New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	CP000730	2080720 =	43 (1.160)	3 (0.090)	3/244	NT	6.8%	intergenic (‑188/+55)	USA300HOU_1938/USA300HOU_1939	hypothetical protein/hypothetical protein
	?	CP000730	2080773 =	41 (1.170)					intergenic (‑241/+2)	USA300HOU_1938/USA300HOU_1939	hypothetical protein/hypothetical protein

AACAAAACCATTCAATCAAAATGATTATTGATTGCGATATATTGTGTTCAATGATATTATTTAAGTGTATCCACAGAATTATACTACACA‑‑‑‑‑‑‑‑ACCCCAAGTCTGGTACCAGCAGACTTGGGGTTATTTATGTGTGTAGGATCATTTTTTATTTTTCCATTTCAGTTCTAACCAAAGTCGAAAAATAATTAGTAAGCCACCTGTAATAAGTGTCATCATCCCTTCTTGCCACCACATCATTACACTACACCTCCGTTCGACTAAAGTATCATACTGAAG  >  CP000730/2080637‑2080912                                                                                                                                                 |                                                                                                                                            aacaaAACCATTCAATCAAAATGATTATTGATTGCGATATATTGTGTTCAATGATATTATTTAAGTGTATCCACAGAATTATACTACACA‑‑‑‑‑‑‑‑ACCCCAAGTCTGGTACCAGCAGACTTGGGGTTATTTATGTGTGTAGGTTCa                                                                                                                                         >  2:407686/1‑141 (MQ=255) aacaaAACCATTCAATCAAAATGATTATTGATTGCGATATATTGTGTTCAATGATATTATTTAAGTGTATCCACAGAATTATACTACACA‑‑‑‑‑‑‑‑ACCCCAAGTCTGGTACCAGCAGACTTGGGGTTATTTATGTGTGTAGGATCa                                                                                                                                         >  1:346843/1‑141 (MQ=255)  ggatgatgacacttattacaggtggcttactaattatttttcgactttggttagaactgaaatggaaaaataaaaaatgatcCTACACA‑‑‑‑‑‑‑‑ACCCCAAGTCTGGTACCAGCAGACTTGGGGTTATTTATGTGTGTAGGATCAt                                                                                                                                        >  2:64188‑M1/83‑141 (MQ=255)       atgacacttattacaggtggcttcctaattatttttcgactttggttagaactgaaatggaaaaataaaaaatgatcCTACACACATAAATAACCCCAAGTCTGGTACCAGCAGACTTGGGGTTATTTATGTGTGTAGGAt                                                                                                                                           >  1:185945‑M1/78‑141 (MQ=255)          aTTCAATCAAAATGATTATTGATTGCGATATATTGTGTTCAATGATATTATTTAAGTGTATCCACAGAATTATACTACACA‑‑‑‑‑‑‑‑ACCCCAAGTCTGGTACCAGCAGACTTGGGGTTATTTATGTGTGTAGGATCATTTTTTAtt                                                                                                                                >  1:64151/1‑141 (MQ=255)              aatccaACTGATTATTGATTGCGATATATTGTCTTCAAAGATACTACACAAGTGTATCGACAGAATTAGACTACACA‑‑‑‑‑‑‑‑ACCCCAAGTCGGGTACCAGCAGACTTGGGGTTATTTATGTGTGTAGGCTCATTTTTTAtttttt                                                                                                                            >  2:152879/1‑140 (MQ=255)               atcaaAATGATTATTGATTGCGATATATTGTGTTCAATGATATTATTTAAGTGTATCCACAGAATTATACTACACA‑‑‑‑‑‑‑‑ACCCCAAGTCTGGTACCAGCAGACTTGGGGTTATTTATGTGTGTAGGATCATTTTTTATTTTTcc                                                                                                                           <  2:201464/141‑1 (MQ=255)               atcaaAATGATTATTGATTGCGATATATTGTGTTCAATGATATTATTTAAGTGTATCCACAGAATTATACTACACA‑‑‑‑‑‑‑‑ACCCCAAGTCTGGTACCAGCAGACTTGGGGTTATTTATGTGTGTAGGATCATTTTTTATTTTTcc                                                                                                                           <  2:201490/141‑1 (MQ=255)                       gATTATTGATTGCGATATATTGTGTTCAATGATATTATTTAAGTGTATCCACAGAATTATACTACACA‑‑‑‑‑‑‑‑ACCCCAAGTCTGGTACCAGCAGACTTGGGGTTATTTATGTGTGTAGGATCATTTTTTATTTTTCTATTTCAGt                                                                                                                   >  2:171154/1‑141 (MQ=255)                         ttattGATTGCGATATATTGTGTTCAATGATATTATTTAAGTGTATCCACAGAATTATACTACACA‑‑‑‑‑‑‑‑ACCCCAAGTCTGGTACCAGCAGACTTGGGGTTATTTATGTGTGTAGGATCATTTTTTATTTTTCCATTTCAGTTc                                                                                                                 <  1:107155/141‑1 (MQ=255)                          tattGATTGCGATATATTGTGTTCAATGATATTATTTAAGTGTATCCACAGAATTATACTACACA‑‑‑‑‑‑‑‑ACCCCAAGTCTGGTACCAGCAGACTTGGGGTTATTTATGTGTGTAGGATCATTTTTTATTTTTCCATTTCAGTTCt                                                                                                                <  1:192593/141‑1 (MQ=255)                          tattGATTGCGATATATTGTGTTCAATGATATTATTTAAGTGTATCCACAGAATTATACTACACA‑‑‑‑‑‑‑‑ACCCCAAGTCTGGTACCAGCAGACTTGGGGTTATTTATGTGTGTAGGATCATTTTTTATTTTTCCATTTCAGTTCt                                                                                                                >  1:123526/1‑141 (MQ=255)                          tattGATTGCGATATATTGTGTTCAATGATATTATTTAAGTGTATCCACAGAATTATACTACACA‑‑‑‑‑‑‑‑ACCCCAAGTCTGGTACCAGCAGACTTGGGGTTATTTATGTGTGTAGGATCATTTTTTATTTTTCCATTTCAGTTCt                                                                                                                <  1:192477/141‑1 (MQ=255)                           tttgaatgCGAAATCTTTTGTTCAATGATATTATTTAAGGGTATCCACAGAATTCTACTCCAGA‑‑‑‑‑‑‑‑ACTCCCAGTCTGCTACCAGCAGACTTTGGGTTATTTATGTGTGTAGGATCATTTTTTATTTTTCCATTTCAGTTCTa                                                                                                               <  2:307912/140‑1 (MQ=255)                            ttgattgCGATATATTGTGTTCAATGATATTATTTAAGTGTATCCACAGAATTATACTACACA‑‑‑‑‑‑‑‑ACCCCAAGTCTGGTACCAGCAGACTTGGGGTTATTTATGTGTGTAGGATCATTTTTTATTTTTCCATTTCAGTTCTaa                                                                                                              >  1:82508/1‑141 (MQ=255)                                  gCGATATATTGTGTTCAATGATATTATTTAAGTGTATCCACAGAATTATACTACACA‑‑‑‑‑‑‑‑ACCCCAAGTCTGGTACCAGCAGACTTGGGGTTATTTATGTGTGTAGGATCATTTTTTATTTTTCCATTTCAGTTCTAACCAAAg                                                                                                        >  1:426476/1‑141 (MQ=255)                                    gATATATTGTGTTCAATGATATTATTTAAGTGTATCCACAGAATTATACTACACA‑‑‑‑‑‑‑‑ACCCCAAGTCTGGTACCAGCAGACTTGGGGTTATTTATGTGTGTAGGATCATTTTTTATTTTTCCATTTCAGTTCTAACCAAAGTc                                                                                                      <  1:278768/141‑1 (MQ=255)                                           tgtgTTCAATGATATTATGTAAGGGTATCCACAGAATTGTAGTAGACA‑‑‑‑‑‑‑‑GGCTGGAGGCGGGTACCAGCAGACTTGGGGTTATTTATGTGTGTAGGAACATTTTTTATTTTTCCATTTCAGTTCTATCCAAAGTCGAAAaat                                                                                               <  2:427562/141‑1 (MQ=255)                                            gtgtTCAATGATATTATTTAAGTGTATCCACAGAATTATACTACACA‑‑‑‑‑‑‑‑ACCCCAAGTCTGGTACCAGCAGACTTTGGGTTATTTATGTGTGTAGGATAATTTTTTATTTTTCCATTTCAGTTCTAACCAAAGTGGAAAaata                                                                                              >  2:39843/1‑141 (MQ=255)                                                acAAAGAAATTATTTAAGTATATCCACAAAAATATAAAACACA‑‑‑‑‑‑‑‑ACCCCAAGTCTGGTACCAGCAGACTTGGGGTTATTTAAGTGTGTAAAAAAATTTATTAATATTCCATTTAAGTTAAAAAAAAAAAAAAAAAATAATTa                                                                                          <  2:148713/140‑1 (MQ=255)                                                   