New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	CP000730	= 1217693	45 (0.920)	3 (0.070)	3/228	NT	7.1%	intergenic (+22/‑415)	USA300HOU_1144/USA300HOU_1145	hypothetical protein/possible 3‑demethylubiquinone‑9 3‑methyltransferase
	?	CP000730	= 1217729	39 (0.910)					intergenic (+58/‑379)	USA300HOU_1144/USA300HOU_1145	hypothetical protein/possible 3‑demethylubiquinone‑9 3‑methyltransferase

AAAAAATAAAACAACTATAGATCATAATGATGATTTATTTAAACATGTAAAGGATATATTACGTAAACAAGAACAAATTTAAAAACAAAAAAGCTATAGTGTTTAATATCAGGGGCTGCTTAACCGCATCCGAATATTACAAACACTATAGCTTTTATTATATAAAAAATTTATTAGCGGATAATTAACTTTATTAAAATCCAACCAATTAAGAATACGAGTAATAGGACTAATACTGGAATCACATAATGTAACATAACGTCCCTCCTTTAACTTA  >  CP000730/1217590‑1217866                                                                                                                                            |                                                                                                                                          aaaaaaTAAAACAACGATAGATCATAATGATGATTTATTTAAACATGTAAAGGATATATTACGTAAACAAGAACAAATTTAAAAACAAAAAAGCTATAGTGTTTAATATCAGGGGCTGCTTAACCGCATCCGAATAGTACa                                                                                                                                          <  1:83292‑M2/141‑2 (MQ=255)    aaaTAAAACAACTATAGATCATAATGATGATTTATTTAAACATGTAAAGGATATATTACGTAAGCAAGAACAAATTTAAAAACAAAAAAGCTATAGTGTTTAATATTAGGCGCTGGTTAACCGCATTAGAATATTAAaaac                                                                                                                                       <  1:99421‑M2/141‑5 (MQ=255)           acaacTATAGATCATAATGGTGATTTATTTAAACATTTAAAGGATATATTACGTAAACAAGAACAAATTTAAAAACAAAAAAGCTATAGTGTTTAATATCAGGGGCTGCTTAACCGCATACGAATATTACaaacactatag                                                                                                                                >  1:295858‑M2/1‑130 (MQ=255)            caacTATAGATCATAATGATGATTTATTTAAACATGTAAAGGATATATTACGTAAACAAGAACAAATTTAAAAACAAAAAAGCTATAGTGTTTAATATCAGGGGCTGCTTAACCGCATCCGAATATTACaaacactatagc                                                                                                                               >  1:541362‑M2/1‑129 (MQ=255)                tataGATCATAATGATGATTTATTTAAACATGTAAAGGATATATTACGTAAACAAGAACAAATTTAAAAACAAAAAAGCTATAGTGTTTAATATCAGGGGCTGCTTAACCGCATCCGAATATTACaaagactatagctttt                                                                                                                           <  2:320908‑M2/141‑17 (MQ=255)                      tCAAAATGATGATTTATTTAAACAAGTAAAGGATATATTACGGAAACAAAAACAAAAAAAAAAACAAAAAAGCTATAGTGTTTAATATCAGGGGCTGCTTAACCGCATCCGAATATTACAAACACTATAGCTTTTATtata                                                                                                                     <  2:156051/141‑1 (MQ=255)                         tAATGATGATTTATTTAAACATGTAAAGGATATATTACGTAAACAAGTACAAATTTAAAAACAAAAAAACTATAGTGTTTAATATCAGAGCCTGCTTAACTGCATCCGAATAGTCCaaaatcgatagcttttttgttttac                                                                                                                  <  1:404815‑M2/141‑26 (MQ=255)                           atgatgATTTATTTAAACATGTAAAGGATATATTACGTAAACAAGAACAAATTTAAAAACAAAAAAGCTATAGTGTTTAATATCAGGGGCTGCTTAACCGCATCCGAATATTACAAACACTATAGCTTTTATTATATaaaa                                                                                                                >  1:281824/1‑141 (MQ=255)                           atgatgATTTATTTAAACATGTAAAGGATATATTACGTAAACAAGAAAAAATTTAAAAACAACAAAGCTATAGTGTTTAATATCAGAGGCTACTTAACCGCATGCGCATATTACAAACAGTCTAGCTTTTATTGTATaaaa                                                                                                                >  2:299252/1‑141 (MQ=255)                                    taattaAACATGTAAAGGATATATTACGTATACAAGAACAAATTTAAAAACAAAAAAGCTATAGTGTTTAATATCAGGGGCTGCTTAACCGCATCCGAATATTACAAACACTATAGCTTTTATTATATAAAAAATttatta                                                                                                       <  2:361668/138‑1 (MQ=255)                                            aaTGTAAAGGATATATTACGTAAACAAGAACAAATTTAAAAACAAAAAAGCTATAGTGTTTAATATCAGGGGCTGCTTAACCGCATCCGAATAGTACAAACACTATAGCTTTTATTATATAAAAAATTTATTAGCGGATaa                                                                                               <  1:191015/140‑1 (MQ=255)                                               ttAAAGGATATATTACCTAAAAAAGAACAAATTACAAAACAAAAAAGCTATAGTGTTTAATATCAGGTGCTGCTTAACCGCATACGAATATTACAAACACTATAGCTTTTATTATATAAAAAATTTATTAGCGGATAATTa                                                                                            <  2:256207/140‑1 (MQ=255)                                                tAAAGGATATATTACGTAAACAAGAACAAATTTAAAAACAAAAAAGCTATAGTGTTTAATATCAGGGGCTGCTTAACCGCATCCGAATATTACAAACACTATAGCTTTTATTATATAAAAAATTTATTAGCGGATAATTaa                                                                                           <  1:101113/141‑1 (MQ=255)                                                 aaaGGATTTATTACGTAAACAAGAACAAATTTAAAAACAAAAAAGCTATAGTGTTTAATATCAGGGGCTGCTTAACCGCATCCGAATATTACAAACACTATAGCTTTTATTATATAAAAAATTTATTAGCGGATAATTAAc                                                                                          <  1:139370/141‑1 (MQ=255)                                                 aaaGGATAGATTACGAAAACAAGAACAAGTTTAAAAACAAAAAAGCTATAGTGTTTAATATCAGGGGGTGCTTAATCGTCAACGAAAATTACAAACGCTATCGAATTTATTATATAAAAAATTTATTAGCGGATAATTAAc                                                                                          <  2:120786/141‑1 (MQ=255)                                                    ggATATATTACGTAAACAAGAACAAATTTAAAAACAAAAAAGCTATAGTGTTTAATATCAGGGGCTGCTTAACCGCATCCGAATATTACAAACACTATAGCTTTTATTATATAAAAAATTTATTAGCGGATAATTAACttt                                                                                       >  1:194629/1‑141 (MQ=255)                                                       tatatTACGTAAACAAGAACAAATTTAAAAACAAAAAAGCTATAGTGTTTAATATCAGGGGCTGCTTAACCGCATCCGAATATTACAAACACTATAGCTTTTATTATATAAAAAATTTATTAGCGGATAATTAACTttatt                                                                                    <  2:351054/141‑1 (MQ=255)                                                       tatatTACGTAAACAAGAACAAATTTAAAAACAAAAAAGCTATAGTGTTTAATAACAGGGGCTGCTTAACCGCATCCGAATATTACAAACACTATAGCTTTTATTATATAAAAAATTTATTAGCGGATAATTAACTttatt                                                                                    <  2:338711/141‑1 (MQ=255)                                                              cGTAAACAAGAACAAATTTAAAAACAAAAAAGCTATAGTGTTTAATATCAGGGGCTGCTTAACCGCATCCGAATATTACAAACACTATAGCTTTTATTATATAAAAAATTTATTAGCGGATAATTAACTTTATTAAAATcc                                                                             <  