New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	2008942 =	40 (0.870)	3 (0.070)	3/232	NT	8.3%	intergenic (+70/+121)	USA300HOU_RS10115/USA300HOU_RS10125	hypothetical protein/Putative multidrug export ATP‑binding/permease protein
	?	USA300TCH1516_ALE	2008991 =	31 (0.750)					intergenic (+119/+72)	USA300HOU_RS10115/USA300HOU_RS10125	hypothetical protein/Putative multidrug export ATP‑binding/permease protein

TGAAGAAGACTTTGATTTATAACATTAAAACAATTTTATCAATTAATGCCACAATGAGATAAACTAATATTGAATCTCGAAATTAAATTTAAAAAAGCAGTAAGATTATTTTC‑‑AATTAAGAAAATC‑TCTTACTGCTTTTTCTATGTTATGACCCCACCATCCTGTTACAAATTTTCTCTTCAAGATTGTACTGAAGTCAAACAACTAATACTTTATAAGTTTTGAATGCTATATAAATGCTCGTAAGCACCTTGTTTTGCAATCAATTCACGATGCGT  >  USA300TCH1516_ALE/2008851‑2009128                                                                                                                                                |                                                                                                                                          tgAAGAAGACTTTGATTTATAACATTAAAACAATTTTATCAATTAATGCCACAATGAGATAAACTAATATTGAATCTCGAAATTAAATTTAAAAAAGCAGTAAGATTATTTTC‑‑AATTAAGAAAATC‑TCTTACTGCTTTTTc                                                                                                                                           >  1:10863/1‑141 (MQ=255)     gaagaCTTTGATTTATAACATTAAAACAATTTTATCAATTAATGCCACAATGAGATAAACTAATATTGAATCTCGAAATTAAATTTAAAAAAGCAGTAAGATTATTTTC‑‑AATTAAGAAAATC‑TCTTACTGCTTTTTCTATg                                                                                                                                       >  1:256473/1‑141 (MQ=255)          tcaaaacttataaagtattagttttttgacttcagtacaatcttgaagagaaaatttgtaacaggatggtggggtcataacatagaaaaagcagtaagattattttcaattaagaaaatctcttactgctttttCTATGtt                                                                                                                                     <  1:270153‑M2/7‑1 (MQ=255)              gATTTATAACATTAAAACAATTTTATCAATTAATGCCACAATGAGATAAACTAATATTGAATCTCGAAATTAAATTTAAAAAAGCAGTAAGATTATTTTC‑‑AATTAAGAAAATC‑TCTTACTGCTTTTTCTATGTTATGAccc                                                                                                                              >  1:63824/1‑141 (MQ=255)                 ttATAACATTAAAACAATTTTATCAATTAATGCCACAATGAGATAAACTAATATTGAATCTCGAAATTAAATTTAAAAAAGCAGTAAGATTATTTTC‑‑AATTAAGAAAATC‑TCTTACTGCTTTTTCTATGTTATGACCccac                                                                                                                           <  2:254263/141‑1 (MQ=255)                 ttATAACATTAAAACAATTTTATCAATTAATGCCACAATGAGATAAACTAATATTGAATCTCGAAATTAAATTTAAAAAAGCAGTAAGATTATTTTC‑‑AATTAAGAAAATC‑TCTTACTGCTTTTTCTATGTTATGACCccac                                                                                                                           >  1:367855/1‑141 (MQ=255)                      aCATTAAAACAATTTTATCAATTAATGCCACAATGAGATAAACTAATATTGAATCTCGAAATTAAATTTAAAAAAGCAGTAAGATTATTTTC‑‑AATTAAGAAAATC‑TCTTACTGCTTTTTCTATGTTATGACCTCACCATcc                                                                                                                      >  2:248900/1‑141 (MQ=255)                            aaaCAATTTTATCAATTAATGCCACAATGAGATAAACTAATATTGAATCTCGAAATTAAATTTAAAAAAGCAGTAAGATTATTTTC‑‑AATTAAGAAAATC‑TCTTACTGCTTTTTCTATGTTATGACCCCACCATCCTGTTAc                                                                                                                >  1:20668/1‑141 (MQ=255)                                aaTTTTATCAATTAATGCCACAATGAGATAAACTAATATTGAATCTCGAAATTAAATTTAAAAAAGCAGTAAGATTATTTTC‑‑AATTAAGAAAATC‑TCTTACTGCTTTTTCTATGTTATGACCCCACCATCCTGTTACAAAt                                                                                                            <  2:193731/141‑1 (MQ=255)                                   