New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	= 891804	45 (0.970)	4 (0.090)	3/250	NT	8.9%	intergenic (+222/‑517)	USA300HOU_RS04385/rnmV_2	hypothetical protein/Ribonuclease M5
	?	USA300TCH1516_ALE	= 2031829	39 (0.880)					intergenic (+295/+195)	USA300HOU_RS10250/USA300HOU_RS10255	hypothetical protein/hypothetical protein

GTAGAAATTGGGAATCCAATTTCTCTTTGTTGGGGCCCACACCCCAACTTGCATTGTCTGTAGAAATTGGGAATCCAATTTCTCTTTGTTGGGGCCCCTGACTAGAATTGAAAAAAGCTTGTTACAAGCGCATTTTCG‑TTCAGTCAACTACTGCCAATATAACTTCGTAGAGCATAGAACATTGATTTATGTCCCCGCCTCTTTTTATCGTATATAGCATGTCCCTTTTTAAAATTACAAGCATAAATATTCAGACTCAAATATAGCCACACGCCTAAACT  >  USA300TCH1516_ALE/2031689‑2031969                                                                                                                                              |                                                                                                                                             gTAGAAATTGGGAATCCAATTTCTCTTTGTTGGGGCCCACACCCCAACTTGCATTGTCTGTAGAAATTGGGAATCCAATTTCTCTTTGTTGGGGCCCCTGACTAGAATTGAAAAAAGCTTGTTACAAGCGCATTTTCG‑TTc                                                                                                                                              >  2:218386/1‑141 (MQ=255)     aaaTTGGGAATCCAATTTCTCTTTGTTGGGGCCCACACCCCAACTTGCATTGTCTGTAGAAATTGGGAATCCAATTTCTCTTTGTTGGGGCCCCTGACTAGAATTGAAAAAAGCTTGTTACAAGCGCATTTTCG‑TTCagtc                                                                                                                                          >  1:611591‑M2/1‑137 (MQ=255)     aaaTTGGGAATCCAACTTCTCTTTGTTGGGGCCCACACCCCAACTTGCATTGTCTGTAGAAATTGGGAATCCAATTTCTCTTTGTTGGGGCCCCTGACTAGAATTGAAAAAAGCTTGTTACAAGCGCATTTTCG‑TTCagtc                                                                                                                                          >  1:654066‑M2/1‑137 (MQ=255)      aaTTGGGAATCCAATTTCTCTTTGTTGGGGCCCACACCCCAACTTGCATTGTCTGTAGAAATTGGGAATCCAATTTCTCTTTGTTGGGGCCCCTGACTAGAATTGAAAAAAGCTTGTTACAAGCGCATTTTCG‑TTCagtca                                                                                                                                         <  1:402418‑M2/141‑6 (MQ=255)       aTTGGTAACCCAATTTCTCTTTGTTGGGCCCCACACCCCAACTTGCATTGTTTGTAGAAATTGGGAATCCAATTTCTCTTTGTTGGGGCCCCTGACTAGAATTGAAAAAAGCTTGTTACAAGCTCGTTTTCG‑TTCAGTCaa                                                                                                                                        <  1:100368/141‑1 (MQ=18)              aTCCAATTTCTCTTTGTTGGGGCCCACACCCCAACTTGCATTGTCTGTAGAAATTGGGAATCCAATTTCTCTTTGTTGGGGCCCCTGACTAGAATTGAAAAAAGCTTGTTACAAGCGCATTTTCG‑TTCAGTCAACTACTGc                                                                                                                                 >  2:58348/1‑141 (MQ=255)                 cAATTTCTCTTTGTTGGGGCCCACACCCCAACTTGCATTGTCTGTAGAAATTGGGAATCCAATTTCTCTTTGTTGGGGCCCCTGACTAGAATTGAAAAAAGCTTGTTACAAGCGCATTTTCG‑TTCAGTCAACTACTGCCaa                                                                                                                              <  1:448404/141‑1 (MQ=255)                 cAATTTCTCTTTGTTGGGGCCCACACCCCAACTTGCATTGTCTGTAGAAATTGGGAATCCAATTTCTCTTTGTTGGGGCCCCTGACTAGAATTGAAAAAAGCTTGTTACAAGCGCATTTTCG‑TTCAGTCAACTACTGCCaa                                                                                                                              <  1:447437/141‑1 (MQ=255)                   aTTTCTCTTTGTTGGGGCCCACACCCCAACTTGCATTGTCTGTAGAAATTGGGAATCCAATTTCTCTTTGTTGGGGCCCCTGACTAGAATTGAAAAAAGCTTGTTACAAGCGCATTTTCG‑TTCAGTCAACTACTGCCAata                                                                                                                            <  1:520525/141‑1 (MQ=255)                     ttCTCTTTGTTGGGGCCCACACCCCAACTTGCATTGTCTGTAGAAATTGGGAATCCAATTTCTCTTTGTTGGGGCCCCTGACTAGAATTGAAAAAAGCTTGTTACAAGCGCATTTTCG‑TTCAGTCAACTACTGCCAAtata                                                                                                                          >  2:327593/1‑141 (MQ=255)                         ctTTGTTGGGGCCCACACCCCAACTTGCATTGTCTGTAGAAATTGGGAATCCAATTTCTCTTTGTTGGGGCCCCTGACTAGAATTGAAAAAAGCTTGTTACAAGCGCATTTTCG‑TTCAGTCAACTACTGCCAATATAACtt                                                                                                                      <  1:508950/141‑1 (MQ=255)                           ttgttgGGGCCCACACCCCAACTTGCATTGTCTGTAGAAATTGGGAATCCAATTTCTCTTTGTTGGGGCCCCTGACTAGAATTGAAAAAAGCTTGTTACAAGCGCATTTTCG‑TTCAGTCAACTACTGCCAATATAACTTCg                                                                                                                    >  2:212084/1‑141 (MQ=255)                           ttgttgGGGCCCACACCCCAACTTGCATTGTCTGTAGAAATTGGGAATCCAATTGCTCTTTGTTGGGGCCCCTGACTAGAATTGAAAAAAGCTTGTTACAAGCGCATTTTCG‑TTCAGTCAACTACTGCCAATATAACTTCg                                                                                                                    >  1:492269/1‑141 (MQ=255)                             gttgGGGCCCACACCCCAACTTGCATTGTCTGTAGAAATTGGGAATCCAATTTCTCTTTGTTGGGGCCCCTGACTAGAATTGAAAAAAGCTTGTTACAAGCGCATTTTCG‑TTCAGTCAACTACTGCCAATATAACTTCGTa                                                                                                                  >  1:31311/1‑141 (MQ=255)                                 gggCCCACACCCCAACTTGCATTGTCTGTAGAAATTGGGAATCCAATTTCTCTTTGTTGGGGCCCCTGACTAGAATTGAAAAAAGCTTGTTACAAGCGCATTTTCG‑TTCAGTCAACTACTGCCAATATAACTTCGTAGAGc                                                                                                              >  1:421464/1‑141 (MQ=255)                                 gggCCCACACCCCAACTTGCATTGTCTGTAGAAATTGGGAATCCAATTTCTCTTTGTTGGGGCCCCTGACTAGAATTGAAAAAAGCTTGTTACAAGCGCATTTTCG‑TTCAGTCAACTACTGCCAATATAACTTCGTAGAGc                                                                                                              >  1:368978/1‑141 (MQ=255)                                   gCCCACACCCCAACTTGCATTGTCTGTAAAAATTAGGAATCTAATTTCTCTTTGTTGGGGCCCCTGACTAGAATTGAAAAAAGCTTGTTACAAGCGCATTTTTG‑TTCAGTCAACTACTGCCAATATAACTTCGTAGAGCAt                                                                                                            >  2:9112/1‑141 (MQ=255)                                      cacaCCCCAACTTGCATTGTCTGTAGAAATTGGGAATCCAATTTCTCTTTGTTGGGGCCCCTGACTAGAATTGAAAAAAGCTTGTTACAAGCGCATTTTCG‑TTCAGTCAACTACTGCCAATATAACTTCGTAGAGCATAGa                                                                                                         >  1:513418/1‑141 (MQ=255)                                              aaCTTGCATTGTCTGTAGAAATTGGGAATCCAATTTCTCTTTGTTGGGGCCCCTGACTAGAATTGAAAAAAGCTTGTTACAAGCGCATTTTCG‑TTCAGTTAACTACTGCCAATATAACTTCGTAGAGCATAGAACATTGAt                                                                                                 >  2:140748/1‑141 (MQ=255)                                                 ttGCATTGTCTGTAGAAATTGGGAATCCAATTTCTCTTTGTTGGGGCCCCTGACTAGAATTGAAAAAGGCTTGTTACAAGCGCATTTTCG‑TTCAGTCAACTACTGCCAATATAACTTCGTAGAGCATAGAACATTGATTTa                                                                                              <  1:703984/141‑1 (MQ=255)                                                  tGCATTGTCTGTAGAAATTGGGAATCCAATTTCTCTTTGTTGGGGCCCCTGACTAGAATTGAAAAAAGCTTGTTACAAGCGCATTTTCG‑TTCAGTCAACTACTGCCAATATAACTTCGTAGAGCATAGAACATTGATTTAt                                                                                             <  1:626998/141‑1 (MQ=255)                                                       tGTCTGTAGAAATTGGGAATCCAATTTCTCTTTGTTGGGGCCCCTGACTAGAATTGAAAAAAGCTTGTTACAAGCGCATTTTCG‑TTCAGTCAACTACTGCCAATATAACTTCGTAGAGCATAGAACATTGATTTATGTccc                                                                                        <  1:680949/141‑1 (MQ=255)                                                         tCTGTAGAAATTGGGAATCCAATTTCTCTTTGTTGGGGCCCCTGACTAGAATTGAAAAAAGCTTGTTACAAGCGCATTTTCG‑TTCAGTCAACTACTGCCAATATAACTTCGTAGAGCATAGAACATTGATTTATGTCCCCg                                                                                      <  1:675747/141‑1 (MQ=255)                                                            gTAGAAATTGGGAATCCAATTTCTCTTTGTTGGGGCCCCTGACTAGAATTGAAAAAAGCTTGTTACAAGCGCATTTTCG‑TTCAGTCAACTACTGCCAATATAACTTCGTAGAGCATAGAACATTGATTTATGTCCCCGCct                                                                                   >  2:75477/1‑141 (MQ=255)                                                              aGAAATTGGGAATCCAATTTCTCTTTGTTGAGGCCCCTGACTAGAATTGAAAAAAGCTTGTTACAAGCGCATTTTCG‑TTCAGTCAACTACTGCCAATATAACTTCGTAGAGCATAGAACATTGATTTATGTCCCCGCctct                                                                                 <  2:155041/141‑1 (MQ=255)                                                                   ttGGGAATCCAATTTCTCTTTGTTGGGGCCCCTGACTAGAATTGAAAAAAGCTTGTTACAAGCGCATTTTCG‑TTCAGTCAACTACTGCCAATATAACTTCGTAGAGCATAGAACATTGATTTATGTCCCCGCCTCTTTTTa                                                                            <  1:387050/141‑1 (MQ=255)                                                                    tGGGAATCCAATTTCTCTTTGTTGGGGCCCCTGACTAGAATTGAAAAAAGCTTGTTACAAGCGCATTTTCG‑TTCAGTCAACTACTGCCAATATAACTTCGTAGAGCATAGAACATTGATTTATGTCCCCGCCTCTTTTTAt                                                                           <  1:771597/141‑1 (MQ=255)                                                                     gggAATCCAATTTCTCTTTGTTGGGGCCCCTGACTAGAATTGAAAAAAGCTTGTTACAAGCGCATTTTCG‑TTCAGTCAACTACTGCCAATATAACTTCGTAGAGCATAGAACATTGATTTATGTCCCCGCCTCTTTTTATc                                                                          <  1:717437/141‑1 (MQ=255)                                                                                ttCTCTTTGTTGGGGCCCCTGACTAGAATTGAAAAAAGCTTGTTACAAGCGCATTTTCG‑TTCAGTCAACTACTGCCAATATAACTTCGTAGAGCATAGAACATTGATTTATGTCCCCGCCTCTTTTTATCGTATATAGCAt                                                               >  2:148297/1‑141 (MQ=255)                                                                                   tctTTGTTGGGGCCCCTGACTAGAATTGAAAAAAGCTTGTTACAAGCGCATTTTCG‑TTCAGTCAACTACTGCCAATATAACTTCGTAGAGCATAGAACATTGATTTATGTCCCCGCCTCTTTTTATCGTATATAGCATGTc                                                            >  1:226616/1‑141 (MQ=255)                                                                                    ctTTGTTGGGGCCCCTGACTAGAATTGAAAAAAGCTTGTTACAAGCGCATTTTCG‑TTCAGTCAACTACTGCCAATATAACTTCGTAGAGCATAGAACATTGATTTATGTCCCCGCCTCTTTTTATCGTATATAGCATGTcc                                                           >  1:584913/1‑141 (MQ=255)                                                                                       tgttgGGGCCCCTGACTAGAATTGAAAAAAGCTTGTTACAAGCGCATTTTCG‑TTCAGTCAACTACTGCCAATATAACTTCGTAGAGCATAGAACATTGATTTATGTCCCCGCCTCTTTTTATCGTATATAGCATGTCCCtt                                                        >  2:324443/1‑141 (MQ=255)                                                                                             ggCCCCTGACTAGAATTGAAAAAAGCTTGTTACAAGCGCATTTTCG‑TTCAGTCAACTACTGCCAATATAACTTCGTAGAGCATAGAACATTGATTTATGTCCCCGCCTCTTTTTATCGTATATAGCATGTCCCTTTTTaaa                                                  <  1:130047/141‑1 (MQ=255)                                                                                                  cTGACTAGAATTGAAAAAAGCTTGTTACAAGCGCATTTTCG‑TTCAGTCAACTACTGCCAATATAACTTCGTAGAGCATAGAACATTGATTTATGTCCCCGCCTCTTTTTATCGTATATAGCATGTCCCTTTTTAAAATTAc                                             >  1:104570/1‑141 (MQ=255)                                                                                                     aCTAGAATTGAAAAAAGCTTGTTACAAGCGCATTTTCG‑TTCAGTCAACTACTGCCAATATAACTTCGTAGAGCATAGAACATTGATTTATGTCCCCGCCTCTTTTTATCGTATATAGCATGTCCCTTTTTAAAATTACAAg                                          <  1:359887/141‑1 (MQ=255)                                                                                                       tAGAATTGAAAAAAGCTTGTTACAAGCGCATTTTCG‑TTCAGTCAACTACTGCCAATATAACTTCGTAGAGCATAGAACATTGATTTATGTCCCCGCCTCTTTTTATCGTATATAGCATGTCCCTTTTTAAAATTACAAGCa                                        <  1:385185/141‑1 (MQ=255)                                                                                                         gAATTGAAAAAAGCTTGTTACAAGCGCATTTTCAATTCtagtcaggggccccaacacagagaatttcgaaaagaaattctacaggcaatgcaagttggggatgggccccaacaaagagaaattggattcccaatttctaca                                       <  2:10665‑M2/141‑104 (MQ=255)                                                                                                           aTTGAAAAAAGCTTGTTACAAGCGCATTTTCAATTCtagtcaggggccccaacacagagaatttcgaaaagaaattctacaggcaatgcaagttggggatgggccccaacaaagagaaattggattcccaatttctacaga                                     <  1:173113‑M2/141‑106 (MQ=255)                                                                                                              gAAAAAAGCTTGTTACAAGCGCATTTTCG‑TTCagtcaggggccccaacatagagaatttcgaaaagaaattctacaggcaatgcgagttggggtgtgggccccaacaaagagaaattggattcccaatttctacagacaat                                 <  1:248756‑M2/141‑110 (MQ=255)                                                                                                                aaaaaGCTTGTTACAAGCGCATTTTCAATTCtagtcaggggccccaacacagagaatttcgaaaagaaattctacaggcaatgcaagttggggatgggccccaacaaagagaaattggattcccaatttctacagacaatg                                <  1:334828‑M2/141‑111 (MQ=255)                                                                                                                   aaGCTTGTTACAAGCGCATTTTCG‑TTCAGTCAACTACTGCCAATATGACTTCGTAGAGCATAGAACATTGATTTATGTCCCCGCCTCTTTTTATCGTATATAGCATGTCCCTTTTTAAAATTACAAGCATAAATATTCAGa                            <  2:335328/141‑1 (MQ=255)                                                                                                                      cTTGTTACAAGCGCATTTTCG‑TTCAGTCAACTACTGCCAATATAACTTCGTAGAGCATAGAACATTGATTTATGTCCCCGCCTCTTTTTATCGTATATAGCATGTCCCTTTTTAAAATTACAAGCATAAATATTCAGACTc                         <  2:63072/141‑1 (MQ=255)                                                                                                                          ttACAAGCGCATTTTCG‑TTCAGTCAACTACTGCCAATATAACTTCGTAGAGCATAGAACATTGATTTATGTCCCCGCCTCTTTTTATCGTATATAGCATGTCCCTTTTTAAAATTACAAGCATAAATATTCAGACTCAAat                     >  2:330900/1‑141 (MQ=255)                                                                                                                               aGCGCATTTTCG‑TTCAGTCAACTACTGCCAATATAACTTCGTAGAGCATAGAACATTGATTTATGTCCCCGCCTCTTTTTATCGTATATAGCATGTCCCTTTTTAAAATTACAAGCATAAATATTCAGACTCAAATATAGc                >  2:133844/1‑141 (MQ=255)                                                                                                                                gcgcATTTTCG‑TTCAGTCAACTACTGCCAATATAACTTCGTAGAGCATAGAACATTGATTTATGTCCCCGCCTCTTTTTATCGTATATAGCATGTCCCTTTTTAAAATTACAAGCATAAATATTCAGACTCAAATATAGcc               >  1:330839/1‑141 (MQ=255)                                                                                                                                gcgcATTTTCG‑TTCAGTCAACTACTGCCAATATAACTTCGTAGAGCATAGAACATTGATTTATGTCCCCGCCTCTTTTTATCGTATATAGCATGTCCCTTTTTAAAATTACAAGCATAAATATTCAGACTCAAATATAGcc               >  2:224299/1‑141 (MQ=255)                                                                                                                                  gcATTTTCG‑TTCAGTCAACTACTGCCAATATAACTTCGTAGAGCATAGAACATTGATTTATGTCCCCGCCTCTTTTTATCGTATATAGCATGTCCCTTTTTAAAATTACAAGCATAAATATTCAGACTCAAATATAGCcac             >  2:93946/1‑141 (MQ=255)                                                                                                                                      tttCG‑TTCAGTCAACTACTGCCAATATAACTTCGTAGAGCATAGAACATTGATTTATGTCCCCGCCTCTTTTTATCGTATATAGCATGTCCCTTTTTAAAATTACAAGCATAAATATTCAGACTCAAATATAGCCACACGc         >  1:440130/1‑141 (MQ=255)                                                                                                                                         cG‑TTCAGTCAACTACTGCCAATATAACTTCGTAGAGCATAGAACATTGATTTATGTCCCCGCCTCTTTTTATCGTATATAGCATGTCCCTTTTTAAAATTACAAGCATAAATATTCAGACTCAAATATAGCCACACGCCTa      >  1:380948/1‑141 (MQ=255)                                                                                                                                         cG‑TTCAGTCAACTACTGCCAATATAACTTCGTAGAGCATAGAACATTGATTTATGTCCCCGCCTCTTTTTATCGTATATAGCATGTCCCTTTTTAAAATTACAAGCATAAATATTCAGACTCAAATATAGCCACACGCCTa      <  1:763996/141‑1 (MQ=255)                                                                                                                                            ttCAGTCAACTACTGCCAATATAACTTCGTAGAGCATAGAACATTGATTTATGTCCCCGCCTCTTTTTATCGTATATAGCATGTCCCTTTTTAAAATTACAAGCATAAATATTCAGACTCAAATATAGCCACACGCCTaaa    <  1:490659/141‑1 (MQ=255)                                                                                                                                            ttCAGTCAACTACTGCCAATATAACTTCGTAGAGCATAGAACATTGATTTATGTCCCCGCCTCTTTTTATCGTATATAGCATGTCCCTTTTTAAAATTACAAGCATAAATATTCAGACTCAAATATAGCCACACGCCTaaa    <  1:490711/141‑1 (MQ=255)                                                                                                                                              cAGTCAACTACTGCCAATATAACTTCGTAGAGCATAGAACATTGATTTATGTCCCCGCCTCTTTTTATCGTATATAGCATGTCCCTTTTTAAAATTACAAGCATAAATATTCAGACTCAAATATAGCCACACGCCTAAACt  <  1:333070/141‑1 (MQ=255)                                                                                                                                              cAGTCAACTACTGCCAATATAACTTCGTAGAGCATAGAACATTGATTTATGTCCCCGCCTCTTTTTATCGTATATAGCATGTCCCTTTTTAAAATTACAAGCATAAATATTCAGACTCAAATATAGCCACACGCCTAAACt  >  2:88495/1‑141 (MQ=255)                                                                                                                                              cAGTCAACTACTGCCAATATAACTTCGTAGAGCATAGAACATTGATTTATGTCCCCGCCTCTTTTTATCGTATATAGCATGTCCCTTTTTAAAATTACAAGCATAAATATTCAGACTCAAATATAGCCACACGCCTAAACt  >  2:88786/1‑141 (MQ=255)                                                                                                                                              |                                                                                                                                             GTAGAAATTGGGAATCCAATTTCTCTTTGTTGGGGCCCACACCCCAACTTGCATTGTCTGTAGAAATTGGGAATCCAATTTCTCTTTGTTGGGGCCCCTGACTAGAATTGAAAAAAGCTTGTTACAAGCGCATTTTCG‑TTCAGTCAACTACTGCCAATATAACTTCGTAGAGCATAGAACATTGATTTATGTCCCCGCCTCTTTTTATCGTATATAGCATGTCCCTTTTTAAAATTACAAGCATAAATATTCAGACTCAAATATAGCCACACGCCTAAACT  >  USA300TCH1516_ALE/2031689‑2031969

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.