New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	CP000730	= 1040370	52 (0.740)	5 (0.080)	5/242	9.1	9.1%	intergenic (‑6787/‑919)	USA300HOU_0983/USA300HOU_0984	competence protein/glycosyltransferase
	?	CP000730	= 1040397	53 (0.840)					intergenic (‑6814/‑892)	USA300HOU_0983/USA300HOU_0984	competence protein/glycosyltransferase
Rejected: Coverage evenness skew score above cutoff.
Rejected: Frequency below/above cutoff threshold.

ACACATGATATGGCTATTGCAAATCAATGTGACGAAATAATAGATTTAGAACAGTATAGAAAAGTAGCATCTATGTGATATCCAAAAGATAAAATTAAAAGCCAATCAATGGGAAATGTTGACTTCAACA‑CTCCGTTTGATTGGCTTTTATACTGTGTTACTAAGTTATGAAAGTAACAACGGCAAACTGAAAAAAAGCAATATAATAATATTTAATACGATTAGTAATAAATGTAATTGATTTTTCGTTTTAATATAGCAAAAAACAATGAC  >  CP000730/1040262‑1040534                                                                                                                                         |                                                                                                                                          acacATGATATGGCTATTGCAAATCAATGTGACGAAATAATAGATTTAGAACAGTATAGAAAAGTAGCATCTATGTGATATCCAAAAGATAAAATTAAAAGCCAATCAATGGGAAATGTTGACTTCAACA‑CTCCGTTTGAt                                                                                                                                      >  1:843788/1‑141 (MQ=255)         tatGGCTATTGCAAATCAATGTGACGAAATAATAGATTTAGAACAGTATAGAAAAGTAGCATCTATGTGATATCCAAAAGATAAAATTAAAAGCCAATCAATGGGAAATGTTGACTTCAACA‑CTCCGTTTGATTGGCtttt                                                                                                                              <  1:724041/141‑1 (MQ=255)          atGGCTATTGCAAATCAATGTGACGAAATAATAGATTTAGAACAGTATAGAAAAGTAGCATCTATGTGATATCCAAAAGATAAAATTAAAAGCCAATCAATGGGAAATGTTGACTTCAACA‑CTCCGTTTGATTGGCTTTta                                                                                                                             >  1:277457/1‑141 (MQ=255)             gCTATTGCAAATCAATGTGACGAAATAATAGATTTAGAACAGTATAGAAAAGTAGCATCTATGTGATATCCAAAAGATAAAATTAAAAGCCAATCAATGGGAAATGTTGACTTCAACA‑CTCCGTTTGATTGGCTTTTATAc                                                                                                                          <  1:637093/141‑1 (MQ=255)              cTATTGCAAATCAATGTGACGAAATAATAGATTTAGAACAGTATAGAAAAGTAGCATCTATGTGATATCCAAAAGATAAAATTAAAAGCCAATCAATGGGAAATGTTGACTTCAACA‑CTCCGTTTGATTGGCTTTTATACt                                                                                                                         >  1:374619/1‑141 (MQ=255)                aTTGTAAATCAATGTGACGAAATAATAGATTTAGAACAGTATAGAAAAGTAGCATCTATGTGATATCCAAAAGATAAAATTAAAAGCCAATAAATGGGAAATGTTTACTTCAACA‑CTCCTTTTGATTGTCTTTTATATtgt                                                                                                                       >  2:141570/1‑141 (MQ=255)                aTTGCAAATCAATGTGACGAAATAATTGATTTAGAACAGTATAGAAAAGTAGCATCTATGTGATATCCAAAAGATAAAATTAAAAGCCAATCAATGGGAAATGTTGACTTCAACA‑CTCCGTTTGATTGGCTTTTATACtgt                                                                                                                       <  1:90202/141‑1 (MQ=255)                  tGCAAATCAATGTGACGAAATAATAGATTTAGAACAGTATAGAAAAGTAGCATCTATGTGCTATCCATCAGATACCATTCACAGTCTATCGCTGGGAAATGTTGACTTCAACA‑CTCCGTTTGATTGGCTTTTATACTgtgt                                                                                                                     <  1:83666/141‑1 (MQ=255)                   gCAAATCAATGTGACGAAATAATAGATTTAGAACAGTATAGAAAAGTAGCATCTATGTGATATCCAAAAGATAAAATTAAAAGCCAATCAATGGGAAATGTTGACTTCAACA‑CTCCGTTTGATTGGCTTTTATACTGTGtt                                                                                                                    >  1:269656/1‑141 (MQ=255)                      