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

TGTTAATACCTACGCTTACGGACCTAGATCAGAATCATTTAGTGGTAATATCGAAAATACAGAAAGCGCAAAAATAATATTTGATATATTCAAGTAAAGCATAAAAAAATTCCCGAGCACTATAACAAGGTGTTCGGGAATTTTTTATGGTTTAATTTAGTACTCAATGTTAGGTGCTTGGTTAACACGTTCTTGGTATTTTTTAAATGCGAAGTATAAACCGCCAACTAATGTTAAAATAACTGCTAATTTTTTCATCATTCAAACTCC  >  CP000730/2772530‑2772799                                                                                                                                     |                                                                                                                                          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                                                                                                   >  1:305355/1‑141 (MQ=255)                                 aaTCATTTAGTGGTAATATCGAAAATACAGAAAGCGCAAAAATAATATTTGATATATTCAAGTAAAGCATAAAAAAATTCCCGAGCACTATAACAAGGTGTTCGGGAATTTTTTATGGTTTAATTTAGTACTCAATGTTAg                                                                                                   >  2:449303/1‑141 (MQ=255)                                 aaTCATTTAGTGGTAATATCGAAAATACAGAAAGCGCAAAAATAATATTTGATATATTCAAGTAAAGCATAAAAAAATTCCCGAGCACTATAACAAGGTGTTCGGGAATTTTTTATGGTTTAATTTAGTACTCAATGTTAg                                                                                                   >  1:397605/1‑141 (MQ=255)                                      tttAGTGGTAATATCGAAAATACAGAAAGCGCAAAAATAATATTTGATATATTCAAGTAAAGCATAAAAAAATTCCCGAGCACTATAACAAGGTGTTCGGGAATTTTTTATGGTTTAATTTAGTACTCAATGTTAGGTGCt                                                                                              <  1:332318/141‑1 (MQ=255)                                      tttAGTGGTAATATCGAAAATACAGAAAGCGCAAAAATAATATTTGATATATTCAAGTAAAGCATAAAAAAATTCCCGAGCACTATAACAAGGTGTTCGGGAATTTTTTATGGTTTAATTTAGTACTCAATGTTAGGTGCt                                                                                              <  1:332289/141‑1 (MQ=255)                                          gTGGTAATATCGAAAATACAGAAAGCGCAAAAATAATATTTGATATATTCAAGTAAAGCATAAAAAAATTCCCGAGCACTATAACAAGGTGTTCGGGAATTTTTTATGGTTTAATTTAGTACTCAATGTTAGGTGCTTGGt                                                                                          >  1:286179/1‑141 (MQ=255)                                          gTGGTAATATCGAAAATACAGAAAGCGCAAAAATAATATTTGATATATTCAAGTAAAGCATAAAAAAATTCCCGAGCACTATAACAAGGTGTTCGGGAATTTTTTATGGTTTAATTTAGTACTCAATGTTAGGTGCTTGGt                                                                                          >  1:72060/1‑141 (MQ=255)                                                   tCGAAAATACAGAAAGCGCAAAAATAATATTTGATATATTCAAGTAAAGCATAAAAAAATTCCCGAGCACTATAACAAGGTGTTCGGGAATTTTTTATGGTTTAATTTAGTACTCAATGTTAGGTGCTTGGTTAACACGtt                                                                                 >  2:86037/1‑141 (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)                                                                                                        aaaaaaTTCCCGAGCACTATAACAAGGTGTTCGGGAATTTTTTATGGTTTAATTTAGTACTCAATGTTAGGTGCTTGGTTAACACGTTCTTGGTATTTTTTAAATGCGAAGTATAAACCGCCAACTAATGTTAAAATAACt                            <  1:318842/141‑1 (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)                                                                                                                     gCACTATAACAAGGTGTtcgggaattttttatggtttacttgaatatatcaaatattatttttgcgctttctgtattttcga                                                                          >  2:179254‑M2/1‑17 (MQ=255)                                                                                                                     gCACTATAACAAGGTGTtcgggaattttttatggtttacttgaatatatcaaatattatttttgcgctttctgtattttcga                                                                          <  1:179254‑M2/82‑66 (MQ=255)                                                                                                                          ataACAAGTTGTTCGGGAATTTTTTATGGTTTAATTTAGTACTCAATGTTAGGTGCTTGGTTAACACGTTCTTGGTATTTTTTAAATGCGAAGTATAAACCGCCAACTAATGTTAAAATAACTGCTAATTTTTTCATCAtt          <  2:426412/141‑1 (MQ=255)                                                                                                                            aaCAAGGTGTTCGGGAATTTTTTATGGTTTAATTTAGTACTCAATGTTAGGTGCTTGGTTAACACGTTCTTGGTATTTTTTAAATGCGAAGTATAAACCGCCAACTAATGTTAAAATAACTGCTAATTTTTTCATCATTCa        <  1:171696/141‑1 (MQ=255)                                                                                                                                  gtgtTCGGGAATTTTTTATGGTTTAATTTAGTACTCAATGTTAGGTGCTTGGTTAACACGTTCTTGGTATTTTTTAAATGCGAAGTATAAACCGCCAACTAATGTTAAAATAACTGCTAATTTTTTCATCATTCAAACTcc  <  2:409294/141‑1 (MQ=255)                                                                                                                                     |                                                                                                                                          TGTTAATACCTACGCTTACGGACCTAGATCAGAATCATTTAGTGGTAATATCGAAAATACAGAAAGCGCAAAAATAATATTTGATATATTCAAGTAAAGCATAAAAAAATTCCCGAGCACTATAACAAGGTGTTCGGGAATTTTTTATGGTTTAATTTAGTACTCAATGTTAGGTGCTTGGTTAACACGTTCTTGGTATTTTTTAAATGCGAAGTATAAACCGCCAACTAATGTTAAAATAACTGCTAATTTTTTCATCATTCAAACTCC  >  CP000730/2772530‑2772799

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.