New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	= 907281	45 (0.870)	4 (0.080)	3/240	NT	8.6%	intergenic (+390/‑39)	USA300HOU_RS04490/USA300HOU_RS04495	hypothetical protein/hypothetical protein
	?	USA300TCH1516_ALE	= 907290	44 (0.920)					intergenic (+399/‑30)	USA300HOU_RS04490/USA300HOU_RS04495	hypothetical protein/hypothetical protein

AATATTGGTGGGTTTGAGGAGTAGCAATAAAATAAAGGAGGTAATTGTGTAAAATATCTCTTTTTGTTATTTCTTATTTATTTACAACCGATAAAATTAAATGTATTATATATATAACGATCTAGCCATAACTCTATTCGGGTTATGGCTACTTTTATAGGGGTAAATTTATGAAGCCATTTGAAAGTCATAATAAACAATTGAAAATTCTAAGAAGAAGAGGAATGGAAGTACCGAGTAGTGCTAAAAGAGATTTAGAAAATGAAAATTATTATAATATC  >  USA300TCH1516_ALE/907150‑907430                                                                                                                                             |                                                                                                                                             aataTTGGTGGGTTTGAGGAGTAGCAATAAAATAAAGGAGGTAATTGTGTAAAATATCTCTTTTTGTTATTTCTTATTTATTTACAACCGATAAAATTAACTGTATTGTATTTATAACGATCTAGCCATAACTCAATTCgg                                                                                                                                              >  2:211853/1‑141 (MQ=255) aataTTGGTGGGCTTGAGGAGTAGCAATAAAATAAAGGAGGTAATTGTGTAAAATATCTCTTTTTGTTATTTCTTATTTATTTACAACCGATAAAATTAAATGTATTATATATATAACGATCTAGCCATAACTCTATTCgg                                                                                                                                              <  1:412661/141‑1 (MQ=255)      tggtggGTTTGAGGAGTAGCAATAAAATAAAGGAGGTAATTGTGTAAAATATCTCTTTTTGTTATTTCTTATTTATTTACAACCGATAAAATTAAATGTATTATATATATAACGATCTAGCCATAACTCTATTCGGgttat                                                                                                                                         >  1:360257‑M2/1‑136 (MQ=255)       ggtggGTTTGAGGAGCAGCAATAAAATAAAGGAGGTAATTGTGTAAAATATCTCTTTTTGTTATTTCTTATTTATTTACAACCGATAAAATTAAATGTATTATATATATAACGATCTAGCCATAACTCTATTCGGgttatg                                                                                                                                        <  1:452910‑M2/141‑7 (MQ=255)          tggtTTGAGGAGGAGCAATAAAATAAAGGAGGTAATTGTGTAAAATATCTCTTTTTGTTATTTCTTATTTATTTACAACCGATAAAATTAAATGTATTATATATATAACGATCTAGCCATAACTCTATTCGGgttatggct                                                                                                                                     >  1:181536‑M2/2‑132 (MQ=255)              ttGAGGAGTAGCAATAAAATAAAGGAGGTAATTGTGTAAAATATCTCTTTTTGTTATTTCTTATTTATTTACAACCGATAAAATTAAATGTATTATATATATAACGATCTAGCCATAACTCTATTCGGGTTATGGCTACtt                                                                                                                                 <  1:20107/141‑1 (MQ=255)                gaggagTAGCAATAAAATAAAGGAGGTAATTGTGTAAAATATCTCTTTTTGTTATTTCTTATTTATTTACAACCGATAAAATTAAATGTATTATATATATAACGATCTAGCCATAACTCTATTCGGGTTATGGCTACtttt                                                                                                                               >  2:452992/1‑141 (MQ=255)                    agTAGCAATAAAATAAAGGAGGTAATTGTGTAAAATATCTCTTTTTGTTATTTCTTATTTATTTACAACCGATAAAATTAAATGTATTATATATATAACGATCTAGCCATAACTCTATTCGGGTTATGGCTACTTTTATAg                                                                                                                           <  1:96353/141‑1 (MQ=255)                     gTAGCAATAAAATAAAGGAGGTAATTGTGTAAAATATCTCTTTTTGTTATTTCTTATTTATTTACAACCGATAAAATTAAATGTATTATATATATAACGATATAGCCATAACTATATTCGGGTTATGGCTACTTTTATAgg                                                                                                                          >  1:7368/1‑141 (MQ=255)                         