Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
JC	USA300TCH1516_ALE	68,656	Δ3 bp	5.4%	coding (772‑774/852 nt)	USA300TCH1516_00061 →	hypothetical protein

New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	68659 =	57 (0.750)	3 (0.050)	3/224	NT	5.4%	coding (775/852 nt)	USA300TCH1516_00061	hypothetical protein
	?	USA300TCH1516_ALE	= 68655	57 (0.880)					coding (771/852 nt)	USA300TCH1516_00061	hypothetical protein

GGGAACACCTGCCGATAACGCCCCGATAGAAAGTTTCCATTCCTCGCTAAAGTCTGAAACTTTTTACATCAATAATGAGCTTAATCACTCTAATCACATTGTAATAGATATTGTCGAAAAGTACATTAAAAACAATAATAATAATAATAATAATCGAATTCAACAAAAACTAGGCTACTTATCCCCTGTAAAATACAGAGAATTAATAGCCTAGAACATGGTGTTTTTATTAAGTTCCCGTTTTAAGGGTTCAGTGCCCTAGGATT  >  USA300TCH1516_ALE/68523‑68788                                                                                                                                     |                                                                                                                                      gggAACACCTGCCGATAACGCCCCGATAGAAAGTTTCCATTCCTCGCTAAAGTCTGAAACTTTTTACATCAATAATGAGCTTAATCACTCTAATCACATTGTAATAGATATTGTCGAAAAGTACATTAAAAACaataataa                                                                                                                               <  2:452619‑M2/141‑9 (MQ=255)      cacCTGCCGATAACGCCCCGATAGAAAGTTTCCATTCCTCGCTAAAGTCTGAAACTTTTTACATCAATAATGAGCTTAATCACTCTAATCACATTGTAATAGATATTGTCGAAAAGTACATTAAAAACaataataataata                                                                                                                          >  1:158120‑M2/1‑128 (MQ=255)           gCCGATAACGCCCCGATAGAAAGTTTCCATTCCTCGCTAAAGTCTGAAACTTTTTACATCAATAATGAGCTTAATCACTCTAATCACATTGTAATAGATATTGTCGAAAAGTACATTAAAAACaataataataataataat                                                                                                                     >  2:375269‑M2/1‑123 (MQ=255)                    gCCCCGATAGAAAGTTTCCATTCCTCGCTAAAGTCTGAAACTTTTTACATCAATAATGAGCTTAATCACTCTAATCACATTGTAATAGATATTGTCGAAAAGTACATTAAAAACAATAATAATAATAATAATAATCGAAtt                                                                                                            >  1:600958/1‑141 (MQ=255)                    gCCCCGATAGAAAGTTTCCATGCCTCGCTAAAGTCTGAAACTTTTTACATCAATAATGAGCTTAATCACTCTAATCACATTGTAATAGATATTGTCGAAAAGTACATTAAAAACAATAATAATAATAATAATAATCGAAtt                                                                                                            <  2:122600/141‑1 (MQ=255)                        cGATAGAAAGTTTCCATTCCTCGCTAAAGTCTGAAACTTTTTACATCAATAATGAGCTTAATCACTCTAATCACATTGTAATAGATATTGTCGAAAAGTACATTAAAAACAATAATAATAATAATAATAATCGAATTcaac                                                                                                        <  1:392529/141‑1 (MQ=255)                             gAAAGTTTCCATTCCTCGCTAAGCCCGGAAACTGTTTACATCAATAATGAGCTTAATCACTCTAATCACATTGTAATAGATATTGTCGAAAAGTACATTAAAAACAATAATAATAATAATAATAATCGAATTCAACaaaaa                                                                                                   >  1:440490/1‑141 (MQ=21)                             gAAAGTTTCCATTCCTCGCTAAAGTCTGAAACTTTTTACATCAATAATGAGCTTAATCACTCTAATCACATTGTAATAGATATTGTCGAAAAGTACATTAAAAACAATAATAATAATAATAATAATCGAATTCAACaaaaa                                                                                                   >  2:846538/1‑141 (MQ=255)                               aaGTTTCCATTCCTCGCTAAAGTCTGAAACTTTTTACATCAATAATGAGCTTAATCACTCTAATCACATTGTAATAGATATTGTCGAAAAGTACATTAAAAACAATAATAATAATAATAATAATCGAATTCAACAAAAACt                                                                                                 <  1:503107/141‑1 (MQ=255)                                   ttCCATTCCTCGCTAAAGTCTGAAACTTTTTACATCAATAATGAGCTTAATCACTCTAATCACATTGTAATAGATATTGTCGAAAAGTACATTAAAAACAATAATAATAATAATAATAATCGAATTCAACAAAAACTAGGc                                                                                             <  1:708434/141‑1 (MQ=255)                                     ccATTCCTCGCTAAAGTCTGAAACTTTTTACATCAATAATGAGCTTAATCACTCTAATCACATTGTAATAGATATTGTCGAAAAGTACATTAAAAACAATAATAATAATAATAATAATCGAATTCAACAAAAACTAGGCTa                                                                                           <  1:537009/141‑1 (MQ=255)                                     ccATTCCTCGCTAAAGTCTGAAACTTTTTACATCAATAATGAGCTTAATCACTCTAATCACATTGTAATAGATATTGTCGAAAAGTACATTAAAAACAACAATAATAATAATAATAATCGAATTCAACAAAAACTAGGCTa                                                                                           <  1:716713/141‑1 (MQ=255)                                       aTTCCTCGCTAAAGTCTGAAACTTTTTACATCAATAATGAGCTTAATCACTCTAATCACATTGTAATAGATATTGTCGAAAAGTACATTAAAAACAATAATAATAATAATAATAATCGAATTCAACAAAAACTAGGCTACt                                                                                         <  2:327233/141‑1 (MQ=255)                                            tCGCTAAAGTCTGAAACTTTTTACATCAATAATGAGCTTAATCACTCTACTCACATTGTAATAGATATTGTCGAAAAGTACATTAAAAACAATAATAATAATAATAATAATCAACTTCAACAAAAAATAGACTACTTATcc                                                                                    >  1:99357/1‑141 (MQ=21)                                              ccTAAAGTCTGAAACTTTTTACATCAATAATGAGCTTAATCACTCTAATCACATTGTAATAGATATTGTCGAAAAGTACATTAAAAACAATAATAATAATAATAATAATCGAATTCAACAAAAACTAGGCTACTTATcccc                                                                                  <  1:759312/140‑1 (MQ=255)                                                tAAAGTCTGAAACTTTTTACATCAATAATGAGCTTAATCACTCTAATCACATTGTAATAGATATTGTCGAAAAGTACATTAAAAACAATAATAATAATAATAATAATCGAATTCAACAAAAACTAGGCTACTTATCCCCTg                                                                                <  2:841250/141‑1 (MQ=255)                                                 aaaGTCTGAAACTTTTTACATCAATAATGAGCTTAATCACTCTAATCACATTGTAATAGATATTGTCGAAAAGTACATTAAAAACAATAATAATAACAATAATAATCGAATTCAATAAAAATTAGGCTACTTATCCCCTGt                                                                               <  1:499628/141‑1 (MQ=255)                                                   aGTCTGAAACTTTTTACATCAATAATGAGCTTAATCACTATAAGGACATTGTAATAGATATTGTCGAAAAGTACATTAAAAACAATAATAATAATAATAATAATCGAATTCAACAAAAACTAGGCTACTTATCCCCTGTaa                                                                             >  1:711801/1‑141 (MQ=255)                                                    gTCTGAAACTTTTTACATCAATAATGAGCTTAATCACTCTAATCACATTGTAATAGATATTGTCGAAAAGTACATTAAAAACaataataataataataatcgaattcaacaaaaactaggctacttatcccctgtaaaata                                                                            >  2:896026‑M2/1‑82 (MQ=255)                                                       