQ=37)                                              cATACTAATAGTAGTTACATAAATTAAAAGGTAGATATTTCTTTTTTATATAAAGGTTTGGCA‑GACATTTCATAACT‑TGCCAAACCTTTATATATCTAATTATCAAACTGCACTAAACTTACCAAAACTGCTTATTCTAtt                                                                                    >  1:240511/1‑141 (MQ=255)                                                tACTAATAGTAGTTACATAAATTAAAAGGTAGATATTTCTTTTTTATATAAAGGTTTGGCA‑GACATTTCATAACT‑TGCCAAACCTTTATATATCTAATTATCAAACTGCACTAAACTTACCAAAACTGCTTATTCTATTAc                                                                                  <  1:394018/141‑1 (MQ=255)                                                   tAATAGTAGTTACATAAATTAAAAGGTAGATATTTCTTTTTTATATAAAGGTTTGGCA‑GACATTTCATAACT‑TGCCAAACCTTTATATATCTAATTATCAAACTGCACTAAACTTACCAAAACTGCTTATTCTATTACCTg                                                                               >  2:290460/1‑141 (MQ=255)                                                    aaTAGGAGTTACATAAATTAAAAGGTAAATATTTCTTTTTTATATAAATGTTTGGCA‑GACATTTCATAACT‑TGCCAAACCTTTATATATCTAATTATCAAACTGCACTAAACTTACCAAAACTGCTTATTCTATTACCTgt                                                                              <  1:748792/141‑2 (MQ=255)                                                      agcagttttggtaagtttagtgcagtttgataattagaTATATAAAGGTTTGGCAAGTTATGAAATGTCT‑‑GCCAAACCTTTATATATCTAATTATCAAACTGCACTAAACTTACCAAAACTGCTTATTCTATTACCTGCCt                                                                            >  1:311918‑M1/39‑141 (MQ=255)                                                        gtagtTACATAAATTAAAAGGTAGATATTTCTTTTTTATATAAAGGTTTGGCA‑GACATTTCATAACT‑TGCCAAACCTTTATATATCTAATTATCAAACTGCACTAAACTTACCAAAACTGCTTATTCTATTACCTGCCTTg                                                                          >  2:285720/1‑141 (MQ=255)                                                                gtaagtttagtgcagtttgataattagaTATATAAAGGTTTGGCA‑‑AGTTATGAAATGTCTGCCAAACCTTTATATATCTAATTATCAAACTGCACTAAACTTACCAAAACTGCTTATTCTATTACCTGCCTTGTCTACctc                                                                  <  1:342905‑M1/113‑1 (MQ=255)                                                                aTAAATTAAAAGGTAGATATTTCTTTTTTATATAAAGGTTTGGCA‑GACATTTCATAACT‑TGCCAAACCTTTATATATCTAATTATCAAACTGCACTAAACTTACCAAAACTGCTTATTCTATTACCTGCCTTGTCTACctc                                                                  <  1:21924/141‑1 (MQ=255)                                                                    aTTAAAAGGTAGATATTTCTTTTTTATATAAAGGTTTGGCA‑GACATTTCATAACT‑TGCCAAACCTTTATATATCTAATTATCAAACTGCACTAAACTTACCAAAACTGCTTATTCTATTACCTGCCTTGTCTACCTCTCCt                                                              >  1:785731/1‑141 (MQ=255)                                                                         aaGGTAGATATTTCTTTTTTATATAAAGGTTTGGCA‑GACATTTCATAACT‑TGCCAAACCTTTATATATCTAATTATCAAACTGCACTAAACTTACCAAAACTGCTTATTCTATTACCTGCCTTGTCTACCTCTCCTGTCGc                                                         >  1:697818/1‑141 (MQ=255)                                                                                      cTTTTTTATATAAAGGTTTGGCA‑GACATTTCATAACT‑TGCCAAACCTTTATATATCTAATTATCAAACTGCACTAAACTTACCAAAACTGCTTATTCTATTACCTGCCTTGTCTACCTCTCCTGTCGCTATATAACGACGt                                            >  2:182565/1‑141 (MQ=255)                                                                                      cTTTTTTATATAAAGGTTTGGCA‑GACATTTCATAACT‑TGCCAAACCTTTATATATCTAATTATCAAACTGCACTAAACTTACCAAAACTGCTTATTCTATTACCTGCCTTGTCTACCTCTCCTGTCGCTATATAACGACGt                                            <  1:214490/141‑1 (MQ=255)                                                                                            TATATAAAGGTTTGGCA‑GACATTTCATAACT‑TGCCAAACCTTTATATATCTAATTATCAAACTGCACTAAACTTACCAAAACTGCTTATTCTATTACCTGCCTTGTCTACCTCTCCTGTCGCTATATAACGACGTTGTCCa                                      <  2:65494‑M1/141‑1 (MQ=255)                                                                                                TAAAGGTTTGGCA‑GACATTTCATAACT‑TGCCAATCCTTTATACATCTTTTTTTCAAACGACACTAAACGTACCAAAACTGCTTATTCTATTACCTGCCTTGTCTACCTCTCCTGTCGCTATATAACGACGTTGTCCACTAt                                  >  1:705634‑M1/1‑141 (MQ=255)                                                                                                  