New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	CP000730	2249230 =	46 (1.100)	3 (0.080)	3/244	NT	6.6%	intergenic (‑223/+176)	USA300HOU_2120/USA300HOU_2121	hypothetical protein/hypothetical protein
	?	CP000730	2249273 =	41 (1.040)					intergenic (‑266/+133)	USA300HOU_2120/USA300HOU_2121	hypothetical protein/hypothetical protein

TAATGTCATGTTTTTCATTTTAAAAATTCAATAGCATTAAATTTTACGTATACACAAATTCGGTCTATAACACGAAACATATCTAGTTACTAAAAATTTCAAAACGATAACCTTTAGTATACCTTTATCAACAAAATGGCAACTCTTATAACA‑TAGTGAAATAAAAGTCGCCATTTAATATTAGTATTACAAAGTATTGCCATATCATAAATTTAATTACTGTTGACTAGAATCGAAAAAAGCTTGTTACAAACGCATATTCAGTCAACT  >  CP000730/2249097‑2249366                                                                                                                                      |                                                                                                                                          tAATGTCATGTTTTTTATTTTTTTAATTCAATAGCATTAAATTTTACGTATACACAAATTCGGTCTATAACACGAAACATATCTAGTTACTAAAAATTTCAAAACGATAACCTTTATTATACCTTTATCAACAAAATAGCa                                                                                                                                    >  2:322066/1‑141 (MQ=255)    tGTCATGTTTTTCATTTTAAAAATTCAATAGCATTAAATTTTACGTATACACAAATTCGGTCTATAACACGAAACATATCTAGTTACTAAAAATTTCAAAACGATAACCTTTAGTATACCTTTATCAACAAAATGGCAAct                                                                                                                                 <  1:471178/141‑1 (MQ=255)      tCATGTTTTTCATTTTAAAAATTCAATAGCATTAAATTTTACGTATACACAAATTCGGTCTATAACACGAAACATATCTAGTTACTAAAAATTTCAAAACGATAACCTTTAGTATACCTTTATCAACAAAATGGCAActct                                                                                                                               >  1:256105/1‑141 (MQ=255)               tCATTTTAAAAATTCAATAGCATTAAATTTTACGTATACACAAATTCGGTCTATAACACGAAACATATCTAGTTACTAAAAATTTCAAAACGATAACCTTTAGTATACCTTTATCAACAAAATGGCAACTCTTATAACA‑Ta                                                                                                                     <  2:275656/141‑1 (MQ=255)               tCATTTTAAAAATTCAATAGCATTAAATTTTACGTATACACAAATTCGGTCTATAACACGAAACATATCTAGTTACTAAAAATTTCAAAACGATAACCTTTAGTATACCTTTATCAACAAAATGGCAACTCTTATAACA‑Ta                                                                                                                     <  2:446477/141‑1 (MQ=255)                 aTTTTAAAAATTCAATAGCATTAAATTTTACGTATACACAGATTCGGTCGATAACAGAAAACAGATCTAGTTAATAAAAATTTCAAAACACTAACCTTTATTATACCTTTATAAAAAAAATGGCAATTCTTATAACA‑TAgg                                                                                                                   >  2:238154/1‑140 (MQ=255)                    ttAAAAATTCAATAGCATTAAATTTTACGTATACACAAATTCGGTCTATAACACGAAACATATCTAGTTACTAAAAATTTCAAAACGATAACCTTTAGTATACCTTTATCAACAAAATGGCAACTCTTATAACA‑TAGTGaa                                                                                                                >  1:139114/1‑141 (MQ=255)                    ttAAAAATTCAATAGCATTAAATTTTACGTATACACAAATTCGGTCTATAACACGAAACATATCTAGTTACTAAAAATTTCAAAACGATAACCTTTAGTATACCTTTATCAACAAAATGGCAACTCTTATAACA‑TAGTGaa                                                                                                                >  2:477838/1‑141 (MQ=255)                     