New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	= 260294	49 (0.770)	3 (0.050)	3/238	NT	6.1%	intergenic (‑408/‑180)	potD_1/pflB	Spermidine/putrescine‑binding periplasmic protein/Formate acetyltransferase
	?	USA300TCH1516_ALE	= 260312	48 (0.820)					intergenic (‑426/‑162)	potD_1/pflB	Spermidine/putrescine‑binding periplasmic protein/Formate acetyltransferase

AAATCTTTCTAAGTGTTGATTTAACGCTTATCAACAATCATTTTTTATAAACAAATATATACTCCTAAATTAACTTTTAAAGCAATGAAAATAGTGAACATTATAACTGTTGTGTAACAG‑AAT‑‑GC‑AATTAGCATATTACTGTTACACAAATTAGTACAGTTTCTATGTTTTGACATACATTTGATGAAAATTGTACATAATTTATGTGAAAAAAATCACAACAAACATGCTACAATGACTATGAAAACGTTAACATAGCATTTCAAATTCAC  >  USA300TCH1516_ALE/260175‑260446                                                                                                                                              |                                                                                                                                       aaaTCTTTCTAAGTGTTGATTTAACGCTTATCAACAATCATTTTTTATAAACAAATATATACTCCTAAATTAACTTTTAAAGCAATGAAAATAGTGAACATTATAACTGTTGTGTAACAG‑AAT‑‑GC‑AATTAGCATATTActg                                                                                                                                     >  1:568920‑M2/1‑138 (MQ=255)  aaTCTTTCTAAGTGTTGATTTAACGCTTATCAACAATCATTTTTTATAAACAAATATATACTCCTAAATTAACTTTTAAAGCAATGAAAATAGTGAACATTATAACTGTTGTGTAACAG‑AAT‑‑GC‑AATTAGCATATTActgt                                                                                                                                    >  1:505311‑M2/1‑137 (MQ=255)  aaTCTTTCTAAGTGTTGATTTAACGCTTATCAACAATCATTTTTTATAAACAAATATATACTCCTAAATTAACTTTTAAAGCAATGAAAATAGTGAACATTATAACTGTTGTGTAACAG‑AAT‑‑GC‑AATTAGAATATTAatgt                                                                                                                                    <  1:275238‑M2/141‑5 (MQ=255)      tttCTAAGTGTTGATTTAACGCTTATCAACAATCATTTTTTATAAACAAATATATACTCCTAAATTAACTTTTAAAGCAATGAAAATAGTGAACATTATAACTGTTGTGTAACAG‑AAT‑‑GC‑AATTAGCATATTActgttaca                                                                                                                                >  1:461531‑M2/1‑133 (MQ=255)        tCTAAGTGTTGATTTAACGCTTATCAACAATCATTTTTTATAAACAAATATATACTCCTAAATTAACTTTTAAAGCAATGAAAATAGTGAACATTATAACTGTTGTGTAACAG‑AAT‑‑GC‑AATTAGCATATTActgttacaca                                                                                                                              >  2:462013‑M2/1‑131 (MQ=255)        tCTAAGTGTTGATTTAACGCTTATCAACAATCATTTTTTATAAACAAATATATACTCCTAAATTAACTTTTAAAGCAATGAAAATAGTGAACATTATAACTGTTGTGTAACAG‑AAT‑‑GC‑AATTAGCATATTActgttacaca                                                                                                                              >  2:462321‑M2/1‑131 (MQ=255)           aaGTGTTGATTTAACGCTTATCAACAATCATTTTTTATAAACAAATATATACTCCTAAATTAACTTTTAAAGCAATGAAAATAGTGAACATTATAACTGTTGTGTAACAG‑AAT‑‑GC‑AATTAGCATATTACTGTTACACAAAt                                                                                                                           <  2:276289/141‑1 (MQ=255)            aGTGTTGATTTAACGCCTATCAACAATCATTTTTTATAAAGAAATATATATTCCTAAATTAACTTTTAAAACAATAAGAATAGAAAACATCATAACTGGTGTGTAACAG‑AAG‑‑GA‑AAGAAGCATATTACTAATACACaaaaa                                                                                                                          >  1:381563/1‑139 (MQ=255)              tgtTGATTTAACGCTTATCAACAATCATTTTTTATAAACAAATATATACTCCTAAATTAACTTTTAAAGCAATGAAAATAGTGAACATTATAACTGTTGTGTAACAG‑AAT‑‑GC‑AATTAGCATATTACTGTTACACAAATTAg                                                                                                                        <  1:443145/141‑1 (MQ=255)               gtTGATTTAACGCTTATCAACAATCATTTTTTATAAACAAATATATACTCCTAAATTAACTTTTAAAGCAATGAAAATAGTGAACATTATAACTGTTGTGTAACAG‑AAT‑‑GC‑AATTAGCATATTACTGTTACACAAATTAGt                                                                                                                       >  1:403900/1‑141 (MQ=255)               gtTGATTTAACGCTTAGCAACAATCATTTTTTATAAACAAATATATACTCCTAAATTAACTTTTAAAGCAATGAAAATAGTGAACATTATAACTGTTGTGTAACAG‑AAT‑‑GC‑AATTAGCATATTACTGTTACACAAATTAGt                                                                                                                       >  1:456557/1‑141 (MQ=255)                ttGATTTAACGCTTATCAACAATCATTTTTTATAAACAAATATATACTCCTAAATTAACTTTTAAAGCAATGAAAATAGTGAACATTATAACTGTTGTGTAACAG‑AAT‑‑GC‑AATTAGCATATTACTGTTACACAAATTAGTa                                                                                                                      <  1:762333/141‑1 (MQ=255)                 tGATTTAACGCTTATCAACAATCATTTTTTATAAACAAATATATACTCCTAAATTAACTTTTAAAGCAATGAAAATAGTGAACATTATAACTGTTGTGTAACAG‑AAT‑‑GC‑AATTAGCATATTACTGTTACACAAATTAGTAc                                                                                                                     <  1:434941/141‑1 (MQ=255)                          gCTTATCAACAATCATTTTTTATAAACAAATATATACTCCTAAATTAACTTTTAAAGCAATGAAAATAGTGAACATTATAACTGTTGTGTAACAG‑AAT‑‑GC‑AATTAGCATATTACTGTTACACAAATTAGTACAGTTTCTAt                                                                                                            <  2:324156/141‑1 (MQ=255)                            ttATCAACAATCATTTTTTATAAACAAATATATTCTCCTAAATTAACTTTTAAAGCAATGAAAATAGTGAACATTATACCTGTTGTGTAACAG‑AAT‑‑GC‑AATTAGCATATTACTGTTACACAAATTAGTACAGTTTCTATGt                                                                                                          <  1:267322/141‑1 (MQ=255)                            ttATCAACAATCATTTTTTATAAACAAATATATACTCCTAAATTAACTTTTAAAGCAATGAAAATAGTGAACATTATAACTGTTGTGTAACAG‑AAT‑‑GC‑AATTAGCATATTACTGTTACACAAATTAGTACAGTTTCTATGt                                                                                                          <  2:571737/141‑1 (MQ=255)                                 aacaaTCATTTTTTATAAACAAATATATACTCCTAAATTAACTTTTAAAGTAATGAAAATAGTGAACATTATAACTGTTGTGTAACAG‑AAT‑‑GC‑AATTAGCATATTACTGTTACACAAATTAGTACAGTTTCTATGTTTTGa                                                                                                     >  2:565165/1‑141 (MQ=255)                                   caaTCATTTTTTATAAACAAATATATACTCCTAAATTAACTTTTAAAGCAATGAAAATAGTGAACATTATAACTGTTGTGTAACAG‑AAT‑‑GC‑AATTAGCATATTACTGTTACACAAATTAGTACAGTTTCTATGTTTTGaca                                                                                                   >  2:103828/1‑141 (MQ=255)                                   aaataatTTTTTATAAACAAATATATACTCCTAAATGAACTTTTAAAGCAATGAAAATAGTGAACATTATAACTGTTGTGTAACAG‑AAT‑‑GC‑AATTACCATATTAATGTTAGATAAATTAGTACAGGTTCGATTTTGGGaca                                                                                                   <  2:448955/140‑1 (MQ=255)                                              tataAACAAATATATACTCCTAAATTAACTTTTAAAGCAATGAAAATAGTGAACATTATAACTGTTGTGTAACAG‑AAT‑‑GC‑AATTAGCATATTACTGTTACACAAATTAGTACAGTTTCTATGTTTTGACATACATTtgatg                                                                                        <  2:730515/141‑1 (MQ=255)                                              tataAAAAAATATATTCCCCCAAATTAACTTTTAAAGCAATGAAAATAGTGAACATTATAACTGTTGTGTAACAG‑AAT‑‑GC‑AATTAGCATATTACTGTTACACAAATTTGTGCGTGGCCTATGTTTTGACATACATTtgatg                                                                                        <  1:184055/141‑1 (MQ=255)                                                 aaaCAAATATATACTCCTAAATTAACTTTTAAAGCAATGAAAATAGTGAACATTATAACTGTTGTGTAACAG‑AAT‑‑GC‑AATTAGCATATTACTGTTACACAAATTAGTACAGTTTCTATGTTTTGACATACATTTGATGaaa                                                                                     <  1:56731/141‑1 (MQ=255)                                                        tatataCTCCTAAATTAACTTTTAAATCAATTAAAATAGTAAACATTATAACTGTTGTGTAACAG‑AAT‑‑GC‑AATTAGCATATTACTGTTACACAAATTAGTACAGTTTCTATGTTTTGACATACATTTGATGAAAATTGTAc                                                                              <  1:182317/141‑1 (MQ=255)                                                            taCTCCTAAATTAACTTTTAAAGCAATGAAAATAGTGAACATTATAACTGTTGTGTAACAGTAATATGCTAATT‑GCAT‑T‑tgttacacaacagttataatgttcactattttcattgctttaaaagttaatttaggagta                                                                             >  1:629436‑M2/1‑80 (MQ=255)                                                            taCTCCTAAATTAACTTTTAAAGCAATGAAAATAGTGAACATTATAACTGTTGTGTAACAGTAATATGC‑TAATTGCAT‑T‑tgttacacaacagttataatgttcactattttcattgctttaaaagttaatttaggagta                                                                             <  2:629436‑M2/140‑61 (MQ=255)                                                            taCTCCTAAATTAACTTTTAAAGCAATGAAAATAGTGAACATTATAACTGTTGTGTAACAG‑AAT‑‑GC‑AATTAGCATATTACTGTTACACAAATTAGTACAGTTTCTATGTTTTGACATACATTTAATGAAAATTGACCATaa                                                                          >  2:740407/1‑141 (MQ=255)                                                                  tAAATTAACTTTTAAAGCAATGAAAATAGTGAACATTATAACTGTTGTGTAACAG‑AAT‑‑GC‑AATTAGCATATTACTGTTACACAAATTAGTACAGTTTCTATGTTTTGACATACATTTGATGAAAATTGTACATAATTTAtt                                                                    >  1:657825/1‑140 (MQ=255)                                                                  tAAATTAACTTTTAAAGCAATGAAAATAGTGAACATTATAACTGTTGTGTAACAG‑AAT‑‑GC‑AATTAGCATATTACTGTTACACAAATTAGTACAGTTTCTATGTTTTGACATACATTTGATGAAAATTGTACATAATTTAtg                                                                    >  1:622675/1‑141 (MQ=255)                                                                  tAAATTAACTTGTAAAGCAATGAAAATAGTGAACATTATAACTGTTGTGTAACAG‑AAT‑‑GC‑AATTAGCATATTACTGTTACACAAATTAGTACAGTTTCTATGTTTTGACATACATTTGATGAAAATTGTACATAATTTAtg                                                                    <  2:593009/141‑1 (MQ=255)                                                                       