New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	CP000730	= 329211	31 (0.840)	3 (0.090)	3/238	NT	9.0%	intergenic (+79/+64)	USA300HOU_0295/USA300HOU_0296	hypothetical membrane protein/hypothetical protein
	?	CP000730	= 329244	32 (0.940)					intergenic (+112/+31)	USA300HOU_0295/USA300HOU_0296	hypothetical membrane protein/hypothetical protein

GACGATAGTGCCACTAGTTGTTACGACTTGGATTATTATAGCTACAATTATACTTTCGTAAACGATTTTGATTAATGGGGAATGTAGAGAACATTTCTTTGTAATTTTATAATCGAATAACATACAAAATAAAGCGACC‑AATTTTGCAGTGTTACGAATTGTAAACTGCGAACTGGTCGCTTTTTATTGATGTCATGATTAATTTAATGGATGTAATTATATGATGAAACTTCTGAAGCAGAGATGGTTCTTGATGAAACGATATATTCACCAATCCAGT  >  CP000730/329072‑329351                                                                                                                                             |                                                                                                                                             gACGATAGTGCCACTAGTTGTTACGACTTGGATTATTATAGCTACAATTATACTTTCGTAAACGATTTTGATTAATGGGGAATGTAGAGAACATTTCTTTGTAATTTTATAATCGAATAACATACAAAATAAAGCGACC‑aa                                                                                                                                             <  1:271712/141‑1 (MQ=255)     aTAGTGCCACTAGTTGTTACGACTTGGATTATTATAGCTACAATTATACTTTCGTAAACGATTTTGATTAATGGGGAATGTAGAGAACATTTCTTTGTAATTTTATAATCGAATAACATACAAAATAAAGCGACC‑AAtttt                                                                                                                                         >  2:241888/1‑141 (MQ=255)         tGCCACTAGTTGTTACGACTTGGATTATTATAGCTACAATTATACTTTCGTAAACGATTTTGATTAATGGGGAATGTAGAGAACATTTCTTTGTAATTTTATAATCGAATAACATACAAAATAAAGCGACC‑AATTTTGCAg                                                                                                                                     <  2:192244/141‑1 (MQ=255)           ccACTAGTTGTTACGACTTGGATTATTATAGCTACAATTATACTTTCGTAAACGATTTTGATTAATGGGGAATGTAGAGAACATTTCTTTGTAATTTTATAATCGAATAACATACAAAATAAAGCGACC‑AATTTTGCAgtg                                                                                                                                   <  1:130007/141‑1 (MQ=255)             aCTAGTTGTTACGACTTGGATTATTATAGCTACAATTATACTTTCGTAAACGATTTTGATTAATGGGGAATGTAGAGAACATTTCTTTGTAATTTTATAATCGAATAACATACAAAATAAAGCGACC‑AATTTTGCAGTGtt                                                                                                                                 <  2:388718/141‑1 (MQ=255)                        cGACTTGGATTATTATAGCTACAATTATACTTTCGTAAACGATTTTGATTAATGGGGAATGTAGAGAACATTTCTTTGTAATTTTATAATCGAATAACATACAAAATAAAGCGACC‑AATTTTGCAGTGTTACGAATTGTaa                                                                                                                      >  2:15269/1‑141 (MQ=255)                           cTTGGATTATTATAGCTACAATTATACTTTCGTAAACGATTTTGATTAATGGGGAATGTAGAGAACATTTCTTTGTAATTTTATAATCGAATAACATACAAAATAAAGCGACCAAttttgcagtttacaattcgtaacact                                                                                                                    <  1:131925‑M1/141‑27 (MQ=255)                             tGGATTATTATAGCTACAATTATACTTTCGTAAACGATTTTGATTAATGGGGAATGTAGAGAACATTTCTTTGTAATTTTATAATCGAATAACATACAAAATAAAGCGACC‑Agttcgcagtttacaattcgtaacactgca                                                                                                                 <  2:297472‑M1/141‑30 (MQ=255)                              ggATTATTATAGCTACAATTATACTTTCGTAAACGATTTTGATTAATGGGGAATGTAGAGAACATTTCTTTGTAATTTTATAATCGAATAACATACAAAATAAAGCGACC‑AATTTTGCAGTGTTACGAATTGTAAACTGCg                                                                                                                >  1:439974/1‑141 (MQ=255)                                  tattatAGCTACAATTATACTTTCGTAAACGATTTTGATTAATGGGGAATGTAGAGAACATTTCTTTGTAATTTTATAATCGAATAACATACAAAATAAAGCGACC‑AATTTTGCAGTGTTACGAATTGTAAACTGCGAACt                                                                                                            >  1:439504‑M2/1‑140 (MQ=255)                                      ataGCTACAATTATACTTTCGTAAACGATTTTGATTAATGGGGAATGTAGAGAACATTTCTTTGTAATTTTATAATCGAATAACATACAAAATAAAGCGACC‑AATTTTGCAGTGTTACGAATTGTAAACTGCGAACtggtc                                                                                                        >  2:5725‑M2/1‑136 (MQ=255)                                         gCTACAATTATACTTTCGTAAACGATTTTGATTAATGGGGAATGTAGAGAACATTTCTTTGTAATTTTATAATCGAATAACATACAAAATAAAGCGACC‑Agttcgcagtttacaattcgtaacactgcaaaattggtcgct                                                                                                     <  1:142239‑M1/141‑42 (MQ=255)                                                 tataCTTTCGTAAACGATTTTGATTAATGGGGAATGTAGAGAACATTTCTTTGTAATTTTATAATCGAATAACATACAAAATAAAGCGACC‑AATTTTGCAGTGTTACGAATTGTAAACTGCGAACTGGTCGCTTTTTATTg                                                                                             >  2:277867/1‑141 (MQ=255)                                                 tataCTTTCGTAAACGATTTTGATTAATGGGGAATGTAGAGAACATTTCTTTGTAATTTTATAATCGAATAACATACAAAATAAAGCGACC‑AATTTTGCAGTGTTACGAATTGTAAACTGCGAACTGGTCGCTTTTTATTg                                                                                             <  1:89079/141‑1 (MQ=255)                                                   taCTTTCGTAAACGATTTTGATTAATGGGGAATGTAGAGAACATTTCTTTGTAATTTTATAATCGAATAACATACAAAATAAAGCGACC‑AATTTTGCAGTGTTACGAATTGTAAACTGCGAACTGGTCGCTTTTTATTGAt                                                                                           >  2:185061/1‑141 (MQ=255)                                                          gTAAACGATTTTGATTAATGGGGAATGTAGAGAACATTTCTTTGTAATTTTATAATCGAATAACATACAAAATAAAGCGACC‑AATTTTGCAGTGTTACGAATTGTAAACTGCGAACTGGTCGCTTTTTATTGATGTCATGa                                                                                    <  2:102236/141‑1 (MQ=255)                                                                   tttGATTAATGGGGAATGTAGAGAACATTTCTTTGTAATTTTATAATCGAATAACATACAAAATAAAGCGACC‑AATTTTGCAGTGTTACGAATTGTAAACTGCGAACTGGTCGCTTTTTATTGATGTCATGAttaatttaa                                                                           <  2:448703/141‑1 (MQ=255)                                                                    ttGATTAATGGGGAATGTAGAGAACATTTCTTTGTAATTTTATAATCGAATAACATACAAAATAAAGCGACC‑AATTTTGCAGTGTTACGAATTGTAAACTGCGAACTGGTCGCTTTTTATTGATGTCATGAttaatttaat                                                                          >  2:338851/1‑141 (MQ=255)                                                                         tAATGGGGAATGTAGAGAACATTTCTTTGTAATTTTATAATCGAATAACATACAAAATAAAGCGACC‑AATTTTGCAGTGTTACGAATTGTAAACTGCGAACTGGTCGCTTTTTATTGATGTCATGATTAATTTAATGGATg                                                                     >  1:72692/1‑141 (MQ=255)                                                                         tAATGGGGAAAGTAGAGAACATTTCTTGGTAATTTTATAATCGAATAACATACAAAATAAAGCGACC‑AATTTTGCAGTGTTACGAATTGTAAACTGCGAACTGGTCGCTTTTTATTGATGTCATGATTAATTTAATGGATg                                                                     >  2:203684/1‑141 (MQ=255)                                                                                          