New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	CP000730	= 1117307	39 (0.600)	4 (0.070)	4/228	NT	9.9%	intergenic (+3093/‑427)	USA300HOU_1046/typA	hypothetical protein/GTP‑binding protein TypA
	?	CP000730	= 1117325	38 (0.660)					intergenic (+3111/‑409)	USA300HOU_1046/typA	hypothetical protein/GTP‑binding protein TypA

ATCGTGGTCTCCATCAAGAAATTAGCAATGATTATTTAGAGCCCCACCATGATGCGTTAATACAATTACATGAACAACGATTT‑AAAAGAAAATCAAAATAATTACCAAAAGCGTAATATGTAGTCCTAACAATTAGGTAACATATTACGCTTTTATACCTTAAATAATAAAAACACGCGCCAATATAAAACCAGTTAAATGTTCATCATGAACATGTGTGGTCTTAAATCAACGCGTGTTATTGTCGATATAACTTATAGCCAATCGTTTTCTCGA  >  CP000730/1117187‑1117462                                                                                                                                            |                                                                                                                                          aTCGTGGTCTCCATCAAGAAATTAGCAATGATTATATAGATCCCCACCAAGATGCGTTAATAAAATTACATGAACAACGATTT‑AAAAGAAAATCAAAATAATTTCCAAAAGCGTAATATGTAGTCCTAACGATTAGGTAac                                                                                                                                         >  2:349431‑M2/1‑139 (MQ=255)     tGGTCTCCATCAAGAAATTAGCAATGATTATTTAGAGCCCCACCATGATGCGTTAATACAATTACATGAACAACGATTT‑AAAAGAAAATCAAAATAATTACCAAAAGCGTAATATGTAGTCCTAACAATTAGGTAacatat                                                                                                                                     >  2:230288‑M2/1‑135 (MQ=255)      ggTCTCCATCAAGAAATTAGCAATGATTATTTAGAGCCCCACCATGATGCGTTAATACAAGTACATGAATAGCGATAG‑AAAAGAAGAGCAAAATAATTACCAAAAGCGTAATATGTAGTGCTAACAATTAGGTAacatatt                                                                                                                                    <  1:664794‑M2/141‑8 (MQ=255)                 aGAAATTAGCAATGATTATTTAGAGCCCCACCATGATGCGTTAATACAATTACATGAACAACGATTT‑AAAAGAAAATCAAAATAATTACCAAAAGCGTAATATGTAGTCCTAACAATTAGGTAACATATTACGCTTTtata                                                                                                                         <  1:251765/141‑1 (MQ=255)                  gAAATTAGCAATGATTATTTAGAGCCCCACCATGATGCGTTAATACAATTACATGAACAACGATTT‑AAAAGAAAATCAAAATAATTACCAAAAGCGTAATATGTAGTCCTAACAATTAGGTAACATATTACGCTTTTATAc                                                                                                                        <  2:83020/141‑1 (MQ=255)                   aaaTTAGCAATGATTATTTAGAGCCCCACCATGATGCGTTAATACAATTACATGAACAACGATTT‑AAAAGAAAATCAAAATAATTACCAAAAGCGTAATATGTAGTCCTAACAATTAGGTAACATATTACGCTTTTATAcc                                                                                                                       <  1:758453/141‑1 (MQ=255)                   aaaTTAGCAATGATTATTTAGAGCCCCACCATGATGCGTTAATACAATTACATGAACAACGATTT‑AAAAGAAAATCAAAATAATTACCAAAAGCGTAATATGTAGTCCTAACAATTAGGTAACATATTACGCTTTTATAcc                                                                                                                       >  1:517739/1‑141 (MQ=255)                    aaTTAGCAATGATTATTTAGAGCCCCACCATGATGCGTTAATACAATTACATGAACAACGATTT‑AAAAGAAAATCAAAATAATTACCAAAAGCGTAATATGTAGTCCTAACAATTAGGTAACATATTACGCTTTTATACCt                                                                                                                      <  1:189968/141‑1 (MQ=255)                      ttAGCAATGATTATTTAGAGCCCCACCATGATGCGTTAATACAATTACATGAACAACGATTT‑AAAAGAAAATCAAAATAATTACCAAAAGCGTAATATGTAGTCCTAACAATTAGGTAACATATTACGCTTTTATACCTTa                                                                                                                    >  2:216309/1‑141 (MQ=255)                       tAGCAATGATTATTTAGAGCCCCACCATGATGCGTTAATACAATTACATGAACAACGATTT‑AAAAGAAAATCAAACTAATTACCCAAAGCGTAATATGTAGTCCTAACAATTAGGTAACATATTACGCTTTTATACCTTaa                                                                                                                   <  2:118406/141‑1 (MQ=255)                        aGCAATGATTATTTAGCGCCCCACCATGAAGCGTTAATAAAATTACATGAACAACGATTT‑AAAAGAAAATCAAAATAATTACCATAAGCGTAAGATGTAGTCCTAACAATTAGGTAACATATTACGCTTTTATACCTTaaa                                                                                                                  <  2:704372/141‑1 (MQ=255)                        aGCAATGATTATTTAGAGCCCCACCATGATGCGTTAATACAATTACATGAACAACGATTT‑AAAAGAAAATCAAAATAATTACCAAAAGCGTAATATGTAGTCCTAACAATTAGGTAACATATTACGCTTTTATACCTTaaa                                                                                                                  <  2:516336/141‑1 (MQ=255)                        aGCAATGATTATTTAGAGCCCCACCATGATGCGTTAATACAATTACATGAACAACGATTT‑AAAAGAAAATCAAAATAATTACCAAAAGCGTAATATGTAGTCCTAACAATTAGGTAACATATTACGCTTTTATACCTTaaa                                                                                                                  <  1:77552/141‑1 (MQ=255)                         gCAATGATTATTTAGAGCCCCACCATGATGCGTTAATACAATTACATGAACAACGATTT‑AAAAGAAAATCAAAATAATTACCAAAAGCGTAATATGTAGTCCTAACAATTAGGTAACATATTACGCTTTTATACCTTAaat                                                                                                                 >  1:394866/1‑141 (MQ=255)                          cAATGATTATTTAGAGCCCCACCATGATGCGTTAATACAATTACATGAACAACGATTT‑AAAAGAAAATCAAAATAATTACCAAAAGCGTAATATGTTA‑CCTAATTGTTAGGACtacatattacgcttttggtaattatttt                                                                                                               >  1:205372‑M2/1‑113 (MQ=255)                           aaTGATTATTTAGAGCCCCACCATGATGCGTTAATACAATTACATGAACAACGATTTAAAAAGAAAATCAAAATAATTACCAAAAGCGTAACAAGTAGTCCTAACAATTAGGCAACATATTACGCTTTTATACCTTAaata                                                                                                                >  1:783547/1‑141 (MQ=255)                                  attTAGAGCCCCACCATGATGCGTTAATACAATTACATGAACAACGATTT‑AAAAGAAAATCAAAATAATTACCAAAAGCGTAATATGTAGTCCTAACAATTAGGTAACATATTACGCTTTTATACCTTAAATAATAAAAac                                                                                                        <  2:421501/141‑1 (MQ=255)                                   tttAGAGCCCCACCATGATGCGTTAATACAATTACATGAACAACGATTT‑AAAAGAAAATCAAAATAATTACCAAAAGCGTAATATGTAGTCCTAACAATTAGGTAACATATTACGCTTTTATACCTTAAATAATAAAAaca                                                                                                       >  2:555775/1‑141 (MQ=255)                                     tAGAGCCCCACCATGATGCGTTAATACAATTACATGAACAACGATTT‑AAAAGAAAATCAAAATAATTACCAAAAGCGTAATATGTAGTCCTAACAATTAGGTAACATATTACGCTTTTATACCTTAAATAATAAAAACAcg                                                                                                     >  1:769286/1‑141 (MQ=255)                                      agagCCCCACCATGATGCGTTAATACAATTACATGAACAACGATTT‑AAAAGAAAATCAAAATAATTACCAAAAGCGTAATATGTAGTCCTAACAATTAGGTAACATATTACGCTTTTATACCTTAAATAATAAAAACAcgc                                                                                                    >  1:507798/1‑141 (MQ=255)                                      