tttATCAATTAATGCCACAATGAGATAAACTAATATTGAATCTCGAAATTAAATTTAAAAAAGCAGTAAGATTATTTTC‑‑AATTAAGAAAATC‑TCTTACTGCTTTTTCTATGTTATGACCCCACCATCCTGTTACAAAtttt                                                                                                         >  1:653858/1‑141 (MQ=255)                                   tttATCAATTAATGCCACAATGAGATAAACTAATATTGAATCTCGAAATTAAATTTAAAAAAGCAGTAAGATTATTTTC‑‑AATTAAGAAAATC‑TCTCACTGCTTTTTCTATGTTATGACCCCACCATCCTGTTACAAAtttt                                                                                                         >  1:653844/1‑141 (MQ=255)                                     tATCAATTAATGCCACAATGAGATAAACTAATATTGAATCTCGAAATTAAATTTAAAAAAGCAGTAAGATTATTTTC‑‑AATTAAGAAAATC‑TCTTACTGCTTTTTCTATGTTATGACCCCACCATCCTGTTACAAATTTtct                                                                                                       >  1:98482/1‑141 (MQ=255)                                      aTCAATTAATGCCACAATGAGATAAACTAATATTGAATCTCGAAATTAAATTTAAAAAAGCAGTAAGATTATTTTC‑‑AATTAAGAAAATC‑TCTTACTGCTTTTTCTATGTTATGACCCCACCATCCTGTTACAAATTTtctc                                                                                                      >  1:749983/1‑141 (MQ=255)                                              aTGCCACAATTAGATAAACTAATATTGAATCTCGAAATTAAATTTAAAAAAGCAGTAAGATTATTTTC‑‑AATTAAGAAAATC‑TCTTACTGCTTTTTCTATGTTATGACCCCACCATCCTGTTACAAATTTTCTCTTCAAGAt                                                                                              <  1:423816/141‑1 (MQ=255)                                               tGCCACAATGAGATAAACTAATATTGAATCTCGAAATTAAATTTAAAAAAGCAGTAAGATTATTTTC‑‑AATTAAGAAAATC‑TCTTACTGCTTTTTCTATGTTATGACCCCACCATCCTGTTACAAATTTTCTCTTCAAGAtt                                                                                             <  2:158727/141‑1 (MQ=255)                                                    caATGAGATAAACTAATATTGAATCTCGAAATTAAATTTAAAAAAGCAGTAAGATTATTTTC‑‑AATTAAGAAAATC‑TCTTACTGCTTTTTCTATGTTATGACCCCACCATCCTGTTACAAATTTTCTCTTCAAGATTGTACt                                                                                        <  2:252972/141‑1 (MQ=255)                                                          gaTAAACTAATATTGAATCTCGAAATTAAATTTAAAAAAGCAGTAAGATTATTTTC‑‑AATTAAGAAAATC‑TCTTACTGCTTTTTCTATGTTATGACCCCACCATCCTGTTACAAATTTTCTCTTCAAGATTGTACTGAAGTc                                                                                  >  1:541375/1‑141 (MQ=255)                                                           aTAAACTAATATTGAATCTCGAAATTAAATTTAAAAAAGCAGTAAGATTATTTTC‑‑AATTAAGAAAATC‑TCTTACTGCTTTTTCTATGTTATGACCCCACCATCCTGTTACAAATTTTCTCTTCAAGATTGTACTGAAGTCa                                                                                 >  2:235706/1‑141 (MQ=255)                                                             aaaCTAATATTGAATCTCGAAATTAAATTTAAAAAAGCAGTAAGATTATTTTC‑‑AATTAAGAAAATC‑TCTTACTGCTTTTTCTATGTTATGACCCCACCATCCTGTTACAAATTTTCTCTTCAAGATTGTACTGAAGTCaaa                                                                               <  1:584136/141‑1 (MQ=255)                                                                      ttGAATCTCGAAATTAAATTTAAAAAAGCAGTAAGATTATTTTC‑‑AATTAAGAAAATC‑TCTTACTGCTTTTTCTATGTTATGACCCCACCATCCTGTTACAAATTTTCTCTTCAAGATTGTACTGAAGTCAAACAACTAATa                                                                      >  1:119102/1‑141 (MQ=255)                                                                      ttGAATCTCGAAATTAAATTTAAAAAAGCAGTAAGATTATTTTC‑‑AATTAAGAAAATC‑TCTTACTGCTTTTTCTATGTTATGACCCCACCATCCTGTTACAAATCTTCTCTTCAAGATTGTACTGAAGTCAAACAACTAATa                                                                      >  1:482730/1‑141 (MQ=255)                                                                       