cAATAAAATAAAGGAGGTAATTGTGTAAAATATCTCTTTTTGTTATTTCTTATTTATTTACAACCGATAAAATTAAATGTATTATATATATAACGATCTAGCCATAACTCTATTCGGGTTATGGCTACTTTTATAGGGGTa                                                                                                                      >  2:251100/1‑141 (MQ=255)                          aataaaataaAGGAGGTAATTGTGTAAAATATCTCTTTTTGTTATTTCTTATTTATTTACAACCGATAAAATTAAATGTATTATATATATAACGATCTAGCCATAACTCTATTCGGGTTATGGCTACTTTTATAGGGGTaa                                                                                                                     <  2:508840/141‑1 (MQ=255)                          aataaaataaAGGAGGTAATTGTGTAAAATACCCCTTTTTGTTATTTCTTATTTATTTACAACCGATAAAATTAAATGTATTATATATATAACGATCTAGCCATAACTCTATTCGGGTTATGGCTACTTTTATAGGGGTat                                                                                                                     <  2:405138/141‑2 (MQ=255)                           ataaaataaaGGAGGTAATTTTGTAAAATATCTCTTTTTGTTATTTCTTATTTATTTACAACCGATAAAATTAAATGTATTATATATATAACGATCTAGCCATAACTCTATTCGGGTTATGGCTACTTTTATAGGGGTaaa                                                                                                                    <  2:408405/141‑1 (MQ=255)                           ataaaataaaGGAGGTAATTGTGTAAAATATCTCTTTTTGTTATTTCTTATTTATTTACAACCGATAAAATTAAATGTATTATATATATAACGATCTAGCCATAACTCTATTCGGGTTATGGCTACTTTTATAGGGGTaaa                                                                                                                    >  2:604817/1‑141 (MQ=255)                               aataaaGGAGGTAATTGTGTAAAATATCTCTTTTTGTTATTTCTTATTTATTTACAACCGATAAAATTAAATGTATTATATATATAACGATCTAGCCATAACTCTATTCGGGTTATGGCTACTTTTATAGGGGTaagatta                                                                                                                >  1:230725/1‑136 (MQ=255)                                   aaGGAGGTAATTGTGTAAAATATCTCTTTTTGTTATTTCTTATTTATTTACAACCGATAAAATTAAATGTATTATATATATAACGATCTAGCCATAACTCTATTCGGGTTATGGCTACTTTTATAGGGGTAAATTTATGaa                                                                                                            >  1:84823/1‑141 (MQ=255)                                       aggTAATTGTGTAAAATATCTCTTTTTGTTATTTCTTATTTATTTACAACCGATAAAATTAAATGTATTATATATATAACGATCTAGCCATAACTCTATTCGGGTTATGGCTACTTTTATAGGGGTAAATTTATGAAGCCa                                                                                                        >  1:462021/1‑141 (MQ=255)                                            aTTGTGTAAAATATCTCTTTTTGTTATTTCTTATTTATTTACAACCGATAAAATTAAATGTATTATATATATAACGATCTAGCCATAACTCTATTCGGGTTATGGCTACTTTTATAGGGGTAAATTTATGAAGCCATTTGa                                                                                                   >  2:363375/1‑141 (MQ=255)                                                  gaaaaTATGTTCTTTTGTTATTTCTTATTTATTTACCACCGATAAAATTAAATGTATTATATATATAACGATCTAGCCATAACTCTATTCGGGTTATGGCTACTTTTATAGGGGTAAATTTATGAAGCCATTTGAAAGTCa                                                                                             <  1:112315/140‑1 (MQ=255)                                                    aaaTATCTCTTTTTGTTATTTCTTATTTATTTACAACCGATAAAATTAAATGTATTATATATATAACGATCTAGCCATAACCCGAATAGAgttatggctagatcgttatatatataatacatttaattttatcggttgtaa                                                                                           >  1:382133‑M2/1‑90 (MQ=255)                                                          ctctTTTTGTTATTTCTTATTTATTTACAACCGATAAAATTAAATGTATTATATATATAACGATCTAGCCATAACTCTATTCGGGTTATGGCTACTTTTATAGGGGTAAATTTATGAAGCCATTTGAAAGTCATAATAAAc                                                                                     <  1:14911/141‑1 (MQ=255)                                                              ttttGTTATTTCTTATTTATTTACAACCGATAAAATTAAATGTATTATATATATAACGATCTAGCCATAACTCTATTCGGGTTATGGCTACTTTTATAGGGGTAAATTTATGAAGCCATTTGAAAGTCATAATAAACAAtt                                                                                 >  2:528609/1‑141 (MQ=255)                                                              ttttGTTATTTCTTATTTATTTACAACCGATAAAATTAAATGTATTATATATATAACGATCTAGCCATAACTCTATTCGGGTTATGGCTACTTTTATAGGGGTAAATTTATGAAGCCATTTGAAAGTCATAATAAACAAtt                                                                                 >  1:515240/1‑141 (MQ=255)                                                                ttttTATTTCGTATTAATTTACAACCGATAAAATTAAATGTATGATATATATAACGATCTAGCCATAACCCGAATAGAgttatggctagatcgttatatatataatacatttaattttatcggttgtaaataaataagaaa                                                                               >  2:538581‑M2/1‑78 (MQ=255)                                                                      tttCTTATTTATTTACAACCGATAAAATTAAATGTATTATATATATAACGATCTAGCCATAACTCTATTCGGGTTATGGCTACTTTTATAGGGGTAAAGTTATGAAGCCATTTGAAAGTCATAATAAACAATTGAAAATTc                                                                         <  1:574078/141‑1 (MQ=255)                                                                       ttCTTATTTATTTACAACCGATAAAATTAAATGTATTATATATATAACGATCTAGCCATAACTCTATTCGGGTTATGGCTACTTTTATAGGGGTAAATTTATGAAGCCATTTGAAAGTCATAATAAACAATTGAAAATTCt                                                                        <  1:93672/141‑1 (MQ=255)                                                                           tatttattTACAACCGATAAAATTAAATCTATTATAAAGATAACGATCTAGCCATAACTCGATTCGGGTTATGGCTACTTTTATAGGGGTAAATTTATGAAGCCATTTGAAAGTCATAAGAAACAATTCAAAATTCTaaga                                                                    <  1:316819/141‑1 (MQ=255)                                                                             tttatttaCAACCGATAAAATTAAATGTATTATATATATAACGATCTAGCCATAACTCTATTCGGGTTATGGCTACTTTTATAGGGGTAAATTTATGAAGCCATTTGAAAGTCATAATAAACAATTGAAAATTCTaagaag                                                                  >  1:244150/1‑141 (MQ=255)                                                                              taatttaCAACCGATAAAATTAAATGTATTATATATATAACGATCTAGCCATAACTCTATTCGGGTTATGGCTACTTTTAAAGGGGTAAATTTATGAAGCCATTTGAAAGTCATAATAAACAATTGAAAATTCTaagaaga                                                                 <  2:578370/139‑1 (MQ=255)                                                                                      aaCCGATAAAATTAAATGTATTATATATATAACGATCTAGCCATAACTCTATTCGGGTTATGGCTACTTTTATAGGGGTAAATTTATGAAGCCATTTGAAAGTCATAATAAACAATTGAAAATTCTAAGAAGAAGAGGAAt                                                         <  1:533768/141‑1 (MQ=255)                                                                                             aaaaTTAAATGTATTATATATATAACGATCTAGCCATAACTCTATTCGGGTTATGGCTACTTTTATAGGGGTAAATTTATGAAGCCATTTGAAAGTCATAATAAACAATTGAAAATTCTAAGAAGAAGAGGAATGGAAGTa                                                  <  2:452910/141‑1 (MQ=255)                                                                                               aaTTAAATGTATTATATATATAACGATCTAGCCATAACTCTATTCGGGTTATGGCTACTTTTATAGGGGTAAATTTATGAAGCCATTTGAAAGTCATAATAAACAATTGAAAATTCTAAGAAGAAGAGGAATGGAAGTAcc                                                <  1:540004/141‑1 (MQ=255)                                                                                               aaTTAAATGTATTATATATATAACGATCTAGCCATAACTCTATTCGGGTTATGGCTACTTTTATAGGGGTAAAATTATGAAGCCATTTGAAAGTCATAATAAACAATTGAAAATTCTAAGAAGAAGAGGAATGGAAGTAcc                                                >  2:217949/1‑141 (MQ=255)                                                                                                   aaaTGTATTATATATATAACGATCTAGCCATAACTCTATTAGGGTTATGGCTACTTATATAGGGGTAAATTTATGAAGCCATTTGAAAGTCATAATAAACAATGGAAAATTCTAAGAAGAAGAGGAATGGAAGTACCGaga                                            >  2:99197/1‑140 (MQ=255)                                                                                                    