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

TAAATTTTACGTATACACAAATTCGGTCTATAACACGAAACATATCTAGTTACTAAAAATTTCAAAACGATAACCTTTAGTATACCTTTATCAACAAAATGGCAACTCTTATAACA‑TAGTGAAATAAAAGTCGCCATTTAATATTAGTATTACAAAGTATTGCCATATCATAAATTTAATTACTGTTGACTAGAATCGAAAAAAGCTTGTTACAAACGCATATTCAGTCAACTACTGGCAACACAACATTGTAGCGCCTTATGTTCCGAAC  >  CP000730/2249134‑2249404                                                                                                                                             |                                                                                                                                    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                                                                                                                              <  1:343933/141‑1 (MQ=255)       ttACGTATACACAAATTCGGTCTATAACACGAAACATATCTAGTTACTAAAAATTTCAAAACGATAACCTTTAGTATACCTTTATCAACAAAATGGCAACTCTTATAACA‑TAGTGAAATAAAAGTCGCCATTTAATATTAg                                                                                                                              <  2:23776/141‑1 (MQ=255)        gactgaatatgcgtttgtaacaagcttttttcgattctagtcaacagtaattaaatttatgatatggcaatactttgtaatactaatattaaatggcaactcttataacatagtgaaataaaagtcgccatttAATATTAg                                                                                                                              <  1:251123‑M2/8‑1 (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                                                                                  >  2:79596/1‑141 (MQ=255)                                                   tACTAAAAATTTCAAAACGATAACCTTTAGTATACCTTTATCAACAAAATGGCAACTCTTATAACA‑TAGTGAAATAAAAGTCGCCATTTAATATTAGTATTACAAAGTATTGCCATATCATAAATTTAATTACTGTTGACt                                                                                  >  1:210925/1‑141 (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                                                       <  2:34584/141‑1 (MQ=255)                                                                              tAGTATACCTTTATCAACAAAATGGCAACTCTTATAACA‑TAGTGAAATAAAAGTCGCCATTTAATATTAGTATTACAAAGTATTGCCATATCATAAATTTAATTACTGTTGACTAGAATCGAAAAAAGCTTGTTACAAACg                                                       >  2:412878/1‑141 (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                                        >  2:224299/1‑141 (MQ=255)                                                                                             aacaaAATGGCAACTCTTATAACA‑TAGTGAAATAAAAGTCGCCATTTAATATTAGTATTACAAAGTATTGCCATATCATAAATTTAATTACTGTTGACTAGAATAGAAAAAAGCTTGTTACAAACGCATATTCAGTCAact                                        <  1:224299/141‑1 (MQ=255)                                                                                                ttaaatggcgacttttatttcactatgttataagagttgccatttAATATTAGTATTACAAAGTATTGCCATATCATAAATTTAATTACTGTTGACTAGAATCGAAAAAAGCTTGTTACAAACGCATATTCAGTCAactac                                      >  1:349959‑M2/46‑141 (MQ=255)                                                                                                  aaatggcgacttttatttcactatgttataagagttgccatttAATATTAGTATTACAAAGTATTGCCATATCATAAATTCAATTACTGTTGACTAGAATCGAAAAAAGCTTGTTACAAACGCATATTCAGTCAACTACTg                                    >  2:351119‑M2/44‑141 (MQ=255)                                                                                                      GCAACTCTTATAACA‑TAGTGAAATAAAAGTCGCCATTTAATATTAGTATTACAAAGTATTGCCATATCATAAATTTAATTACTGTTGACTAGAATCGAAAAAAGCTTGTTACAAACGCATATTCAGTCAACTACTGGCAac                               <  2:351483‑M1/141‑1 (MQ=255)                                                                                                       