2:132104/141‑1 (MQ=255)                                                                  aaCAATAACAAATTTAAAAACAAAAAAGCTATAGTGTTTAATATCAGGGGCTGCTTAACTGAATCCGAATATTACAAACACTATAGTTATTATTAAAAAAAAAATTTATTAGCGGATAATTAACTTTATTAAAATccaacc                                                                         <  2:177519/141‑1 (MQ=255)                                                                   aCAAGAACAAATTTAAAAACAAAAAAGCTATAGTGTTTAATATCAGGGGCTGCTTAACCGCATCCGAATATTACAAACACTATAGCTTTTATTATATAAAAAATTTATTAGCGGATAATTAACTTTATTAAAATccaacca                                                                        >  1:56757/1‑141 (MQ=255)                                                                   aCAAGAACAAATTTAAAAACAAAAAAGCTATAGTGTTTAATATCAGGGGCTGCTTAACCGCATCCGAATATTACAAACACTACAGCTTTTATTACATAAAAAATTTATTAGCGGATAATTAAATTTATTAAAATccaacca                                                                        >  2:186421/1‑141 (MQ=255)                                                                     aaaaaCAAATTTAAAAAAAAAAAAGCTATAGTGTTTAATATCAGGGGCTGCTTAACCGCATCCGAATATTACAAACACTATAGCTTTTATTATATAAAAAATTTATTAGCGGATAATTAACTTTATTAAAATCCAACCAAt                                                                      <  2:88894/138‑1 (MQ=255)                                                                       gAACAAATTTAAAAACAAAAAAGCTATAGTGTTTAATATCAGGGGCTGCTTAACCGCATCCGAATATTACAAACACTATAGCTTTTATTATATAAAAAATTTATTAGCGGATAATTAACTTTATTAAAATCCAACCAATTa                                                                    <  1:209964/141‑1 (MQ=255)                                                                       aaaCAAATTTAAAAACAAAAAAGCTATAGTGTTTAATATCAGGGGCTGCTTAACCGCAACCGAATATTACAAACACTATAGCTTTTATTATATAAAAAATTTATTAGCGGATAATTAACTTTATTAAAATCCAACCAATTa                                                                    <  2:143812/140‑1 (MQ=255)                                                                         aCAAATTTAAAAACAAAAAAGCTATAGTGTTTAATATCAGGGGCTGCTTAACCGCATCCGAATATTACAAACACTATAGCTTTTATTATATAAAAAATTTATTAGCGGATAATTAACTTTATTAAAATCCAACCAATTAAg                                                                  >  1:293194/1‑141 (MQ=255)                                                                           aaagtaaaaaaCAAAAAAGCCATAGTGTTTAATATCAGGGGCTGCTTAACCGCATCCGAATATTACAAACACTATAGCTTTTATTATATAAAAAATTTATTAGCGGATAATTAACTTTATTAAAATCCAACCAATTAAGaa                                                                <  2:94032/135‑1 (MQ=255)                                                                           aaaTTTAAAAAAAAAAAAGCTATAGTGTTTAATATCAGGGGCTGCTTAACCGCATCCGAATATTACAAACACTATAGCTTTTATTATATAAAAAATTTATTAGCGGATAATTAACTTTATTAAAATCCAACCAATTAAGaa                                                                <  1:175284/141‑1 (MQ=255)                                                                                tAAAAACAAAAAAGCTATAGTGTTTAATATCAGGGGCTGCTTAACCGCATCCGAATATTACaaacactatagcttttttgtttttaaatatgttcttgtttacgtaatatcccccggagatgtttaaataaatcatcatta                                                           >  2:404815‑M2/1‑61 (MQ=255)                                                                                    aaCAAAAAAGCTATAGTGTTTAATATCAGGGGCTGCTTAACCGCATCCGAATATTACAAACACTATAGCTTTTATTATATAAAAAATTTATTAGCGGATAATTAACTTTATTAAAATCCAACCAATTAAGAATACGAGTaa                                                       >  1:242349/1‑141 (MQ=255)                                                                                      cAAAAAAGCTATAGTGTTTAATATCAGGGGCTGCTTAACCGCATCCGACTATTACAAACACTATAGCTTTTATTATATAAAAAATTTATTAGCGGATAATTAACTTTATTAAAATCCAACCAATTAAGAATAAGAGCAAtg                                                     >  1:90522/1‑140 (MQ=255)                                                                                      cAAAAAAGCTATAGTGTTTAATATCAGGGGCTGCTTAACCGCATCCGAATATTACAAACACTATAGCTTTTATTATATAAAAAATTTATTAGCGGATAATTAACTTTATTAAAATCCAACCAATTAAGAATACGAGTAAtt                                                     >  2:50864/1‑140 (MQ=255)                                                                                      cAAAAAAGCTATAGTGTTTAATATCAGGGGCTGCTTAACCGCATCCGAATATTACAAACACTATAGCTTTTATTATATAAAAAATTTATTAGCGGATAATTAACTTTATTAAAATCCAACCAATTAAGAATACGAGTAATa                                                     <  1:462506/141‑1 (MQ=255)                                                                                         aaaaGCTATAGTGTTTAATATCAGGGGCTGCTTAACCGCATCCGAATATTACAAACACTATAGCTTTTATTATATAAAAAATTTATTAGCGGATAATTAACTTTATGAAAATCCAACCAATTAAGAATACGAGTAATAGGa                                                  <  2:235655/141‑1 (MQ=255)                                                                                                 taGTGTTTAATATCAGGGGGTGATTAACAGCATCAGAATAATACAAACAGTATAGCTTTTATTATATAAAAAATTTATTAGCGGATAATTAACTTTATTAAAATCCAACCAATTAAGAATACGAGTAATAGGACTAATACt                                          >  1:113545/1‑141 (MQ=255)                                                                                                     gtTTAATATCATTTGCTGCATAACCGCATCCAAATATTACaaacactatagcttttttgtttttaaatttgttcttgtttacgtaatatatcctttacatgtttaaataaatcatcattatgatctatagttgttttattt                                      >  2:99421‑M2/1‑40 (MQ=255)                                                                                                          atatCAGGGGCTGCTTAACCGCATCCGAATATTACAAACACTATAGCTTTTATTATATAAAAAATTTATTAGCGGATAATTAACTTTATTAAAATCCAACCAATTAAGAATACGAGTAATAGGACTAATACTGGAATcaca                                 >  1:300860/1‑141 (MQ=255)                                                                                                            atCAGGGGCTGCTTAACCGCATCCGAATATTACAAACACTATAGCTTTTATTATATAAAAAATTTATTAGCGGATAATTAACTTTATTAAAATCCAACCAATTAAGAATAAGAGTAATAGGACTACTACTGGAATCACATa                               >  1:13607/1‑141 (MQ=255)                                                                                                             tCAGGGGCTGCTTAACCGCATCCGAATATTACAAACACTATAGCTTTTATTATATAAAAAATTTATTAGCGGATAATTAACTTTATTAAAATCCAACCAATTAAGAATACGAGTAATAGGACTAATACTGGAATCACATaa                              >  1:232125/1‑141 (MQ=255)                                                                                                               aGGGGCTGCTTAACCGCATCCGAATATTACAAACACTATAGCTTTTATTATATAAAAAATTTATTAGCGGATAATTAACTTTATTAAAATCCAACCAATTAAGAATACGAGTAATAGGACTAATACTGGAATCACATAATg                            >  1:506343/1‑141 (MQ=255)                                                                                                               aGGGGCTGCTTAACCGCATCCGAATATTACAAACACTATAGCTTTTATTATATAAAAAATTTATTAGCGGATAATTAACTTTATTAAAATCAAATCAATTAAGAATACGAGTAATAGGACTAATACTGGAATCACATAATg                            <  1:445017/141‑1 (MQ=255)                                                                                                                      gctTAACCGCATCCGAATATTACAAACACTATAGCTTTTATTATATAAAAAATTTATTAGCGGATAATTAACTTTATTAAAATCCAACCAATTAAGAATACGAGTAATAGGACTAATACTGGAATCACATAATGTAACATa                     >  1:30984/1‑141 (MQ=255)                                                                                                                         tAACCGTATCCGAATATTACAAACACTATAGCTTATATTATATAAAAAATTTATTAGCGGATAATTAACTTTATTAAAATCCAACCAATTAAGAATACGAGTAATAGGACTAATACTGGAATCACATAATGGAACATAACg                  <  2:74674/141‑1 (MQ=255)                                                                                                                         tAACCGCATCCGAATATTACAAACACTATAGCTTTTATTATATAAAAAATTTATTAGCGGATAATTAACTTTATTAAAATCCAACCAATTAAGAATACGAGTAATAGGACTAATACTGGAATCACATAATGTAACATAACg                  >  1:267214/1‑141 (MQ=255)                                                                                                                           aCCGCATCCGAATATTACAAACACTATAGCTTTTATTATATAAAAAATTTATTAGCGGATAATTAACTTTATTAAAATCCAACCAATTAAGAATACGAGTAATAGGACTAATACTGGAATCACATAATGTAACATAACGTc                <  1:500569/141‑1 (MQ=255)                                                                                                                                 tctgAATACTACAAACACTATAGCTTTTATTATATAAAAAATTTATTAGCGGATAATTAACTTTATTAAAATCCAACCAATTAAGAATACGAGTAATAGGACTAATACTGGAATCACATAATGTAACATAACGTCcctcct          <  1:285458/138‑1 (MQ=255)                                                                                                                                      atatTACAAACACTATAGCTTTTATTATATAAAAAATTTATTAGCGGATAATTAACTTTATTAAAATCCAACCAATTAAGAATACGAGTAATAGGACTAATACTGGAATCACATAATGTAACATAACGTCCCTCCTTTAAc     >  2:481123/1‑141 (MQ=255)                                                                                                                                       aatTACAAACACTATAGCTTTTATTATATAAAAAATTTATTAGCGGATAATTAACTTTATTAAAATCCAACCAATTAAGAATACGAGTAATAGGACTAATACTGGAATCACATAATGTAACATAACGTCCCTCCTTTAACt    <  2:316470/140‑1 (MQ=255)                                                                                                                                        atTACAAACACTATAGCTTTTATTATATAAAAAATTTATTAGCGGATAATTAACTTTATTAAAATCCAACCAATTAAGAATACGAGTAATAGGACTAATACTGGAATCACATAATGTAACATAACGTCCCCCCTATAACtt   >  2:323153/1‑141 (MQ=255)                                                                                                                                         ttACAAACACTATAGCTTTTATTATATCAAAAATTTATTAGCGGCTTCTTTATCTGATTAAAATCCAACCAATTAAGAATACGAGTAATAGGACTAATACTGGAATCACATAATGTAACATAACGTTCCTCCTTTAACtta  <  1:299252/141‑1 (MQ=255)                                                                                                                                            |                                                                                                                                          AAAAAATAAAACAACTATAGATCATAATGATGATTTATTTAAACATGTAAAGGATATATTACGTAAACAAGAACAAATTTAAAAACAAAAAAGCTATAGTGTTTAATATCAGGGGCTGCTTAACCGCATCCGAATATTACAAACACTATAGCTTTTATTATATAAAAAATTTATTAGCGGATAATTAACTTTATTAAAATCCAACCAATTAAGAATACGAGTAATAGGACTAATACTGGAATCACATAATGTAACATAACGTCCCTCCTTTAACTTA  >  CP000730/1217590‑1217866

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ 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.