tGAAACTTTTTACATCAATAATGAGCTTAATCACTCTAATCACATTGTAATAGATATTGTCGAAAAGTACATTAAAAACAATAATAATAATAATAATAATCGAATTCAACAAAAACTAGGCTACTTATCCCCTGTAAAATa                                                                         <  1:910486/141‑1 (MQ=255)                                                           aCTTTTTACATCAATAATGAGCTTAATCACTCTAATCACATTGTAATAGATATTGTCGAAAAGTACATTAAAAACAATAATAATAATAATAATAATCGAATTCAACAAAAACTAGGCTACTTATCCCCTGTAAAATACaga                                                                     <  1:41936/141‑1 (MQ=255)                                                           aCTTATTACATCAATAGTTATCTGAACCACTCTAAACACATTGTAATAGATAATGACGAAAAGTAAATTAAAAACAATAATAATAATAATAATAATCGAATTCAACAAAATCTAGGCTACTCATCCCCTCTAAATTACaga                                                                     <  2:340557/141‑1 (MQ=21)                                                              ttttACATCAATAATGAGCTTAATCACTCTAATCACATTGTAATAGCAATTGTCGAAAAGTACATTACAAACAATAATAATAATAATAATAATCGAATTCAACAAAAACTAGGCTACTTATCCCCTGTAAAATACagagca                                                                  >  1:558145/1‑139 (MQ=255)                                                                     tCAATAATGAGCTTAATCACTCTAATCACATTGTAATAGATATTGTCGAAAAGTACATTAAAAACAATAATAATAATAATAATAATCGAATTCAACAAAAACTAGGCTACTTATCCCCTGTAAAATACAGAGAATTAATAg                                                           >  2:98304/1‑141 (MQ=255)                                                                     tCAATAATGAGCTTAATCACTCTAATCACATTGTAATAGATATTGTCGAAAAGTACATTAAAAACAATAATAATAATAATAATAATCGAATTCAACAAAAACTAGGCTACTTATACCCTGTAAAATACAGAGAATTAATAg                                                           >  1:143491/1‑141 (MQ=255)                                                                       aatagtGAGCTTAATCACTATAAGCACATTGTAATAGATATTGTCGAAAAGTACATTAAAAACAATAATAATAATAATAATAATCGAATTCAACAAAAACTAGGCTACTTATCCCCTGTAAAATACAGAGAATTAATAGcc                                                         <  1:656810/141‑1 (MQ=255)                                                                         taatGAGCTTAATCACTCTAATCACATTGTAATAGATATTGTCGAAAAGTACATTAAAAACAATAATAATAATAATAATAATCGAATTCAACAAAAACTAGGCTACTTATCCCCTGTAAAATACAGAGAATTAATAGCCTa                                                       >  2:865647/1‑141 (MQ=255)                                                                          aatGAGCTTAATCAGTCTAATCACATTGTAATAGATATTGTCGAAAAGTACATTAAAAACAATAATAATAATAATAATAATCGAATTCAACAAAAACTAGGCTACTTATCCCCTGTAAAATACAGAGAATTAATAGCCTAg                                                      <  2:343893/141‑1 (MQ=255)                                                                           atGAGCTTAATCACTCTAATCACATTGTAATAGATATTGTCGAAAAGTACATTAAAAACAATAATAATAATAATAATAATCGAATTCAACAAAAACTAGGCTACTTATCCCCTGTAAAATACAGAGAATTAATAGCCTAGa                                                     <  1:33232/141‑1 (MQ=255)                                                                           atGAGCTTAATCACTCTAATCACATTGTAATAGATATTGTCGAAAAGTACATTAAAAACAATAATAATAATAATAATAATCGAATTCAACAAAAACTAGGCTACTTATCCCCTGTAAAATACAGAGAATTAATAGCCTAGa                                                     <  1:110353/141‑1 (MQ=255)                                                                           atGAGCTTAATCACTCTAATCACATTGTAATAGATATTGTCGAAAAGTACATTAAAAACAATAATAATAATAATAATAATCGAATTCAACAAAAACTAGGCTACTTATCCCCTGTAAAATACAGAGAATTAATAGCCTAGa                                                     >  2:15232/1‑141 (MQ=255)                                                                             gAGCTTAATCACTCTAATCACATTGTAATAGATATTGTCGAAAAGTACATTAAAAACaataataataataataatcgaattcaacaaaaactaggctacttatcccctgtaaaatacagagaattaatagcctagaacatg                                                   <  1:238835‑M2/141‑85 (MQ=255)                                                                               gCTTAATCACTCTAATCACATTGTAATAGATATTGTCGAAAAGTACATTAAAAACAATAATAATAATAATAATAATCGAATTCAACAAAAACTAGGCTACTTATCCCCTGTAAAATACAGAGAATTAATAGCCTAGAACAt                                                 >  1:731917/1‑141 (MQ=255)                                                                               gCTTAATCACTCTAATCACATTGTAATAGATATTGTCGAAAAGTACATTAAAAACAATAATAATAATAATAATAATCGAATTCAACAAAAACTAGGCTACTTATCCCCTGTAAAATACAGAGAAGTAATAGCCTAGAACAt                                                 <  1:452619/141‑1 (MQ=255)                                                                                  tAATCACTCTAATCACATTTTAATAGATATTGTCGAAAACTACATTAAAAACAATAATAATAATAATAATAATCGAATTCAACAAAAACTAGGCTACTTATCCCCTGTAAAATACAGAGAATTAATAGCCTAGAACATGgt                                              <  2:398052/141‑1 (MQ=255)                                                                                  tAATCACTCTAATCACATTGTAATAGATATTGTCGAAAAGTACATTAAAAACAATAATAATAATAATAATAATCGAATTCAACAAAAACTAGGCTACTTATCCCCTGTAAAATACAGAGAATTAATAGCCTAGAACATGgt                                              <  2:879421/141‑1 (MQ=255)                                                                                     caccgctAATCACATTGTAAAAGATAATGTCGAAGAGTACATTAAAAACAATAATAATGATAATAATAATCGAATTCAACAAAAACTAGGCTACCTCTCCCCTGTAAAATACAGAGAATTAATAGCCTAGAACATGGTGtt                                           <  2:484334/136‑1 (MQ=21)                                                                                          ctAATCACATTGTAATAGATATTGTCGAAAATTACATTAAAAACAATAATAATAATAATAATAATCGAATTCAACAAAAACTAGGCTACTTATCCCCTGTAAAATACAGAGAATTAATAGCCTAGAACATGGTGTTTttat                                      >  1:39088/1‑141 (MQ=255)                                                                                             aTCACATTGTAATAGATATTGTCGAAAAGTACATTAAAAACAATACTAATAATAATAATAATCGAATTCAACAAAAACTAGGCTACTTATCCCCTGTAAAATACAGAGAATTAATAGCCTAGAACATGGTGTTTTTATTaa                                   <  2:890018/141‑1 (MQ=255)                                                                                             aTCACATTGTAATAGATATTGTCGAAAAGTACATTAAAAACAATAATAATAATAATAATAATCGAATTCAACAAAAACTAGGCTACTTATCCCCTGTAAAATACAGAGAATTAATAGCCTAGAACATGGTGTTTTTATTaa                                   <  2:293081/141‑1 (MQ=255)                                                                                             aTCACATTGTAATAGATATTGTCGAAAAGTACATTAAAAACAATAATAATAATAATAATAATCGAATTCAACAAAAACTAGGCTACTTATCCCCTGTAAAATACAGAGAATTAATAGCCTAGAACATGGTGTTTTTATTaa                                   <  1:724993/141‑1 (MQ=255)                                                                                             aTCACACTGTAATAGATATTGTCGAAAAGTACATTAAAAACAATAATAATAATAATAATAATCGAATTCAACAACAACTAGGCTACTTATCCCCTGTAAAATACAGAGAATTAATAGCCTAGAACATGGTGTTTTTATTaa                                   <  2:499574/141‑1 (MQ=255)                                                                                                 