tAACTTTTAAAGAAATGAAAATAGTGAACATTATATCTGTTGTGTAACAG‑AAT‑‑GC‑AATTAGCATATTACTGTTACACAAATTAGTACAGTTTCTATGTTTTGACATACATTTGATGAAAATTGTACATAATTTATGTGaaa                                                               <  1:79267/141‑1 (MQ=255)                                                                           ttttAAAGCAATGAAAATAGTGAACATTATAACTGTTGTGTAACAG‑AAT‑‑GC‑AATTAGCATATTACTGTTACACAAATTAGTACAGTTTCTATGTTTTGACATACATTTGATGAAAATTGTACATAATTTATGTGaaaaaaa                                                           >  1:733320/1‑141 (MQ=255)                                                                             ttAAAGCAATGAAAATAGTGAACATGATAACTGTTGTGTAACAG‑AAT‑‑GC‑AATTAGCATATTACTGTTACACAAATTAGTACAGTTTCTATGTTTTGACATACATTTGATGAAAATTGTACATAATTTATGTGAAAAAAATc                                                         <  2:36734/141‑1 (MQ=255)                                                                                 aGCAATGAAAATAGTGAACATTATAACTGTTGTGTAACAG‑AAT‑‑GC‑AATTAGCATATTTCTGTTACACAAATTAGTACAGTTTTTATGTTTTGACATACATTTGATGAAAATTGTACATAATTTATGTGAAAAAAATCacaa                                                     <  2:220920/141‑1 (MQ=255)                                                                                 aGCAATGAAAATAGTGAACATTATAACTGTTGTGTAACAG‑AAT‑‑GC‑AATTAGCATATTACTGTTACACAAATTAGTACAGTTTCTATGTTTTGACATACATTTGATGAAACTTGTACATAATTTATGTAAAAAAAATCacaa                                                     >  2:747506/1‑141 (MQ=255)                                                                                   cAATGAAAATAGTGAACATTATAACTGTTGTGTAACAG‑AAT‑‑GC‑AATTAGCATATTACTGTTACACAAATTAGTACAGTTTCTATGTTTTGACATACATTTGATGAAAATTGTACATAATTTATGTGAAAAAAATCacaaca                                                   <  1:54064/141‑1 (MQ=255)                                                                                      tGAAAATAGTGAACATTATAACTGTTGTGTAACAG‑AAT‑‑GC‑AATTAGCATATTACTGTTACACAAATTAGTACAGTTTCTATGTTTTAACATACATTAGATGAAAATTGTACATAATTTATAGGAAAATAATCACagcaaac                                                >  2:217765/1‑141 (MQ=255)                                                                                        aaaaTAGTGAACATTATAACTGTTGTGTAACAG‑AAT‑‑GC‑AATTAGCATATTACTGTTACACAAATTAGTACAGTTTCTATGTTTTGACATACATTTGATGAAAATTGTACATAATTTATGTGAAAAAAATCACAACAAACAt                                              >  2:340430/1‑141 (MQ=255)                                                                                         aaaTAGTGAACATTATAACTTTTGTGTAACAG‑AAT‑‑GC‑AATTAGCATATTACTGTTACACAAATTAGTACAGTTTCTATGTTTTGACATACATTTGATGAAAATTGTACATAATTTATGTGAAAAAAATCACAACAAACATg                                             <  1:668010/141‑1 (MQ=255)                                                                                         aaaTAGTGAACATTATAACTGTTGTGTAACAG‑AAT‑‑GC‑AATTAGCATATTACTGTTACACAAATTAGTACAGTTTCTATGTTTTGACATACATTTGATGAAAATTGTACATAATTTATGTGAAAAAAATCACAACAAACATg                                             >  2:169284/1‑141 (MQ=255)                                                                                          aaTAGTGAACATTATAACTGTTGTGTAACAG‑AAT‑‑GC‑AATTAGCATATTACTGTTACACAAATTAGTACAGTTTCTATGTTTTGACATACATTTGATGAAAATTGTACATAATTTATGTGAAAAAAATCACAACAAACATGc                                            >  1:735993/1‑141 (MQ=255)                                                                                             