aTGATATTATTTAAGTGTATCCACAGAATTATACTACACA‑‑‑‑‑‑‑‑ACCCCAAGTCTGGTACCAGCAGACTTGGGGTTATTTATGTGTGTAGGATCATTTTTTATTTTTCCATTTCAGTTCTAACCAAAGTCGAAAAATAATTAGTa                                                                                       >  1:251466/1‑141 (MQ=255)                                                         ttattTAAGTGTATCCACAGAATTATACTACACA‑‑‑‑‑‑‑‑ACCCCAAGTCTGGTACCAGCAGACTTGGGGTTATTTATGTGTGTAGGATCATTTTTTATTTTTCCATTTCAGTTCTAACCAAAGTCGAAAAATAATTAGTAAGCCAc                                                                                 <  1:306207/141‑1 (MQ=255)                                                           attTAAGTGTATCCACAGAATTATACTACACA‑‑‑‑‑‑‑‑ACCCCAAGTCTGGTACCAGCAGACTTGGGGTTATTTATGTGTGTAGGATCATTTTTTATTTTTTTATTTTTGTTTTATCTAAAGTCGAAAAATAATTAGTAAGCCATCt                                                                               >  2:355220/1‑141 (MQ=255)                                                           attTAAGTGTATCCACAGAATTATACTACACA‑‑‑‑‑‑‑‑ACCCCAAGTCTGGTACCAGCAGACTTGGGGTTATTTATGTGTGTAGGATCATTTTTTATTTTACCATTTCAGTTCTAACCAAAGTCGAAAAATAATTAGTAAGCCACCt                                                                               <  1:377018/141‑1 (MQ=255)                                                           attTAAAAGTATCCACAGAATTATACTACACA‑‑‑‑‑‑‑‑ACCCCAAGTCTGGTACCAGCAGACTTGGGGTTATTTATGTGTGTAGGATCATTTTTTATTTTTCCATTTCAGTTCTAAAAAAAAAAAAAAAATAATTAGTAAGCCACCt                                                                               <  2:372277/141‑1 (MQ=255)                                                              tAAGTGTATCCACAGAATTATACTACACA‑‑‑‑‑‑‑‑ACCCCAAGTCTGGTACCAGCAGACTTGGGGTTATTTATGTGTGTAGGATCATTTTTTATTTTTCCATTTCAGTTCTAACCAAAGTCGAAAAATAATTAGTAAGCCACCTGta                                                                            <  2:289770/141‑1 (MQ=255)                                                               aaGTGTATCCACAGAATTATACTACACA‑‑‑‑‑‑‑‑ACCCCAAGTCTGGTACCAGCAGACTTGGGGTTATTTATGTGTGTAGGATCATTTTTTATTTTTCCATTTCAGTTCTAACCAAAGTCGAAAAATAATTAGTAAGCCACCTGtaa                                                                           >  2:57940/1‑141 (MQ=255)                                                                 gtgtATCCACAGCATTATACTACACA‑‑‑‑‑‑‑‑ACCCCAAGTCTGGTACCAGCAGACTTGGAGTTATTGATGTGTGTAGGCTCATTTTTTATTTTCCCCTTTCAGTTCTAACCAGAGTCGAAAAATAATTAGTAAGCCACCTGtaaca                                                                         <  2:158689/141‑3 (MQ=255)                                                                 gtgtATCCACAGAATTATACTACACA‑‑‑‑‑‑‑‑ACCCCAAGTCTGGTACCAGCAGACTTGGGGTTATTTATGTGTGTAGGATCATTTTTTATTTTTCCATTTCAGTTCTAACCAAAGTCGAAAAATAATTAGTAAGCCACCTGtaata                                                                         <  2:158688/141‑1 (MQ=255)                                                                 gggtATCCACAGAATTATACTACACA‑‑‑‑‑‑‑‑ACACCAAGTCGGGTACCAGCAGACTTGGGGTTATTTATGTGTGTAGGATCATTTTTTATTTTTCCATTTCAGTTCTAACCAAAGTCGAAAACTAATTAGTTAGCCACCTGtaatc                                                                         <  2:19261/139‑2 (MQ=255)                                                                   ttATCCACAGAATTATACTACACA‑‑‑‑‑‑‑‑ACCCCAAGTCTGGTACCAGCAGACTTGGGGTTATTTATGTGTGTAGGATCATTTTTTATTTTTCCATTTCAGTTCTAAAAAAAAAAAAAAAATAATTAGTAAGCCACCTGTAATAAg                                                                       <  2:33218/140‑1 (MQ=255)                                                                   gtATCCACAGAATTATACTACACA‑‑‑‑‑‑‑‑ACCCCAAGTCTGGTACCAGCAGACTTGGGGTTATTTATGTGTGTAGGATTATTTTTTATTTTTCCATTTCAGTTCTAACCAAAGTCGAAAAATAATTAGTAATCCACCTGTAATAAg                                                                       >  2:69468/1‑141 (MQ=255)                                                                             aaTTATACTACACA‑‑‑‑‑‑‑‑ACCCCAAGTCTGGTACCAGCAGACTTGGGGTTATTTATGTGTGTAGGATCATTTTTTATTTTTCTATTTTAGTTCTAACCAAAGTCGAAAAATAATTAGTAAGCCACCTGTAATAAGTatcatcatc                                                             >  2:128707/1‑141 (MQ=255)                                                                                 atcctacacacataaataaccccaagtctgctggtaccagacttggggttatttatgtgtgtagGATCATTTTTTATTTTTCCATTTCAGTTCTAACCAAAGTCGAAAAATAATTAGGAAGCCACCTGTAATAAGTGtcat                                                                 >  1:185945‑M2/65‑141 (MQ=255)                                                                                  tactacACA‑‑‑‑‑‑‑‑ACCCCAAGTCTGGTACCAGCAGACTTGGGGTTATTTATGTGTGTAGGATCATTTTTTATTTTTCCATTTCAGTTCTAACCAAAGTCGAAAAATAATTAGTAAGCCACCTGTAATAAGTGTCATCATCCcttc                                                        <  2:21329/141‑1 (MQ=255)                                                                                     TACACA‑‑‑‑‑‑‑‑ACCCCAAGTCTGGTACCAGCAGACTTGGGGTTATTTATGTGTGTAGGATCATTTTTTATTTTTCCATTTCAGTTCTAACCAAAGTCGAAAAATAATTAGTAAGCCACCTGTAATAAGTGTCATCATCCCTTCTTg                                                     >  1:50031‑M1/1‑141 (MQ=255)                                                                                      atgatcctacacacataaataaccccaagtctgctggtaccagacttggggttgtgtagGATCATTTTTTATTTTTCCATTTCAGTTCTAACCAAAGTCGAAAAATAATTAGTAAGCCACCTGTAATAAGTGTCATCATcc                                                            >  2:64188‑M2/60‑141 (MQ=255)                                                                                       CACA‑‑‑‑‑‑‑‑ACCCCAAGTCTGGTACCAGCAGACTTGGGGTTATTTATGTGTGTAGGATCATTTTTTATTTTTCCATTTCAGTTCTAACCAAAGTCGAAAAATAATTAGTAAGCCACCTGTAATAAGTGTCATCATCCCTTCTTGcc                                                   >  2:82508‑M1/1‑141 (MQ=255)                                                                                                    ccccAAGTCTGGTACCAGCAGACTTGGGGTTATTTATGTGTGTAGGATCATTTTTTTTTTTTTTTTTTCAGTTCTAACCAAAGTCGAAAAATAATTAGTAAGCCACCTGTAATAAGTGTCATCATCCCTTCTTGCcaccac                                              >  2:105083/1‑141 (MQ=255)                                                                                                    ccccAAGTCTGGTACCAGCAGACTTGGGGTTATTTATGTGTGTAGGATCATTTTTTATTTTTCCATTTCAGTTCTAACCAAAGTCGAAAAATAATTAGTAAGCCACCTGTAATAAGTGTCATCATCCCTTCTTGCcaccac                                              >  2:124394/1‑141 (MQ=255)                                                                                                       aataaccccaagtctgctggtaccagacttggggttgtgtagGATCATTTTTTATTTTTCCATTTCAGTTCTAACCAAAGTCGAAAAATAATTAGTAAGCCACCTGTAATAAGTGTCATCATCCCTTCTTGCCACCAcatc                                           <  1:64188‑M2/99‑1 (MQ=255)                                                                                                        aaGTCTGGTACCAGCAGACTTGGGGTTATTTATGTGTGTAGGATCATTTTTTATTTTTCCATTTCAGTTCTAACCAAAGTCGAAAAATAATTAGTAAGCCACCTGTAATAAGTGTCATCATCCCTTCTTGCCACCAcatca                                          >  1:353408/1‑141 (MQ=255)                                                                                                           tCTGGTACCAGCAGACTTGGGGTTATTTATGTGTGTAGGATCATTTTTTATTTTTCCATTTCAGTTCTAACCAAAGTCGAAAAATAATTAGTAAGCCACCTGTAATAAGTGTCATCATCCCTTCTTGCCACCACATCATta                                       >  1:259529/1‑141 (MQ=255)                                                                                                              