aaCATTTCTTTGTAATTTTATAATCGAATAACATACAAAATAAAGCGACC‑AATTTTGCAGTGTTACGAATTGTAAACTGCGAACTGGTCGCTTTTTATTGATGTCATGATTAATTTAATGGATGTAATTATATGATGAAAc                                                    <  1:201952/141‑1 (MQ=255)                                                                                             aTTTCTTTGTAATTTTATAATCGAATAACATACAAAATAAAGCGACC‑AATTTTGCAGTGTTACGAATTGTAAACTGCGAACTGGTCGCTTTTTATTGATGTCATGATTAATTTAATGGATGTAATTATATGATGAAAAttt                                                 >  2:414550/1‑140 (MQ=255)                                                                                                  tttGTAATTTTATAATCGAATAACATACAAAATAAAGCGACC‑AATTTTGCAGTGTTACGAATTGTAAACTGCGAACTGGTCGCTTTTTATTGATGTCATGATTAATTTAATGGATGTAATTATATGATGAAACTTCTGAAg                                            >  2:31368/1‑141 (MQ=255)                                                                                                        aTTTTATAATCGAATAACATACAAAATAAAGCGACC‑ACTTTTGCAGTGTTACGAATTGTAAACTGCGAACTGGTCGCTTTATATTGATGTCATGATTAATTTAATGGATGTAATTATATGATGAAACTTCTGAAGCagata                                      <  2:376325/141‑3 (MQ=255)                                                                                                          tttATAATCGAATAACATACAAAATAAAGCGACC‑AATTTTGCAGTGTTACGAATTGTAAACTGCGAACTGGTCGCTTTTTATTGATGTCATGATTAATTTAATGGATGTAATTATATGATGAAACTTCTGAAGCAGAGATg                                    <  1:455792/141‑1 (MQ=255)                                                                                                          tttATAATCGAATAACATACAAAATAAAGCGACC‑AATTTTGCAGTGTTACGAATTGTAAACTGCGAACTGGTCGCTTTTTATTGATGTCATGATTAATTTAATGGATGTAATTATATGATGAAACTTCTGAAGCAGAGATg                                    <  2:280561/141‑1 (MQ=255)                                                                                                               aaTCGAATAACATACAAAATAAAGCGACC‑AATTTTGCAGTGTTACGAATTGTAAACTGCGAACTGGTCGCTTTTTATTGATGTCATGATTAATTTAATGGATGTAATTATATGATGAAACTTCTGAAGCAGAGATGGTTCt                               <  1:289774/141‑1 (MQ=255)                                                                                                                 tCGAATAACATACAAAATAAAGCGACC‑AATTTTGCAGTGTTACGAATAGTAAACTGCGAACTGGACGCTTTTTATTGATGTCTTGATTAATTTAATAGATGTAATTATATGATGAAACTTGTGAAGCAGAGATGGTTCTtg                             >  1:284267/1‑141 (MQ=255)                                                                                                                  cGAATAACATACAAAATAAAGCGACC‑AATTTTGCAGTGTTACGAATTGTAAACTGCGAACTGGTCGCTTTTTATTGATGTCATGATTAATTTAATGGATGTAATTATATGATGAAACTTCTGAAGCAGAGATGGTTCTtga                            >  2:124454/1‑141 (MQ=255)                                                                                                                    aaTAACATACAAAATAAAGCGACC‑AATTTTGCAGTGTTACGAATTGTAAACTGCGAACTGGTCGCTTTTTATTGATGTCATGATTAATTTAATGGATGTAATTATATGATGAAACTTCTGAAGCAGAGATGGTTCTtgatg                          <  2:59758/141‑1 (MQ=255)                                                                                                                     aTAACATACAAAATAAAGCGACC‑AATTTTGCAGTGTTACGAATTGTAAACTGCGAACTGGTCGCTTTTTATTGATGTCATGATTAATTTAATGGATGTAATTATATGATGAAACTTCTGAAGCAGAGATGGTTCTtgatga                         <  2:294384/141‑1 (MQ=255)                                                                                                                          aTACAAAATAAAGCGACC‑AATTTTGCAGTGTTACGAATTGTAAAc                                                                                                                    >  2:323682/1‑45 (MQ=255)                                                                                                                          