New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	895785 =	22 (0.790)	39 (1.600)	25/246	0.1	63.8%	coding (806/822 nt)	metQ_2	Methionine‑binding lipoprotein MetQ
	?	USA300TCH1516_ALE	= 909740	25 (1.030)					intergenic (‑663/‑371)	USA300HOU_RS04500/csbD_1	hypothetical protein/Stress response protein CsbD

AGTGCGAAAGATAATCCTTATGCAAACTTAATTGCTGTTAAAGAAGGACATCAAGATGATAAGAAAATCAAAGCATTAATTGAAGTATTACAATCTAAAGATATTCAAGACTTCATTAATGAAAAATACAATGGTGCAGTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACGATTAAGGGGTTATTTTTGTGGTATTGAAAATAAAAAAGGGCACAAAAGGGGCAGTATATGCAAATTATCGAATTTTAAACAAAAAAA  >  USA300TCH1516_ALE/895646‑895923                                                                                                                                            |                                                                                                                                           gttgttttcaagggcaaaaaaagggcataattttgaaacaaagggcaagggtatgaataataaattatcttgaaaattttataaatgcatatataacaatgttttgattgcccttgaacttccttgataatctggctaatt                                                                                                                                           <  2:186661‑M1/2‑1 (MQ=255)  ttgttttcaagggcaaaaaaagggcataattttgaaacaaagggcaagggtatgaataataaattatcttgaaaattttataaatgcatatataataatgttttgattgcccttgaacttacttgataatctggctcattt                                                                                                                                          <  2:302333‑M1/3‑2 (MQ=255)  ttgttttcaagggcaaaaaaagggcataattttgaaacaaagggcaagggtatgaataataaattatcttgaaaattttataaatgcatatataacaatgttttgattgcccttgaacttccttgataatctggctaatta                                                                                                                                          <  1:119285‑M1/3‑1 (MQ=255)  gTGCGAAAGATAATCCTTATGCAAACTTAATTGCTGTTAAAGAAGGACATCAAGATGATAAGAAAATCAAAGCATTAATTGAAGTATTACAATCTAAAGATATTCAAGACTTCATTAATGAAAAATACAATGGTGCAGTTa                                                                                                                                          >  1:134510/1‑141 (MQ=255)                   tATGCAAACTTAATTGCTGTTAAAGAAGGACATCAAGATGATAAGAAAATCAAAGCATTAATTGAAGTATTACAATCTAAAGATATTCAAGACTTCATTAATGAAAAATACAATGGTGCAGTTATTCCTGCTAAATAATAc                                                                                                                         >  1:1500/1‑141 (MQ=255)                        ggtataattttgaaacaaagggaaagggtatgaataataaattatcttgaaaattttataaatgcatatataacaatgttttgattgcccttgaacttccttgataatctggctaaTTATTCCTGCTAAATAATACCAAtt                                                                                                                    >  2:109442‑M1/117‑141 (MQ=255)                           cTTAATTGCTGTTAAAGAATGACATCAAGATGATAAGAAAATCAAAGCATTAATTGAAGTATTACAATCTAAAGATAATCAAGACTTCATTAATGAAAAATACAATGGTGCAGTTATTCCTGCTATATAATACCAATtaaa                                                                                                                 <  1:14776/141‑1 (MQ=255)                           cTTAATTGCTGTTAAAGAAGGACATCAAGATGATAAGAAAATCAAAGCATTAATTGAAGTATTACAATCTAAAGATATTCAAGACTTCATTAATGAAAAATACAATGGTGCAGTTATTCCTGCTAAATAATACCAATtaaa                                                                                                                 <  1:168314/141‑1 (MQ=255)                            taattttgaaacaaagggcaaggtgatgaataataaattatcttgaaaattttataaatgcatatataacaatgttttgattgcccttgaacttccttgataatctggctaaTTATTCCTGCTAAATAATACCAATtaaat                                                                                                                >  2:36025‑M1/113‑141 (MQ=255)                            taattttgaaacaaagggcaagggtatgaataataaattatcttgaaaattttataaatgcatatataacaatgttttgattgcccttgaacttccttgataatctggctaaTTATTCCTGCTAAATAATACCAATtaaat                                                                                                                >  2:303256‑M1/113‑141 (MQ=255)                             aattttgaaacaaagggcaagggtatgaataataaattatcttgaaaattttataaatgcatatataacaatgttttgattgcccttgaacttccttgataatctggctaaTTATTCCTGCTAAATAATACCAATtaaata                                                                                                               >  1:217205‑M1/112‑141 (MQ=255)                             