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

ATTAGCTTTTTCACATATCATAGATCTGATGCAGACATTGAAATTGTTGAAGAAGACTTTGATTTATAACATTAAAACAATTTTATCAATTAATGCCACAATGAGATAAACTAATATTGAATCTCGAAATTAAATTTAAAAAAGCAGTAAGATTATTTTC‑‑AATTAAGAAAATC‑TCTTACTGCTTTTTCTATGTTATGACCCCACCATCCTGTTACAAATTTTCTCTTCAAGATTGTACTGAAGTCAAACAACTAATACTTTATAAGTTTTGAATGCTAT  >  USA300TCH1516_ALE/2008804‑2009082                                                                                                                                           |                                                                                                                                                acgcatcgtgaattgattgcaaaacaaggtgcttacgagcatttatatagcattcaaaacttataaagtattagttgtttgacttcagtacaatcttgaagagaaaatttgtaacaggatggtggggtcataacatagaaa                                                                                                                                               <  1:500241‑M1/3‑1 (MQ=255) aTTAGCTTTTTCACATATCATAGATCTGATGCAGACATTGAAATTGTTGAAGAAGACTTTGATTTATAACATTAAAACAATTTTATCAATTAATGCCACAATGAGATAAACTAATATTGAATCTCGAAATTAAATTTaaaa                                                                                                                                               >  1:35588/1‑141 (MQ=255)   gcatcgtgaattgattgcaaaacaaggtgcttacgagcatttatatagcattgaaggcttagagggtagtggttgtttgacgtcagtacaatcttgaagagaaaatttgtaacaggatggtggggtcataacatagaaaaa                                                                                                                                             >  2:13212‑M1/137‑141 (MQ=255)   gcatcgtgaattgattgcaaaacaaggtgcttacgagcatttatatagcattcaaaacttataaagtattagttgtttgacttcagtacaatcttgaagagaaaatttgtaacaggatggtggggtcataacatagaaaaa                                                                                                                                             >  1:714329‑M1/137‑141 (MQ=255)   gcatcgtgaattgattgcaaaacaaggtgcttacgagcatttatatagcattaaaaacttacaaagtgttagttgtttgacttcagtacaatctttaagagaaaatttgtaacaggatggtggggtcataacatagaaaaa                                                                                                                                             >  2:64524‑M1/137‑141 (MQ=255)          ttCACATATCATAGATCTGATGCAGACATTGAAATTGTTGAAGAAGACTTTGATTTATAACATTAAAACAATTTTATCAATTAATGCCACAATGAGATAAACTAATATTGAATCTCGAAATTAAATTTAAAAAAGCAGTaa                                                                                                                                      >  1:530781/1‑141 (MQ=255)           tCACATATCATAGATCTGATGCAGACATTGAAATTGTTGAAGAAGACTTTGATTTATAACATTAAAACAATTTTATCAATTAATGCCACAATGAGATAAACTAATATTGAATCTCGAAATTAAATTTAAAAAAGCAGTAAg                                                                                                                                     >  2:329871/1‑141 (MQ=255)            cacaTATCATAGATCTGATGCAGACATTGAAATTGTTGAAGAAGACTTTGATTTATAACATTAAAACAATTTTATCAATTAATGCCACAATGAGATAAACTAATATTGAATCTCGAAACTAAATTTAAAAAAGCAGTAAGa                                                                                                                                    >  1:132981/1‑141 (MQ=255)              caTATCATAGATCTGATGCAGACATTGAAATTGTTGAAGAAGACTTTGATTTATAACATTAAAACAATTTTATCAATTAATGCCACAATGAGATAAACTAATATTGAATCTCGAAATTAAATTTAAAAAAGCAGTAAGatt                                                                                                                                  >  2:24192/1‑141 (MQ=255)                 atCATAGATCTGATGCAGACATTGAAATTGTTGAAGAAGACTTTGATTTATAACATTAAAACAATTTTATCAATTAATGCCACAATGAGATAAACTAATATTGAAGCTCGAAATTAAATTTAAAAAAGCAGTAAGattatt                                                                                                                               <  1:686795/141‑1 (MQ=255)                          cTGATGCAGACATTGAAATTGTTGAAGAAGACTTTGATTTATAACATTAAAACAATTTTATCAATTAATGCCACAATGAGATAAACGAATATTGAATCTCGAAATTAAATTTAAAAAAGCAGTAAGATTATTTTC‑‑AATTaa                                                                                                                    >  1:173789/1‑141 (MQ=255)                           tGATGCAGACATTGAAATTGTTGAAGAAGACTTTGATTTATAACATTAAAACAATTTTATCAATTAATGCCACAATGCGCAAGACTAATATTGAATCTCGAAATTAAATTTAAAAAAGCAGTAAGATTATTTTC‑‑AATTAAg                                                                                                                   >  1:213766/1‑141 (MQ=255)                           tGATGCAGACATTGAAATTGTTGAAGAAGACTTTGATTTATAACATTAAAACAATTTTATCAATTAATGCCACAATGCAATAGGCGAATATTGAATCTCGAAATTAAATTTAAAAAAGCAGTAAGATTATTTTC‑‑AATTAAg                                                                                                                   >  1:213867/1‑141 (MQ=255)                           tGATGCACACATTGAAATTGTTGAAGAAGACTTTGATTTATAACATTAAAACAATTTTATCAATTAATGCCACAATGAGATAAACTAATATTGAATCTCGAAATTAAATTTAAAAAAGCAGTAAGATTATTTTC‑‑AATTAAg                                                                                                                   >  1:622802/1‑141 (MQ=255)                               gcttacgagcatttatttagcattcaaaacttataaagtattagttgtttgacttcagtacaatcttgaagagaaaatttgtaacaggatggtggggtcataacatagAAAAAGCAGTAAGATTATTTTC‑‑AATTAAGaaaa                                                                                                               >  1:507401‑M1/109‑141 (MQ=255)                                    cATTGAAATTGTTGAAGAAGACTTTGATTTATAACATTAAAACAATTTTATCAATTAATGCCACAATGAGATAAACTAATATTGAATCTCGAAATTAAATTTAAAAAAGCAGTAAGATTATTTTC‑‑AATTAAGAAAATc‑tct                                                                                                         <  2:4715/141‑1 (MQ=255)                                       tGAAATTGTTGAAGAAGACTTTGATTTATAACATTAAAACAATTTTATCAATTAATGCCACAATGAGATAAACTAATATTGAATCTCGAAATTAAATTTAAAAAAGCAGTAAGATTATTTTC‑‑AATTAAGAAAATC‑TCTTAc                                                                                                      <  2:288555/141‑1 (MQ=255)                                          aaTTGTTGAAGAAGACTTTGATTTATAACATTAAAACAATTTTATCAATTAATGCCACAATGAGATAAACTAATATTGAATCTCGAAATTAAATTTAAAAAAGCAGTAAGATTATTTTC‑‑AATTAAGAAAATC‑TCTTACTGc                                                                                                   <  1:661871/141‑1 (MQ=255)                                           aTTGTTGAAGAAGACTTTGATTTATAACATTAAAACAATTTTATCAATTAATGCCACAATGAGATAAACTAATATTGAATCTCGAAATTAAATTTAAAAAAGCAGTAAGATTATTTTC‑‑AATTAAGAAAATC‑TCTTACTGCt                                                                                                  <  2:191908/141‑1 (MQ=255)                                             tgttgAAGAAGACTTTGATTTATAACATTAAAACAATTTTATCAATTAATGCCACAATGAGATAAACTAATATTGAATCTCGAAATTAAATTTAAAAAAGCAGTAAGCTTATTTTC‑‑AATTAAGAAAATC‑TCTTACTGCttt                                                                                                <  1:409506/141‑1 (MQ=255)                                              gttgAAGAAGACTTTGATTTATAACATTAAAACAATTTTATCAATTAATGCCACAATGAGATAAACTAATATTGAATCTCGAAATTAAATTTAAAAAAGCAGTAAGATTATTTTC‑‑AATTAAGAAAATC‑TCTTACTGCtttt                                                                                               >  1:719154/1‑141 (MQ=255)                                               atagcattcaaaacttataaagtattagttgtttgacttcagtacaatcttgaagagaaaatttgtaacaggatggtggggtcataacatagAAAAAGCAGTAAGATTATTTTC‑‑AATTAAGAAAATC‑TCTTACTGCttttt                                                                                              >  1:109000‑M1/93‑141 (MQ=255)                                                tgAAGAAGACTTTGATTTATAACATTAAAACAATTTTATCAATTAATGCCACAATGAGATAAACTAATATTGAATCTCGAAATTAAATTTAAAAAAGCAGTAAGATTATTTTC‑‑AATTAAGAAAATC‑TCTTACTGCTTTTTc                                                                                             >  1:10863/1‑141 (MQ=255)                                                    gaagaCTTTGATTTATAACATTAAAACAATTTTATCAATTAATGCCACAATGAGATAAACTAATATTGAATCTCGAAATTAAATTTAAAAAAGCAGTAAGATTATTTTC‑‑AATTAAGAAAATC‑TCTTACTGCTTTTTCTATg                                                                                         >  1:256473/1‑141 (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        >  2:174808/1‑141 (MQ=255)                                                                                                                                     aattTAAAAAAGCAGTAAGATTATTTTC‑‑AATTAAGAAAATC‑TCTTACTGCTTTTTCTATGTTATGACCCCACCATCCTGTTACAAATTTTCTCTTCAAGATTGTACTGAAGTCAAACAACTAATACTTTATAAGTTTTGaa        >  1:60102/1‑141 (MQ=255)                                                                                                                                        ttAAAAAAGCAGTAAGATTATTTTC‑‑AATTAAGAAAATC‑TCTTACTGCTTTTTCTATGTTATGACCCCACCATCCTGTTACAAATTTTCTCTTCAAGATTGTACTGAAGTCAAACAACTAATACTTTATAAGTTTTGAATGc     <  1:236616/141‑1 (MQ=255)                                                                                                                                           AAAAAGCAGTAAGATTATTTTC‑‑AATTAAGAAAATC‑TCTTACTGCTTTTTCTATGTTATGACCCCACCATCCTGTTACAAATTTTCTCTTCAAGATTGTACTGAAGTCAAACAACTAATACTTTATAAGTTTTGAATGCtat  <  1:60926‑M1/141‑1 (MQ=255)                                                                                                                                           |                                                                                                                                                ATTAGCTTTTTCACATATCATAGATCTGATGCAGACATTGAAATTGTTGAAGAAGACTTTGATTTATAACATTAAAACAATTTTATCAATTAATGCCACAATGAGATAAACTAATATTGAATCTCGAAATTAAATTTAAAAAAGCAGTAAGATTATTTTC‑‑AATTAAGAAAATC‑TCTTACTGCTTTTTCTATGTTATGACCCCACCATCCTGTTACAAATTTTCTCTTCAAGATTGTACTGAAGTCAAACAACTAATACTTTATAAGTTTTGAATGCTAT  >  USA300TCH1516_ALE/2008804‑2009082

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.