aGTGAACATTAGAACTGTTGTGTAACAG‑AAT‑‑GC‑AATTAGCATATTACTGTTACACAAATTAGTACAGTTTCTATGTTTTGACATACATTTGATGAAAATTGTACATAATTTATGTGAAAAAAATCACAACAAACATGCTAc                                         <  2:275238/141‑1 (MQ=255)                                                                                               tGAACATTATAACTGTTGTGTAACAG‑AAT‑‑GC‑AATTAGCATATTACTGTTACACAAATTAGTACAGTTTCTATGTTTTGACATACATTTGATGAAAATTGTACATAATTTATGTGAAAAAAATCACAACAAACATGCTACaa                                       <  1:70400/141‑1 (MQ=255)                                                                                                      tataACTGTTGTGTAACAG‑AAT‑‑GC‑AATTAGCATATTACTGTTACACAAATTAGTACAGTTTCTATGTTTTGACATACATTTGATGAAAATTGTACATAATTTATGTGAAAAAAATCACAACAAACATGCTACAATGACTAt                                <  1:565165/141‑1 (MQ=255)                                                                                                         aaCTGTTGTGTAACAG‑AAT‑‑GC‑AATTAGCATATTACTGTTACACAAATTAGTACAGTTTCTATGTTTTGACATACATTTGATGAAAATTGTACATAATTTATGTGAAAAAAATCACAACAAACATGCTACAATGACTATGaa                             >  1:112119/1‑141 (MQ=255)                                                                                                          aCTGTTGTGTAACAG‑AAT‑‑GC‑AATTAGCATATTACTGTTACACAAATTAGTACAGTTTCTATGTTTTGACATACATTTGATGAAAATTGTACATAATTTATGTGAAAAAAATCACAACAAACATGCTACAATGACTATGaaa                            <  2:55595/141‑1 (MQ=255)                                                                                                           cTGTTGTGTAACAG‑AAT‑‑GT‑AATTAGCATATTActgttacacaacagttataatgttcactattttcattgctttaaaagttaatttaggagtatatatttgtttataaaaaatgattgttgataagcgttaaatcaacact                           >  2:381563‑M2/1‑32 (MQ=255)                                                                                                             gttgtGTAACAG‑AAT‑‑GC‑CATTAGCATATTACTGTTACACAAATTAGTACAGTTTCTATGTTTTGACATACATTTGATGAAAATTGTACATAATTTATGTGAAAAAAATCACAACAAACATGCTACAATGACTATGAAAACg                         >  2:594469/1‑141 (MQ=255)                                                                                                                gtgtAACAG‑AAT‑‑GC‑AATTAGCATATTACTGTTACACAAATTAGTACAGTTTCTATGTTTTGACATACATTTGATGAAAATTGTACATAATTTATGTGAAAAAAATCACAACAAACATGCTACAATGACTATGAAAACGTTa                      >  1:479814/1‑141 (MQ=255)                                                                                                                  gtAACAG‑AAT‑‑GC‑AATTAGCATATTACTGTTACACAAATTAGTACAGTTTCTATGTTTTGACATACATTTGATGAAAATTGTACATAATTTATGTGAAAAAAATCACACCAAACATGCTACAATGACTATGAAAACGTTAAc                    >  1:15089/1‑141 (MQ=255)                                                                                                                  gtAACAG‑AAT‑‑GC‑AATTAGCATATTACTGTTACACAAATTAGTACAGTTTCTATGTTTTGACATACATTTGATGAAAATTGTACATAATTTATGTGAAAAAAATCACAACAAACATGCTACAATGACTATGAAAACGTTAAc                    <  2:78645/141‑1 (MQ=255)                                                                                                                     aCAG‑TAT‑‑GC‑AAGTAGCATATTTCTGTTACACAAATTAGTACAGTTACCATGATGTGACATACATTTGATGAAAACTGTACATGATTTTTGTGAAAGAAATCACACAAAAAAAGCTACACAGAAGATGAAAAGGTTAACATa                 >  2:304037/1‑141 (MQ=255)                                                                                                                     