gctggtaccagACTTGGGGTTATTTATGTGTGTAGGATCATTTTTTATTTTTCCATTTCAGTTCTAACCAAAGTCGAAAAATAATTAGTAAGCCACCTGTAATAAGTGTCATCATCCCTTCTTGCCACCACATCATtacac                                    >  2:399489/9‑141 (MQ=255)                                                                                                              gctggtaccagACTTGGGGTTATTTATGTGTGTAGGATCATTTTTTATTTTTCCATTTCAGTTCTAACCAAAGTCGAAAAATAATTAGTAAGCCACCTGTAATAAGTGTCATCATCCCTTCTTGCCACCACATCATtacac                                    >  1:74155/9‑141 (MQ=255)                                                                                                               gTACCAGCAGACTTGGGGTTATTTATGTGTGTAGGATCATTTTTTATTTTTCCATTTCAGTTCTAACCAAAGTCGAAAAATAATTAGTAAGCCACCTGTAATAAGTGTCATCATCCCTTCTTGCCACCACATCATtacact                                   >  1:142300/1‑141 (MQ=255)                                                                                                                         aCTTGGGGTTATTTATGTGTGTAGGATCATTTTTTATTTTTCCATTTCAGTTCTAACCAAAGTCGAAAAATAATTAGTAAGCCACCTGTAATAAGTGTCATCATCCCTTCTTGCCACCACATCATTACACTACACCTCCGt                         <  2:343784/141‑1 (MQ=255)                                                                                                                              gggTTATTTATGTGTGTAGGATCATTTTTTATTTTTCCATTTCAGTTCTAACCAAAGTCGAAAAATAATTAGTAAGCCACCTGTAATAAGTGTCATCATCCCTTCTTGCCACCACATCATTACACTACACCTCCGTTCGAc                    <  2:439851/141‑1 (MQ=255)                                                                                                                                gTTATTTATGTGTGTAGGATCATTTTTTATTTTTCCATTTCAGTTCTAACCAAAGTCGAAAAATAATTAGTAAGCCACCTGTAATAAGTGTCATCATCCCTTCTTGCCACCACATCATTACACTACACCTCCGTTCGACTa                  <  2:381591/141‑1 (MQ=255)                                                                                                                                  tatttatGTGTGTAGGATCATTTTTTATTTTTCCATTTCAGTTCTAACCAAAGTCGAAAAATAATTAGTAAGCCACCTGTAATAAGTGTCATCATCCCTTCTTGCCACCACATCATTACACTACACCTCCGTTCGACTaaa                >  1:113543/1‑141 (MQ=255)                                                                                                                                             gtagGATCATTTTTTATTTTTCCATTTCAGTTCTAACCAAAGTCGAAAAATAATTAGTAAGCCACCTGTAATAAGTGTCATCATCCCTTCTTGCCACCACATCATTACACTACACCTCCGTTCGACTAAAGTATCATACTg     <  1:112743‑M2/137‑1 (MQ=255)                                                                                                                                              aagGATCATTTTTTATTTTTCCATTTCAGTTCTAACCAAAGTCGAAAAATAATTAGTAAGCCACCTGTAATAAGTGTCATCATCCCTTCTTGCCACCACATCATTACACTACACCTCCGTTCGACTAAAGTATCATACTGa    <  2:433847‑M2/138‑1 (MQ=255)                                                                                                                                                gGATCATTTTTTATTTTTCCATTTCAGTTCTAACCAAAGTCGAAAAATAATTAGTAAGCCACCTGTAATAAGTGTCATCATCCCTTCTTGCCACCACATCATTACACTACACCTCCGTTCGACTAAAGTATCATACTGAAg  <  1:69568‑M2/140‑1 (MQ=255)                                                                                                                                                 |                                                                                                                                            AACAAAACCATTCAATCAAAATGATTATTGATTGCGATATATTGTGTTCAATGATATTATTTAAGTGTATCCACAGAATTATACTACACA‑‑‑‑‑‑‑‑ACCCCAAGTCTGGTACCAGCAGACTTGGGGTTATTTATGTGTGTAGGATCATTTTTTATTTTTCCATTTCAGTTCTAACCAAAGTCGAAAAATAATTAGTAAGCCACCTGTAATAAGTGTCATCATCCCTTCTTGCCACCACATCATTACACTACACCTCCGTTCGACTAAAGTATCATACTGAAG  >  CP000730/2080637‑2080912

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