New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	CP000730	= 1709558	55 (0.620)	6 (0.070)	4/244	NT	10.2%	intergenic (‑97/+365)	sem/USA300HOU_1604	enterotoxin/hypothetical protein
	?	CP000730	= 1709579	54 (0.640)					intergenic (‑118/+344)	sem/USA300HOU_1604	enterotoxin/hypothetical protein

TGTAAAAATTCCTTCTAACAATAATATTAAAATAAATCCTGTTAAATATTTAACTTCAAACTCCCCCAAAACAATTATTAATTTACATTTGAGAGCGAGACATAAATGATAAAGAACCGCTTATGGTTTATTATGTAGTGGTTCTTGAGCCTACAATTTTGATTATGTATCACGCTCATAATACTTTTCAATTTGAAATACTCTGTTCGCAATTATTAGTTGAGTTATATCAACCAATACAGTGTATACCTAAAAATTCCAAACCGT  >  CP000730/1709441‑1709707                                                                                                                                           |                                                                                                                                 tGTAAAAATTCCTTCTAACAATAATATTAAAATAAATCCTGTTAAATATTTAACTTCAAACTCCCCCACAACAATTATTAATTTACATTTGAGAGCGAGACATAAATGATAAAGAACCGCTTATGGTTTATTATGTAGTgg                                                                                                                                >  1:733094‑M2/1‑139 (MQ=255) tGTAAAAATTCCTTCTAACAATAATATTAAAATAAATCCTGTTAAATATTTAACTTCAAACTCCCCCAAAACAATTATTAATTTACATTTGAGAGCGAGACATAAATGATAAAGAACCGCTTATGGTTTATTATGTAGTgg                                                                                                                                >  1:733110‑M2/1‑139 (MQ=255)  gTAAAAATTCCTTCTAACAATAATATTAAAATAAATCCTGTTAAATATTTAACTTCAAACTCCCCCAAAACAATTATTAATTTACATTTGAGAGCGAGACATAAATGATAAAGAACCGCTTATGGTTTATTATGTAGTggt                                                                                                                               <  1:994716‑M2/141‑4 (MQ=255)        aTTCCTTCTAACAATAATATTAAAATAAATCCTGTTAAATATTTAACTTCAAACTCCCCCAAAACAATTATTAATTTACATTTGAGAGCGAGACATAAATGATAAAGAACCGCTTATGGTTTATTATGTAGTGGTTCTTGa                                                                                                                         >  2:754259/1‑141 (MQ=255)             ttCTAACAATAATATTAAAATAAATCCTGTTAAATATTTAACTTCAAACTCCCCCAAAACAATTATTAATTTACATTTGAGAGCGAGACATAAATGATAAAGAACCGCTTATGGTTTATTATGTAGTGGTTCTTGAGCCTa                                                                                                                    <  1:661858/141‑1 (MQ=255)              tCTAACAATAATATTAAAATAAATCCTGTTAAATATTTAACTTCAAACTCCCCCAAAACAATTATTAATTTACATTTGAGAGCGAGACATAAATGATAAAGAACCGCTTATGGTTTATTATGTAGTGGTTCTTGAGCCTAc                                                                                                                   <  2:631828/141‑1 (MQ=255)              tCTAACAATAATATTAAAATAAATCCTGTTAAATATTTAACTTCAAACTCCCCCAAAACAATTATTAATTTACATTTGAGAGCGAGACATAAATGATAAAGAACCGCTTATGGTTTATTATGTAGTGGTTCTTGAGCCTAc                                                                                                                   <  2:866374/141‑1 (MQ=255)              tCTAACAATAATATTAAAATAAATCCTGTTAAATATTTAACTTCAAACTCCCCCAAAACAATTATTAATTTACATTTGAGAGCGAGACATAAATGATAAAGAACCGCTTATGGTTTATTATGTAGTGGTTCTTGAGCCTAc                                                                                                                   <  2:545182/141‑1 (MQ=255)                tAACAATAATATTAAAATAAATCCTGTTAAATATTTAACTTCAAACTCCCCCAAAACAATTATTAATTTACATTTGAGAGCGAGACATAAATGATAAAGAACCGCTTATGGTTTATTATGTAGTGGTTCTTGAGCCTACaa                                                                                                                 <  2:25001/141‑1 (MQ=255)                      taataTTAAAATAAATCCTGTTCAATATTTAACTTCAAACTCCCCCAAAACAATTATTAATTTACATTTGAGAGCGAGACATAAATGAGAAAGAACCGCTTATGGTTTATTATGTAGTGGTTCTTGAGCCTACAATTTTGa                                                                                                           <  2:376390/141‑1 (MQ=255)                      taataTTAAAATAAATCCTGTTAAATATTTAACTTCAAACTCCCCCAAAACAATTATTAATTTACATTTGAGAGCGAGACATAAATGATAAAGAACCGCTTATGGTTTATTATGTAGTGGTTCTTGAGCCTACAATTTTGa                                                                                                           >  2:95693/1‑141 (MQ=255)                            tAAAATAAATCCTGTTAAATATTTAACTTCAAACTCCCCCAAAACAATTATTAATTTACATTTGAGAGCGAGACATAAATGATAAAGAACCGCTTATGGTTTATTATGTAGTGGTTCTTGAGCCTACAATTTTGATTATGt                                                                                                     <  2:737074/141‑1 (MQ=255)                              aaataaatCCTGTTAAATATTTAACTTCAAACTCCCCCAAAACAATTATTAATTTACATTTGAGAGCGAGACATAAATGATAAAGAACCGCTTATGGTTTATTATGTAGTGGTTCTTGAGCCTACAATTTTGATTATGTAt                                                                                                   >  1:732069/1‑141 (MQ=255)                               aataaatCCTGTTAAATATTTAACTTCAAACTCCCCCAAAACAATTATTAATTTACATTTGAGAGCGAGACATAAATGATAAAGAACCGCTTATGGTTTATTATGTAGTGGTTCTTGAGCCTACAATTTTGATTATGTATc                                                                                                  >  1:999066/1‑141 (MQ=255)                                ataaatCCTGTTAAATATTTAACTTCAAACTCCCCCAAAACAATTATTAATTTACATTTGAGAGCGAGACATAAATGATAAAGAACCGCTTATGGTTTATTATGTAGTGGTTCTAGAGCCTACAATTTTGATTATGTATCa                                                                                                 >  1:1080956/1‑141 (MQ=255)                                     tCCTGTTAAATATTTAACTTCAAACTCCCCCAAAACAATTATTAATTTACATTTGAGAGCGAGACATAAATGATAAAGAACCGCTTATGGTTTATTATGTAGTGGTTCTTGAGCCTACAATTTTGATTATGTATCACGCTc                                                                                            >  2:498862/1‑141 (MQ=255)                                      ccTGTTAAATATTTAACTTCAAACTCCCCCAAAACAATTATTAATTTACATTTGAGAGCGAGACATAAATGATAAAGAACCGCTTATGGTTTATTATGTAGTGGTTCTTGAGCCTACAATTTTGATTATGTATCACGCTCa                                                                                           <  2:464593/141‑1 (MQ=255)                                       cTGTTAAATATTTAACTTCAAACTCCCCCAAAACAATTATTAATTTACATTTGAGAGCGAGACATAAATGATAAAGAACCGCTTATGGTTTATTATGTAGTGGTTCTTGAGCCTACAATTTTGATTATGTATCACGCTCat                                                                                          >  1:319188/1‑141 (MQ=255)                                       cTGTTAAATATTTAACTTCAAACTCCCCCAAAACAATTATTAATTTACATTTGAGAGCGAGACATAAATGATAAAGAACCGCTTATGGTTTATTATGTAGTGGTTCTTGAGCCTACAATTTTGATTATGTATCACGCTCat                                                                                          <  1:16393/141‑1 (MQ=255)                                          ttAAATATTTAACTTCAAACTCCCCCAAAACAATTATTAATTTACATTTGAGAGCGAGACATAAATGATAAAGAACCGCTTATGGTTTATTATGTAGTGGTTCTTGAGCCTACAATTTTGATTATGTATCACGCTCataat                                                                                       <  2:191851/141‑1 (MQ=255)                                          