New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	CP000730	418185 =	46 (1.240)	3 (0.090)	3/242	NT	6.5%	intergenic (+38/+48)	ychF/USA300HOU_0385	possible GTP‑binding protein/hypothetical protein
	?	CP000730	418213 =	43 (1.240)					intergenic (+66/+20)	ychF/USA300HOU_0385	possible GTP‑binding protein/hypothetical protein

GTGGCGAAAGTGGCGCTAAAGAAGCGGGCAGACAACGATTAGAAGGTAAAGAATATATTATGCAAGATGGCGATATCGTTCATTTCAGATTTAATGTATAAACGATAGAGTGAAGTTAATTAAATAGTATATATGTAGAAGAGGCGGAATCAATTG‑TTC‑GCCTCTTTTAATTATGCGTATAATTTATTAAAAGAATGGAATAATTTTACTCGCGTTAATAATATCTTGAGTGCTGAAAAATTGTTTGCCTTCGCCAGTATAAGCAGGCTCTAAAACA  >  CP000730/418047‑418323                                                                                                                                           |                                                                                                                                             gtggCGAAAGTGGCGCTAAAGAAGCGGGCAGACAACGATTAGAAGGTAAAGAATATATTATGCAAGATGGCGATATCGTTCATTTCAGATTTAATGTATAAACGATAGAGTGAAGTTAATTAAATAGTATATATGTagaag                                                                                                                                            <  2:378586/141‑1 (MQ=255) gtggCGAAAGTGGCGCTAAAGAAGCGGGCAGACAACGATTAGAAGGTAAAGAATATATTATGCAAGATGGCGATATCGTTCATTTCAGATTTAATGTATAAACGATAGAGTGAAGTTAATTAAATAGTATATATGTagaag                                                                                                                                            <  1:1223/141‑1 (MQ=255) gtggCGAAAGTGGCGCTAAAGAAGCGGGCAGACAACGATTAGAAGGTAAAGAATATATTATGCAAGATGGCGATATCGTTCATTTCAGATTTAATGTATAAACGATAGAGTGAAGTTAATTAAATAGTATATATGTagaag                                                                                                                                            <  1:97399/141‑1 (MQ=255)   ggCGAAAGTGGCGCTAAAGAAGCGGGCAGACAACGATTAGAAGGTAAAGAATATATTATGCAAGATGGCGATATCGTTCATTTCAGATTTAATGTATAAACGATAGAGTGAAGTTAATTAAATAGTATATATGTAGAagag                                                                                                                                          >  1:83466/1‑141 (MQ=255)    gCGAAAGCGGCGCTAAAGAAGCGGGCAGACAACGATTAGAAGGTAAAGAATATATTATGCAAGATGGCGATATCGTTCATTTCAGATTTAATGTATAAACGATAGAGTGAAGTTAATTAAATAGTATATATGTAGAAGAgg                                                                                                                                         <  1:412852/141‑1 (MQ=255)      gAAAGTGGCGCTAAAGAAGCGGGCAGACAACGATTAGAAGGTAAAGAATATATTATGCAAGATGGCGATATCGTTCATTTCAGATTTAATGTATAAACGATAGAGTGAAGTTAATTAAATAGTATATATGTAGAAGAGGCg                                                                                                                                       <  1:446990/141‑1 (MQ=255)        aaGTGGCGCTAAAGAAGCGGGCAGACAACGATTAGAAGGTAAAGAATATATTATGCAAGATGGCGATATCGTTCATTTCAGATTTAATGTATAAACGATAGAGTGAAGTTAATTAAATAGTATATATGTAGAAGAGGCGGa                                                                                                                                     >  2:41392/1‑141 (MQ=255)               gcTAAAGAAGCGGGCAGACAACGATTAGAAGGTAAAGAATATATTATGCAAGATGGCGATATCGTTCATTTCAGATTTAATGTATAAACGATAGAGTGAAGTTAATTAAATAGTATATATGTAGAAGAGGCgaacaattga                                                                                                                              <  2:102637/141‑10 (MQ=255)               gcTAAAGAAGCGGGCAGACAACGATTAGAAGGTAAAGAATATATTATGCAAGATGGCGATATCGTTCATTTCAGATTTAATGTATAAACGATAGAGTGAAGTTAATTAAATAGTATAAATGTAGAAGAGGCGGAATCAAtt                                                                                                                              >  2:454072/1‑141 (MQ=255)                  