tAAAAATTCAATAGCATTAAATTTTACGTATACACAAATTCGGTCTATAACACGAAACATATCTAGTTACTAAAAATTTCAAAACGATAACCTTTAGTATACCTTTATCAACAAAATGGCAACTCTTATAACA‑TAGTGaaa                                                                                                               <  1:87981/141‑1 (MQ=255)                       aaaaTTCAATAGCATTAAATTTTACGTATACACAAATTCGGTCTATAACACGAAACATATCTAGTTACTAAAAATTTCAAAACGATAACCTTTAGTATACCTTTATCAACAAAATGGCAACTCTTATAACA‑TAGTGAAATa                                                                                                             >  1:292940/1‑141 (MQ=255)                        aaaTTCAATAGCATTAAATTTTACGTATACACAAATTCGGTCTATAACACGAAACATATCTAGTTACTAAAAATTTCAAAACGATAACCTTTAGTATACCTTTATCAACAAAATGGCAACTCTTATAACA‑TAGTGAAATaa                                                                                                            <  2:246363/141‑1 (MQ=255)                          aTTCAATAGCATTAAATTTTACGTATACACAAATTCGGTCTATAACACGAAACATATCTAGTTACTAAAAATTTCAAAACGATAACCTTTAGTATACCTTTATCAACAAAATGGCAACTCTTATAACA‑TAGTGAAATaaaa                                                                                                          <  2:330162/141‑1 (MQ=255)                            tCAATAGCATTAAATTTTACGTATACACAAATTCGGTCTATAACACGAAACATATCTAGTTACTAAAAATTTCAAAACGATAACCTTTAGTATACCTTTATCAACAAAATGGCAACTCTTATAACA‑TAGTGAAATAAAAGt                                                                                                        >  2:55200/1‑141 (MQ=255)                                    cagtagttgactgaatatgcgtttgtaacaagcttttttcgattctagtcaacagtaattgaatttatgatatggcaatactttgtaatactaatattAAATGGCAACTCTTATAACA‑TAGTGAAATAAAAGTCGCCAttt                                                                                                >  2:351119‑M1/99‑141 (MQ=255)                                      gtagttgactgaatatgcgtttgtaacaagcttttttcgattctagtcaacagtaattaaatttatgatatggcaatactttgtaatactaatattAAATGGCAACTCTTATAACA‑TAGTGAAATAAAAGTCGCCATTTaa                                                                                              >  1:349959‑M1/97‑141 (MQ=255)                                        aaTTTTACGTATACACAAATTCGGTCTATAACACGAAACATATCTATTTACTAAAAATTTCAAAACGATAACCTTTAGTATACCTTTATCAACAAAATGGCAACTCTTATAACA‑TAGTGAAATAAAAGTCGCCATTTAata                                                                                            <  2:468911/141‑1 (MQ=255)                                        aaTTTTACGTATACACAAATTCGGTCTATAACACGAAACATATCTAGTTACTAAAAATTTCAAAACGATAACCTTTCGTATACCTTTATCAACAAAATGGCAACTCTTATAACA‑TAGTGAAATAAAAGTCGCCATTTAata                                                                                            <  2:380634/141‑1 (MQ=255)                                          ttttACGTATACACAAATTCGGTCTATAACACGAAACATATCTAGTTACTAAAAATTTCAAAACGATAACCTTTAGTATACCTTTATCAACAAAATGGCAACTCTTATAACA‑TAGTGAAATAAAAGTCGCCATTTAATAtt                                                                                          >  2:276743/1‑141 (MQ=255)                                            ttACGTATACACAAATTCGGTCTATAACACGAAACATATCTAGTTACTAAAAATTTCAAAACGATAACCTTTAGTATACCTTTATCAACAAAATGGCAACTCTTATAACA‑TAGTGAAATAAAAGTCGCCATTTAATATTAg                                                                                        <  2:23776/141‑1 (MQ=255)                                            ttACGTATACACAAATTCGGTCTATAACACGAAACATATCTAGTTACTAAAAATTTCAAAACGATAACCTTTAGTATACCTTTATCAACAAAATGGCAACTCTTATAACA‑TAGTGAAATAAAAGTCGCCATTTAATATTAg                                                                                        <  1:343933/141‑1 (MQ=255)                                                  ataCACAAATTCGGTCTATAACACGAAACATATCTAGTTACTAAAAATTTCAAAACGATAACCTTTAGTATACCTTTATCAACAAAATGGCAACTCTTATAACA‑TAGTGAAATAAAAGTCGCCATTTAATATTAGTATTAc                                                                                  <  2:493193/141‑1 (MQ=255)                                                   taCACAAATTCGGTCTATAACACGATACATATCTAGTTACTAAAAATTTCAAAACGATAACCTTTAGTATACCTTTATCAACAAAATGGCCACTCTTATAACA‑TAGTGAAATAAAAGTCGCCATTTAATTTTAGTATTACa                                                                                 <  2:275135/141‑1 (MQ=255)                                                       caAATTCTCTCTATAAAACTAAACATATCTAGTTACTAAAAATTTAAAAACGATAACCTTTAGTATACCTTTATCAACAAAATGGCAACTCTTATAACA‑TAGTGAAATAAAAGTCGCCATTTAATATTAGTATTACAAAGt                                                                             <  2:458719/141‑1 (MQ=255)                                                            tCGGTCTATAACACGAAACATATCTAGTTACTAAAAATTTCAAAACGATAACCTTTAGTATACCTTTATCAACAAAATGGCAACTCTTATAACA‑TAGTGAAATAAAAGTCGCCATTTAATATTAGTATTACAAAGTATTGc                                                                        >  1:436664/1‑141 (MQ=255)                                                              ggTCTATAACACGAAACATATCTAGTTACTAAAAATTTCAAAACGATAACCTTTAGTATACCTTTATCAACAAAATGGCAACTCTTATAACA‑TAGTGAAATAAAAGTCGCCATTTAATATTAGTATTACAAAGTATTGCCa                                                                      <  1:148052/141‑1 (MQ=255)                                                                        acGAAACATATCTAGTTACTAAAAATTTCAAAACGATAACCTTTAGTATACATTTATCAACAAAATGGCAAATCTTATAACA‑TAGTGAAATAAAAGTCGCCATTTAATATTAGTATTACACAGTATCGCCATATCATAAAt                                                            >  1:149970/1‑141 (MQ=255)                                                                                tatCTAGTTACTAAAAATTTCAAAACGATAACCTTTAGTATACCTTTATCAACAAAATGGCAACTCTTATAACA‑TAGTGAAATAAAAGTCGCCATTTAATATTAGTATTACAAAGTATTGCCATATCATAAATTTAATTAc                                                    >  1:315204/1‑141 (MQ=255)                                                                                     aGTTACTAAAAATTTCAAAACGATAACCTTTAGTATACCTTTATCAACAAAATGGCAACTCTTATAACA‑TAGTGAAATAAAAGTCGCCATTTAATATTAGTATTACAAAGTATTGCCATATCATAAATTTAATTACTGTTg                                               <  1:432371/141‑1 (MQ=255)                                                                                     aGTTACTAAAAATTTCAAAACGATAACCTTTAGTATACCTTTATCAACAAAATGGCAACTCTTATAACA‑CAGTGAAATAAAAGTCGCCATTTAATATTAGTATTACAAAGTATTGCCATATCATAAATTTAATTACTGTTg                                               <  1:50794/141‑1 (MQ=255)                                                                                        tACTAAAAATTTCAAAACGATAACCTTTAGTATACCTTTATCAACACAATGGCAACTCTTATAACA‑TAGTGAAATAAAAGTCGCCATTTAATATTAGTATTACAAAGTATTGCCATATCATAAATTTAATTACTGTTGACt                                            >  2:323037/1‑141 (MQ=255)                                                                                        tACTAAAAATTTCAAAACGATAACCTTTAGTATACCTTTATCAACAAAATGGCAACTCTTATAACA‑TAGTGAAATAAAAGTCGCCATTTAATATTAGTATTACAAAGTATTGCCATATCATAAATTTAATTACTGTTGACt                                            >  1:210925/1‑141 (MQ=255)                                                                                        