CAACTCTTATAACA‑TAGTGAAATAAAAGTCGCCATTTAATATTAGTATTACAAAGTATTGCCATATCATAAATTTAATTACTGTTGACTAGAATCGAAAAAAGCTTGTTACAAACGCATATTCAGTCAACTACTGGCAaca                              <  1:305286‑M1/141‑1 (MQ=255)                                                                                                        aaCTCTTATAACA‑TAGTGAAATAAAAGTCGCCATTTAATATTAGTATTACAAAGTATTGCCATATCATAAATTTAATTACTGTTGACTAGAATCGAAAAAAGCTTGTTACAAACGCATATTCAGTCAACTACTGGcaacac                             <  1:164149/141‑1 (MQ=255)                                                                                                                       aGTGAAATAAAAGTCGCCATTTAATATTAGTATTACAAAGTATTGCCATATCATAAATTTAATTACTGTTGACTAGAATCGAAAAAAGCTTGTTACAAACGCATATTCAGTCAACTACTGGCAACACAACATTGTAGCGcc               >  2:152487/1‑141 (MQ=255)                                                                                                                          gAAATAAAAGTCGCCATTTAATATTAGTATTACAAAGTATTGCCATATCATAAATTTAATTACTGTTGACTAGAATCGAAAAAAGCTTGTTACAAACGCATATTCAGTCAACTACTGGCAACACAACATTGTAGCGCCTTa            <  1:266214/141‑1 (MQ=255)                                                                                                                             aTAAAAGTCGCCATTTAATATTAGTATTACAAAGTATTGCCATATCATAAATTTAATTACTGTTGACTAGAATCGAAAAAAGCTTGTTACAAACGCATATTCAGTCAACTACTGGCAACACAACATTGTAGCGCCTTATGt         >  2:252121/1‑141 (MQ=255)                                                                                                                               aaaaGTCGCCATTTAATATTAGTATTATAACGTATTACTATATCATAAATTTAATTACTGTTGACTAGAATCGAAAACAGCTTGTTACAAACGCATATTCAGTCAACTACTGGCAACACAACATTGTAGCGCCTTATGTTc       >  2:464137/1‑141 (MQ=255)                                                                                                                                aaaGTCGCCATTTAATATTAGTATTACAAAGTATTGCCATATCATAAATTTAATTACTGTTGACTAGAATCGAAAAAAGCTTGTTACAAACGCATATTCTGTCAACTACTGGCAACACAACATTGTAGCGCCATATGTTcc      >  2:10725/1‑141 (MQ=255)                                                                                                                                aaaGTCGCCATTTAATATTAGTATTACAAAGTATTGCCATATCATAAATTTAATTACTGTTGACTAGAATCGAAAAAAGCTTGTTACAAACGCATATTCAGTCAACTACTGGCAACACAACATTGTAGCGCCTTATGTTcc      <  1:138910/141‑1 (MQ=255)                                                                                                                                 aaGTCGCCATTTAATATTAGTATTACAAAGTATTGCCATATCATAAATTTAATTACTGTTGACTAGAATCGAAAAAAGCTTGTTGCAAACGCATATTCAGTCAACTACTGGCAACACAACATTGTAGCGCCTTATGTTCCg     >  1:388145/1‑141 (MQ=255)                                                                                                                                  aGTCGCCATTTAATATTAGTATTACAAAGTATTGCCATATCATAAATTTAATTACTGTTGACTAGAATCGAAAAAAGCTTGTTACAAACGCATATTCAGTCAACTACTGGCAACACAACATTGTAGCGCCTTATGTTCCGa    >  2:46301/1‑141 (MQ=255)                                                                                                                                    tCGCCATTTAATATTAGTATTACAAAGTATTGCCATATCATAAATTTAATTACTGTTGACTAGAATCGAAAAAAGCTTGTTACAAACGCATATTCAGTCAACTACTGGCAACACAACATTGTAGCGCCTTATGTTCCGAAc  >  1:92901/1‑141 (MQ=255)                                                                                                                                             |                                                                                                                                    TAAATTTTACGTATACACAAATTCGGTCTATAACACGAAACATATCTAGTTACTAAAAATTTCAAAACGATAACCTTTAGTATACCTTTATCAACAAAATGGCAACTCTTATAACA‑TAGTGAAATAAAAGTCGCCATTTAATATTAGTATTACAAAGTATTGCCATATCATAAATTTAATTACTGTTGACTAGAATCGAAAAAAGCTTGTTACAAACGCATATTCAGTCAACTACTGGCAACACAACATTGTAGCGCCTTATGTTCCGAAC  >  CP000730/2249134‑2249404

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.