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

GCAGACAACGATTAGAAGGTAAAGAATATATTATGCAAGATGGCGATATCGTTCATTTCAGATTTAATGTATAAACGATAGAGTGAAGTTAATTAAATAGTATATATGTAGAAGAGGCGGAATCAATTG‑TTC‑GCCTCTTTTAATTATGCGTATAATTTATTAAAAGAATGGAATAATTTTACTCGCGTTAATAATATCTTGAGTGCTGAAAAATTGTTTGCCTTCGCCAGTATAAGCAGGCTCTAAAACAAGATTAGCCTTTGCACAATA  >  CP000730/418074‑418343                                                                                                                                              |                                                                                                                                   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)                                                                                 tccattcttttaataaattatacgcataattaaaagaggcggaatcaattgttcgcctcttTTAATTATGCGTATAATTTATTAAAAGAATGGAATAATTTTACTCGCGTTAATAATATCTTGAGt                                                                    >  2:389475‑M2/62‑126 (MQ=255)                                                                                 tccattcttttaataaattatacgcataattaaaagaggcggaatcaattgttcgcctcttTTAATTATGCGTATAATTTATTAAAAGAATGGAATAATTTTACTCGCGTTAATAATATCTTGAGt                                                                    <  1:389475‑M2/65‑1 (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                             >  1:238063/1‑141 (MQ=255)                                                                                                       tatatGTAGAAGAGGCGGAATCAATTG‑TTC‑GCCTCTTTTAATTATGCGTATAATTTATTAAAAGAATGGAATAATTTTACTCGCGTTAATAATATCTTGAGTGCTGAAAAATTGTTTGCCTTCGCCAGTATAAGCAGGctc                             >  1:439310/1‑141 (MQ=255)                                                                                                             tAGAAGAGGCGGAATCAATTG‑TTC‑GCCTCTTTTAATTATGCGTATAATTTATTAAAAGAATGGAATAATTTTACTCGCGTTAATAATATCTTGAGTGCTGAAAAATTGTTTGCCTTCGCCAGTATAAGCAGGCTCTAAAAc                       >  1:265518/1‑141 (MQ=255)                                                                                                              agaagaGGCGGAATCAATTG‑TTC‑GCCTCTTTTAATTATGCGTATAATTTATTAAAAGAATGGAATAATTTTACTCGCGTTAATAATATCTTGAGTGCTGAAAAATTGTTTGCCTTCGCCAGTATAAGCAGGCTCTAAAACa                      >  1:281373/1‑141 (MQ=255)                                                                                                                  GAGGCGGAATCAATTG‑TTC‑GCCTCTTTTAATTATGCGTATAATTTATTAAAAGAATGGAATAATTTTACTCGCGTTAATAATATCTTGAGTGCTGAAAAATTGTTTGCCTTCGCCAGTATAAGCAGGCTCTAAAACAAGAt                  >  2:48112‑M1/1‑141 (MQ=255)                                                                                                                     GCGGAATCAATTG‑TTC‑GCCTCTTTTAATTATGCGTATAATTTATTAAAAGAATGGAATAATTTTACTCGCGTTAATAATATCTTGAGTGCTGAAAAATTGTTTGCCTTCGCCAGTATAAGCAGGCTCTAAAACAAGATTAg               <  2:197190‑M1/141‑1 (MQ=255)                                                                                                                          aacaattgattccgcctcttTTAATTATGCGTATAATTTATTAAAAGAATGGAGTAATTTTACTCTCGTTAATAATATCTTGAGTGCTGAAAAATTGTTTGCCTTCGCCAGTATAAGGAGGCTCTAAAACAAGAGTAGCCt            >  2:109560‑M2/21‑141 (MQ=255)                                                                                                                              aTTG‑TTC‑GCCTCTTTTAATTATGCGTATAATTTATTAAAAGAATGGAATAATTTTACTCGCGTTAATAATATCTTGAGTGCTGAAAAATTGTTTGCCTTCGCCAGTATAAGCAGGCTCTAAAACAAGATTAGCCTTTGcac      >  1:447966/1‑141 (MQ=255)                                                                                                                              aTTG‑TTC‑GCCTCTTTTAATTATGCGTATAATTTATTAAAAGAATGGAATAATTTTACTCGCGTTAATAATATCTTGAGTGCTGAAAAATTGTTTGCCTTCGCCAGTATAAGCAGGCTCTAAAACAAGATTAGCCTTTGcac      >  1:45434/1‑141 (MQ=255)                                                                                                                              aTTG‑TTC‑GCCTCTTTTAATTATGCGTATAATTTATTAAAAGAATGGAATAATTTTACTCGCGTTAATAATATCTTGAGTGCTGAAAAATTGTTTGCCTTCGCCAGTATAAGCAGGCTCTAAAACAAGATTAGCCTTTGcac      >  2:237161/1‑141 (MQ=255)                                                                                                                                   ttC‑GCCTCTTTTAATTATGCGTATAATTTATTAAAAGAATGGAATAATTTTACTCGCGTTAATAATATCTTGAGTGCTGAAAAATTGTTTGCCTTCGCCAGTATAAGCAGGCTCTAAAACAAGATTAGCCTTTGCACAATa  <  1:84952/141‑1 (MQ=255)                                                                                                                                              |                                                                                                                                   GCAGACAACGATTAGAAGGTAAAGAATATATTATGCAAGATGGCGATATCGTTCATTTCAGATTTAATGTATAAACGATAGAGTGAAGTTAATTAAATAGTATATATGTAGAAGAGGCGGAATCAATTG‑TTC‑GCCTCTTTTAATTATGCGTATAATTTATTAAAAGAATGGAATAATTTTACTCGCGTTAATAATATCTTGAGTGCTGAAAAATTGTTTGCCTTCGCCAGTATAAGCAGGCTCTAAAACAAGATTAGCCTTTGCACAATA  >  CP000730/418074‑418343

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.