tACTAAAAATTTCAAAACGATAACCTTTAGTATACCTTTATCAACAAAATGGCAACTCTTATAACA‑TAGTGAAATAAAAGTCGCCATTTAATATTAGTATTACAAAGTATTGCCATATCATAAATTTAATTACTGTTGACt                                            >  2:79596/1‑141 (MQ=255)                                                                                             aaaaTTTCAAAACGATAACCTTTAGTATACCTTTATCAACAAAATGGCAACTCTTATAACA‑TAGTGAAATAAAAGTCGCCATTTAATATTAGTATTACAAAGTATTGCCATATCATAAATTTAATTACTGTTGACTAGAAt                                       >  2:316885/1‑141 (MQ=255)                                                                                                  ttCAAAACGATAACCTTTAGTATACCTTTATCAACAAAATGGCAACTCTTATAACA‑TAGTGAAATAAAAGTCGCCATTTAATATTAGTATTACAAAGTATTGCCATATCATAAATTTAATTACTGTTGACTAGAATCGaaa                                  >  2:214957/1‑141 (MQ=255)                                                                                                    cAAAACGATAACCTTTAGTATACCTTTATCAACAAAATGGCAACTCTTATAACA‑TAGTGAAATAAAAGTCGCCATTTAATATTAGTATTACAAAGTATTGCCATATCATAAATTTAATTACTGTTGACTAGAATCGaaaaa                                >  1:402687/1‑141 (MQ=255)                                                                                                    cAAAACGATAACCTTTAGTATACCTTTATCAACAAAATGGCAACTCTTATAACA‑TAGTGAAATAAAAATCGCCATTTAAAATTAGTATTACAAAGTATTACCATATCATAAATATAATTACTGTTGACTAGAATCGaaaaa                                >  2:188118/1‑141 (MQ=255)                                                                                                          gATAACCTTTAGTATACCTTTATCAACAAAATGGCAACTCTTATAACA‑TAGTGAAATAAAAGTCGCCATTTAATATTAg                                                                                        >  2:305709/1‑79 (MQ=255)                                                                                                          gATAACCTTTAGTATACCTTTATCAACAAAATGGCAACTCTTATAACA‑TAGTGAAATAAAAGTCGCCATTTAATATTAg                                                                                        <  1:305709/79‑1 (MQ=255)                                                                                                              aCCTTTAGTATACCTTTATCAACAAAATGGCAACTCTTATAACA‑TAGTGAAATAAAAGTCGCCATTTAATATTAGTATTACAAAGTATTGCCATATCATAAATTTAATTACTGTTGACTAGAATCGAAAAAAGCTTGTTAc                      >  1:461839/1‑141 (MQ=255)                                                                                                                 tttAGTATACCTTTATCAACAAAATGGCAACTCTTATAACA‑TAGTGAAATAAAAGTCGCCATTTAATATTAGTATTACAAAGTATTGCCATATCATAAATTTAATTACTGTTAAAAAAAAAAAAAAAAAGCTTGTTACaaa                   <  2:489823/141‑1 (MQ=255)                                                                                                                   tAGTATACCTTTATCAACAAAATGGCAACTCTTATAACA‑TAGTGAAATAAAAGTCGCCATTTAATATTAGTATTACAAAGTATTGCCATATCATAAATTTAATTACTGTTGACTAGAATCGAAAAAAGCTTGTTACAAACg                 >  2:412878/1‑141 (MQ=255)                                                                                                                   tAGTATACCTTTATCAACAAAATGGCAACTCTTATAACA‑TAGTGAAATAAAAGTCGCCATTTAATATTAGTATTACAAAGTATTGCCATATCATAAATTTAATTACTGTTGACTAGAATCGAAAAAAGCTTGTTACAAACg                 <  2:34584/141‑1 (MQ=255)                                                                                                                    aGTATACCTTTATCAACAAAATGGCAACTCTTATAACA‑TAGTGAAATAAAAGTCGCCATTTAATATTAGTATTACAAAGTATTGCCATATCATAAATTTAATTACTGTTGACTAGAATCGAAAAAAGCTTGTTACAAACGc                <  1:477838/141‑1 (MQ=255)                                                                                                                    aGTATACCTTTATCAACAAAATGGCAACTCTTATAACA‑TAGTGAAATAAAAGTCGCCACTTAATATTAGTATTACAAAGTATTGCCCTATCATAAATTTAATTACTGTTGACTAGAATCGAAAAAAGCTTGTTACAAACGc                <  2:379182/141‑1 (MQ=255)                                                                                                                     gTATACCTTTATCAACAAAATGGCAACTCTTATAACA‑TAGTGAAATAAAAGTCGCCATTTAATATTAGTATTACAAAGTATTGCCATATCATAAATTTAATTACTGTTGACTAGAATCGAAAAAAGCTTGTTACAAACGCa               <  1:166928/141‑1 (MQ=255)                                                                                                                       ataCCTTTATCAACAAAATGGCAACTCTTATAACA‑TAGTGAAATAAAAGTCGCCATTTAATATTAGTATTACAAAGTATTGCCATATCATAAATTTAATTACTGTTGACTAGAATCGAAAAAAGCTTGTTACAAACGCata             <  2:91355/141‑1 (MQ=255)                                                                                                                              tATCAACAAAATGGCAACTCTTATAACA‑TAGTGAAATAAAAGTCGCCATTTAATATTAGTATTACAAAGTATTGCCATATCATAAATTTAATTACTGTTGACTAGAATCGAAAAAAGCTTGTTACAAACGCATATTCAGTc      <  1:184189/141‑1 (MQ=255)                                                                                                                              ctaatattAAATGGCGACTTTTATTTCACTA‑TGTTATAAGAGTTGCCATTTAATATTAGTATTACAAAGTATTGCCATATCATAAATTTAATTACTGTTGACTAGAATCGAAAAAAGCTTGTTACAAACGCATATTCAGTc      <  1:251123‑M1/133‑1 (MQ=255)                                                                                                                               aTCAACAAAATGGCAACTCTTATAACA‑TAGTGAAATAAAAGTCGCCATTTAATATTAGTATTACAAAGTATTGCCATATCATAAATTTAATTACTGTTGACTAGAATCGAAAAAAGCTTGTTACAAACGCATATTCAGTCa     >  2:330250/1‑141 (MQ=255)                                                                                                                                  aacaaAATGGCAACTCTTATAACA‑TAGTGAAATAAAAGTCGCCATTTAATATTAGTATTACAAAGTATTGCCATATCATAAATTTAATTACTGTTGACTAGAATCGAAAAAAGCTTGTTACAAACGCATATTCAGTCAact  >  1:59675/1‑141 (MQ=255)                                                                                                                                  aacaaAATGGCAACTCTTATAACA‑TAGTGAAATAAAAGTCGCCATTTAATATTAGTATTACAAAGTATTGCCATATCATAAATTTAATTACTGTTGACTAGAATAGAAAAAAGCTTGTTACAAACGCATATTCAGTCAact  <  1:224299/141‑1 (MQ=255)                                                                                                                                  aacaaAATGGCAACTCTTATAACA‑TAGTGAAATAAAAGTCGCCATTTAATATTAGTATTACAAAGTATTGCCATATCATAAATTTAATTACTGTTGACTAGAATAGAAAAAAGCTTGTTACAAACGCATATTCAGTCAact  >  2:224299/1‑141 (MQ=255)                                                                                                                                      |                                                                                                                                          TAATGTCATGTTTTTCATTTTAAAAATTCAATAGCATTAAATTTTACGTATACACAAATTCGGTCTATAACACGAAACATATCTAGTTACTAAAAATTTCAAAACGATAACCTTTAGTATACCTTTATCAACAAAATGGCAACTCTTATAACA‑TAGTGAAATAAAAGTCGCCATTTAATATTAGTATTACAAAGTATTGCCATATCATAAATTTAATTACTGTTGACTAGAATCGAAAAAAGCTTGTTACAAACGCATATTCAGTCAACT  >  CP000730/2249097‑2249366

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.