tGAATCTCGAAATTAAATTTAAAAAAGCAGTAAGATTATTTTC‑‑AATTAAGAAAATC‑TCTTACTGCTTTTTCTATGTTATGACCCCACCATCCTGTTACAAATTTTCTCTTCAAGATTGTACTGAAGTCAAACAACTAATAc                                                                     >  1:545273/1‑141 (MQ=255)                                                                                  attaaattTAAAAAAGCAGTAAGATTATTTTC‑‑AATTAAGAAAATC‑TCTTACTGCTTTTTCTATGTTATGACCCCACCATCCTGTTACAAATTTTCTCTTCAAGATTGTACTGAAGTCAAACAACTAATACTTTATAAGttt                                                          <  1:237879/141‑1 (MQ=255)                                                                                  attaaattTAAAAAAGCAGTAAGATTATTTTC‑‑AATTAAGAAAATC‑TCTTACTGCTTTTTCTATGTTATGACCCCACCATCCTGTTACAAATTTTCTCTTCAAGATTGTACTGAAGTCAAACAACTAATACTTTATAAGttt                                                          <  1:229563/141‑1 (MQ=255)                                                                                     aacatagAAAAAGCAGTAAGAG‑ATTTTCTTAATT‑‑GAAAATAATCTTACTGCTTTTTCTATGTTATGACCCCACCATCCTGTTACAAATTTTCTCTTCAAGATTGTACTGAAGTCAAAAAACTAATACTTTATAAGTTTTGa                                                       <  1:270153‑M1/134‑1 (MQ=255)                                                                                      aattTAAAAAAGCAGTAAGATTATTTTC‑‑AATTAAGAAAATC‑TCTTACTGCTTTTTCTATGTTATGACCCCACCATCCTGTTACAAATTTTCTCTTCAAGATTGTACTGAAGTCAAACAACTAATACTTTATAAGTTTTGaa                                                      >  1:60102/1‑141 (MQ=255)                                                                                      aattTAAAAAAGCAGTAAGATTATTTTC‑‑AATTAAGAAAATC‑TCTTACTGCTTTTTCTATGTTATGACCCCACCATCCTGTTACAAATTTTCTCTTCAAGATTGTACTGAAGTCAAACAACTAATACTTTATAAGTTTTGaa                                                      >  2:174808/1‑141 (MQ=255)                                                                                         ttAAAAAAGCAGTAAGATTATTTTC‑‑AATTAAGAAAATC‑TCTTACTGCTTTTTCTATGTTATGACCCCACCATCCTGTTACAAATTTTCTCTTCAAGATTGTACTGAAGTCAAACAACTAATACTTTATAAGTTTTGAATGc                                                   <  1:236616/141‑1 (MQ=255)                                                                                            AAAAAGCAGTAAGATTATTTTC‑‑AATTAAGAAAATC‑TCTTACTGCTTTTTCTATGTTATGACCCCACCATCCTGTTACAAATTTTCTCTTCAAGATTGTACTGAAGTCAAACAACTAATACTTTATAAGTTTTGAATGCtat                                                <  1:60926‑M1/141‑1 (MQ=255)                                                                                               aaaaagcagtaagagattttcttaattgaaaataatcttactgctttttCTATGTTATGACCCCACCATCCTGTTACAAATTTTCTCTTCAAGATTGTACTGAAGTCAAACAACTAATACTTTATAAGTTTTGAATGCtat                                                >  1:109000‑M2/50‑141 (MQ=255)                                                                                                AGCAGTAAGATTATTTTC‑‑AATTAAGAAAATC‑TCTTACTGCTTTTTCTATGTTATGACCCCACCATCCTGTTACAAATTTTCTCGTATAGATTGTACTGAAGTCAAACAACTAATACTTTATAAGTTTTGAATGCTATATaa                                            <  1:173687‑M1/141‑1 (MQ=255)                                                                                                 GCAGTAAGATTATTTTC‑‑AATTAAGAAAATC‑TCTTACTGCTTTTTCTATGTTATGACCCCACCATCCTGTTACAAATTTTCTCTTCAAGATTGTACTGAAGTCAAACAACTAATACTTTATAAGTTTTGAATGCTATATaaa                                           <  1:105563‑M1/141‑1 (MQ=255)                                                                                                            attTTC‑‑AATTAAGAAAATC‑TCTTACTGCTTTTTCTATGTTATGACCCCACCATCCTGTTACAAATTTTCTCTTCAAGATTGTACTGAAGTCAAACAACTAATACTTTATAAGTTTTGAATGCTATATAAATGCTCGTAAGc                                <  2:118165/141‑1 (MQ=255)                                                                                                             ttttC‑‑AATTAAGAAAATC‑TCTTACTGCTTTTTCTATGTTATGACCCCACCATCCTGTTACAAATTTTCTCTTCAAGATTGTACTGAAGTCAAACAACTAATACTTTATAAGTTTTGAATGCTATATAAATGCTCGTAAGCa                               <  