agagCCCCACCATGATGCGTTAATACAATTACATGAACAACGATTT‑AAAAGAAAATCAAAATAATTACCAAAAGCGTAATATGTAGTCCTAACAATTAGGTAACATATTACGCTTTTATACCTTAAATAATAAAAACAcgc                                                                                                    >  2:202550/1‑141 (MQ=255)                                          ccccACCATGATGCGTTAATACAATTACATGAACAACGATTT‑AAAAGAAAATCAAAATAATTACCAAAAGCGTAATATGTAGTCCTAACAATTAGGTAACATATTACGCTTTTATACCTTAAATAATAAAAACACGCGcct                                                                                                <  1:746574/141‑2 (MQ=255)                                           cccACCATGATGCGTTAATACAATTACATGAACAACGATTT‑AAAAGAAAATCAAAATAATTACCAAAAGCGTAATAAGTAGTCCTAACAATTAGGTAACATATTACGCTTTTATACCTTAAATAATAAAAACACGCGCCaa                                                                                               >  1:2616/1‑141 (MQ=255)                                            ccaccaTGATGCGTTAATACAATTACATGAACAACGATTT‑AAAAGAAAATCAAAATAATTACCAAAAGCGTAATATGTAGTCCTAACAATTAGGTAACATATTACGCTTTTATACCTTAAATAATAAAAACACGCGCCAat                                                                                              >  2:659049/1‑141 (MQ=255)                                            ccaccaTGATGCGTTAATACAATTACATGAACAACGATTT‑AAAAGAAAATCAAAATAATTACCAAAAGCGTAATATGTAGTCCTAACAATTAGGTAACATATTACGCTTTTATACCCTAAATAATAAAAACACACGCCAat                                                                                              >  2:228900/1‑141 (MQ=255)                                                  tgatgCGTTAATACAATTACATGAACAACGATTT‑AAAAGAAAATCAAAATAATTACCAAAAGCGTAATATGTAGTCCTAACAATTAGGTAACATATTACGCTTTTATACCTTAAATAATAAAAACACGCGCCAATATaaaa                                                                                        >  2:477652/1‑141 (MQ=255)                                                       cGTTAATACAATTACATGAACAACGATTT‑AAAAGAAAATCAAAATAATTACCAAAAGCGTAATATGTAGTCCTAACAATTAGGTAACATATTACGCTTTTATACCTTAAATAATAAAAACACGCGCCAATATAAAACCAGt                                                                                   <  2:127606/141‑1 (MQ=255)                                                            aTACAATTACATGAACAACGATTT‑AAAAGAAAATCAAAATAATTATCAAAAGCGTAATATGTAGTCCTAACAATTAGGTAACATATTACGCTTTTATACCTTAAATAATAAAAACCCGCGCCAATATAATGCCAGTTAAAt                                                                              <  2:161959/141‑1 (MQ=255)                                                              aCAATTACATGAACAACGATTT‑AAAAGAAAATCAAAATAATTACCAAAAGCGTAATATGTAGTCCTAACAATTAGGTAACATATTACGCTTTTATACCTTAAATAATaaa                                                                                                           <  1:212874/110‑1 (MQ=255)                                                              aCAATTACATGAACAACGATTT‑AAAAGAAAATCAAAATAATTACCAAAAGCGTAATATGTAGTCCTAACAATTAGGTAACATATTACGCTTTTATACCTTAAATAATaaa                                                                                                           >  2:212874/1‑110 (MQ=255)                                                                    aCATGAACAACGATTT‑AAAAGAAAATCAAAATAATTACCAAAAGCGTAATATGTTA‑CCTAATTGTTAGGACtacatattacgcttttggtaattattttgattttcttttaaatcgttgttcatgtaattgtattaacgca                                                                     >  2:765046‑M2/1‑71 (MQ=255)                                                                     cATGAACAACGATTT‑AAAAGAAAATCAAAATAATTACCAAAAGCGTAATATGTAGTCCTAACAATTAGGTAACATATTACGCTTTTATACCTTAAATAATAAAAACACGCGCCAATATAAAACCAGTTAAATGTTcatcat                                                                     <  1:216309/141‑1 (MQ=255)                                                                         aacaacGATTT‑AAAAGAAAATCAAAATAATTACCAAAAGCGTAATATGTAGTCCTAACAATTAGGTAACATATTACGCTTTTATACCTTAAATAATAAAAACACGCGCCAATATAAAACCAGTTAAATGTTCATCATGAAc                                                                 >  1:565321/1‑141 (MQ=255)                                                                                     aaaaGAAAATCAAAATAATTACCAAAAGCGTAATATGTAGTCCTAACAATTAGGTAACATATTACGCTTTTATACCTTAAATAATAAAAACACGCGCCAATATAAAACCAGTTAAATGTTCATCATGAACATGTGTGGTCt                                                      >  1:183068/1‑141 (MQ=255)                                                                                      aaaGAAAATCAAAATAATTACCAAAAGCGTAATATGTAGTCCTAACAATTAGGTAACATATTACGCTTTTATACCTTAAATAATAAAAACACGCGCCAATATAAAACCAGTTAAATGTTCATCATGAACATGTGTGGTCtt                                                     >  2:180867/1‑141 (MQ=255)                                                                                      aaaGAAAATCAAAATAATTACCAAAAGCGTAATATGTAGTCCTAACAATTAGGTAACATATTACGCTTTTATACCTTAAATAATAAAAACACGCGCCAATATAAAACCAGTTAAATGTTCATCATGAACATGTGTGGTCtt                                                     >  1:111503/1‑141 (MQ=255)                                                                                         gAAAATCAAAACAATCAACAAAAGCGTAATCTGTAGTCCTAACAATTAGGTAACATATTACGCTTTTATACCTTAAATAATAAACACAAGCGACCCCATCACACCAGTCACATGTTCATCATGAACATGTGTGGTCTTaaa                                                  <  2:664794/141‑1 (MQ=255)                                                                                               cAAAATAATTACCAAAAGCGTAATATGTAGTCCTAACAATTAGGTAACATATTACGCTTTTATACCTTAAATAATAAAAACACGCGCCAATATAAAACCAGTTAAATGTTCATCATGAACATGTGTGGTCTTAAATCAAcg                                            >  1:266972/1‑141 (MQ=255)                                                                                                 aaaTAATTACCAAAAGCGTAATATGTAGTCCTAACAATTAGGTAACATATTACGCTTTTATACCTTAAATAATAAAAACACGCGCCAATATAAAACCAGTTAAATGTTCATCATGAACATGTGTGGTCTTAAATCAAcgcg                                          <  2:125270/141‑1 (MQ=255)                                                                                                       ttACCAAAAGCGTAATATGTAGTCCTAACAATTAGGTAACATATTACGCTTTTATACCTTAAATAATAAAAACACGCGCCAATATAAAACCAGTTAAATGTTCATCATGAACATGTGTGGTCTTAAATCAACGCGTGTTAt                                    >  2:164462/1‑141 (MQ=255)                                                                                                          ccAAAAGCGTAATATGTAGTCCTAACAATTAGGTAACATATTACGCTTTTATACCTTAAATAATAAAAACACGCGCCAATATAAAACCAGTTAAATGTTCATCATGAACATGTGTGGTCTTAAATCAACGCGTGTTATTGt                                 >  1:466041/1‑141 (MQ=255)                                                                                                                  gTAATATGTAGTCCTAACAATTAGGTAACATATTACGCTTTTATACCTTAAATAATAAAAACACGCGCCAATATAAAACCAGTTAAATGTTCATCATGAACATGTGTGGTCTTAAATCAACGCGTGTTATTGTCGATATaa                         >  2:782302/1‑141 (MQ=255)                                                                                                                      tatGTAGTCCTAACAATTAGGTAacatattacgcttttggtagttattttgatgttcttttaaatcgttgttcttgtaattgtattaacgcatcctcgcgaggcgctgaataatcattgctaatttcttgatggagaccac                     <  2:37133‑M2/141‑119 (MQ=255)                                                                                                                      