ttAAATATTTAACTTCAAACTCCCCCAAAACAATTATTAATTTACATTTGAGAGCGAGACATAAATGATAAAGAACCGCTTATGGTTTATTATGTAGTGGTTCTTGAGCCTACAATTTTGATTATGTATCACGCTCataat                                                                                       >  1:867682/1‑141 (MQ=255)                                                 tttAACTTCAAACTCCCCCAAAACAATTATTAATTTACATTTGAGAGCGAGACATAAATGATAAAGAACCGCTTATGGTTTATTATGTAGTGGTTCTTGAGCCTACAATTTTGATTATGTATCACGCTCATAATCCTTTTc                                                                                >  1:414072/1‑141 (MQ=255)                                                 tttAACTTCAAACTCCCCCAAAACAATTATTAATTTACATTTGAGAGCGAGACATAAATGATAAAGAACCGCTTATGGTTTATTATGTAGTGGTTCTTGAGCCTACAATTTTGATTATGTATCACGCTCATAATACTTTTc                                                                                <  2:452010/141‑1 (MQ=255)                                                     aCTTCAAACTCCCCCAAAACAATTATTAATTTACATTTGAGAGCGAGACATAAATGATAAAGAACCGCTTATGGTTTATTATGTAGTGGTTCTTGAGCCTACAATTTTGATTATGTATCACGCTCATAATACTTTTCatct                                                                            >  2:39293/1‑138 (MQ=255)                                                       ttCAAACTCCCCCAAAACAATTATTAATTTACATTTGAGAGCGAGACATAAATGATAAAGAACCGCTTATGGTTTATTATGTAGTGGTTCTTGAGCCTACAATTTTGATTATGTATCACGCTCATAATACTTTTCAATTTg                                                                          <  2:1027815/141‑1 (MQ=255)                                                           aaCTCCCCCAAAACAATTATTAATTTACATTTGAGAGCGAGACATAAATGATAAAGAACCGCTTATGGTTTATTATGTAGTGGTTCTTGAGCCTACAATTTTGATTATGTATCACGCTCATAATACTTTTCAATTTGAAAt                                                                      >  2:1033461/1‑141 (MQ=255)                                                             cTCCCCCAAAACAATTATTAATTTACATTTGAGAGCGAGACATAAATGATAAAGAACCGCTTATGGTTTATTATGTAGTGGTTCTTGAGCCTACAATTTTGATTATGTATCACGCTCATAATACTTTTCAATTTGAAATAc                                                                    >  1:252105/1‑141 (MQ=255)                                                               cccccAAAACAATTATTAATTTACATTTGAGAGCGAGACATAAATGATAAAGAACCGCTTATGGTTTATTATGTAGTGGTTCTTGAGCCTACAATTTTGATTATGTATCACACTCATAATACTTTTCAATTTGAAATActc                                                                  >  2:55999/1‑141 (MQ=255)                                                                   cAAAACAATTATTAATTTACATTTGAGAGCGAGACATAAATGATAAAGAACCGCTTATGGTTTATTATGTAGTGGTTCTTGAGCCTACAATTTTGATTATGTATCACGCTCATAATACTTTTCAATTTGAAATACTCTGtt                                                              >  2:77299/1‑141 (MQ=255)                                                                    aaaaCAATTATTAATTTACATTTGAGAGCGAGACATAAATGATAAAGAACCGCTTATGGTTTATTATGTAGTGGTTCTTGAGCCTACAATTTTGATTATGTATCACGCTCATAATACTTTTCAATTTGAAATACTCTGTTc                                                             <  2:469303/141‑1 (MQ=255)                                                                     aatcAATTATTAATTTACATTGCATAGCTAGACATAAATGATAAAGAGCCTCTTATTGTTTGTTATGTAGTTGTTCTTGAGCTTACAATTGTGATTATGTATCGCGCTCATAATACTTTTCAATTTGAAATACTGTGTTCg                                                            <  2:875076/138‑1 (MQ=255)                                                                          attattAATTTACATTTGAGAGCGAGACATAAATGATAAAGAACCGCTTATGGTTTATTATGTAGTGGTTCTTGAGCCTACAATTTTGATTATGTATCACGCTCATAATACTTTTCAATTTGAAATACTCTGTTCGCAatt                                                       <  2:795806/141‑1 (MQ=255)                                                                           ttattaATTTACATTTGAGAGCGAGACATAAATGATAAAGAACCGCTTATGGTTTATTATGTAGTGGTTCTTGAGCCTACAATTTTGATTATGTATCACGCTCATAATACTTTTCAATTTGAAATACTCTGTTCGCAatta                                                      <  1:491853/141‑1 (MQ=255)                                                                           ttattaATTTACATTTGAGAGCGAGACATAAATGATAAAGAACCGCTTATGGTTTATTATGTAGTGGTTCTTGAGCCTACAATTTTGATTATGTATCACGCTCATAATACTTTTCAATTTGAAATACTCTGTTCGCAatta                                                      <  1:337357/141‑1 (MQ=255)                                                                           ttattaATTTACATTTGAGAGCGAGACATAAATGATAAAGAACCGCTTATGGTTTATTATGTAGTGGTTCTTGAGCCTACAATTTTGATTATGTATCACGCTCATAATACTTTTCAATTTGAAATACTCTGTTCGCAatta                                                      <  1:337487/141‑1 (MQ=255)                                                                                aaTTTACATTTGAGAGCGAGAGATGAATGATAAAGAACCGCTTATGGTTTATTATGTATTGGTTCTTGAGCCTACAATTTTGATTATGTATCACGCTCATAATACTTTTCAATTTGAAAGACTCTGTTCGCAATTATTAGt                                                 <  2:1041619/141‑1 (MQ=255)                                                                                 aTTTACATTTGAGAGCGAGACATAAATGATAAAGAACCGCTTATGGTTTATTATGTAGTGGTTCTTGAGCCTACAATTTTGATTATGTATCACGCTCATAATACTTTTCAATTTGAAATACTCTGTTCGCAATTATTAGtt                                                <  1:1080327/141‑1 (MQ=255)                                                                                  tttACATTTGAGAGCGAGACATAAATGATAAAGAACCGCTTATGGTTTATTATGTAGTGGTTCTTGAGCCTACAATTTTGATTATGTATCACGCTCATAATACTTTTCAATTTGAAATACTCTGTTCGCAATTATTAGTTg                                               >  2:650635/1‑141 (MQ=255)                                                                                            agagCGAGACATAAATGATAAAGAACCGCTTATGGTTTATTATGTAGTGGTTCTTGAGCCTACAATTTTGATTATGTATCACGCTCATAATACTTTTCAATTTGAAATACTCTGTTCGCAATTATTAGTTGAGTTATATCa                                     >  2:714118/1‑141 (MQ=255)                                                                                             gagCGAGACATAAATGATAAAGAACCGCTTATGGTTTATTATGTAGTGGTTCTTGAGCCTACAATTTTGATTATGTATCACGCTCATAATACTTTTCAATTTGAAATACTCTGTTCGCAATTATTAGTTGAGTTATATCaa                                    <  2:1003788/141‑1 (MQ=255)                                                                                             gagCGAGACATAAATGATAAAGAACCGCTTATGGTTTATTATGTAGTGGTTCTTGAGCCTACAATTTTGATTATGTATCACGCTCATAATACTTTTCAATTTGAAATACTCTGTTCGCAATCATTACTTGAGTTATATCaa                                    >  2:373523/1‑141 (MQ=255)                                                                                              agCGAGACATAAATGATAAAGAACCGCTTATGGTTTATTATGTAGTGGTTCTTGAGCCCACAATTTTGATTATGTATCACGCTCATAATACTTTTCAATTTGAAATACTCTGTTCGCAATTATTAGTTGAGTTATATCAAc                                   <  1:924997/141‑1 (MQ=255)                                                                                                cGAGACATAAATGATAAAGAACCGCTTATGGTTTATTATGTAGTGGTTCTTGAGCCTACAATTTTGATTATGTATCACGCTCATAATACTTTTCAATTTGAAATACTCTGTTCGCAATTATTAGTTGAGTTATATCAACCa                                 >  2:936105/1‑141 (MQ=255)                                                                                                