New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	CP000730	= 2772645	36 (0.970)	4 (0.120)	4/232	NT	10.5%	intergenic (+19/+41)	phoB/USA300HOU_2627	alkaline phosphatase/hypothetical protein
	?	CP000730	= 2772662	36 (1.080)					intergenic (+36/+24)	phoB/USA300HOU_2627	alkaline phosphatase/hypothetical protein

TTCCGATGGACATACAGGCGAGGATGTTAATACCTACGCTTACGGACCTAGATCAGAATCATTTAGTGGTAATATCGAAAATACAGAAAGCGCAAAAATAATATTTGATATATTCAAGTAAAGCATAAAAAAATTCCCGAGCACTATAACAAGGTGTTCGGGAATTTTTTATGGTTTAATTTAGTACTCAATGTTAGGTGCTTGGTTAACACGTTCTTGGTATTTTTTAAATGCGAAGTATAAACCGCCAACTAATGTTAAAATAACTGCTAATTTT  >  CP000730/2772506‑2772782                                                                                                                                            |                                                                                                                                          ttCCGATGGACATACAGGCGAGGATGTTAATACCTACGCTTACGGACCTAGATCAGAATCATTTAGTGGTAATATCGAAAATACAGAAAGCGCAAAAATAATATTTGATATATTCAAGTAAAGCATAAAAAAATTCCCGAg                                                                                                                                          >  2:19025/1‑141 (MQ=255)    cGATGGACATACAGGCGAGGATGTTAATACCTACGCTTACGGACCTAGATCAGAATCATTTAGTGGTAATATCGAAAATACAGAAAGCGCAAAAATAATATTTGATATATTCAAGTAAAGCATAAAAAAATTCCCGAGCAc                                                                                                                                       <  1:14458/141‑1 (MQ=255)            aTACAGGCGAGGATGTTAATACCTACGCTTACGGACCTAGATCAGAATCATTTAGTGGTAATATCGAAAATACAGAAAGCGCAAAAATAATATTTGATATATTCAAGTAAAGCATAAAAAAATTCCCGAGCACTATAACaa                                                                                                                               <  1:97881/141‑1 (MQ=255)                         tGTTAATACCTACGCTTACGGACCTAGATCAGAATCATTTAGTGGTAATATCGAAAATACAGAAAGCGCAAAAATAATATTTGATATATTCAAGTAAAGCATAAAAAAATTCCCGAGCACTATAACAAGGTGTtcgggaat                                                                                                                  <  2:323723‑M2/141‑9 (MQ=255)                          gTTAATACCTACGCTTACGGACCTAGATCAGAATCATTTAGTGGTAATATCGAAAATACAGAAAGCGCAAAAATAATATTTGATATATTCAAGTAAAGCATAAAAAAATTCCCGAGCACTATAACAAGGTGTtcgggaatt                                                                                                                 >  2:13822‑M2/1‑132 (MQ=255)                           ttAATACCTACGCTTACGGACCTAGATCAGAATCATTTAGTGGTAATATCGAAAATACAGAAAGCGCAAAAATAATATTTGATATATTCAAGTAAAGCATAAAAAAATTCCCGAGCACTATAACAAGGTGTtcgggaattt                                                                                                                <  1:159097‑M2/141‑11 (MQ=255)                             aaTACCTACGCTTACGGACCTAGATCAGAATCATTTAGTGGTAATATGGAAAATACAGAAAGCGCAAAAATAATATTTGATATATTCAAGTAAAGCATAAAAAAATTCCCGAGCACTATAACAAGGTGGtcgggaagtttt                                                                                                              <  1:395231‑M2/141‑13 (MQ=255)                              aTACCTACGCTTACGGACCTAGATCAGAATCATTTAGTGGTAATATCGAAAATACAGAAAGCGCAAAAATAATATTTGATATATTCAAGTAAAGCATAAAAAAATTCCCGAGCACTATAACAAGGTGTtcgggaatttttt                                                                                                             >  2:175226‑M2/1‑128 (MQ=255)                                aCCTACGCTTACGGACCTAGATCAGAATCATTTAGTGGTAATATCGAAAATACAGAAAGCGCAAAAATAATATTTGATATATTCAAGTAAAGCATAAAAAAATTCCCGAGCACTATAACAAGGTGTTCGGGAATTTTTTAt                                                                                                           <  2:48180/141‑1 (MQ=255)                                  