tatGTAGTCCTAACAATTAGGTAACATATTACGCTTTTATACCTTAAATAATAAAAACACGCGCCAATATAAAACCAGTTAAATGTTCATCATGAACATGTGTGGTCTTAAATCAACGCGTGTTATTGTCGATATAACTta                     >  1:276579/1‑141 (MQ=255)                                                                                                                       atGTAGTCCTAACAATNAGGTAacatattncgcttttggtaattattttgattttcttttaaatcgttgttcatgtaattgtattaacgcatcatggtggggctctaaataatcattgctaatttcttgatggagaccacg                    <  1:475601‑M2/141‑120 (MQ=255)                                                                                                                         gTAGTCCTAACAATTAGGTAACATATTACGCTTTTATACCTTAAATAATAAAAACACGCGCCAATATAAAACCAGTTAAATGTTCATCATGAACATGTGTGGTCTTAAATCAACGCGTGTTATTGTCGATATAACTTATAg                  <  1:640717/141‑1 (MQ=255)                                                                                                                                    aaTTAGGTAACATATTACGCTTTTATACCTTAAATAATAAAAACACGCGCCAATATAAAACCAGTTAAATGTTCATCATGAACATGTGTGGTCTTAAATCAACGCGTGTTATTGTCGATATAACTTATAGCCAATCGtttt       >  2:176595/1‑141 (MQ=255)                                                                                                                                      ttAGGTAACATATTACGCTTTTATACCTTAAATAATAAAAACACGCGCCAATATAAAACCAGTTAAATGTTCATCATGAACATGTGTGGTCTTAAATCAACGCGTGTTATTGTCGATATAACTTATAGCCAATCGTTTtct     >  1:249663/1‑141 (MQ=255)                                                                                                                                      ttAGGTAACATATTACGCTTTTATACCTTAAATAATAAAAACACGCGCCAATATAAAACCAGTTAAATGTTCATCATGAACATGTGTGGTCTTAAATCAACGCGTGTTATTGTCGATATAACTTATAGCCAATCGTTTtct     >  1:249682/1‑141 (MQ=255)                                                                                                                                         ggTAACATATTACGCTTTTATACCTTAAATAATAAAAACACGCGCCAATATAAAACCAGTTAAATGTTCATCATGAACATGTGTGGTCTTAAATCAACGCGTGTTATTGTCGATATAACTTATAGCCAATCGTTTTCTCGa  >  2:563471/1‑141 (MQ=255)                                                                                                                                         ggTAACATATTACGCTTTTATACCTTAAATAATAAAAACACGCGCCAATATAAAACCAGTTAAATGTTCATCATGAACATGTGTGGTCTTAAATCAACGCGTGTTATTGTCGATATAACTTATAGCCAATCGTTTTCTCGa  >  2:497269/1‑141 (MQ=255)                                                                                                                                         ggTAACATATTACGCTTTTATACCTTAAATAATAAAAACACGCGCCAATATAAAACCAGTTAAATGTTCATCATGAACATGTGTGGTCTTAAATCAACGCGTGTTATTGTCGATATAACTTATAGCCAATCGTTTTCTCGa  >  1:406457/1‑141 (MQ=255)                                                                                                                                         ggTAACATATTACGCTTTTATACCTTAAATAATAAAAACACGCGCCAATATAAAACCAGTTAAATGTTCATCATGAACATGTGTGGTCTTAAATCAACGCGTGTTATTGTCGATATAACTTATAGCCAATCGTTTTCTCGa  >  2:137989/1‑141 (MQ=255)                                                                                                                                            |                                                                                                                                          ATCGTGGTCTCCATCAAGAAATTAGCAATGATTATTTAGAGCCCCACCATGATGCGTTAATACAATTACATGAACAACGATTT‑AAAAGAAAATCAAAATAATTACCAAAAGCGTAATATGTAGTCCTAACAATTAGGTAACATATTACGCTTTTATACCTTAAATAATAAAAACACGCGCCAATATAAAACCAGTTAAATGTTCATCATGAACATGTGTGGTCTTAAATCAACGCGTGTTATTGTCGATATAACTTATAGCCAATCGTTTTCTCGA  >  CP000730/1117187‑1117462

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