caTTGTAATAGATATTGTCGAAAAGTACATTAAAAACAATAATAATAATAATAATAATCGAATTCAACAAAAACTAGGCTACTTATCCCCTGTAAAATACAGAGAATTAATAGCCTAGAACATGGTGTTTTTATTAAGTTc                               <  2:768567/141‑1 (MQ=255)                                                                                                 caTTGTAATAGATATTGTCGAAAAGTACATTAAAAACAATAATAATAATAATAATAATCGAATTCAACAAAAACTAGGCTACTTATCCCCTGTAAAATACAGAGAATTAATAGCCTAGAACATGGTGTTTTTATTAAGTTc                               <  2:892788/141‑1 (MQ=255)                                                                                                 caTCGTAAAAGATATTGTCGAAAAGTACATTAAAAACAATAATAATAATAATAATAATCGAATTCAACAAAAACTAGGCTACTTATCCCCTGTAAAATACAGAGAATTAATAGCCTAGAACATGGTGTTTTTATTAAGTTc                               <  2:86573/141‑1 (MQ=255)                                                                                                      tAATAGATATTGTCGAAAAGTACATTAAAAACAATAATAATAATAATAATAATCGAATTCAACAAAAACTAGGCTACTTATCCCCTGTAAAATACAGAGAATTAATAGCCTAGAACATGGTGTTTTTATTAAGTTCCCGtt                          <  1:513177/141‑1 (MQ=255)                                                                                                        agagagATTGTCGAAAAGTACATTAAAAACAATAATAATAATAATAATAATCGAATTCAACAAAAACTAGGCTACTTATCCCCTGTAAAATACAGAGAATTAATAGCCTAGAACATGGTGTTTTTATTAAGTTCCCGtttt                        <  2:254580/139‑1 (MQ=255)                                                                                                        aTAGATATTGTCGAAAAGTACATTAAAAACAATAATAATAATAATAATAATCGAATTCAACAAAAACTAGGCTACTTATCCCCTGTAAAATACAGAGAATTAATAGCCTAGAACATGGTGTTTTTATTAAGTTCCCGtttt                        <  1:258489/141‑1 (MQ=255)                                                                                                               ttGTCGAAAAGTACATTAAAAACAATAATAATAATAATAATAATCGAATTCAACAAAAACTAGGCTACTTATCCCCTGTAAAATACAGAGAATTAATAGCCTAGAACATGGTGTTTTTATTAAGTTCCCGTTTTAAGGGtt                 <  2:453883/141‑1 (MQ=255)                                                                                                               ttGTCGAAAAGTACATTAAAAACAATAATAATAATAATAATAATCGAATTCAACAAAAACTAGGCTACTTATCCCCTGTAAAATACAGAGAATTAATAGCCTAGAACATGGTGTTTTTATTAAGTTCCCGTTTTAAGGGtt                 >  1:270477/1‑141 (MQ=255)                                                                                                                tGTCGAAAAGTACATTAAAAACAATAATAATAATAATAATAATCGAATTCAACAAAAACTAGGCTACTTATCCCCTGTAAAATACAGAGAATTAATAGCCTAGAACATGGTGTTTTTATTAAGTTCCCGTTTTAAGGGTTc                <  1:528787/141‑1 (MQ=255)                                                                                                                 gTCGAAAAGTACATTAAAAACAATAATAATAATAATAATAATCGAATTCAACAAAAACTAGGCTACTTATCCCCTGTAAAATACAGAGAATTAATAGCCTAGAACATGGTGTTTTTATTAAGTTCCCGTTTTAAGGGTTCa               >  1:460384/1‑141 (MQ=255)                                                                                                                 gTCGAAAAGTACATCAAAACCAATAATAATAATAATAATAATCGAATTCAACAAAAACTAGGCTACTTATCCCCTGTAAAATACAGAGAATTAATAGCCTAGAACATGGTGTCTTTACTAAGTTCCCTTTTTAAGGGTTCa               >  2:218819/1‑141 (MQ=18)                                                                                                                  tCGAAAAGTACATTAAAAACAATAATAATAATAATAATAATCGAATTCAACAAAAACTAGGCTACTTATCCCCTGTAAAATACAGAGAATTAATAGCCTAGAACATGGTGTTTTTATTAAGTTCCCGTTTTAAGGGTTCAg              <  2:147311/141‑1 (MQ=255)                                                                                                                  gcGAAAAGTACATTAAAAACAATAATAATAATAATAATAATCGAATTCAACAAAAACTAGGCTACTTATCCCCTGTAAAATACAGAGAATTAATAGCCTAGAACATGGTGTTTTTATTAAGTTCCCGTTTTAAGGGTTCAg              <  1:540152/140‑1 (MQ=255)                                                                                                                  acGAAAAGTACATTAAAAACAATAATAATACTAATAATCATCGAATTCACCAAAAACTAGGCTCCTTATCCCCTGTAAACTACAGAGAATTAATAGCCTAGAACATGGTGTTTTTATTAAGTTCCCGTTTTAAGGGTTCAg              <  2:39319/140‑1 (MQ=18)                                                                                                                   cGAAAAGTACATTAAAAACAATAATAATAATAATAATAATCGAATTCAACAAAAACTAGGCTACTTATCCCCTGTAAAATACAGAGAATTAATAGCCTAGAACATGGTGTTTTTATTAAGTTCCCGTTTTAAGGGTTCAGt             >  1:502679/1‑141 (MQ=255)                                                                                                                     aaaaGTACATTAAAAACAATAATAATAATAATAATAATCGAATTCAACAAAAACTAGGCTACTTATCCCCTGTAAAATACAGAGAATTAATAGCCTAGAACATGGTGTTTTTATTAAGTTCCCGTTTTAAGGGTTCAGTGc           <  1:740682/141‑1 (MQ=255)                                                                                                                     aaaaGTACATTAAAAACAATAATAATAATAATAATAATCGAATTCAACAAAAACTAGGCTACTTATCCCCTGTAAAATACAGAGAATTAATAGCCTAGAACATGGTGTTTTTATTAAGTTCCCGTTTTAAGGATTCAGTGc           >  1:714654/1‑141 (MQ=255)                                                                                                                      aaaGTACATTAAAAACAATAATAATAATAATAATAATCGAATTCAACAAAAACTAGGCTACTTATCCCCTGTAAAAAACAGAGAATTAATAGCCTAGAACATGGTGTTTTTATTAAGTTCCCGTTTTAAGGGTTCAGTGcc          >  2:897088/1‑141 (MQ=255)                                                                                                                       aaGTACATTAGAAAAaataataataataataatcgaattcaacaaaaactaggctacttatcccctgtaaaatacagagaattaatagcctagaacatggtgtttttattaagttcccgttttaagggttaagtgccctag         <  2:618117‑M2/141‑127 (MQ=255)                                                                                                                             aTTAAAAACAATAATAATAATAATAATAATCGAATTCAACAAAAACTAGGCTACTTATCCCCTGTAAAATACAGAGAATTAATAGCCTAGAACATGGTGTTTTTATTAAGTTCCCGTTTTAAGGGTTCAGTGCCCTAGGAt   >  1:49719/1‑141 (MQ=255)                                                                                                                              ttAACAAAAATAATAAAAATAATAAGATTCGACATCAACAAACACTAGGCTACTTATCCCCTGTAAAATACAGAGAATTAATAGCCTAGAACATGGTGTTTTTATTAAGTTCCCGTTTTAAGGGTTCAGTGCCCTAGGAtt  <  1:317403/141‑1 (MQ=17)                                                                                                                                     |                                                                                                                                      GGGAACACCTGCCGATAACGCCCCGATAGAAAGTTTCCATTCCTCGCTAAAGTCTGAAACTTTTTACATCAATAATGAGCTTAATCACTCTAATCACATTGTAATAGATATTGTCGAAAAGTACATTAAAAACAATAATAATAATAATAATAATCGAATTCAACAAAAACTAGGCTACTTATCCCCTGTAAAATACAGAGAATTAATAGCCTAGAACATGGTGTTTTTATTAAGTTCCCGTTTTAAGGGTTCAGTGCCCTAGGATT  >  USA300TCH1516_ALE/68523‑68788

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.