aattttgaaacaaagggcaagggtatgaataataaattatcttgaaaattttataaatgcatatataacaatgttttgattgcccttgaactaccttgataatctggctaaTTATTCCTGCTAAATAATACCAATtaaata                                                                                                               >  2:212635‑M1/112‑141 (MQ=255)                              aaTTGCTGTTAAAGAAGGACATCAAGATGATAAGAAAATCAAAGCATTAATTGAAGTATTACAATCTAAAGATATTCAAGACTTCATTAATGAAAAATACAATGGTGCAGTTATTCCTGCTAAATAATACCAATtaaataa                                                                                                              >  2:291455/1‑141 (MQ=255)                              aaTTGCTGTTAAAGAAGGACATCAAGATGATAAGAAAATCAAAGCATTAATTGAAGTATTACAATCTAAAGATATTCAAGACTTCATTAATGAAAAATACAATGGTGCAGTTATTCCTGCTAAATAATACCAATtaaataa                                                                                                              >  1:157157/1‑141 (MQ=255)                               ttttgaaacaaagggcaagtgtatgaataataaattatcttgaaaattttataaatgcatatataacaatgttttgattgcccttgaacttccttgataatctggctaaTTATTCCTGCTAAATAATACCAATtaaataaa                                                                                                             >  2:210122‑M1/110‑141 (MQ=255)                               ttttgaaacaaagggcaagggtatgaataataaattatcttgaaaattttataaatgcatatataacaatgttttgattgcccttgaacttccttgataatatggctaaTTATTCCTGCTAAATAATACCAATtaaataaa                                                                                                             >  1:169249‑M1/110‑141 (MQ=255)                                ttGCAGTTAAAGAAGGACATCAAGATAATAAGAAAATCAAAGCATTAATTGAAGTATTACAATCTAAAGATATTCAAGACTTCATTAATGAAAAATACAATGGTGCAGTTATTCCTGCTAAATAATACCAATTAAATacaa                                                                                                            <  2:315989/141‑1 (MQ=255)                                  gCTGTTAAAGAAGGACATCAAGATGATAAGAAAATCAAAGCATTAATTGAAGTATTACAATCTAAAGATATTCAAGACTTCATTAATGAAAAATACAATGGTGCAGTTATTCCTGCTAAATAATACCAATTAAATAAAAAt                                                                                                          <  1:169769/141‑1 (MQ=255)                                           gaagGACATCAAGATGATAAGAAAATCAAAGCATTAATTGAAGTATTACAATCTAAAGATATTCAAGACTTCATTAATGAAAAATACAATGGTGCAGTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTtaa                                                                                                 <  2:41730/141‑1 (MQ=255)                                             agGACATCAAGATGATAAGAAAATCAAAGCATTAATTGAAGTATTACAATCTAAAGATATTCAAGACTTCATTAATGAAAAATACAATGGTGCAGTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTtaata                                                                                               >  1:261259/1‑141 (MQ=255)                                              caagggtatgaataataaattatcttgaaaattttataaatgcatatataacaatgttttgattgcccttgaacttccttgataatctggctaaTTATTCCTGCTAAATAATACCAATTAAATAAAACTACCCCTtactaa                                                                                              <  2:142569‑M1/47‑1 (MQ=255)                                              caagggtatgaataataaattatcttgaaaattttataaatgcatatataacaatgttttgattgccattgaacttccttgataatctggctaaTTATTCCTGCTAAATAATACCAATTAAATAAAAATATCCTTtaataa                                                                                              <  2:300361‑M1/47‑1 (MQ=255)                                                  ggtatgaataataaattatcttgaaaattttataaatgcatatataacaatgttttgattgcccttgaacttccttgataatctggctaaTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATaacaac                                                                                          >  2:72464‑M1/91‑141 (MQ=255)                                                       gatgatAAGAAAATCAAAGCATTAATTGAAGTATTACAATCTAAAGATATTCAAGACTTCATTAATGAAAAATACAATGGTGCAGTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACGATTa                                                                                     >  1:3378/1‑141 (MQ=255)                                                        aagatTAGCAAATAAAAGCAATAAATAAAGTATTAAAATCTCACGATATTCAAGACTTCATAAATGAAAAATAAAATAACGTAGTTATTACTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATAACCACGATTaa                                                                                    <  2:64244/139‑1 (MQ=255)                                                             taaagtatcttgaaaattttataaatgcatatataacaatgttttgattgcccttgaacttccttgataatctggctaaTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACGATTAAGGGGt                                                                               >  2:141270‑M1/80‑141 (MQ=255)                                                                  tatcttgaaaattttataaatgcatatataacaatgttttgattgcccttgaacttccttgataatctggctaaTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACGATTAAGGGGTTAttt                                                                          >  1:193601‑M1/75‑141 (MQ=255)                                                                   atcttgaaaattttataaatgcatatataacaatgttttgattgcccttgaacttccttgataatctggctaaTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACGATTAAGGGGTTAtttt                                                                         >  1:186661‑M1/74‑141 (MQ=255)                                                                     cttgaaaattttataaatgcatatataacaatgttttgattgcccttgaacttccttgataatctggctaaTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACGATTAAGGGGTTATTTTtg                                                                       >  1:150909‑M1/72‑141 (MQ=255)                                                                     cttgaaaattttataaatgcatatataacaatgttttgattgcccttgaacttccttgataatctggctaaTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACGATTAAGGGGTTATTTTtg                                                                       >  1:301372‑M1/72‑141 (MQ=255)                                                                      ttgaaaattttataaatgcatatataacaatgttttgattgcccttgaacttccttgataatctggctaaTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACGATTAACGGGTTATTTTtgt                                                                      <  1:175824‑M1/71‑1 (MQ=255)                                                                            ttAATTGAAGTATTACAATCTAAAGATATTCAAGACTTCATTAATGAAAAATACAATGGTGCAGTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACGATTAAGGGGTTATTTTTGTGGTAtt                                                                >  1:32436/1‑141 (MQ=255)                                                                                tataaatgcatatataacaatggtttgattgcccgtgaatttccttgagaatctggctaaTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACGATTAAGGGGTTATTTTTGTGGTATTGaaa                                                            >  2:77860‑M1/61‑141 (MQ=255)                                                                                 ataaatgcatatataacaatgttttgattgcccttgaacttccttgataatctggctaaTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACGATTAAGGGGTTATTTTTGTGGTATTGaaaa                                                           <  1:276703‑M1/82‑1 (MQ=255)                                                                                              tCTAAAGATATTCAAGACTTCATTAATGAAAAATACAATGAAGCAGTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACGATTAAGGGGTTATTTTTGTGGTATTGAAAATAAAAAAGGGcac                                              <  2:175780/141‑1 (MQ=255)                                                                                               aacaatgttttgattgcccttgaacttccttgataatctggctaaTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACGATTAAGGGGTTATTTTTGTGGTATTGAAAATAAAAAAGGGcaca                                             <  1:6635‑M1/96‑1 (MQ=255)                                                                                                  aatgttttgattgcgcttgaacttccttgataatctggctaaTTATTCCTGCTAAATAATACAAATTAAATAAAAATACCCTTTAATAACAACGATTAAGGGGTTATTTTTGTGGTATTGAAAATAAAAAAGGGCACaaaa                                          >  2:161024‑M1/43‑141 (MQ=255)                                                                                                  aatgttttgattgcccttgaacttccttgataatctggctaaTTATTCCTGCTTAATAATACGATTTGAGTATGAGTACCCTTTCATAGCACCGATTAAGGGGTTATTTTTGTGGTATTGAAAATAAAAAAGGGCACaaaa                                          >  1:70717‑M1/43‑141 (MQ=255)                                                                                                  aaggttttgattgctcttgaacttccttgataatctggctaaTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACGATTAAGGGGTTATTTTTGTGGTATTGAAAAGAAGAAAGGGCACaaaa                                          >  2:282338‑M1/43‑141 (MQ=255)                                                                                                  aaggttttgattgcccttgaacttccttgataatctggctaaTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACGATTAAGGGGTTATTTTTGTGGTATTGAAAATAAAAAAGGGCACaaaa                                          >  2:269436‑M1/43‑141 (MQ=255)                                                                                                  aaGATATTCAAGACTTCATTAATGAAAAATACAATGGTGCAGTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACGATTAAGGGGTTATTTTTGTGGTATTGAAAATAAAAAAGGGCACaaaa                                          <  1:297616/141‑1 (MQ=255)                                                                                                   aGATATTCAAGACTTCATTAATGAAAAATACAATGGTGCAGTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACGATTAAGATGTTATTTATGTGCAAATGAAAATAAAAAAGGACACAACAg                                         >  2:51748/1‑141 (MQ=255)                                                                                                   aGATATTCAAGACTTCAGTAATGAAAAATACAATGGTGCAGTTATGCCTGCGAAAAAAGACCAATAAAATAAAAATACCCGTGAATAACAACGAGTAAGGGGTTATTTTTGTGGTATTGAAAATAAAAAAGGGCACAAAAg                                         <  1:55956/141‑1 (MQ=255)                                                                                                     atatTCAAGACTTCATTAATGAAAAATACAATGGTGCAGTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACGATTAAGGGGTTATTTTTGTGGTATTGAAAATAAAAAAGGGCACAAAAggg                                       >  1:144340/1‑141 (MQ=255)                                                                                                      ttttgattgcccttgaacttccttgataatctggctaaTTATTCCTGCTAAATAATACCAGTTAAATAAAAATACCCTTTAATAACAACGATTAATGTGTTCTTTTTATGGTCTGGAAAATAAAACAGGGCACAaaagtgg                                      <  2:183241‑M1/103‑4 (MQ=255)                                                                                                        ttgattgcccttgaacttccttgataatctggctaaTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACGATTAAGGTGTTATTTTTTTGGTATTGAAACTAAAAAAGAGCACAAAAGTGgcc                                    <  2:2348‑M1/105‑2 (MQ=255)                                                                                                        ttgattgcccttgaacttccttgataatctggctaaTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACGATTAAGGGGTTATTTTTGTGGTATTGAAAATAAAAAAGGGCACACAAGGGGCa                                    <  2:186039‑M1/105‑1 (MQ=255)                                                                                                        ttgattgcccttgaacttccttgataatctggctaaTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACGATTAAGGGGTTATTATTATGGTATTGAAAATAAAAAAGGTCATAAAAGGGGCa                                    <  2:41966‑M1/105‑1 (MQ=255)                                                                                                        ttgattgcccttgaacttccttgataatctggctaaTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACGATTAAGGGCTTATTTTTGTTCTATTCAAACTAACAAAGGTCACAaaagggtca                                    <  2:305152‑M1/105‑4 (MQ=255)                                                                                                        ttgattgcccttgaacttccttgataatctggctaaTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCATTTAATAACAAGTACTAAGGGGCTATTGTGAGGGTATTGAAAATAAAACAgagcacaaaaaggtaa                                    <  2:296076‑M1/105‑7 (MQ=255)                                                                                                         tgattgcccttgaacttccttgataatctggctaaTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACGATTAAGGGGTTATTTTTGTGGTATTGAAAATAAAAAAGGGCACAAAAGGGGCAg                                   <  2:28703‑M1/106‑1 (MQ=255)                                                                                                         tgattgcccttgaacttacttgataatctggctaaTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACGATTAAGGGGTTATTTTTGTGGTATTGAAAATAAAAAAGGAAACAAAAAGGACAg                                   <  2:133525‑M1/106‑1 (MQ=255)                                                                                                               cccttgaacttccttgataatctggctaaTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACGATTAAGGGGTTATTTTTGTGGTATTGAAAATAAAAAAGGTCACAAAAGGtgcagtttgtg                             <  2:184341‑M1/112‑6 (MQ=255)                                                                                                                ccttgaacttccttgataatctggctaaTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACGATTAAGGGGTTATTTTTATGGTATTGAAAATAAGAAAGGGCACAAAAGGGGAAGTACAtga                            <  2:100028‑M1/113‑2 (MQ=255)                                                                                                                 tCATTAATGAAAAATACAATGGTGCAGTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACGATTAAGGGGTTATTTTTGTGGTATTGAAAATAAAAAAGGGCACAAAAGGGGCAGTATATGCa                           >  1:268528/1‑141 (MQ=255)                                                                                                                       cttccttgataatctggctaaTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACGATTAAGGTGTTATTTTTGTGTTATTGAAAATAAAAAAGAGCACAAAAGGTGTAGTATATGCAAATTAt                     <  2:84539‑M1/120‑1 (MQ=255)                                                                                                                       cttccttgataatctggctaaTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACGATTAAGGGGTTATTTTTGTGGTATTGAAAATAAAAAAGTGCACAAAAGGGGCAGTATATGCAAATTAt                     <  2:84462‑M1/120‑1 (MQ=255)                                                                                                                         gAAAAATACAATGGTGCAGTTATTCCTGCTAAATAATACCACTTACATAGAAAGACCCTTTAATAACAACGATTAAGGGGTTATTTTTGTGGTATTGAAAATAAAAAAGGGCACAAAAGGGGCAGTATATGCAAATTATCg                   <  1:303877/141‑1 (MQ=255)                                                                                                                         gAAAAATACAATGGTGCAGTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACGATTAAGGGGTTATTTTTGTGGTATTGAAAATAAAAAAGGGCACAAAAGGGGCAGTATATGCAAATTATCg                   <  1:257585/141‑1 (MQ=255)                                                                                                                          ccttgataatctggctaaTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACGATTAAGGGGTTATTTTTGTGCCCTACATTATTTTTTAGGGCACAAAAGGGGCAGTATATGCAAATTATCGa                  <  1:219863‑M1/123‑1 (MQ=255)                                                                                                                             tgataatctggctaaTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTCATAACAACGATTAAGGGGTTATTTTTGTGGTATTGAAAATAAAAAAGGGCACAAAAGGGGCAGTATATGCAAATTATCGAAtt               <  1:288178‑M1/126‑1 (MQ=255)                                                                                                                                    ctggctaaTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACGATTAAGGGGTTATTTTTGTGGTATTGAAAATAAAAAAGGGCACAAAAGGGGCAGTATATGAAAATTATCGAATTTTAAACa        <  2:46923‑M1/133‑1 (MQ=255)                                                                                                                                     tggctaaTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACGATTAAGGGGTTATTTTTGTGGTATTGAAAATAAAAAAGGGCACAAAAGGGGCAGTATATGCAAATTATCGAATTTTAAACaa       <  1:198589‑M1/134‑1 (MQ=255)                                                                                                                                          aGTTATTCCTGCTAAATAATACCAAGTAAATAAAAATACTCTTTAATAACAACGACTAAGGGGTTATTTTTTTGGTATTGAAAATAAAAAAGGGCACAAAAGGGGCAATACATGCAAATTATCGAATTTTAAACaaaaaaa  >  2:192687/1‑141 (MQ=255)                                                                                                                                            |                                                                                                                                           AGTGCGAAAGATAATCCTTATGCAAACTTAATTGCTGTTAAAGAAGGACATCAAGATGATAAGAAAATCAAAGCATTAATTGAAGTATTACAATCTAAAGATATTCAAGACTTCATTAATGAAAAATACAATGGTGCAGTTATTCCTGCTAAATAATACCAATTAAATAAAAATACCCTTTAATAACAACGATTAAGGGGTTATTTTTGTGGTATTGAAAATAAAAAAGGGCACAAAAGGGGCAGTATATGCAAATTATCGAATTTTAAACAAAAAAA  >  USA300TCH1516_ALE/895646‑895923

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ 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.