AAGGTTTGGCA‑GACATTTCATAACT‑TGCCAAACCTTTATATATCTAATTATCAAACTGCACTAAACTTACCAAAACTGCTTATTCTATTACCTGCCTTGTCTACCTCTCCTGTCGCTATATAACGACGTTGTCCACTATTa                                >  1:769401‑M1/1‑141 (MQ=255)                                                                                                  AAGGTTTGGCA‑GACATTTCATAACT‑TGCCAAACCTTTATATATCTAATTATCAAACTGCACTAAACTTACCAAAACTGCTTATTCTATTACCTGCCTTGTCTACCTCTCCTGTCGCTATATAACGACGTTGTCCACTATTa                                >  2:111956‑M1/1‑141 (MQ=255)                                                                                                  AAGGTTTGGCA‑GACATTTCATAACT‑TGCAAAACCTTTATATATCTAATTATCAAACTGCACTAAACTTACCAAAACTGCTTATTCTATTACCTGCCTTGTCTACCTCTCCTGTCGCTATATAACGACGTTGTCCACTATTa                                >  1:25699‑M1/1‑141 (MQ=255)                                                                                                      TTTGGCA‑GACATTTCATAACT‑TGCCAAACCTTTATATATCTAATTATCAAACTGCACTAAACTTACCAAAACTGCTTATTCTATTACCTGCCTTGTCTACCTCTCCTGTCGCTATATAACGACGTTGTCCACTATTAGCaa                            >  1:631097‑M1/1‑141 (MQ=255)                                                                                                            A‑GACATTTCATAACT‑TGCCAAACCTTTATATATCTAATTATCAAACTGCACTAAACTTACCAAAACTGCTTATTCTATTACCTGCCTTGTCTACCTCTCCTGTCGCTATATAACGACGTTGTCCACTATTAGCAATATAAg                      >  1:127202‑M1/1‑141 (MQ=255)                                                                                                              aagttatgaaatgtctgccaaacctttatataTCTAATTATCAAACTGCACTAAACTTACCAAAACTGCTTATTCTATTACCTGCCTTGTCTACCTCTCCTGTCGCTATATAACGACGTTGTCCACTATTAGCAATATAAg                      >  2:218438‑M2/33‑141 (MQ=255)                                                                                                                 aTTTCATAACT‑TGCCAAACCTTTATATATCTAATTATCAAACTGCACTAAACTTACCAAAACTGCTTATTCTATTACCTGCCTTGTCTACCTCTCCTGTCGCTATATAACGACGTTGTCCACTATTAGCAATATAAGTAAt                  <  1:243586/141‑1 (MQ=255)                                                                                                                 aTTTCATAACT‑TGCCAAACCTTTATATATCTAATTATCAAACTGCACTAAACTTACCAAAACTGCTTATTCTATTACCTGCCTTGTCTACCTCTCCTGTCGCTATATAACGACGTTGTCCACTATTAGCAATATAAGTAAt                  <  1:185352/141‑1 (MQ=255)                                                                                                                    tCATAACT‑TGCCAAACCTTTATATATCTAATTATCAAACTGCACTAAACTTACCAAAACTGCTTATTCTATTACCTGCCTTGTCTACCTCTCCTGTCGCTATATAACGACGTTGTCCACTATTAGCAATATAAGTAATCCa               <  1:77981/141‑1 (MQ=255)                                                                                                                    tCATAACT‑TGCCAAACCTTTATATATCTAATTATCAAACTGCACTAAACTTACCAAAACTGCTTATTCTATTACCTGCCTTGTCTACCTCTCCTGTCGCTATATAACGACGTTGTCCACTATTAGCAATATAAGTAATCCa               >  1:18673/1‑141 (MQ=255)                                                                                                                      aTAACT‑TGCCAAACCTTTATATATCTAATTATCAAACTGCACTAAACTTACCAAAACTGCTTATTCTATTACCTGCCTTGTCTACCTCTCCTGTCGCTATATAACGACGTTGTCCACTATTAGCAATATAAGTAATCCATc             >  1:287686/1‑141 (MQ=255)                                                                                                                               ccaaacctttatataTCTAATTATCAAACTGCACTAAACTTACCAAAACTGCTTATTCTATTACCTGCCTTGTCTACCTCTCCTGTCGCTATATAACGACGTTGTCCACTATTAGCAATATAAGTAATCCATCTATAGCCa     <  1:119558‑M2/126‑1 (MQ=255)                                                                                                                                  aacctttatataTCTAATTATCAAACTGCACTAAACTTACCAAAACTGCTTATTCTATTACCTGCCTTGTCTACCTCTCCTGTCGCTATATAACGACGTTGTCCACTATTAGCAATATAAGTAATCCATCTATAGCCATTa  <  2:293086‑M2/129‑1 (MQ=255)                                                                                                                                              |                                                                                                                                 AATCATCTTATGTAATTAATGGTCCTGGAAAAACTAATGAATATGCATACTAATAGTAGTTACATAAATTAAAAGGTAGATATTTCTTTTTTATATAAAGGTTTGGCA‑GACATTTCATAACT‑TGCCAAACCTTTATATATCTAATTATCAAACTGCACTAAACTTACCAAAACTGCTTATTCTATTACCTGCCTTGTCTACCTCTCCTGTCGCTATATAACGACGTTGTCCACTATTAGCAATATAAGTAATCCATCTATAGCCATTA  >  USA300TCH1516_ALE/2087931‑2088198

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.