1:683146/141‑1 (MQ=255)                                                                                                              tttC‑‑AATTAAGAAAATC‑TCTTACTGCTTTTTCTATGTTATGACCCCACCATCCTGTTACAAATTTTCTCTTCAAGATTGTACTGAAGTCAAACAACTAATACTTTATAAGTTTTGAATGCTATATAAATGCTCGTAAGCAc                              >  1:308993/1‑141 (MQ=255)                                                                                                               ttttcttaattgaaaataatcttactgctttttCTATGTTATGACCCCACCATCCTGTTACAAATTTTCTCTTCAAGATTGTACTGAAGTCAAACAACTAATACTTTATAAGTTTTGAATGCTAAATAAATGCTCGTAAGc                                >  1:507401‑M2/34‑141 (MQ=255)                                                                                                                    aaTTAAGAAAATC‑TCTTACTGCTTTTTCTATGTTATGACCCCACCATCCTGTTACAAATTTTCTCTTCAAGATTGTACTGAAGTCAAACAACTAATACTTTATAAGTTTTGAATGCTATATAAATGCTCGTAAGCACCTTg                          <  1:446220/141‑1 (MQ=255)                                                                                                                       tAAGAAAATC‑TCTTACTGCTTTTTCTATGTTATGACCCCACCATCCTGTTACAAATTTTCTCTTCAAGATTGTACTGAAGTCAAACAACTAATACTTTATAAGTTTTGAATGCTATATAAATGCTCGTAAGCACCTTGttt                       <  1:780381/141‑1 (MQ=255)                                                                                                                         aGAAAATC‑TCTTACTGCTTTTTCTATGTTATGACCCCACCATCCTGTTACAAATTTTCTCTTCAAGATGGTACTGAAGTCAAACAACTAATACTTTATAAGTTGTGAATGCTATATAAATGCTCGTAAGCACCTTGTTTTg                     >  1:395011/1‑141 (MQ=255)                                                                                                                           aaaaTC‑TCTTACTGCTTTTTCTATGTTATGACCCCACCATCCTGTTACAAATTTTCTCTTCAAGATTGTACTGAAGTCAAACAACTAATACTTTATAAGTTTTGAATGCTATATAAATGCTCGTAAGCACCTTGTTTTGca                   <  2:315411/141‑1 (MQ=255)                                                                                                                                           tttttCTATGTTATGACCCCACCATCCTGTTACAAATTTTCTCTTCAAGATTGTACTGACGTCAAACAACCACTACCCTCTAAGCCTTCAATGCTATATAAATGCTCGTAAGCACCTTGTTTTGCAATCAATTCACGATGc    >  2:13212‑M2/6‑141 (MQ=255)                                                                                                                                           tttttCTATGTTATGACCCCACCATCCTGTTACAAATTTTCTCTTCAAGATTGTACTGAAGTCAAACAACTAATACTTTATAAGTTTTGAATGCTATATAAATGCTCGTAAGCACCTTGTTTTGCAATCAATTCACGATGc    >  1:714329‑M2/6‑141 (MQ=255)                                                                                                                                           tttttCTATGTTATGACCCCACCATCCTGTTACAAATTTTCTCTTAAAGATTGTACTGAAGTCAAACAACTAACACTTTGTAAGTTTTTAATGCTATATAAATGCTCGTAAGCACCTTGTTTTGCAATCAATTCACGATGc    >  2:64524‑M2/6‑141 (MQ=255)                                                                                                                                             tttCTATGTTATGACCCCACCATCCTGTTACAAATTTTCTCTTCAAGATTGTACTGAAGTCAAACAACTAATACTTTATAAGTTTTGAATGCTATATAAATGCTCGTAAGCACCTTGTTTTGCAATCAATTCACGATGCGt  <  1:500241‑M2/138‑1 (MQ=255)                                                                                                                                                |                                                                                                                                          TGAAGAAGACTTTGATTTATAACATTAAAACAATTTTATCAATTAATGCCACAATGAGATAAACTAATATTGAATCTCGAAATTAAATTTAAAAAAGCAGTAAGATTATTTTC‑‑AATTAAGAAAATC‑TCTTACTGCTTTTTCTATGTTATGACCCCACCATCCTGTTACAAATTTTCTCTTCAAGATTGTACTGAAGTCAAACAACTAATACTTTATAAGTTTTGAATGCTATATAAATGCTCGTAAGCACCTTGTTTTGCAATCAATTCACGATGCGT  >  USA300TCH1516_ALE/2008851‑2009128

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 37 ≤ 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.