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

GTAAAATGTATAAAACATACTTCTTTAAAAAAGGAGAGTCTAAATCATCTTATGTAATTAATGGTCCTGGAAAAACTAATGAATATGCATACTAATAGTAGTTACATAAATTAAAAGGTAGATATTTCTTTTTTATATAAAGGTTTGGCA‑GACATTTCATAACT‑TGCCAAACCTTTATATATCTAATTATCAAACTGCACTAAACTTACCAAAACTGCTTATTCTATTACCTGCCTTGTCTACCTCTCCTGTCGCTATATAACGACGTTGTCCA  >  USA300TCH1516_ALE/2087889‑2088162                                                                                                                                      |                                                                                                                                               gTAAAATGTATAAAACATACTTCTTTAAAAAAGGAGAGTCTAAATCATCTTATGTAATTAATGGTCCTGGAAAAACTAATGAATATGCATACTAATAGTAGTTACATAAATTAAAAGGTAGATATTTCTTTTTTATATaaa                                                                                                                                         >  1:502696/1‑141 (MQ=255) gTAAAATGTATAAAACATACTTCTTTAAAAAAGGAGAGTCTAAATCATCTTATGTAATTAATGGTCCTGGAAAAACTAATGAATATGCATACTAATAGTAGTTACATAAATTAAAAGGTAGATATTTCTTTTTTATATaaa                                                                                                                                         >  1:152004/1‑141 (MQ=255)     taatggctatagatggattacttatattgctaatagtggacaacgtcgttatatagcgacaggagaggtagacaaggcaggtaatagaataagcagttttggtaagtttagtgcagtttgataattagaTATATAAAGGtt                                                                                                                                     <  2:293086‑M1/12‑1 (MQ=255)        tggctatagatggattacttatattgctaatagtggacaacgtcgttatatagcgacaggagaggtagacaaggcaggtaatagaataagcagttttggtaagtttagtgcagtttgataattagaTATATAAAGGTTTgg                                                                                                                                  <  1:119558‑M1/15‑1 (MQ=255)                  tACTTCTTTAAAAAAGGAGAGTCTAAATCATCTTATGTAATTAATGGTCCTGGAAAAACTAATGAATATGCATACTAATAGTAGTTACATAAATTAAAAGGTAGATATTTCTTTTTTATATAAAGGTTTGGCA‑GACATTTc                                                                                                                       <  1:311865/141‑1 (MQ=255)                      tcttTAAAAAAGGAGAGTCTAAATCATCTTATGTAATTAATGGTCCTGGAAAAACTAATGAATATGCATACTAATAGTAGTTACATAAATTAAAAGGTAGATATTTCTTTTTTATATAAAGGTTTGGCA‑GACATTTCATaa                                                                                                                   >  1:212915/1‑141 (MQ=255)                         cttatattgctaatagtggacaacgtcgttatatagcgacaggagaggtagacaaggcaggtaatagaataagcagttttggtaagtttagtgcagtttgataattagaTATATAAAGGTTTGGCA‑GACATTTCATAACt‑t                                                                                                               >  2:218438‑M1/110‑141 (MQ=255)                          tAAAAAAGGAGAGTCTAAATCATCTTATGTAATTAATGGTCCTGGAAAAACTAATGAATATGCATACTAATAGTAGTTACATAAATTAAAAGGTAGATATTTCTTTTTTATATAAAGGTTTGGCA‑GACATTTCATAACT‑Tg                                                                                                              <  1:594726/141‑1 (MQ=255)                            aaaaaGGAGAGTCTAAATCATCTTATGTAATTAATGGTCCTGGAAAAACTAATGAATATGCATACTAATAGTAGTTACATAAATTAAAAGGTAGATATTTCTTTTTTATATAAAGGTTTGGCA‑GACATTTCATAACT‑TGcc                                                                                                            <  1:222403/141‑1 (MQ=255)                                   agagTCTAAATCATCTTATGTAATTAATGGTCCTGGAAAAACTAATGAATATGCATACTAATAGTAGTTACATAAATTAAAAGGTAGATATTTCTTTTTTATATAAAGGTTTGGCA‑GACATTTCATAACT‑TGCCAAACCtt                                                                                                     <  1:154647/141‑1 (MQ=255)                                     agTCTAAATCATCTTATGTAATTAATGGTCCTGGAAAAACTAATGAATATGCATACTAATAGTAGTTACATAAATTAAAAGGTAGATATTTCTTTTTTATATAAAGGTTTGGCA‑GACATTTCATAACT‑TGCCAAACCTTta                                                                                                   <  1:287023/141‑1 (MQ=255)                                     agTCTAAATCATCTTATGTAATTAATGGTCCTGGAAAAACTAATGAATATGCATACTAATAGTAGTTACATAAATTAAAAGGTAGATATTTCTTTTTTATATAAAGGTTTGGCA‑GACATTTCATAACT‑TGCCAAACCTTta                                                                                                   <  1:105959/141‑1 (MQ=255)                                      gTCTAAATCATCTTATGTAATTAATGGTCCTGGAAAAACTAATGAATATGCATACTAGTAGTAGTTACATAAATTAAAAGGTAGATATTTCTTTTTTATATAAAGGTTTGGCA‑GACATTTCATAACT‑TGCCAAACCTTtat                                                                                                  >  1:695295/1‑141 (MQ=255)                                           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)                                                                            cTAATGAATATGCATACTAATAGTAGTTACATAAATTAAAAGGTAGATATTTCTTTTTTATATAAAGGTTTGGCA‑GACATTTCATAACT‑TGCCAAACCTTTATATATCTAATTATCAAACTGCACTAAACTTACCAAAACt                                                            >  1:328167/1‑141 (MQ=255)                                                                               aTGAATATGCATACTAATAGTAGTTACATAAATTAAAAGGTAGATATTTCTTTTTTATATAAAGGTATGGCA‑GACATTTCATAACT‑TGCCAAACCTTTATATATCTAATTATCAAACTGCACTAAACTTACCAAAACTgta                                                         >  1:584545/1‑139 (MQ=255)                                                                                tGAATATGCATACTAATAGTAGTTACATAAATTAAAAGGTAGATATTTCTTTTTTATATAAAGGTTTGGCA‑GACATTTCATAACT‑TGCCAAACCTTTATATATCTAATTATCAAACTGCACTAAACTTACCAAAACTGCtt                                                        <  1:259184/141‑1 (MQ=255)                                                                                tGAATATGCATACTAATAGTAGTTACATAAATTAAAAGGTAGATATTTCTTTTTTATATAAAGGTTTGGCA‑GACATTTCATAACT‑TGCCAAACCTTTATATATCTAATTATCAAACTGCACTAAACTTACCAAAACTGCtt                                                        <  1:715601/141‑1 (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)                                                                                                                                      |                                                                                                                                               GTAAAATGTATAAAACATACTTCTTTAAAAAAGGAGAGTCTAAATCATCTTATGTAATTAATGGTCCTGGAAAAACTAATGAATATGCATACTAATAGTAGTTACATAAATTAAAAGGTAGATATTTCTTTTTTATATAAAGGTTTGGCA‑GACATTTCATAACT‑TGCCAAACCTTTATATATCTAATTATCAAACTGCACTAAACTTACCAAAACTGCTTATTCTATTACCTGCCTTGTCTACCTCTCCTGTCGCTATATAACGACGTTGTCCA  >  USA300TCH1516_ALE/2087889‑2088162

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.