aaTCAATGTGACGAAATAATAGATTTAGAACAGTATAGAAAAGTAGCATCTATGTGATATCCAAAAGATAAAATTAAAAGCCAATCAATGGGAAATGTTGACTTCAACA‑CTCCGTTTGATTGGCTTTTATACTGTGTTACt                                                                                                                 >  1:529974/1‑141 (MQ=255)                        tCAATGTGACGAAATAATAGATTTAGAACAGTATAGAAAAGTAGCATCTATGTGATATCCAAAAGATAAAATTAAAAGCCAATCAATGGGAAATGTTGACTTCAACA‑CTCCGTTTGATTGGCTTTTATACTGTGTTACTaa                                                                                                               <  2:48593/141‑1 (MQ=255)                        tCAATGTGACGAAATAATAGATTTAGAACAGTATAGAAAAGTAGCATCTATGTGATATCCAAAAGATAAAATTAAAAGCCAATCAATGGGAAATGTTGACTTCAACA‑CTCCGTTTGATTGGCTTTTATACTGTGTTACTaa                                                                                                               >  2:577587/1‑141 (MQ=255)                         cAATGTGACGAAATAATAGATTTAGAACAGTATAGAAAAGTAGCATCTATGTGATATCCAAAAGATAAAATTAAAAGCCAATCAATGGGAAATGTTGACTTCAACA‑CTCCGTTTGATTGGCTTTTATACTGTGTTACTAAg                                                                                                              <  1:743722/141‑1 (MQ=255)                                  gAAATAATAGATTTAGAACAGTATAGAAAAGTAGCATCTATGTGATATCCAAAAGATAAAATTAAAAGCCAATCAAACGG‑AGTGTTGAAGTCAACATTTCCCATTGATTGGCTTTtaat                                                                                                                           >  1:730749/1‑117 (MQ=17)                                  gAAATAATAGATTTAGAACAGTATAGAAAAGTAGCATCTATGTGATATCCAAAAGATAAAATTAAAAGCCAATCAAACGG‑AGTGTTGAAGTCAACATTTCCCATTGATTGGCTTTtaat                                                                                                                           <  2:730749/119‑3 (MQ=17)                                         taGATTTAGAACAGTATAGAAAAGTAGCATCTATGTGATATCGAAAAGATAAAATTAAAAGCCAATCAATGGGAAATGTTGACTTCAACA‑CTCCGTTTGATTGGCTTTTATACTGTGTTACTAAGTTATGAAAGTaacaac                                                                                              >  1:726320/1‑141 (MQ=255)                                                    cAGTATAGAAAAGTAGCATCTATGTGATATCCAAAAGATAAAATTAAAAGCCAATCAATGGGAAATGTTGACTTCAACA‑CTCCGTTTGATTGGCTTTTATACTGTGTTACTAAGTTATGAAAGTAACAACGGCAAACTGaa                                                                                   >  2:569258/1‑141 (MQ=255)                                                    cAGTATAGAAAAGTAGCATCTATGTGATATCCAAAAGATAAAATTAAAAGCCAATCAATGGGAAATGTTGACTTCAACA‑CTCCGTTTGATTGGCTTTTATACTGTGTTACTAAGTTATGAAAGTAACAACGGCAAACTGaa                                                                                   <  2:655035/141‑1 (MQ=255)                                                     aGTATAGAAAAGTAGCATCTATGTGATATCCAAAAGATAAAATTAAAAGCCAATCAATGGGAAATGTTGACTTCAACA‑CTCCGTTTGATTGGCTTTTATACTGTGTTACTAAGTTATGAAAGTAACAACGGCAAACTGaaa                                                                                  >  2:172269/1‑141 (MQ=255)                                                     aGTATAGAAAAGTAGCATCTATGTGATATCCAAAAGATAAAATTAAAAGCCAATCAATGGGAAATGTTGACTTCAACA‑CTCCGTTTGATTGGCTTTTATACTGTGTTACTAAGTTAGGAAAGTAACAACGGCAAACTGaaa                                                                                  >  2:212938/1‑141 (MQ=255)                                                         taGAAAAGTAGCATCTATGTGATATCCAAAAGATAAAATTAAAAGCCAATCAATGGGAAATGTTGACTTCAACA‑CTCCGTTTGATTGGCTTTTATACTGTGTTACTAAGTTATGAAAGTAACAACGGCAAACTGaaaaaaa                                                                              <  2:564820/141‑1 (MQ=255)                                                           gAAAAGTAGCATCTATGTGATATCCAAAAGATAAAATTAAAAGCCAATCAATGGGAAATGTTGACTTCAACA‑CTCCGTTTGATTGGCTTTTATACTGTGTTACTAAGTTATGAAAGTAACAACGGCAAACTGAAAAAAAGc                                                                            >  2:468940/1‑141 (MQ=255)                                                                gTAGCATCTATGTGATATCCAAAAGATAAAATTAAAAGCCAATCAATGGGAAATGTTGACTTCAACA‑CTCCGTTTGATTGGCTTTTATACTGTGTTACTAAGTTATGAAAGTAACAACGGCAAACTGAAAAAAAGCAatat                                                                       >  1:779851/1‑141 (MQ=255)                                                                 tAGCATCTATGTGATATCCAAAAGATAAAATTAAAAGCCAATCAATGGGAAATGTTGACTTCAACA‑CTCCGTTTGATTGGCTTTTATACTGTGTTACTAAGTTATGAAAGTAACAACGGCAAACTGAAAAAAAGCAAtata                                                                      <  2:529974/141‑1 (MQ=255)                                                                  aGCATCTATGTGATATCCAAAAGATAAAATTAAAAGCCAATCAATGGGAAATGTTGACTTCAACA‑CTCCGTTTGATTGGCTTTTATACTGTGTTACTAAGTTATGAAAGTAACAACGGCAAACTGAAAAAAAGNAATataa                                                                     >  2:632993/1‑141 (MQ=255)                                                                   gCATCTATGTGATATCCAAAAGATAAAATTAAAAGCCAATCAATGGGAAATGTTGACTTCAACA‑CTCCGTTTGATTGGCTTTTATACTGTGTTACTAAGTTATGAAAGTAACAACGGCAAACTGAAAAAAAGCAATataat                                                                    >  2:400371/1‑141 (MQ=255)                                                                    cATCTATGTGATATCCAAAAGATAAAATTAAAAGCCAATCAATGGGAAATGTTGACTTCAACA‑CTCCGTTTGATTGGCTTTTATACTGTGTTACTAAGTTATGAAAGTAACAACGGCAAACTGAAAAAAAGCAATataata                                                                   >  2:767398/1‑141 (MQ=255)                                                                                   cAAAAGATAAAATTAAAAGCCAATCAATGGGAAATGTTGACTTCAACA‑CTCCGTTTGATTGGCTTTTATACTGTGTTACTAAGTTATGAAAGTAACAACGGCAAACTGAAAAAAAGCAATATAATAATATTTAATACGAtt                                                    >  2:166720/1‑141 (MQ=255)                                                                                      aaGATAAAATTAAAAGCAAATCAATGGGAAATGTTGACTTCAACA‑CTCCGTTTGATTGGCTTTTATACTGTGTTACTAAGTTATGAAAGTAACAACGGCAAACTGAAAAAAAGCAATATAATAATATTTAATACGATTAGt                                                 >  1:772166/1‑141 (MQ=255)                                                                                       aGATAAAATTAAAAGCCAATCAATGGGAAATGTTGACTTCAACA‑CTCCGTTTGATTGGCTTTTATACTGTGTTACTAAGTTATGAAAGTAACAATGGCAAACTGAAAAAAAGCAATATAATAATATTTAATACGATTAGta                                                >  1:237543/1‑141 (MQ=255)                                                                                         aTAAAATTAAAAGCCAATCAATGGGAAATGTTGACTTCAACA‑CTCCGTTTGATTGGCTTTTATACTGTGTTACTAAGTTATGAAAGTAACAACGGCAAACTGAAAAAAAGCAATATAATAATATTTAATACGATTAGtaat                                              <  1:347606/141‑1 (MQ=255)                                                                                           aaaaTTAAAAGCCAATCAATGGGAAATGTTGACTTCAACA‑CTCCGTTTGATTGGCTTTTATACTGTGTTACTAAGTTATGAAAGTAACAACGGCAAACTGAAAAAAAGCAATATAATAATATTTAATACGATTAGtaataa                                            >  1:447871/1‑141 (MQ=255)                                                                                            aaaTTAAAAGCCAATCAATGGGAAATGTTGACTTCAACA‑CTCCGTTTGATTGGCTTTTATACTGTGTTACTAAGTTATGAAAGTAACAACGGCAAACTGAAAAAAAGCAATATAATAATATTTAATACGATTAGTAATaaa                                           >  2:536501/1‑141 (MQ=255)                                                                                                tAAAAGCCAATCAATGGGAAATGTTGACTTCAACA‑CTCCGTTTGATTGACTTTTATACTGTGTAACTAAGTTATGAAAGTAACAAAGAAAAAAAGAAAAAAAGCAATATAATAATATTTAATACGATTAGTAATAAATGTa                                       <  2:176390/141‑1 (MQ=255)                                                                                                  aaaGCCAATCAATGGGAATAGTTGACTTCAACT‑CTCCGTTTGATTGGCTTTTATACTGTGTTACTAAGTTATGAAAGTAACAACGGCAAACTGAAAAAAAGCAATATAATAATATTTAATACGATTAGTAATAAATGTAAt                                     <  1:91721/141‑1 (MQ=255)                                                                                                     gCCAATCAATGGGAAATGTTGACTTCAACA‑CTCCGTTTGATTGGCTTTTATACTGTGTTACTAAGTTATGAAAGTAACAACGGCAAACTGAAAAAAAGCAATATAATAATATTTAATACGATTAGTAATAAATGTAATTGa                                  <  2:782275/141‑1 (MQ=255)                                                                                                     gCCAATCAATGGGAAATGTTGACTTCAACA‑CTCCGTTTGATTGGCTTTTATACTGTGTTACTAAGTTATGAAAGTAACAACGGCAAACAGAAAAAAAGCAATATAATAATATTTAATACGATTAGTAATAAATGTAATTGa                                  <  2:374619/141‑1 (MQ=255)                                                                                                      ccAATCAATGGGAAATGTTGACTTCAACA‑CTCCGTTTGATTGGCTTTTATACTGTGTTACTAAGTTATGAAAGTAACAACGGCAAACTGAAAAAAAGCAATATAATAATATTTAATACGATTAGTAATAAATGTAATTGAt                                 >  2:40902/1‑141 (MQ=255)                                                                                                      ccAATCAATGGGAAATGTTGACTTCAACA‑CTCCGTTTGATTGGCTTTTATACTGTGTTACTAAGTTATGAAAGTAACAACGGCAAACTGAAAAAAAGCAATATAATAATATTTAATACGATTAGTAATAAATGTAATTGAt                                 >  2:709386/1‑141 (MQ=255)                                                                                                         atcaatGGGAAATGTTGACTTCAACA‑CTCCGTTTGATTGGCTTTTATACTGTGTTACTAAGTTATGAAAGTAACAACGGCAAACTGAAAAAAAGCAATATAATAATATTTAATACGATTAGTAATAAATGTAATTGAtttt                              <  1:190612/141‑1 (MQ=255)                                                                                                           caatGGGAAATGTTGACTTCAACA‑CTCCGTTTGATTGGCTTTTATACTGTGTTACTAAGTTATGAAAGTAACAACGGCAAACTGAAAAAAAGCAATATAATAATATTTAATACGATTAGTAATAAATGTAATTGATTTTTc                            <  1:400371/141‑1 (MQ=255)                                                                                                           caatGGGAAATGTTGACTTCAACA‑CTCCGTTTGATTGGCTTTTATACTGTGTTACTAAGTTATGAAAGTAACAACGGCAAACTGAAAAAAAGCAATATAATAATATTTAATACGATTAGTAATAAATGTAATTGATTTTTc                            <  1:362057/141‑1 (MQ=255)                                                                                                             atGGGAAATGTTGACTTCAACA‑CTCCGTTTGATTGGCTTTTATACTGTGTTACTAAGTTATGAAAGTAACAACGGCAAACTGAAAAAAAGCAATATAATAATATTTAATACGATTAGTAATAAATGTAATTGAtttttttt                          >  2:419662/1‑138 (MQ=255)                                                                                                             atGGAAAATGTTGACTTCAACA‑CTCCGTTTGATTGGCTTTTATACTGTGTTACTAAGTTATGAAAGTAACAACGACAAAAAAAAAAAAAGCAATATAATAATATTTAATACGATTAGTAATAAATGTAATTGATTTTTCGt                          <  2:257761/141‑1 (MQ=255)                                                                                                                ggAAATGTTGACTTCAACA‑CTCCGTTTGATTGGCTTTTATACTGTATTACTAAGTTATGAAAGTAACAACGGCAAACAGAAAAAAAGCAATATAATAATATTTAATACGATTAGTAATAAATGTAATTGATTTTTCGattt                       >  1:677788/1‑141 (MQ=255)                                                                                                                     tGTTGACTTCAACA‑CTCCGTTTGATTGGCTTTTATACTGTGTTACTAAGTTATGAAAGTAACAACGGCAAACTGAAAAAAAGCAATATAATAATATTTAATACGATTAGTAATAAATGTAATTGATTTTTCGTTTTAatat                  <  2:81400/141‑1 (MQ=255)                                                                                                                     tGTTGACTTCAACA‑CTCCGTTTGATTGGCTTTTATACTGTGTTACTAAGTTATGAAAGTAACAACGGCAAACTGAAAAAAAGCAATATAATAATATTTAATACGATTAGTAATAAATGTAATTGATTTTTCGTTTTAatat                  <  1:767398/141‑1 (MQ=255)                                                                                                                      