aaTGTATTATATATATAACGATCTAGCCATAACTCTATTCGGGTTATGGCTACTTTTATAGGGGTAAATTTATGAAGCCATTTGAAAGTCATAATAAACAATTGAAAATTCTAAGAAGAAGAGGAATGGAAGTACCGagta                                           <  2:515240/141‑1 (MQ=255)                                                                                                    aaTGTATTATATATATAACGATCTAGCCATAACTCTATTCGGGTTATGGCTACTGTTAGAAGGGTAAATTTATGAAGCCATTTGACAGTCGTCATCAACAATTGCAAATTCTAAGAATAAGAGGAATGGAAGTACCGagta                                           >  1:507677/1‑141 (MQ=255)                                                                                                      tGTATTATATATATAACGATCTAGCCATAACTCTATTCGGGTTATGGCTACTTTTATAGGGGTAAATTTATGAAGCCATTTGAAAGTCATAATAAACAATTGAAAATTCTAAGAAGAAGAGGAATCGAAGTACCGagtagt                                         <  1:452992/141‑1 (MQ=255)                                                                                                      tGTATTATATATATAACGATCTAGCCAAAACTCTATTCGGGTTATGGCTACTTTTATAGGGGTAAATTTATGAAGCCATTTGAAAGTCATAATAAACAATTGAAAATTCTAAGAAGAAGAGGAATGGAAGTACCGagtagt                                         <  1:204188/141‑1 (MQ=255)                                                                                                         attatATATATAACGATCTAGCCATAACTCTATTCGGGTTATGGCTACTTTTATAGGGGTAAATTTATGAAGCCATTTGAAAGTCATAATAAACAATTGAAAATTCTAAGAAGAAGGGGAATGGAAGTACCGAGTAGTGCt                                      >  1:421771/1‑141 (MQ=255)                                                                                                          ttatATATATAACGATCTAGCCATAACTCTATTCGGGTTATGGCTACTTTTATAGGGGTAAATTTATGAAGCCATTTGAAAGTCATAATAAACAATTGAAAATTCTAAGAAGAAGAGGAATGGAAGTACCGAGTAGTGCTa                                     <  1:241635/141‑1 (MQ=255)                                                                                                                 tataACGATCTAGCCATAACTCTATTCGGGTTATGGCTACTTTTATAGGGGTAAATTTATGAAGCCATTTGAAAGTCATAATAAACAATTGAAAATTCTAAGAAGAAGAGGAATGGAAGTACCGAGTAGTGCTAAAAgaga                              >  1:271846/1‑141 (MQ=255)                                                                                                                 tataACGATCTAGCCATAACTCTATTCGGGTTATGGCTACTTTTATAGGGGTAAATTTATGAAGCCATTTGAAAGTCATAATAAACAATTGAAAATTCTAAGAAGAAGAGGAATGGAAGTACCGAGTAGTGCTAAAAgaga                              >  1:489564/1‑141 (MQ=255)                                                                                                                     aCGATCTAGCCATAACTCTATTCGGGTTATGGCTACTTTTATAGGGGTAAATTTATGAAGCCATTTGAAAGTCATAATAAACAATTGAAAATTCTAAGAAGAAGAGGAATGGAAGTACCGAGTAGTGCTAAAAGAGATTTa                          >  2:411570/1‑141 (MQ=255)                                                                                                                     aCGATCCAGCCATAAATGTAGCCGGGTGATAGCTACTTTTAGAGGGGTAAATTTATGAAGCCATTTGTAAGTCATAATAAACAATTGAAAATTCTAAGAAGAAGAGGAATGGAAGTACCGAGTAGTGCTAAAAGAGATTTa                          <  1:9663/141‑1 (MQ=255)                                                                                                                         tCTAGCCATAACTCTATTCGTGTTATGGCTACTTTTATAGGGGTAAATTTATGAAGCCATTTGAAAGTCATAATAAACAATTGAAAATTCTAAGAAGAAGAGGAATGGAAGTACCGAGTAGTGCTAAAAGAGATTTAgaaa                      >  1:373216/1‑141 (MQ=255)                                                                                                                          cTAGCCATAACTCTATTCGGGTTATGGCTACTTTTATAGGGGTAAATTTATGAAGCCATTTGAAAGTCATAATAAACAATTGAAAATTCTAAGAAGAAGAGGAATGGAAGTACCGAGTAGTGCTAAAAGAGATTTAgaaaa                     >  1:162234/1‑141 (MQ=255)                                                                                                                          cTAGCCATAACTCTATTCGGGTTATGGCTACTTTTATAGGGGTAAATTTATGAAGCCATTTGAAAGTCATAATAAACAATTGAAAATTCTAAGAAGAAGAGGAATGGAAGTACCGAGTAGTGCTAAAAGAGATTTAgaaaa                     <  2:236325/141‑1 (MQ=255)                                                                                                                            aGCCATAACTCTATTCGGGTTATGGCTACTTTTATAGGGGTAAATTTATGAAGCCATTTGAAAGTCATAATAAACAATTGAAAATTCTAAGAAGAAGAGGAATGGAAGTACCGAGTAGTGCTAAAAGAGATTTAgaaaatg                   >  2:397629/1‑141 (MQ=255)                                                                                                                              ccATAACTCTATTCGGGTTATGGCTACTTTTATAGGGGTAAATTTATGAAGCCATTTGAAAGTCATAATAAACAATTGAAAATTCTAAGAAGAAGAGGAATGGAAGTACCGAGTAGTGCTAAAAGAGATTTAgaaaatgaa                 >  2:427865/1‑141 (MQ=255)                                                                                                                              ccATAACTCTATTCGGGTTATGGCTACTTTTATAGGGGTAAATTTATGAAGCCATTTGAAAGTCATAATAAACAATTGAAAATTCCAAGAAGAAGAGGAATGGAAGTACCGAGTAGTGCTAAAAGAGATTTAgaaaatgaa                 <  1:25065/141‑1 (MQ=255)                                                                                                                                aTAACTTTATTCGGGTTGTGGCCACTTTTAAAGGAGTAAAATTATGAAGCCACTTGAAAGTCATAATAAACAATTGCAAATTTTGCGAAGAAGGGGAAGCGGAGTTCCAATGAGTGCTAAAAGAGATTTAgaaaatgaaaa               <  2:431174/141‑1 (MQ=255)                                                                                                                                  acctctATTTCGGTTATGGCTACTTTTATAGGGGTAAATTTATGAAGCCATTTGAAAGTCATAATAAACAATTGAAAATTCTAAGAAGAAGAGGAATGGAAGTACCGAGTAGTGCTAAAAGAGATTTAGAAAATGAAAatt             <  1:62448/139‑1 (MQ=255)                                                                                                                                     tctATTCGGGTTATGGCTACTTTTATAGGGGTAAATTTATGAAGCCATTTGAAAGTCATAATAAACAATTGAAAATTCTAAGAAGAAGAGGAATGGGAGTACCGAGTAATGCTAAAAGAGATTTAGAAAATGAAAattatt          >  2:178994/1‑141 (MQ=255)                                                                                                                                        aTTCGGgttatggctagatcgttatatatataatacatttaattttatcggttgtaaataaataagaaataacaaaaagagatattttacacaattacctcctttattttattgctactcctcaaacccaccaatattatc       <  1:361909‑M2/141‑136 (MQ=255)                                                                                                                                        aTTCGGgttatggctagatcgttatatatataatacatttaattttatcggttgtaaataaataagaaataacaaaaagagatattttacacaattacctcctttattttattgctactcctcaaacccaccaatattatc       <  2:289330‑M2/141‑136 (MQ=255)                                                                                                                                          tCGGGTTATGGCTACTTTTATAGGGGTAAATTTATGAAGCCATTTGAAAGTCATAATAAACAATTGAAAATTCTAAGAAGAAGAGGAATGGAAGTACCGAGTAGTGCTAAAAGAGATTTAGAAAATGAAAATTATTataat     <  1:25578/141‑1 (MQ=255)                                                                                                                                             ggTTATGGCTACTTTTATAGGGGTAAATTTATGAAGCCATTTGAAAGTCATAATAAACAATTGAAAATTCTAAGAAGAAGAGGAATGGAAGTACCGAGTAGTGCTAAAAGAGATTTAGAAAATGAAAATTATTATAATATc  >  1:64377/1‑141 (MQ=255)                                                                                                                                             |                                                                                                                                             AATATTGGTGGGTTTGAGGAGTAGCAATAAAATAAAGGAGGTAATTGTGTAAAATATCTCTTTTTGTTATTTCTTATTTATTTACAACCGATAAAATTAAATGTATTATATATATAACGATCTAGCCATAACTCTATTCGGGTTATGGCTACTTTTATAGGGGTAAATTTATGAAGCCATTTGAAAGTCATAATAAACAATTGAAAATTCTAAGAAGAAGAGGAATGGAAGTACCGAGTAGTGCTAAAAGAGATTTAGAAAATGAAAATTATTATAATATC  >  USA300TCH1516_ALE/907150‑907430

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.