cTACGCTTACGGACCTAGATCAGAATCATTTAGTGGTAATATCGAAAATACAGAAAGCGCAAAAATAATATTTGATATATTCAAGTAAAGCATAAAAAAATTCCCGAGCACTATAACAAGGTGTTCGGGAATTTTTTATgg                                                                                                         <  1:205796/141‑1 (MQ=255)                                     cGCTTACGGACCTAGATCAGAATCATTTAGTGGTAATATCGAAAATACAGAAAGCGCAAAAATAATATTTGATATATTCAAGTAAAGCATAAAAAAATTCCCGAGCACTATAACAAGGTGTTCGGGCATTTTTTATGGttt                                                                                                      >  2:374076/1‑141 (MQ=255)                                       cTTACGGACCTAGATCAGAATCATTTAGTGGTAATATCGAAAATACAGAAAGCGCAAAAATAATATTTGATATATTCAAGTAAAGCATAAAAAAATTCCCGAGCACTATAACAAGGTGTTCGGGAATTTTTTATGGTTTaa                                                                                                    >  1:330345/1‑141 (MQ=255)                                          aCGGACCTAGATCAGAATCATTTAGTGGTAATATCGAAAATACAGAAAGCGCAAAAATAATATTTGATATATTCAAGTAAAGCATAAAAAAATTCCCGAGCACTATAACAAGGTGTTCGGGAATTTTTTATGGTTTAAttt                                                                                                 <  2:241421/141‑1 (MQ=255)                                           cGGACCTAGATCAGAATCATTTAGTGGTAATATCGAAAATACAGAAAGCGCAAAAATAATATTTGATATATTCAAGTAAAGCATAAAAAAATTCCCGAGCACTATAACAAGGTGTTCGGGAATTTTTTATGGTTTAATTTa                                                                                                >  2:199331/1‑141 (MQ=255)                                           cGGACCTAGATCAGAATCATTTAGTGGTAATATCGAAAATACAGAAAGCGCAAAAATAATATTTGATATATTCAAGTAAAGCATAAAAAAATTCCCGAGCACTATAACAAGGTGTTCGGGAATTTTTTATGGTTTAATTTa                                                                                                >  2:171696/1‑141 (MQ=255)                                               ccTAGATCAGAATCATTTAGTGGTAATATCGAAAATACAGAAAGCGCAAAAATAATATTTGATATATTCAAGTAAAGCATAAAAAAATTCCCGAGCACTATAACAAGGTGTTCGGGAATTTTTTATGGTTTAATTTAGTAc                                                                                            >  2:70689/1‑141 (MQ=255)                                                cTAGATCAGAATCATTTAGTGGTAATATCGAAAATACAGAAAGCGCAAAAATAATATTTGATATATTCAAGTAAAGCATAAAAAAATTCCCGAGCACTATAACAAGGTGTTCGGGAATTTTTTATGGTTTAATTTAGTACt                                                                                           <  1:318609/141‑1 (MQ=255)                                                         aaTCATTTAGTGGTAATATCGAAAATACAGAAAGCGCAAAAATAATATTTGATATATTCAAGTAAAGCATAAAAAAATTCCCGAGCACTATAACAAGGTGTTCGGGAATTTTTTATGGTTTAATTTAGTACTCAATGTTAg                                                                                  >  2:449303/1‑141 (MQ=255)                                                         aaTCATTTAGTGGTAATATCGAAAATACAGAAAGCGCAAAAATAATATTTGATATATTCAAGTAAAGCATAAAAAAATTCCCGAGCACTATAACAAGGTGTTCGGGAATTTTTTATGGTTTAATTTAGTACTCAATGTTAg                                                                                  >  1:305355/1‑141 (MQ=255)                                                         aaTCATTTAGTGGTAATATCGAAAATACAGAAAGCGCAAAAATAATATTTGATATATTCAAGTAAAGCATAAAAAAATTCCCGAGCACTATAACAAGGTGTTCGGGAATTTTTTATGGTTTAATTTAGTACTCAATGTTAg                                                                                  >  1:397605/1‑141 (MQ=255)                                                              tttAGTGGTAATATCGAAAATACAGAAAGCGCAAAAATAATATTTGATATATTCAAGTAAAGCATAAAAAAATTCCCGAGCACTATAACAAGGTGTTCGGGAATTTTTTATGGTTTAATTTAGTACTCAATGTTAGGTGCt                                                                             <  1:332289/141‑1 (MQ=255)                                                              tttAGTGGTAATATCGAAAATACAGAAAGCGCAAAAATAATATTTGATATATTCAAGTAAAGCATAAAAAAATTCCCGAGCACTATAACAAGGTGTTCGGGAATTTTTTATGGTTTAATTTAGTACTCAATGTTAGGTGCt                                                                             <  1:332318/141‑1 (MQ=255)                                                                  gTGGTAATATCGAAAATACAGAAAGCGCAAAAATAATATTTGATATATTCAAGTAAAGCATAAAAAAATTCCCGAGCACTATAACAAGGTGTTCGGGAATTTTTTATGGTTTAATTTAGTACTCAATGTTAGGTGCTTGGt                                                                         >  1:72060/1‑141 (MQ=255)                                                                  gTGGTAATATCGAAAATACAGAAAGCGCAAAAATAATATTTGATATATTCAAGTAAAGCATAAAAAAATTCCCGAGCACTATAACAAGGTGTTCGGGAATTTTTTATGGTTTAATTTAGTACTCAATGTTAGGTGCTTGGt                                                                         >  1:286179/1‑141 (MQ=255)                                                                       aaTATCGAAAATACAGAAAGCGCAAAAATAATATTTGATATATTCAAGTAAAGCATAAAAAAATTCCCGAacaccttgttatagtgctcgggaa                                                                                                                   <  2:187676‑M1/94‑25 (MQ=255)                                                                       aaTATCGAAAATACAGAAAGCGCAAAAATAATATTTGATATATTCAAGTAAAGCATAAAAAAATTCCCGAacaccttgttatagtgctcgggaa                                                                                                                   >  1:187676‑M1/1‑70 (MQ=255)                                                                           tCGAAAATACAGAAAGCGCAAAAATAATATTTGATATATTCAAGTAAAGCATAAAAAAATTCCCGAGCACTATAACAAGGTGTTCGGGAATTTTTTATGGTTTAATTTAGTACTCAATGTTAGGTGCTTGGTTAACACGtt                                                                >  2:86037/1‑141 (MQ=255)                                                                           tCGAAAATACAGAAAGCGCAAAAATAATATTTGATATATTCAAGTAAACCAT‑AAAAAATTCCCGAacaccttgttatagtgc                                                                                                                          <  1:179254‑M1/82‑18 (MQ=255)                                                                           tCGAAAATACAGAAAGCGCAAAAATAATATTTGATATATTCAAGTAAACCAT‑AAAAAATTCCCGAacaccttgttatagtgc                                                                                                                          >  2:179254‑M1/1‑65 (MQ=255)                                                                              aaaaTACAGAAAGCGCAAAAATAATATTTGATATATTCAAGTAAAGCATAAAAAAATTCCCGAGCACTATAACAAGGTGTTCGGGAATTTTTTATGGTTTAATTTAGTACTCAATGTTAGGTGCTTGGTTAACACGTTCtt                                                             >  2:105307/1‑141 (MQ=255)                                                                               aaaTACAGAAAGCGCAAAAATAATATTTGATATATTCAAGTAAAGCATAAAAAAATTCCCGAGCACTATAACAAGGTGTTCGGGAATTTTTTATGGTTTAATTTAGTACTCAATGTTAGGTGCTTGGTTAACACGTTCTTg                                                            >  1:366591/1‑141 (MQ=255)                                                                                      gAACGCGCAAAACGAATAGTAGATATATTCAAGTAAAGCATAAAAAAATTCCCGAGCACTATATCAAGGTGTTCGGGAATTATTTATGCTTTAATTTAGTACTTAATGTTAGGTGCTTGGTTAACACGTACTTGGTAtttt                                                     <  2:237013/141‑1 (MQ=255)                                                                                      gAAAGCGCAAAAATAATATTTGATATATTCAAGTAAAGCATAAAAAAATTCCCGAGCACTATAACAAGGTGTTCGGGAATTTTTTATGGTTTAATTTAGTACTCAATGTTAGGTGCTTGGTTAACACGTTCTTGGTAtttt                                                     >  1:436913/1‑141 (MQ=255)                                                                                                   taataTTTGATATATTCAAGTAAAGCATAAAAAAATTCCCGAGCACTATAACAAGGTGTTCGGGAATTTTTTATGGTTTAATTTAGTACTCAATGTTAGGTGCTTGGTTAACACGTTCTTGGTATTTTTTAAATGCGAAGt                                        <  1:426775/141‑1 (MQ=255)                                                                                                      tatTTGATATATTCAAGTAAAGCATAAAAAAATTCCCGAGCACTATAACAAGGTGTTCGGGAATTTTTTATGGTTTAATTTAGTACTCAATGTTAGGTGCTTGGTTAACACGTTCTTGGTATTTTTTAAATGCGAAGtata                                     >  1:22827/1‑141 (MQ=255)                                                                                                        tttGATATATTCAAGTAAAGCATAAAAAAATTCCCGAGCACTATAACAAGGTGTTCGGGAATTTTTTATGGTTTAATTTAGTACTCAATGTTAGGTGCTTGGTTAACACGTTCTTGGTATTTTTTAAATGCGAAGTATaaa                                   >  2:218855/1‑141 (MQ=255)                                                                                                          tGATATATTCAAGTAAAGCATAAAAAAATTCCCGAGCACTATAACAAGGTGTTCTGGAATTTTTTATGGTTTAATTTAGTACTCAATGTTAGGTGCTTGGTTAACACGTTCTTGGTATTTTTTAAATGTGAAGTATAAAcc                                 >  2:238622/1‑141 (MQ=255)                                                                                                                  tCAAGTAAAGCATAAAAAAATTCCCGAGCACTATAACAAGGTGTTCGGGAATTTTTTATGGTTTAATTTAGTACTCAATGTTAGGTGCTTCGTTAACACGTTCTTGGTATTNTTTNAATGCGAANTATAAACCGCCAACTa                         <  1:374071/141‑1 (MQ=255)                                                                                                                      gTAAAGCATAAAAAAATTCCCGAGCACTATAACAAGGTGTTCGGGAATTTTTTATGGTTTAATTTAGTACTCAATGTTAGGTGCTTGGTTAACACGTTCTTGGTATTTTTTAAATGCGAAGTATAAACCGCCAACTAATGt                     <  2:320552/141‑1 (MQ=255)                                                                                                                       tAAAGCATAAAAAAATTCCCGAGCACTATAACAAGGTGTTCGGGAATTTTTTATGGTTTAATTTAGTACTCAATGTTAGGTGCTTGGTTAACACGTTCTTGGTATTTTTTAAATGCGAAGTATAAACCGCCAACTAATGtt                    <  1:449303/141‑1 (MQ=255)                                                                                                                          aGCATAAAAAAATTCCCGAGCACTATAACAAGGTGTTCGGGAATTTTTTATGGTTTAATTTAGTACTCAATGTTAGGTGCTTGGTTAACACGTTCTTGGTATTTTTTAAATGCGAAGTATAAACCGCCAACTAATGTTaaa                 <  1:398086/141‑1 (MQ=255)                                                                                                                          aGCATAAAAAAATTCCCGAGCACTATAACAAGGTGTTCGGGAATTTTTTATGGTTTAATTTAGTACTCAATGTTAGGTGCTTGGTTAACACGTTCTTGGTATTTTTTAAATGCGAAGTATAAACCGCCAACTAATGTTaaa                 <  1:397989/141‑1 (MQ=255)                                                                                                                           gCATAAAAAAATTCCCGAGCACTATAACAAGGTGTTCGGGAATTTTTTATGGTTTAATTTAGTACTCAATGTTAGGTGCTTGGTTAACACGTTCTTGGTATTTTTTAAATGCGAAGTATAAACCGCCAACTAATGTTaaaa                >  2:23137/1‑141 (MQ=255)                                                                                                                              tAAAAAAATTCCCGAGCACTATAACAAGGGGTTCGGGAATTTTTTATGGTTTAATTTAGTACTCAATGTTAGGTGCTTGGTTAACACGTTCTTGGTATTTTTTAAATGCGAAGTATAAACCGCCAACTAATTTTAAATTaa             >  2:139413/1‑141 (MQ=255)                                                                                                                                aaaaaaTTCCCGAacaccttgttatagtgctcgggaatttttttatgctttacttgaatatatcaaatattatttttgcgctttctgtattttcgatattaccactaaatgattctgatctaggtccgtaagcgtaggtat           >  2:175226‑M1/1‑13 (MQ=255)                                                                                                                                aaaaaaTTCCCGAGCACTATAACAAGGTGTTCGGGAATTTTTTATGGTTTAATTTAGTACTCAATGTTAGGTGCTTGGTTAACACGTTCTTGGTATTTTTTAAATGCGAAGTATAAACCGCCAACTAATGTTAAAATAACt           <  1:318842/141‑1 (MQ=255)                                                                                                                                 aaaacTTCCCGAccaccttgttatagtgctcgggaatttttttatgctttacttgaatatatcaaatattatttttgcgctttctgtattttccatattaccactaaatgattctgatctaggtccgtaagcgtaggtatt          <  1:395231‑M1/141‑130 (MQ=255)                                                                                                                                   aaaTTCCCGAacaccttgttatagtgctcgggaatttttttatgctttacttgaatatatcaaatattatttttgcgctttctgtattttcgatattaccactaaatgattctgatctaggtccgtaagcgtaggtattaa        <  1:159097‑M1/141‑132 (MQ=255)                                                                                                                                    aaTTCCCGAacaccttgttatagtgctcgggaatttttttatgctttacttgaatatatcaaatattatttttgcgctttctgtattttcgatattaccactaaatgattctgatctaggtccgtaagcgtaggtattaac       >  2:13822‑M1/1‑9 (MQ=255)                                                                                                                                     aTTCCCGAacaccttgttatagtgctcgggaatttttttatgctttacttgaatatatcaaatattatttttgcgctttctgtattttcgatattaccactaaatgattctgatctaggtccgtaagcgtaggtattaaca      <  2:323723‑M1/141‑134 (MQ=255)                                                                                                                                     aTTCCCGAGCACTATAACAAGGTGTTCGGGAATTTTTTATGGTTTAATTTAGTACTCAATGTTAGGTGCTTGGTTAACACGTTCTTGGTATTTTTTAAATGCGAAGTATAAACCGCCAACTAATGTTAAAATAACTGCTaa      >  2:432809/1‑141 (MQ=255)                                                                                                                                     aTTCCCGAGCACTATAACAAGGTGTTCGGGAATTTTTTATGGTTTAATTTAGTACTCAATGTTAGGTGCTTGGTTAACACGTTCTTGGTATTTTTTAAATGCGAAGTATAAACCGCCAACTAATGTTAAAATAACTGCTaa      <  2:24023/141‑1 (MQ=255)                                                                                                                                      ttCCCGAGCACTATAACAAGGTGTtcgggaatttttttatgctttacttgaatatatcaaatattatttttgcgctttctgtattttcgatatt                                                    <  2:187676‑M2/94‑71 (MQ=255)                                                                                                                                      ttCCCGAGCACTATAACAAGGTGTtcgggaatttttttatgctttacttgaatatatcaaatattatttttgcgctttctgtattttcgatatt                                                    >  1:187676‑M2/1‑24 (MQ=255)                                                                                                                                         ccGAGCACTATAACAAGGTGTTCGGGAATTTTTTATGGTTTAATTTAGTACTCAATGTTAGGTGCTTGGTTAACACGTTCTTGGTATTTTTTAAATGCGAAGTATAAACCGCCAACTAATGTTAAAATAACTGCTAAtttt  <  1:199331/141‑1 (MQ=255)                                                                                                                                            |                                                                                                                                          TTCCGATGGACATACAGGCGAGGATGTTAATACCTACGCTTACGGACCTAGATCAGAATCATTTAGTGGTAATATCGAAAATACAGAAAGCGCAAAAATAATATTTGATATATTCAAGTAAAGCATAAAAAAATTCCCGAGCACTATAACAAGGTGTTCGGGAATTTTTTATGGTTTAATTTAGTACTCAATGTTAGGTGCTTGGTTAACACGTTCTTGGTATTTTTTAAATGCGAAGTATAAACCGCCAACTAATGTTAAAATAACTGCTAATTTT  >  CP000730/2772506‑2772782

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.