aggctactcttgttttagagcctccttatactggcgaaggcaaacaatttttcagcactcaagatattattaacgagagtaaaattactccattcttttaataaattatacgcataattaaAAGAGGCGGAATCAATTG‑tt                                                                                                                          >  2:109560‑M1/122‑141 (MQ=255)                  aaaGAAGCTGGCAGACAACGATTAGAAGGTAAAGAATATATTATGCAAGATGGCGATATCGTTCATTTCAGATTTAATGTATAAACGATAGAGTGAAGTTAATTAAATAGTATATATGTAGAAGAGGCgaacaattgattc                                                                                                                           <  2:365884/141‑13 (MQ=255)                         ggggCAGACAAGGATTATAAGGTAAAGAACATATTATGCAAGATGGCGATATCGTTCATTTAAGATTTAATGTATAAACGATAGTGGGAAGTTATGTAAATAGTATTTATGTAGAAGTGGTAGAACCAATTG‑TTC‑GCctct                                                                                                                  <  2:279131/140‑1 (MQ=255)                            gCAGACAACGATTAGAAGGTAAAGAATATATTATGCAAGATGGCGATATCGTTCATTTCAGATTTAATGTATAAACGATAGAGTGAAGTTAATTAAATAGTATATATGTAGAAGAGGCGGAATCAATTG‑TTC‑GCCTCtttt                                                                                                               >  2:125075/1‑141 (MQ=255)                                  aaCGATTAGAAGGTAAAGAATATAGTATGCGAGATGGCGATATCGTTCATTTCAGAGTTAATGTATACACGATAGAGTGTAGTTAATTAAATAGTATATATGTAGAAGAGGCGGAATCAATTG‑CTC‑CCCTCTTTTAGTTAt                                                                                                         >  2:87691/1‑141 (MQ=255)                                           aaGGTAAAGAATATATTATGCAAGATGGCGATATCGTTCATTTCAGATTTAATGTATAAACGATAGAGTGAAGTTAATTAAATAGTATATATGTAGAAGAGGCGGAATCAATTG‑TTC‑GCCTCTTTTAATTATGCGTATAAt                                                                                                >  1:88826/1‑141 (MQ=255)                                            aGGTAAAGAATATATTATGCAAGATGGCGATATCGTTCATTTCAGATTTAATGTATAAACGATAGAGTGAAGTTAATTAAATAGTATATATGTAGAAGAGGCGGAATCAATTG‑TTC‑GCCTCTTTTAATTATGCGTATAAtt                                                                                               >  1:108572/1‑141 (MQ=255)                                               tAAAGAATATATTATGCAAGATGGCGATATCGTTCATTTCAGATTTAATGTATAAACGATAGAGTGAAGTTAATTAAATAGTATATATGTAGAAGAGGCGGAATCAATTG‑TTC‑GCCTCTTTTAATTATGCGTATAATttat                                                                                            <  2:229414/141‑1 (MQ=255)                                                aaaGAATATATTATGCAAGATGGCGATATCGTTCATTTCAGATTTAATGTATAAACGATAGAGTGAAGTTAATTAAATAGTATATATGTAGAAGAGGCGGAATCAATTG‑TTC‑GCCTCTTTTAATTATGCGTATAATttatt                                                                                           >  2:438789/1‑141 (MQ=255)                                                   gAATATATTATGCAAGATGGCGATATCGTTCATTTCAGATTTAATGTATAAACGATAGAGTGAAGTTAATTAAATAGTATATATGTAGAAGAGGCGGAATCAATTG‑TTC‑GCCTCTTTTAATTATGCGTATAATTTATTaaa                                                                                        <  1:36323/141‑1 (MQ=255)                                                      tatatTATGCAAGATGGCGATATCGTTCATTTCAGATTTAATGTATAAACGATAGAGTGAAGTTAATTAAATAGTATATATGTAGAAGAGGCGGAATCAATTG‑TTC‑GCCTCTTTTAATTATGCGTATAATttattatttaa                                                                                     >  1:75281/1‑136 (MQ=255)                                                                  ggtGGCGATATCGTTCATGTCAGATTTAATGTATAAACTATAGAGTGAAGTTAATTAAATAGTATATATGTAGAAGAGGCGGAATCAATTG‑TTC‑GCCTCTTTTAATTATGCGTATAATTTATTAAAAGAATGGAATAAttt                                                                         <  2:11696/139‑1 (MQ=255)                                                                  gATGGCGATATCGTTCATTTCAGATTTAATGTATAAACGATAGAGTGAAGTTAATTAAATAGTATATATGTAGAAGCGGCGGAATCAATTG‑TTC‑GCCTCTTTTAATTATGCGTATAATTTATTAAAAGAATGGAATAAttt                                                                         >  2:437308/1‑141 (MQ=255)                                                                     ggCGATATCGTTCATTTCAGATTTAATGTATAAACGATAGAGTGAAGTTAATTAAATAGTATATATGTAGAAGAGGCGGAATCAATTG‑TTC‑GCCTCTTTTAATTATGCGTATAATTTATTAAAAGAATGGAATAATTTTAc                                                                      >  2:131349/1‑141 (MQ=255)                                                                      gCGATATCGTTCATTTCAGATTTAATGTATAAACGATAGAGTGAAGTTAATTAAATAGTATATATGTAGAAGAGGCGGAATCAATTG‑TTC‑GCCTCTTTTAATTATGCGTATAATTTATTAAAAGAATGGAATAATTTTACt                                                                     >  1:435536/1‑141 (MQ=255)                                                                       cGATAGCGTTCATTTCAGATTTAATGTAACATGGATAGAGTGAGGTTAATCAGATCATATATATGTAGAAGAGGCGGAATCAATTG‑TTC‑GCCTCTTTTAATTATGCGTATAGTTTATTAAAAAAATGGAATAATCTTCCTc                                                                    >  2:70834/1‑141 (MQ=255)                                                                          actcaagatattattaacgcgagtaaaattattccattcttttaataaattatacgcataattaaAAGAGGCG‑AA‑CAATTGATTCCGCCTCTTTTAATTATGCGTATAATTTATTAAAAGAATGGa                                                                                <  1:389475‑M1/61‑1 (MQ=255)                                                                          actcaagatattattaacgcgagtaaaattattccattcttttaataaattatacgcataattaaAAGAGGCG‑AA‑CAATTGATTCCGCCTCTTTTAATTATGCGTATAATTTATTAAAAGAATGGa                                                                                >  2:389475‑M1/66‑126 (MQ=255)                                                                           atCGTTCATTTCAGATTTAATGTATAAACGATAGAGTGAAGTTAATTAAATAGTATATATGTAGAAGAGGCGGAATCAATTG‑TTC‑GCCTCTTTTAATTATGCGTATAATTTATTAAAAGAATGGAATAATTTTACTCGCGt                                                                <  1:265963/141‑1 (MQ=255)                                                                           atCGTTCATTTCAGATTTAATGTATAAAAGAGCGAGTGAAGTTAATTAAATAGTATATATGTAGAAGAGGCGGAATCAATTG‑TTC‑GCCTCTTTTAATTATGCGTATAATTTATTAAAAGAATGGAATAATTTTACTCGCGt                                                                >  2:358965/1‑141 (MQ=255)                                                                              gTTCATTTCAGATTTAATGTATAAACGATAGAGTGAAGTTAATTAAATAGTATATATGTAGAAGAGGCGGAATCAATTG‑TTC‑GCCTCTTTTAATTATGCGTATAATTTATTAAAAGAATGGAATGATTTTACTCGCGtaaa                                                             <  2:83466/141‑4 (MQ=255)                                                                              gTTCATTTCAGATTTAATGTATAAACGATAGAGTGAAGTTAATTAAATAGTATATATGTAGAAGAGGCGGAATCAATTG‑TTC‑GCCTCTTTTAATTATGCGTATAATTTATTAAAAGAATGGAATAATTTTACTCGCGTtaa                                                             <  2:417471/141‑1 (MQ=255)                                                                              gTTCATTTCAGATTTAATGTATAAACGATAGAGTGAAGTTAATTAAATAGTATATATGTAGAAGAGGCGGAATCAATTG‑TTC‑GCCTCTTTTAATTATGCGTATAATTTATTAAAAGAATGGAATAATTTTACTCGCGTtaa                                                             <  1:302021/141‑1 (MQ=255)                                                                              gTTCATTTCAGATTTAATGTATAAACGATAGAGTGAAGTTAATTAAATAGTATATATGTAGAAGAGGCGGAATCAATTG‑TTC‑GCCTCTTTTAATTATGCGTATAATTTATTAAAAGAATGGAATAATTTTACTCGCGTtaa                                                             <  1:286757/141‑1 (MQ=255)                                                                                 cATTTCAGATTTAATGTATAAACGATAGAGTGAAGTTAATTAAATAGTATATATGTAGAAGAGGCGGAATCAATTG‑TTC‑GCCTCTTTTAATTATGCGTATAATTTATTAAAAGAATGGAATAATTTTACTCGCGTtaataa                                                          <  1:6820/141‑1 (MQ=255)                                                                                 cATTTCAGATTTAATGTATAAACGATAGAGTGAAGTTAATTAAATAGTATATATGTAGAAGAGGCGGAATCAATTG‑TTC‑GCCTCTTTTAATTATGCGTATAATTTATTAAAAGAATGGAATAATTTTACTCGCGTtaataa                                                          <  1:330999/141‑1 (MQ=255)                                                                                   tttCAGATTTAATGTATAAACGATAGAGTGAAGTTAATTAAATAGTATATATGTAGAAGAGGCGGAATCAATTG‑TTC‑GCCTCTTTTAATTATGCGTATAATTTATTAAAAGAATGGAATAATTTTACTCGCGTTAataata                                                        <  1:411008/141‑1 (MQ=255)                                                                                       aGATTTAATGTATAAACGATAGAGTGAAGTTAATTAAATAGTATATATGTAGAAGAGGCGGAATCAATTG‑TTC‑GCCTCTTTTAATTATGCGTATAATTTATTAAAAGAATGGAATAATTTTACTCGCGTTAATAATATCtt                                                    >  2:84952/1‑141 (MQ=255)                                                                                           ttAATGTATAAACGATAGAGTGAAGTTAATTAAATAGTATATATGTAGAAGAGGCGGAATCAATTG‑TTC‑GCCTCTTTTAATTATGCGTATAATTTATTAAAAGAATGGAATAATTTTACTCGCGTTAATAATATCTTGAGt                                                <  1:426994/141‑1 (MQ=255)                                                                                           ttAATGTATAAACGATAGAGTGAAGTTAATTAAATAGTATATATGTAGAAGAGGCGGAATCAATTG‑TTC‑GCCTCTTTTAATTATGCGTATAATTTATTAAAAGAATGGAATAATTTTACTCGCGTTAATAATATCTTGAGt                                                >  2:294271/1‑141 (MQ=255)                                                                                             aaTGTATAAACGATAGAGTTAAGTTAATTAAATAGTATATATGTAGAAGAGGCGGAATCAATTG‑TTC‑GCCTCTTTTAATTATGCGTATAATTTATTAAAAGAATGGAATAATTTTACTCGCGTTAATAATATCTTGAGTGc                                              <  1:251191/141‑1 (MQ=255)                                                                                                gTATAAACGATAGAGTGAAGTTAATTAAATAGTATATATGTAGAAGAGGCGGAATCAATTG‑TTC‑GCCTCTTTTAATTATGCGTATAATTTATTAAAAGAATGGAATAATTTTACTCGCGTTAATAATATCTTGAGTGCTGa                                           <  1:173253/141‑1 (MQ=255)                                                                                                  ataAACGATAGAGTGAAGTTAATTAAATAGTATATATGTAGAAGAGGCGGAATCAATTG‑TTC‑GCCTCTTTTAATTATGCGTATAATTTATTAAAAGAATGGAATAATTTTACTCGCGTTAATAATATCTTGAGTGCTGaaa                                         >  2:338682/1‑141 (MQ=255)                                                                                                    aaaCGATAGAGTGAAGTTAATTAAATAGTATATATGTAGAAGAGGCGGAATCAATTG‑TTC‑GCCTCTTTTAATTATGCGTATAATTTATTAAAAGAATGGAATAATTTTACTCGCGTTAATAATATCTTGAGTGCTGaaaaa                                       <  2:323664/141‑1 (MQ=255)                                                                                                    aaaCGATAGAGTGAAGTTAATTAAATAGTATATATGTAGAAGAGGCGGAATCAATTG‑TTC‑GCCTCTTTTAATTATGCGTATAATTTATTAAAAGAATGGAATAATTTTACTCGCGTTAATAATATCTTGAGTGCTGaaaaa                                       >  1:436816/1‑141 (MQ=255)                                                                                                     aaCGATAGAGTGAAGTTAATTAAATAGTATATATGTAGAAGAGGCGGAATCAATTG‑TTC‑GCCTCTTTTAATTATGCGTATAATTTATTAAAAGAATGGAATAATTTTACTCGCGTTAATAATATCTTGAGTGCTGAAAAAt                                      <  2:16642/141‑1 (MQ=255)                                                                                                         aTAGAGTGAAGTTAATTAAATAGTATATATGTAGAAGAGGCGGAATCAATTG‑TTC‑GCCTCTTTTAATTATGCGTATAATTTATTAAAAGAATGGAATAATTTTACTCGCGTTAATAATATCTTGAGTGCTGAAAAATTGtt                                  <  1:354016/141‑1 (MQ=255)                                                                                                          tAGAGTGAAGTTAATTAAATAGTATATATGTAGAAGAGGCGGAATCAATTG‑TTC‑GCCTCTTTTAATTATGCGTATAATTTATTAAAAGAATGGAATAATTTTACTCGCGTTAATAATATCTTGAGTGCTGAAAAATTGttt                                 >  1:292518/1‑141 (MQ=255)                                                                                                                 aaGTTAATTAAATAGTATATATGTAGAAGAGGCGGAATCAATTG‑TTC‑GCCTCTTTTAATTATGCGTATAATTTATTAAAAGAATGGAATAATTTTACTCGCGTTAATAATATCTTGAGTGCTGAAAAATTGTTTGCCTTCg                          >  1:51777/1‑141 (MQ=255)                                                                                                                            aTAGTATATATGTAGAAGAGGCGGAATCAATTG‑TTC‑GCCTCTTTTAATTATGCGTATAATTTATTAAAAGAATGGAATAATTTTACTCGCGTTAATAATATCTTGAGTGCTGAAAAATTGTTTGCCTTCGCCAGTATAAGc               <  2:306468/141‑1 (MQ=255)                                                                                                                              aGTATATATGTAGAAGAGGCGGAATCAATTG‑TTC‑GCCTCTTTTAATTATGCGTATAATTTATTAAAAGAATGGAATAATTTTACTCGCGTTAATAATATCTTGAGTGCTGAAAAATTGTTTGCCTTCGCCAGTATAAGCAg             <  2:88826/141‑1 (MQ=255)                                                                                                                                 atatatGTAGAAGAGGCGGAATCAATTG‑TTC‑GCCTCTTTTAATTATGCGTATAATTTATTAAAAGAATGGAATAATTTTACTCGCGTTAATAATATCTTGAGTGCTGAAAAATTGTTTGCCTTCGCCAGTATAAGCAGGct          <  1:57960/141‑1 (MQ=255)                                                                                                                                  tatatGTAGAAGAGGCGGAATCAATTG‑TTC‑GCCTCTTTTAATTATGCGTATAATTTATTAAAAGAATGGAATAATTTTACTCGCGTTAATAATATCTTGAGTGCTGAAAAATTGTTTGCCTTCGCCAGTATAAGCAGGctc         >  1:439310/1‑141 (MQ=255)                                                                                                                                  tatatGTAGAAGAGGCGGAATCAATTG‑TTC‑GCCTCTTTTAATTATGCGTATAATTTATTAAAAGAATGGAATAATTTTACTCGCGTTAATAATATCTTGAGTGCTGAAAAATTGTTTGCCTTCGCCAGTATAAGCAGGctc         >  1:238063/1‑141 (MQ=255)                                                                                                                                        tAGAAGAGGCGGAATCAATTG‑TTC‑GCCTCTTTTAATTATGCGTATAATTTATTAAAAGAATGGAATAATTTTACTCGCGTTAATAATATCTTGAGTGCTGAAAAATTGTTTGCCTTCGCCAGTATAAGCAGGCTCTAAAAc   >  1:265518/1‑141 (MQ=255)                                                                                                                                         agaagaGGCGGAATCAATTG‑TTC‑GCCTCTTTTAATTATGCGTATAATTTATTAAAAGAATGGAATAATTTTACTCGCGTTAATAATATCTTGAGTGCTGAAAAATTGTTTGCCTTCGCCAGTATAAGCAGGCTCTAAAACa  >  1:281373/1‑141 (MQ=255)                                                                                                                                           |                                                                                                                                             GTGGCGAAAGTGGCGCTAAAGAAGCGGGCAGACAACGATTAGAAGGTAAAGAATATATTATGCAAGATGGCGATATCGTTCATTTCAGATTTAATGTATAAACGATAGAGTGAAGTTAATTAAATAGTATATATGTAGAAGAGGCGGAATCAATTG‑TTC‑GCCTCTTTTAATTATGCGTATAATTTATTAAAAGAATGGAATAATTTTACTCGCGTTAATAATATCTTGAGTGCTGAAAAATTGTTTGCCTTCGCCAGTATAAGCAGGCTCTAAAACA  >  CP000730/418047‑418323

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.