gTTGACTTCAACA‑CTCCGTTTGATTGGCTTTTATACTGTGTTACTAAGTTATGAAAGTAACAACGGCAAACTGAAAAAAAGCAATATAATAATATTTAATACGATTAGTAATAAATGTAATTGATTTTTCGTTTTAAtata                 >  2:10574/1‑141 (MQ=255)                                                                                                                      gTTGACTTCAACA‑CTCCGTTTGATTGGCTTTTATACTGTGTTACTAAGTTATGAAAGTAACAACGGCAAACTGAAAAAAAGCAATATAATAATATTTAATACGATTAGTAATAAATGTAATTGATTTTTCGTTTTAAtata                 >  1:834732/1‑141 (MQ=255)                                                                                                                      gTTGACTTCAACA‑CTCCGTTTGATTGGCTTTTATACTGTGTTACTAAGTTATGAAAGTAAAAACGGCAAACTGAAAAAAAGCAATATAATAATATTTAATACGATTAGTAATAAATGTAATTGATTTTTCGTTTTAAtata                 >  2:642045/1‑141 (MQ=255)                                                                                                                       ttGACTTCAACA‑CTCCGTTTGATTGGCTTTTATACtgt                                                                                                                       >  1:767062/1‑38 (MQ=255)                                                                                                                       ttGACTTCAACA‑CTCCGTTTGATTGGCTTTTATACtgt                                                                                                                       <  2:767062/38‑1 (MQ=255)                                                                                                                        tGACTTCAACA‑CTCCGTTTGATTGGCTTTTATACTGTGTTACTAAGTTATGAAAGTAACAACGGCAAACTGAAAAAAAGCAATATAATAATATTTAATACGATTAGTAATAAATGTAATTGATTTTTCGTTTTATTATAGc               >  2:271297/1‑141 (MQ=255)                                                                                                                         gACTTCAACA‑CTCCGTTTGATTGGCTTTTATACTGTGTTACTAAGTTATGAAAGTAACAACGGCAAACTGAAAAAAAGCAATATAATAATATTTAATACGATTAGTAATAAATGTAATTGATTTTTCGTTTTAATATAGCa              <  1:536501/141‑1 (MQ=255)                                                                                                                         gACTTCAACA‑CTCCGTTTGATTGGCTTTTATACTGTGTTACTAAGTTATGAAAGTAACAACGGCAAACTGAAAAAAAGCAATATAATAATATTTAATACGATTAGTAATAAATGTAATTGATTTTTCGTTTTAATATAGCa              <  1:256219/141‑1 (MQ=255)                                                                                                                         gACTTCAACA‑CTCCGTTTGATTGGCTTTTATACTGTGTTACTAAGTTATGAAAGTAACAACGGAAAACTAAAAAAAAGCAATATAATAATATTTAATACGATTAGTAATAAATGTAATTGATTTTTCGTTTTAATATAGCa              <  2:110985/141‑1 (MQ=255)                                                                                                                                  a‑cTCCGTTTGATTGGCTTTTATACTGTGGTAATAATTTGGGTAAGTTACAACGGCAAACTGAAAAAAAGCAATATAATAATATTTAATACGATTAGTAATAAATGTAATTGATTTTTCGTTTTAATATAGCAAAAAACAAt     >  2:464259/1‑141 (MQ=255)                                                                                                                                      ccGTTTGATTGGCTTTTATACTGTGTTACTAAGTTATGAAAGTAACAACGGCAAACTGAAAAAAAGCAATATAATAATATTTAATACGATTAGTAATAAATGTAATTGATTTTTCGTTTTAATATAGCAAAAAACAATGAc  >  1:732084/1‑141 (MQ=255)                                                                                                                                         |                                                                                                                                          ACACATGATATGGCTATTGCAAATCAATGTGACGAAATAATAGATTTAGAACAGTATAGAAAAGTAGCATCTATGTGATATCCAAAAGATAAAATTAAAAGCCAATCAATGGGAAATGTTGACTTCAACA‑CTCCGTTTGATTGGCTTTTATACTGTGTTACTAAGTTATGAAAGTAACAACGGCAAACTGAAAAAAAGCAATATAATAATATTTAATACGATTAGTAATAAATGTAATTGATTTTTCGTTTTAATATAGCAAAAAACAATGAC  >  CP000730/1040262‑1040534

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