cGAGACATAAATGATAAAGAACCGCTTATGGTTTATTATGTAGTGGTTCTTGAGCCTACAATTTTGATTATGTATCACGCTCATAATACTTTTCAATTTGAAATACTCTGTTCGCAATTATTAGTTGAGTTATATCAACCa                                 >  1:780514/1‑141 (MQ=255)                                                                                                 gagaCATAAATGATAAAGAACCGCTTATGGTTTATTATGTAGTGGTTCTTGAGCCTACAATTTTGATTATGTATCACGCTCATAATACTTTTCAATTTGAAATACTCTGTTCGCAATTATTGGTTGatataactcaactaa                                <  1:760151/141‑15 (MQ=255)                                                                                                    aCATAAATGATAAAGAACCGCTTATGGTTTATTATGTAGTGGTTCTTGAGCCTACAATTTTGATTATGTATCACGCTCATAATACTTTTCAATTTGAAATACTCTGTTCGCAATTATTAGTTGAGTTATATCAACCAATAc                             >  2:861122/1‑141 (MQ=255)                                                                                                      aTAAATGATAAAGAACCGCTTATGGTTTATTATGTAGTGGTTCTTGAGCCTACAATTTTGATTATGTATCACGCTCATAATACTTTTCAATTTGAAATACTCTGTTCGCAATTATTAGTTGAGTTATATCAACCAATACAg                           >  2:734312/1‑141 (MQ=255)                                                                                                          aTGATAAAGAACCGCTTATGGTTTATTATGAAGTGGTTCTTGAGCCTACAATTTTGATTATGTATCACGCTCATAATACTTTTCAATTTGAAATACTCTGTTCGCAATTATTAGTTGAGTTATATCAACCAATACAGTGta                       <  2:517149/141‑1 (MQ=255)                                                                                                           tGATAAAGAACCGCTTATGGTTTATTATGTAGTggttctttatcatttatgtctcgctctcaaatgtaaattaataattgttttgggggagtttgaagttaaatatttaacaggatttattttaatattattgttagaagg                      <  2:2584‑M2/141‑109 (MQ=255)                                                                                                            gATAAAGAACCGCTTATGGTTTATTATGTAGTggttctttatcatttatgtctcgctctcaaatgtaaattaataattgttttgggggagtttgaagttaaatatttaacaggatttattttaatattattgttagaagga                     <  2:452908‑M2/141‑110 (MQ=255)                                                                                                            gATAAAGAACCGCTTATGGTTTATTATGTAGTggttctttatcatttatgtctcgctctcaaatgtaaattaataattgttttgggggagtttgaagttaaatatttaacaggatttattttaatattattgttagaagga                     <  2:200952‑M2/141‑110 (MQ=255)                                                                                                              tAAAGAACCGCTTATGGTTTATTATGTAGTGGTTCTTGAGCCTACAATTTTGATTATGTATCACGCTCATAATACTTTTCAATTTGAAATACTCTGTTCGCAATTATTAGTTGAGTTATATCAACCAATACAGTGTATAcc                   <  2:782025/141‑1 (MQ=255)                                                                                                                 aGAACCGCTTATGGTTTATTATGTAGTGGTTCTTGAGCCTACAATTTTGATTATGTATCACGCTCATAATACTTTTCAATTTGAAATACTCTGTTCGCAATTATTAGTTGAGTTATATCAACCAATACAGTGTATACCTaa                >  2:741864/1‑141 (MQ=255)                                                                                                                   aaCCGCTTATGGTTTATTATGTAGTGGTTCTTGAGCCTACAATTTTGATTATGTATCACGCTCATAATACTTTTCAATTTGAAATACTCTGTTCGCAATTATTAGTTGAGTTATATCAACCAATACAGTGTATACCTaaaa              >  1:829946/1‑141 (MQ=255)                                                                                                                    aCCGCTTATGGTTTATTATGTAGTggttctttatcatttatgtctcgctctcaaatgtaaattaataattgttttgggggagtttgaagttaaatatttaacaggatttattttaatattattgttagaaggaatttttac             <  2:464388‑M2/141‑118 (MQ=255)                                                                                                                     ccGCTTATGGTTTATTATGTAGTGGTTCTTGAGCCTACAATTTTGATTATGTATCACGCTCATAATACTTTTCAATTTGAAATACTCTGTTCGCAATTATTAGTTGAGTTATATCAACCAATACAGTGTATACCTAAAAAt            <  2:303612/141‑1 (MQ=255)                                                                                                                      cGCTTATGGTTTATTATGTAGTggttctttatcatttatgtctcgctctcaaatgtaaattaataattgttttgggggagtttgaagttaaatatttaacaggatttattttaatattattgttagaaggaatttttacaa           <  1:1042393‑M2/141‑120 (MQ=255)                                                                                                                      cGCTTATGGTTTATTATGTAGTggttctttatcatttatgtctcgctctcaaatgtaaattaataattgttttgggggagtttgaagttaaatatttaacaggatttattttaatattattgttagaaggaatttttacaa           <  2:198376‑M2/141‑120 (MQ=255)                                                                                                                         ttATGGTTTATTATGTAGTGGTTCTTGAGCCTACAATTTTGATTATGTATCACGCTCATAATACTTTTCAATTTGAAATACTCTGTTCGCGATTATTAGTTGAGTTATATCAACCAATACAGTGTATACCTAAAAATTCCa        <  2:1026652/141‑1 (MQ=255)                                                                                                                         ttATGGTTTATTATGTAGTGGTTCTTGAGCCTACAATTTTGATTATGTATCACGCTCATAATACTTTTCAATTTGAAATACTCTGTTCGCAATTATTAGTTGAGTTATATCAACCAATACAGTGTATACCTAAAAATTCCa        >  2:830713/1‑141 (MQ=255)                                                                                                                          tATGGTTTATTATGTAGTGGTTCTTGAGCCTACAATTTTCATTATGTATCACGCTCATAATACTTTTCAATTTGAAATACTCTGTTCGCAATTATTAGTTGAGTTATATCAACCAATACAGTGTATACCTAAAAATTCCaa       <  1:802603/141‑1 (MQ=255)                                                                                                                           aTGGTTTATTATGTAGTGGTTCTTGAGCCTACAATTTTGATTATGTATCACGCTCATAATACTTTTCAATTTGAAATACTCTGTTCGCAATTATTAGTTGAGTTATATCAACCAATACAGTGTATACCTAAAAATTCCaaa      >  2:1045130/1‑141 (MQ=255)                                                                                                                              gTTTATTATGTAGTGGTTCTTGAGCCTACAATTTTGATTATGTATCACGCTCATAATACTTTTCAATTTGAAATACTCTGTTCGCAATTATTAGTTGAGTTATATCAACCAATACAGTGTATACCTAAAAATTCCAAACCg   <  1:545454/141‑1 (MQ=255)                                                                                                                               tttATTATGTAGTGGTTCATAAACATACAATTTTGATTATGTATCACGATCATAATACTATTCAATTTGAAATACTCTGTCCGCAATTATTAGTTGAGTTATATCCTCCAATAAAAAAAAAAAAAAAAAATTCCAAACCGt  <  2:613680/141‑1 (MQ=255)                                                                                                                                           |                                                                                                                                 TGTAAAAATTCCTTCTAACAATAATATTAAAATAAATCCTGTTAAATATTTAACTTCAAACTCCCCCAAAACAATTATTAATTTACATTTGAGAGCGAGACATAAATGATAAAGAACCGCTTATGGTTTATTATGTAGTGGTTCTTGAGCCTACAATTTTGATTATGTATCACGCTCATAATACTTTTCAATTTGAAATACTCTGTTCGCAATTATTAGTTGAGTTATATCAACCAATACAGTGTATACCTAAAAATTCCAAACCGT  >  CP000730/1709441‑1709707

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ 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.