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.

GTCGATGAAAATAAAGTGCTGATTTTAGCAACACATGATATGGCTATTGCAAATCAATGTGACGAAATAATAGATTTAGAACAGTATAGAAAAGTAGCATCTATGTGATATCCAAAAGATAAAATTAAAAGCCAATCAATGGGAAATGTTGACTTCAACA‑CTCCGTTTGATTGGCTTTTATACTGTGTTACTAAGTTATGAAAGTAACAACGGCAAACTGAAAAAAAGCAATATAATAATATTTAATACGATTAGTAATAAATGTAATTGATTTTTCGT  >  CP000730/1040232‑1040510                                                                                                                                           |                                                                                                                                              gtCGATGAAAATAAAGTGCTGATTTTAGCAACACATGATATGGCTATTGCAAATCAATGTGACGAAATAATAGATTTAGAACAGTATAGAAAAGTAGCATCTATGTGATATCCAAAAGATAAAATTAAAAGCCAATCAATg                                                                                                                                             <  2:657286/141‑1 (MQ=255)         aaaTAAAGTGCTGATTTTAGCAACACATGATATGGCTATTGCAAATCAATGTGACGAAATAATAGATTTAGAACAGTATAGAAAAGTAGCATCTATGTGATATCCAAAAGATAAAATTAAAAGCCAATCAATGGGAAATGt                                                                                                                                     <  1:452284/141‑1 (MQ=255)          aaTAAAGTGCTGATTTTAGCAACACATGATATGGCTATTGCAAATCAATGTGACGAAATAATAGATTTAGAACAGTATAGAAAAGTAGCATCTATGTGATATCCAAAAGATAAAATTAAAAGCCAATCAATGGGAAATGtt                                                                                                                                    >  1:174102/1‑141 (MQ=255)          aaTAAAGTGCTGATTTTAGCAACACATGATATGGCTATTGCAAATCAATGTGACGAAATAATAGATTTAGAACAGTATAGAAAAGTAGCATCTATGTGATATCCAAAAGATAAAATTAAAAGCCAATCAATGGGAAATGtt                                                                                                                                    <  1:221903/141‑1 (MQ=255)           aTAAAGTGCTGATTTTAGCAACACATGATATGGCTATTGCAAATCAATGTGACGAAATAATAGATTTAGAACAGTATAGAAAAGTAGCATCTATGTGATATCCAAAAGATAAAATTAAAAGCCAATCAATGGGAAATGTTg                                                                                                                                   >  1:165491/1‑141 (MQ=255)               aGTGCTGATTTTAGCAACACATGATATGGCTATTGCAAATCAATGTGACGAAATAATAGATTTAGAACAGTATAGAAAAGTAGCATCTATGTGATATCCAAAAGATAAAATTAAAAGCCAATCAATGGGAAATGTTGACtt                                                                                                                               <  1:669769/141‑1 (MQ=255)                 tGCTGATTTTAGCAACACATGATATGGCTATTGCAAATCAATGTGACGAAATAATAGATTTAGAACAGTATAGAAAAGTAGCATCTATGTGATATCCAAAAGATAAAATTAAAAGCCAATCAATGGGAAATGTTGACTTCa                                                                                                                             <  1:414145/141‑1 (MQ=255)                       ttttAGCAACACATGATATGGCTATTGCAAATCAATGTGACGAAATAATAGATTTAGAACAGTATAGAAAAGTAGCATCTATGTGATATCCAACAAATGAAAGGAAAAGCCAATCAATGGGAAATGTTGACTTCAACA‑CTc                                                                                                                      <  1:617819/141‑1 (MQ=255)                       ttttAGCAACACATGATATGGCTATTGCAAATCAATGTGACGAAATAATAGATTTAGAACAGTATAGAAAAGTAGCATCTATGTGATATCCAAAAGATAAAATTAAAAGCCAATCAATGGGAAATGTTGACTTCAACA‑CTc                                                                                                                      <  1:469051/141‑1 (MQ=255)                       ttttAGCAACACATGATATGGCTATTGCAAATCAATGTGACGAAATAATAGATTTAGAACAGTATAGAAAAGTAGCATCTATGTGATATCCAAAAGATAAAATTAAAAGCCAATCAATGGGAAATGTTGACTTCAACA‑CTc                                                                                                                      >  1:48385/1‑141 (MQ=255)                               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                                                                                       >  2:577587/1‑141 (MQ=255)                                                      tCAATGTGACGAAATAATAGATTTAGAACAGTATAGAAAAGTAGCATCTATGTGATATCCAAAAGATAAAATTAAAAGCCAATCAATGGGAAATGTTGACTTCAACA‑CTCCGTTTGATTGGCTTTTATACTGTGTTACTaa                                                                                       <  2:48593/141‑1 (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                                                           <  2:655035/141‑1 (MQ=255)                                                                                  cAGTATAGAAAAGTAGCATCTATGTGATATCCAAAAGATAAAATTAAAAGCCAATCAATGGGAAATGTTGACTTCAACA‑CTCCGTTTGATTGGCTTTTATACTGTGTTACTAAGTTATGAAAGTAACAACGGCAAACTGaa                                                           >  2:569258/1‑141 (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    <  1:362057/141‑1 (MQ=255)                                                                                                                                         caatGGGAAATGTTGACTTCAACA‑CTCCGTTTGATTGGCTTTTATACTGTGTTACTAAGTTATGAAAGTAACAACGGCAAACTGAAAAAAAGCAATATAATAATATTTAATACGATTAGTAATAAATGTAATTGATTTTTc    <  1:400371/141‑1 (MQ=255)                                                                                                                                           atGGGAAATGTTGACTTCAACA‑CTCCGTTTGATTGGCTTTTATACTGTGTTACTAAGTTATGAAAGTAACAACGGCAAACTGAAAAAAAGCAATATAATAATATTTAATACGATTAGTAATAAATGTAATTGAtttttttt  >  2:419662/1‑138 (MQ=255)                                                                                                                                           atGGAAAATGTTGACTTCAACA‑CTCCGTTTGATTGGCTTTTATACTGTGTTACTAAGTTATGAAAGTAACAACGACAAAAAAAAAAAAAGCAATATAATAATATTTAATACGATTAGTAATAAATGTAATTGATTTTTCGt  <  2:257761/141‑1 (MQ=255)                                                                                                                                           |                                                                                                                                              GTCGATGAAAATAAAGTGCTGATTTTAGCAACACATGATATGGCTATTGCAAATCAATGTGACGAAATAATAGATTTAGAACAGTATAGAAAAGTAGCATCTATGTGATATCCAAAAGATAAAATTAAAAGCCAATCAATGGGAAATGTTGACTTCAACA‑CTCCGTTTGATTGGCTTTTATACTGTGTTACTAAGTTATGAAAGTAACAACGGCAAACTGAAAAAAAGCAATATAATAATATTTAATACGATTAGTAATAAATGTAATTGATTTTTCGT  >  CP000730/1040232‑1040510

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.