aTACAAAATAAAGCGACC‑AATTTTGCAGTGTTACGAATTGTAAAc                                                                                                                    <  1:323682/45‑1 (MQ=255)                                                                                                                            aCAAAATAAAGCGACC‑AATTTTGCAGTGTTACGAATTGTAAACTGCGAACTGGTCGCTTTTTATCGATGTCATGATTAATTTAATGGATGTAATTATATGATGAAACTTCTGAAGCAGAGATGGTTCTTGATGAAACGata                  >  2:14865/1‑141 (MQ=255)                                                                                                                                   aaaGCGACC‑AATCTTGCAGTGTTACGAATTGTAAACTGCGAACTGGTCGCTCTTTATTGATGTCATAATTAACTTAATGGATGTAATTATATGATGAAACTTCTGAAGCAGAGATGGTTCTTGATGAAACGATATATTCAc           >  2:412179/1‑141 (MQ=255)                                                                                                                                    aaGCGACC‑AATTTTGCAGTGTTACGAATTGTAAACTGCGAACTGGTCGCTTTTTATTGATGTCATGATTAATTTAATGGATGTAATTATATGATGAAACTTCTGAAGCAGAGATGGTTCTTGATGAAACGATATATTCAcc          >  2:290984/1‑141 (MQ=255)                                                                                                                                     aGCGACC‑AATTTTGCAGTGTTACGAATTGTAAACTGCGAACtggtcgctttattttgtatgttattcgattataaaattacaaagaaatgttctctacattccccattaatcaaaatcgtttacgaaagtataattgtagc         <  1:142239‑M2/141‑101 (MQ=255)                                                                                                                                     aGCGACC‑AATTTTGCAGTGTTACGAATTGTAAACTGCGAACTGGTCGCTTTTTATTGATGTCATGATTAATTTAATGGATGTAATTATATGATGAAACTTCTGAAGCAGAGATGGTTCTTGATGAAACGATATATTCACCa         >  2:52614/1‑141 (MQ=255)                                                                                                                                       cGACC‑AATTTTGCAGTGTTACGAATTGTAAACTGCGAACTGGTCGCTTTTTATTGATGTCATGATTAATTTAATGGATGTAATTATATGATGAAACTTCTGAAGCAGAGATGGTTCTTGATGAAACGATATATTCACCAAt       >  1:181192/1‑141 (MQ=255)                                                                                                                                        gACC‑Agttcgcagtttacaattcgtaacactgcaaaattggtcgctttattttgtatgttattcgattataaaattacaaagaaatgttctctacattccccattaatcaaaatcgtttacgaaagtataattgtagctat      >  2:5725‑M1/1‑5 (MQ=255)                                                                                                                                           c‑AATTTTGCAGTGTTACGAATTGTAAACTGCGAACTGGTCGCTTTTTATTGATGTCATGATTAATTTAATGGATGTAATTATATGATGAAACTTCTGAAGCAGAGATGGTTCTTGATGAAACGATATATTCACCAATCCAg   <  2:183341/141‑1 (MQ=255)                                                                                                                                             agttcgcagtttacaattcgtaacactgcaaaattggtcgctttattttgtatgttattcgattataaaattacaaagaaatgttctctacattccccattaatcaaaatcgtttacgaaagtataattgtagctataata  >  1:439504‑M1/1‑1 (MQ=255)                                                                                                                                             |                                                                                                                                             GACGATAGTGCCACTAGTTGTTACGACTTGGATTATTATAGCTACAATTATACTTTCGTAAACGATTTTGATTAATGGGGAATGTAGAGAACATTTCTTTGTAATTTTATAATCGAATAACATACAAAATAAAGCGACC‑AATTTTGCAGTGTTACGAATTGTAAACTGCGAACTGGTCGCTTTTTATTGATGTCATGATTAATTTAATGGATGTAATTATATGATGAAACTTCTGAAGCAGAGATGGTTCTTGATGAAACGATATATTCACCAATCCAGT  >  CP000730/329072‑329351

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.