aCAG‑AAT‑‑GC‑AATTAGCATATTACTGTTACACAAATTAGTACAGTTTCTATGTTTTGACATACATTTGATGAAAATTGTACATAATTTATGTGAAAAAAATCACAACAAACATGCTACAATGACTATGAAAACGTTAActcc                 >  2:377878/1‑138 (MQ=255)                                                                                                                     aCAG‑AAT‑‑GC‑AATTAGCATATTACTGTTACACAAATTAGTACAGTTTCTATGTTTTGACATACATTTGATGAAAATTGTACATAATTTATGTGAAAAAAATCACAACAAACATGCTACAATGACTATGAAAACGTTAACATa                 >  1:628697/1‑141 (MQ=255)                                                                                                                      cAG‑AAT‑‑GC‑AATTAGCATATTACTGTTACACAAATTAGTACAGTTTCTATGTTTTGACATACATTTGATGAAAATTGTACATAATTTATGTGAAAAAAATCACAACAAACATGCTACAAAGACTATGAAAACGTTAAAATAg                >  1:134115/1‑141 (MQ=255)                                                                                                                          aaT‑‑GC‑TATTAGTATATTACTGTTACATAATGTAGTACAGTTTCTATGTTTTGACATACATTTGATGAAAATTGTACTTAATTTATGTGAAAAAAATCACAACAAACATGCTACAATGACTATGAAAACGTTAACATAGCAt             <  2:74030/141‑1 (MQ=255)                                                                                                                               gC‑AATTAGCATATTACTGTTACACAAATTAGTACAGTTTCTATGTTTTGACATACATTTGATGAAAATTGTACATAATTTATGTGAAAAAAATCACAACAAACATGCTACAATGACTATGAAAACGTTAACATAGCATTTc          >  2:647966/1‑141 (MQ=255)                                                                                                                                   aTTAGCAGATTACTTTTACACAAATTAGGACAGTTTCTATGTTTTGACATACATTTGATGAAAATTGTACATAATTTATGTGAAAAAAATTACAAGTATTACAGTACAATGACTATGAAAAAGTTAACATAGCATTTGaaa       >  2:538215/1‑141 (MQ=255)                                                                                                                                      aGCATATTACTGTTACACAAATTAGTACAGTTTCTATGTTTTGACATACATTTGATGAAAATTGTACATAATTTATGTGAAAAAAATCACAACAAACATGCTACAATGACTATGAAAACGTTAACATAGCATTTCAAATTc    >  2:20242/1‑141 (MQ=255)                                                                                                                                        cATATTACTGTTACACAAATTAGTACAGTTTCTATGTTTTGACATACATTTGATGAAAATTGTACATAATTTATGTGAAAAAAATCACAACAAACATGCTACAATGACTATGAAAACGTTAGCATACCATTTCAAATTcac  <  1:422897/141‑1 (MQ=255)                                                                                                                                        aatatTACTGTTACACAAATTAGTACAGTTTCTATGTTTTGACATACATTTGACGAAAATTGTACATAATTTATGTGAAAAAAATCACCACAAAACTGCTACAAGGACTATGAAAACGTTAACATAGCATTTCAAATTcac  <  2:504325/140‑1 (MQ=255)                                                                                                                                              |                                                                                                                                       AAATCTTTCTAAGTGTTGATTTAACGCTTATCAACAATCATTTTTTATAAACAAATATATACTCCTAAATTAACTTTTAAAGCAATGAAAATAGTGAACATTATAACTGTTGTGTAACAG‑AAT‑‑GC‑AATTAGCATATTACTGTTACACAAATTAGTACAGTTTCTATGTTTTGACATACATTTGATGAAAATTGTACATAATTTATGTGAAAAAAATCACAACAAACATGCTACAATGACTATGAAAACGTTAACATAGCATTTCAAATTCAC  >  USA300TCH1516_ALE/260175‑260446

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ 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.